FreeINCHI: 119| 6.37k|{ 120| 6.37k| if (!out) ------------------ | Branch (120:9): [True: 0, False: 6.37k] ------------------ 121| 0| { 122| 0| return; 123| 0| } 124| | 125| 6.37k| if (out->szInChI) ------------------ | Branch (125:9): [True: 5.02k, False: 1.34k] ------------------ 126| 5.02k| { 127| 5.02k| inchi_free( out->szInChI ); ------------------ | | 1152| 5.02k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 5.02k, False: 0] | | | Branch (1152:50): [Folded, False: 5.02k] | | ------------------ ------------------ 128| 5.02k| } 129| 6.37k| if (out->szLog) ------------------ | Branch (129:9): [True: 6.28k, False: 89] ------------------ 130| 6.28k| { 131| 6.28k| inchi_free( out->szLog ); ------------------ | | 1152| 6.28k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.28k, False: 0] | | | Branch (1152:50): [Folded, False: 6.28k] | | ------------------ ------------------ 132| 6.28k| } 133| 6.37k| if (out->szMessage) ------------------ | Branch (133:9): [True: 6.28k, False: 89] ------------------ 134| 6.28k| { 135| 6.28k| inchi_free( out->szMessage ); ------------------ | | 1152| 6.28k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.28k, False: 0] | | | Branch (1152:50): [Folded, False: 6.28k] | | ------------------ ------------------ 136| 6.28k| } 137| | 138| 6.37k| memset( out, 0, sizeof( *out ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 139| 6.37k|} FreeStructFromINCHI: 174| 6.37k|{ 175| 6.37k| if (!out) ------------------ | Branch (175:9): [True: 0, False: 6.37k] ------------------ 176| 0| { 177| 0| return; 178| 0| } 179| | 180| 6.37k| if (out->atom) ------------------ | Branch (180:9): [True: 1.75k, False: 4.61k] ------------------ 181| 1.75k| { 182| 1.75k| inchi_free( out->atom ); ------------------ | | 1152| 1.75k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.75k, False: 0] | | | Branch (1152:50): [Folded, False: 1.75k] | | ------------------ ------------------ 183| 1.75k| } 184| 6.37k| if (out->stereo0D) ------------------ | Branch (184:9): [True: 386, False: 5.98k] ------------------ 185| 386| { 186| 386| inchi_free( out->stereo0D ); ------------------ | | 1152| 386|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 386, False: 0] | | | Branch (1152:50): [Folded, False: 386] | | ------------------ ------------------ 187| 386| } 188| 6.37k| if (out->szLog) ------------------ | Branch (188:9): [True: 6.28k, False: 89] ------------------ 189| 6.28k| { 190| 6.28k| inchi_free( out->szLog ); ------------------ | | 1152| 6.28k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.28k, False: 0] | | | Branch (1152:50): [Folded, False: 6.28k] | | ------------------ ------------------ 191| 6.28k| } 192| 6.37k| if (out->szMessage) ------------------ | Branch (192:9): [True: 6.28k, False: 89] ------------------ 193| 6.28k| { 194| 6.28k| inchi_free( out->szMessage ); ------------------ | | 1152| 6.28k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.28k, False: 0] | | | Branch (1152:50): [Folded, False: 6.28k] | | ------------------ ------------------ 195| 6.28k| } 196| | 197| 6.37k| memset( out, 0, sizeof( *out ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 198| 6.37k|} CheckINCHI: 812| 12.7k|{ 813| 12.7k| int ret = INCHI_VALID_NON_STANDARD; 814| 12.7k| int ret_i2i; 815| 12.7k| inchi_InputINCHI inchi_inp; 816| 12.7k| inchi_Output inchi_out; 817| 12.7k| size_t slen, pos_slash1 = 0; 818| 12.7k| char *str = NULL; 819| 12.7k| size_t i; 820| 12.7k| size_t slen0; 821| 12.7k| char pp; 822| | 823| | /* .. non-empty */ 824| 12.7k| if (szINCHI == NULL) ------------------ | Branch (824:9): [True: 0, False: 12.7k] ------------------ 825| 0| { 826| 0| return INCHI_INVALID_PREFIX; 827| 0| } 828| | 829| 12.7k| slen = strlen( szINCHI ); 830| | 831| | 832| | /* .. has valid prefix */ 833| 12.7k| if (slen < LEN_INCHI_STRING_PREFIX + 3) ------------------ | | 739| 12.7k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (833:9): [True: 2, False: 12.7k] ------------------ 834| 2| { 835| 2| return INCHI_INVALID_PREFIX; 836| 2| } 837| 12.7k| if (memcmp( szINCHI, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 738| 12.7k|#define INCHI_STRING_PREFIX "InChI=" ------------------ if (memcmp( szINCHI, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 739| 12.7k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (837:9): [True: 26, False: 12.7k] ------------------ 838| 26| { 839| 26| return INCHI_INVALID_PREFIX; 840| 26| } 841| | 842| | /* .. has InChI version 1 */ 843| | /* if (!isdigit(szINCHI[LEN_INCHI_STRING_PREFIX]) ) */ 844| 12.7k| if (szINCHI[LEN_INCHI_STRING_PREFIX] != '1') ------------------ | | 739| 12.7k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (844:9): [True: 0, False: 12.7k] ------------------ 845| 0| { 846| 0| return INCHI_INVALID_VERSION; 847| 0| } 848| | 849| | /* Determine the InChI calculation-class designator. 850| | * Historical InChI=1/... remains accepted as non-standard input. 851| | */ 852| 12.7k| pos_slash1 = LEN_INCHI_STRING_PREFIX + 1; ------------------ | | 739| 12.7k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ 853| | 854| 12.7k| if (szINCHI[pos_slash1] == 'S') ------------------ | Branch (854:9): [True: 72, False: 12.6k] ------------------ 855| 72| { 856| 72| ret = INCHI_VALID_STANDARD; 857| 72| pos_slash1++; 858| 72| } 859| 12.6k| else if (szINCHI[pos_slash1] == 'B') ------------------ | Branch (859:14): [True: 48, False: 12.5k] ------------------ 860| 48| { 861| 48| ret = INCHI_VALID_BETA; 862| 48| pos_slash1++; 863| 48| } 864| 12.5k| else if (szINCHI[pos_slash1] == 'N') ------------------ | Branch (864:14): [True: 0, False: 12.5k] ------------------ 865| 0| { 866| 0| ret = INCHI_VALID_NON_STANDARD; 867| 0| pos_slash1++; 868| 0| } 869| | 870| | /* Molecular Inorganics subversion designator */ 871| 12.7k| if (szINCHI[pos_slash1] == 'B') ------------------ | Branch (871:9): [True: 0, False: 12.7k] ------------------ 872| 0| { 873| 0| pos_slash1++; 874| 0| } 875| | 876| | /* .. has trailing slash in the right place */ 877| 12.7k| if (szINCHI[pos_slash1] != '/') ------------------ | Branch (877:9): [True: 0, False: 12.7k] ------------------ 878| 0| { 879| 0| return INCHI_INVALID_LAYOUT; 880| 0| } 881| | 882| | /* .. the rest of source string contains valid literals */ 883| | 884| | 885| | /* adjust line len so we not check trailing whitespaces */ 886| 12.7k| i = slen - 1; 887| 12.7k| while (isspace(UCINT szINCHI[i--])) slen--; ------------------ | Branch (887:12): [True: 646, False: 12.7k] ------------------ 888| | 889| | /* Treat possible SaveOpt letters */ 890| 12.7k| slen0 = slen; 891| 12.7k| if (( szINCHI[slen - 3] == '\\' ) && ------------------ | Branch (891:9): [True: 28, False: 12.6k] ------------------ 892| 28| ( szINCHI[slen - 2] >= 'A' ) && ( szINCHI[slen - 2] <= 'Z' ) && ------------------ | Branch (892:9): [True: 26, False: 2] | Branch (892:41): [True: 26, False: 0] ------------------ 893| 26| ( szINCHI[slen - 1] >= 'A' ) && ( szINCHI[slen - 1] <= 'Z' ) ------------------ | Branch (893:9): [True: 26, False: 0] | Branch (893:41): [True: 26, False: 0] ------------------ 894| 12.7k| ) 895| 26| { 896| 26| slen0 = slen - 3; 897| 26| } 898| | 899| 12.7k| int prev_is_slash = 1; 900| 4.80M| for (i = pos_slash1 + 1; i < slen0; i++) ------------------ | Branch (900:30): [True: 4.79M, False: 12.5k] ------------------ 901| 4.79M| { 902| 4.79M| pp = szINCHI[i]; 903| 4.79M|#if ( FIX_GAF_2020_GENERIC==1 ) 904| 4.79M| if (prev_is_slash) ------------------ | Branch (904:13): [True: 88.0k, False: 4.70M] ------------------ 905| 88.0k| { 906| | /* After slash: */ 907| 88.0k| if (pp == '0') ------------------ | Branch (907:17): [True: 4, False: 88.0k] ------------------ 908| 4| { 909| | /* '0' is never allowed */ 910| 4| return INCHI_INVALID_LAYOUT; 911| 4| } 912| 88.0k| if (i > pos_slash1 + 1) ------------------ | Branch (912:17): [True: 75.3k, False: 12.7k] ------------------ 913| 75.3k| { 914| | /* Not in main formula layer... */ 915| 75.3k| if (!islower(pp)) ------------------ | Branch (915:21): [True: 34, False: 75.2k] ------------------ 916| 34| { 917| | /* only lowercase letters are allowed */ 918| 34| return INCHI_INVALID_LAYOUT; 919| 34| } 920| 75.3k| } 921| 88.0k| } 922| 4.79M| prev_is_slash = (pp != '/') ? 0 : 1; ------------------ | Branch (922:25): [True: 4.71M, False: 76.1k] ------------------ 923| 4.79M|#endif 924| 4.79M| if (pp >= 'A' && pp <= 'Z') continue; ------------------ | Branch (924:13): [True: 2.92M, False: 1.86M] | Branch (924:26): [True: 191k, False: 2.73M] ------------------ 925| 4.60M| if (pp >= 'a' && pp <= 'z') continue; ------------------ | Branch (925:13): [True: 2.73M, False: 1.86M] | Branch (925:26): [True: 2.73M, False: 0] ------------------ 926| 1.86M| if (pp >= '0' && pp <= '9') continue; ------------------ | Branch (926:13): [True: 780k, False: 1.08M] | Branch (926:26): [True: 762k, False: 17.5k] ------------------ 927| 1.10M| switch (pp) 928| 1.10M| { 929| 703k| case '(': case ')': ------------------ | Branch (929:13): [True: 370k, False: 731k] | Branch (929:23): [True: 333k, False: 768k] ------------------ 930| 710k| case '*': case '+': ------------------ | Branch (930:13): [True: 4.31k, False: 1.09M] | Branch (930:23): [True: 2.76k, False: 1.09M] ------------------ 931| 992k| case ',': case '-': ------------------ | Branch (931:13): [True: 213k, False: 888k] | Branch (931:23): [True: 67.8k, False: 1.03M] ------------------ 932| 1.08M| case '.': case '/': ------------------ | Branch (932:13): [True: 15.8k, False: 1.08M] | Branch (932:23): [True: 76.1k, False: 1.02M] ------------------ 933| 1.08M|#if ( FIX_GAF_2020_GENERIC==1 ) 934| 1.10M| case ';': case '?': continue; ------------------ | Branch (934:13): [True: 8.26k, False: 1.09M] | Branch (934:23): [True: 9.20k, False: 1.09M] ------------------ 935| |#else 936| | case ';': case '=': 937| | case '?': case '@': continue; 938| |#endif 939| 112| default: return INCHI_INVALID_LAYOUT; ------------------ | Branch (939:13): [True: 112, False: 1.10M] ------------------ 940| 1.10M| } 941| 1.10M| } 942| | 943| 12.5k| if (strict) ------------------ | Branch (943:9): [True: 0, False: 12.5k] ------------------ 944| 0| { 945| 0| char opts[] = "?FixedH ?RecMet ?SUU ?SLUUD"; 946| 0| extract_inchi_substring( &str, szINCHI, slen ); 947| 0| if (NULL == str) ------------------ | Branch (947:13): [True: 0, False: 0] ------------------ 948| 0| { 949| 0| ret = INCHI_FAIL_I2I; 950| 0| goto fin; 951| 0| } 952| | 953| 0| inchi_inp.szInChI = str; 954| 0| opts[0] = opts[8] = opts[16] = opts[21] = INCHI_OPTION_PREFX; ------------------ | | 231| 0|#define INCHI_OPTION_PREFX '-' ------------------ 955| 0| inchi_inp.szOptions = opts; 956| | 957| 0| ret_i2i = GetINCHIfromINCHI( &inchi_inp, &inchi_out ); 958| | 959| 0| if (( ( ret_i2i != inchi_Ret_OKAY ) && ( ret_i2i != inchi_Ret_WARNING ) ) || !inchi_out.szInChI) ------------------ | Branch (959:15): [True: 0, False: 0] | Branch (959:48): [True: 0, False: 0] | Branch (959:86): [True: 0, False: 0] ------------------ 960| 0| { 961| 0| ret = INCHI_FAIL_I2I; 962| 0| } 963| 0| else 964| 0| { 965| 0| const char *in_str = inchi_inp.szInChI; 966| 0| const char *out_str = inchi_out.szInChI; 967| | 968| | /* 969| | * Historical non-standard InChI=1/ input is normalized 970| | * to the explicit InChI=1N/ form during InChI-to-InChI 971| | * conversion. Ignore only this prefix difference. 972| | */ 973| 0| if (!strncmp(in_str, "InChI=1/", 8) && ------------------ | Branch (973:17): [True: 0, False: 0] ------------------ 974| 0| !strncmp(out_str, "InChI=1N/", 9)) ------------------ | Branch (974:17): [True: 0, False: 0] ------------------ 975| 0| { 976| 0| in_str += 8; 977| 0| out_str += 9; 978| 0| } 979| | 980| 0| if (strcmp(in_str, out_str)) ------------------ | Branch (980:17): [True: 0, False: 0] ------------------ 981| 0| { 982| 0| ret = INCHI_FAIL_I2I; 983| 0| } 984| 0| } 985| 0| } 986| | 987| 12.5k|fin:if (strict) ------------------ | Branch (987:9): [True: 0, False: 12.5k] ------------------ 988| 0|{ 989| 0| if (NULL != str) ------------------ | Branch (989:9): [True: 0, False: 0] ------------------ 990| 0| inchi_free( str ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 991| 0|} 992| | 993| 12.5k| return ret; 994| 12.5k|} parse_options_string: 1042| 12.7k|{ 1043| 12.7k| char *p; 1044| 12.7k| char *pArgCurChar; 1045| 12.7k| int bInsideQuotes; 1046| 12.7k| int bCopyCharToArg; 1047| 12.7k| int nNumBackSlashes; 1048| 12.7k| int i; 1049| | 1050| 12.7k| i = 0; 1051| 12.7k| argv[i++] = ""; /* zeroth argument is not used */ 1052| 12.7k| p = cmd; 1053| 12.7k| bInsideQuotes = 0; 1054| | 1055| | /* arguments, one by one */ 1056| 25.4k| while (i < maxargs - 1) ------------------ | Branch (1056:12): [True: 25.4k, False: 0] ------------------ 1057| 25.4k| { 1058| | /* bypass spaces */ 1059| 38.2k| while (*p == ' ' || *p == '\t') ------------------ | Branch (1059:16): [True: 12.7k, False: 25.4k] | Branch (1059:29): [True: 0, False: 25.4k] ------------------ 1060| 12.7k| { 1061| 12.7k| p++; 1062| 12.7k| } 1063| 25.4k| if (!*p) ------------------ | Branch (1063:13): [True: 12.7k, False: 12.7k] ------------------ 1064| 12.7k| { 1065| 12.7k| break; 1066| 12.7k| } 1067| | 1068| | /* scan an argument */ 1069| 12.7k| argv[i++] = pArgCurChar = p; /* store preliminary ptr to arg */ 1070| | 1071| 171k| while (1) ------------------ | Branch (1071:16): [True: 171k, Folded] ------------------ 1072| 171k| { 1073| 171k| bCopyCharToArg = 1; 1074| 171k| nNumBackSlashes = 0; 1075| 171k| while (*p == '\\') ------------------ | Branch (1075:20): [True: 0, False: 171k] ------------------ 1076| 0| { 1077| 0| ++p; 1078| 0| ++nNumBackSlashes; 1079| 0| } 1080| | 1081| | /* each pair of backslashes => one backslash; one more backslash => literal quote */ 1082| 171k| if (*p == '\"') ------------------ | Branch (1082:17): [True: 0, False: 171k] ------------------ 1083| 0| { 1084| | /* one " found */ 1085| 0| if (nNumBackSlashes % 2 == 0) ------------------ | Branch (1085:21): [True: 0, False: 0] ------------------ 1086| 0| { 1087| 0| if (bInsideQuotes) ------------------ | Branch (1087:25): [True: 0, False: 0] ------------------ 1088| 0| { 1089| 0| if (*( p + 1 ) == '\"') ------------------ | Branch (1089:29): [True: 0, False: 0] ------------------ 1090| 0| { 1091| 0| p++; 1092| 0| } 1093| 0| else 1094| 0| { 1095| 0| bCopyCharToArg = 0; 1096| 0| } 1097| 0| } 1098| 0| else 1099| 0| { 1100| 0| bCopyCharToArg = 0; 1101| 0| } 1102| 0| bInsideQuotes = !bInsideQuotes; 1103| 0| } 1104| 0| nNumBackSlashes /= 2; /* divide nNumBackSlashes by two */ 1105| 0| } 1106| 171k| while (nNumBackSlashes--) ------------------ | Branch (1106:20): [True: 0, False: 171k] ------------------ 1107| 0| { 1108| 0| *pArgCurChar++ = '\\'; 1109| 0| } 1110| 171k| if (!*p) ------------------ | Branch (1110:17): [True: 12.7k, False: 159k] ------------------ 1111| 12.7k| { 1112| 12.7k| break; 1113| 12.7k| } 1114| 159k| if (!bInsideQuotes && ( *p == ' ' || *p == '\t' )) ------------------ | Branch (1114:17): [True: 159k, False: 0] | Branch (1114:37): [True: 0, False: 159k] | Branch (1114:50): [True: 0, False: 159k] ------------------ 1115| 0| { 1116| 0| p++; 1117| | /* move to the next char because this char may become 1118| | * zero due to *pArgCurChar++ = '\0'; line below */ 1119| 0| break; 1120| 0| } 1121| 159k| if (bCopyCharToArg) ------------------ | Branch (1121:17): [True: 159k, False: 0] ------------------ 1122| 159k| { 1123| 159k| *pArgCurChar++ = *p; 1124| 159k| } 1125| 159k| ++p; 1126| 159k| } 1127| 12.7k| *pArgCurChar++ = '\0'; /* argument zero termination */ 1128| 12.7k| } 1129| | 1130| | /* The last argument is NULL */ 1131| 12.7k| argv[i] = NULL; 1132| | 1133| 12.7k| return i; 1134| 12.7k|} InpAtom0DToInchiAtom: 1680| 1.75k|{ 1681| 1.75k| int num_stereo_centers, num_stereo_bonds, num_inp_stereo0D, i, m, m1, m2, n, ret = 0; 1682| | 1683| | /* count stereobonds, allenes. cumulenes. and stereoatoms */ 1684| 1.75k| num_stereo_centers = num_stereo_bonds = ret = 0; 1685| | 1686| 1.75k| *atom = NULL; 1687| 1.75k| *num_atoms = 0; 1688| 1.75k| *stereo0D = NULL; 1689| 1.75k| *num_stereo0D = 0; 1690| | 1691| 132k| for (i = 0; i < num_inp_atoms; i++) ------------------ | Branch (1691:17): [True: 130k, False: 1.75k] ------------------ 1692| 130k| { 1693| 130k| if (at[i].p_parity) ------------------ | Branch (1693:13): [True: 224, False: 130k] ------------------ 1694| 224| { 1695| | /* stereocenter */ 1696| 224| num_stereo_centers++; 1697| 224| } 1698| 130k| else 1699| 130k| { 1700| 130k| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) ------------------ | | 873| 261k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1700:25): [True: 130k, False: 14] | Branch (1700:53): [True: 738, False: 130k] ------------------ 1701| 738| { 1702| 738| ; 1703| 738| } 1704| 130k| num_stereo_bonds += m; 1705| 130k| } 1706| 130k| } 1707| | 1708| 1.75k| num_stereo_bonds /= 2; 1709| 1.75k| num_inp_stereo0D = num_stereo_bonds + num_stereo_centers; 1710| | 1711| 1.75k| if (num_inp_atoms > 0) ------------------ | Branch (1711:9): [True: 1.75k, False: 0] ------------------ 1712| 1.75k| { 1713| 1.75k| *atom = (inchi_Atom *) inchi_calloc( num_inp_atoms, sizeof( ( *atom )[0] ) ); ------------------ | | 1146| 1.75k|#define inchi_calloc calloc ------------------ 1714| 1.75k| } 1715| | 1716| 1.75k| *num_atoms = num_inp_atoms; 1717| | 1718| 1.75k| if (num_inp_stereo0D > 0) ------------------ | Branch (1718:9): [True: 386, False: 1.36k] ------------------ 1719| 386| { 1720| 386| *stereo0D = (inchi_Stereo0D *) inchi_calloc( num_inp_stereo0D, sizeof( ( *stereo0D )[0] ) ); ------------------ | | 1146| 386|#define inchi_calloc calloc ------------------ 1721| 386| } 1722| | 1723| 1.75k| if ((num_inp_atoms && !( *atom )) || (num_inp_stereo0D > 0 && !( *stereo0D ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1723:10): [True: 1.75k, False: 0] | Branch (1723:27): [True: 0, False: 1.75k] | Branch (1723:43): [True: 386, False: 1.36k] | Branch (1723:67): [True: 0, False: 386] ------------------ 1724| 0| { 1725| | /* allocation failed */ 1726| 0| ret = -1; 1727| 0| goto exit_function; 1728| 0| } 1729| | 1730| | /* copy atom properties */ 1731| 132k| for (i = 0; i < num_inp_atoms; i++) ------------------ | Branch (1731:17): [True: 130k, False: 1.75k] ------------------ 1732| 130k| { 1733| 130k| ( *atom )[i].num_bonds = at[i].valence; 1734| 250k| for (m = 0; m < at[i].valence; m++) ------------------ | Branch (1734:21): [True: 120k, False: 130k] ------------------ 1735| 120k| { 1736| 120k| ( *atom )[i].bond_type[m] = at[i].bond_type[m]; 1737| 120k| ( *atom )[i].neighbor[m] = at[i].neighbor[m]; 1738| 120k| } 1739| 130k| ( *atom )[i].charge = at[i].charge; 1740| |#if USE_BCF 1741| | memcpy_s( ( *atom )[i].elname, ATOM_EL_LEN, at[i].elname, ATOM_EL_LEN ); /* djb-rwth: function replaced with its safe C11 variant */ 1742| |#else 1743| 130k| memcpy( ( *atom )[i].elname, at[i].elname, ATOM_EL_LEN ); ------------------ | | 71| 130k|#define ATOM_EL_LEN 6 /* length of ASCIIZ element symbol field */ ------------------ 1744| 130k|#endif 1745| 130k| if (at[i].iso_atw_diff) ------------------ | Branch (1745:13): [True: 704, False: 129k] ------------------ 1746| 704| { 1747| 704| ( *atom )[i].isotopic_mass = ISOTOPIC_SHIFT_FLAG + ( at[i].iso_atw_diff > 0 ? at[i].iso_atw_diff - 1 : at[i].iso_atw_diff ); ------------------ | | 73| 704|#define ISOTOPIC_SHIFT_FLAG 10000 /* add to isotopic mass if isotopic_mass = */ ------------------ | Branch (1747:66): [True: 682, False: 22] ------------------ 1748| 704| } 1749| 130k| ( *atom )[i].num_iso_H[0] = at[i].num_H; 1750| 521k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 72| 521k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (1750:21): [True: 391k, False: 130k] ------------------ 1751| 391k| { 1752| 391k| ( *atom )[i].num_iso_H[m + 1] = at[i].num_iso_H[m]; 1753| 391k| } 1754| 130k| ( *atom )[i].radical = at[i].radical; 1755| 130k| } 1756| | 1757| | /* stereo */ 1758| 132k| for (i = n = 0; i < num_inp_atoms; i++) ------------------ | Branch (1758:21): [True: 130k, False: 1.75k] ------------------ 1759| 130k| { 1760| 130k| if (at[i].p_parity) ------------------ | Branch (1760:13): [True: 224, False: 130k] ------------------ 1761| 224| { 1762| 224| if (n < num_inp_stereo0D) ------------------ | Branch (1762:17): [True: 223, False: 1] ------------------ 1763| 223| { 1764| 223| ( *stereo0D )[n].central_atom = i; 1765| 223| ( *stereo0D )[n].parity = at[i].p_parity; 1766| 223| ( *stereo0D )[n].type = INCHI_StereoType_Tetrahedral; 1767| 1.11k| for (m = 0; m < MAX_NUM_STEREO_ATOM_NEIGH; m++) ------------------ | | 877| 1.11k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1767:29): [True: 892, False: 223] ------------------ 1768| 892| { 1769| 892| ( *stereo0D )[n].neighbor[m] = at[i].p_orig_at_num[m] - 1; 1770| 892| } 1771| 223| n++; 1772| 223| } 1773| 1| else 1774| 1| { 1775| 1| ret |= 1; 1776| 1| break; 1777| 1| } 1778| 224| } 1779| 130k| else 1780| 130k| { 1781| 130k| for (m1 = 0; m1 < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m1]; m1++) ------------------ | | 873| 261k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1781:26): [True: 130k, False: 14] | Branch (1781:55): [True: 738, False: 130k] ------------------ 1782| 738| { 1783| | /* find the opposite atom at the other end of double bond, allene, or cumulene */ 1784| 738| int chain[12], len = 0, nxt_neigh, nxt, cur; 1785| 738| cur = chain[len++] = i; 1786| 738| nxt_neigh = at[cur].sb_ord[m1]; 1787| | 1788| 738| do 1789| 759| { 1790| | /* add next atom */ 1791| 759| chain[len++] = nxt = at[cur].neighbor[nxt_neigh]; 1792| 759| nxt_neigh = ( at[nxt].neighbor[0] == cur ); 1793| 759| cur = nxt; 1794| | /* find nxt_neigh */ 1795| 759| } 1796| 759| while (!at[cur].sb_parity[0] && ------------------ | Branch (1796:24): [True: 21, False: 738] ------------------ 1797| 21| len < 12 && ------------------ | Branch (1797:24): [True: 21, False: 0] ------------------ 1798| 21| at[cur].valence == 2); ------------------ | Branch (1798:24): [True: 21, False: 0] ------------------ 1799| | 1800| 738| if (at[cur].sb_parity[0] && len <= 4 && i < cur /* count bonds only one time */) ------------------ | Branch (1800:21): [True: 738, False: 0] | Branch (1800:45): [True: 738, False: 0] | Branch (1800:57): [True: 367, False: 371] ------------------ 1801| 367| { 1802| | /* double bond, cumulene, or allene has been found */ 1803| 413| for (m2 = 0; m2 < MAX_NUM_STEREO_BONDS && at[cur].sb_parity[m2]; m2++) ------------------ | | 873| 826|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1803:34): [True: 413, False: 0] | Branch (1803:63): [True: 412, False: 1] ------------------ 1804| 412| { 1805| 412| if (chain[len - 2] == at[cur].neighbor[(int) at[cur].sb_ord[m2]]) ------------------ | Branch (1805:29): [True: 366, False: 46] ------------------ 1806| 366| { 1807| 366| if (n < num_inp_stereo0D) ------------------ | Branch (1807:33): [True: 366, False: 0] ------------------ 1808| 366| { 1809| 366| int parity1 = at[i].sb_parity[m1]; 1810| 366| int parity2 = at[cur].sb_parity[m2]; 1811| 366| int parity; 1812| 366| if (( INCHI_PARITY_ODD == parity1 || INCHI_PARITY_EVEN == parity1 ) && ------------------ | Branch (1812:39): [True: 137, False: 229] | Branch (1812:70): [True: 110, False: 119] ------------------ 1813| 247| ( INCHI_PARITY_ODD == parity2 || INCHI_PARITY_EVEN == parity2 )) ------------------ | Branch (1813:39): [True: 33, False: 214] | Branch (1813:70): [True: 214, False: 0] ------------------ 1814| 247| { 1815| | /* well-defined parity */ 1816| 247| parity = ( parity1 == parity2 ) ? INCHI_PARITY_EVEN : INCHI_PARITY_ODD; ------------------ | Branch (1816:46): [True: 105, False: 142] ------------------ 1817| 247| } 1818| 119| else 1819| 119| { 1820| 119| parity = inchi_max( parity1, parity2 ); ------------------ | | 138| 119|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 119] | | ------------------ ------------------ 1821| 119| } 1822| 366| ( *stereo0D )[n].central_atom = ( len == 3 ) ? chain[1] : NO_ATOM; ------------------ | | 369| 728|#define NO_ATOM (-1) /* non-existent (central) atom */ ------------------ | Branch (1822:65): [True: 4, False: 362] ------------------ 1823| 366| ( *stereo0D )[n].parity = parity; 1824| 366| ( *stereo0D )[n].type = len == 3 ? INCHI_StereoType_Allene : INCHI_StereoType_DoubleBond; ------------------ | Branch (1824:57): [True: 4, False: 362] ------------------ 1825| 366| ( *stereo0D )[n].neighbor[0] = at[i].sn_orig_at_num[m1] - 1; 1826| 366| ( *stereo0D )[n].neighbor[1] = i; 1827| 366| ( *stereo0D )[n].neighbor[2] = cur; 1828| 366| ( *stereo0D )[n].neighbor[3] = at[cur].sn_orig_at_num[m2] - 1; 1829| 366| n++; 1830| 366| } 1831| 0| else 1832| 0| { 1833| 0| ret |= 1; 1834| 0| } 1835| 366| break; 1836| 366| } 1837| 412| } 1838| 367| } 1839| 738| } 1840| 130k| } 1841| 130k| } 1842| | 1843| 1.75k| *num_stereo0D = n; 1844| | 1845| 1.75k|exit_function: 1846| 1.75k| if (ret < 0) ------------------ | Branch (1846:9): [True: 0, False: 1.75k] ------------------ 1847| 0| { 1848| 0| if (*atom) ------------------ | Branch (1848:13): [True: 0, False: 0] ------------------ 1849| 0| { 1850| 0| inchi_free( *atom ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1851| 0| } 1852| 0| if (*stereo0D) ------------------ | Branch (1852:13): [True: 0, False: 0] ------------------ 1853| 0| { 1854| 0| inchi_free( *stereo0D ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1855| 0| } 1856| 0| *atom = NULL; 1857| 0| *stereo0D = NULL; 1858| 0| *num_atoms = 0; 1859| 0| *num_stereo0D = 0; 1860| 0| } 1861| | 1862| 1.75k| return ret; 1863| 1.75k|} GetINCHIfromINCHI: 2120| 6.37k|{ 2121| 6.37k| STRUCT_DATA struct_data; 2122| 6.37k| STRUCT_DATA *sd = &struct_data; 2123| | 2124| 6.37k| static char szMainOption[] = " ?InChI2InChI"; 2125| | 2126| 6.37k| INCHI_CLOCK ic; 2127| 6.37k| CANON_GLOBALS CG; 2128| | 2129| 6.37k| int i; 2130| 6.37k| char szSdfDataValue[MAX_SDF_VALUE + 1]; 2131| 6.37k| unsigned long ulDisplTime = 0; /* infinite, milliseconds */ 2132| | 2133| 6.37k| INPUT_PARMS inp_parms; 2134| 6.37k| INPUT_PARMS *ip = &inp_parms; 2135| | 2136| 6.37k| int bReleaseVersion = bRELEASE_VERSION; ------------------ | | 238| 6.37k|#define bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */ ------------------ 2137| 6.37k| int nRet = 0, nRet1; 2138| | 2139| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2140| | int num_repeat = REPEAT_ALL; 2141| |#endif 2142| | 2143| 6.37k| const char *argv[INCHI_MAX_NUM_ARG + 1]; 2144| 6.37k| int argc; 2145| 6.37k| char *szOptions = NULL; 2146| | 2147| 6.37k| INCHI_IOSTREAM inchi_file[3], *out_file = inchi_file, *log_file = inchi_file + 1, *input_file = inchi_file + 2; 2148| | 2149| |#if( TRACE_MEMORY_LEAKS == 1 ) 2150| | _CrtSetDbgFlag( _CRTDBG_CHECK_ALWAYS_DF | _CRTDBG_LEAK_CHECK_DF | _CRTDBG_ALLOC_MEM_DF ); 2151| |/* for execution outside the VC++ debugger uncomment one of the following two */ 2152| | 2153| |#ifdef MY_REPORT_FILE 2154| | _CrtSetReportMode( _CRT_WARN, _CRTDBG_MODE_FILE ); 2155| | _CrtSetReportFile( _CRT_WARN, MY_REPORT_FILE ); 2156| | _CrtSetReportMode( _CRT_ERROR, _CRTDBG_MODE_FILE ); 2157| | _CrtSetReportFile( _CRT_ERROR, MY_REPORT_FILE ); 2158| | _CrtSetReportMode( _CRT_ASSERT, _CRTDBG_MODE_FILE ); 2159| | _CrtSetReportFile( _CRT_ASSERT, MY_REPORT_FILE ); 2160| |#else 2161| | _CrtSetReportMode( _CRT_WARN | _CRT_ERROR, _CRTDBG_MODE_DEBUG ); 2162| |#endif 2163| | 2164| | /* turn on floating point exceptions */ 2165| |#if ( !defined(__STDC__) || __STDC__ != 1 ) 2166| | { 2167| | /* Get the default control word. */ 2168| | int cw = _controlfp( 0, 0 ); 2169| | 2170| | /* Set the exception masks OFF, turn exceptions on. */ 2171| | /*cw &=~(EM_OVERFLOW|EM_UNDERFLOW|EM_INEXACT|EM_ZERODIVIDE|EM_DENORMAL);*/ 2172| | cw &= ~( EM_OVERFLOW | EM_UNDERFLOW | EM_ZERODIVIDE | EM_DENORMAL ); 2173| | 2174| | /* Set the control word. */ 2175| | _controlfp( cw, MCW_EM ); 2176| | } 2177| |#endif 2178| |#endif 2179| | 2180| 6.37k| memset( out, 0, sizeof( *out ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2181| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2182| |repeat: 2183| | FreeINCHI( out ); 2184| | inchi_ios_close( out_file ); 2185| | inchi_ios_close( log_file ); 2186| | inchi_ios_reset( input_file ); /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2187| |#endif 2188| | 2189| | /* Initialize internal for this function I/O streams as string buffers */ 2190| 6.37k| inchi_ios_init( input_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1016| 6.37k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2191| 6.37k| inchi_ios_init( out_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1016| 6.37k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2192| 6.37k| inchi_ios_init( log_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1016| 6.37k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2193| | 2194| 6.37k| sd->bUserQuit = 0; 2195| | 2196| | /* clear original input structure */ 2197| | /* memset( inchi_file, 0, sizeof(inchi_file) ); */ 2198| 6.37k| memset( sd, 0, sizeof( *sd ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2199| 6.37k| memset( ip, 0, sizeof( *ip ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2200| 6.37k| memset( szSdfDataValue, 0, sizeof( szSdfDataValue ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2201| | 2202| 6.37k| memset( &ic, 0, sizeof( ic ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2203| 6.37k| memset( &CG, 0, sizeof( CG ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2204| | 2205| 6.37k| szMainOption[1] = INCHI_OPTION_PREFX; ------------------ | | 231| 6.37k|#define INCHI_OPTION_PREFX '-' ------------------ 2206| | 2207| 6.37k| if (!inpInChI) ------------------ | Branch (2207:9): [True: 0, False: 6.37k] ------------------ 2208| 0| { 2209| 0| nRet = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2210| 0| goto exit_function; 2211| 0| } 2212| | 2213| | /* options */ 2214| 6.37k| if (inpInChI) ------------------ | Branch (2214:9): [True: 6.37k, False: 0] ------------------ 2215| 6.37k| { 2216| 6.37k| int opt_len = (int) ( ( inpInChI->szOptions ? strlen( inpInChI->szOptions ) : 0 ) + sizeof( szMainOption ) + 1 ); ------------------ | Branch (2216:33): [True: 0, False: 6.37k] ------------------ 2217| 6.37k| szOptions = (char*) inchi_calloc( (long long)opt_len + 1, sizeof( szOptions[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 6.37k|#define inchi_calloc calloc ------------------ 2218| 6.37k| if (szOptions) ------------------ | Branch (2218:13): [True: 6.37k, False: 0] ------------------ 2219| 6.37k| { 2220| 6.37k| if (inpInChI->szOptions) ------------------ | Branch (2220:17): [True: 0, False: 6.37k] ------------------ 2221| 0| { 2222| 0| strcpy( szOptions, inpInChI->szOptions ); 2223| 0| } 2224| 6.37k| strcat( szOptions, szMainOption ); 2225| 6.37k| argc = parse_options_string( szOptions, argv, INCHI_MAX_NUM_ARG ); ------------------ | | 11| 6.37k|#define INCHI_MAX_NUM_ARG 32 ------------------ 2226| 6.37k| } 2227| 0| else 2228| 0| { 2229| 0| nRet = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 2230| 0| goto translate_RetVal; /* emergency exit */ 2231| 0| } 2232| 6.37k| } 2233| 0| else 2234| 0| { 2235| 0| argc = 1; 2236| 0| argv[0] = ""; 2237| 0| argv[1] = NULL; 2238| 0| } 2239| | 2240| 6.37k| if ((argc == 1 ------------------ | Branch (2240:10): [True: 0, False: 6.37k] ------------------ 2241| 0|#ifdef TARGET_API_LIB 2242| 0| && ( !inpInChI || !inpInChI->szInChI )) ------------------ | Branch (2242:14): [True: 0, False: 0] | Branch (2242:27): [True: 0, False: 0] ------------------ 2243| 6.37k|#endif 2244| | 2245| 6.37k| || (argc == 2 && ( argv[1][0] == INCHI_OPTION_PREFX ) && ------------------ | | 231| 6.37k|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (2245:13): [True: 6.37k, False: 0] | Branch (2245:26): [True: 6.37k, False: 0] ------------------ 2246| 6.37k| ( !strcmp( argv[1] + 1, "?" ) || !inchi_stricmp( argv[1] + 1, "help" ) ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2246:11): [True: 0, False: 6.37k] | Branch (2246:42): [True: 0, False: 6.37k] ------------------ 2247| 0| { 2248| 0| HelpCommandLineParms( log_file ); 2249| 0| out->szLog = log_file->s.pStr; 2250| 0| memset( log_file, 0, sizeof( *log_file ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2251| 0| nRet = _IS_EOF; ------------------ | | 15| 0|#define _IS_EOF -1 /* end of file */ ------------------ 2252| 0| inchi_free(szOptions); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2253| 0| goto translate_RetVal; 2254| 0| } 2255| | 2256| 6.37k| nRet1 = ReadCommandLineParms( argc, argv, ip, szSdfDataValue, 2257| 6.37k| &ulDisplTime, bReleaseVersion, log_file ); 2258| | 2259| 6.37k| if (szOptions) ------------------ | Branch (2259:9): [True: 6.37k, False: 0] ------------------ 2260| 6.37k| { 2261| | /* argv pointed to strings in szOptions */ 2262| 6.37k| inchi_free( szOptions ); ------------------ | | 1152| 6.37k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.37k, False: 0] | | | Branch (1152:50): [Folded, False: 6.37k] | | ------------------ ------------------ 2263| 6.37k| szOptions = NULL; 2264| 6.37k| } 2265| | /* INChI DLL specific */ 2266| 6.37k| ip->bNoStructLabels = 1; 2267| | 2268| 6.37k| if (0 > nRet1) ------------------ | Branch (2268:9): [True: 0, False: 6.37k] ------------------ 2269| 0| { 2270| 0| goto exit_function; 2271| 0| } 2272| | 2273| 6.37k| if (ip->bNoStructLabels) ------------------ | Branch (2273:9): [True: 6.37k, False: 0] ------------------ 2274| 6.37k| { 2275| 6.37k| ip->pSdfLabel = NULL; 2276| 6.37k| ip->pSdfValue = NULL; 2277| 6.37k| } 2278| 0| else if (ip->nInputType == INPUT_INCHI_XML || ------------------ | Branch (2278:14): [True: 0, False: 0] ------------------ 2279| 0| ip->nInputType == INPUT_INCHI_PLAIN || ------------------ | Branch (2279:13): [True: 0, False: 0] ------------------ 2280| 0| ip->nInputType == INPUT_CMLFILE || ------------------ | Branch (2280:13): [True: 0, False: 0] ------------------ 2281| 0| ip->nInputType == INPUT_INCHI) ------------------ | Branch (2281:13): [True: 0, False: 0] ------------------ 2282| 0| { 2283| | /* the input may contain both the header and the label of the structure */ 2284| 0| if (!ip->pSdfLabel) ------------------ | Branch (2284:13): [True: 0, False: 0] ------------------ 2285| 0| { 2286| 0| ip->pSdfLabel = ip->szSdfDataHeader; 2287| 0| } 2288| 0| if (!ip->pSdfValue) ------------------ | Branch (2288:13): [True: 0, False: 0] ------------------ 2289| 0| { 2290| 0| ip->pSdfValue = szSdfDataValue; 2291| 0| } 2292| 0| } 2293| | 2294| 6.37k| if (ip->nInputType && ip->nInputType != INPUT_INCHI) ------------------ | Branch (2294:9): [True: 6.37k, False: 0] | Branch (2294:27): [True: 0, False: 6.37k] ------------------ 2295| 0| { 2296| 0| inchi_ios_eprint( log_file, "Input type set to INPUT_INCHI\n" ); 2297| 0| ip->nInputType = INPUT_INCHI; 2298| 0| } 2299| | 2300| 6.37k| if (!inpInChI->szInChI) ------------------ | Branch (2300:9): [True: 0, False: 6.37k] ------------------ 2301| 0| { 2302| 0| nRet = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2303| 0| goto exit_function; 2304| 0| } 2305| 6.37k| else 2306| 6.37k| { 2307| 6.37k| const int strict = 0; 2308| 6.37k| nRet = CheckINCHI( inpInChI->szInChI, strict ); 2309| 6.37k| if (nRet != INCHI_VALID_STANDARD && ------------------ | Branch (2309:13): [True: 6.33k, False: 35] ------------------ 2310| 6.33k| nRet != INCHI_VALID_NON_STANDARD && ------------------ | Branch (2310:13): [True: 113, False: 6.22k] ------------------ 2311| 113| nRet != INCHI_VALID_BETA) ------------------ | Branch (2311:13): [True: 89, False: 24] ------------------ 2312| 89| { 2313| 89| nRet = _IS_ERROR; ------------------ | | 12| 89|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2314| 89| goto exit_function; 2315| 89| } 2316| 6.37k| } 2317| | 2318| | 2319| 6.28k| PrintInputParms( log_file, ip ); 2320| | 2321| | /********************************/ 2322| | /* InChI -> InChI */ 2323| | /********************************/ 2324| | 2325| | /* input_file simulation */ 2326| 6.28k| input_file->s.pStr = inpInChI->szInChI; 2327| 6.28k| input_file->s.nUsedLength = (int) strlen( input_file->s.pStr ) + 1; 2328| 6.28k| input_file->s.nAllocatedLength = input_file->s.nUsedLength; 2329| 6.28k| input_file->s.nPtr = 0; 2330| | 2331| | /* buffer for the message */ 2332| 6.28k| out->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( out->szMessage[0] ) ); ------------------ | | 1146| 6.28k|#define inchi_calloc calloc ------------------ out->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( out->szMessage[0] ) ); ------------------ | | 2102| 6.28k|#define MAX_MSG_LEN 512 ------------------ 2333| 6.28k| if (!out->szMessage) ------------------ | Branch (2333:9): [True: 0, False: 6.28k] ------------------ 2334| 0| { 2335| 0| inchi_ios_eprint( log_file, "Cannot allocate output message buffer.\n" ); 2336| 0| nRet = -1; 2337| 0| } 2338| 6.28k| else 2339| 6.28k| { 2340| 6.28k| nRet = ReadWriteInChI( &ic, &CG, input_file, out_file, log_file, 2341| 6.28k| ip, sd, 2342| 6.28k| NULL, 0, NULL, 2343| 6.28k| NULL, NULL, 2344| 6.28k| out->szMessage, MAX_MSG_LEN, ------------------ | | 2102| 6.28k|#define MAX_MSG_LEN 512 ------------------ 2345| 6.28k| NULL /*out->WarningFlags*/ ); 2346| 6.28k| } 2347| | 2348| 6.28k| if (nRet >= 0 && out_file->s.pStr) ------------------ | Branch (2348:9): [True: 5.12k, False: 1.16k] | Branch (2348:22): [True: 5.02k, False: 93] ------------------ 2349| 5.02k| { 2350| | /* success */ 2351| 5.02k| char* p = NULL; 2352| | /* djb-rwth: fixing oss-fuzz issue #40971 */ 2353| 5.02k| int p_len, out_szinchi_len; 2354| 5.02k| out_szinchi_len = strlen(out_file->s.pStr); 2355| 5.02k| out->szInChI = out_file->s.pStr; 2356| 5.02k| out->szAuxInfo = NULL; 2357| | 2358| 5.02k| for (p = strchr( out->szInChI, '\n' ); p; p = strchr( p + 1, '\n' )) ------------------ | Branch (2358:48): [True: 5.02k, False: 0] ------------------ 2359| 5.02k| { 2360| 5.02k| p_len = strlen(p); 2361| 5.02k| if ((p_len >= 8) && !memcmp( p, "\nAuxInfo", 8 )) ------------------ | Branch (2361:17): [True: 0, False: 5.02k] | Branch (2361:33): [True: 0, False: 0] ------------------ 2362| 0| { 2363| 0| *p = '\0'; /* remove LF after INChI */ 2364| 0| out->szAuxInfo = p + 1; /* save pointer to AuxInfo */ 2365| 0| } 2366| 5.02k| else if (out->szAuxInfo || !p[1]) ------------------ | Branch (2366:22): [True: 0, False: 5.02k] | Branch (2366:40): [True: 5.02k, False: 0] ------------------ 2367| 5.02k| { 2368| | /* remove LF after aux info or from the last char */ 2369| 5.02k| *p = '\0'; 2370| 5.02k| break; 2371| 5.02k| } 2372| 5.02k| } 2373| 5.02k| out_file->s.pStr = NULL; 2374| 5.02k| } 2375| | 2376| | /* 2377| | out->szLog = log_file->pStr; 2378| | log_file->pStr = NULL; 2379| | */ 2380| | 2381| 6.37k|exit_function:; 2382| | 2383| 31.8k| for (i = 0; i < MAX_NUM_PATHS; i++) ------------------ | | 58| 31.8k|#define MAX_NUM_PATHS 4 ------------------ | Branch (2383:17): [True: 25.4k, False: 6.37k] ------------------ 2384| 25.4k| { 2385| 25.4k| if (ip->path[i]) ------------------ | Branch (2385:13): [True: 0, False: 25.4k] ------------------ 2386| 0| { 2387| 0| inchi_free( (char*) ip->path[i] ); /* cast deliberately discards 'const' qualifier */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2388| 0| ip->path[i] = NULL; 2389| 0| } 2390| 25.4k| } 2391| | 2392| 6.37k| SetBitFree( &CG ); 2393| | 2394| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2395| | if (num_repeat-- > 0) 2396| | { 2397| | goto repeat; 2398| | } 2399| |#endif 2400| | 2401| 6.37k|#ifdef TARGET_API_LIB 2402| | /* output */ 2403| | 2404| 6.37k| if (log_file->s.pStr && log_file->s.nUsedLength > 0) ------------------ | Branch (2404:13): [True: 6.28k, False: 89] | Branch (2404:33): [True: 6.28k, False: 0] ------------------ 2405| 6.28k| { 2406| 17.5k| while (log_file->s.nUsedLength && '\n' == log_file->s.pStr[log_file->s.nUsedLength - 1]) ------------------ | Branch (2406:20): [True: 17.5k, False: 0] | Branch (2406:47): [True: 11.3k, False: 6.28k] ------------------ 2407| 11.3k| { 2408| 11.3k| log_file->s.pStr[--log_file->s.nUsedLength] = '\0'; /* remove last LF */ 2409| 11.3k| } 2410| 6.28k| if (out) ------------------ | Branch (2410:17): [True: 6.28k, False: 0] ------------------ 2411| 6.28k| { 2412| 6.28k| out->szLog = log_file->s.pStr; 2413| 6.28k| log_file->s.pStr = NULL; 2414| 6.28k| } 2415| 6.28k| } 2416| | 2417| 6.37k|#endif 2418| | 2419| 6.37k|translate_RetVal: 2420| | 2421| | /* close internal output streams */ 2422| 6.37k| inchi_ios_close( out_file ); 2423| 6.37k| inchi_ios_close( log_file ); 2424| 6.37k| inchi_ios_reset( input_file ); /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2425| | 2426| 6.37k| switch (nRet) 2427| 6.37k| { 2428| 9| case -3: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2428:9): [True: 9, False: 6.36k] ------------------ 2429| 1.15k| case -2: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2429:9): [True: 1.15k, False: 5.21k] ------------------ 2430| 0| case -1: nRet = inchi_Ret_FATAL; break; /* Severe error: no Structure has been created (typically; break; memory allocation failed) */ ------------------ | Branch (2430:9): [True: 0, False: 6.37k] ------------------ 2431| 5.20k| default: ------------------ | Branch (2431:9): [True: 5.20k, False: 1.16k] ------------------ 2432| | /* 2433| | if ( !outStruct->atom || !outStruct->num_atoms ) 2434| | { 2435| | nRet = inchi_Ret_EOF; 2436| | } 2437| | else 2438| | { 2439| | int m,n,t=0; 2440| | for ( m=0; m < 2; m ++ ) 2441| | { 2442| | for ( n=0; n < 2; n ++ ) 2443| | { 2444| | if ( outStruct->WarningFlags[m][n] ) { 2445| | t ++; 2446| | } 2447| | } 2448| | } 2449| | nRet = t? inchi_Ret_WARNING : inchi_Ret_OKAY; 2450| | } 2451| | */ 2452| 5.20k| break; 2453| 6.37k| } 2454| | 2455| 6.37k| return nRet; 2456| 6.37k|} GetStructFromINCHIEx: 2491| 6.37k|{ 2492| 6.37k| INCHI_CLOCK ic; 2493| 6.37k| CANON_GLOBALS CG; 2494| 6.37k| STRUCT_DATA struct_data; 2495| 6.37k| STRUCT_DATA *sd = &struct_data; 2496| 6.37k| INPUT_PARMS inp_parms; 2497| 6.37k| INPUT_PARMS *ip = &inp_parms; 2498| 6.37k| INCHI_IOSTREAM inchi_file[3]; 2499| 6.37k| INCHI_IOSTREAM *out_file = inchi_file, *log_file = inchi_file + 1, *input_file = inchi_file + 2; 2500| 6.37k| int i, nRet = 0, nRet1; 2501| | /* djb-rwth: removing redundant variables/code */ 2502| 6.37k| int bReleaseVersion = bRELEASE_VERSION; /* djb-rwth: ignoring LLVM warning: variable used in function call */ ------------------ | | 238| 6.37k|#define bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */ ------------------ 2503| 6.37k| unsigned long ulDisplTime = 0; /* infinite, milliseconds */ 2504| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2505| | int num_repeat = REPEAT_ALL; 2506| |#endif 2507| 6.37k| static char szMainOption[] = " ?InChI2Struct"; 2508| 6.37k| char szSdfDataValue[MAX_SDF_VALUE + 1]; 2509| 6.37k| const char *argv[INCHI_MAX_NUM_ARG + 1]; 2510| 6.37k| int argc; 2511| 6.37k| char *szOptions = NULL; 2512| | /* conversion result */ 2513| 6.37k| inp_ATOM *at = NULL; 2514| 6.37k| int num_at = 0; 2515| 6.37k| OAD_Polymer *polymer = NULL; 2516| 6.37k| OAD_V3000 *v3000 = NULL; 2517| | 2518| |#if( TRACE_MEMORY_LEAKS == 1 ) 2519| | _CrtSetDbgFlag( _CRTDBG_CHECK_ALWAYS_DF | _CRTDBG_LEAK_CHECK_DF | _CRTDBG_ALLOC_MEM_DF ); 2520| | 2521| |/* for execution outside the VC++ debugger uncomment one of the following two */ 2522| |#ifdef MY_REPORT_FILE 2523| | _CrtSetReportMode( _CRT_WARN, _CRTDBG_MODE_FILE ); 2524| | _CrtSetReportFile( _CRT_WARN, MY_REPORT_FILE ); 2525| | _CrtSetReportMode( _CRT_ERROR, _CRTDBG_MODE_FILE ); 2526| | _CrtSetReportFile( _CRT_ERROR, MY_REPORT_FILE ); 2527| | _CrtSetReportMode( _CRT_ASSERT, _CRTDBG_MODE_FILE ); 2528| | _CrtSetReportFile( _CRT_ASSERT, MY_REPORT_FILE ); 2529| |#else 2530| | _CrtSetReportMode( _CRT_WARN | _CRT_ERROR, _CRTDBG_MODE_DEBUG ); 2531| |#endif 2532| | 2533| | /* turn on floating point exceptions */ 2534| |#if ( !defined(__STDC__) || __STDC__ != 1 ) 2535| | { 2536| | /* Get the default control word. */ 2537| | int cw = _controlfp( 0, 0 ); 2538| | 2539| | /* Set the exception masks OFF, turn exceptions on. */ 2540| | /*cw &=~(EM_OVERFLOW|EM_UNDERFLOW|EM_INEXACT|EM_ZERODIVIDE|EM_DENORMAL);*/ 2541| | cw &= ~( EM_OVERFLOW | EM_UNDERFLOW | EM_ZERODIVIDE | EM_DENORMAL ); 2542| | 2543| | /* Set the control word. */ 2544| | _controlfp( cw, MCW_EM ); 2545| | } 2546| |#endif 2547| |#endif 2548| | 2549| 6.37k| memset( outStruct, 0, sizeof( *outStruct ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2550| | 2551| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2552| | repeat: 2553| | FreeStructFromINCHI( &outStruct ); 2554| | inchi_ios_reset( input_file ); /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2555| | inchi_ios_close( out_file ); 2556| | inchi_ios_close( log_file ); 2557| |#endif 2558| | 2559| 6.37k| sd->bUserQuit = 0; 2560| | 2561| | /* Initialize internal for this function I/O streams as string buffers */ 2562| 6.37k| inchi_ios_init( input_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1016| 6.37k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2563| 6.37k| inchi_ios_init( out_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1016| 6.37k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2564| 6.37k| inchi_ios_init( log_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1016| 6.37k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2565| | 2566| | /* clear original input structure */ 2567| 6.37k| memset( sd, 0, sizeof( *sd ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2568| 6.37k| memset( ip, 0, sizeof( *ip ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2569| 6.37k| memset( szSdfDataValue, 0, sizeof( szSdfDataValue ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2570| | 2571| 6.37k| memset( &ic, 0, sizeof( ic ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2572| 6.37k| memset( &CG, 0, sizeof( CG ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2573| | 2574| 6.37k| szMainOption[1] = INCHI_OPTION_PREFX; ------------------ | | 231| 6.37k|#define INCHI_OPTION_PREFX '-' ------------------ 2575| | 2576| 6.37k| if (!inpInChI) ------------------ | Branch (2576:9): [True: 0, False: 6.37k] ------------------ 2577| 0| { 2578| 0| nRet = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2579| 0| goto exit_function; 2580| 0| } 2581| | 2582| | /* options */ 2583| 6.37k| if (inpInChI /*&& inpInChI->szOptions*/) ------------------ | Branch (2583:9): [True: 6.37k, False: 0] ------------------ 2584| 6.37k| { 2585| | /* fix bug discovered by Burt Leland 2008-12-23 */ 2586| 6.37k| int opt_len = ( inpInChI->szOptions ? strlen( inpInChI->szOptions ) : 0 ) + sizeof( szMainOption ) + 1; ------------------ | Branch (2586:25): [True: 0, False: 6.37k] ------------------ 2587| 6.37k| szOptions = (char*)inchi_calloc((long long)opt_len + 1, sizeof(szOptions[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 6.37k|#define inchi_calloc calloc ------------------ 2588| 6.37k| if (szOptions) ------------------ | Branch (2588:13): [True: 6.37k, False: 0] ------------------ 2589| 6.37k| { 2590| 6.37k| if (inpInChI->szOptions) ------------------ | Branch (2590:17): [True: 0, False: 6.37k] ------------------ 2591| | /* fix bug discovered by Burt Leland 2008-12-23 */ 2592| 0| strcpy(szOptions, inpInChI->szOptions); 2593| 6.37k| strcat(szOptions, szMainOption); 2594| 6.37k| argc = parse_options_string( szOptions, argv, INCHI_MAX_NUM_ARG ); ------------------ | | 11| 6.37k|#define INCHI_MAX_NUM_ARG 32 ------------------ 2595| 6.37k| } 2596| 0| else 2597| 0| { 2598| 0| nRet = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 2599| 0| goto translate_RetVal; /* emergency exit */ 2600| 0| } 2601| 6.37k| } 2602| 0| else 2603| 0| { 2604| 0| argc = 1; 2605| 0| argv[0] = ""; 2606| 0| argv[1] = NULL; 2607| 0| } 2608| | 2609| 6.37k| if ((argc == 1 ------------------ | Branch (2609:10): [True: 0, False: 6.37k] ------------------ 2610| 0|#ifdef TARGET_API_LIB 2611| 0| && ( !inpInChI || !inpInChI->szInChI )) ------------------ | Branch (2611:14): [True: 0, False: 0] | Branch (2611:27): [True: 0, False: 0] ------------------ 2612| 6.37k|#endif 2613| 6.37k| || (argc == 2 && ( argv[1][0] == INCHI_OPTION_PREFX ) && ------------------ | | 231| 6.37k|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (2613:13): [True: 6.37k, False: 0] | Branch (2613:26): [True: 6.37k, False: 0] ------------------ 2614| 6.37k| ( !strcmp( argv[1] + 1, "?" ) || !inchi_stricmp( argv[1] + 1, "help" ) ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2614:11): [True: 0, False: 6.37k] | Branch (2614:42): [True: 0, False: 6.37k] ------------------ 2615| 0| { 2616| 0| HelpCommandLineParms( log_file ); 2617| 0| outStruct->szLog = log_file->s.pStr; 2618| 0| nRet = _IS_EOF; ------------------ | | 15| 0|#define _IS_EOF -1 /* end of file */ ------------------ 2619| 0| goto translate_RetVal; 2620| 0| } 2621| | 2622| 6.37k| nRet1 = ReadCommandLineParms( argc, argv, ip, szSdfDataValue, 2623| 6.37k| &ulDisplTime, bReleaseVersion, 2624| 6.37k| log_file ); 2625| | 2626| 6.37k| if (szOptions) ------------------ | Branch (2626:9): [True: 6.37k, False: 0] ------------------ 2627| 6.37k| { 2628| | /* argv pointed to strings in szOptions */ 2629| 6.37k| inchi_free( szOptions ); ------------------ | | 1152| 6.37k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.37k, False: 0] | | | Branch (1152:50): [Folded, False: 6.37k] | | ------------------ ------------------ 2630| 6.37k| szOptions = NULL; 2631| 6.37k| } 2632| | 2633| | /* INChI DLL specific */ 2634| 6.37k| ip->bNoStructLabels = 1; 2635| | 2636| 6.37k| if (0 > nRet1) ------------------ | Branch (2636:9): [True: 0, False: 6.37k] ------------------ 2637| 0| { 2638| 0| goto exit_function; 2639| 0| } 2640| | 2641| 6.37k| if (ip->bNoStructLabels) ------------------ | Branch (2641:9): [True: 6.37k, False: 0] ------------------ 2642| 6.37k| { 2643| 6.37k| ip->pSdfLabel = NULL; 2644| 6.37k| ip->pSdfValue = NULL; 2645| 6.37k| } 2646| 0| else if (ip->nInputType == INPUT_INCHI_XML || ------------------ | Branch (2646:14): [True: 0, False: 0] ------------------ 2647| 0| ip->nInputType == INPUT_INCHI_PLAIN || ------------------ | Branch (2647:13): [True: 0, False: 0] ------------------ 2648| 0| ip->nInputType == INPUT_CMLFILE || ------------------ | Branch (2648:13): [True: 0, False: 0] ------------------ 2649| 0| ip->nInputType == INPUT_INCHI) ------------------ | Branch (2649:13): [True: 0, False: 0] ------------------ 2650| 0| { 2651| | /* the input may contain both the header and the label of the structure */ 2652| 0| if (!ip->pSdfLabel) ------------------ | Branch (2652:13): [True: 0, False: 0] ------------------ 2653| 0| ip->pSdfLabel = ip->szSdfDataHeader; 2654| 0| if (!ip->pSdfValue) ------------------ | Branch (2654:13): [True: 0, False: 0] ------------------ 2655| 0| ip->pSdfValue = szSdfDataValue; 2656| 0| } 2657| | 2658| 6.37k| if (ip->nInputType && ip->nInputType != INPUT_INCHI) ------------------ | Branch (2658:9): [True: 6.37k, False: 0] | Branch (2658:27): [True: 0, False: 6.37k] ------------------ 2659| 0| { 2660| 0| inchi_ios_eprint( log_file, "Input type set to INPUT_INCHI\n" ); 2661| 0| ip->nInputType = INPUT_INCHI; 2662| 0| } 2663| | 2664| 6.37k| if (!inpInChI->szInChI) ------------------ | Branch (2664:9): [True: 0, False: 6.37k] ------------------ 2665| 0| { 2666| 0| nRet = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2667| 0| goto exit_function; 2668| 0| } 2669| 6.37k| else 2670| 6.37k| { 2671| 6.37k| const int strict = 0; /* do not use strict mode, it may be too alarmous */ 2672| 6.37k| nRet = CheckINCHI( inpInChI->szInChI, strict ); 2673| 6.37k| if (nRet == INCHI_VALID_STANDARD || nRet == INCHI_VALID_NON_STANDARD || nRet == INCHI_VALID_BETA) /* djb-rwth: removing redundant code */ ------------------ | Branch (2673:13): [True: 35, False: 6.33k] | Branch (2673:45): [True: 6.22k, False: 113] | Branch (2673:81): [True: 24, False: 89] ------------------ 2674| 6.28k| { 2675| 6.28k| ; 2676| 6.28k| } 2677| 89| else 2678| 89| { 2679| 89| nRet = _IS_ERROR; ------------------ | | 12| 89|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2680| 89| goto exit_function; 2681| 89| } 2682| 6.37k| } 2683| | 2684| 6.28k| PrintInputParms( log_file, ip ); 2685| | 2686| | /*********************************/ 2687| | /* InChI -> Structure conversion */ 2688| | /*********************************/ 2689| | 2690| | /* input_file simulation */ 2691| | 2692| | /* 2693| | that was incorrect simulation, and correct one is much simpler, see below 2694| | input_file->s.pStr = inpInChI->szInChI; 2695| | input_file->s.nUsedLength = (int) strlen(input_file->s.pStr)+1; 2696| | input_file->s.nAllocatedLength = input_file->s.nUsedLength; 2697| | input_file->s.nPtr = 0; 2698| | */ 2699| 6.28k| inchi_ios_print_nodisplay( input_file, inpInChI->szInChI ); 2700| | 2701| | /* buffer for the message */ 2702| | /* outStruct->szMessage = (char *)inchi_calloc( MAX_MSG_LEN, sizeof(outStruct->szMessage[0])); */ 2703| | 2704| 6.28k| outStruct->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( char ) ); ------------------ | | 1146| 6.28k|#define inchi_calloc calloc ------------------ outStruct->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( char ) ); ------------------ | | 2102| 6.28k|#define MAX_MSG_LEN 512 ------------------ 2705| 6.28k| if (!outStruct->szMessage) ------------------ | Branch (2705:9): [True: 0, False: 6.28k] ------------------ 2706| 0| { 2707| 0| inchi_ios_eprint( log_file, "Cannot allocate output message buffer.\n" ); 2708| 0| nRet = -1; 2709| 0| } 2710| 6.28k| else 2711| 6.28k| { 2712| 6.28k| int num_bonds; 2713| 6.28k| nRet = ReadWriteInChI( &ic, &CG , input_file, out_file, log_file, 2714| 6.28k| ip, sd, &at, &num_at, &num_bonds, 2715| 6.28k| &polymer, &v3000, 2716| 6.28k| outStruct->szMessage, 2717| 6.28k| MAX_MSG_LEN, outStruct->WarningFlags ); ------------------ | | 2102| 6.28k|#define MAX_MSG_LEN 512 ------------------ 2718| | 2719| 6.28k| if (nRet >= 0 && polymer && at && (num_at > 0)) /* djb-rwth: fixing oss-fuzz issue #68329, #68286 */ ------------------ | Branch (2719:13): [True: 1.82k, False: 4.45k] | Branch (2719:26): [True: 143, False: 1.68k] | Branch (2719:37): [True: 143, False: 0] | Branch (2719:43): [True: 143, False: 0] ------------------ 2720| 143| { 2721| 143| OAD_Polymer_SmartReopenCyclizedUnits( polymer, at, 2722| 143| num_at, &num_bonds ); 2723| 143| } 2724| 6.28k| } 2725| | 2726| 6.28k| if (nRet >= 0 && at && num_at) ------------------ | Branch (2726:9): [True: 1.82k, False: 4.45k] | Branch (2726:22): [True: 1.75k, False: 73] | Branch (2726:28): [True: 1.75k, False: 0] ------------------ 2727| 1.75k| { 2728| | /* success */ 2729| 1.75k| nRet = InpAtom0DToInchiAtom( at, num_at, 2730| 1.75k| &outStruct->num_atoms, 2731| 1.75k| &outStruct->atom, 2732| 1.75k| &outStruct->num_stereo0D, 2733| 1.75k| &outStruct->stereo0D ); 2734| | 2735| 1.75k| if (at) ------------------ | Branch (2735:13): [True: 1.75k, False: 0] ------------------ 2736| 1.75k| { 2737| 1.75k| inchi_free( at ); ------------------ | | 1152| 1.75k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.75k, False: 0] | | | Branch (1152:50): [Folded, False: 1.75k] | | ------------------ ------------------ 2738| 1.75k| at = NULL; 2739| 1.75k| } 2740| | 2741| 1.75k| if (nRet >= 0 && polymer) ------------------ | Branch (2741:13): [True: 1.75k, False: 0] | Branch (2741:26): [True: 143, False: 1.61k] ------------------ 2742| 143| { 2743| | /* Check for and then replace ZZ for star atoms if Polymer extension is supplied */ 2744| 17.7k| for (i = 0; i < outStruct->num_atoms; i++) ------------------ | Branch (2744:25): [True: 17.5k, False: 143] ------------------ 2745| 17.5k| { 2746| 17.5k| if (!strcmp( outStruct->atom[i].elname, "Zz" )) ------------------ | Branch (2746:21): [True: 196, False: 17.3k] ------------------ 2747| 196| { 2748| 196| strcpy( outStruct->atom[i].elname, "*" ); 2749| 196| } 2750| 17.5k| } 2751| 143| } 2752| | 2753| 1.75k| if (nRet >= 0) ------------------ | Branch (2753:13): [True: 1.75k, False: 0] ------------------ 2754| 1.75k| { 2755| 1.75k| if (polymer || v3000) ------------------ | Branch (2755:17): [True: 143, False: 1.61k] | Branch (2755:28): [True: 0, False: 1.61k] ------------------ 2756| 143| { 2757| 143| nRet = SetInChIExtInputByExtOrigAtData( polymer, v3000, 2758| 143| &outStruct->polymer, 2759| 143| &outStruct->v3000, 2760| 143| outStruct->num_atoms ); /* pair to SetExtOrigAtDataByInChIExtInput */ 2761| 143| FreeExtOrigAtData( polymer, v3000 ); 2762| 143| polymer = NULL; 2763| 143| v3000 = NULL; 2764| 143| } 2765| 1.75k| } 2766| 1.75k| if (nRet < 0) ------------------ | Branch (2766:13): [True: 0, False: 1.75k] ------------------ 2767| 0| { 2768| 0| inchi_ios_eprint( log_file, "Final structure conversion failed\n" ); 2769| 0| } 2770| 1.75k| } 2771| 6.28k| outStruct->szLog = log_file->s.pStr; 2772| | 2773| 6.37k|exit_function:; 2774| | 2775| 31.8k| for (i = 0; i < MAX_NUM_PATHS; i++) ------------------ | | 58| 31.8k|#define MAX_NUM_PATHS 4 ------------------ | Branch (2775:17): [True: 25.4k, False: 6.37k] ------------------ 2776| 25.4k| { 2777| 25.4k| if (ip->path[i]) ------------------ | Branch (2777:13): [True: 0, False: 25.4k] ------------------ 2778| 0| { 2779| 0| inchi_free( (char*) ip->path[i] ); /* cast deliberately discards 'const' qualifier */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2780| 0| ip->path[i] = NULL; 2781| 0| } 2782| 25.4k| } 2783| | 2784| 6.37k| SetBitFree( &CG ); 2785| | 2786| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2787| | if (num_repeat-- > 0) 2788| | { 2789| | goto repeat; 2790| | } 2791| |#endif 2792| | 2793| 6.37k|#ifdef TARGET_API_LIB 2794| | /* output */ 2795| 6.37k| if (log_file->s.pStr && log_file->s.nUsedLength > 0) ------------------ | Branch (2795:9): [True: 6.28k, False: 89] | Branch (2795:29): [True: 6.28k, False: 0] ------------------ 2796| 6.28k| { 2797| 12.8k| while (log_file->s.nUsedLength && ------------------ | Branch (2797:16): [True: 12.8k, False: 0] ------------------ 2798| 12.8k| '\n' == log_file->s.pStr[log_file->s.nUsedLength - 1]) ------------------ | Branch (2798:17): [True: 6.56k, False: 6.28k] ------------------ 2799| 6.56k| { 2800| 6.56k| log_file->s.pStr[--log_file->s.nUsedLength] = '\0'; /* remove last LF */ 2801| 6.56k| } 2802| 6.28k| if (outStruct) ------------------ | Branch (2802:13): [True: 6.28k, False: 0] ------------------ 2803| 6.28k| { 2804| 6.28k| outStruct->szLog = log_file->s.pStr; 2805| 6.28k| log_file->s.pStr = NULL; 2806| 6.28k| } 2807| 6.28k| } 2808| 6.37k|#endif 2809| | 2810| 6.37k|translate_RetVal: 2811| | 2812| | /* Close internal I/O streams */ 2813| | /* that was incorrect also 2814| | inchi_ios_reset(input_file); */ /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2815| 6.37k| inchi_ios_close( input_file ); 2816| 6.37k| inchi_ios_close( out_file ); 2817| 6.37k| inchi_ios_close( log_file ); 2818| | 2819| 6.37k| switch (nRet) 2820| 6.37k| { 2821| 3.44k| case -3: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2821:9): [True: 3.44k, False: 2.92k] ------------------ 2822| 1.01k| case -2: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2822:9): [True: 1.01k, False: 5.36k] ------------------ 2823| 0| case -1: nRet = inchi_Ret_FATAL; break; /* Severe error: no Structure has been created (typically; break; memory allocation failed) */ ------------------ | Branch (2823:9): [True: 0, False: 6.37k] ------------------ 2824| 1.91k| default: ------------------ | Branch (2824:9): [True: 1.91k, False: 4.45k] ------------------ 2825| 1.91k| if (outStruct) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (2825:17): [True: 1.91k, False: 0] ------------------ 2826| 1.91k| { 2827| 1.91k| if (!outStruct->atom || !outStruct->num_atoms) ------------------ | Branch (2827:21): [True: 162, False: 1.75k] | Branch (2827:41): [True: 0, False: 1.75k] ------------------ 2828| 162| { 2829| 162| nRet = inchi_Ret_EOF; 2830| 162| } 2831| 1.75k| else 2832| 1.75k| { 2833| 1.75k| int m, n, t = 0; 2834| 5.26k| for (m = 0; m < 2; m++) ------------------ | Branch (2834:33): [True: 3.50k, False: 1.75k] ------------------ 2835| 3.50k| { 2836| 10.5k| for (n = 0; n < 2; n++) ------------------ | Branch (2836:37): [True: 7.01k, False: 3.50k] ------------------ 2837| 7.01k| { 2838| 7.01k| if (outStruct->WarningFlags[m][n]) ------------------ | Branch (2838:33): [True: 1.54k, False: 5.47k] ------------------ 2839| 1.54k| { 2840| 1.54k| t++; 2841| 1.54k| } 2842| 7.01k| } 2843| 3.50k| } 2844| 1.75k| nRet = t ? inchi_Ret_WARNING : inchi_Ret_OKAY; ------------------ | Branch (2844:28): [True: 1.47k, False: 279] ------------------ 2845| 1.75k| } 2846| 1.91k| break; 2847| 1.91k| } 2848| 6.37k| } 2849| | 2850| 6.37k| return nRet; 2851| 6.37k|} GetStructFromINCHI: 2862| 6.37k|{ 2863| 6.37k| int ret = 0; 2864| | 2865| 6.37k| inchi_OutputStructEx outex; 2866| 6.37k| memset( out, 0, sizeof( *out ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2867| | 2868| 6.37k| ret = GetStructFromINCHIEx( inpInChI, &outex ); 2869| | 2870| 6.37k| out->szLog = outex.szLog; 2871| 6.37k| out->szMessage = outex.szMessage; 2872| 6.37k| out->WarningFlags[0][0] = outex.WarningFlags[0][0]; 2873| 6.37k| out->WarningFlags[0][1] = outex.WarningFlags[0][1]; 2874| 6.37k| out->WarningFlags[1][0] = outex.WarningFlags[1][0]; 2875| 6.37k| out->WarningFlags[1][1] = outex.WarningFlags[1][1]; 2876| | 2877| 6.37k| if (ret == inchi_Ret_OKAY || ret == inchi_Ret_WARNING) ------------------ | Branch (2877:9): [True: 279, False: 6.09k] | Branch (2877:34): [True: 1.47k, False: 4.61k] ------------------ 2878| 1.75k| { 2879| 1.75k| out->num_atoms = outex.num_atoms; 2880| 1.75k| out->atom = outex.atom; 2881| 1.75k| out->num_stereo0D = outex.num_stereo0D; 2882| 1.75k| out->stereo0D = outex.stereo0D; 2883| 1.75k| } 2884| | 2885| 6.37k| return ret; 2886| 6.37k|} SetInChIExtInputByExtOrigAtData: 3267| 143|{ 3268| 143| int k, m, err = 0; 3269| | 3270| | /* Polymers */ 3271| 143| if (orp && orp->n > 0) ------------------ | Branch (3271:9): [True: 143, False: 0] | Branch (3271:16): [True: 143, False: 0] ------------------ 3272| 143| { 3273| | /* djb-rwth: fixing oss-fuzz issue #67695, #66748 */ 3274| 143| inchi_Input_Polymer* iip_tmp = (inchi_Input_Polymer*) inchi_calloc( 1, sizeof( inchi_Input_Polymer ) ); ------------------ | | 1146| 143|#define inchi_calloc calloc ------------------ 3275| 143| inchi_Input_PolymerUnit** units_tmp = (inchi_Input_PolymerUnit**) inchi_calloc( orp->n, sizeof( ( *iip )->units[0] ) ); ------------------ | | 1146| 143|#define inchi_calloc calloc ------------------ 3276| 143| int** uk_al_tmp = (int**)inchi_malloc((orp->n) * sizeof(int*)); ------------------ | | 1143| 143|#define inchi_malloc malloc ------------------ 3277| 143| inchi_Input_PolymerUnit** unitk = (inchi_Input_PolymerUnit**)inchi_malloc((orp->n) * sizeof(inchi_Input_PolymerUnit*)); ------------------ | | 1143| 143|#define inchi_malloc malloc ------------------ 3278| | 3279| 143| if (!iip_tmp || !units_tmp || !uk_al_tmp || !unitk) ------------------ | Branch (3279:13): [True: 0, False: 143] | Branch (3279:25): [True: 0, False: 143] | Branch (3279:39): [True: 0, False: 143] | Branch (3279:53): [True: 0, False: 143] ------------------ 3280| 0| { 3281| 0| err = 9001; 3282| 0| goto preexitf; 3283| 0| } 3284| | /* *iip = iip_tmp; */ 3285| 143| iip_tmp->n = orp->n; 3286| 143| iip_tmp->units = units_tmp; 3287| 143| memset(units_tmp, 0, sizeof( *units_tmp) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3288| 598| for (k = 0; k < orp->n; k++) ------------------ | Branch (3288:21): [True: 455, False: 143] ------------------ 3289| 455| { 3290| 455| int q = 0; 3291| 455| unitk[k] = (inchi_Input_PolymerUnit*)inchi_calloc(1, sizeof(inchi_Input_PolymerUnit)); ------------------ | | 1146| 455|#define inchi_calloc calloc ------------------ 3292| 455| OAD_PolymerUnit *groupk = orp->units[k]; 3293| | /* unitk = ( *iip )->units[k]; */ 3294| 455| if (!unitk[k]) ------------------ | Branch (3294:17): [True: 0, False: 455] ------------------ 3295| 0| { 3296| 0| err = 9001; 3297| 0| goto preexitf; 3298| 0| } 3299| 455| iip_tmp->units[k] = unitk[k]; 3300| 455| memset( unitk[k], 0, sizeof(*unitk[k])); /* djb-rwth: memset_s C11/Annex K variant? */ 3301| 455| unitk[k]->id = groupk->id; 3302| 455| unitk[k]->type = groupk->type; 3303| 455| unitk[k]->subtype = groupk->subtype; 3304| 455| unitk[k]->conn = groupk->conn; 3305| 455| unitk[k]->label = groupk->label; 3306| 2.27k| for (q = 0; q < 4; q++) ------------------ | Branch (3306:25): [True: 1.82k, False: 455] ------------------ 3307| 1.82k| { 3308| 1.82k| unitk[k]->xbr1[q] = groupk->xbr1[q]; 3309| 1.82k| unitk[k]->xbr2[q] = groupk->xbr2[q]; 3310| 1.82k| } 3311| 455| strcpy( unitk[k]->smt, groupk->smt); 3312| 455| unitk[k]->na = groupk->na; 3313| 455| uk_al_tmp[k] = (int*)inchi_calloc(unitk[k]->na, sizeof(int)); ------------------ | | 1146| 455|#define inchi_calloc calloc ------------------ 3314| 455| if (!uk_al_tmp[k]) ------------------ | Branch (3314:17): [True: 0, False: 455] ------------------ 3315| 0| { 3316| 0| err = 9001; 3317| 0| goto preexitf; 3318| 0| } 3319| 455| unitk[k]->alist = uk_al_tmp[k]; 3320| 1.94k| for (m = 0; m < unitk[k]->na; m++) ------------------ | Branch (3320:25): [True: 1.48k, False: 455] ------------------ 3321| 1.48k| { 3322| 1.48k| uk_al_tmp[k][m] = groupk->alist[m]; 3323| 1.48k| } 3324| 455| unitk[k]->nb = groupk->nb; 3325| 455| if (unitk[k]->nb > 0) ------------------ | Branch (3325:17): [True: 104, False: 351] ------------------ 3326| 104| { 3327| 104| unitk[k]->blist = (int*)inchi_calloc(2 * (long long)unitk[k]->nb, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 104|#define inchi_calloc calloc ------------------ 3328| 104| if (!unitk[k]->blist) ------------------ | Branch (3328:21): [True: 0, False: 104] ------------------ 3329| 0| { 3330| 0| err = 9001; 3331| 0| goto preexitf; 3332| 0| } 3333| 520| for (m = 0; m < 2 * groupk->nb; m++) ------------------ | Branch (3333:29): [True: 416, False: 104] ------------------ 3334| 416| { 3335| 416| unitk[k]->blist[m] = groupk->blist[m]; 3336| 416| } 3337| 104| } 3338| 351| else 3339| 351| { 3340| 351| unitk[k]->blist = NULL; 3341| 351| } 3342| | 3343| 455| inchi_free(unitk[k]); ------------------ | | 1152| 455|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 455, False: 0] | | | Branch (1152:50): [Folded, False: 455] | | ------------------ ------------------ 3344| 455| inchi_free(uk_al_tmp[k]); ------------------ | | 1152| 455|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 455, False: 0] | | | Branch (1152:50): [Folded, False: 455] | | ------------------ ------------------ 3345| 455| } 3346| | /* djb-rwth: avoiding memory leak */ 3347| 143| preexitf: 3348| | /* djb-rwth: fixing GHI #165 */ 3349| 143| if (iip_tmp && *iip) /* djb-rwth: fixing oss-fuzz issue #455987437 */ ------------------ | Branch (3349:13): [True: 143, False: 0] | Branch (3349:24): [True: 0, False: 143] ------------------ 3350| 0| { 3351| 0| memcpy(*iip, iip_tmp, sizeof(inchi_Input_Polymer)); 3352| 0| } 3353| 143| inchi_free(iip_tmp); ------------------ | | 1152| 143|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 143, False: 0] | | | Branch (1152:50): [Folded, False: 143] | | ------------------ ------------------ 3354| 143| inchi_free(units_tmp); ------------------ | | 1152| 143|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 143, False: 0] | | | Branch (1152:50): [Folded, False: 143] | | ------------------ ------------------ 3355| 143| inchi_free(uk_al_tmp); ------------------ | | 1152| 143|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 143, False: 0] | | | Branch (1152:50): [Folded, False: 143] | | ------------------ ------------------ 3356| 143| inchi_free(unitk); ------------------ | | 1152| 143|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 143, False: 0] | | | Branch (1152:50): [Folded, False: 143] | | ------------------ ------------------ 3357| 143| if (err) ------------------ | Branch (3357:13): [True: 0, False: 143] ------------------ 3358| 0| { 3359| 0| goto exitf; 3360| 0| } 3361| 143| } 3362| | 3363| 143| if (orv) ------------------ | Branch (3363:9): [True: 0, False: 143] ------------------ 3364| 0| { 3365| 0| int nn; 3366| 0| *iiv = (inchi_Input_V3000 *) inchi_calloc( 1, sizeof(inchi_Input_V3000) ); /* djb-rwth: fixing the incorrect type of variable */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3367| 0| if (!*iiv) ------------------ | Branch (3367:13): [True: 0, False: 0] ------------------ 3368| 0| { 3369| 0| err = 9001; 3370| 0| goto exitf; 3371| 0| } 3372| 0| memset( *iiv, 0, sizeof( **iiv ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3373| | 3374| 0| ( *iiv )->n_collections = orv->n_collections; 3375| 0| ( *iiv )->n_haptic_bonds = orv->n_haptic_bonds; 3376| 0| ( *iiv )->n_non_haptic_bonds = orv->n_non_haptic_bonds; 3377| 0| ( *iiv )->n_sgroups = orv->n_sgroups; 3378| 0| ( *iiv )->n_non_star_atoms = orv->n_non_star_atoms; 3379| 0| ( *iiv )->n_star_atoms = orv->n_star_atoms; 3380| 0| ( *iiv )->n_steabs = orv->n_steabs; 3381| 0| ( *iiv )->n_sterac = orv->n_sterac; 3382| 0| ( *iiv )->n_sterel = orv->n_sterel; 3383| 0| ( *iiv )->n_3d_constraints = orv->n_3d_constraints; 3384| | 3385| 0| if (orv->atom_index_orig) ------------------ | Branch (3385:13): [True: 0, False: 0] ------------------ 3386| 0| { 3387| 0| ( *iiv )->atom_index_orig = (int *) inchi_calloc( nat, sizeof( int ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3388| 0| if (NULL == ( *iiv )->atom_index_orig) ------------------ | Branch (3388:17): [True: 0, False: 0] ------------------ 3389| 0| { 3390| 0| err = 9001; 3391| 0| goto exitf; 3392| 0| } 3393| 0| memcpy( ( *iiv )->atom_index_orig, orv->atom_index_orig, nat ); 3394| 0| } 3395| 0| if (orv->atom_index_fin) ------------------ | Branch (3395:13): [True: 0, False: 0] ------------------ 3396| 0| { 3397| 0| ( *iiv )->atom_index_fin = (int *) inchi_calloc( nat, sizeof( int ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3398| 0| if (NULL == ( *iiv )->atom_index_fin) ------------------ | Branch (3398:17): [True: 0, False: 0] ------------------ 3399| 0| { 3400| 0| err = 9001; 3401| 0| goto exitf; 3402| 0| } 3403| 0| memcpy( ( *iiv )->atom_index_fin, orv->atom_index_fin, nat ); 3404| 0| } 3405| 0| if (orv->n_haptic_bonds && orv->lists_haptic_bonds) ------------------ | Branch (3405:13): [True: 0, False: 0] | Branch (3405:36): [True: 0, False: 0] ------------------ 3406| 0| { 3407| 0| ( *iiv )->lists_haptic_bonds = (int **) inchi_calloc( orv->n_haptic_bonds, sizeof( int* ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3408| 0| if (NULL == ( *iiv )->lists_haptic_bonds) ------------------ | Branch (3408:17): [True: 0, False: 0] ------------------ 3409| 0| { 3410| 0| err = 9001; 3411| 0| goto exitf; 3412| 0| } 3413| 0| for (m = 0; m < orv->n_haptic_bonds; m++) ------------------ | Branch (3413:25): [True: 0, False: 0] ------------------ 3414| 0| { 3415| 0| int *lst = NULL; 3416| 0| int *mol_lst = orv->lists_haptic_bonds[m]; 3417| 0| nn = mol_lst[2] + 3; 3418| 0| lst = ( *iiv )->lists_haptic_bonds[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3419| 0| if (NULL == lst) ------------------ | Branch (3419:21): [True: 0, False: 0] ------------------ 3420| 0| { 3421| 0| err = 9001; 3422| 0| goto exitf; 3423| 0| } 3424| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3424:29): [True: 0, False: 0] ------------------ 3425| 0| { 3426| 0| lst[k] = mol_lst[k]; 3427| 0| } 3428| 0| } 3429| 0| } 3430| 0| if (orv->n_steabs && orv->lists_steabs) ------------------ | Branch (3430:13): [True: 0, False: 0] | Branch (3430:30): [True: 0, False: 0] ------------------ 3431| 0| { 3432| 0| ( *iiv )->lists_steabs = (int **) inchi_calloc( orv->n_steabs, sizeof( int* ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3433| 0| if (NULL == ( *iiv )->lists_steabs) { err = 9001; goto exitf; } ------------------ | Branch (3433:17): [True: 0, False: 0] ------------------ 3434| 0| for (m = 0; m < orv->n_steabs; m++) ------------------ | Branch (3434:25): [True: 0, False: 0] ------------------ 3435| 0| { 3436| 0| int *lst = NULL; 3437| 0| int *mol_lst = orv->lists_steabs[m]; 3438| 0| nn = mol_lst[1] + 2; 3439| 0| lst = ( *iiv )->lists_steabs[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3440| 0| if (NULL == lst) ------------------ | Branch (3440:21): [True: 0, False: 0] ------------------ 3441| 0| { 3442| 0| err = 9001; 3443| 0| goto exitf; 3444| 0| } 3445| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3445:29): [True: 0, False: 0] ------------------ 3446| 0| { 3447| 0| lst[k] = mol_lst[k]; 3448| 0| } 3449| 0| } 3450| 0| } 3451| 0| if (orv->n_sterac && orv->lists_sterac) ------------------ | Branch (3451:13): [True: 0, False: 0] | Branch (3451:30): [True: 0, False: 0] ------------------ 3452| 0| { 3453| 0| ( *iiv )->lists_sterac = (int **) inchi_calloc( orv->n_sterac, sizeof( int* ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3454| 0| if (NULL == ( *iiv )->lists_sterac) { err = 9001; goto exitf; } ------------------ | Branch (3454:17): [True: 0, False: 0] ------------------ 3455| 0| for (m = 0; m < orv->n_sterac; m++) ------------------ | Branch (3455:25): [True: 0, False: 0] ------------------ 3456| 0| { 3457| 0| int *lst = NULL; 3458| 0| int *mol_lst = orv->lists_sterac[m]; 3459| 0| nn = mol_lst[1] + 2; 3460| 0| lst = ( *iiv )->lists_sterac[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3461| 0| if (NULL == lst) ------------------ | Branch (3461:21): [True: 0, False: 0] ------------------ 3462| 0| { 3463| 0| err = 9001; 3464| 0| goto exitf; 3465| 0| } 3466| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3466:29): [True: 0, False: 0] ------------------ 3467| 0| { 3468| 0| lst[k] = mol_lst[k]; 3469| 0| } 3470| 0| } 3471| 0| } 3472| 0| if (orv->n_sterel && orv->lists_sterel) ------------------ | Branch (3472:13): [True: 0, False: 0] | Branch (3472:30): [True: 0, False: 0] ------------------ 3473| 0| { 3474| 0| ( *iiv )->lists_sterel = (int **) inchi_calloc( orv->n_sterel, sizeof( int* ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3475| 0| if (NULL == ( *iiv )->lists_sterel) { err = 9001; goto exitf; } ------------------ | Branch (3475:17): [True: 0, False: 0] ------------------ 3476| 0| for (m = 0; m < orv->n_sterel; m++) ------------------ | Branch (3476:25): [True: 0, False: 0] ------------------ 3477| 0| { 3478| 0| int *lst = NULL; 3479| 0| int *mol_lst = orv->lists_sterel[m]; 3480| 0| nn = mol_lst[1] + 2; 3481| 0| lst = ( *iiv )->lists_sterel[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 3482| 0| if (NULL == lst) ------------------ | Branch (3482:21): [True: 0, False: 0] ------------------ 3483| 0| { 3484| 0| err = 9001; 3485| 0| goto exitf; 3486| 0| } 3487| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3487:29): [True: 0, False: 0] ------------------ 3488| 0| { 3489| 0| lst[k] = mol_lst[k]; 3490| 0| } 3491| 0| } 3492| 0| } 3493| 0| } 3494| | 3495| 143|exitf: 3496| 143| if (err) ------------------ | Branch (3496:9): [True: 0, False: 143] ------------------ 3497| 0| { 3498| 0| FreeInChIExtInput( *iip, *iiv ); 3499| 0| } 3500| | 3501| 143| return err; 3502| 143|} CreateCompositeNormAtom: 1943| 811|{ 1944| 811| int i, j, jj, k, n, m, tot_num_at, tot_num_H, cur_num_at, cur_num_H; /* djb-rwth: removing redundant variables */ 1945| 811| int num_comp[TAUT_NUM + 1], num_taut[TAUT_NUM + 1], num_del[TAUT_NUM + 1], num_at[TAUT_NUM + 1], num_inp_at[TAUT_NUM + 1]; 1946| 811| int ret = 0, indicator = 1; 1947| 811| inp_ATOM *at, *at_from; 1948| 811| memset( num_comp, 0, sizeof( num_comp ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1949| 811| memset( num_taut, 0, sizeof( num_taut ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1950| 811| memset( num_del, 0, sizeof( num_taut ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1951| | /* count taut and non-taut components */ 1952| 2.43k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 2.43k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1952:17): [True: 1.62k, False: 811] ------------------ 1953| 1.62k| { 1954| 1.62k| num_comp[j] = num_taut[j] = 0; 1955| 74.5k| for (i = 0; i < num_components; i++) ------------------ | Branch (1955:21): [True: 72.8k, False: 1.62k] ------------------ 1956| 72.8k| { 1957| 72.8k| if (all_inp_norm_data[i][j].bExists) ------------------ | Branch (1957:17): [True: 71.4k, False: 1.40k] ------------------ 1958| 71.4k| { 1959| 71.4k| num_del[j] += ( 0 != all_inp_norm_data[i][j].bDeleted ); 1960| 71.4k| num_comp[j] ++; 1961| 71.4k| num_taut[j] += ( 0 != all_inp_norm_data[i][j].bTautomeric ); 1962| 71.4k| } 1963| 72.8k| } 1964| 1.62k| } 1965| | 1966| | /* count intermediate taut structure components */ 1967| 811| if (num_comp[TAUT_YES] > num_del[TAUT_YES] && num_taut[TAUT_YES]) ------------------ | | 575| 811|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (num_comp[TAUT_YES] > num_del[TAUT_YES] && num_taut[TAUT_YES]) ------------------ | | 575| 811|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (num_comp[TAUT_YES] > num_del[TAUT_YES] && num_taut[TAUT_YES]) ------------------ | | 575| 706|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1967:9): [True: 706, False: 105] | Branch (1967:51): [True: 69, False: 637] ------------------ 1968| 69| { 1969| | /* 1970| | num_comp[TAUT_INI] = num_comp[TAUT_YES] - num_del[TAUT_YES]; 1971| | */ 1972| | 1973| 207| for (i = 0, j = TAUT_YES; i < num_components; i++) ------------------ | | 575| 69|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1973:35): [True: 138, False: 69] ------------------ 1974| 138| { 1975| 138| if (all_inp_norm_data[i][j].bExists && ------------------ | Branch (1975:17): [True: 138, False: 0] ------------------ 1976| 138| ( all_inp_norm_data[i][j].bDeleted || ------------------ | Branch (1976:19): [True: 0, False: 138] ------------------ 1977| 138| (all_inp_norm_data[i][j].bTautomeric && ------------------ | Branch (1977:22): [True: 69, False: 69] ------------------ 1978| 69| all_inp_norm_data[i][j].at_fixed_bonds && ------------------ | Branch (1978:21): [True: 69, False: 0] ------------------ 1979| 69| all_inp_norm_data[i][j].bTautPreprocessed) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1979:21): [True: 47, False: 22] ------------------ 1980| 47| { 1981| 47| num_comp[TAUT_INI] ++; ------------------ | | 576| 47|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ 1982| 47| } 1983| 138| } 1984| 69| } 1985| | 1986| | /* count atoms and allocate composite atom data */ 1987| 3.24k| for (jj = 0; jj <= TAUT_INI; jj++) ------------------ | | 576| 3.24k|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ | Branch (1987:18): [True: 2.43k, False: 811] ------------------ 1988| 2.43k| { 1989| 2.43k| num_at[jj] = num_inp_at[jj] = 0; 1990| 2.43k| j = inchi_min( jj, TAUT_YES ); ------------------ | | 139| 2.43k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 811, False: 1.62k] | | ------------------ ------------------ 1991| 2.43k| if (num_comp[jj]) ------------------ | Branch (1991:13): [True: 972, False: 1.46k] ------------------ 1992| 972| { 1993| 72.5k| for (i = 0; i < num_components; i++) ------------------ | Branch (1993:25): [True: 71.5k, False: 972] ------------------ 1994| 71.5k| { 1995| 71.5k| if (all_inp_norm_data[i][j].bDeleted) ------------------ | Branch (1995:21): [True: 35.0k, False: 36.5k] ------------------ 1996| 35.0k| { 1997| 35.0k| continue; 1998| 35.0k| } 1999| | /* find k = the normaized structure index */ 2000| 36.5k| if (jj == TAUT_INI) ------------------ | | 576| 36.5k|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ | Branch (2000:21): [True: 94, False: 36.4k] ------------------ 2001| 94| { 2002| 94| if (all_inp_norm_data[i][j].bExists && ------------------ | Branch (2002:25): [True: 94, False: 0] ------------------ 2003| 94| all_inp_norm_data[i][j].at_fixed_bonds) ------------------ | Branch (2003:26): [True: 94, False: 0] ------------------ 2004| 94| { 2005| 94| k = j; 2006| 94| } 2007| 0| else 2008| 0| { 2009| 0| if (all_inp_norm_data[i][ALT_TAUT( j )].bExists && !all_inp_norm_data[i][ALT_TAUT( j )].bDeleted && ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ if (all_inp_norm_data[i][ALT_TAUT( j )].bExists && !all_inp_norm_data[i][ALT_TAUT( j )].bDeleted && ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2009:29): [True: 0, False: 0] | Branch (2009:76): [True: 0, False: 0] ------------------ 2010| 0| !all_inp_norm_data[i][j].bDeleted) ------------------ | Branch (2010:33): [True: 0, False: 0] ------------------ 2011| 0| { 2012| 0| k = ALT_TAUT( j ); ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 2013| 0| } 2014| 0| else 2015| 0| { 2016| 0| if (all_inp_norm_data[i][j].bExists) ------------------ | Branch (2016:33): [True: 0, False: 0] ------------------ 2017| 0| { 2018| 0| k = j; 2019| 0| } 2020| 0| else 2021| 0| { 2022| 0| continue; 2023| 0| } 2024| 0| } 2025| 0| } 2026| 94| } 2027| 36.4k| else 2028| 36.4k| { 2029| 36.4k| if (all_inp_norm_data[i][j].bExists) ------------------ | Branch (2029:25): [True: 36.4k, False: 9] ------------------ 2030| 36.4k| { 2031| 36.4k| k = j; 2032| 36.4k| } 2033| 9| else 2034| 9| { 2035| 9| if (all_inp_norm_data[i][ALT_TAUT( j )].bExists && !all_inp_norm_data[i][ALT_TAUT( j )].bDeleted) ------------------ | | 577| 9|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 9|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 9] | | ------------------ ------------------ if (all_inp_norm_data[i][ALT_TAUT( j )].bExists && !all_inp_norm_data[i][ALT_TAUT( j )].bDeleted) ------------------ | | 577| 9|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 9|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 9] | | ------------------ ------------------ | Branch (2035:29): [True: 9, False: 0] | Branch (2035:76): [True: 9, False: 0] ------------------ 2036| 9| { 2037| 9| k = ALT_TAUT( j ); ------------------ | | 577| 9|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 9|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 9] | | ------------------ ------------------ 2038| 9| } 2039| 0| else 2040| 0| { 2041| 0| continue; 2042| 0| } 2043| 9| } 2044| 36.4k| } 2045| 36.5k| num_inp_at[jj] += all_inp_norm_data[i][k].num_at; /* all atoms including terminal H */ 2046| 36.5k| num_at[jj] += all_inp_norm_data[i][k].num_at - all_inp_norm_data[i][k].num_removed_H; 2047| 36.5k| } 2048| 972| if (num_inp_at[jj]) ------------------ | Branch (2048:17): [True: 867, False: 105] ------------------ 2049| 867| { 2050| 867| if (!CreateCompAtomData( composite_norm_data + jj, num_inp_at[jj], num_components, jj == TAUT_INI )) ------------------ | | 576| 867|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ | Branch (2050:21): [True: 0, False: 867] ------------------ 2051| 0| goto exit_error; 2052| 867| composite_norm_data[jj].num_removed_H = num_inp_at[jj] - num_at[jj]; 2053| 867| } 2054| 972| } 2055| 2.43k| } 2056| | 2057| | /* fill out composite atom */ 2058| 3.24k| for (jj = 0; jj <= TAUT_INI; jj++, indicator <<= 1) ------------------ | | 576| 3.24k|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ | Branch (2058:18): [True: 2.43k, False: 811] ------------------ 2059| 2.43k| { 2060| 2.43k| j = inchi_min( jj, TAUT_YES ); ------------------ | | 139| 2.43k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 811, False: 1.62k] | | ------------------ ------------------ 2061| 2.43k| if (num_comp[jj]) ------------------ | Branch (2061:13): [True: 972, False: 1.46k] ------------------ 2062| 972| { 2063| 972| tot_num_at = 0; 2064| 972| tot_num_H = 0; 2065| 72.5k| for (i = 0; i < num_components; i++) ------------------ | Branch (2065:25): [True: 71.5k, False: 972] ------------------ 2066| 71.5k| { 2067| 71.5k| if (all_inp_norm_data[i][j].bDeleted) ------------------ | Branch (2067:21): [True: 35.0k, False: 36.5k] ------------------ 2068| 35.0k| { 2069| 35.0k| composite_norm_data[jj].nNumRemovedProtons += all_inp_norm_data[i][j].nNumRemovedProtons; 2070| 140k| for (n = 0; n < NUM_H_ISOTOPES; n++) ------------------ | | 72| 140k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2070:33): [True: 105k, False: 35.0k] ------------------ 2071| 105k| { 2072| 105k| composite_norm_data[jj].nNumRemovedProtonsIsotopic[n] += all_inp_norm_data[i][j].nNumRemovedProtonsIsotopic[n]; 2073| 105k| } 2074| 35.0k| continue; 2075| 35.0k| } 2076| | /* djb-rwth: removing redundant code */ 2077| 36.5k| k = TAUT_NUM; /* djb-rwth: ignoring LLVM warning: value used */ ------------------ | | 573| 36.5k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ 2078| | /* find k = the normaized structure index */ 2079| 36.5k| if (jj == TAUT_INI) ------------------ | | 576| 36.5k|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ | Branch (2079:21): [True: 94, False: 36.4k] ------------------ 2080| 94| { 2081| 94| if (all_inp_norm_data[i][j].bExists && all_inp_norm_data[i][j].at_fixed_bonds) ------------------ | Branch (2081:25): [True: 94, False: 0] | Branch (2081:60): [True: 94, False: 0] ------------------ 2082| 94| { 2083| 94| k = j; 2084| 94| } 2085| 0| else 2086| 0| { 2087| 0| if (all_inp_norm_data[i][ALT_TAUT( j )].bExists) ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2087:29): [True: 0, False: 0] ------------------ 2088| 0| { 2089| 0| k = ALT_TAUT( j ); ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 2090| 0| } 2091| 0| else 2092| 0| { 2093| 0| if (all_inp_norm_data[i][j].bExists && !all_inp_norm_data[i][ALT_TAUT( j )].bDeleted) ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2093:33): [True: 0, False: 0] | Branch (2093:68): [True: 0, False: 0] ------------------ 2094| 0| { 2095| 0| k = j; 2096| 0| } 2097| 0| else 2098| 0| { 2099| 0| continue; 2100| 0| } 2101| 0| } 2102| 0| } 2103| 94| } 2104| 36.4k| else 2105| 36.4k| { 2106| 36.4k| if (all_inp_norm_data[i][j].bExists) ------------------ | Branch (2106:25): [True: 36.4k, False: 9] ------------------ 2107| 36.4k| { 2108| 36.4k| k = j; 2109| 36.4k| } 2110| 9| else 2111| 9| { 2112| 9| if (all_inp_norm_data[i][ALT_TAUT( j )].bExists && !all_inp_norm_data[i][ALT_TAUT( j )].bDeleted) ------------------ | | 577| 9|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 9|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 9] | | ------------------ ------------------ if (all_inp_norm_data[i][ALT_TAUT( j )].bExists && !all_inp_norm_data[i][ALT_TAUT( j )].bDeleted) ------------------ | | 577| 9|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 9|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 9] | | ------------------ ------------------ | Branch (2112:29): [True: 9, False: 0] | Branch (2112:76): [True: 9, False: 0] ------------------ 2113| 9| { 2114| 9| k = ALT_TAUT( j ); ------------------ | | 577| 9|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 9|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 9] | | ------------------ ------------------ 2115| 9| } 2116| 0| else 2117| 0| { 2118| 0| continue; 2119| 0| } 2120| 9| } 2121| 36.4k| } 2122| | /* copy main atoms */ 2123| 36.5k| cur_num_H = all_inp_norm_data[i][k].num_removed_H; /* number of terminal H atoms */ 2124| 36.5k| cur_num_at = all_inp_norm_data[i][k].num_at - cur_num_H; /* number of all but explicit terminal H atoms */ 2125| | 2126| 36.5k| if (( tot_num_at + cur_num_at ) > num_at[jj] || ------------------ | Branch (2126:21): [True: 0, False: 36.5k] ------------------ 2127| 36.5k| ( num_at[jj] + tot_num_H + cur_num_H ) > num_inp_at[jj]) ------------------ | Branch (2127:21): [True: 0, False: 36.5k] ------------------ 2128| 0| { 2129| 0| goto exit_error; /* miscount */ 2130| 0| } 2131| 36.5k| at = composite_norm_data[jj].at + tot_num_at; /* points to the 1st destination atom */ 2132| 36.5k| at_from = ( jj == TAUT_INI && k == TAUT_YES && all_inp_norm_data[i][k].at_fixed_bonds ) ? ------------------ | | 576| 73.1k|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ at_from = ( jj == TAUT_INI && k == TAUT_YES && all_inp_norm_data[i][k].at_fixed_bonds ) ? ------------------ | | 575| 36.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2132:29): [True: 94, False: 36.4k] | Branch (2132:47): [True: 94, False: 0] | Branch (2132:64): [True: 94, False: 0] ------------------ 2133| 36.4k| all_inp_norm_data[i][k].at_fixed_bonds : all_inp_norm_data[i][k].at; 2134| 36.5k| memcpy( at, at_from, sizeof( composite_norm_data[0].at[0] ) * cur_num_at ); /* copy atoms except terminal H */ 2135| | /* shift neighbors of main atoms */ 2136| 75.6k| for (n = 0; n < cur_num_at; n++, at++) ------------------ | Branch (2136:29): [True: 39.1k, False: 36.5k] ------------------ 2137| 39.1k| { 2138| 44.5k| for (m = 0; m < at->valence; m++) ------------------ | Branch (2138:33): [True: 5.38k, False: 39.1k] ------------------ 2139| 5.38k| { 2140| 5.38k| at->neighbor[m] += tot_num_at; 2141| 5.38k| } 2142| 39.1k| } 2143| | /* copy explicit H */ 2144| 36.5k| if (cur_num_H) ------------------ | Branch (2144:21): [True: 282, False: 36.2k] ------------------ 2145| 282| { 2146| 282| at = composite_norm_data[jj].at + num_at[jj] + tot_num_H; /* points to the 1st destination atom */ 2147| 282| memcpy( at, at_from + cur_num_at, sizeof( composite_norm_data[0].at[0] ) * cur_num_H ); 2148| | /* shift neighbors of explicit H atoms */ 2149| 597| for (n = 0; n < cur_num_H; n++, at++) ------------------ | Branch (2149:33): [True: 315, False: 282] ------------------ 2150| 315| { 2151| 630| for (m = 0; m < at->valence; m++) ------------------ | Branch (2151:37): [True: 315, False: 315] ------------------ 2152| 315| { 2153| 315| at->neighbor[m] += tot_num_at; 2154| 315| } 2155| 315| } 2156| 282| } 2157| | /* composite counts */ 2158| 36.5k| composite_norm_data[jj].bHasIsotopicLayer |= all_inp_norm_data[i][k].bHasIsotopicLayer; 2159| 36.5k| composite_norm_data[jj].num_isotopic += all_inp_norm_data[i][k].num_isotopic; 2160| 36.5k| composite_norm_data[jj].num_bonds += all_inp_norm_data[i][k].num_bonds; 2161| 36.5k| composite_norm_data[jj].bTautomeric += ( j == jj ) && all_inp_norm_data[i][k].bTautomeric; ------------------ | Branch (2161:56): [True: 36.4k, False: 94] | Branch (2161:71): [True: 69, False: 36.3k] ------------------ 2162| 36.5k| composite_norm_data[jj].nNumRemovedProtons += all_inp_norm_data[i][k].nNumRemovedProtons; 2163| 146k| for (n = 0; n < NUM_H_ISOTOPES; n++) ------------------ | | 72| 146k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2163:29): [True: 109k, False: 36.5k] ------------------ 2164| 109k| { 2165| 109k| composite_norm_data[jj].nNumRemovedProtonsIsotopic[n] += all_inp_norm_data[i][k].nNumRemovedProtonsIsotopic[n]; 2166| 109k| composite_norm_data[jj].num_iso_H[n] += all_inp_norm_data[i][k].num_iso_H[n]; 2167| 109k| } 2168| | /* 2169| | composite_norm_data[j].num_at += cur_num_at + cur_num_H; 2170| | composite_norm_data[j].num_removed_H += cur_num_H; 2171| | */ 2172| | /* total count */ 2173| 36.5k| tot_num_at += cur_num_at; 2174| 36.5k| tot_num_H += cur_num_H; 2175| | /* offset for the next component */ 2176| 36.5k| if (composite_norm_data[jj].nOffsetAtAndH) ------------------ | Branch (2176:21): [True: 36.4k, False: 94] ------------------ 2177| 36.4k| { 2178| 36.4k| composite_norm_data[jj].nOffsetAtAndH[2 * i] = tot_num_at; 2179| 36.4k| composite_norm_data[jj].nOffsetAtAndH[2 * i + 1] = num_at[jj] + tot_num_H; 2180| 36.4k| } 2181| 36.5k| } 2182| 972| if (tot_num_at != num_at[jj] || ------------------ | Branch (2182:17): [True: 0, False: 972] ------------------ 2183| 972| num_at[jj] + tot_num_H != num_inp_at[jj]) ------------------ | Branch (2183:18): [True: 0, False: 972] ------------------ 2184| 0| { 2185| 0| goto exit_error; /* miscount */ 2186| 0| } 2187| 972| composite_norm_data[jj].bExists = ( tot_num_at > 0 ); 2188| 972| ret |= indicator; 2189| 972| } 2190| 2.43k| } 2191| 811| return ret; 2192| | 2193| 0|exit_error: 2194| 0| return ret; 2195| 811|} CreateCompAtomData: 2203| 867|{ 2204| 867| FreeCompAtomData( inp_at_data ); 2205| 867| if (( inp_at_data->at = CreateInpAtom( num_atoms ) ) && ------------------ | Branch (2205:9): [True: 867, False: 0] ------------------ 2206| 867| ( num_components <= 1 || bIntermediateTaut || ------------------ | Branch (2206:11): [True: 0, False: 867] | Branch (2206:34): [True: 47, False: 820] ------------------ 2207| 820| ( inp_at_data->nOffsetAtAndH = (AT_NUMB*) inchi_calloc( 2 * ( (long long)num_components + 1 ), sizeof( inp_at_data->nOffsetAtAndH[0] ) ) ) )) /* djb-rwth: cast operator added */ ------------------ | | 1146| 820|#define inchi_calloc calloc ------------------ | Branch (2207:9): [True: 820, False: 0] ------------------ 2208| 867| { 2209| | 2210| 867| inp_at_data->num_at = num_atoms; 2211| 867| inp_at_data->num_components = ( num_components > 1 ) ? num_components : 0; ------------------ | Branch (2211:39): [True: 867, False: 0] ------------------ 2212| 867| return 1; 2213| 867| } 2214| 0| FreeCompAtomData( inp_at_data ); 2215| | 2216| 0| return 0; 2217| 867|} RestoreEdgeFlow: 408| 65.9k|{ 409| | /*flow1 = edge->flow;*/ /* output from BNS */ 410| 65.9k| switch (bChangeFlow & BNS_EF_CHNG_RSTR) ------------------ | | 372| 65.9k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 65.9k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 65.9k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ | Branch (410:13): [True: 65.9k, False: 0] ------------------ 411| 65.9k| { 412| 0| case 0: ------------------ | Branch (412:9): [True: 0, False: 65.9k] ------------------ 413| | /* the flow has not been permitted to change inside the BNS */ 414| | /* nothing to do */ 415| | /*flow1 = edge->flow;*/ /* output from BNS, the original flow value */ 416| | /*flow2 = flow1 + delta;*/ /* the flow would be changed to this value by the BNS if permitted */ 417| 0| break; 418| 1.27k| case BNS_EF_CHNG_FLOW: ------------------ | | 370| 1.27k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ | Branch (418:9): [True: 1.27k, False: 64.6k] ------------------ 419| | /* the flow has been changed by the BNS; update flow0 */ 420| | /*flow2 = edge->flow;*/ /* output from BNS, the changed value */ 421| | /*flow1 = flow2 - delta;*/ /* the original flow value before the BNS */ 422| 1.27k| edge->flow0 = edge->flow; /* SAVE NEW EDGE FLOW AS THE INITIAL FLOW FROM CHEM. BONDS */ 423| 1.27k| break; 424| 64.6k| case BNS_EF_CHNG_RSTR: ------------------ | | 372| 64.6k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 64.6k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 64.6k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ | Branch (424:9): [True: 64.6k, False: 1.27k] ------------------ 425| | /* the flow has been changed by the BNS; requested to change it back */ 426| | /*flow2 = edge->flow;*/ /* output from BNS, the changed value */ 427| | /*flow1 = flow2 - delta;*/ /* the original flow value before the BNS */ 428| 64.6k| edge->flow = edge->flow - delta; /* CHANGE EDGE FLOW BACK (RESTORE) */ 429| 64.6k| break; 430| 0| case BNS_EF_RSTR_FLOW: ------------------ | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ ------------------ | Branch (430:9): [True: 0, False: 65.9k] ------------------ 431| | /* the flow has not been permitted to change inside the BNS */ 432| | /* nothing to do */ 433| | /*flow1 = edge->flow;*/ /* output from BNS, the original flow value */ 434| | /*flow2 = flow1 + delta;*/ /* the flow would be changed to this value by the BNS if permitted */ 435| 0| break; 436| 65.9k| } 437| | 438| 65.9k| return 0; 439| 65.9k|} SetAtomBondType: 450| 68.3k|{ 451| 68.3k| int flow1, flow2, tmp, ret = 0; 452| 68.3k| int bond_mark = 0, bond_type, new_bond_type; /* djb-rwth: addressing LLVM warning */ 453| | 454| 68.3k| if (!edge->pass || !bond_type21) ------------------ | Branch (454:9): [True: 0, False: 68.3k] | Branch (454:24): [True: 0, False: 68.3k] ------------------ 455| 0| { 456| 0| return 0; 457| 0| } 458| | 459| 68.3k| switch (bChangeFlow & BNS_EF_CHNG_RSTR) ------------------ | | 372| 68.3k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 68.3k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 68.3k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 460| 68.3k| { 461| 28.6k| case 0: /* the flow has not been permitted to change inside the BNS: simulated in case of check one bond */ ------------------ | Branch (461:9): [True: 28.6k, False: 39.6k] ------------------ 462| 28.6k| case BNS_EF_RSTR_FLOW: /* the flow has not been permitted to change inside the BNS: obsolete mode, unexpected bChangeFlow */ ------------------ | | 371| 28.6k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ ------------------ | Branch (462:9): [True: 0, False: 68.3k] ------------------ 463| 28.6k| flow1 = edge->flow0; /* output from BNS, the original (old) flow value */ 464| 28.6k| flow2 = flow1 + delta; /* the flow would be changed to this value by the BNS if permitted */ 465| 28.6k| break; 466| 598| case BNS_EF_CHNG_FLOW: /* the flow has been changed by the BNS */ ------------------ | | 370| 598|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ | Branch (466:9): [True: 598, False: 67.7k] ------------------ 467| 39.6k| case BNS_EF_CHNG_RSTR: /* the flow has been changed by the BNS; requested to change it back */ ------------------ | | 372| 39.6k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 39.6k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 39.6k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ | Branch (467:9): [True: 39.1k, False: 29.2k] ------------------ 468| 39.6k| flow2 = edge->flow; /* output from BNS, the changed (new) value */ 469| 39.6k| flow1 = edge->flow0; /* the original flow (old) value before the BNS */ 470| 39.6k| break; 471| 0| default: ------------------ | Branch (471:9): [True: 0, False: 68.3k] ------------------ 472| 0| return 0; /* added 2006-03-21 */ 473| 68.3k| } 474| | 475| 68.3k| if (( bChangeFlow & BNS_EF_CHNG_BONDS ) && ( bChangeFlow & BNS_EF_ALTR_NS ) != BNS_EF_ALTR_NS) ------------------ | | 373| 68.3k|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ ------------------ if (( bChangeFlow & BNS_EF_CHNG_BONDS ) && ( bChangeFlow & BNS_EF_ALTR_NS ) != BNS_EF_ALTR_NS) ------------------ | | 382| 598|#define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 374| 598|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ | | ------------------ | | #define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 377| 598|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_CHNG_BONDS ) && ( bChangeFlow & BNS_EF_ALTR_NS ) != BNS_EF_ALTR_NS) ------------------ | | 382| 598|#define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 374| 598|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ | | ------------------ | | #define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 377| 598|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: | | ------------------ ------------------ | Branch (475:9): [True: 598, False: 67.7k] | Branch (475:48): [True: 278, False: 320] ------------------ 476| 278| { 477| | /* Set new bond types according to the new flow values */ 478| 278| new_bond_type = flow2 + BOND_SINGLE; ------------------ | | 177| 278|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 278|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ 479| 278| if (*bond_type12 != new_bond_type) ------------------ | Branch (479:13): [True: 277, False: 1] ------------------ 480| 277| { 481| 277| *bond_type12 = *bond_type21 = new_bond_type; 482| 277| ret++; 483| 277| } 484| 278| } 485| 68.1k| else 486| 68.1k| { 487| 68.1k| if (bChangeFlow & BNS_EF_ALTR_BONDS) ------------------ | | 374| 68.1k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ | Branch (487:13): [True: 51.9k, False: 16.1k] ------------------ 488| 51.9k| { 489| 51.9k| if (flow1 == flow2) ------------------ | Branch (489:17): [True: 5, False: 51.9k] ------------------ 490| 5| { 491| 5| goto exit_function; 492| 5| } 493| | /* Update alternating bond information */ 494| 51.9k| if (flow1 > flow2) ------------------ | Branch (494:17): [True: 25.7k, False: 26.1k] ------------------ 495| 25.7k| { 496| | /* Make sure flow2 > flow1 */ 497| 25.7k| tmp = flow1; 498| 25.7k| flow1 = flow2; 499| 25.7k| flow2 = tmp; 500| 25.7k| } 501| | /* djb-rwth: removing redundant code */ 502| 51.9k| switch (bond_type = ( *bond_type12 & BOND_TYPE_MASK )) ------------------ | | 189| 51.9k|#define BOND_TYPE_MASK 0x0f ------------------ 503| 51.9k| { 504| 11.6k| case BOND_SINGLE: ------------------ | | 177| 11.6k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 11.6k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (504:17): [True: 11.6k, False: 40.2k] ------------------ 505| 22.5k| case BOND_DOUBLE: ------------------ | | 178| 22.5k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 22.5k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (505:17): [True: 10.8k, False: 41.0k] ------------------ 506| 25.6k| case BOND_TRIPLE: ------------------ | | 179| 25.6k|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 25.6k|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (506:17): [True: 3.13k, False: 48.8k] ------------------ 507| | /* assume that the input bond type fits either flow1 or flow2 */ 508| 25.6k| if (flow1 == 0 && flow2 == 1) ------------------ | Branch (508:25): [True: 20.9k, False: 4.74k] | Branch (508:39): [True: 20.1k, False: 758] ------------------ 509| 20.1k| { 510| 20.1k| if (bChangeFlow & BNS_EF_SET_NOSTEREO) ------------------ | | 377| 20.1k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ | Branch (510:29): [True: 10.6k, False: 9.50k] ------------------ 511| 10.6k| { 512| 10.6k| bond_mark = BOND_MARK_ALT12NS; ------------------ | | 197| 10.6k|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ 513| 10.6k| bond_type = BOND_ALT12NS; ------------------ | | 186| 10.6k|#define BOND_ALT12NS 9 ------------------ 514| 10.6k| } 515| 9.50k| else 516| 9.50k| { 517| 9.50k| bond_mark = BOND_MARK_ALT12; ------------------ | | 193| 9.50k|#define BOND_MARK_ALT12 0x10 ------------------ 518| 9.50k| bond_type = BOND_ALTERN; ------------------ | | 180| 9.50k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 9.50k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ 519| 9.50k| } 520| 20.1k| } 521| 5.49k| else 522| 5.49k| { 523| 5.49k| if (flow1 == 0 && flow2 == 2) ------------------ | Branch (523:29): [True: 758, False: 4.74k] | Branch (523:43): [True: 758, False: 0] ------------------ 524| 758| { 525| 758| bond_mark = BOND_MARK_ALT13; ------------------ | | 195| 758|#define BOND_MARK_ALT13 0x30 ------------------ 526| 758| bond_type = BOND_ALT_13; ------------------ | | 183| 758|#define BOND_ALT_13 6 /* single/triple */ ------------------ 527| 758| } 528| 4.74k| else 529| 4.74k| { 530| 4.74k| if (flow1 == 1 && flow2 == 2) ------------------ | Branch (530:33): [True: 4.74k, False: 0] | Branch (530:47): [True: 4.74k, False: 0] ------------------ 531| 4.74k| { 532| 4.74k| bond_mark = BOND_MARK_ALT23; ------------------ | | 196| 4.74k|#define BOND_MARK_ALT23 0x40 ------------------ 533| 4.74k| bond_type = BOND_ALT_23; ------------------ | | 184| 4.74k|#define BOND_ALT_23 7 /* double/triple */ ------------------ 534| 4.74k| } 535| 0| else 536| 0| { 537| 0| return BNS_BOND_ERR; /* error */ ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 538| 0| } 539| 4.74k| } 540| 5.49k| } 541| 25.6k| break; 542| 25.6k| case BOND_TAUTOM: ------------------ | | 185| 14.9k|#define BOND_TAUTOM 8 ------------------ | Branch (542:17): [True: 14.9k, False: 37.0k] ------------------ 543| 14.9k| if (flow1 == 0 && flow2 == 1) ------------------ | Branch (543:25): [True: 14.9k, False: 5] | Branch (543:39): [True: 14.9k, False: 0] ------------------ 544| 14.9k| { 545| 14.9k| bond_mark = BOND_MARK_ALT12NS; ------------------ | | 197| 14.9k|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ 546| 14.9k| } 547| 5| else 548| 5| if (flow1 == 1 && flow2 == 2) { ------------------ | Branch (548:29): [True: 5, False: 0] | Branch (548:43): [True: 5, False: 0] ------------------ 549| 5| bond_mark = BOND_MARK_ALT23; ------------------ | | 196| 5|#define BOND_MARK_ALT23 0x40 ------------------ 550| 5| } 551| 0| else { 552| 0| return BNS_BOND_ERR; /* error */ ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 553| 0| } 554| 14.9k| break; 555| 14.9k| default: ------------------ | Branch (555:17): [True: 11.3k, False: 40.6k] ------------------ 556| 11.3k| new_bond_type = bond_type; 557| 11.3k| bond_mark = ( *bond_type12 & BOND_MARK_MASK ); ------------------ | | 198| 11.3k|#define BOND_MARK_MASK 0x70 ------------------ 558| 11.3k| switch (bond_mark) 559| 11.3k| { 560| 4.26k| case BOND_MARK_ALT12: ------------------ | | 193| 4.26k|#define BOND_MARK_ALT12 0x10 ------------------ | Branch (560:25): [True: 4.26k, False: 7.06k] ------------------ 561| 4.26k| if (( bChangeFlow & BNS_EF_SET_NOSTEREO ) && flow1 == 0 && flow2 == 1) ------------------ | | 377| 4.26k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ | Branch (561:33): [True: 617, False: 3.64k] | Branch (561:74): [True: 580, False: 37] | Branch (561:88): [True: 580, False: 0] ------------------ 562| 580| { 563| 580| bond_mark = BOND_MARK_ALT12NS; ------------------ | | 197| 580|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ 564| 580| new_bond_type = BOND_ALT12NS; ------------------ | | 186| 580|#define BOND_ALT12NS 9 ------------------ 565| 580| break; 566| 580| } 567| 7.08k| case BOND_MARK_ALT12NS: ------------------ | | 197| 7.08k|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (567:25): [True: 3.40k, False: 7.92k] ------------------ 568| 7.08k| if (flow1 == 2 || flow2 == 2) ------------------ | Branch (568:33): [True: 0, False: 7.08k] | Branch (568:47): [True: 560, False: 6.52k] ------------------ 569| 560| { 570| 560| bond_mark = BOND_MARK_ALT123; ------------------ | | 194| 560|#define BOND_MARK_ALT123 0x20 ------------------ 571| 560| new_bond_type = BOND_ALT_123; ------------------ | | 182| 560|#define BOND_ALT_123 5 /* single/double/triple */ ------------------ 572| 560| } 573| 7.08k| break; 574| 760| case BOND_MARK_ALT13: ------------------ | | 195| 760|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (574:25): [True: 760, False: 10.5k] ------------------ 575| 760| if (flow1 == 1 || flow2 == 1) ------------------ | Branch (575:33): [True: 429, False: 331] | Branch (575:47): [True: 329, False: 2] ------------------ 576| 758| { 577| 758| bond_mark = BOND_MARK_ALT123; ------------------ | | 194| 758|#define BOND_MARK_ALT123 0x20 ------------------ 578| 758| new_bond_type = BOND_ALT_123; ------------------ | | 182| 758|#define BOND_ALT_123 5 /* single/double/triple */ ------------------ 579| 758| } 580| 760| break; 581| 2.09k| case BOND_MARK_ALT23: ------------------ | | 196| 2.09k|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (581:25): [True: 2.09k, False: 9.23k] ------------------ 582| 2.09k| if (flow1 == 0 || flow2 == 0) ------------------ | Branch (582:33): [True: 792, False: 1.29k] | Branch (582:47): [True: 0, False: 1.29k] ------------------ 583| 792| { 584| 792| bond_mark = BOND_MARK_ALT123; ------------------ | | 194| 792|#define BOND_MARK_ALT123 0x20 ------------------ 585| 792| new_bond_type = BOND_ALT_123; ------------------ | | 182| 792|#define BOND_ALT_123 5 /* single/double/triple */ ------------------ 586| 792| } 587| 2.09k| break; 588| 817| case BOND_MARK_ALT123: ------------------ | | 194| 817|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (588:25): [True: 817, False: 10.5k] ------------------ 589| 817| break; 590| | 591| 0| case 0: /* special case: second alt bond testing */ ------------------ | Branch (591:25): [True: 0, False: 11.3k] ------------------ 592| 0| if (flow1 == 0 && flow2 == 1) ------------------ | Branch (592:33): [True: 0, False: 0] | Branch (592:47): [True: 0, False: 0] ------------------ 593| 0| { 594| 0| bond_mark = BOND_MARK_ALT12; ------------------ | | 193| 0|#define BOND_MARK_ALT12 0x10 ------------------ 595| 0| } 596| 0| else 597| 0| { 598| 0| if (flow1 == 0 && flow2 == 2) ------------------ | Branch (598:37): [True: 0, False: 0] | Branch (598:51): [True: 0, False: 0] ------------------ 599| 0| { 600| 0| bond_mark = BOND_MARK_ALT13; ------------------ | | 195| 0|#define BOND_MARK_ALT13 0x30 ------------------ 601| 0| } 602| 0| else 603| 0| { 604| 0| if (flow1 == 1 && flow2 == 2) ------------------ | Branch (604:41): [True: 0, False: 0] | Branch (604:55): [True: 0, False: 0] ------------------ 605| 0| { 606| 0| bond_mark = BOND_MARK_ALT23; ------------------ | | 196| 0|#define BOND_MARK_ALT23 0x40 ------------------ 607| 0| } 608| 0| else 609| 0| { 610| 0| return BNS_BOND_ERR; /* error */ ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 611| 0| } 612| 0| } 613| 0| } 614| 0| break; 615| | 616| 0| default: ------------------ | Branch (616:25): [True: 0, False: 11.3k] ------------------ 617| 0| return BNS_BOND_ERR; /* error */ ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 618| 11.3k| } 619| | 620| 11.3k| switch (bond_type) 621| 11.3k| { 622| 0| case BOND_TAUTOM: ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (622:25): [True: 0, False: 11.3k] ------------------ 623| 0| break; 624| 4.26k| case BOND_ALTERN: ------------------ | | 180| 4.26k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 4.26k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (624:25): [True: 4.26k, False: 7.06k] ------------------ 625| 7.66k| case BOND_ALT12NS: ------------------ | | 186| 7.66k|#define BOND_ALT12NS 9 ------------------ | Branch (625:25): [True: 3.40k, False: 7.92k] ------------------ 626| 8.47k| case BOND_ALT_123: ------------------ | | 182| 8.47k|#define BOND_ALT_123 5 /* single/double/triple */ ------------------ | Branch (626:25): [True: 817, False: 10.5k] ------------------ 627| 9.23k| case BOND_ALT_13: ------------------ | | 183| 9.23k|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (627:25): [True: 760, False: 10.5k] ------------------ 628| 11.3k| case BOND_ALT_23: ------------------ | | 184| 11.3k|#define BOND_ALT_23 7 /* double/triple */ ------------------ | Branch (628:25): [True: 2.09k, False: 9.23k] ------------------ 629| 11.3k| bond_type = new_bond_type; 630| 11.3k| break; 631| 0| default: ------------------ | Branch (631:25): [True: 0, False: 11.3k] ------------------ 632| 0| return BNS_BOND_ERR; /* error */ ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 633| 11.3k| } 634| 51.9k| } 635| | 636| 51.9k| new_bond_type = bond_type | bond_mark; 637| 51.9k| if (new_bond_type != *bond_type12) ------------------ | Branch (637:17): [True: 40.8k, False: 11.1k] ------------------ 638| 40.8k| { 639| 40.8k| *bond_type12 = *bond_type21 = new_bond_type; 640| 40.8k| ret++; 641| 40.8k| } 642| 51.9k| } 643| 68.1k| } 644| | 645| 68.3k|exit_function: 646| | 647| 68.3k| return ret; 648| 68.3k|} RunBalancedNetworkSearch: 655| 567k|{ 656| 567k| int pass, delta = 0, nSumDelta; 657| | 658| 567k| nSumDelta = 0; 659| 690k| for (pass = 0; pass < pBNS->max_altp; pass++) ------------------ | Branch (659:20): [True: 690k, False: 2] ------------------ 660| 690k| { 661| 690k| pBNS->alt_path = pBNS->altp[pass]; 662| 690k| pBNS->bChangeFlow = 0; 663| 690k| delta = BalancedNetworkSearch( pBNS, pBD, bChangeFlow ); 664| 690k| ReInitBnData( pBD ); 665| 690k| if (0 < delta) ------------------ | Branch (665:13): [True: 122k, False: 567k] ------------------ 666| 122k| { 667| 122k| pBNS->num_altp++; 668| 122k| nSumDelta += abs( delta ); 669| 122k| } 670| 567k| else 671| 567k| { 672| 567k| break; 673| 567k| } 674| 690k| } 675| | 676| 567k| if (IS_BNS_ERROR( delta )) ------------------ | | 67| 567k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 567k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 567k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 567k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 567k, False: 0] | | | Branch (67:44): [True: 2, False: 567k] | | ------------------ ------------------ 677| 2| { 678| 2| return delta; 679| 2| } 680| | 681| 567k| if (bInchiTimeIsOver( pBNS->ic, pBNS->ulTimeOutTime )) ------------------ | Branch (681:9): [True: 0, False: 567k] ------------------ 682| 0| { 683| 0| return BNS_TIMEOUT; ------------------ | | 63| 0|#define BNS_TIMEOUT (BNS_ERR + 14) /*(-9985)*/ /* v. 1.05 */ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 684| 0| } 685| | 686| 567k| return nSumDelta; /* number of eliminated pairs of "dots" */ 687| 567k|} SetAtomRadAndChemValFromVertexCapFlow: 694| 40|{ 695| 40| BNS_VERTEX *vert = pBNS->vert + v1; 696| 40| inp_ATOM *at = atom + v1; 697| 40| S_CHAR cValue; 698| 40| int nChanges = 0; 699| | 700| | /* Set only on the 1st pass */ 701| 40| if (!vert->st_edge.pass) ------------------ | Branch (701:9): [True: 0, False: 40] ------------------ 702| 0| { 703| 0| return 0; 704| 0| } 705| | 706| | /* Adjust chem_bonds_valence */ 707| 40| cValue = at->chem_bonds_valence - at->valence; 708| 40| if (cValue >= 0 && cValue != vert->st_edge.flow) ------------------ | Branch (708:9): [True: 40, False: 0] | Branch (708:24): [True: 40, False: 0] ------------------ 709| 40| { 710| 40| at->chem_bonds_valence = at->valence + vert->st_edge.flow; 711| 40| nChanges++; 712| 40| } 713| | 714| | /* Adjist radical */ 715| 40| switch (vert->st_edge.cap - vert->st_edge.flow) 716| 40| { 717| 40| case 0: ------------------ | Branch (717:9): [True: 40, False: 0] ------------------ 718| 40| cValue = 0; 719| 40| break; 720| 0| case 1: ------------------ | Branch (720:9): [True: 0, False: 40] ------------------ 721| 0| cValue = RADICAL_DOUBLET; ------------------ | | 76| 0|#define RADICAL_DOUBLET 2 ------------------ 722| 0| break; 723| 0| case 2: ------------------ | Branch (723:9): [True: 0, False: 40] ------------------ 724| 0| cValue = RADICAL_TRIPLET; ------------------ | | 77| 0|#define RADICAL_TRIPLET 3 ------------------ 725| 0| break; 726| 0| default: ------------------ | Branch (726:9): [True: 0, False: 40] ------------------ 727| 0| return BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 728| 40| } 729| 40| if (cValue != at->radical) ------------------ | Branch (729:9): [True: 40, False: 0] ------------------ 730| 40| { 731| 40| at->radical = cValue; 732| 40| nChanges++; 733| 40| } 734| | 735| 40| return nChanges; 736| 40|} AddChangedAtHChargeBNS: 744| 197|{ 745| 197| int i, mask, num; 746| 1.62k| for (i = 0, num = 0; i < num_atoms; i++) ------------------ | Branch (746:26): [True: 1.43k, False: 197] ------------------ 747| 1.43k| { 748| 1.43k| if (mark[i]) ------------------ | Branch (748:13): [True: 450, False: 980] ------------------ 749| 450| { 750| 450| mark[i] = 0; 751| 450|#if ( FIX_NORM_BUG_ADD_ION_PAIR == 1 ) 752| | /* add ignoring adjacent charges */ 753| 450| at[i].at_type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, -2 ); 754| |#else 755| | at[i].at_type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); 756| |#endif 757| 450| num++; 758| 450| } 759| 1.43k| } 760| | 761| 197| return num; 762| 197|} EliminatePlusMinusChargeAmbiguity: 778| 197|{ 779| 197| int pass, i, v0, v1, v2, ineigh1, /*ineigh0,*/ /*ineigh2,*/ 780| 197| vLast, n, delta, ret, err = 0; 781| 197| int nFound, k; 782| 197| BNS_EDGE *edge; 783| | 784| 394| for (pass = pBNS->num_altp - 1, ret = 0; 0 <= pass; pass--) ------------------ | Branch (784:46): [True: 197, False: 197] ------------------ 785| 197| { 786| | 787| 197| pBNS->alt_path = pBNS->altp[pass]; 788| 197| v1 = ALTP_START_ATOM( pBNS->alt_path ); ------------------ | | 103| 197|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 789| 197| n = ALTP_PATH_LEN( pBNS->alt_path ); ------------------ | | 101| 197|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 790| 197| delta = ALTP_DELTA( pBNS->alt_path ); ------------------ | | 112| 197|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 791| 197| vLast = ALTP_END_ATOM( pBNS->alt_path ); ------------------ | | 102| 197|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 792| 197| v0 = v2 = NO_VERTEX; /* negative number */ ------------------ | | 118| 197|#define NO_VERTEX -2 ------------------ 793| | 794| 1.40k| for (i = 0; i < n; i++, delta = -delta, v0 = v1, v1 = v2 /*, ineigh0 = ineigh1*/) ------------------ | Branch (794:21): [True: 1.20k, False: 197] ------------------ 795| 1.20k| { 796| 1.20k| ineigh1 = ALTP_THIS_ATOM_NEIGHBOR( pBNS->alt_path, i ); /* v1->v2 neighbor */ ------------------ | | 104| 1.20k|#define ALTP_THIS_ATOM_NEIGHBOR(altp,X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[0] /* 0 <= X < path_len */ ------------------ 797| | /*ineigh2 = ALTP_NEXT_ATOM_NEIGHBOR(pBNS->alt_path, i);*/ /* v2->v1 neighbor */ 798| 1.20k| edge = pBNS->edge + pBNS->vert[v1].iedge[ineigh1]; 799| | /* follow the BN Structure, not the inp_ATOM, to take care of swithching to 800| | t-groups, c-groups or other fictitious edges/vertices 801| | */ 802| 1.20k| v2 = edge->neighbor12 ^ v1; 803| 1.20k| if (v1 < num_atoms && ------------------ | Branch (803:17): [True: 771, False: 434] ------------------ 804| 771| ( (v0 >= num_atoms && ( pBNS->vert[v0].type & BNS_VERT_TYPE_C_GROUP )) || ------------------ | | 49| 237|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (804:20): [True: 237, False: 534] | Branch (804:39): [True: 207, False: 30] ------------------ 805| 564| (v2 >= num_atoms && ( pBNS->vert[v2].type & BNS_VERT_TYPE_C_GROUP ) ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 49| 235|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (805:20): [True: 235, False: 329] | Branch (805:39): [True: 112, False: 123] ------------------ 806| 319| { 807| 319| int cgPos = 0, cgNeg = 0; 808| 319| int neighPos = -1, neighNeg = -1; 809| 319| BNS_EDGE *edgePos, *edgeNeg; 810| 319| nFound = 0; 811| 1.28k| for (k = pBNS->vert[v1].num_adj_edges - 1; k >= 0 && ( neighPos < 0 || neighNeg < 0 ); k--) ------------------ | Branch (811:60): [True: 1.18k, False: 96] | Branch (811:72): [True: 961, False: 223] | Branch (811:88): [True: 0, False: 223] ------------------ 812| 961| { 813| 961| BNS_EDGE *next_edge = pBNS->edge + pBNS->vert[v1].iedge[k]; 814| 961| int v = next_edge->neighbor12 ^ v1; 815| 961| if (pBNS->vert[v].type & BNS_VERT_TYPE_C_GROUP) ------------------ | | 49| 961|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (815:25): [True: 542, False: 419] ------------------ 816| 542| { 817| 542| if (pBNS->vert[v].type & BNS_VERT_TYPE_C_NEGATIVE) ------------------ | | 54| 542|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (817:29): [True: 319, False: 223] ------------------ 818| 319| { 819| 319| cgNeg = v; 820| 319| neighNeg = k; 821| 319| nFound++; 822| 319| } 823| 223| else 824| 223| { 825| 223| cgPos = v; 826| 223| neighPos = k; 827| 223| nFound++; 828| 223| } 829| 542| } 830| 961| } 831| 319| if (2 == nFound && neighPos >= 0 && neighNeg >= 0) ------------------ | Branch (831:21): [True: 223, False: 96] | Branch (831:36): [True: 223, False: 0] | Branch (831:53): [True: 223, False: 0] ------------------ 832| 223| { 833| | /* both c-groups have been found */ 834| 223| edgePos = pBNS->edge + pBNS->vert[v1].iedge[neighPos]; 835| 223| edgeNeg = pBNS->edge + pBNS->vert[v1].iedge[neighNeg]; 836| 223| if (edgePos->flow < edgeNeg->flow) ------------------ | Branch (836:25): [True: 0, False: 223] ------------------ 837| 0| { 838| | /* ambiguity found; replace (+cg)--N==(-cg) with (+cg)==N--(-cg) */ 839| 0| int dflow = edgeNeg->flow - edgePos->flow; 840| | 841| 0| edgePos->flow += dflow; 842| 0| pBNS->vert[cgPos].st_edge.cap += dflow; 843| 0| pBNS->vert[cgPos].st_edge.flow += dflow; 844| | 845| 0| edgeNeg->flow -= dflow; 846| 0| pBNS->vert[cgNeg].st_edge.cap -= dflow; 847| 0| pBNS->vert[cgNeg].st_edge.flow -= dflow; 848| 0| ret++; 849| 0| } 850| 223| } 851| 319| } 852| 1.20k| } 853| | 854| 197| if (v2 != vLast) ------------------ | Branch (854:13): [True: 0, False: 197] ------------------ 855| 0| { 856| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 857| 0| } 858| 197| } 859| | 860| 197| return err ? err : ret; ------------------ | Branch (860:12): [True: 0, False: 197] ------------------ 861| 197|} AddOrRemoveExplOrImplH: 872| 5.11k|{ 873| 5.11k| int i, iso, tot_num_iso_H, 874| 5.11k| num_H, /* number of H before the removal, including explicit H */ 875| 5.11k| nNum2Remove, /* number of H to remove */ 876| 5.11k| nNumRemovedExplicitH; /* djb-rwth: removing redundant variables */ 877| 5.11k| S_CHAR num_iso_H[NUM_H_ISOTOPES]; 878| 5.11k| inp_ATOM *at_H; 879| | 880| 5.11k| if (!nDelta) ------------------ | Branch (880:9): [True: 0, False: 5.11k] ------------------ 881| 0| { 882| 0| return 0; 883| 0| } 884| | /* add */ 885| 5.11k| if (nDelta > 0) ------------------ | Branch (885:9): [True: 4.21k, False: 900] ------------------ 886| 4.21k| { 887| 4.21k| at[at_no].num_H += nDelta; 888| 4.21k| t_group_info->tni.nNumRemovedProtons--; 889| 4.21k| return nDelta; 890| 4.21k| } 891| | /* remove */ 892| 900| nNum2Remove = -nDelta; 893| 900| nNumRemovedExplicitH = t_group_info->tni.nNumRemovedExplicitH; /* number of explicit H saved separately in 894| | at[num_atoms+i], i=0..nNumRemovedExplicitH-1 */ 895| 900| tot_num_iso_H = NUM_ISO_H( at, at_no ); ------------------ | | 55| 900|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) ------------------ 896| 900| num_H = at[at_no].num_H; 897| | /* 898| | tot_num_iso_H = NUM_ISO_H(at,at_no); 899| | num_H = at[at_no].num_H; 900| | nNumAtomExplicitH = 0; 901| | nNumRemovedExplicitH = t_group_info->tni.nNumRemovedExplicitH; 902| | tot_num_explicit_iso_H = 0; 903| | */ 904| | 905| 900| at_H = at + num_atoms; 906| 900| memcpy(num_iso_H, at[at_no].num_iso_H, sizeof(num_iso_H)); 907| | /* Remove all explicit H, otherwise a false stereo can occur. 908| | Example: remove H(+) from the following substructure: 909| | 910| | H H 911| | A / A / 912| | >X==N(+) produces false stereogenic bond: >X==N 913| | B \ B 914| | H 915| | 916| | To avoid this effect all explicit H atoms must be removed 917| | */ 918| | 919| | /* djb-rwth: removing redundant code */ 920| 1.36k| for (i = 0; i < nNumRemovedExplicitH; ) ------------------ | Branch (920:17): [True: 461, False: 900] ------------------ 921| 461| { 922| 461| if (at_H[i].neighbor[0] == at_no) ------------------ | Branch (922:13): [True: 307, False: 154] ------------------ 923| 307| { 924| 307| int m, k, orig_no = at_H[i].orig_at_number; 925| 307| nNumRemovedExplicitH--; 926| | /* djb-rwth: removing redundant code */ 927| 307| if (nNumRemovedExplicitH > i) ------------------ | Branch (927:17): [True: 60, False: 247] ------------------ 928| 60| { 929| 60| inp_ATOM at_i = at_H[i]; 930| 60| memmove(at_H + i, at_H + i + 1, sizeof(at_H[0]) * ((long long)nNumRemovedExplicitH - i)); /* djb-rwth: cast operator added */ 931| 60| at_H[nNumRemovedExplicitH] = at_i; /* save removed H (for debugging purposes?) */ 932| 60| } 933| | /* Adjust 0D parities */ 934| 307| if (at[at_no].sb_parity[0]) ------------------ | Branch (934:17): [True: 81, False: 226] ------------------ 935| 81| { 936| 163| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[at_no].sb_parity[m]; m++) ------------------ | | 873| 326|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (936:29): [True: 163, False: 0] | Branch (936:57): [True: 82, False: 81] ------------------ 937| 82| { 938| 82| if (at[at_no].sn_orig_at_num[m] == orig_no) ------------------ | Branch (938:25): [True: 65, False: 17] ------------------ 939| 65| { 940| 65| if (at[at_no].valence >= MIN_NUM_STEREO_BOND_NEIGH) ------------------ | | 875| 65|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (940:29): [True: 30, False: 35] ------------------ 941| 30| { 942| 30| at[at_no].sn_ord[m] = k = ( at[at_no].sb_ord[m] == 0 ); 943| 30| at[at_no].sn_orig_at_num[m] = at[(int) at[at_no].neighbor[k]].orig_at_number; 944| 30| if (ATOM_PARITY_WELL_DEF( at[at_no].sb_parity[m] )) ------------------ | | 259| 30|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 30|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 30|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 30, False: 0] | | | Branch (259:75): [True: 13, False: 17] | | ------------------ ------------------ 945| 13| { 946| 13| at[at_no].sb_parity[m] = 3 - at[at_no].sb_parity[m]; 947| 13| } 948| 30| } 949| 35| else 950| 35| { 951| 35| at[at_no].sn_ord[m] = -99; /* no sb neighbor exists anymore */ 952| 35| at[at_no].sn_orig_at_num[m] = 0; 953| 35| if (ATOM_PARITY_WELL_DEF( at[at_no].sb_parity[m] )) ------------------ | | 259| 35|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 35|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 35|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 35, False: 0] | | | Branch (259:75): [True: 25, False: 10] | | ------------------ ------------------ 954| 25| { 955| 25| int pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; 956| 25| if (0 < get_opposite_sb_atom( at, at_no, at[at_no].sb_ord[m], ------------------ | Branch (956:37): [True: 25, False: 0] ------------------ 957| 25| &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord )) 958| 25| { 959| 25| at[at_no].sb_parity[m] = 960| 25| at[pnxt_atom].sb_parity[pinxt_sb_parity_ord] = AB_PARITY_UNDF; ------------------ | | 222| 25|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 961| 25| } 962| 25| } 963| 35| } 964| 65| } 965| 82| } 966| 81| } 967| | /* do not increment i here: we have shifted next at_H[] element 968| | to the ith position and decremented nNumRemovedExplicitH */ 969| 307| } 970| 154| else 971| 154| { 972| 154| i++; 973| 154| } 974| 461| } 975| | 976| 1.85k| for (iso = -1; iso < NUM_H_ISOTOPES && 0 < nNum2Remove; iso++) ------------------ | | 25| 3.70k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (976:20): [True: 1.84k, False: 11] | Branch (976:44): [True: 954, False: 889] ------------------ 977| 954| { 978| | /* Each pass removes up to one H */ 979| 954| if (iso < 0) ------------------ | Branch (979:13): [True: 900, False: 54] ------------------ 980| 900| { 981| | /* Try to remove non-isotopic */ 982| 1.77k| while (tot_num_iso_H < num_H && 0 < nNum2Remove) ------------------ | Branch (982:20): [True: 1.06k, False: 706] | Branch (982:45): [True: 873, False: 194] ------------------ 983| 873| { 984| | /* Non-isotopic H exists */ 985| 873| num_H--; 986| 873| t_group_info->tni.nNumRemovedProtons++; 987| 873| nNum2Remove--; 988| 873| } 989| 900| } 990| 54| else 991| 54| { 992| | /* Remove isotopic */ 993| 74| while (num_iso_H[iso] && num_H && 0 < nNum2Remove) ------------------ | Branch (993:20): [True: 23, False: 51] | Branch (993:38): [True: 21, False: 2] | Branch (993:47): [True: 20, False: 1] ------------------ 994| 20| { 995| | /* Isotopic H exists */ 996| 20| num_H--; 997| 20| num_iso_H[iso] --; 998| 20| t_group_info->tni.nNumRemovedProtonsIsotopic[iso] ++; 999| 20| t_group_info->tni.nNumRemovedProtons++; 1000| 20| nNum2Remove--; 1001| 20| } 1002| 54| } 1003| 954| } 1004| |#if ( bRELEASE_VERSION != 1 ) 1005| | if (nNum2Remove) 1006| | { 1007| | int stop = 1; /* Program error */ 1008| | } 1009| |#endif 1010| 900| if (nDelta + nNum2Remove < 0) ------------------ | Branch (1010:9): [True: 893, False: 7] ------------------ 1011| 893| { 1012| 893| at[at_no].num_H = num_H; 1013| 893| memcpy(at[at_no].num_iso_H, num_iso_H, sizeof(at[0].num_iso_H)); 1014| 893| t_group_info->tni.nNumRemovedExplicitH = nNumRemovedExplicitH; 1015| 893| } 1016| | 1017| 900| return nDelta + nNum2Remove; 1018| 5.11k|} SubtractOrChangeAtHChargeBNS: 1029| 394|{ 1030| 394| int pass, i, v0, v1, v2, ineigh1, /*ineigh2,*/ vLast, n, delta, ret, err = 0; 1031| 394| BNS_EDGE *edge; 1032| 394| int nDeltaH, nDeltaCharge; 1033| 394| int mask, type; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1034| | 1035| 788| for (pass = pBNS->num_altp - 1, ret = 0; 0 <= pass; pass--) ------------------ | Branch (1035:46): [True: 394, False: 394] ------------------ 1036| 394| { 1037| | 1038| 394| pBNS->alt_path = pBNS->altp[pass]; 1039| 394| v1 = ALTP_START_ATOM( pBNS->alt_path ); ------------------ | | 103| 394|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 1040| 394| n = ALTP_PATH_LEN( pBNS->alt_path ); ------------------ | | 101| 394|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 1041| 394| delta = ALTP_DELTA( pBNS->alt_path ); ------------------ | | 112| 394|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 1042| 394| vLast = ALTP_END_ATOM( pBNS->alt_path ); ------------------ | | 102| 394|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 1043| 394| v0 = v2 = NO_VERTEX; ------------------ | | 118| 394|#define NO_VERTEX -2 ------------------ 1044| | 1045| 2.80k| for (i = 0; i < n; i++, delta = -delta, v0 = v1, v1 = v2) ------------------ | Branch (1045:21): [True: 2.41k, False: 394] ------------------ 1046| 2.41k| { 1047| 2.41k| ineigh1 = ALTP_THIS_ATOM_NEIGHBOR( pBNS->alt_path, i ); /* v1->v2 neighbor */ ------------------ | | 104| 2.41k|#define ALTP_THIS_ATOM_NEIGHBOR(altp,X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[0] /* 0 <= X < path_len */ ------------------ 1048| | /*ineigh2 = ALTP_NEXT_ATOM_NEIGHBOR(pBNS->alt_path, i);*/ /* v2->v1 neighbor */ 1049| 2.41k| edge = pBNS->edge + pBNS->vert[v1].iedge[ineigh1]; 1050| | /* follow the BN Structure, not the inp_ATOM, to take care of swithching to 1051| | t-groups, c-groups or other fictitious edges/vertices 1052| | */ 1053| 2.41k| v2 = edge->neighbor12 ^ v1; 1054| 2.41k| if (v1 < num_atoms && ( v0 >= num_atoms || v2 >= num_atoms )) ------------------ | Branch (1054:17): [True: 1.54k, False: 868] | Branch (1054:37): [True: 474, False: 1.06k] | Branch (1054:56): [True: 466, False: 602] ------------------ 1055| 940| { 1056| 940| nDeltaH = nDeltaCharge = 0; 1057| 940| if (v0 >= num_atoms) ------------------ | Branch (1057:21): [True: 474, False: 466] ------------------ 1058| 474| { 1059| | /* delta(v0-v1) = -delta(v1-v2) along the alternating path */ 1060| 474| if (pBNS->vert[v0].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 474|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (1060:25): [True: 38, False: 436] ------------------ 1061| 38| { 1062| 38| nDeltaH -= delta; 1063| 38| } 1064| 436| else 1065| 436| { 1066| 436| if (pBNS->vert[v0].type & BNS_VERT_TYPE_C_GROUP) ------------------ | | 49| 436|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (1066:29): [True: 414, False: 22] ------------------ 1067| 414| { 1068| 414| nDeltaCharge += delta; 1069| 414| } 1070| 436| } 1071| 474| } 1072| 940| if (v2 >= num_atoms) ------------------ | Branch (1072:21): [True: 474, False: 466] ------------------ 1073| 474| { 1074| 474| if (pBNS->vert[v2].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 474|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (1074:25): [True: 228, False: 246] ------------------ 1075| 228| { 1076| 228| nDeltaH += delta; 1077| 228| } 1078| 246| else 1079| 246| { 1080| 246| if (pBNS->vert[v2].type & BNS_VERT_TYPE_C_GROUP) ------------------ | | 49| 246|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (1080:29): [True: 224, False: 22] ------------------ 1081| 224| { 1082| 224| nDeltaCharge -= delta; 1083| 224| } 1084| 246| } 1085| 474| } 1086| 940| if (nDeltaH || nDeltaCharge) ------------------ | Branch (1086:21): [True: 266, False: 674] | Branch (1086:32): [True: 634, False: 40] ------------------ 1087| 900| { 1088| 900| if (bSubtract) ------------------ | Branch (1088:25): [True: 450, False: 450] ------------------ 1089| 450| { 1090| 450| if (!mark[v1]) ------------------ | Branch (1090:29): [True: 450, False: 0] ------------------ 1091| 450| { 1092| | /* first time the atom has been encountered: subtract */ 1093| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1094| 450|#if ( FIX_NORM_BUG_ADD_ION_PAIR == 1 ) 1095| 450| type = GetAtomChargeType(at, v1, nAtTypeTotals, &mask, 2); 1096| |#else 1097| | type = GetAtomChargeType(at, v1, nAtTypeTotals, &mask, 1); 1098| |#endif 1099| 450| ret++; /* number of changed atoms */ 1100| 450| mark[v1] ++; 1101| 450| } 1102| 450| } 1103| 450| else 1104| 450| { 1105| | /* Change */ 1106| 450| at[v1].charge += nDeltaCharge; 1107| 450| if (nDeltaH) ------------------ | Branch (1107:29): [True: 133, False: 317] ------------------ 1108| 133| { 1109| 133| AddOrRemoveExplOrImplH( nDeltaH, at, num_atoms, (AT_NUMB) v1, t_group_info ); 1110| 133| } 1111| 450| ret++; /* number of changed atoms */ 1112| 450| } 1113| 900| } 1114| 940| } 1115| 2.41k| } 1116| | 1117| 394| if (v2 != vLast) ------------------ | Branch (1117:13): [True: 0, False: 394] ------------------ 1118| 0| { 1119| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1120| 0| } 1121| 394| } 1122| | 1123| 394| return err ? err : ret; ------------------ | Branch (1123:12): [True: 0, False: 394] ------------------ 1124| 394|} SetBondsFromBnStructFlow: 1134| 26.1k|{ 1135| 26.1k| int pass, i, v0, v1, v2, ineigh1, ineigh2, vLast, n, delta, ret, ret_val, err = 0; 1136| 26.1k| BNS_EDGE *edge; 1137| 26.1k| int bChangeFlowAdd; /* djb-rwth: removing redundant variables */ 1138| 26.1k| int bChangeFlow = ( bChangeFlow0 & ~BNS_EF_SET_NOSTEREO ); ------------------ | | 377| 26.1k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ 1139| | /* 1140| | bCheckMovingRad = (bChangeFlow & BNS_EF_ALTR_NS) == BNS_EF_ALTR_NS && 1141| | pBNS->tot_st_cap > pBNS->tot_st_flow; 1142| | */ 1143| 53.1k| for (pass = pBNS->num_altp - 1, ret = 0; 0 <= pass; pass--) ------------------ | Branch (1143:46): [True: 26.9k, False: 26.1k] ------------------ 1144| 26.9k| { 1145| 26.9k| pBNS->alt_path = pBNS->altp[pass]; 1146| 26.9k| v1 = ALTP_START_ATOM( pBNS->alt_path ); ------------------ | | 103| 26.9k|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 1147| 26.9k| n = ALTP_PATH_LEN( pBNS->alt_path ); ------------------ | | 101| 26.9k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 1148| 26.9k| delta = ALTP_DELTA( pBNS->alt_path ); ------------------ | | 112| 26.9k|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 1149| 26.9k| vLast = ALTP_END_ATOM( pBNS->alt_path ); ------------------ | | 102| 26.9k|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 1150| 26.9k| if (( bChangeFlow0 & BNS_EF_SET_NOSTEREO ) && ------------------ | | 377| 26.9k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ | Branch (1150:13): [True: 9.69k, False: 17.2k] ------------------ 1151| 9.69k| ( pBNS->vert[v1].st_edge.cap0 > pBNS->vert[v1].st_edge.flow0 || ------------------ | Branch (1151:15): [True: 3.44k, False: 6.25k] ------------------ 1152| 6.25k| pBNS->vert[vLast].st_edge.cap0 > pBNS->vert[vLast].st_edge.flow0 )) ------------------ | Branch (1152:15): [True: 4.03k, False: 2.22k] ------------------ 1153| 7.47k| { 1154| | /* djb-rwth: removing redundant code */ 1155| 7.47k| bChangeFlowAdd = BNS_EF_SET_NOSTEREO; ------------------ | | 377| 7.47k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ 1156| 7.47k| ret |= 2; 1157| 7.47k| } 1158| 19.4k| else 1159| 19.4k| { 1160| 19.4k| bChangeFlowAdd = 0; 1161| 19.4k| } 1162| | /* start vertex */ 1163| 26.9k| if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 26.9k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 26.9k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 26.9k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 26.9k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 26.9k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 26.9k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ | Branch (1163:13): [True: 26.7k, False: 217] ------------------ 1164| 26.7k| { 1165| | /* Restore s-v1 edge flow to the BNS this pass input value */ 1166| 26.7k| ; /*pBNS->vert[v1].st_edge.flow -= delta;*/ 1167| 26.7k| } 1168| 217| else 1169| 217| { 1170| 217| if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ | Branch (1170:17): [True: 217, False: 0] ------------------ 1171| 217| { 1172| 217| if (v1 < num_atoms) ------------------ | Branch (1172:21): [True: 20, False: 197] ------------------ 1173| 20| { 1174| | /* Will produce wrong result if called for v1 next time? */ 1175| 20| ret_val = SetAtomRadAndChemValFromVertexCapFlow( pBNS, at, v1 ); 1176| 20| if (ret_val < 0) ------------------ | Branch (1176:25): [True: 0, False: 20] ------------------ 1177| 0| { 1178| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1179| 0| } 1180| 20| else 1181| 20| { 1182| 20| ret |= ( ret_val > 0 ); 1183| 20| } 1184| 20| } 1185| | /*pBNS->vert[v1].st_edge.flow0 = pBNS->vert[v1].st_edge.flow;*/ 1186| 217| } 1187| 217| } 1188| | 1189| 26.9k| pBNS->vert[v1].st_edge.pass = 0; 1190| | 1191| 26.9k| v0 = v2 = NO_VERTEX; ------------------ | | 118| 26.9k|#define NO_VERTEX -2 ------------------ 1192| 90.7k| for (i = 0; i < n; i++, delta = -delta, v0 = v1, v1 = v2) ------------------ | Branch (1192:21): [True: 63.8k, False: 26.9k] ------------------ 1193| 63.8k| { 1194| 63.8k| ineigh1 = ALTP_THIS_ATOM_NEIGHBOR( pBNS->alt_path, i ); /* v1->v2 neighbor */ ------------------ | | 104| 63.8k|#define ALTP_THIS_ATOM_NEIGHBOR(altp,X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[0] /* 0 <= X < path_len */ ------------------ 1195| 63.8k| ineigh2 = ALTP_NEXT_ATOM_NEIGHBOR( pBNS->alt_path, i ); /* v2->v1 neighbor */ ------------------ | | 105| 63.8k|#define ALTP_NEXT_ATOM_NEIGHBOR(altp,X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[1] ------------------ 1196| 63.8k| edge = pBNS->edge + pBNS->vert[v1].iedge[ineigh1]; 1197| | /* follow the BN Structure, not the inp_ATOM, to take care of swithching to 1198| | t-groups, c-groups or other fictitious edges/vertices 1199| | */ 1200| | 1201| 63.8k| v2 = edge->neighbor12 ^ v1; 1202| | 1203| | /* change at->chem_bonds_valence 2004-03-08 */ 1204| 63.8k| if (( bChangeFlow & BNS_EF_CHNG_BONDS ) && v1 < num_atoms) ------------------ | | 373| 63.8k|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ ------------------ | Branch (1204:17): [True: 1.27k, False: 62.5k] | Branch (1204:56): [True: 837, False: 434] ------------------ 1205| 837| { 1206| 837| if (v0 >= num_atoms && v2 < num_atoms) ------------------ | Branch (1206:21): [True: 237, False: 600] | Branch (1206:40): [True: 233, False: 4] ------------------ 1207| 233| { 1208| 233| at[v1].chem_bonds_valence += delta; /* change in v1-v2 bond order */ 1209| 233| } 1210| 604| else 1211| 604| { 1212| 604| if (v0 < num_atoms && v2 >= num_atoms && v0 != NO_VERTEX) ------------------ | | 118| 233|#define NO_VERTEX -2 ------------------ | Branch (1212:25): [True: 600, False: 4] | Branch (1212:43): [True: 233, False: 367] | Branch (1212:62): [True: 233, False: 0] ------------------ 1213| 233| { 1214| 233| at[v1].chem_bonds_valence -= delta; /* change in v0-v1 bond order */ 1215| 233| } 1216| 604| } 1217| 837| } 1218| | 1219| 63.8k| if (!edge->pass) ------------------ | Branch (1219:17): [True: 620, False: 63.2k] ------------------ 1220| 620| { 1221| 620| continue; 1222| 620| } 1223| | 1224| 63.2k| if (v1 < num_atoms && ineigh1 < at[v1].valence && ------------------ | Branch (1224:17): [True: 57.1k, False: 6.06k] | Branch (1224:35): [True: 39.6k, False: 17.4k] ------------------ 1225| 39.6k| v2 < num_atoms && ineigh2 < at[v2].valence) ------------------ | Branch (1225:18): [True: 39.6k, False: 0] | Branch (1225:36): [True: 39.6k, False: 0] ------------------ 1226| 39.6k| { 1227| 39.6k| if (( bChangeFlow0 & BNS_EF_ALTR_NS ) == BNS_EF_ALTR_NS && ------------------ | | 382| 39.6k|#define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 374| 39.6k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ | | ------------------ | | #define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 377| 39.6k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: | | ------------------ ------------------ if (( bChangeFlow0 & BNS_EF_ALTR_NS ) == BNS_EF_ALTR_NS && ------------------ | | 382| 79.3k|#define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 374| 39.6k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ | | ------------------ | | #define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 377| 39.6k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: | | ------------------ ------------------ | Branch (1227:21): [True: 11.2k, False: 28.4k] ------------------ 1228| 11.2k| ( bChangeFlow0 & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 11.2k|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 11.2k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 11.2k|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 11.2k|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ ( bChangeFlow0 & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 11.2k|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 11.2k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 11.2k|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 11.2k|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ | Branch (1228:21): [True: 533, False: 10.7k] ------------------ 1229| 533| { 1230| | /* 2004-07-02 special mode: save new ring bonds and mark as non-stereo non-ring bonds */ 1231| 533| if (at[v1].nRingSystem != at[v2].nRingSystem) ------------------ | Branch (1231:25): [True: 320, False: 213] ------------------ 1232| 320| { 1233| | /* Non-ring bond (bridge) */ 1234| 320| bChangeFlowAdd = BNS_EF_ALTR_NS; ------------------ | | 382| 320|#define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 374| 320|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ | | ------------------ | | #define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 377| 320|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: | | ------------------ ------------------ 1235| 320| } 1236| 213| else 1237| 213| { 1238| | /* Ring bond */ 1239| 213| bChangeFlowAdd = 0; 1240| 213| } 1241| 533| } 1242| | /* Change bonds on the first pass only: in this case all flow correspond to the BNS output */ 1243| 39.6k| ret_val = SetAtomBondType( edge, &at[v1].bond_type[ineigh1], &at[v2].bond_type[ineigh2], delta, bChangeFlow | bChangeFlowAdd ); 1244| 39.6k| if (ret_val < 0) ------------------ | Branch (1244:21): [True: 0, False: 39.6k] ------------------ 1245| 0| { 1246| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1247| 0| } 1248| 39.6k| else 1249| 39.6k| { 1250| 39.6k| ret |= ( ret_val > 0 ); 1251| 39.6k| } 1252| 39.6k| } 1253| 63.2k| edge->pass = 0; 1254| 63.2k| } 1255| | 1256| 26.9k| if (v2 != vLast) ------------------ | Branch (1256:13): [True: 0, False: 26.9k] ------------------ 1257| 0| { 1258| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1259| 0| } 1260| 26.9k| else 1261| 26.9k| { 1262| 26.9k| if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 26.9k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 26.9k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 26.9k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 26.9k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 26.9k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 26.9k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ | Branch (1262:17): [True: 26.7k, False: 217] ------------------ 1263| 26.7k| { 1264| | /* Restore v2-t edge flow to the BNS this pass input value */ 1265| | /* "+=" instead of "-=" explanation: delta must have same sign as at the last edge */ 1266| 26.7k| ; /*pBNS->vert[v2].st_edge.flow += delta; */ 1267| 26.7k| } 1268| 217| else 1269| 217| { 1270| 217| if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ | Branch (1270:21): [True: 217, False: 0] ------------------ 1271| 217| { 1272| 217| if (v2 < num_atoms) ------------------ | Branch (1272:25): [True: 20, False: 197] ------------------ 1273| 20| { 1274| 20| ret_val = SetAtomRadAndChemValFromVertexCapFlow( pBNS, at, v2 ); 1275| 20| if (ret_val < 0) ------------------ | Branch (1275:29): [True: 0, False: 20] ------------------ 1276| 0| { 1277| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1278| 0| } 1279| 20| else 1280| 20| { 1281| 20| ret |= ( ret_val > 0 ); 1282| 20| } 1283| 20| } 1284| | /*pBNS->vert[v2].st_edge.flow0 = pBNS->vert[v2].st_edge.flow;*/ 1285| 217| } 1286| 217| } 1287| 26.9k| } 1288| 26.9k| pBNS->vert[v2].st_edge.pass = 0; 1289| 26.9k| } 1290| | 1291| 26.1k| return err ? err : ret; ------------------ | Branch (1291:12): [True: 0, False: 26.1k] ------------------ 1292| 26.1k|} RestoreBnStructFlow: 1491| 27.7k|{ 1492| 27.7k| int pass, i, v1, v2, ineigh1, ineigh2, vLast, n, delta, ret, err = 0; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 1493| 27.7k| BNS_EDGE *edge; 1494| | 1495| 56.3k| for (pass = pBNS->num_altp - 1, ret = 0; 0 <= pass; pass--) ------------------ | Branch (1495:46): [True: 28.6k, False: 27.7k] ------------------ 1496| 28.6k| { 1497| 28.6k| pBNS->alt_path = pBNS->altp[pass]; 1498| 28.6k| v1 = ALTP_START_ATOM( pBNS->alt_path ); ------------------ | | 103| 28.6k|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 1499| 28.6k| n = ALTP_PATH_LEN( pBNS->alt_path ); ------------------ | | 101| 28.6k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 1500| 28.6k| delta = ALTP_DELTA( pBNS->alt_path ); ------------------ | | 112| 28.6k|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 1501| 28.6k| vLast = ALTP_END_ATOM( pBNS->alt_path ); ------------------ | | 102| 28.6k|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 1502| 28.6k| v2 = NO_VERTEX; ------------------ | | 118| 28.6k|#define NO_VERTEX -2 ------------------ 1503| | /* starting vertex */ 1504| 28.6k| if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 28.6k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 28.6k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 28.6k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 28.6k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 28.6k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 28.6k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ | Branch (1504:13): [True: 28.4k, False: 217] ------------------ 1505| 28.4k| { 1506| 28.4k| pBNS->vert[v1].st_edge.flow -= delta; /* restore s-v1 edge flow to the BNS input value */ 1507| 28.4k| } 1508| 217| else 1509| 217| { 1510| 217| if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ | Branch (1510:17): [True: 20, False: 197] ------------------ 1511| 20| { 1512| 20| pBNS->vert[v1].st_edge.flow0 = pBNS->vert[v1].st_edge.flow; 1513| 20| } 1514| 217| } 1515| | 1516| | /* Augmenting path edges */ 1517| 94.5k| for (i = 0; i < n; i++, delta = -delta, v1 = v2) ------------------ | Branch (1517:21): [True: 65.9k, False: 28.6k] ------------------ 1518| 65.9k| { 1519| 65.9k| ineigh1 = ALTP_THIS_ATOM_NEIGHBOR( pBNS->alt_path, i ); /* v1->v2 neighbor */ ------------------ | | 104| 65.9k|#define ALTP_THIS_ATOM_NEIGHBOR(altp,X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[0] /* 0 <= X < path_len */ ------------------ 1520| 65.9k| ineigh2 = ALTP_NEXT_ATOM_NEIGHBOR(pBNS->alt_path, i); /* v2->v1 neighbor */ /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 105| 65.9k|#define ALTP_NEXT_ATOM_NEIGHBOR(altp,X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[1] ------------------ 1521| 65.9k| edge = pBNS->edge + pBNS->vert[v1].iedge[ineigh1]; 1522| 65.9k| v2 = edge->neighbor12 ^ v1; 1523| 65.9k| RestoreEdgeFlow( edge, delta, bChangeFlow ); 1524| 65.9k| edge->pass = 0; 1525| 65.9k| } 1526| | 1527| | /* Ending vertex */ 1528| 28.6k| if (v2 != vLast) ------------------ | Branch (1528:13): [True: 0, False: 28.6k] ------------------ 1529| 0| { 1530| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1531| 0| } 1532| 28.6k| else 1533| 28.6k| { 1534| 28.6k| if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 28.6k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 28.6k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 28.6k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_CHNG_RSTR ) == BNS_EF_CHNG_RSTR) ------------------ | | 372| 28.6k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 28.6k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 28.6k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ | Branch (1534:17): [True: 28.4k, False: 217] ------------------ 1535| 28.4k| { 1536| | /* Restore v2-t edge flow to the original value */ 1537| | /* "+=" instead of "-=" explanation: delta must have same sign as at the last edge */ 1538| 28.4k| pBNS->vert[v2].st_edge.flow += delta; 1539| 28.4k| } 1540| 217| else 1541| 217| { 1542| 217| if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ if (( bChangeFlow & BNS_EF_SAVE_ALL ) == BNS_EF_SAVE_ALL) ------------------ | | 381| 217|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 217|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 217|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 217|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ | Branch (1542:21): [True: 20, False: 197] ------------------ 1543| 20| { 1544| 20| pBNS->vert[v2].st_edge.flow0 = pBNS->vert[v2].st_edge.flow; 1545| 20| } 1546| 217| } 1547| 28.6k| } 1548| 28.6k| } 1549| | 1550| 27.7k| return err ? err : ret; ------------------ | Branch (1550:12): [True: 0, False: 27.7k] ------------------ 1551| 27.7k|} bNeedToTestTheFlow: 1558| 89.6k|{ 1559| 89.6k| int nBondType = ( BOND_TYPE_MASK & bond_type ); ------------------ | | 189| 89.6k|#define BOND_TYPE_MASK 0x0f ------------------ 1560| 89.6k| int nBondAttrib = ( BOND_MARK_MASK & bond_type ); ------------------ | | 198| 89.6k|#define BOND_MARK_MASK 0x70 ------------------ 1561| | 1562| 89.6k| if (bTestForNonStereoBond) ------------------ | Branch (1562:9): [True: 38.5k, False: 51.0k] ------------------ 1563| 38.5k| { 1564| 38.5k| if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 180| 25.5k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 64.1k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 186| 25.5k|#define BOND_ALT12NS 9 ------------------ | Branch (1564:13): [True: 12.9k, False: 25.5k] | Branch (1564:28): [True: 0, False: 25.5k] | Branch (1564:56): [True: 0, False: 25.5k] ------------------ 1565| 12.9k| { 1566| 12.9k| switch (nTestFlow) ------------------ | Branch (1566:21): [True: 12.9k, False: 0] ------------------ 1567| 12.9k| { 1568| 3.23k| case 0: /* single: can be 1 (single)? */ ------------------ | Branch (1568:17): [True: 3.23k, False: 9.76k] ------------------ 1569| 3.23k| if (nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 197| 6.47k|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1569:25): [True: 1.85k, False: 1.38k] ------------------ 1570| 1.38k| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 194| 4.62k|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1570:26): [True: 372, False: 1.01k] ------------------ 1571| 1.01k| nBondAttrib == BOND_MARK_ALT13) ------------------ | | 195| 1.01k|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1571:26): [True: 1, False: 1.01k] ------------------ 1572| 2.22k| { 1573| 2.22k| return 0; /* yes, already checked */ 1574| 2.22k| } 1575| 1.01k| break; 1576| | 1577| 8.02k| case 1: /* double: can be 2 (double)? */ ------------------ | Branch (1577:17): [True: 8.02k, False: 4.97k] ------------------ 1578| 8.02k| if (nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 197| 16.0k|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1578:25): [True: 6.22k, False: 1.80k] ------------------ 1579| 1.80k| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 194| 9.82k|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1579:26): [True: 207, False: 1.59k] ------------------ 1580| 1.59k| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 196| 1.59k|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1580:26): [True: 601, False: 995] ------------------ 1581| 7.02k| { 1582| 7.02k| return 0; /* yes, already checked */ 1583| 7.02k| } 1584| 995| break; 1585| 1.73k| case 2: /* triple: can be 3 (triple)? */ ------------------ | Branch (1585:17): [True: 1.73k, False: 11.2k] ------------------ 1586| 1.73k| if (nBondAttrib == BOND_MARK_ALT13 || ------------------ | | 195| 3.47k|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1586:25): [True: 0, False: 1.73k] ------------------ 1587| 1.73k| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 194| 3.47k|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1587:26): [True: 274, False: 1.46k] ------------------ 1588| 1.46k| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 196| 1.46k|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1588:26): [True: 732, False: 731] ------------------ 1589| 1.00k| { 1590| 1.00k| return 0; /* yes, already checked */ 1591| 1.00k| } 1592| 731| break; 1593| 12.9k| } 1594| 12.9k| } 1595| 38.5k| } 1596| 51.0k| else 1597| 51.0k| { 1598| 51.0k| if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 180| 37.0k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 88.1k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 186| 37.0k|#define BOND_ALT12NS 9 ------------------ | Branch (1598:13): [True: 13.9k, False: 37.0k] | Branch (1598:28): [True: 0, False: 37.0k] | Branch (1598:56): [True: 0, False: 37.0k] ------------------ 1599| 13.9k| { 1600| 13.9k| switch (nTestFlow) ------------------ | Branch (1600:21): [True: 13.9k, False: 0] ------------------ 1601| 13.9k| { 1602| 5.34k| case 0: /* single: can be 1 (single)? */ ------------------ | Branch (1602:17): [True: 5.34k, False: 8.64k] ------------------ 1603| 5.34k| if (nBondAttrib == BOND_MARK_ALT12 || ------------------ | | 193| 10.6k|#define BOND_MARK_ALT12 0x10 ------------------ | Branch (1603:25): [True: 2.81k, False: 2.53k] ------------------ 1604| 2.53k| nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 197| 7.88k|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1604:26): [True: 2.07k, False: 461] ------------------ 1605| 461| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 194| 5.81k|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1605:26): [True: 326, False: 135] ------------------ 1606| 135| nBondAttrib == BOND_MARK_ALT13) ------------------ | | 195| 135|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1606:26): [True: 0, False: 135] ------------------ 1607| 5.21k| { 1608| 5.21k| return 0; 1609| 5.21k| } 1610| 135| break; 1611| | 1612| 7.56k| case 1: /* double: can be 2 (double)? */ ------------------ | Branch (1612:17): [True: 7.56k, False: 6.43k] ------------------ 1613| 7.56k| if (nBondAttrib == BOND_MARK_ALT12 || ------------------ | | 193| 15.1k|#define BOND_MARK_ALT12 0x10 ------------------ | Branch (1613:25): [True: 3.21k, False: 4.35k] ------------------ 1614| 4.35k| nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 197| 11.9k|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1614:26): [True: 3.54k, False: 811] ------------------ 1615| 811| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 194| 8.37k|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1615:26): [True: 526, False: 285] ------------------ 1616| 285| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 196| 285|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1616:26): [True: 126, False: 159] ------------------ 1617| 7.40k| { 1618| 7.40k| return 0; /* yes */ 1619| 7.40k| } 1620| 159| break; 1621| 1.08k| case 2: /* triple: can be 3 (triple)? */ ------------------ | Branch (1621:17): [True: 1.08k, False: 12.9k] ------------------ 1622| 1.08k| if (nBondAttrib == BOND_MARK_ALT13 || ------------------ | | 195| 2.16k|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1622:25): [True: 0, False: 1.08k] ------------------ 1623| 1.08k| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 194| 2.16k|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1623:26): [True: 426, False: 658] ------------------ 1624| 658| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 196| 658|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1624:26): [True: 226, False: 432] ------------------ 1625| 652| { 1626| 652| return 0; 1627| 652| } 1628| 432| break; 1629| 13.9k| } 1630| 13.9k| } 1631| 51.0k| } 1632| | 1633| 66.1k| return 1; 1634| 89.6k|} nBondsValenceInpAt: 1641| 1.41M|{ 1642| 1.41M| int j, bond_type, nBondsValence = 0, nAltBonds = 0, nNumWrong = 0; 1643| 2.14M| for (j = 0; j < at->valence; j++) ------------------ | Branch (1643:17): [True: 727k, False: 1.41M] ------------------ 1644| 727k| { 1645| 727k| bond_type = at->bond_type[j] & BOND_TYPE_MASK; ------------------ | | 189| 727k|#define BOND_TYPE_MASK 0x0f ------------------ 1646| 727k| switch (bond_type) 1647| 727k| { 1648| 0| case 0: /* for structure from InChI reconstruction */ ------------------ | Branch (1648:13): [True: 0, False: 727k] ------------------ 1649| 477k| case BOND_SINGLE: ------------------ | | 177| 477k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 477k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1649:13): [True: 477k, False: 250k] ------------------ 1650| 648k| case BOND_DOUBLE: ------------------ | | 178| 648k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 648k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1650:13): [True: 171k, False: 556k] ------------------ 1651| 727k| case BOND_TRIPLE: ------------------ | | 179| 727k|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 727k|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (1651:13): [True: 79.1k, False: 648k] ------------------ 1652| 727k| nBondsValence += bond_type; 1653| 727k| break; 1654| 0| case BOND_ALTERN: ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (1654:13): [True: 0, False: 727k] ------------------ 1655| 0| nAltBonds++; 1656| 0| break; 1657| 0| default: ------------------ | Branch (1657:13): [True: 0, False: 727k] ------------------ 1658| 0| nNumWrong++; 1659| 727k| } 1660| 727k| } 1661| 1.41M| switch (nAltBonds) 1662| 1.41M| { 1663| 1.41M| case 0: ------------------ | Branch (1663:9): [True: 1.41M, False: 0] ------------------ 1664| 1.41M| break; 1665| 0| case 1: ------------------ | Branch (1665:9): [True: 0, False: 1.41M] ------------------ 1666| 0| nBondsValence += 1; /* 1 or greater than 3 is wrong */ 1667| 0| nNumWrong++; 1668| 0| break; 1669| 0| default: ------------------ | Branch (1669:9): [True: 0, False: 1.41M] ------------------ 1670| 0| nBondsValence += nAltBonds + 1; 1671| 0| break; 1672| 1.41M| } 1673| 1.41M| if (nNumAltBonds) ------------------ | Branch (1673:9): [True: 1.09M, False: 318k] ------------------ 1674| 1.09M| { 1675| 1.09M| *nNumAltBonds = nAltBonds; 1676| 1.09M| } 1677| 1.41M| if (nNumWrongBonds) ------------------ | Branch (1677:9): [True: 1.09M, False: 318k] ------------------ 1678| 1.09M| { 1679| 1.09M| *nNumWrongBonds = nNumWrong; 1680| 1.09M| } 1681| | 1682| 1.41M| return nBondsValence; 1683| 1.41M|} BnsAdjustFlowBondsRad: 1694| 288k|{ 1695| 288k| int bError = 0, nOrigDelta = 0, ret, num_removed; 1696| | 1697| 288k|#if( CHECK_AROMBOND2ALT == 1 ) 1698| 288k| int *pcValMinusBondsVal = NULL; 1699| 288k| int i, nValMinusBondsVal, nAltBonds, bIgnore, valen, is_rad, excess; 1700| | 1701| | /* Find valence excess (it may only be due to aromatic bonds) */ 1702| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1702:17): [True: 1.09M, False: 288k] ------------------ 1703| 1.09M| { 1704| 1.09M| valen = nBondsValenceInpAt( at + i, &nAltBonds, &bIgnore ); 1705| 1.09M| nValMinusBondsVal = (int) at[i].chem_bonds_valence - valen; 1706| 1.09M| bIgnore += ( nAltBonds > 3 ); 1707| 1.09M| if (!bIgnore && nValMinusBondsVal > 0) ------------------ | Branch (1707:13): [True: 1.09M, False: 0] | Branch (1707:25): [True: 0, False: 1.09M] ------------------ 1708| 0| { 1709| 0| if (!pcValMinusBondsVal && ------------------ | Branch (1709:17): [True: 0, False: 0] ------------------ 1710| 0| !( pcValMinusBondsVal = (int *) inchi_calloc( num_atoms, sizeof( pcValMinusBondsVal[0] ) ) )) ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ | Branch (1710:18): [True: 0, False: 0] ------------------ 1711| 0| { 1712| 0| bError = BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1713| 0| goto exit_function; 1714| 0| } 1715| | /* Mark atoms that have extra unsatisfied valence due to aromatic bonds */ 1716| 0| is_rad = ( at[i].radical == RADICAL_DOUBLET ); ------------------ | | 76| 0|#define RADICAL_DOUBLET 2 ------------------ 1717| 0| excess = nValMinusBondsVal + is_rad; 1718| 0| pcValMinusBondsVal[i] = excess; 1719| 0| } 1720| 1.09M| } 1721| 288k|#endif /* CHECK_AROMBOND2ALT */ 1722| | 1723| | /* Match bonds to valences */ 1724| 288k| do 1725| 288k| { 1726| 288k| num_removed = 0; 1727| 288k| ret = RunBalancedNetworkSearch( pBNS, pBD, BNS_EF_CHNG_FLOW ); ------------------ | | 370| 288k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ 1728| 288k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 288k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 288k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 288k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 288k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 288k, False: 0] | | | Branch (67:44): [True: 0, False: 288k] | | ------------------ ------------------ 1729| 0| { 1730| 0| bError = ret; 1731| 0| } 1732| 288k| else 1733| 288k| { 1734| 288k| nOrigDelta += ret; 1735| 288k| num_removed = pBNS->num_altp; /* number of augmenting paths */ 1736| 288k| if (ret > 0) ------------------ | Branch (1736:17): [True: 19, False: 288k] ------------------ 1737| 19| { 1738| | /* save new bonds in at[] and flows in pBNS and at[] */ 1739| 19| ret = SetBondsFromBnStructFlow( pBNS, at, num_atoms, BNS_EF_SAVE_ALL ); /* must include 1: 5=(4|1) */ ------------------ | | 381| 19|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 19|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 19|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 19|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ 1740| 19| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 19|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 19|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 19|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 19|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 19, False: 0] | | | Branch (67:44): [True: 0, False: 19] | | ------------------ ------------------ 1741| 0| { 1742| 0| bError = ret; 1743| 0| } 1744| 19| ret = RestoreBnStructFlow( pBNS, BNS_EF_SAVE_ALL ); /* must include 1: 5=(4|1) */ ------------------ | | 381| 19|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 19|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 19|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 19|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ 1745| 19| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 19|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 19|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 19|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 19|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 19, False: 0] | | | Branch (67:44): [True: 0, False: 19] | | ------------------ ------------------ 1746| 0| { 1747| 0| bError = ret; 1748| 0| } 1749| 19| } 1750| 288k| ReInitBnStructAltPaths( pBNS ); 1751| 288k| } 1752| 288k| } while (num_removed && num_removed == pBNS->max_altp && !bError); ------------------ | Branch (1752:14): [True: 19, False: 288k] | Branch (1752:29): [True: 0, False: 19] | Branch (1752:62): [True: 0, False: 0] ------------------ 1753| | 1754| 288k|#if( CHECK_AROMBOND2ALT == 1 ) 1755| | /* Check whether aromatic bonds have been replaced with alternating bonds */ 1756| 288k| if (!bError && pcValMinusBondsVal) ------------------ | Branch (1756:9): [True: 288k, False: 0] | Branch (1756:20): [True: 0, False: 288k] ------------------ 1757| 0| { 1758| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1758:21): [True: 0, False: 0] ------------------ 1759| 0| { 1760| 0| if (!pcValMinusBondsVal[i]) ------------------ | Branch (1760:17): [True: 0, False: 0] ------------------ 1761| 0| { 1762| 0| continue; 1763| 0| } 1764| 0| valen = nBondsValenceInpAt( at + i, &nAltBonds, &bIgnore ); 1765| 0| nValMinusBondsVal = (int) at[i].chem_bonds_valence - valen; 1766| 0| is_rad = ( at[i].radical == RADICAL_DOUBLET ); ------------------ | | 76| 0|#define RADICAL_DOUBLET 2 ------------------ 1767| 0| excess = nValMinusBondsVal + is_rad; 1768| 0| if (bIgnore || ------------------ | Branch (1768:17): [True: 0, False: 0] ------------------ 1769| 0| ( pcValMinusBondsVal[i] - excess ) != 1) ------------------ | Branch (1769:17): [True: 0, False: 0] ------------------ 1770| 0| { 1771| | /* radical excess has not been reduced */ 1772| 0| bError = BNS_ALTBOND_ERR; ------------------ | | 61| 0|#define BNS_ALTBOND_ERR (BNS_ERR + 13) /*(-9986)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1773| 0| break; 1774| 0| } 1775| 0| } 1776| 0| } 1777| | 1778| 288k|exit_function: 1779| 288k| if (pcValMinusBondsVal) ------------------ | Branch (1779:9): [True: 0, False: 288k] ------------------ 1780| 0| { 1781| 0| inchi_free( pcValMinusBondsVal ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1782| 0| } 1783| 288k|#endif /* CHECK_AROMBOND2ALT */ 1784| | 1785| 288k| return bError ? bError : nOrigDelta; ------------------ | Branch (1785:12): [True: 0, False: 288k] ------------------ 1786| 288k|} BnsTestAndMarkAltBonds: 1797| 293k|{ 1798| 293k| int ret, iat, ineigh, neigh; 1799| 293k| int nMinFlow, nMaxFlow, nTestFlow, nCurFlow; 1800| 293k| int iedge, bError, nDots, nChanges, bTestForNonStereoBond; /* djb-rwth: removing redundant variables */ 1801| | 1802| | /* Normalize bonds and find tautomeric groups */ 1803| 293k| bError = 0; 1804| 293k| nChanges = 0; 1805| 293k| bTestForNonStereoBond = pBNS->tot_st_cap > pBNS->tot_st_flow; 1806| | 1807| 1.42M| for (iat = 0; iat < num_atoms && !bError; iat++) ------------------ | Branch (1807:19): [True: 1.12M, False: 293k] | Branch (1807:38): [True: 1.12M, False: 0] ------------------ 1808| 1.12M| { 1809| 1.66M| for (ineigh = 0; ineigh < at[iat].valence && !bError; ineigh++) ------------------ | Branch (1809:26): [True: 539k, False: 1.12M] | Branch (1809:54): [True: 539k, False: 0] ------------------ 1810| 539k| { 1811| 539k| neigh = at[iat].neighbor[ineigh]; 1812| 539k| if (neigh < iat) ------------------ | Branch (1812:17): [True: 269k, False: 269k] ------------------ 1813| 269k| { 1814| 269k| continue; /* we have already tested the bond */ 1815| 269k| } 1816| 269k| iedge = pBNS->vert[iat].iedge[ineigh]; 1817| 269k| if (IS_FORBIDDEN( pBNS->edge[iedge].forbidden, pBNS )) ------------------ | | 41| 269k|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (41:48): [True: 8.36k, False: 261k] | | ------------------ ------------------ 1818| 8.36k| { 1819| 8.36k| continue; 1820| 8.36k| } 1821| 261k| if (nBondTypeToTest && ( at[iat].bond_type[ineigh] & BOND_TYPE_MASK ) != nBondTypeToTest) ------------------ | | 189| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (1821:17): [True: 0, False: 261k] | Branch (1821:36): [True: 0, False: 0] ------------------ 1822| 0| { 1823| 0| continue; 1824| 0| } 1825| 261k| nMinFlow = nMinFlow2Check( pBNS, iedge ); 1826| 261k| nMaxFlow = nMaxFlow2Check( pBNS, iedge ); 1827| 261k| nCurFlow = nCurFlow2Check( pBNS, iedge ); 1828| 261k| if (nMinFlow == nMaxFlow) ------------------ | Branch (1828:17): [True: 192k, False: 69.0k] ------------------ 1829| 192k| { 1830| 192k| if (nMaxFlow && bTestForNonStereoBond) ------------------ | Branch (1830:21): [True: 67.7k, False: 124k] | Branch (1830:33): [True: 12.2k, False: 55.4k] ------------------ 1831| 12.2k| { 1832| 12.2k| nTestFlow = nMaxFlow - (int) ( pBNS->tot_st_cap - pBNS->tot_st_flow ); /* temporary use of nTestFlow */ 1833| 12.2k| nMinFlow = inchi_max( 0, nTestFlow ); ------------------ | | 138| 12.2k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 2.31k, False: 9.91k] | | ------------------ ------------------ 1834| 12.2k| } 1835| 180k| else 1836| 180k| { 1837| 180k| continue; 1838| 180k| } 1839| 192k| } 1840| 252k| for (nTestFlow = nMinFlow; nTestFlow <= nMaxFlow && !bError; nTestFlow++) ------------------ | Branch (1840:40): [True: 170k, False: 81.3k] | Branch (1840:65): [True: 170k, False: 0] ------------------ 1841| 170k| { 1842| 170k| if (nTestFlow == nCurFlow) ------------------ | Branch (1842:21): [True: 81.3k, False: 89.6k] ------------------ 1843| 81.3k| { 1844| 81.3k| continue; 1845| 81.3k| } 1846| 89.6k| if (!bNeedToTestTheFlow( at[iat].bond_type[ineigh], nTestFlow, bTestForNonStereoBond )) ------------------ | Branch (1846:21): [True: 23.5k, False: 66.1k] ------------------ 1847| 23.5k| { 1848| 23.5k| continue; 1849| 23.5k| } 1850| | /* djb-rwth: removing redundant code */ 1851| 66.1k| nDots = bSetFlowToCheckOneBond( pBNS, iedge, nTestFlow, fcd ); 1852| | 1853| 66.1k| if (IS_BNS_ERROR( nDots )) ------------------ | | 67| 66.1k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 66.1k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 66.1k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 66.1k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 66.1k, False: 0] | | | Branch (67:44): [True: 5.08k, False: 61.0k] | | ------------------ ------------------ 1854| 5.08k| { 1855| 5.08k| if (nDots == BNS_CANT_SET_BOND) ------------------ | | 57| 5.08k|#define BNS_CANT_SET_BOND (BNS_ERR + 9) /*(-9990)*/ | | ------------------ | | | | 47| 5.08k|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (1855:25): [True: 5.08k, False: 0] ------------------ 1856| 5.08k| { 1857| 5.08k| ret = bRestoreFlowAfterCheckOneBond( pBNS, fcd ); 1858| 5.08k| if (!IS_BNS_ERROR( ret )) ------------------ | | 67| 5.08k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 5.08k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 5.08k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 5.08k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 5.08k, False: 0] | | | Branch (67:44): [True: 0, False: 5.08k] | | ------------------ ------------------ 1859| 5.08k| { 1860| 5.08k| continue; 1861| 5.08k| } 1862| 5.08k| } 1863| 0| bError = nDots; 1864| 0| } 1865| 61.0k| else 1866| 61.0k| { 1867| 61.0k| if (nDots > 0) ------------------ | Branch (1867:25): [True: 59.4k, False: 1.56k] ------------------ 1868| 59.4k| { 1869| 59.4k| ret = RunBalancedNetworkSearch( pBNS, pBD, bChangeFlow ); 1870| 59.4k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 59.4k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 59.4k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 59.4k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 59.4k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 59.4k, False: 0] | | | Branch (67:44): [True: 0, False: 59.4k] | | ------------------ ------------------ 1871| 0| { 1872| 0| bError = ret; 1873| 0| } 1874| 59.4k| else 1875| 59.4k| { 1876| 59.4k| if (ret > 0) ------------------ | Branch (1876:33): [True: 17.5k, False: 41.8k] ------------------ 1877| 17.5k| { 1878| 17.5k| if (2 * ret == nDots) ------------------ | Branch (1878:37): [True: 16.9k, False: 656] ------------------ 1879| 16.9k| { 1880| 16.9k| ret = bSetBondsAfterCheckOneBond( pBNS, fcd, nTestFlow, at, num_atoms, bChangeFlow ); 1881| 16.9k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 16.9k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 16.9k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 16.9k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 16.9k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 16.9k, False: 0] | | | Branch (67:44): [True: 0, False: 16.9k] | | ------------------ ------------------ 1882| 0| { 1883| 0| bError = ret; 1884| 0| } 1885| 16.9k| else 1886| 16.9k| { 1887| 16.9k| nChanges += ( ret & 1 ); 1888| 16.9k| ret = SetBondsFromBnStructFlow( pBNS, at, num_atoms, bChangeFlow ); 1889| 16.9k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 16.9k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 16.9k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 16.9k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 16.9k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 16.9k, False: 0] | | | Branch (67:44): [True: 0, False: 16.9k] | | ------------------ ------------------ 1890| 0| { 1891| 0| bError = ret; 1892| 0| } 1893| 16.9k| else 1894| 16.9k| { 1895| 16.9k| if (ret >= 0) ------------------ | Branch (1895:49): [True: 16.9k, False: 0] ------------------ 1896| 16.9k| { 1897| 16.9k| nChanges += ( ret & 1 ); 1898| | /* djb-rwth: removing redundant code */ 1899| 16.9k| } 1900| 0| else 1901| 0| { 1902| 0| bError = ret; 1903| 0| } 1904| 16.9k| } 1905| 16.9k| } 1906| 16.9k| } 1907| | /* typically 2*ret < nDots; 2*ret > nDots should not happen. Check later */ 1908| 17.5k| ret = RestoreBnStructFlow( pBNS, bChangeFlow & BNS_EF_CHNG_RSTR ); ------------------ | | 372| 17.5k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 17.5k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 17.5k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 1909| 17.5k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 17.5k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 17.5k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 17.5k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 17.5k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 17.5k, False: 0] | | | Branch (67:44): [True: 0, False: 17.5k] | | ------------------ ------------------ 1910| 0| { 1911| 0| bError = ret; 1912| 0| } 1913| 17.5k| } 1914| 59.4k| } 1915| | /* --- Reinitialize to repeat the calculations --- */ 1916| 59.4k| ReInitBnStructAltPaths( pBNS ); 1917| 59.4k| } 1918| | 1919| 1.56k| else 1920| 1.56k| { 1921| 1.56k| if (nDots == 0) ------------------ | Branch (1921:29): [True: 1.56k, False: 0] ------------------ 1922| 1.56k| { 1923| 1.56k| ret = bSetBondsAfterCheckOneBond( pBNS, fcd, nTestFlow, at, num_atoms, bChangeFlow ); 1924| 1.56k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 1.56k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.56k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.56k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.56k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.56k, False: 0] | | | Branch (67:44): [True: 0, False: 1.56k] | | ------------------ ------------------ 1925| 0| { 1926| 0| bError = ret; 1927| 0| } 1928| 1.56k| else 1929| 1.56k| { 1930| 1.56k| nChanges += ( ret & 1 ); 1931| 1.56k| } 1932| 1.56k| } 1933| 1.56k| } 1934| 61.0k| } 1935| | 1936| 61.0k| ret = bRestoreFlowAfterCheckOneBond( pBNS, fcd ); 1937| | 1938| 61.0k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 61.0k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 61.0k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 61.0k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 61.0k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 61.0k, False: 0] | | | Branch (67:44): [True: 0, False: 61.0k] | | ------------------ ------------------ 1939| 0| { 1940| 0| bError = ret; 1941| 0| } 1942| | 1943| 61.0k| } /* for (nTestFlow = */ 1944| 81.3k| } /* for (ineigh = */ 1945| 1.12M| } /* for (iat = */ 1946| | 1947| 293k| return bError ? bError : nChanges; ------------------ | Branch (1947:12): [True: 0, False: 293k] ------------------ 1948| 293k|} SetForbiddenEdges: 1973| 376k|{ 1974| | 1975| | 1976| 376k| int i, j, neigh, num_found; 1977| 376k| BNS_IEDGE iedge; 1978| | /*S_CHAR edge_forbidden_mask = BNS_EDGE_FORBIDDEN_MASK;*/ 1979| 376k| S_CHAR edge_forbidden_mask = forbidden_mask; 1980| | 1981| 376k| pBNS->edge_forbidden_mask |= forbidden_mask; 1982| | 1983| 376k| num_found = 0; 1984| | 1985| 2.30M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1985:17): [True: 1.93M, False: 376k] ------------------ 1986| 1.93M| { 1987| | /* acetyl */ 1988| 1.93M| if (at[i].el_number == EL_NUMBER_C && 3 == at[i].valence && ------------------ | | 13| 3.86M|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1988:13): [True: 195k, False: 1.73M] | Branch (1988:47): [True: 10.7k, False: 184k] ------------------ 1989| 10.7k| 4 == at[i].chem_bonds_valence) ------------------ | Branch (1989:14): [True: 9.47k, False: 1.29k] ------------------ 1990| 9.47k| { 1991| 9.47k| int num_O = 0; 1992| 9.47k| int bond_to_O_val = 0; 1993| 9.47k| int forbidden_bond_pos = -1; 1994| 9.47k| int forbidden_bond_val = -1; 1995| 37.9k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (1995:25): [True: 28.4k, False: 9.47k] ------------------ 1996| 28.4k| { 1997| 28.4k| neigh = at[i].neighbor[j]; 1998| 28.4k| if (at[neigh].el_number == EL_NUMBER_O && ------------------ | | 15| 56.8k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1998:21): [True: 3.88k, False: 24.5k] ------------------ 1999| 3.88k| at[neigh].valence == 1) ------------------ | Branch (1999:22): [True: 2.43k, False: 1.45k] ------------------ 2000| 2.43k| { 2001| 2.43k| num_O++; 2002| 2.43k| bond_to_O_val += ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 2.43k|#define BOND_TYPE_MASK 0x0f ------------------ 2003| 2.43k| } 2004| 25.9k| else 2005| 25.9k| { 2006| 25.9k| forbidden_bond_pos = j; 2007| 25.9k| forbidden_bond_val = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 25.9k|#define BOND_TYPE_MASK 0x0f ------------------ 2008| 25.9k| } 2009| 28.4k| } 2010| 9.47k| if (2 == num_O && 3 == bond_to_O_val && 1 == forbidden_bond_val) ------------------ | Branch (2010:17): [True: 804, False: 8.67k] | Branch (2010:31): [True: 782, False: 22] | Branch (2010:53): [True: 782, False: 0] ------------------ 2011| 782| { 2012| 782| iedge = pBNS->vert[i].iedge[forbidden_bond_pos]; 2013| 782| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2014| 782| num_found++; 2015| 782| } 2016| 9.47k| } 2017| 1.92M| else 2018| 1.92M| { 2019| | /* nitro */ 2020| 1.92M| if (at[i].el_number == EL_NUMBER_N && 3 == at[i].valence && ------------------ | | 14| 3.84M|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2020:17): [True: 196k, False: 1.72M] | Branch (2020:51): [True: 14.5k, False: 181k] ------------------ 2021| 14.5k| ( 4 == at[i].chem_bonds_valence || 5 == at[i].chem_bonds_valence )) ------------------ | Branch (2021:19): [True: 2.23k, False: 12.3k] | Branch (2021:52): [True: 7.79k, False: 4.54k] ------------------ 2022| 10.0k| { 2023| 10.0k| int num_O = 0; 2024| 10.0k| int bond_to_O_val = 0; 2025| 10.0k| int forbidden_bond_pos = -1; 2026| 10.0k| int forbidden_bond_val = -1; 2027| 40.1k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (2027:29): [True: 30.0k, False: 10.0k] ------------------ 2028| 30.0k| { 2029| 30.0k| neigh = at[i].neighbor[j]; 2030| 30.0k| if (at[neigh].el_number == EL_NUMBER_O && ------------------ | | 15| 60.1k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2030:25): [True: 1.30k, False: 28.7k] ------------------ 2031| 1.30k| at[neigh].valence == 1) ------------------ | Branch (2031:26): [True: 774, False: 531] ------------------ 2032| 774| { 2033| 774| num_O++; 2034| 774| bond_to_O_val += ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 774|#define BOND_TYPE_MASK 0x0f ------------------ 2035| 774| } 2036| 29.3k| else 2037| 29.3k| { 2038| 29.3k| forbidden_bond_pos = j; 2039| 29.3k| forbidden_bond_val = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 29.3k|#define BOND_TYPE_MASK 0x0f ------------------ 2040| 29.3k| } 2041| 30.0k| } 2042| 10.0k| if (2 == num_O && ( 3 == bond_to_O_val || 4 == bond_to_O_val ) && 1 == forbidden_bond_val) ------------------ | Branch (2042:21): [True: 31, False: 10.0k] | Branch (2042:37): [True: 11, False: 20] | Branch (2042:59): [True: 20, False: 0] | Branch (2042:83): [True: 23, False: 8] ------------------ 2043| 23| { 2044| 23| iedge = pBNS->vert[i].iedge[forbidden_bond_pos]; 2045| 23| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2046| 23| num_found++; 2047| 23| } 2048| 10.0k| } 2049| 1.92M| } 2050| 1.93M| } 2051| | 2052| |#ifdef FIX_SRU_CYCLIZING_PS_BONDS_IN_BNS 2053| | if (nebend > 1) 2054| | num_found += fix_explicitly_indicated_bonds( nebend, ebend, pBNS, at, num_atoms ); 2055| |#endif 2056| | 2057| 376k|#if ( REMOVE_ION_PAIRS_FIX_BONDS == 1 ) 2058| 376k| num_found += fix_special_bonds( pBNS, at, num_atoms, edge_forbidden_mask ); 2059| 376k|#endif 2060| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 2061| | num_found += TempFix_NH_NH_Bonds( pBNS, at, num_atoms ); 2062| |#endif 2063| | 2064| 376k| return num_found; 2065| 376k|} fix_special_bonds: 2150| 376k|{ 2151| 376k| int num_changes = 0; 2152| | 2153| 376k|#define MAX_NEIGH 6 2154| | 2155| 376k| int i, k, n1, n2, n3, i1, i2, i3, i4, bond_type; /* djb-rwth: removing redundant variables */ 2156| 376k| inp_ATOM *a; 2157| 376k| int j[3], m[3], num_O, k_O, num_N, num_OH, num_OM, num_X, num_other, k_N; 2158| | 2159| 376k| BNS_IEDGE iedge; 2160| | /*S_CHAR edge_forbidden_mask = BNS_EDGE_FORBIDDEN_MASK;*/ 2161| 376k| S_CHAR edge_forbidden_mask = forbidden_mask; 2162| | 2163| 376k| pBNS->edge_forbidden_mask |= edge_forbidden_mask; 2164| | 2165| 2.30M| for (i = 0, a = at; i < num_atoms; i++, a++) ------------------ | Branch (2165:25): [True: 1.93M, False: 376k] ------------------ 2166| 1.93M| { 2167| | 2168| 1.93M| if (!a->charge && !a->radical && ------------------ | Branch (2168:13): [True: 1.71M, False: 219k] | Branch (2168:27): [True: 1.68M, False: 24.0k] ------------------ 2169| 1.68M| 2 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 1.68M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.68M|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2169:14): [True: 60.9k, False: 1.62M] ------------------ 2170| 60.9k| 0 == num_of_H( at, i ) && ------------------ | Branch (2170:14): [True: 50.2k, False: 10.6k] ------------------ 2171| 50.2k| 2 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 50.2k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 50.2k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2171:14): [True: 36.6k, False: 13.6k] ------------------ 2172| 36.6k| ion_el_group( at[i].el_number ) == EL_NUMBER_N ) ------------------ | | 14| 36.6k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2172:14): [True: 18.3k, False: 18.2k] ------------------ 2173| 18.3k| { 2174| | /* Found N(V), no H */ 2175| 18.3k| if (2 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2175:17): [True: 1.80k, False: 16.5k] ------------------ 2176| 1.80k| { 2177| | /* #N= */ 2178| | /* fix bonds: double and triple: =N# so that bonds cannot be changed by the normalization */ 2179| 1.80k|#if ( FIX_N_V_METAL_BONDS_GPF == 1 ) 2180| 1.80k| if (0 > ( i1 = nNoMetalNeighIndex( at, i ) ) || ------------------ | Branch (2180:21): [True: 0, False: 1.80k] ------------------ 2181| 1.80k| 0 > ( i2 = nNoMetalOtherNeighIndex( at, i, n1 = a->neighbor[i1]/* non-metal neighbor #1 */ ) )) ------------------ | Branch (2181:22): [True: 3, False: 1.79k] ------------------ 2182| 3| { 2183| | /*num_err ++; */ /* do not count would-be original InChI v.1 buffer overflow GPF */ 2184| 3| continue; /* v1 bug: 2 bonds to metal yield i1 < 0 and/or i2 < 0 => bounds violation */ 2185| 3| } 2186| |#else 2187| | i1 = nNoMetalNeighIndex( at, i ); 2188| | n1 = a->neighbor[i1]; /* non-metal neighbor #1 */ 2189| | i2 = nNoMetalOtherNeighIndex( at, i, n1 ); 2190| |#endif 2191| 1.79k| n2 = a->neighbor[i2]; /* non-metal neighbor #2 */ 2192| | /* forbid all edges to non-metals */ 2193| 1.79k| iedge = pBNS->vert[i].iedge[i1]; 2194| 1.79k| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; /* fix bond to neighbor #1 */ 2195| 1.79k| iedge = pBNS->vert[i].iedge[i2]; 2196| 1.79k| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; /* fix bond to neighbor #1 */ 2197| 1.79k| num_changes++; /* added 11-15-2005 */ 2198| | /* i n3 */ 2199| | /* forbid single bond edge beyond the neighboring =N- as in #N=N- */ 2200| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2201| 1.79k| if (( at[i].bond_type[i1] & BOND_TYPE_MASK ) == BOND_TYPE_DOUBLE) ------------------ | | 189| 1.79k|#define BOND_TYPE_MASK 0x0f ------------------ if (( at[i].bond_type[i1] & BOND_TYPE_MASK ) == BOND_TYPE_DOUBLE) ------------------ | | 33| 1.79k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2201:21): [True: 1.03k, False: 768] ------------------ 2202| 1.03k| { 2203| 1.03k| i3 = i1; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2204| 1.03k| n3 = n1; 2205| 1.03k| } 2206| 768| else 2207| 768| { 2208| 768| i3 = i2; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2209| 768| n3 = n2; 2210| 768| } 2211| 1.79k| if (0 == NUMH( at, n3 ) && 2 == nNoMetalNumBonds( at, n3 ) && ------------------ | | 56| 3.59k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.79k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2211:21): [True: 1.79k, False: 8] | Branch (2211:44): [True: 1.51k, False: 277] ------------------ 2212| 1.51k| 3 == nNoMetalBondsValence( at, n3 ) && ------------------ | Branch (2212:22): [True: 918, False: 595] ------------------ 2213| 918| ion_el_group( at[n3].el_number ) == EL_NUMBER_N && ------------------ | | 14| 2.71k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2213:22): [True: 817, False: 101] ------------------ 2214| 817| 0 <= ( k = nNoMetalOtherNeighIndex( at, n3, i ) )) ------------------ | Branch (2214:22): [True: 709, False: 108] ------------------ 2215| 709| { 2216| | /* found =N- ; forbid the edge*/ 2217| 709| iedge = pBNS->vert[n3].iedge[k]; 2218| 709| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2219| 709| num_changes++; 2220| 709| } 2221| 1.79k| } 2222| 16.5k| else if (3 == nNoMetalNumBonds( at, i ) && ------------------ | Branch (2222:22): [True: 9.60k, False: 6.94k] ------------------ 2223| | /* | */ 2224| | /* found =N= */ 2225| | /* locate all non-metal neighbors */ 2226| 9.60k| 0 <= ( j[0] = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (2226:23): [True: 9.59k, False: 3] ------------------ 2227| 9.59k| 0 <= ( j[1] = nNoMetalOtherNeighIndex( at, i, m[0] = a->neighbor[j[0]] ) ) && ------------------ | Branch (2227:23): [True: 9.58k, False: 16] ------------------ 2228| 9.58k| 0 <= ( j[2] = nNoMetalOtherNeighIndex2( at, i, m[0], m[1] = a->neighbor[j[1]] ) )) ------------------ | Branch (2228:23): [True: 8.64k, False: 940] ------------------ 2229| 8.64k| { 2230| | /* Count specific neighbors: N(V)=N, N(V)-N N(V)=O, and N(V)-N */ 2231| | 2232| | /* if there is a single neighbor connected by a double bond, namely 2233| | N(V)=N and/or N(V)=O, then fix the bond(s). 2234| | If N(V)=O was fixed then do not fix another bond */ 2235| 8.64k| m[2] = a->neighbor[j[2]]; 2236| 8.64k| num_O = num_N = 0; 2237| 34.5k| for (k = 0; k < 3; k++) ------------------ | Branch (2237:29): [True: 25.9k, False: 8.64k] ------------------ 2238| 25.9k| { 2239| 25.9k| n1 = m[k]; 2240| 25.9k| i1 = j[k]; /* djb-rwth: ignoring LLVM warning: variable used */ 2241| 25.9k| if (ion_el_group( at[n1].el_number ) == EL_NUMBER_N) ------------------ | | 14| 25.9k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2241:25): [True: 14.8k, False: 11.1k] ------------------ 2242| 14.8k| { 2243| 14.8k| k_N = k; 2244| 14.8k| num_N++; 2245| 14.8k| } 2246| 11.1k| else if (ion_el_group( at[n1].el_number ) == EL_NUMBER_O && ------------------ | | 15| 22.2k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2246:30): [True: 3.29k, False: 7.81k] ------------------ 2247| 3.29k| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2247:30): [True: 2.59k, False: 701] ------------------ 2248| 2.59k| { 2249| 2.59k| k_O = k; 2250| 2.59k| num_O++; 2251| 2.59k| } 2252| 25.9k| } 2253| 8.64k| num_other = 0; 2254| 8.64k| if (1 == num_O && ------------------ | Branch (2254:21): [True: 1.07k, False: 7.56k] ------------------ 2255| 1.07k| 0 == at[n1 = m[k_O]].charge && ------------------ | Branch (2255:22): [True: 961, False: 111] ------------------ 2256| 961| 0 == at[n1].radical && ------------------ | Branch (2256:22): [True: 851, False: 110] ------------------ 2257| 851| BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_O]] & BOND_TYPE_MASK ) ------------------ | | 33| 851|#define BOND_TYPE_DOUBLE 2 ------------------ BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_O]] & BOND_TYPE_MASK ) ------------------ | | 189| 851|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2257:22): [True: 835, False: 16] ------------------ 2258| 8.64k| ) 2259| 835| { 2260| | /* Fix bond to neighbor =O */ 2261| 835| iedge = pBNS->vert[i].iedge[i1]; 2262| 835| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2263| 835| num_changes++; 2264| 835| num_other++; /* indicator: double to a terminal O has been fixed */ 2265| 835| } 2266| 8.64k| if (!num_other && ------------------ | Branch (2266:21): [True: 7.80k, False: 835] ------------------ 2267| 7.80k| num_O <= 1 && ------------------ | Branch (2267:22): [True: 7.04k, False: 763] ------------------ 2268| 7.04k| 1 == num_N && ------------------ | Branch (2268:22): [True: 1.92k, False: 5.12k] ------------------ 2269| 1.92k| 0 == at[n1 = m[k_N]].charge && ------------------ | Branch (2269:22): [True: 1.08k, False: 838] ------------------ 2270| 1.08k| 0 == at[n1].radical && ------------------ | Branch (2270:22): [True: 808, False: 275] ------------------ 2271| 808| BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_N]] & BOND_TYPE_MASK )) ------------------ | | 33| 808|#define BOND_TYPE_DOUBLE 2 ------------------ BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_N]] & BOND_TYPE_MASK )) ------------------ | | 189| 808|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2271:22): [True: 422, False: 386] ------------------ 2272| 422| { 2273| | /* Fix bond to neighbor =N */ 2274| 422| iedge = pBNS->vert[i].iedge[i1]; 2275| 422| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2276| 422| num_changes++; 2277| 422| } 2278| 8.64k| } 2279| 7.90k| else if (4 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2279:22): [True: 6.87k, False: 1.02k] ------------------ 2280| 6.87k| { 2281| | /* | */ 2282| | /* found -N=N- */ 2283| | /* | */ 2284| | /* locate non-metal neighbor connected by a double bond; 2285| | * if it is =N- then fix the double bond and the single bond beyond the neighbor 2286| | */ 2287| 6.87k| num_N = 0; 2288| 6.87k| num_other = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 2289| 34.3k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (2289:30): [True: 27.5k, False: 6.87k] ------------------ 2290| 27.5k| { 2291| 27.5k| if (BOND_TYPE_DOUBLE == ( at[i].bond_type[i1] & BOND_TYPE_MASK ) && ------------------ | | 33| 27.5k|#define BOND_TYPE_DOUBLE 2 ------------------ if (BOND_TYPE_DOUBLE == ( at[i].bond_type[i1] & BOND_TYPE_MASK ) && ------------------ | | 189| 27.5k|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2291:25): [True: 6.74k, False: 20.7k] ------------------ 2292| 6.74k| !is_el_a_metal( at[n1 = (int) at[i].neighbor[i1]].el_number ) && ------------------ | Branch (2292:26): [True: 6.50k, False: 236] ------------------ 2293| 6.50k| ion_el_group( at[n1].el_number ) == EL_NUMBER_N) ------------------ | | 14| 6.50k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2293:26): [True: 2.94k, False: 3.56k] ------------------ 2294| 2.94k| { 2295| 2.94k| num_N++; 2296| 2.94k| n2 = n1; 2297| 2.94k| i2 = i1; 2298| 2.94k| } 2299| 27.5k| } 2300| 6.87k| if (1 == num_N && 0 == NUMH( at, n2 ) && ------------------ | | 56| 9.68k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 2.80k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2300:21): [True: 2.80k, False: 4.06k] | Branch (2300:35): [True: 2.63k, False: 170] ------------------ 2301| 2.63k| 2 == nNoMetalNumBonds( at, n2 ) && ------------------ | Branch (2301:22): [True: 642, False: 1.99k] ------------------ 2302| 642| 3 == nNoMetalBondsValence( at, n2 ) && ------------------ | Branch (2302:22): [True: 628, False: 14] ------------------ 2303| 628| 0 <= ( i3 = nNoMetalOtherNeighIndex( at, n2, i ) ) && ------------------ | Branch (2303:22): [True: 561, False: 67] ------------------ 2304| 561| BOND_TYPE_SINGLE == ( at[n2].bond_type[i3] & BOND_TYPE_MASK )) ------------------ | | 32| 561|#define BOND_TYPE_SINGLE 1 ------------------ BOND_TYPE_SINGLE == ( at[n2].bond_type[i3] & BOND_TYPE_MASK )) ------------------ | | 189| 561|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2304:22): [True: 561, False: 0] ------------------ 2305| 561| { 2306| | /* fix the single bond beyond the N(V) neighbor N(V)=N- */ 2307| 561| iedge = pBNS->vert[n2].iedge[i3]; 2308| 561| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2309| 561| num_changes++; 2310| | /* fix the double bond */ 2311| 561| iedge = pBNS->vert[i].iedge[i2]; 2312| 561| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2313| 561| num_changes++; 2314| 561| } 2315| 6.87k| } 2316| 18.3k| } 2317| | 2318| 1.91M| else if (!a->charge && !a->radical && ------------------ | Branch (2318:18): [True: 1.69M, False: 219k] | Branch (2318:32): [True: 1.66M, False: 24.0k] ------------------ 2319| 1.66M| 2 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 1.66M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.66M|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2319:19): [True: 42.6k, False: 1.62M] ------------------ 2320| 42.6k| 0 == num_of_H( at, i ) && ------------------ | Branch (2320:19): [True: 31.9k, False: 10.6k] ------------------ 2321| 31.9k| 2 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 31.9k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 31.9k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2321:19): [True: 18.2k, False: 13.6k] ------------------ 2322| 18.2k| a->el_number != EL_NUMBER_O && ion_el_group( a->el_number ) == EL_NUMBER_O && ------------------ | | 15| 1.93M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ a->el_number != EL_NUMBER_O && ion_el_group( a->el_number ) == EL_NUMBER_O && ------------------ | | 15| 1.92M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2322:19): [True: 16.4k, False: 1.84k] | Branch (2322:50): [True: 4.98k, False: 11.4k] ------------------ 2323| 4.98k| 3 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2323:19): [True: 2.69k, False: 2.28k] ------------------ 2324| 2.69k| { 2325| | /* Found S(IV), no H, one double bond, total 3 bonds */ 2326| | /* OH 2327| | / 2328| | in O=S (X != O) fix single bond O-X (type 1) 2329| | \ 2330| | X 2331| | 2332| | X 2333| | / 2334| | in Z=S (X, Y != OH) fix double bond Z=S (type 2) 2335| | \ 2336| | Y 2337| | */ 2338| 2.69k| num_N = 0; /* number of non-metal neighbors connected by a double bond */ 2339| 2.69k| num_OH = 0; /* number of neighbors OH connected by a single bond */ 2340| 2.69k| num_OM = 0; /* number of charged neighbors O connected by a single bond */ 2341| 2.69k| num_O = 0; /* number of neighbors =O connected by a double bond */ 2342| 2.69k| num_other = 0; 2343| | 2344| 10.7k| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2344:26): [True: 8.07k, False: 2.69k] ------------------ 2345| 8.07k| { 2346| 8.07k| n1 = (int) a->neighbor[i1]; 2347| 8.07k| if (is_el_a_metal( at[n1].el_number )) ------------------ | Branch (2347:21): [True: 1.31k, False: 6.75k] ------------------ 2348| 1.31k| { 2349| 1.31k| continue; 2350| 1.31k| } 2351| | 2352| 6.75k| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 189| 6.75k|#define BOND_TYPE_MASK 0x0f ------------------ 2353| | 2354| 6.75k| if (BOND_TYPE_DOUBLE == bond_type) ------------------ | | 33| 6.75k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2354:21): [True: 2.46k, False: 4.29k] ------------------ 2355| 2.46k| { 2356| 2.46k| num_N++; 2357| 2.46k| n2 = n1; 2358| 2.46k| i2 = i1; 2359| 2.46k| if (ion_el_group( at[n1].el_number ) == EL_NUMBER_O) ------------------ | | 15| 2.46k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2359:25): [True: 1.13k, False: 1.32k] ------------------ 2360| 1.13k| { 2361| 1.13k| num_O++; 2362| 1.13k| } 2363| 2.46k| } 2364| 4.29k| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 32| 4.29k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2364:26): [True: 4.25k, False: 46] ------------------ 2365| 4.25k| 1 == nNoMetalNumBonds( at, n1 ) && ------------------ | Branch (2365:27): [True: 942, False: 3.30k] ------------------ 2366| 942| 1 == nNoMetalBondsValence( at, n1 ) && ------------------ | Branch (2366:27): [True: 942, False: 0] ------------------ 2367| 942| ion_el_group( at[n1].el_number ) == EL_NUMBER_O) ------------------ | | 15| 942|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2367:27): [True: 411, False: 531] ------------------ 2368| 411| { 2369| 411| if (0 == at[n1].charge) ------------------ | Branch (2369:25): [True: 134, False: 277] ------------------ 2370| 134| { 2371| 134| num_OH++; 2372| 134| n3 = n1; 2373| 134| i3 = i1; /* djb-rwth: ignoring LLVM warning: variable used */ 2374| 134| } 2375| 277| else 2376| 277| { 2377| 277| num_OM++; 2378| 277| } 2379| 411| } 2380| 3.88k| else 2381| 3.88k| { 2382| 3.88k| num_other++; 2383| | /* djb-rwth: removing redundant code */ 2384| 3.88k| i4 = i1; 2385| 3.88k| } 2386| 6.75k| } /* for (i1 = */ 2387| | 2388| 2.69k| if (1 == num_N && 1 == num_O && 1 == num_OH + num_OM) ------------------ | Branch (2388:17): [True: 2.45k, False: 235] | Branch (2388:31): [True: 1.13k, False: 1.31k] | Branch (2388:45): [True: 351, False: 786] ------------------ 2389| 351| { 2390| 351| if (1 == num_other) ------------------ | Branch (2390:21): [True: 218, False: 133] ------------------ 2391| 218| { 2392| | /* type 1: fix the single bond S-X */ 2393| 218| iedge = pBNS->vert[i].iedge[i4]; 2394| 218| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2395| 218| num_changes++; 2396| 218| } 2397| 351| } 2398| 2.34k| else if (1 == num_N && !num_OH && !num_OM) ------------------ | Branch (2398:22): [True: 2.10k, False: 235] | Branch (2398:36): [True: 2.05k, False: 50] | Branch (2398:47): [True: 2.05k, False: 5] ------------------ 2399| 2.05k| { 2400| 2.05k| int bFound = 0; /* flag */ 2401| 2.05k| int bDoNotFixAnyBond = 0; /* flag */ 2402| | /* Avoid case N=S-NH or N=S-N(-); N = N, P, As, Sb */ 2403| 2.05k| if (ion_el_group( at[n2].el_number ) == EL_NUMBER_N) ------------------ | | 14| 2.05k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2403:21): [True: 1.02k, False: 1.02k] ------------------ 2404| 1.02k| { 2405| 1.02k| U_CHAR el_number = at[n2].el_number; 2406| 4.11k| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2406:34): [True: 3.08k, False: 1.02k] ------------------ 2407| 3.08k| { 2408| 3.08k| n1 = (int) a->neighbor[i1]; 2409| 3.08k| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 189| 3.08k|#define BOND_TYPE_MASK 0x0f ------------------ 2410| 3.08k| if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 32| 3.08k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2410:29): [True: 2.05k, False: 1.02k] ------------------ 2411| 2.05k| ( NUMH( at, n1 ) || -1 == at[n1].charge ) && ------------------ | | 56| 4.11k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 2.05k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ | | | Branch (56:21): [True: 90, False: 1.96k] | | ------------------ ------------------ | Branch (2411:49): [True: 442, False: 1.52k] ------------------ 2412| 532| el_number == at[n1].el_number) ------------------ | Branch (2412:30): [True: 521, False: 11] ------------------ 2413| 521| { 2414| 521| i3 = i1; /* djb-rwth: ignoring LLVM warning: variable used */ 2415| 521| n3 = n1; 2416| 521| bFound++; 2417| 521| } 2418| 3.08k| } 2419| 1.02k| } 2420| | /* Exception: check if Z==X and they belong to the same ring system */ 2421| 8.20k| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2421:30): [True: 6.15k, False: 2.05k] ------------------ 2422| 6.15k| { 2423| 6.15k| if (i1 != i2) ------------------ | Branch (2423:25): [True: 4.10k, False: 2.05k] ------------------ 2424| 4.10k| { 2425| 4.10k| n1 = (int) a->neighbor[i1]; 2426| 4.10k| if (at[n2].el_number == at[n1].el_number && ------------------ | Branch (2426:29): [True: 1.90k, False: 2.19k] ------------------ 2427| 1.90k| at[n2].nRingSystem == at[n1].nRingSystem) ------------------ | Branch (2427:30): [True: 362, False: 1.54k] ------------------ 2428| 362| { 2429| 362| bDoNotFixAnyBond++; 2430| 362| } 2431| 4.10k| } 2432| 6.15k| } 2433| 2.05k| if (bDoNotFixAnyBond) ------------------ | Branch (2433:21): [True: 280, False: 1.77k] ------------------ 2434| 280| { 2435| 280| ; /* do nothing */ 2436| 280| } 2437| 1.77k| else if (bFound) ------------------ | Branch (2437:26): [True: 495, False: 1.27k] ------------------ 2438| 495| { 2439| 495| if (1 == bFound && ------------------ | Branch (2439:25): [True: 486, False: 9] ------------------ 2440| 486| 0 <= ( i4 = nNoMetalOtherNeighIndex2( at, i, n2, n3 ) )) ------------------ | Branch (2440:26): [True: 470, False: 16] ------------------ 2441| 470| { 2442| | /* fix bond i4 */ 2443| 470| iedge = pBNS->vert[i].iedge[i4]; 2444| 470| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2445| 470| num_changes++; 2446| 470| } 2447| 495| } 2448| 1.27k| else 2449| 1.27k| { 2450| | /* fix the double bond >S=X */ 2451| 1.27k| iedge = pBNS->vert[i].iedge[i2]; 2452| 1.27k| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2453| 1.27k| num_changes++; 2454| | /* -- test later -- 2455| | if ( 2 == nNoMetalNumBonds( at, n2 ) && 2456| | 0 <= ( i3 = nNoMetalOtherNeighIndex( at, n2, i ) ) ) { 2457| | iedge = pBNS->vert[n2].iedge[i3]; 2458| | pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2459| | num_changes ++; 2460| | } 2461| | -------------------*/ 2462| 1.27k| } 2463| 2.05k| } 2464| 2.69k| } 2465| | 2466| 1.91M| else if (!a->charge && !a->radical && ------------------ | Branch (2466:18): [True: 1.69M, False: 219k] | Branch (2466:32): [True: 1.66M, False: 24.0k] ------------------ 2467| 1.66M| 4 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 1.66M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.66M|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2467:19): [True: 10.5k, False: 1.65M] ------------------ 2468| 10.5k| 0 == num_of_H( at, i ) && ------------------ | Branch (2468:19): [True: 7.67k, False: 2.90k] ------------------ 2469| 7.67k| 4 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 7.67k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 7.67k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2469:19): [True: 5.69k, False: 1.97k] ------------------ 2470| 5.69k| a->el_number != EL_NUMBER_O && ion_el_group( a->el_number ) == EL_NUMBER_O && ------------------ | | 15| 1.91M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ a->el_number != EL_NUMBER_O && ion_el_group( a->el_number ) == EL_NUMBER_O && ------------------ | | 15| 1.91M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2470:19): [True: 5.68k, False: 10] | Branch (2470:50): [True: 3.02k, False: 2.66k] ------------------ 2471| 3.02k| 4 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2471:19): [True: 1.67k, False: 1.35k] ------------------ 2472| 1.67k| { 2473| | /* Found S(VI), no H, two double bonds or one triple bond */ 2474| | /* O 2475| | || 2476| | in O=S--Y- (X, Y -- non-terminal) fix single bonds S-X, S-Y (type 1) 2477| | \ 2478| | X-- 2479| | 2480| | O 2481| | || 2482| | in O=S--O(-) (X -- non-terminal) fix single bond S-X (type 2) 2483| | \ 2484| | X-- 2485| | 2486| | O 2487| | || 2488| | in O=S--OH (X -- non-terminal) fix single bond S-X (type 3) 2489| | \ 2490| | X-- 2491| | 2492| | */ 2493| 1.67k| int iN[4]; /* indexes of non-terminal neighbors connected by a single bond */ 2494| 1.67k| num_N = 0; /* number of non-metal neighbors connected by a double bond */ 2495| 1.67k| num_OH = 0; /* number of neighbors OH connected by a single bond */ 2496| 1.67k| num_OM = 0; /* number of non-terminal neighbors connected by a single bond */ 2497| 1.67k| num_O = 0; /* number of neighbors =O connected by a double bond */ 2498| 1.67k| num_X = 0; /* number of terminal atom X != O connected by a single bond */ 2499| 1.67k| num_other = 0; 2500| 8.36k| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2500:26): [True: 6.69k, False: 1.67k] ------------------ 2501| 6.69k| { 2502| 6.69k| n1 = (int) a->neighbor[i1]; 2503| 6.69k| if (is_el_a_metal( at[n1].el_number )) ------------------ | Branch (2503:21): [True: 571, False: 6.12k] ------------------ 2504| 571| { 2505| 571| continue; 2506| 571| } 2507| 6.12k| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 189| 6.12k|#define BOND_TYPE_MASK 0x0f ------------------ 2508| 6.12k| if (BOND_TYPE_DOUBLE == bond_type) ------------------ | | 33| 6.12k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2508:21): [True: 2.91k, False: 3.20k] ------------------ 2509| 2.91k| { 2510| 2.91k| num_N++; 2511| 2.91k| if (( 0 == at[n1].charge ------------------ | Branch (2511:27): [True: 2.34k, False: 576] ------------------ 2512| 576|#if ( S_VI_O_PLUS_METAL_FIX_BOND == 1 ) 2513| 576| || (1 == at[n1].charge && 2 == at[n1].valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2513:31): [True: 254, False: 322] | Branch (2513:53): [True: 50, False: 204] ------------------ 2514| 2.91k|#endif 2515| 2.91k| ) && 2516| 2.39k| 0 == at[n1].radical && ------------------ | Branch (2516:26): [True: 2.36k, False: 25] ------------------ 2517| 2.36k| 0 == num_of_H( at, n1 ) && ------------------ | Branch (2517:26): [True: 2.31k, False: 47] ------------------ 2518| 2.31k| ion_el_group( at[n1].el_number ) == EL_NUMBER_O && ------------------ | | 15| 5.23k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2518:26): [True: 2.02k, False: 291] ------------------ 2519| 2.02k| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2519:26): [True: 1.56k, False: 460] ------------------ 2520| 1.56k| { 2521| 1.56k| num_O++; 2522| 1.56k| } 2523| 2.91k| } 2524| 3.20k| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 32| 3.20k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2524:26): [True: 2.95k, False: 248] ------------------ 2525| 2.95k| 1 == nNoMetalNumBonds( at, n1 ) && ------------------ | Branch (2525:27): [True: 1.02k, False: 1.92k] ------------------ 2526| 1.02k| ion_el_group( at[n1].el_number ) == EL_NUMBER_O && ------------------ | | 15| 4.23k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2526:27): [True: 664, False: 364] ------------------ 2527| 664| 1 >= num_of_H( at, n1 ) && ------------------ | Branch (2527:27): [True: 659, False: 5] ------------------ 2528| 659| 1 == ( ( 0 == at[n1].charge ) && 1 == num_of_H( at, n1 ) ) ------------------ | Branch (2528:27): [True: 547, False: 112] | Branch (2528:34): [True: 176, False: 483] | Branch (2528:60): [True: 65, False: 111] ------------------ 2529| 659| + ( ( -1 == at[n1].charge ) && 0 == num_of_H( at, n1 ) )) ------------------ | Branch (2529:31): [True: 483, False: 176] | Branch (2529:58): [True: 482, False: 1] ------------------ 2530| 547| { 2531| 547| num_OH++; /* -OH or -O(-) */ 2532| 547| } 2533| 2.65k| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 32| 2.65k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2533:26): [True: 2.41k, False: 248] ------------------ 2534| 2.41k| 1 < nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2534:27): [True: 1.92k, False: 481] ------------------ 2535| 1.92k| { 2536| 1.92k| iN[num_OM++] = i1; /* non-terminal neighbor connected by a single bond */ 2537| 1.92k| } 2538| 729| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 32| 729|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2538:26): [True: 481, False: 248] ------------------ 2539| 481| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2539:27): [True: 481, False: 0] ------------------ 2540| 481| { 2541| 481| num_X++; /* other terminal neighbor connected by a single bond */ 2542| 481| } 2543| 248| else 2544| 248| { 2545| 248| num_other++; 2546| 248| } 2547| 6.12k| } 2548| 1.67k| if (num_N == num_O && 2 == num_O && 2 == num_OH + num_OM + num_X && 0 == num_other) ------------------ | Branch (2548:17): [True: 659, False: 1.01k] | Branch (2548:35): [True: 476, False: 183] | Branch (2548:49): [True: 279, False: 197] | Branch (2548:81): [True: 279, False: 0] ------------------ 2549| 279| { 2550| 630| for (i2 = 0; i2 < num_OM; i2++) ------------------ | Branch (2550:30): [True: 351, False: 279] ------------------ 2551| 351| { 2552| 351| i1 = iN[i2]; 2553| | /* fix bond i1 */ 2554| 351| iedge = pBNS->vert[i].iedge[i1]; 2555| 351| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2556| 351| num_changes++; 2557| 351| } 2558| 279| } 2559| 1.67k| } 2560| | 2561| 1.90M| else if (!a->charge && !a->radical && ------------------ | Branch (2561:18): [True: 1.68M, False: 219k] | Branch (2561:32): [True: 1.66M, False: 24.0k] ------------------ 2562| 1.66M| 6 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 1.66M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.66M|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2562:19): [True: 2.66k, False: 1.66M] ------------------ 2563| 2.66k| 0 == num_of_H( at, i ) && ------------------ | Branch (2563:19): [True: 1.48k, False: 1.18k] ------------------ 2564| 1.48k| 6 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 56| 1.48k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.48k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2564:19): [True: 1.19k, False: 292] ------------------ 2565| 1.19k| a->el_number != EL_NUMBER_O && ion_el_group( a->el_number ) == EL_NUMBER_O && ------------------ | | 15| 1.91M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ a->el_number != EL_NUMBER_O && ion_el_group( a->el_number ) == EL_NUMBER_O && ------------------ | | 15| 1.91M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2565:19): [True: 1.18k, False: 8] | Branch (2565:50): [True: 48, False: 1.13k] ------------------ 2566| 48| 5 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2566:19): [True: 45, False: 3] ------------------ 2567| 45| { 2568| | /* Found S(VIII), no H, three double bonds or two triple bond */ 2569| | /* 2570| | 2571| | O 2572| | || 2573| | in O=S--Y-- (X, Y -- non-terminal) fix single bond S-X, S-Y (type 4) 2574| | //\ 2575| | O X-- 2576| | 2577| | note: this structure is a mistakenly drawn structure 2578| | 2579| | O O 2580| | || || 2581| | O=S--O--Y-- or O=S--Y-- 2582| | \ \ 2583| | X-- O--X-- 2584| | 2585| | 2586| | */ 2587| 45| int iN[5]; /* indexes of non-terminal neighbors connected by a single bond */ 2588| 45| num_N = 0; /* number of non-metal neighbors connected by a double bond */ 2589| 45| num_OH = 0; /* number of neighbors OH connected by a single bond */ 2590| 45| num_OM = 0; /* number of non-terminal neighbors connected by a single bond */ 2591| 45| num_O = 0; /* number of neighbors =O connected by a double bond */ 2592| 45| num_X = 0; /* number of terminal atom X != O connected by a single bond */ 2593| 45| num_other = 0; 2594| 270| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2594:26): [True: 225, False: 45] ------------------ 2595| 225| { 2596| 225| n1 = (int) a->neighbor[i1]; 2597| 225| if (is_el_a_metal( at[n1].el_number )) ------------------ | Branch (2597:21): [True: 92, False: 133] ------------------ 2598| 92| { 2599| 92| continue; 2600| 92| } 2601| 133| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 189| 133|#define BOND_TYPE_MASK 0x0f ------------------ 2602| 133| if (BOND_TYPE_DOUBLE == bond_type) ------------------ | | 33| 133|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2602:21): [True: 57, False: 76] ------------------ 2603| 57| { 2604| 57| num_N++; 2605| 57| if (( 0 == at[n1].charge ------------------ | Branch (2605:27): [True: 46, False: 11] ------------------ 2606| 11|#if ( S_VI_O_PLUS_METAL_FIX_BOND == 1 ) 2607| 11| || (1 == at[n1].charge && 2 == at[n1].valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2607:31): [True: 1, False: 10] | Branch (2607:53): [True: 0, False: 1] ------------------ 2608| 57|#endif 2609| 57| ) 2610| 46| && 0 == at[n1].radical && ------------------ | Branch (2610:29): [True: 46, False: 0] ------------------ 2611| 46| 0 == num_of_H( at, n1 ) && ------------------ | Branch (2611:26): [True: 45, False: 1] ------------------ 2612| 45| ion_el_group( at[n1].el_number ) == EL_NUMBER_O && ------------------ | | 15| 102|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2612:26): [True: 36, False: 9] ------------------ 2613| 36| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2613:26): [True: 35, False: 1] ------------------ 2614| 35| { 2615| 35| num_O++; 2616| 35| } 2617| 57| } 2618| 76| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 32| 76|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2618:26): [True: 33, False: 43] ------------------ 2619| 33| 1 == nNoMetalNumBonds( at, n1 ) && ------------------ | Branch (2619:27): [True: 18, False: 15] ------------------ 2620| 18| ion_el_group( at[n1].el_number ) == EL_NUMBER_O && ------------------ | | 15| 94|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2620:27): [True: 7, False: 11] ------------------ 2621| 7| 1 >= num_of_H( at, n1 ) && ------------------ | Branch (2621:27): [True: 7, False: 0] ------------------ 2622| 7| 1 == ( ( 0 == at[n1].charge ) && 1 == num_of_H( at, n1 ) ) ------------------ | Branch (2622:27): [True: 7, False: 0] | Branch (2622:34): [True: 3, False: 4] | Branch (2622:60): [True: 3, False: 0] ------------------ 2623| 7| + ( ( -1 == at[n1].charge ) && 0 == num_of_H( at, n1 ) )) ------------------ | Branch (2623:31): [True: 4, False: 3] | Branch (2623:58): [True: 4, False: 0] ------------------ 2624| 7| { 2625| 7| num_OH++; /* -OH or -O(-) */ 2626| 7| } 2627| 69| else 2628| 69| { 2629| 69| if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 32| 69|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2629:25): [True: 26, False: 43] ------------------ 2630| 26| 1 < nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2630:26): [True: 15, False: 11] ------------------ 2631| 15| { 2632| | 2633| 15| iN[num_OM++] = i1; /* non-terminal neighbor connected by a single bond */ 2634| 15| } 2635| 54| else 2636| 54| { 2637| 54| if (BOND_TYPE_SINGLE == bond_type && 1 == nNoMetalNumBonds( at, n1 )) ------------------ | | 32| 54|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2637:29): [True: 11, False: 43] | Branch (2637:62): [True: 11, False: 0] ------------------ 2638| 11| { 2639| | 2640| 11| num_X++; /* other terminal neighbor connected by a single bond */ 2641| 11| } 2642| 43| else 2643| 43| { 2644| 43| num_other++; 2645| 43| } 2646| 54| } 2647| 69| } 2648| 133| } 2649| 45| if (num_N == num_O && 3 == num_O && 2 == num_OH + num_OM + num_X && 0 == num_other) ------------------ | Branch (2649:17): [True: 24, False: 21] | Branch (2649:35): [True: 4, False: 20] | Branch (2649:49): [True: 0, False: 4] | Branch (2649:81): [True: 0, False: 0] ------------------ 2650| 0| { 2651| 0| for (i2 = 0; i2 < num_OM; i2++) ------------------ | Branch (2651:30): [True: 0, False: 0] ------------------ 2652| 0| { 2653| 0| i1 = iN[i2]; 2654| | /* fix bond i1 */ 2655| 0| iedge = pBNS->vert[i].iedge[i1]; 2656| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2657| 0| num_changes++; 2658| 0| } 2659| 0| } 2660| 45| } 2661| | 2662| 1.93M| } /* for (i = */ 2663| | 2664| 376k| return num_changes; 2665| 376k|} is_Z_atom: 2747| 699k|{ 2748| 699k| switch ( el_number ) 2749| 699k| { 2750| 123k| case EL_NUMBER_C: /* fallthrough */ ------------------ | | 13| 123k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (2750:9): [True: 123k, False: 576k] ------------------ 2751| 422k| case EL_NUMBER_N: ------------------ | | 14| 422k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2751:9): [True: 298k, False: 401k] ------------------ 2752| 483k| case EL_NUMBER_P: ------------------ | | 18| 483k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (2752:9): [True: 60.9k, False: 639k] ------------------ 2753| 487k| case EL_NUMBER_AS: ------------------ | | 22| 487k|#define EL_NUMBER_AS ((U_CHAR)33) ------------------ | Branch (2753:9): [True: 4.13k, False: 695k] ------------------ 2754| 489k| case EL_NUMBER_SB: ------------------ | | 25| 489k|#define EL_NUMBER_SB ((U_CHAR)51) ------------------ | Branch (2754:9): [True: 2.81k, False: 697k] ------------------ 2755| 551k| case EL_NUMBER_S: ------------------ | | 19| 551k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2755:9): [True: 61.2k, False: 638k] ------------------ 2756| 558k| case EL_NUMBER_SE: ------------------ | | 23| 558k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2756:9): [True: 7.21k, False: 692k] ------------------ 2757| 572k| case EL_NUMBER_TE: ------------------ | | 26| 572k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2757:9): [True: 13.6k, False: 686k] ------------------ 2758| 572k| case EL_NUMBER_CL: ------------------ | | 20| 572k|#define EL_NUMBER_CL ((U_CHAR)17) ------------------ | Branch (2758:9): [True: 600, False: 699k] ------------------ 2759| 573k| case EL_NUMBER_BR: ------------------ | | 24| 573k|#define EL_NUMBER_BR ((U_CHAR)35) ------------------ | Branch (2759:9): [True: 255, False: 699k] ------------------ 2760| 588k| case EL_NUMBER_I: ------------------ | | 27| 588k|#define EL_NUMBER_I ((U_CHAR)53) ------------------ | Branch (2760:9): [True: 15.6k, False: 684k] ------------------ 2761| |#if ( ALL_NONMETAL_Z == 1 ) 2762| | case EL_NUMBER_B: 2763| | case EL_NUMBER_O: 2764| | case EL_NUMBER_SI: 2765| | case EL_NUMBER_GE: 2766| | case EL_NUMBER_F: 2767| | case EL_NUMBER_AT: 2768| |#endif 2769| 588k| return 1; 2770| 111k| default: ------------------ | Branch (2770:9): [True: 111k, False: 588k] ------------------ 2771| 111k| return 0; 2772| 699k| } 2773| 699k|} IsZOX: 2780| 18.8k|{ 2781| 18.8k| inp_ATOM *at_Z = atom + atom[at_x].neighbor[ord]; 2782| | 2783| 18.8k| int i, neigh, num_O; 2784| | 2785| 91.7k| for (i = 0, num_O = 0; i < at_Z->valence; i++) ------------------ | Branch (2785:28): [True: 72.8k, False: 18.8k] ------------------ 2786| 72.8k| { 2787| 72.8k| neigh = at_Z->neighbor[i]; 2788| 72.8k| if (neigh == at_x) ------------------ | Branch (2788:13): [True: 18.8k, False: 53.9k] ------------------ 2789| 18.8k| { 2790| 18.8k| continue; 2791| 18.8k| } 2792| 53.9k| if (atom[neigh].valence == 1 && ------------------ | Branch (2792:13): [True: 37.6k, False: 16.2k] ------------------ 2793| 37.6k| atom[neigh].chem_bonds_valence == 2 && ------------------ | Branch (2793:14): [True: 18.7k, False: 18.9k] ------------------ 2794| 18.7k| atom[neigh].charge == 0 && ------------------ | Branch (2794:14): [True: 10.2k, False: 8.48k] ------------------ 2795| 10.2k| atom[neigh].radical == 0 && ------------------ | Branch (2795:14): [True: 10.1k, False: 80] ------------------ 2796| 10.1k| ( atom[neigh].el_number == EL_NUMBER_O || ------------------ | | 15| 20.3k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2796:16): [True: 6.44k, False: 3.71k] ------------------ 2797| 3.71k| atom[neigh].el_number == EL_NUMBER_S || ------------------ | | 19| 13.8k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2797:16): [True: 2.51k, False: 1.19k] ------------------ 2798| 1.19k| atom[neigh].el_number == EL_NUMBER_SE || ------------------ | | 23| 11.3k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2798:16): [True: 717, False: 482] ------------------ 2799| 482| atom[neigh].el_number == EL_NUMBER_TE )) ------------------ | | 26| 482|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2799:16): [True: 313, False: 169] ------------------ 2800| 9.98k| { 2801| 9.98k| num_O++; 2802| 9.98k| } 2803| 53.9k| } 2804| | 2805| 18.8k| return num_O; 2806| 18.8k|} GetAtomChargeType: 2843| 1.76M|{ 2844| | 2845| 1.76M| inp_ATOM *at = atom + at_no; 2846| 1.76M|#if ( FIX_NORM_BUG_ADD_ION_PAIR == 1 ) 2847| 1.76M| int i, neigh, mask, type, num_z, num_m, num_o, delta = bSubtract > 0 ? -1 : 1; /* 0 or -2 => add, 1 or 2 => subtract */ ------------------ | Branch (2847:60): [True: 5.78k, False: 1.76M] ------------------ 2848| 1.76M| int32_t bit; /* djb-rwth: fixing coverity ID #499579 */ 2849| 1.76M| int bNoAdjIon = ( bSubtract == 0 || bSubtract == 1 ); ------------------ | Branch (2849:23): [True: 1.76M, False: 6.23k] | Branch (2849:41): [True: 5.33k, False: 900] ------------------ 2850| |#else 2851| | int i, neigh, mask, bit, type, num_z, num_m, num_o, delta = bSubtract ? -1 : 1; 2852| |#endif 2853| 1.76M| int bUnsatNHasTerminalO = 0; 2854| | 2855| 1.76M| type = ATT_NONE; ------------------ | | 30| 1.76M|#define ATT_NONE 0x0000 ------------------ 2856| 1.76M| mask = 0; 2857| | 2858| 1.76M| if (at->radical && at->radical != RADICAL_SINGLET) ------------------ | | 75| 79.8k|#define RADICAL_SINGLET 1 ------------------ | Branch (2858:9): [True: 79.8k, False: 1.68M] | Branch (2858:24): [True: 79.8k, False: 0] ------------------ 2859| 79.8k| { 2860| 79.8k| goto exit_function; 2861| 79.8k| } 2862| | 2863| 1.68M| if (is_el_a_metal( at->el_number )) ------------------ | Branch (2863:9): [True: 379k, False: 1.30M] ------------------ 2864| 379k| { 2865| 379k| goto exit_function; 2866| 379k| } 2867| 1.30M| if (at->charge < -1 || at->charge > 1) ------------------ | Branch (2867:9): [True: 825, False: 1.30M] | Branch (2867:28): [True: 185, False: 1.30M] ------------------ 2868| 1.01k| { 2869| 1.01k| goto exit_function; 2870| 1.01k| } 2871| | 2872| 1.30M| if (!at->valence && at->charge == 1 && !at->num_H && !at->radical && at->el_number == EL_NUMBER_H) ------------------ | | 11| 175k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (2872:9): [True: 640k, False: 667k] | Branch (2872:25): [True: 175k, False: 464k] | Branch (2872:44): [True: 175k, False: 132] | Branch (2872:58): [True: 175k, False: 0] | Branch (2872:74): [True: 175k, False: 85] ------------------ 2873| 175k| { 2874| | /* a proton H+ (#1) */ 2875| 175k| type = ATT_PROTON; ------------------ | | 43| 175k|#define ATT_PROTON 0x1000 ------------------ 2876| 175k| mask = ATBIT_Proton; ------------------ | | 119| 175k|#define ATBIT_Proton (1 << ATTOT_NUM_Proton) ------------------ 2877| 175k| goto count_mask_bits; 2878| 175k| } 2879| | 2880| 1.13M| if ( !at->valence && at->charge == -1 && ------------------ | Branch (2880:11): [True: 464k, False: 667k] | Branch (2880:27): [True: 287, False: 464k] ------------------ 2881| 287| !at->num_H && !at->radical && ------------------ | Branch (2881:11): [True: 35, False: 252] | Branch (2881:25): [True: 35, False: 0] ------------------ 2882| 35| ( at->el_number == EL_NUMBER_F || at->el_number == EL_NUMBER_CL || ------------------ | | 16| 70|#define EL_NUMBER_F ((U_CHAR)9) ------------------ ( at->el_number == EL_NUMBER_F || at->el_number == EL_NUMBER_CL || ------------------ | | 20| 66|#define EL_NUMBER_CL ((U_CHAR)17) ------------------ | Branch (2882:13): [True: 4, False: 31] | Branch (2882:45): [True: 0, False: 31] ------------------ 2883| 31| at->el_number == EL_NUMBER_BR || at->el_number == EL_NUMBER_I ) ------------------ | | 24| 66|#define EL_NUMBER_BR ((U_CHAR)35) ------------------ at->el_number == EL_NUMBER_BR || at->el_number == EL_NUMBER_I ) ------------------ | | 27| 31|#define EL_NUMBER_I ((U_CHAR)53) ------------------ | Branch (2883:13): [True: 0, False: 31] | Branch (2883:46): [True: 2, False: 29] ------------------ 2884| 1.13M| ) 2885| 6| { 2886| | /* a halogen anion Hal- (#2) */ 2887| 6| type = ATT_HalAnion; ------------------ | | 44| 6|#define ATT_HalAnion 0x2000 ------------------ 2888| 6| mask = ATBIT_HalAnion; ------------------ | | 120| 6|#define ATBIT_HalAnion (1 << ATTOT_NUM_HalAnion) ------------------ 2889| 6| goto count_mask_bits; 2890| 6| } 2891| 1.13M|#if ( HAL_ACID_H_XCHG == 1 ) 2892| | /* halogen/chalcogen acid */ 2893| 1.13M| if ((!at->valence && at->charge == 0 && 1 == at->num_H && !at->radical && ------------------ | Branch (2893:10): [True: 464k, False: 667k] | Branch (2893:26): [True: 464k, False: 498] | Branch (2893:45): [True: 1.18k, False: 463k] | Branch (2893:63): [True: 1.18k, False: 0] ------------------ 2894| 1.18k| ( at->el_number == EL_NUMBER_F || ------------------ | | 16| 2.36k|#define EL_NUMBER_F ((U_CHAR)9) ------------------ | Branch (2894:11): [True: 568, False: 614] ------------------ 2895| 614| at->el_number == EL_NUMBER_CL || ------------------ | | 20| 1.79k|#define EL_NUMBER_CL ((U_CHAR)17) ------------------ | Branch (2895:11): [True: 0, False: 614] ------------------ 2896| 614| at->el_number == EL_NUMBER_BR || ------------------ | | 24| 1.79k|#define EL_NUMBER_BR ((U_CHAR)35) ------------------ | Branch (2896:11): [True: 418, False: 196] ------------------ 2897| 196| at->el_number == EL_NUMBER_I )) || ------------------ | | 27| 196|#define EL_NUMBER_I ((U_CHAR)53) ------------------ | Branch (2897:11): [True: 114, False: 82] ------------------ 2898| 1.13M| (!at->valence && at->charge == 0 && 2 == at->num_H && !at->radical && ------------------ | Branch (2898:11): [True: 463k, False: 667k] | Branch (2898:27): [True: 463k, False: 498] | Branch (2898:46): [True: 442, False: 462k] | Branch (2898:64): [True: 442, False: 0] ------------------ 2899| 442| ( at->el_number == EL_NUMBER_O || ------------------ | | 15| 884|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2899:12): [True: 135, False: 307] ------------------ 2900| 307| at->el_number == EL_NUMBER_S || ------------------ | | 19| 749|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2900:12): [True: 265, False: 42] ------------------ 2901| 42| at->el_number == EL_NUMBER_SE || ------------------ | | 23| 484|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2901:12): [True: 16, False: 26] ------------------ 2902| 26| at->el_number == EL_NUMBER_TE )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 26| 26|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2902:12): [True: 26, False: 0] ------------------ 2903| 1.13M| ) 2904| 1.54k| { 2905| | /* a halogen/chalcogen acid (#3) */ 2906| 1.54k| type = ATT_HalAcid; ------------------ | | 45| 1.54k|#define ATT_HalAcid 0x4000 ------------------ 2907| 1.54k| mask = ATBIT_HalAcid; ------------------ | | 121| 1.54k|#define ATBIT_HalAcid (1 << ATTOT_NUM_HalAcid) ------------------ 2908| 1.54k| goto count_mask_bits; 2909| 1.54k| } 2910| 1.13M|#endif 2911| | 2912| 1.13M| if (detect_unusual_el_valence( at->el_number, at->charge, at->radical, ------------------ | Branch (2912:9): [True: 78.1k, False: 1.05M] ------------------ 2913| 1.13M| at->chem_bonds_valence, at->num_H, at->valence )) 2914| 78.1k| { 2915| 78.1k| goto exit_function; /* unusual valence state */ 2916| 78.1k| } 2917| | 2918| | /* Check neighbors */ 2919| 1.75M| for (i = 0, num_z = 0, num_m = 0, num_o = 0; i < at->valence; i++) ------------------ | Branch (2919:50): [True: 941k, False: 811k] ------------------ 2920| 941k| { 2921| 941k| neigh = at->neighbor[i]; 2922| 941k|#if ( FIX_NORM_BUG_ADD_ION_PAIR == 1 ) 2923| 941k| if (atom[neigh].charge < -1 || atom[neigh].charge > 1) ------------------ | Branch (2923:13): [True: 3.93k, False: 937k] | Branch (2923:40): [True: 13.1k, False: 924k] ------------------ 2924| 17.0k| { 2925| 17.0k| goto exit_function; /* neighboring charge */ 2926| 17.0k| } 2927| 924k| if (atom[neigh].charge && at->charge) ------------------ | Branch (2927:13): [True: 322k, False: 601k] | Branch (2927:35): [True: 98.8k, False: 223k] ------------------ 2928| 98.8k| { 2929| 98.8k| if (bNoAdjIon) ------------------ | Branch (2929:17): [True: 98.8k, False: 0] ------------------ 2930| 98.8k| { 2931| 98.8k|#if ( FIX_RENUM_BUG_FOR_CASE_OF_ACIDIC_OH_AT_P_PLUS == 1 ) 2932| 98.8k| goto count_mask_bits; 2933| | /*update_some_attype_totals(nAtTypeTotals, mask, delta, at->charge);*/ 2934| 0|#endif 2935| 0| goto exit_function; /* neighboring charge */ 2936| 98.8k| } 2937| 0| type = ATT_NONE; ------------------ | | 30| 0|#define ATT_NONE 0x0000 ------------------ 2938| 0| mask = 0; 2939| 0| goto count_mask_bits; 2940| 98.8k| } 2941| |#else 2942| | if (atom[neigh].charge < -1 || atom[neigh].charge > 1 || atom[neigh].charge && at->charge) 2943| | { 2944| | goto exit_function; /* neighboring charge */ 2945| | } 2946| |#endif 2947| 825k| if (detect_unusual_el_valence( atom[neigh].el_number, atom[neigh].charge, atom[neigh].radical, ------------------ | Branch (2947:13): [True: 125k, False: 699k] ------------------ 2948| 825k| atom[neigh].chem_bonds_valence, atom[neigh].num_H, 2949| 825k| atom[neigh].valence )) 2950| 125k| { 2951| | /* neighbor in unusual valence state */ 2952| 125k| goto exit_function; 2953| 125k| } 2954| 699k| if (is_Z_atom( atom[neigh].el_number )) ------------------ | Branch (2954:13): [True: 588k, False: 111k] ------------------ 2955| 588k| { 2956| 588k| num_z++; 2957| 588k| } 2958| 699k| if (is_el_a_metal( atom[neigh].el_number )) ------------------ | Branch (2958:13): [True: 31.8k, False: 668k] ------------------ 2959| 31.8k| { 2960| 31.8k| num_m++; 2961| 31.8k| } 2962| 699k| num_o += ( atom[neigh].el_number == EL_NUMBER_O ); ------------------ | | 15| 699k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ 2963| 699k| if (at->el_number == EL_NUMBER_N && at->valence == 2 && !at->charge && ------------------ | | 14| 1.39M|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2963:13): [True: 315k, False: 383k] | Branch (2963:45): [True: 172k, False: 143k] | Branch (2963:65): [True: 108k, False: 64.5k] ------------------ 2964| | /*at->valence < at->chem_bonds_valence &&*/ 2965| 108k| atom[neigh].valence == 1 && atom[neigh].chem_bonds_valence == 2 && ------------------ | Branch (2965:14): [True: 18.2k, False: 90.1k] | Branch (2965:42): [True: 10.0k, False: 8.19k] ------------------ 2966| 10.0k| ( atom[neigh].el_number == EL_NUMBER_O || ------------------ | | 15| 20.0k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2966:16): [True: 640, False: 9.40k] ------------------ 2967| 9.40k| atom[neigh].el_number == EL_NUMBER_S || ------------------ | | 19| 19.4k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2967:16): [True: 1.71k, False: 7.69k] ------------------ 2968| 7.69k| atom[neigh].el_number == EL_NUMBER_SE || ------------------ | | 23| 17.7k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2968:16): [True: 295, False: 7.39k] ------------------ 2969| 7.39k| atom[neigh].el_number == EL_NUMBER_TE )) ------------------ | | 26| 7.39k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2969:16): [True: 602, False: 6.79k] ------------------ 2970| 3.25k| { 2971| 3.25k| bUnsatNHasTerminalO++; 2972| 3.25k| } 2973| 699k| } /* eof check neighbors */ 2974| | 2975| | /* O, S, Se, Te */ 2976| 811k| if ( at->el_number == EL_NUMBER_O || ------------------ | | 15| 1.62M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2976:10): [True: 206k, False: 604k] ------------------ 2977| 604k| at->el_number == EL_NUMBER_S || ------------------ | | 19| 1.41M|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2977:10): [True: 71.5k, False: 532k] ------------------ 2978| 532k| at->el_number == EL_NUMBER_SE || ------------------ | | 23| 1.34M|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2978:10): [True: 4.55k, False: 528k] ------------------ 2979| 528k| at->el_number == EL_NUMBER_TE ) ------------------ | | 26| 528k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2979:10): [True: 7.92k, False: 520k] ------------------ 2980| 290k| { 2981| 290k| if (at->charge == 1) ------------------ | Branch (2981:13): [True: 5.44k, False: 285k] ------------------ 2982| 5.44k| { 2983| 5.44k| if (at->num_H) ------------------ | Branch (2983:17): [True: 1.45k, False: 3.99k] ------------------ 2984| 1.45k| { 2985| | /* #4 */ 2986| 1.45k| type = ATT_O_PLUS; ------------------ | | 42| 1.45k|#define ATT_O_PLUS 0x0800 /**< -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */ ------------------ 2987| 1.45k| mask |= ATBIT_OH_Plus; ------------------ | | 117| 1.45k|#define ATBIT_OH_Plus (1 << ATTOT_NUM_OH_Plus) ------------------ 2988| 1.45k| } 2989| 3.99k| else 2990| 3.99k| { 2991| | /* #5 */ 2992| 3.99k| type = ATT_O_PLUS; ------------------ | | 42| 3.99k|#define ATT_O_PLUS 0x0800 /**< -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */ ------------------ 2993| 3.99k| mask |= ATBIT_O_Plus; ------------------ | | 118| 3.99k|#define ATBIT_O_Plus (1 << ATTOT_NUM_O_Plus) ------------------ 2994| 3.99k| } 2995| 5.44k| } 2996| 285k| else 2997| 285k| { 2998| | /* at->charge != 1 */ 2999| 285k| if (at->valence > 1) ------------------ | Branch (2999:17): [True: 19.7k, False: 265k] ------------------ 3000| 19.7k| { 3001| 19.7k| goto exit_function; /* not a terminal atom #C1 */ 3002| 19.7k| } 3003| 265k| else 3004| 265k| { 3005| 265k| if (at->valence && !( num_z || num_o )) ------------------ | Branch (3005:21): [True: 73.0k, False: 192k] | Branch (3005:39): [True: 65.1k, False: 7.87k] | Branch (3005:48): [True: 6.10k, False: 1.76k] ------------------ 3006| 1.76k| { 3007| 1.76k| if (num_m == at->valence) ------------------ | Branch (3007:25): [True: 541, False: 1.22k] ------------------ 3008| 541| { 3009| 541| goto exit_function; /* #C2 */ 3010| 541| } 3011| 1.22k| goto count_mask_bits; /* #C3 count charges, no donor or acceptor found */ 3012| 1.76k| } 3013| 263k| else 3014| 263k| { 3015| | /* Here at->neigh[0] is one of: O, or Z={C, N, P, As, Sb, S, Se, Te, Cl, Br, I} */ 3016| 263k| if (at->valence) ------------------ | Branch (3016:25): [True: 71.2k, False: 192k] ------------------ 3017| 71.2k| { 3018| 71.2k| neigh = at->neighbor[0]; /* Z or O only */ 3019| 71.2k| if (!atom[neigh].charge && atom[neigh].el_number == EL_NUMBER_C && ------------------ | | 13| 135k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (3019:29): [True: 64.1k, False: 7.15k] | Branch (3019:52): [True: 14.3k, False: 49.8k] ------------------ 3020| 14.3k| atom[neigh].chem_bonds_valence > atom[neigh].valence) ------------------ | Branch (3020:30): [True: 11.5k, False: 2.73k] ------------------ 3021| 11.5k| { 3022| | /* =C-OH, #C-OH, =C-O(-), #C-O(-), -C=O, =C=O; O = O, S, Se, Te */ 3023| 11.5k| type = ATT_ACIDIC_CO; ------------------ | | 31| 11.5k|#define ATT_ACIDIC_CO 0x0001 ------------------ 3024| 11.5k| if (at->num_H == 1) ------------------ | Branch (3024:33): [True: 2.68k, False: 8.89k] ------------------ 3025| 2.68k| { 3026| 2.68k| mask |= ( ATBIT_COH ); /* #6: =C-OH, #C-OH; O=O,S,Se,Te */ ------------------ | | 98| 2.68k|#define ATBIT_COH (1 << ATTOT_NUM_COH) ------------------ 3027| | /*nAtTypeTotals[ATTOT_NUM_COH] ++;*/ 3028| 2.68k| } 3029| 8.89k| else 3030| 8.89k| { 3031| 8.89k| if (at->charge == -1) ------------------ | Branch (3031:37): [True: 5.99k, False: 2.89k] ------------------ 3032| 5.99k| { 3033| 5.99k| mask |= ( ATBIT_CO_Minus ); /* #7: =C-O(-), #C-O(-); O=O,S,Se,Te */ ------------------ | | 109| 5.99k|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) ------------------ 3034| | /*nAtTypeTotals[ATTOT_NUM_CO_Minus] ++;*/ 3035| 5.99k| } 3036| 2.89k| else 3037| 2.89k| { 3038| 2.89k| if (!at->num_H && !at->charge) ------------------ | Branch (3038:41): [True: 2.88k, False: 14] | Branch (3038:55): [True: 2.88k, False: 0] ------------------ 3039| 2.88k| { 3040| 2.88k| mask |= ( ATBIT_CO ); /* #8 -C=O, =C=O; O=O,S,Se,Te */ ------------------ | | 105| 2.88k|#define ATBIT_CO (1 << ATTOT_NUM_CO) ------------------ 3041| | /*nAtTypeTotals[ATTOT_NUM_CO] ++;*/ 3042| 2.88k| } 3043| 14| else 3044| 14| { 3045| 14| mask |= ( ATBIT_Errors ); ------------------ | | 124| 14|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3046| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3047| 14| } 3048| 2.89k| } 3049| 8.89k| } 3050| 11.5k| } 3051| 59.6k| else 3052| 59.6k| { 3053| 59.6k| if (!atom[neigh].charge && ------------------ | Branch (3053:33): [True: 52.5k, False: 7.15k] ------------------ 3054| 52.5k| ( atom[neigh].el_number == EL_NUMBER_O || ------------------ | | 15| 105k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (3054:35): [True: 5.53k, False: 46.9k] ------------------ 3055| 46.9k| atom[neigh].el_number == EL_NUMBER_S || ------------------ | | 19| 99.5k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (3055:35): [True: 6.87k, False: 40.1k] ------------------ 3056| 40.1k| atom[neigh].el_number == EL_NUMBER_SE || ------------------ | | 23| 92.6k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (3056:35): [True: 1.85k, False: 38.2k] ------------------ 3057| 38.2k| atom[neigh].el_number == EL_NUMBER_TE ) && ------------------ | | 26| 38.2k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (3057:35): [True: 730, False: 37.5k] ------------------ 3058| 14.9k| atom[neigh].chem_bonds_valence == atom[neigh].valence) ------------------ | Branch (3058:34): [True: 8.59k, False: 6.39k] ------------------ 3059| 8.59k| { 3060| | /* -O-OH, -O-O(-); O = O, S, Se, Te */ 3061| 8.59k| type = ATT_OO; ------------------ | | 33| 8.59k|#define ATT_OO 0x0004 ------------------ 3062| 8.59k| if (at->num_H == 1) ------------------ | Branch (3062:37): [True: 3.05k, False: 5.54k] ------------------ 3063| 3.05k| { 3064| 3.05k| mask |= ( ATBIT_OOH ); /* #9 -O-OH */ ------------------ | | 101| 3.05k|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) ------------------ 3065| | /*nAtTypeTotals[ATTOT_NUM_OOH] ++;*/ 3066| 3.05k| } 3067| 5.54k| else 3068| 5.54k| { 3069| 5.54k| if (at->charge == -1) ------------------ | Branch (3069:41): [True: 5.53k, False: 14] ------------------ 3070| 5.53k| { 3071| 5.53k| mask |= ( ATBIT_OO_Minus ); /* #10 -O-O(-) */ ------------------ | | 112| 5.53k|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) ------------------ 3072| | /*nAtTypeTotals[ATTOT_NUM_OO_Minus] ++;*/ 3073| 5.53k| } 3074| 14| else 3075| 14| { 3076| 14| mask |= ( ATBIT_Errors ); ------------------ | | 124| 14|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3077| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3078| 14| } 3079| 5.54k| } 3080| 8.59k| } 3081| 51.0k| else 3082| 51.0k| { 3083| 51.0k| if (!atom[neigh].charge && ------------------ | Branch (3083:37): [True: 43.9k, False: 7.15k] ------------------ 3084| 43.9k| atom[neigh].chem_bonds_valence == atom[neigh].valence && ------------------ | Branch (3084:38): [True: 7.09k, False: 36.8k] ------------------ 3085| 7.09k| atom[neigh].el_number == EL_NUMBER_C && ------------------ | | 13| 58.1k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (3085:38): [True: 2.73k, False: 4.36k] ------------------ 3086| 2.73k| at->el_number != EL_NUMBER_O) ------------------ | | 15| 2.73k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (3086:38): [True: 2.53k, False: 193] ------------------ 3087| 2.53k| { 3088| | /* >C-S(-), >C-SH; S = S, Se, Te */ 3089| 2.53k| type = ATT_ACIDIC_S; ------------------ | | 32| 2.53k|#define ATT_ACIDIC_S 0x0002 ------------------ 3090| 2.53k| if (at->num_H == 1) ------------------ | Branch (3090:41): [True: 634, False: 1.90k] ------------------ 3091| 634| { 3092| 634| mask |= ( ATBIT_CSH ); /* #11: >C-SH, >CH-SH, -CH2-SH; S = S, Se, Te */ ------------------ | | 99| 634|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) ------------------ 3093| | /*nAtTypeTotals[ATTOT_NUM_CSH] ++;*/ 3094| 634| } 3095| 1.90k| else 3096| 1.90k| { 3097| 1.90k| if (at->charge == -1) ------------------ | Branch (3097:45): [True: 1.90k, False: 0] ------------------ 3098| 1.90k| { 3099| 1.90k| mask |= ( ATBIT_CS_Minus ); /* #12: >C-S(-), >CH-S(-), -CH2-S(-); S = S, Se, Te */ ------------------ | | 110| 1.90k|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) ------------------ 3100| | /*nAtTypeTotals[ATTOT_NUM_CS_Minus] ++;*/ 3101| 1.90k| } 3102| 0| else 3103| 0| { 3104| 0| mask |= ( ATBIT_Errors ); ------------------ | | 124| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3105| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3106| 0| } 3107| 1.90k| } 3108| 2.53k| } 3109| 48.5k| else 3110| 48.5k| { 3111| 48.5k| if (atom[neigh].el_number == EL_NUMBER_N && ------------------ | | 14| 97.1k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (3111:41): [True: 16.4k, False: 32.1k] ------------------ 3112| 16.4k| atom[neigh].valence == 2 && ------------------ | Branch (3112:42): [True: 6.07k, False: 10.3k] ------------------ 3113| 6.07k| ( !atom[neigh].num_H || (atom[neigh].num_H == 1 && atom[neigh].charge == 1) )) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3113:44): [True: 5.73k, False: 337] | Branch (3113:67): [True: 293, False: 44] | Branch (3113:93): [True: 105, False: 188] ------------------ 3114| 5.84k| { 3115| | /* N or N(-) or NH(+) neighbor */ 3116| 5.84k| type = ATT_NO; /* single bond only */ ------------------ | | 35| 5.84k|#define ATT_NO 0x0010 ------------------ 3117| 5.84k| if (at->num_H == 1) ------------------ | Branch (3117:45): [True: 409, False: 5.43k] ------------------ 3118| 409| { 3119| 409| mask |= ( ATBIT_NOH ); /* #13: =N-OH, =NH(+)-OH, #N(+)-OH, -N(-)-OH; O = O, S, Se, Te */ ------------------ | | 103| 409|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) ------------------ 3120| | /*nAtTypeTotals[ATTOT_NUM_NOH] ++;*/ 3121| 409| } 3122| 5.43k| else 3123| 5.43k| { 3124| 5.43k| if (at->charge == -1) ------------------ | Branch (3124:49): [True: 1.07k, False: 4.35k] ------------------ 3125| 1.07k| { 3126| 1.07k| mask |= ( ATBIT_NO_Minus ); /* #14: =N-O(-); O = O, S, Se, Te */ ------------------ | | 114| 1.07k|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) ------------------ 3127| | /*nAtTypeTotals[ATTOT_NUM_NO_Minus] ++;*/ 3128| 1.07k| } 3129| 4.35k| else 3130| 4.35k| { 3131| 4.35k| if (atom[neigh].charge == 1 || atom[neigh].charge == 0) ------------------ | Branch (3131:53): [True: 1.07k, False: 3.28k] | Branch (3131:80): [True: 3.24k, False: 35] ------------------ 3132| 4.32k| { 3133| 4.32k| mask |= ( ATBIT_NO ); /* #15: =N(+)=O, -NH(+)=O -N=O */ ------------------ | | 107| 4.32k|#define ATBIT_NO (1 << ATTOT_NUM_NO) ------------------ 3134| | /*nAtTypeTotals[ATTOT_NUM_NO] ++;*/ 3135| 4.32k| } 3136| 35| else 3137| 35| { 3138| 35| mask |= ( ATBIT_Errors ); ------------------ | | 124| 35|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3139| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3140| 35| } 3141| 4.35k| } 3142| 5.43k| } 3143| 5.84k| } 3144| 42.7k| else 3145| 42.7k| { 3146| 42.7k| if (atom[neigh].el_number == EL_NUMBER_N) ------------------ | | 14| 42.7k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (3146:45): [True: 10.5k, False: 32.1k] ------------------ 3147| 10.5k| { 3148| 10.5k| type = ATT_N_O; /* #16: single bond only */ ------------------ | | 36| 10.5k|#define ATT_N_O 0x0020 ------------------ 3149| 10.5k| if (at->num_H == 1) ------------------ | Branch (3149:49): [True: 367, False: 10.2k] ------------------ 3150| 367| { 3151| 367| mask |= ( ATBIT_N_OH ); /* #16: -NH-OH, >N-OH or >N(+)charge == -1) ------------------ | Branch (3156:53): [True: 5.64k, False: 4.57k] ------------------ 3157| 5.64k| { 3158| 5.64k| mask |= ( ATBIT_N_O_Minus ); /* #17: -NH-O(-), >N-O(-); O = O, S, Se, Te */ ------------------ | | 115| 5.64k|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) ------------------ 3159| | /*nAtTypeTotals[ATTOT_NUM_NO_Minus] ++;*/ 3160| 5.64k| } 3161| 4.57k| else 3162| 4.57k| { 3163| 4.57k| if (atom[neigh].charge == 1) ------------------ | Branch (3163:57): [True: 1.51k, False: 3.05k] ------------------ 3164| 1.51k| { 3165| 1.51k| mask |= ( ATBIT_N_O ); /* #18: >N(+)=O */ ------------------ | | 108| 1.51k|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) ------------------ 3166| | /*nAtTypeTotals[ATTOT_NUM_NO] ++;*/ 3167| 1.51k| } 3168| 3.05k| else 3169| 3.05k| { 3170| 3.05k| mask |= ( ATBIT_Errors ); ------------------ | | 124| 3.05k|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3171| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3172| 3.05k| } 3173| 4.57k| } 3174| 10.2k| } 3175| 10.5k| } 3176| 32.1k| else 3177| 32.1k| { 3178| 32.1k| if ( atom[neigh].el_number != EL_NUMBER_C && ------------------ | | 13| 64.2k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (3178:50): [True: 31.5k, False: 606] ------------------ 3179| 31.5k| atom[neigh].el_number != EL_NUMBER_O && ------------------ | | 15| 63.6k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (3179:50): [True: 30.9k, False: 576] ------------------ 3180| 30.9k| !is_el_a_metal( atom[neigh].el_number ) && ------------------ | Branch (3180:50): [True: 30.6k, False: 260] ------------------ 3181| 30.6k| atom[neigh].chem_bonds_valence > atom[neigh].valence) ------------------ | Branch (3181:50): [True: 29.3k, False: 1.31k] ------------------ 3182| 29.3k| { 3183| | /* =Z-OH, #Z-OH, =Z-O(-), #Z-O(-), -Z=O, =Z=O; 3184| | =Z(+)-OH, #Z(+)-OH, =Z-O(-), #Z-O(-), -Z(+)=O, =Z(+)=O; O = O, S, Se, Te */ 3185| | /* neigh = Z\{N,C} = P, As, Sb, S, Se, Te, Cl, Br, I */ 3186| 29.3k| if (at->chem_bonds_valence == 1 && IsZOX( atom, at_no, 0 )) ------------------ | Branch (3186:53): [True: 18.8k, False: 10.4k] | Branch (3186:84): [True: 9.43k, False: 9.45k] ------------------ 3187| 9.43k| { 3188| 9.43k| type = ATT_ZOO; ------------------ | | 34| 9.43k|#define ATT_ZOO 0x0008 ------------------ 3189| 9.43k| if (at->num_H == 1) ------------------ | Branch (3189:57): [True: 2.25k, False: 7.17k] ------------------ 3190| 2.25k| { 3191| 2.25k| mask |= ( ATBIT_ZOOH ); /* 18: O=Z-OH; O=O,S,Se,Te; Z may have charge */ ------------------ | | 102| 2.25k|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) ------------------ 3192| | /*nAtTypeTotals[ATTOT_NUM_ZOOH] ++;*/ 3193| 2.25k| } 3194| 7.17k| else 3195| 7.17k| { 3196| 7.17k| if (at->charge == -1) ------------------ | Branch (3196:61): [True: 7.17k, False: 0] ------------------ 3197| 7.17k| { 3198| 7.17k| mask |= ( ATBIT_ZOO_Minus ); /* 19: O=Z-O(-); O = O, S, Se, Te */ ------------------ | | 113| 7.17k|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) ------------------ 3199| | /*nAtTypeTotals[ATTOT_NUM_ZOO_Minus] ++;*/ 3200| 7.17k| } 3201| 0| else 3202| 0| { 3203| 0| mask |= ( ATBIT_Errors ); ------------------ | | 124| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3204| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3205| 0| } 3206| 7.17k| } 3207| 9.43k| } 3208| 19.9k| else 3209| 19.9k| { 3210| 19.9k| type = ATT_OTHER_ZO; ------------------ | | 40| 19.9k|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ ------------------ 3211| 19.9k| if (at->num_H == 1) ------------------ | Branch (3211:57): [True: 450, False: 19.4k] ------------------ 3212| 450| { 3213| 450| mask |= ( ATBIT_ZOH ); /* 20: =Z-OH, #Z-OH; O=O,S,Se,Te; Z may have charge */ ------------------ | | 100| 450|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) ------------------ 3214| | /*nAtTypeTotals[ATTOT_NUM_ZOH] ++;*/ 3215| 450| } 3216| 19.4k| else 3217| 19.4k| { 3218| 19.4k| if (at->charge == -1) ------------------ | Branch (3218:61): [True: 9.31k, False: 10.1k] ------------------ 3219| 9.31k| { 3220| 9.31k| mask |= ( ATBIT_ZO_Minus ); /* 21: =Z-O(-), #Z-O(-); O = O, S, Se, Te */ ------------------ | | 111| 9.31k|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) ------------------ 3221| | /*nAtTypeTotals[ATTOT_NUM_ZO_Minus] ++;*/ 3222| 9.31k| } 3223| 10.1k| else 3224| 10.1k| { 3225| 10.1k| if (at->num_H == 0) ------------------ | Branch (3225:65): [True: 10.1k, False: 18] ------------------ 3226| 10.1k| { 3227| 10.1k| mask |= ( ATBIT_ZO ); /* 22: -Z=O, =Z=O; O=O,S,Se,Te; Z may have charge */ ------------------ | | 106| 10.1k|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) ------------------ 3228| | /*nAtTypeTotals[ATTOT_NUM_ZO] ++;*/ 3229| 10.1k| } 3230| 18| else 3231| 18| { 3232| 18| mask |= ( ATBIT_Errors ); ------------------ | | 124| 18|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3233| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3234| 18| } 3235| 10.1k| } 3236| 19.4k| } 3237| 19.9k| } 3238| 29.3k| } 3239| 2.75k| else 3240| 2.75k| { 3241| 2.75k| if (at->charge == -1 && !is_el_a_metal( atom[neigh].el_number )) ------------------ | Branch (3241:53): [True: 1.46k, False: 1.29k] | Branch (3241:73): [True: 1.37k, False: 87] ------------------ 3242| 1.37k| { 3243| | /* >Z-O(-); O=O,S,Se,Te */ 3244| 1.37k| type = ATT_OTHER_NEG_O; ------------------ | | 39| 1.37k|#define ATT_OTHER_NEG_O 0x0100 ------------------ 3245| 1.37k| mask |= ( ATBIT_O_Minus ); /* 23: -Z-O(-); O=O,S,Se,Te */ ------------------ | | 116| 1.37k|#define ATBIT_O_Minus (1 << ATTOT_NUM_O_Minus) ------------------ 3246| | /*nAtTypeTotals[ATTOT_NUM_ZO_Minus] ++;*/ 3247| 1.37k| } 3248| 2.75k| } 3249| 32.1k| } 3250| 42.7k| } 3251| 48.5k| } 3252| 51.0k| } 3253| 59.6k| } 3254| 71.2k| } 3255| | 3256| 192k| else 3257| 192k| { 3258| 192k| if (at->charge == -1 && at->num_H == 1) ------------------ | Branch (3258:29): [True: 225, False: 192k] | Branch (3258:49): [True: 211, False: 14] ------------------ 3259| 211| { 3260| 211| type = ATT_OH_MINUS; ------------------ | | 41| 211|#define ATT_OH_MINUS 0x0400 /**< OH(-), O=O,S,Se,Te */ ------------------ 3261| 211| mask |= ( ATBIT_O_Minus ); /* 25: HO(-); O=O,S,Se,Te */ ------------------ | | 116| 211|#define ATBIT_O_Minus (1 << ATTOT_NUM_O_Minus) ------------------ 3262| 211| } 3263| 192k| } 3264| 263k| } 3265| 265k| } 3266| 285k| } 3267| 290k| } 3268| | 3269| 520k| else 3270| 520k| { 3271| | /* P, N, neutral valence = 3 (not 5) */ 3272| 520k| if (( at->el_number == EL_NUMBER_N || ------------------ | | 14| 1.04M|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (3272:15): [True: 188k, False: 331k] ------------------ 3273| 331k| at->el_number == EL_NUMBER_P ) && ------------------ | | 18| 331k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (3273:15): [True: 22.8k, False: 308k] ------------------ 3274| 211k| 0 <= at->valence && at->valence <= 3 && ------------------ | Branch (3274:14): [True: 211k, False: 0] | Branch (3274:34): [True: 203k, False: 7.87k] ------------------ 3275| 203k| at->chem_bonds_valence + at->num_H == 3 + at->charge) ------------------ | Branch (3275:14): [True: 135k, False: 68.1k] ------------------ 3276| 135k| { 3277| 135k| if (at->valence && !( num_z /*|| num_o == at->valence*/ )) ------------------ | Branch (3277:17): [True: 135k, False: 51] | Branch (3277:32): [True: 769, False: 134k] ------------------ 3278| 769| { 3279| 769| if (num_m == at->valence) ------------------ | Branch (3279:21): [True: 163, False: 606] ------------------ 3280| 163| { 3281| 163| goto exit_function; 3282| 163| } 3283| 606| goto count_mask_bits; /* N(III), N(-)(II), N(+)(IV) and same P that have only oxygen neighbors are ignored here */ 3284| 769| } 3285| 134k| type = ( at->el_number == EL_NUMBER_N ) ? ATT_ATOM_N : ATT_ATOM_P; ------------------ | | 14| 134k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ type = ( at->el_number == EL_NUMBER_N ) ? ATT_ATOM_N : ATT_ATOM_P; ------------------ | | 37| 121k|#define ATT_ATOM_N 0x0040 ------------------ type = ( at->el_number == EL_NUMBER_N ) ? ATT_ATOM_N : ATT_ATOM_P; ------------------ | | 38| 147k|#define ATT_ATOM_P 0x0080 ------------------ | Branch (3285:20): [True: 121k, False: 12.8k] ------------------ 3286| 134k| switch (at->charge) 3287| 134k| { 3288| 32.7k| case -1: ------------------ | Branch (3288:17): [True: 32.7k, False: 102k] ------------------ 3289| 32.7k| if (at->el_number == EL_NUMBER_N) ------------------ | | 14| 32.7k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (3289:25): [True: 29.6k, False: 3.09k] ------------------ 3290| 29.6k| { 3291| 29.6k| mask |= ( ATBIT_N_Minus ); /* 26: -NH(-), =N(-), >N(-) */ ------------------ | | 95| 29.6k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) ------------------ 3292| 29.6k| if (at->num_H) ------------------ | Branch (3292:29): [True: 1.58k, False: 28.0k] ------------------ 3293| 1.58k| { 3294| 1.58k| mask |= ( ATBIT_NP_H ); /* 27: -NH(-) */ ------------------ | | 94| 1.58k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ 3295| 1.58k| } 3296| 28.0k|#if ( FIX_NP_MINUS_BUG == 1 ) 3297| 28.0k| else 3298| 28.0k| { 3299| 28.0k| if (at->valence == 1 && at->chem_bonds_valence >= 2 && ( at->bond_type[0] & BOND_MARK_ALL )) ------------------ | | 191| 23.7k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ | Branch (3299:33): [True: 23.7k, False: 4.34k] | Branch (3299:53): [True: 23.7k, False: 0] | Branch (3299:84): [True: 84, False: 23.6k] ------------------ 3300| 84| { 3301| 84| type |= ATT_NP_MINUS_V23; /* =N(-) created by normalization 2010-03-11 DT */ ------------------ | | 47| 84|#define ATT_NP_MINUS_V23 0x8000 /**< =N(-) or =P(-) where = previously was triple */ ------------------ 3302| 84| } 3303| 28.0k| } 3304| 29.6k|#endif 3305| 29.6k| } 3306| | /*nAtTypeTotals[ATTOT_NUM_N_Minus] += (at->el_number == EL_NUMBER_N);*/ 3307| 32.7k| break; 3308| 73.6k| case 0: ------------------ | Branch (3308:17): [True: 73.6k, False: 61.1k] ------------------ 3309| 73.6k| if (at->num_H) ------------------ | Branch (3309:25): [True: 7.77k, False: 65.8k] ------------------ 3310| 7.77k| { 3311| 7.77k| mask |= ( ATBIT_NP_H ); /* 28: -NH2, =NH, >NH */ ------------------ | | 94| 7.77k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ 3312| | /*nAtTypeTotals[ATTOT_NUM_NP_H] ++;*/ 3313| 7.77k| } 3314| 65.8k| else 3315| 65.8k| { 3316| 65.8k| if (bUnsatNHasTerminalO == 1) ------------------ | Branch (3316:29): [True: 3.08k, False: 62.7k] ------------------ 3317| 3.08k| { 3318| 3.08k| mask |= ( ATBIT_ON ); /* 29: -N=O,-N=OH(+) only, not =N-OH */ ------------------ | | 97| 3.08k|#define ATBIT_ON (1 << ATTOT_NUM_ON) ------------------ 3319| 3.08k| } 3320| 62.7k| else 3321| 62.7k| { 3322| 62.7k| mask |= ( ATBIT_NP ); /* 30: -P=O,-P=OH(+), >N- =N- (incl. =N-OH) , #N */ ------------------ | | 96| 62.7k|#define ATBIT_NP (1 << ATTOT_NUM_NP) ------------------ 3323| | /*nAtTypeTotals[ATTOT_NUM_NP] ++;*/ 3324| 62.7k| } 3325| 65.8k| } 3326| 73.6k| break; /* ignore neutral N or P */ 3327| 28.3k| case 1: ------------------ | Branch (3327:17): [True: 28.3k, False: 106k] ------------------ 3328| 28.3k| if (at->num_H) ------------------ | Branch (3328:25): [True: 1.20k, False: 27.1k] ------------------ 3329| 1.20k| { 3330| 1.20k| mask |= ( ATBIT_NP_Proton ); /* 31: NH4(+), -NH3(+), =NH2(+), >NH2(+), =NH(+)-, >NH(+)-, #NH(+) */ ------------------ | | 93| 1.20k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) ------------------ 3331| | /*nAtTypeTotals[ATTOT_NUM_NP_Proton] ++;*/ 3332| 1.20k| } 3333| 27.1k| else 3334| 27.1k| { 3335| 27.1k| if (at->chem_bonds_valence > at->valence) ------------------ | Branch (3335:29): [True: 27.1k, False: 0] ------------------ 3336| 27.1k| { 3337| 27.1k| mask |= ( ATBIT_NP_Plus ); /* =N(+)=, #N(+)-, =N(+)< */ ------------------ | | 92| 27.1k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) ------------------ 3338| | /*nAtTypeTotals[ATTOT_NUM_NP_Plus] ++;*/ 3339| 27.1k| } 3340| 0| else 3341| 0| { 3342| 0| type = 0; /* 32: ignore onium cations >N(+)< */ 3343| 0| } 3344| 27.1k| } 3345| 28.3k| break; 3346| 0| default: ------------------ | Branch (3346:17): [True: 0, False: 134k] ------------------ 3347| 0| mask |= ( 1 << ATTOT_NUM_Errors ); 3348| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3349| 0| break; 3350| 134k| } 3351| 134k| } 3352| 520k| } 3353| | 3354| 1.06M|count_mask_bits: 3355| 1.06M| if (nAtTypeTotals) ------------------ | Branch (3355:9): [True: 623k, False: 443k] ------------------ 3356| 623k| { 3357| 623k| if (mask && !( mask & ( ATBIT_Errors ) )) ------------------ | | 124| 97.0k|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ | Branch (3357:13): [True: 97.0k, False: 526k] | Branch (3357:21): [True: 95.8k, False: 1.21k] ------------------ 3358| 95.8k| { 3359| 3.25M| for (i = 0, bit = 1; i < ATTOT_ARRAY_LEN; i++, bit <<= 1) ------------------ | Branch (3359:34): [True: 3.16M, False: 95.8k] ------------------ 3360| 3.16M| { 3361| 3.16M| if (bit & mask) ------------------ | Branch (3361:21): [True: 96.2k, False: 3.06M] ------------------ 3362| 96.2k| { 3363| 96.2k| nAtTypeTotals[i] += delta; 3364| 96.2k| } 3365| 3.16M| } 3366| 95.8k| } 3367| | 3368| | /* Count charges */ 3369| 623k| if (at->charge) ------------------ | Branch (3369:13): [True: 86.3k, False: 536k] ------------------ 3370| 86.3k| { 3371| 86.3k| nAtTypeTotals[ATTOT_TOT_CHARGE] += delta * at->charge; 3372| 86.3k| nAtTypeTotals[ATTOT_NUM_CHARGES] += delta; 3373| 86.3k| } 3374| 623k| } 3375| | 3376| 1.06M| if (pMask) ------------------ | Branch (3376:9): [True: 1.06M, False: 0] ------------------ 3377| 1.06M| { 3378| 1.06M| *pMask = mask; 3379| 1.06M| } 3380| | 3381| 1.76M|exit_function: 3382| 1.76M| if (mask & ( ATBIT_Errors )) ------------------ | | 124| 1.76M|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ | Branch (3382:9): [True: 3.13k, False: 1.76M] ------------------ 3383| 3.13k| { 3384| 3.13k| type = 0; 3385| 3.13k| if (nAtTypeTotals) ------------------ | Branch (3385:13): [True: 1.21k, False: 1.92k] ------------------ 3386| 1.21k| { 3387| 1.21k| nAtTypeTotals[ATTOT_NUM_Errors] += 1; 3388| 1.21k| } 3389| 3.13k| } 3390| | 3391| | 3392| 1.76M| return type; 3393| 1.06M|} SimpleRemoveHplusNPO: 3401| 665|{ 3402| 665| int i, mask, type, num_removed; 3403| 4.32k| for (i = 0, num_removed = 0; i < num_atoms; i++) ------------------ | Branch (3403:34): [True: 3.66k, False: 665] ------------------ 3404| 3.66k| { 3405| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3406| 3.66k| if (( PR_SIMPLE_TYP & ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) ) ) && ------------------ | | 137| 3.66k|#define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 37| 3.66k|#define ATT_ATOM_N 0x0040 | | ------------------ | | #define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 38| 3.66k|#define ATT_ATOM_P 0x0080 | | ------------------ | | #define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 42| 3.66k|#define ATT_O_PLUS 0x0800 /**< -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */ | | ------------------ ------------------ | Branch (3406:13): [True: 1.31k, False: 2.34k] ------------------ 3407| 1.31k| ( PR_SIMPLE_MSK & mask )) ------------------ | | 136| 1.31k|#define PR_SIMPLE_MSK (ATBIT_NP_Proton | ATBIT_OH_Plus) | | ------------------ | | | | 93| 1.31k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | ------------------ | | #define PR_SIMPLE_MSK (ATBIT_NP_Proton | ATBIT_OH_Plus) | | ------------------ | | | | 117| 1.31k|#define ATBIT_OH_Plus (1 << ATTOT_NUM_OH_Plus) | | ------------------ ------------------ | Branch (3407:13): [True: 683, False: 635] ------------------ 3408| 683| { 3409| |#if ( bRELEASE_VERSION == 0 ) 3410| | if (at[i].charge != 1 || at[i].num_H == 0) 3411| | { 3412| | return -1; /* program error */ 3413| | } 3414| |#endif 3415| 683| type = GetAtomChargeType(at, i, nAtTypeTotals, &mask, 1); /* subtract at[i] */ /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3416| 683| at[i].charge = 0; 3417| 683| AddOrRemoveExplOrImplH( -1, at, num_atoms, (AT_NUMB) i, t_group_info ); 3418| | /*at[i].num_H --;*/ 3419| 683| num_removed++; 3420| 683|#if ( FIX_NORM_BUG_ADD_ION_PAIR == 1 ) 3421| 683| type = GetAtomChargeType(at, i, nAtTypeTotals, &mask, 0); /* add changed at[i] */ /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3422| |#else 3423| | type = GetAtomChargeType(at, i, nAtTypeTotals, &mask, 1); /* bug: subtract instead of add */ /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3424| |#endif 3425| | /* 3426| | if ( nAtTypeTotals ) { 3427| | nAtTypeTotals[ATTOT_NUM_NP_Proton] --; 3428| | if ( at[i].num_H ) { 3429| | nAtTypeTotals[ATTOT_NUM_NP_H] ++; 3430| | } else { 3431| | nAtTypeTotals[ATTOT_NUM_NP] ++; 3432| | } 3433| | nAtTypeTotals[ATTOT_TOT_CHARGE] --; 3434| | nAtTypeTotals[ATTOT_NUM_CHARGES] --; 3435| | } 3436| | */ 3437| 683| } 3438| 3.66k| } 3439| | 3440| 665| return num_removed; 3441| 665|} bIsAtomTypeHard: 3450| 1.13k|{ 3451| 1.13k| int mask; 3452| 1.13k| if (( nType & GetAtomChargeType( at, endpoint, NULL, &mask, 0 ) ) && ( mask & nMask ) ------------------ | Branch (3452:9): [True: 302, False: 828] | Branch (3452:74): [True: 296, False: 6] ------------------ 3453| |#if ( OPPOSITE_CHARGE_IN_CGROUP == 0 ) 3454| | && ( at[endpoint].charge == nCharge || !at[endpoint].charge ) 3455| |#endif 3456| 1.13k| ) 3457| 296| { 3458| 296| return 1; 3459| 296| } 3460| | 3461| 834| return 0; 3462| 1.13k|} bIsHDonorAccAtomType: 3467| 565|{ 3468| 565| if (bIsAtomTypeHard( at, endpoint, PR_HARD_TYP_H, PR_HARD_MSK_H, 0 )) ------------------ | | 197| 565|#define PR_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 150| 565|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 565|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define PR_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 148| 565|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 565|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 565|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 565|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 565|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 565|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 565|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ if (bIsAtomTypeHard( at, endpoint, PR_HARD_TYP_H, PR_HARD_MSK_H, 0 )) ------------------ | | 196| 565|#define PR_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 139| 565|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 565|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 565|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 565|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 565|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 565|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define PR_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 141| 565|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 565|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 565|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 565|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 565|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 565|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 565|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 565|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 565| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 565|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 565|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 565|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 565|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 565| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 565|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 565|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 565|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 565|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 565| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 565|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 565|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 565|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ | Branch (3468:9): [True: 148, False: 417] ------------------ 3469| 148| { 3470| | /* Obtain donor/acceptor info */ 3471| 148| int neutral_valence = at[endpoint].chem_bonds_valence + at[endpoint].num_H - at[endpoint].charge; 3472| 148| if (neutral_valence != 2 /* O, S, Se, Te */ && ------------------ | Branch (3472:13): [True: 146, False: 2] ------------------ 3473| 146| neutral_valence != 3 /* N, P */) ------------------ | Branch (3473:14): [True: 1, False: 145] ------------------ 3474| 1| { 3475| 1| return -1; /* wrong endpoint neutral valence */ 3476| 1| } 3477| 147| else 3478| 147| { 3479| 147| int edge_flow = at[endpoint].num_H; 3480| 147| int num_bonds = at[endpoint].valence; 3481| 147| int edge_cap = neutral_valence - num_bonds; /* does not allow to reduce -NH3(+) to #N or -OH(+)- to -O- */ 3482| 147| edge_flow = inchi_min( edge_flow, edge_cap ); ------------------ | | 139| 147|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 84, False: 63] | | ------------------ ------------------ 3483| | /* what this means: */ 3484| 147| if (edge_cap) ------------------ | Branch (3484:17): [True: 96, False: 51] ------------------ 3485| 96| { 3486| 96| if (edge_cap > edge_flow) ------------------ | Branch (3486:21): [True: 81, False: 15] ------------------ 3487| 81| { 3488| 81| *cSubType |= SALT_ACCEPTOR; ------------------ | | 64| 81|#define SALT_ACCEPTOR 4 ------------------ 3489| 81| } 3490| 96| if (edge_flow) ------------------ | Branch (3490:21): [True: 37, False: 59] ------------------ 3491| 37| { 3492| 37| *cSubType |= SALT_DONOR_H; ------------------ | | 62| 37|#define SALT_DONOR_H 1 ------------------ 3493| 37| } 3494| 96| return 4; 3495| 96| } 3496| 147| } 3497| 148| } 3498| | 3499| 468| return -1; 3500| 565|} bIsNegAtomType: 3505| 565|{ 3506| 565| int sub_type = 0; 3507| 565| if (bIsAtomTypeHard( at, endpoint, PR_HARD_TYP_NEG, PR_HARD_MSK_NEG, -1 )) ------------------ | | 194| 565|#define PR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 150| 565|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 565|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define PR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 148| 565|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 565|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 565|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 565|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 565|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 565|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 565|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ if (bIsAtomTypeHard( at, endpoint, PR_HARD_TYP_NEG, PR_HARD_MSK_NEG, -1 )) ------------------ | | 193| 565|#define PR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 139| 565|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 565|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 565|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 565|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 565|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 565|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define PR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 141| 565|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 565|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 565|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 565|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 565|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 565|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 565|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 565|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 565| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 565|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 565|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 565|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 565|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 565| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 565|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 565|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 565|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 565|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 565| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 565|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 565|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 565|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ | Branch (3507:9): [True: 148, False: 417] ------------------ 3508| 148| { 3509| | /* Obtain donor/acceptor info */ 3510| 148| int neutral_valence = at[endpoint].chem_bonds_valence + at[endpoint].num_H - at[endpoint].charge; 3511| 148| if (neutral_valence != 2 /* O, S, Se, Te */ && ------------------ | Branch (3511:13): [True: 146, False: 2] ------------------ 3512| 146| neutral_valence != 3 /* N, P */) ------------------ | Branch (3512:14): [True: 1, False: 145] ------------------ 3513| 1| { 3514| 1| return -1; /* wrong endpoint neutral valence */ 3515| 1| } 3516| 147| else 3517| 147| { 3518| 147| int edge_flow = ( at[endpoint].charge == -1 ); 3519| 147| int num_bonds = at[endpoint].valence; 3520| 147| int edge_cap = neutral_valence - num_bonds - at[endpoint].num_H; /* does not allow to reduce -NH3(+) to #N or -OH(+)- to -O- */ 3521| 147| edge_flow = inchi_min( edge_flow, edge_cap ); ------------------ | | 139| 147|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 75, False: 72] | | ------------------ ------------------ 3522| | /* what this means: */ 3523| 147| if (edge_cap) ------------------ | Branch (3523:17): [True: 84, False: 63] ------------------ 3524| 84| { 3525| 84| if (edge_cap > edge_flow) ------------------ | Branch (3525:21): [True: 75, False: 9] ------------------ 3526| 75| { 3527| 75| sub_type |= SALT_ACCEPTOR; ------------------ | | 64| 75|#define SALT_ACCEPTOR 4 ------------------ 3528| 75| } 3529| 84| if (edge_flow) ------------------ | Branch (3529:21): [True: 11, False: 73] ------------------ 3530| 11| { 3531| 11| sub_type |= SALT_DONOR_Neg; ------------------ | | 63| 11|#define SALT_DONOR_Neg 2 ------------------ 3532| 11| } 3533| 84| if (sub_type) ------------------ | Branch (3533:21): [True: 84, False: 0] ------------------ 3534| 84| { 3535| 84| *cSubType |= sub_type; 3536| 84| return 4; 3537| 84| } 3538| 84| } 3539| 147| } 3540| 148| } 3541| | 3542| 480| return -1; 3543| 565|} bIsHardRemHCandidate: 3548| 565|{ 3549| 565| int ret1, ret2, ret; 3550| 565| int sub_type = 0; 3551| 565| ret1 = bIsHDonorAccAtomType( at, i, &sub_type ); 3552| 565| ret2 = bIsNegAtomType( at, i, &sub_type ); 3553| 565| ret = inchi_max( ret1, ret2 ); ------------------ | | 138| 565|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 15, False: 550] | | ------------------ ------------------ 3554| 565| if (ret > 0 && sub_type) ------------------ | Branch (3554:9): [True: 99, False: 466] | Branch (3554:20): [True: 99, False: 0] ------------------ 3555| 99| { 3556| 99| *cSubType |= sub_type; 3557| 99| return ret; 3558| 99| } 3559| 466| return -1; 3560| 565|} CreateCGroupInBnStruct: 3570| 110k|{ 3571| 110k| int k, c_point, cg, centerpoint, fictpoint, type, ret = 0; 3572| 110k| int num_cg = 1; 3573| 110k| int num_edges = pBNS->num_edges; 3574| 110k| int num_vertices = pBNS->num_vertices; /* new c-group bns-ID */ 3575| 110k| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing charge c-group */ 3576| 110k| BNS_VERTEX *vertex_cpoint; 3577| 110k| BNS_EDGE *edge; /* edge between that vertex and the tautomeric c_point */ 3578| 110k| int mask, num_CPoints; 3579| | 3580| | /* Debug: check overflow */ 3581| 110k| if (num_vertices + num_cg >= pBNS->max_vertices) ------------------ | Branch (3581:9): [True: 0, False: 110k] ------------------ 3582| 0| { 3583| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3584| 0| } 3585| | 3586| | /* Count new c-group edges */ 3587| 407k| for (c_point = 0, num_CPoints = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3587:40): [True: 296k, False: 110k] ------------------ 3588| 296k| { 3589| 296k| if (( nType & GetAtomChargeType( at, c_point, NULL, &mask, 0 ) ) && ( mask & nMask ) ------------------ | Branch (3589:13): [True: 30.6k, False: 265k] | Branch (3589:77): [True: 29.5k, False: 1.15k] ------------------ 3590| |#if ( OPPOSITE_CHARGE_IN_CGROUP == 0 ) 3591| | && ( at[c_point].charge == nCharge || !at[c_point].charge ) 3592| |#endif 3593| 296k| ) 3594| 29.5k| { 3595| 29.5k| num_CPoints++; 3596| 29.5k| } 3597| 296k| } 3598| | 3599| 110k| if (!num_CPoints) ------------------ | Branch (3599:9): [True: 94.6k, False: 16.1k] ------------------ 3600| 94.6k| { 3601| 94.6k| return 0; 3602| 94.6k| } 3603| | 3604| | /* Clear the new vertex */ 3605| 16.1k| memset( pBNS->vert + num_vertices, 0, 1 * sizeof( pBNS->vert[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3606| | 3607| | /* *old* Make sure the last t-group has the largest t-group ID: 3608| | this is necessary to correctly add new edges and vertices for testing augmenting paths 3609| | */ 3610| | 3611| | /**************************************/ 3612| | /* initialize new fictitious vertex */ 3613| | /* representing c-point group */ 3614| | /**************************************/ 3615| | 3616| 16.1k| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 3617| | 3618| 32.2k| for (cg = 0; cg < num_cg; cg++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (3618:18): [True: 16.1k, False: 16.1k] ------------------ 3619| 16.1k| { 3620| | /* 3621| | vert_ficpoint-1 is the last vertex; 3622| | vert_ficpoint is the being added vertex 3623| | Note: nGroupNumber are not contiguous 3624| | */ 3625| 16.1k| vert_ficpoint = pBNS->vert + num_vertices + cg; 3626| 16.1k| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 3627| 16.1k| vert_ficpoint->max_adj_edges = num_CPoints + BNS_ADD_EDGES; ------------------ | | 89| 16.1k|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 3628| 16.1k| vert_ficpoint->num_adj_edges = 0; 3629| 16.1k| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 3630| 16.1k| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 3631| 16.1k| vert_ficpoint->type = BNS_VERT_TYPE_C_GROUP | ( ( nCharge < 0 ) ? BNS_VERT_TYPE_C_NEGATIVE : 0 ); ------------------ | | 49| 16.1k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ vert_ficpoint->type = BNS_VERT_TYPE_C_GROUP | ( ( nCharge < 0 ) ? BNS_VERT_TYPE_C_NEGATIVE : 0 ); ------------------ | | 54| 8.93k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (3631:57): [True: 8.93k, False: 7.19k] ------------------ 3632| 16.1k| } 3633| | 3634| | /************************************************/ 3635| | /* Connect c-points to the fictitious vertices */ 3636| | /* representing c-point groups; set caps, flows */ 3637| | /************************************************/ 3638| 16.1k| cg = 1; 3639| 108k| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3639:23): [True: 92.1k, False: 16.1k] ------------------ 3640| 92.1k| { 3641| 92.1k| if (( nType & ( type = GetAtomChargeType( at, c_point, NULL, &mask, 0 ) ) ) && ( mask & nMask ) ------------------ | Branch (3641:13): [True: 30.4k, False: 61.7k] | Branch (3641:88): [True: 29.5k, False: 910] ------------------ 3642| |#if ( OPPOSITE_CHARGE_IN_CGROUP == 0 ) 3643| | && ( at[c_point].charge == nCharge || !at[c_point].charge ) 3644| |#endif 3645| 92.1k| ) 3646| 29.5k| { 3647| 29.5k| ; 3648| 29.5k| } 3649| 62.6k| else 3650| 62.6k| { 3651| 62.6k| continue; 3652| 62.6k| } 3653| | 3654| 29.5k| fictpoint = cg + num_vertices - 1; /* c-group vertex index */ 3655| 29.5k| vert_ficpoint = pBNS->vert + fictpoint; /* c-group vertex */ 3656| 29.5k| vertex_cpoint = pBNS->vert + c_point; /* c_point vertex */ 3657| | 3658| | /* Debug: check overflow */ 3659| 29.5k| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (3659:13): [True: 0, False: 29.5k] ------------------ 3660| 29.5k| num_edges >= pBNS->max_edges || ------------------ | Branch (3660:14): [True: 0, False: 29.5k] ------------------ 3661| 29.5k| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (3661:14): [True: 0, False: 29.5k] ------------------ 3662| 29.5k| vertex_cpoint->num_adj_edges >= vertex_cpoint->max_adj_edges) ------------------ | Branch (3662:14): [True: 0, False: 29.5k] ------------------ 3663| 0| { 3664| | /* djb-rwth: removing redundant code */ 3665| 0| break; 3666| 0| } 3667| 29.5k| vertex_cpoint->type |= BNS_VERT_TYPE_C_POINT; ------------------ | | 48| 29.5k|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ 3668| 29.5k| if (( KNOWN_ACIDIC_TYPE & type ) && nCharge < 0) ------------------ | | 140| 29.5k|#define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 31| 29.5k|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 32| 29.5k|#define ATT_ACIDIC_S 0x0002 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 33| 29.5k|#define ATT_OO 0x0004 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 34| 29.5k|#define ATT_ZOO 0x0008 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 35| 29.5k|#define ATT_NO 0x0010 | | ------------------ ------------------ | Branch (3668:13): [True: 1.47k, False: 28.0k] | Branch (3668:45): [True: 1.47k, False: 0] ------------------ 3669| 1.47k| { 3670| 1.47k| vertex_cpoint->type |= pBNS->type_TACN; 3671| 1.47k| } 3672| | 3673| |#if ( FIX_CPOINT_BOND_CAP != 1 ) /* { */ 3674| | /* Set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 3675| | /* if their current capacity is zero */ 3676| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 3677| | for (k = 0; k < vertex_cpoint->num_adj_edges; k++) 3678| | { 3679| | int iedge = vertex_cpoint->iedge[k]; 3680| | if (!pBNS->edge[iedge].cap) 3681| | { 3682| | /* single bond, possibly between c_point and centerpoint */ 3683| | centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 3684| | if (centerpoint < pBNS->num_atoms && 3685| | pBNS->vert[centerpoint].st_edge.cap >= 1) 3686| | { 3687| | int bond_type = ( at[c_point].bond_type[k] & BOND_TYPE_MASK ); 3688| | if (bond_type == BOND_TAUTOM || 3689| | bond_type == BOND_ALTERN || 3690| | bond_type == BOND_SINGLE) 3691| | { 3692| | pBNS->edge[iedge].cap = 1; 3693| | } 3694| | } 3695| | } 3696| | } 3697| |#endif /* } FIX_CPOINT_BOND_CAP */ 3698| | 3699| | /* Create a new edge connecting c_point to the new fictitious c-group vertex vert_ficpoint */ 3700| 29.5k| edge = pBNS->edge + num_edges; 3701| 29.5k| edge->cap = 1; 3702| 29.5k| edge->flow = 0; 3703| 29.5k| edge->pass = 0; 3704| 29.5k|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 3705| 29.5k| edge->forbidden &= pBNS->edge_forbidden_mask; /* remove previous temporary ban */ 3706| 29.5k|#endif 3707| | 3708| | /* nCharge = +1: mark edge to c-point having no (+)-moveable charge with flow=1 */ 3709| | /* nCharge = -1: mark edge to c-point having -1 moveable charge with flow=1 */ 3710| | 3711| 29.5k| if ((nCharge == 1 && at[c_point].charge != 1) || (nCharge == -1 && at[c_point].charge == -1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3711:14): [True: 13.0k, False: 16.4k] | Branch (3711:30): [True: 9.60k, False: 3.45k] | Branch (3711:59): [True: 16.4k, False: 3.45k] | Branch (3711:76): [True: 4.71k, False: 11.7k] ------------------ 3712| | /*if ( !CHARGED_CPOINT(at,c_point) )*/ 3713| 14.3k| { 3714| | /* Increment new edge flow, update st_edges of the adjacent vertices */ 3715| 14.3k| edge->flow++; 3716| | /* Increment c-group vertex st-flow & cap */ 3717| 14.3k| vert_ficpoint->st_edge.flow++; 3718| 14.3k| vert_ficpoint->st_edge.cap++; 3719| | /* Increment c-point vertex st-flow & cap */ 3720| 14.3k| vertex_cpoint->st_edge.flow++; 3721| 14.3k| vertex_cpoint->st_edge.cap++; 3722| 14.3k| } 3723| | 3724| 29.5k|#if ( FIX_CPOINT_BOND_CAP == 1 ) /* { */ 3725| | /* Set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 3726| | /* if their current capacity is zero */ 3727| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 3728| 90.0k| for (k = 0; k < vertex_cpoint->num_adj_edges; k++) ------------------ | Branch (3728:21): [True: 60.5k, False: 29.5k] ------------------ 3729| 60.5k| { 3730| 60.5k| int iedge = vertex_cpoint->iedge[k]; 3731| 60.5k| VertexFlow nNewCap = vertex_cpoint->st_edge.cap; 3732| 60.5k| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 3733| 60.5k| if (!pBNS->edge[iedge].cap) ------------------ | Branch (3733:17): [True: 9.52k, False: 51.0k] ------------------ 3734| 9.52k| { 3735| | /* Single bond, possibly between c_point and centerpoint */ 3736| 9.52k| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (3736:21): [True: 9.52k, False: 0] ------------------ 3737| 9.52k| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (3737:22): [True: 3.50k, False: 6.01k] ------------------ 3738| 3.50k| { 3739| 3.50k| nNewCap = inchi_min( pBNS->vert[centerpoint].st_edge.cap, nNewCap ); ------------------ | | 139| 3.50k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 3.50k] | | ------------------ ------------------ 3740| 3.50k| nNewCap = inchi_min( nNewCap, MAX_BOND_EDGE_CAP ); ------------------ | | 139| 3.50k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 3.50k, False: 0] | | ------------------ ------------------ 3741| 3.50k| pBNS->edge[iedge].cap = nNewCap; 3742| 3.50k| } 3743| 9.52k| } 3744| |#if ( FIX_CPOINT_BOND_CAP2 == 1 ) /* multiple bond */ 3745| | else 3746| | { 3747| | if (centerpoint < pBNS->num_atoms && 3748| | edge->flow && pBNS->edge[iedge].cap < MAX_BOND_EDGE_CAP) 3749| | { 3750| | pBNS->edge[iedge].cap++; 3751| | } 3752| | } 3753| |#endif 3754| 60.5k| } 3755| 29.5k|#endif /* } FIX_CPOINT_BOND_CAP */ 3756| | 3757| | /* Connect edge to c_point and fictpoint and increment the counters of neighbors and edges */ 3758| 29.5k| edge->neighbor1 = c_point; /* the smallest out of v1=endopoint and v2=num_vertices */ 3759| 29.5k| edge->neighbor12 = c_point ^ fictpoint; /* v1 ^ v2 */ 3760| 29.5k| vertex_cpoint->iedge[vertex_cpoint->num_adj_edges] = num_edges; 3761| 29.5k| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 3762| 29.5k| edge->neigh_ord[0] = vertex_cpoint->num_adj_edges++; 3763| 29.5k| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 3764| 29.5k| edge->cap0 = edge->cap; 3765| 29.5k| edge->flow0 = edge->flow; 3766| 29.5k| } 3767| | 3768| 16.1k| ret = pBNS->num_vertices; /* new c-group atom number */ 3769| 16.1k| pBNS->num_edges = num_edges; 3770| 16.1k| pBNS->num_vertices += num_cg; 3771| 16.1k| pBNS->num_c_groups += num_cg; 3772| | 3773| 16.1k| return ret; 3774| 110k|} CreateTGroupInBnStruct: 3783| 93.6k|{ 3784| 93.6k| int ret = 0; 3785| | /* ret = ReInitBnStruct( pBNS ); */ 3786| 93.6k| int k, endpoint, tg, centerpoint, fictpoint; 3787| 93.6k| int num_tg = 1; 3788| 93.6k| int num_edges = pBNS->num_edges; 3789| 93.6k| int num_vertices = pBNS->num_vertices; 3790| 93.6k| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing t-group */ 3791| 93.6k| BNS_VERTEX *vert_endpoint; 3792| 93.6k| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 3793| 93.6k| int mask, num_endpoints, neutral_valence, edge_flow, edge_cap, num_bonds; 3794| | 3795| | /* Debug: check overflow */ 3796| 93.6k| if (num_vertices + num_tg >= pBNS->max_vertices) ------------------ | Branch (3796:9): [True: 0, False: 93.6k] ------------------ 3797| 0| { 3798| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3799| 0| } 3800| | 3801| | /* Count new t-group edges */ 3802| 294k| for (endpoint = 0, num_endpoints = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (3802:43): [True: 200k, False: 93.6k] ------------------ 3803| 200k| { 3804| 200k| if (( nType & GetAtomChargeType( at, endpoint, NULL, &mask, 0 ) ) && ( mask & nMask ) ------------------ | Branch (3804:13): [True: 16.9k, False: 183k] | Branch (3804:78): [True: 16.4k, False: 495] ------------------ 3805| 200k| ) 3806| 16.4k| { 3807| 16.4k| num_endpoints++; 3808| 16.4k| } 3809| 200k| } 3810| | 3811| 93.6k| if (!num_endpoints) ------------------ | Branch (3811:9): [True: 84.8k, False: 8.77k] ------------------ 3812| 84.8k| { 3813| 84.8k| return 0; 3814| 84.8k| } 3815| | 3816| | /* Since t-group IDs may be not contiguous, clear all vertices that will be added. 3817| | all-zeroes-vertex will be ignored by the BNS 3818| | */ 3819| 8.77k| memset( pBNS->vert + num_vertices, 0, num_tg * sizeof( pBNS->vert[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3820| | 3821| | /* *old* Make sure the last t-group has the largest t-group ID: 3822| | this is necessary to correctly add new edges and vertices for testing augmenting paths 3823| | */ 3824| | 3825| | /**************************************/ 3826| | /* Initialize new fictitious vertex */ 3827| | /* representing t-point group */ 3828| | /**************************************/ 3829| 8.77k| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 3830| | 3831| 17.5k| for (tg = 0; tg < num_tg; tg++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (3831:18): [True: 8.77k, False: 8.77k] ------------------ 3832| 8.77k| { 3833| | /* 3834| | vert_ficpoint-1 is the last vertex; 3835| | vert_ficpoint is the vertex that is being added 3836| | Note: nGroupNumber are not contiguous 3837| | */ 3838| 8.77k| vert_ficpoint = pBNS->vert + num_vertices + tg; 3839| 8.77k| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 3840| 8.77k| vert_ficpoint->max_adj_edges = num_endpoints + BNS_ADD_EDGES + BNS_ADD_SUPER_TGROUP; ------------------ | | 89| 8.77k|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ vert_ficpoint->max_adj_edges = num_endpoints + BNS_ADD_EDGES + BNS_ADD_SUPER_TGROUP; ------------------ | | 85| 8.77k|#define BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */ ------------------ 3841| 8.77k| vert_ficpoint->num_adj_edges = 0; 3842| 8.77k| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 3843| 8.77k| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 3844| 8.77k| vert_ficpoint->type |= BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 8.77k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 3845| 8.77k| } 3846| | 3847| 8.77k| tg = 1; 3848| 58.8k| for (endpoint = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (3848:24): [True: 50.1k, False: 8.76k] ------------------ 3849| 50.1k| { 3850| 50.1k| if (( nType & GetAtomChargeType( at, endpoint, NULL, &mask, 0 ) ) && ( mask & nMask )) ------------------ | Branch (3850:13): [True: 16.8k, False: 33.2k] | Branch (3850:78): [True: 16.4k, False: 414] ------------------ 3851| 16.4k| { 3852| 16.4k| ; 3853| 16.4k| } 3854| 33.6k| else 3855| 33.6k| { 3856| 33.6k| continue; 3857| 33.6k| } 3858| 16.4k| fictpoint = tg + num_vertices - 1; 3859| 16.4k| vert_ficpoint = pBNS->vert + fictpoint; 3860| 16.4k| vert_endpoint = pBNS->vert + endpoint; 3861| | /* Debug: check overflow */ 3862| 16.4k| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (3862:13): [True: 0, False: 16.4k] ------------------ 3863| 16.4k| num_edges >= pBNS->max_edges || ------------------ | Branch (3863:14): [True: 0, False: 16.4k] ------------------ 3864| 16.4k| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (3864:14): [True: 0, False: 16.4k] ------------------ 3865| 16.4k| vert_endpoint->num_adj_edges >= vert_endpoint->max_adj_edges) ------------------ | Branch (3865:14): [True: 0, False: 16.4k] ------------------ 3866| 0| { 3867| | /* djb-rwth: removing redundant code */ 3868| 0| break; 3869| 0| } 3870| | 3871| | /* Obtain donor/acceptor info */ 3872| 16.4k| neutral_valence = at[endpoint].chem_bonds_valence + at[endpoint].num_H - at[endpoint].charge; 3873| 16.4k| if (neutral_valence != 2 /* O, S, Se, Te */ && ------------------ | Branch (3873:13): [True: 13.0k, False: 3.38k] ------------------ 3874| 13.0k| neutral_valence != 3 /* N, P */) ------------------ | Branch (3874:14): [True: 6, False: 13.0k] ------------------ 3875| 6| { 3876| | /* djb-rwth: removing redundant code */ 3877| 6| break; 3878| 6| } 3879| 16.4k| edge_flow = at[endpoint].num_H; 3880| 16.4k| num_bonds = at[endpoint].valence; 3881| 16.4k| edge_cap = neutral_valence - num_bonds; /* does not allow to reduce -NH3(+) to #N or -OH(+)- to -O- */ 3882| | 3883| 16.4k| if (3 == neutral_valence /* N or P */ && 1 < num_bonds) ------------------ | Branch (3883:13): [True: 13.0k, False: 3.38k] | Branch (3883:50): [True: 8.23k, False: 4.82k] ------------------ 3884| 8.23k| { 3885| 8.23k| edge_cap++; /* allow -NH2(+)- => -N=, >NH(+)- => >N- */ 3886| 8.23k| } 3887| 16.4k| edge_flow = inchi_min( edge_flow, edge_cap ); ------------------ | | 139| 16.4k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 15.9k, False: 541] | | ------------------ ------------------ 3888| | /* 3889| | if ( !nGetEndpointInfo( at, endpoint, &eif ) ) { 3890| | ret = BNS_BOND_ERR; 3891| | break; 3892| | } 3893| | */ 3894| 16.4k| vert_endpoint->type |= BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 16.4k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 3895| | 3896| | /* Create a new edge connecting endpoint to the new fictitious t-group vertex vert_ficpoint */ 3897| 16.4k| edge = pBNS->edge + num_edges; 3898| 16.4k| edge->cap = edge_cap; 3899| 16.4k| edge->flow = edge_flow; 3900| 16.4k| edge->pass = 0; 3901| 16.4k|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 3902| 16.4k| edge->forbidden &= pBNS->edge_forbidden_mask; 3903| 16.4k|#endif 3904| | 3905| | /* Adjust st_flow and st_cap of the adjacent vertices */ 3906| | /* Adjust t-group vertex st-flow & cap */ 3907| 16.4k| vert_ficpoint->st_edge.flow += edge->flow; 3908| 16.4k| vert_ficpoint->st_edge.cap += edge->flow; 3909| | /* adjust endpoint vertex st-flow & cap */ 3910| 16.4k| vert_endpoint->st_edge.flow += edge->flow; 3911| 16.4k| vert_endpoint->st_edge.cap += edge->flow; 3912| | 3913| | /* Adjust edge cap & flow according to the number of H and number of bonds */ 3914| 71.3k| for (k = 0; k < vert_endpoint->num_adj_edges; k++) ------------------ | Branch (3914:21): [True: 54.9k, False: 16.4k] ------------------ 3915| 54.9k| { 3916| 54.9k| int iedge = vert_endpoint->iedge[k]; 3917| 54.9k| VertexFlow nNewCap = vert_endpoint->st_edge.cap; 3918| 54.9k| if (!pBNS->edge[iedge].cap) ------------------ | Branch (3918:17): [True: 3.15k, False: 51.7k] ------------------ 3919| 3.15k| { 3920| | /* single bond, possibly between endpoint and centerpoint */ 3921| 3.15k| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ endpoint ); 3922| 3.15k| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (3922:21): [True: 3.15k, False: 0] ------------------ 3923| 3.15k| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (3923:22): [True: 341, False: 2.81k] ------------------ 3924| 341| { 3925| 341| nNewCap = inchi_min( pBNS->vert[centerpoint].st_edge.cap, nNewCap ); ------------------ | | 139| 341|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 341] | | ------------------ ------------------ 3926| 341| nNewCap = inchi_min( nNewCap, MAX_BOND_EDGE_CAP ); ------------------ | | 139| 341|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 341, False: 0] | | ------------------ ------------------ 3927| 341| pBNS->edge[iedge].cap = nNewCap; 3928| 341| } 3929| 3.15k| } 3930| 54.9k| } 3931| | 3932| | /* Connect edge to endpoint and fictpoint and increment the counters of neighbors and edges */ 3933| 16.4k| edge->neighbor1 = endpoint; /* the smallest out of v1=endopoint and v2=num_vertices */ 3934| 16.4k| edge->neighbor12 = endpoint ^ fictpoint; /* v1 ^ v2 */ 3935| 16.4k| vert_endpoint->iedge[vert_endpoint->num_adj_edges] = num_edges; 3936| 16.4k| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 3937| 16.4k| edge->neigh_ord[0] = vert_endpoint->num_adj_edges++; 3938| 16.4k| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 3939| 16.4k| edge->cap0 = edge->cap; 3940| 16.4k| edge->flow0 = edge->flow; 3941| 16.4k| } 3942| | 3943| 8.77k| ret = pBNS->num_vertices; /* new t-group atom number */ 3944| 8.77k| pBNS->num_edges = num_edges; 3945| 8.77k| pBNS->num_vertices += num_tg; 3946| 8.77k| pBNS->num_t_groups += num_tg; 3947| | 3948| 8.77k| return ret; 3949| 93.6k|} RemoveLastGroupFromBnStruct: 3957| 24.9k|{ 3958| 24.9k| int ret = 0; 3959| | /* ret = ReInitBnStruct( pBNS ); */ 3960| 24.9k| int k, endpoint, /*centerpoint, fictpoint,*/ iedge; 3961| 24.9k| int num_edges = pBNS->num_edges; 3962| 24.9k| int num_vertices = pBNS->num_vertices; 3963| 24.9k| BNS_VERTEX *vert_ficpoint /*, *ver_ficpont_prev*/; /* fictitious vertex describing t-group */ 3964| 24.9k| BNS_VERTEX *vert_endpoint; 3965| 24.9k| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 3966| | /*int mask, num_endpoints, neutral_valence, edge_flow, edge_cap, num_bonds;*/ 3967| 24.9k| int is_t_group = 0, is_c_group = 0; 3968| | 3969| | /* Debug: check overflow */ 3970| 24.9k| if (pBNS->num_added_atoms + pBNS->num_c_groups + pBNS->num_t_groups + num_atoms >= pBNS->max_vertices) ------------------ | Branch (3970:9): [True: 0, False: 24.9k] ------------------ 3971| 0| { 3972| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3973| 0| } 3974| | 3975| 24.9k| if (tg + 1 != num_vertices) ------------------ | Branch (3975:9): [True: 0, False: 24.9k] ------------------ 3976| 0| { 3977| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3978| 0| } 3979| | 3980| 24.9k| vert_ficpoint = pBNS->vert + tg; 3981| | 3982| 24.9k| if (vert_ficpoint->type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 24.9k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (3982:9): [True: 8.77k, False: 16.1k] ------------------ 3983| 8.77k| { 3984| 8.77k| is_t_group = 1; 3985| 8.77k| } 3986| 24.9k| if (vert_ficpoint->type & BNS_VERT_TYPE_C_GROUP) ------------------ | | 49| 24.9k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (3986:9): [True: 16.1k, False: 8.77k] ------------------ 3987| 16.1k| { 3988| 16.1k| is_c_group = 1; 3989| 16.1k| if (vert_ficpoint->type & BNS_VERT_TYPE_C_NEGATIVE) ------------------ | | 54| 16.1k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (3989:13): [True: 8.93k, False: 7.19k] ------------------ 3990| 8.93k| { 3991| 8.93k| is_c_group = 2; 3992| 8.93k| } 3993| 16.1k| } 3994| | 3995| 70.8k| for (k = vert_ficpoint->num_adj_edges - 1; 0 <= k; k--) ------------------ | Branch (3995:48): [True: 45.9k, False: 24.9k] ------------------ 3996| 45.9k| { 3997| 45.9k| iedge = vert_ficpoint->iedge[k]; 3998| 45.9k| if (iedge + 1 != num_edges) ------------------ | Branch (3998:13): [True: 0, False: 45.9k] ------------------ 3999| 0| { 4000| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4001| 0| } 4002| 45.9k| edge = pBNS->edge + iedge; 4003| 45.9k| endpoint = edge->neighbor12 ^ tg; 4004| 45.9k| vert_endpoint = pBNS->vert + endpoint; 4005| | /* adjust st_flow, st_cap */ 4006| 45.9k| vert_endpoint->st_edge.cap0 = 4007| 45.9k| vert_endpoint->st_edge.cap -= edge->flow; 4008| 45.9k| vert_endpoint->st_edge.flow0 = 4009| 45.9k| vert_endpoint->st_edge.flow -= edge->flow; 4010| 45.9k| if (pBNS->type_TACN && ( vert_endpoint->type & pBNS->type_TACN ) == pBNS->type_TACN) ------------------ | Branch (4010:13): [True: 45.9k, False: 0] | Branch (4010:32): [True: 1.47k, False: 44.4k] ------------------ 4011| 1.47k| { 4012| 1.47k| vert_endpoint->type ^= pBNS->type_TACN; 4013| 1.47k| } 4014| 45.9k| if (is_t_group) ------------------ | Branch (4014:13): [True: 16.4k, False: 29.4k] ------------------ 4015| 16.4k| { 4016| 16.4k| vert_endpoint->type ^= ( vert_ficpoint->type & BNS_VERT_TYPE_ENDPOINT ); ------------------ | | 46| 16.4k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 4017| 16.4k| } 4018| 45.9k| if (is_c_group) ------------------ | Branch (4018:13): [True: 29.4k, False: 16.4k] ------------------ 4019| 29.4k| { 4020| 29.4k| vert_endpoint->type ^= ( vert_ficpoint->type & BNS_VERT_TYPE_C_POINT ); ------------------ | | 48| 29.4k|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ 4021| 29.4k| } 4022| | /* Remove edge */ 4023| 45.9k| if (edge->neigh_ord[0] + 1 != vert_endpoint->num_adj_edges) ------------------ | Branch (4023:13): [True: 0, False: 45.9k] ------------------ 4024| 0| { 4025| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4026| 0| } 4027| 45.9k| vert_endpoint->num_adj_edges--; 4028| 45.9k| memset( edge, 0, sizeof( *edge ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4029| 45.9k| num_edges--; 4030| 45.9k| if (1 == is_t_group && endpoint < num_atoms) ------------------ | Branch (4030:13): [True: 16.4k, False: 29.4k] | Branch (4030:32): [True: 16.4k, False: 0] ------------------ 4031| 16.4k| { 4032| 16.4k| at->endpoint = 0; 4033| 16.4k| } 4034| 45.9k| if (1 == is_c_group && endpoint < num_atoms) ------------------ | Branch (4034:13): [True: 13.0k, False: 32.8k] | Branch (4034:32): [True: 13.0k, False: 0] ------------------ 4035| 13.0k| { 4036| 13.0k| at->c_point = 0; 4037| 13.0k| } 4038| 45.9k| } 4039| 24.9k| memset( vert_ficpoint, 0, sizeof( *vert_ficpoint ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4040| 24.9k| num_vertices--; 4041| | 4042| 24.9k| pBNS->num_edges = num_edges; 4043| 24.9k| pBNS->num_vertices = num_vertices; 4044| 24.9k| if (is_t_group) ------------------ | Branch (4044:9): [True: 8.77k, False: 16.1k] ------------------ 4045| 8.77k| { 4046| 8.77k| pBNS->num_t_groups--; 4047| 8.77k| } 4048| 24.9k| if (is_c_group) ------------------ | Branch (4048:9): [True: 16.1k, False: 8.77k] ------------------ 4049| 16.1k| { 4050| 16.1k| pBNS->num_c_groups--; 4051| 16.1k| } 4052| | 4053| 24.9k| return ret; 4054| 24.9k|} SetInitCapFlowToCurrent: 4060| 4.60k|{ 4061| 4.60k| int i, j; 4062| 4.60k| BNS_EDGE *pEdge = NULL; 4063| 36.0k| for (i = 0; i < pBNS->num_vertices; i++) ------------------ | Branch (4063:17): [True: 31.4k, False: 4.60k] ------------------ 4064| 31.4k| { 4065| 31.4k| pBNS->vert[i].st_edge.flow0 = pBNS->vert[i].st_edge.flow; 4066| 31.4k| pBNS->vert[i].st_edge.cap0 = pBNS->vert[i].st_edge.cap; 4067| 78.9k| for (j = 0; j < pBNS->vert[i].num_adj_edges; j++) ------------------ | Branch (4067:21): [True: 47.5k, False: 31.4k] ------------------ 4068| 47.5k| { 4069| 47.5k| pEdge = pBNS->edge + pBNS->vert[i].iedge[j]; 4070| 47.5k| pEdge->cap0 = pEdge->cap; 4071| 47.5k| pEdge->flow0 = pEdge->flow; 4072| 47.5k| } 4073| 31.4k| } 4074| | 4075| 4.60k| return 0; 4076| 4.60k|} SimpleRemoveAcidicProtons: 4098| 41.8k|{ 4099| 41.8k| int i, j, max_j = -1, mask, type, num_removed; 4100| 41.8k| int num[AR_SIMPLE_STEPS + 1], num_tot; 4101| | 4102| 83.7k| for (j = 0; ArTypMask[2 * j]; j++) ------------------ | Branch (4102:17): [True: 41.8k, False: 41.8k] ------------------ 4103| 41.8k| { 4104| 41.8k| num[max_j = j] = 0; 4105| 41.8k| } 4106| | 4107| 117k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4107:17): [True: 75.7k, False: 41.8k] ------------------ 4108| 75.7k| { 4109| 75.7k| if (!at[i].charge && at[i].num_H && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4109:13): [True: 22.3k, False: 53.4k] | Branch (4109:30): [True: 867, False: 21.4k] | Branch (4109:45): [True: 454, False: 413] ------------------ 4110| 454| { 4111| 768| for (j = 0; j <= max_j; j++) ------------------ | Branch (4111:25): [True: 454, False: 314] ------------------ 4112| 454| { 4113| 454| if (( type & ArTypMask[2 * j] ) && ( mask && ArTypMask[2 * j + 1] )) ------------------ | Branch (4113:21): [True: 140, False: 314] | Branch (4113:54): [True: 140, False: 0] | Branch (4113:62): [True: 140, False: 0] ------------------ 4114| 140| { 4115| 140| num[j] ++; 4116| 140| break; 4117| 140| } 4118| 454| } 4119| 454| } 4120| 75.7k| } 4121| 83.6k| for (j = 0, num_tot = 0; j <= max_j; j++) ------------------ | Branch (4121:30): [True: 41.8k, False: 41.7k] ------------------ 4122| 41.8k| { 4123| 41.8k| if (( num_tot += num[j] ) >= num2remove) ------------------ | Branch (4123:13): [True: 98, False: 41.7k] ------------------ 4124| 98| { 4125| 98| max_j = j; 4126| 98| break; 4127| 98| } 4128| 41.8k| } 4129| 41.8k| if (!num_tot) ------------------ | Branch (4129:9): [True: 41.7k, False: 103] ------------------ 4130| 41.7k| { 4131| 41.7k| return 0; 4132| 41.7k| } 4133| 639| for (i = 0, num_removed = 0; i < num_atoms && num_removed < num2remove; i++) ------------------ | Branch (4133:34): [True: 615, False: 24] | Branch (4133:51): [True: 536, False: 79] ------------------ 4134| 536| { 4135| 536| if (!at[i].charge && at[i].num_H && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4135:13): [True: 421, False: 115] | Branch (4135:30): [True: 113, False: 308] | Branch (4135:45): [True: 105, False: 8] ------------------ 4136| 105| { 4137| 107| for (j = 0; j <= max_j; j++) ------------------ | Branch (4137:25): [True: 105, False: 2] ------------------ 4138| 105| { 4139| 105| if (num[j] && ( type & ArTypMask[2 * j] ) && ( mask && ArTypMask[2 * j + 1] )) ------------------ | Branch (4139:21): [True: 105, False: 0] | Branch (4139:31): [True: 103, False: 2] | Branch (4139:64): [True: 103, False: 0] | Branch (4139:72): [True: 103, False: 0] ------------------ 4140| 103| { 4141| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 4142| 103| type = GetAtomChargeType(at, i, pAATG->nAtTypeTotals, &mask, 1); /* subtract at[i] */ 4143| 103| num[j] --; 4144| 103| at[i].charge--; 4145| 103| AddOrRemoveExplOrImplH( -1, at, num_atoms, (AT_NUMB) i, pAATG->t_group_info ); 4146| | /*at[i].num_H --;*/ 4147| 103| num_removed++; 4148| 103| type = GetAtomChargeType(at, i, pAATG->nAtTypeTotals, &mask, 0); /* add changed at[i] */ /* ! THIS CHANGES pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] */ 4149| 103| break; 4150| 103| } 4151| 105| } 4152| 105| } 4153| 536| } 4154| | 4155| | /* 4156| | pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] -= num_removed; 4157| | pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] += num_removed; 4158| | */ 4159| | 4160| 103| return num_removed; 4161| 41.8k|} bHasAcidicHydrogen: 4166| 1.00M|{ 4167| 1.00M| int bFound = 0, j, type, mask; 4168| 1.00M| if (!at[i].charge && at[i].num_H && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4168:9): [True: 908k, False: 100k] | Branch (4168:26): [True: 6.55k, False: 901k] | Branch (4168:41): [True: 2.15k, False: 4.39k] ------------------ 4169| 2.15k| { 4170| 2.37k| for (j = 0; ArTypMask[2 * j]; j++) ------------------ | Branch (4170:21): [True: 2.15k, False: 227] ------------------ 4171| 2.15k| { 4172| 2.15k| if (( type & ArTypMask[2 * j] ) && ( mask & ArTypMask[2 * j + 1] )) ------------------ | Branch (4172:17): [True: 1.93k, False: 215] | Branch (4172:48): [True: 1.92k, False: 12] ------------------ 4173| 1.92k| { 4174| 1.92k| bFound++; 4175| 1.92k| break; 4176| 1.92k| } 4177| 2.15k| } 4178| 2.15k| } 4179| | 4180| 1.00M| return bFound; 4181| 1.00M|} bHasOtherExchangableH: 4186| 312|{ 4187| 312| int bFound = 0, type, mask; 4188| 312| if (at[i].num_H && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4188:9): [True: 312, False: 0] | Branch (4188:24): [True: 24, False: 288] ------------------ 4189| 24| { 4190| 24| if (( type & ATT_ATOM_N ) && ( mask & ATBIT_NP_H )) ------------------ | | 37| 24|#define ATT_ATOM_N 0x0040 ------------------ if (( type & ATT_ATOM_N ) && ( mask & ATBIT_NP_H )) ------------------ | | 94| 11|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ | Branch (4190:13): [True: 11, False: 13] | Branch (4190:38): [True: 11, False: 0] ------------------ 4191| 11| { 4192| 11| bFound++; 4193| 11| } 4194| 24| } 4195| | 4196| 312| return bFound; 4197| 312|} SimpleAddAcidicProtons: 4222| 10.8k|{ 4223| 10.8k| int i, j, max_j = -1, mask, type, num_added; 4224| 10.8k| int num[AR_SIMPLE_STEPS + 1], num_tot; 4225| | 4226| 32.4k| for (j = 0; AaTypMask[2 * j]; j++) ------------------ | Branch (4226:17): [True: 21.6k, False: 10.8k] ------------------ 4227| 21.6k| { 4228| 21.6k| num[max_j = j] = 0; 4229| 21.6k| } 4230| | 4231| 73.3k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4231:17): [True: 62.5k, False: 10.8k] ------------------ 4232| 62.5k| { 4233| 62.5k| if (at[i].charge == -1 && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4233:13): [True: 16.2k, False: 46.2k] | Branch (4233:35): [True: 8.55k, False: 7.70k] ------------------ 4234| 8.55k| { 4235| 16.6k| for (j = 0; j <= max_j; j++) ------------------ | Branch (4235:25): [True: 12.6k, False: 4.05k] ------------------ 4236| 12.6k| { 4237| 12.6k| if (( type & AaTypMask[2 * j] ) && ( mask && AaTypMask[2 * j + 1] )) ------------------ | Branch (4237:21): [True: 4.50k, False: 8.12k] | Branch (4237:54): [True: 4.50k, False: 0] | Branch (4237:62): [True: 4.50k, False: 0] ------------------ 4238| 4.50k| { 4239| 4.50k| num[j] ++; 4240| 4.50k| break; 4241| 4.50k| } 4242| 12.6k| } 4243| 8.55k| } 4244| 62.5k| } 4245| 25.1k| for (j = 0, num_tot = 0; j <= max_j; j++) ------------------ | Branch (4245:30): [True: 17.9k, False: 7.15k] ------------------ 4246| 17.9k| { 4247| 17.9k| if (( num_tot += num[j] ) >= num2add) ------------------ | Branch (4247:13): [True: 3.66k, False: 14.3k] ------------------ 4248| 3.66k| { 4249| 3.66k| max_j = j; 4250| 3.66k| break; 4251| 3.66k| } 4252| 17.9k| } 4253| 10.8k| if (!num_tot) ------------------ | Branch (4253:9): [True: 6.88k, False: 3.93k] ------------------ 4254| 6.88k| { 4255| 6.88k| return 0; 4256| 6.88k| } 4257| 19.0k| for (i = 0, num_added = 0; i < num_atoms && num_added < num2add; i++) ------------------ | Branch (4257:32): [True: 18.3k, False: 650] | Branch (4257:49): [True: 15.0k, False: 3.28k] ------------------ 4258| 15.0k| { 4259| 15.0k| if (at[i].charge == -1 && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4259:13): [True: 4.85k, False: 10.2k] | Branch (4259:35): [True: 4.39k, False: 468] ------------------ 4260| 4.39k| { 4261| 4.76k| for (j = 0; j <= max_j; j++) ------------------ | Branch (4261:25): [True: 4.57k, False: 193] ------------------ 4262| 4.57k| { 4263| 4.57k| if (num[j] && ( type & AaTypMask[2 * j] ) && ( mask && AaTypMask[2 * j + 1] )) ------------------ | Branch (4263:21): [True: 4.35k, False: 216] | Branch (4263:31): [True: 4.19k, False: 161] | Branch (4263:64): [True: 4.19k, False: 0] | Branch (4263:72): [True: 4.19k, False: 0] ------------------ 4264| 4.19k| { 4265| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 4266| 4.19k| type = GetAtomChargeType(at, i, pAATG->nAtTypeTotals, &mask, 1); /* subtract at[i] */ 4267| 4.19k| num[j] --; 4268| 4.19k| at[i].charge++; 4269| 4.19k| AddOrRemoveExplOrImplH( 1, at, num_atoms, (AT_NUMB) i, pAATG->t_group_info ); 4270| | /*at[i].num_H ++;*/ 4271| 4.19k| num_added++; 4272| 4.19k| type = GetAtomChargeType(at, i, pAATG->nAtTypeTotals, &mask, 0); /* add changed at[i] */ 4273| 4.19k| break; 4274| 4.19k| } 4275| 4.57k| } 4276| 4.39k| } 4277| 15.0k| } 4278| | 4279| | /* 4280| | pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] += num_added; 4281| | pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] -= num_added; 4282| | */ 4283| | 4284| 3.93k| return num_added; 4285| 10.8k|} bHasAcidicMinus: 4290| 1.00M|{ 4291| 1.00M| int bFound = 0, j, type, mask; 4292| 1.00M| if (at[i].charge == -1 && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4292:9): [True: 25.5k, False: 980k] | Branch (4292:31): [True: 2.01k, False: 23.5k] ------------------ 4293| 2.01k| { 4294| 4.87k| for (j = 0; AaTypMask[2 * j]; j++) ------------------ | Branch (4294:21): [True: 3.44k, False: 1.42k] ------------------ 4295| 3.44k| { 4296| 3.44k| if (( type & AaTypMask[2 * j] ) && ( mask & AaTypMask[2 * j + 1] )) ------------------ | Branch (4296:17): [True: 599, False: 2.84k] | Branch (4296:48): [True: 592, False: 7] ------------------ 4297| 592| { 4298| 592| bFound++; 4299| 592| break; 4300| 592| } 4301| 3.44k| } 4302| 2.01k| } 4303| | 4304| 1.00M| return bFound; 4305| 1.00M|} HardRemoveAcidicProtons: 4324| 41.7k|{ 4325| 41.7k| int cg_Plus = 0; 4326| 41.7k| int cg_Minus = 0; 4327| 41.7k| int tg_H_Other = 0; 4328| 41.7k| int tg_H_Acid = 0; 4329| | 4330| 41.7k| int ret = 0, ret2; 4331| 41.7k| int nDelta, nNumMoved2AcidH = 0, nNumNeutralized = 0, nPrevNumCharges; /* djb-rwth: removing redundant variables */ 4332| | 4333| 41.7k| int nPosCharges, nPosCharges2; 4334| 41.7k| int nNegCharges, nNegCharges2; 4335| | /* 4336| | int nNumNP_H, nNumNP_H2; 4337| | int nNumOS_H, nNumOS_H2; 4338| | */ 4339| | 4340| 41.7k| nPosCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4341| 41.7k| nNegCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4342| | /* 4343| | nNumNP_H = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4344| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4345| | nNumOS_H = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4346| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4347| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4348| | */ 4349| | 4350| | /* Prevent free exchange H <-> (-) */ 4351| 41.7k| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 49| 41.7k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 54| 41.7k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4352| 41.7k| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 41.7k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4353| 41.7k| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 55| 41.7k|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4354| | 4355| | /* Create (+) charge group */ 4356| 41.7k| cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_POS, AR_HARD_MSK_POS, 1 ); ------------------ | | 202| 41.7k|#define AR_HARD_TYP_POS ATTYP_N | | ------------------ | | | | 150| 41.7k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 41.7k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ ------------------ cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_POS, AR_HARD_MSK_POS, 1 ); ------------------ | | 201| 41.7k|#define AR_HARD_MSK_POS ATBIT_MSK_NP | | ------------------ | | | | 139| 41.7k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 41.7k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 41.7k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 41.7k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 41.7k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 41.7k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ ------------------ 4357| | 4358| | /* create (-) charge group */ 4359| | /* 4360| | if ( nAtTypeTotals[ATTOT_NUM_CO_Minus] + 4361| | nAtTypeTotals[ATTOT_NUM_CS_Minus] + 4362| | nAtTypeTotals[ATTOT_NUM_ZO_Minus] + 4363| | nAtTypeTotals[ATTOT_NUM_N_Minus] ) 4364| | */ 4365| | 4366| 41.7k| cg_Minus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_NEG, AR_HARD_MSK_NEG, -1 ); ------------------ | | 205| 41.7k|#define AR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 150| 41.7k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 41.7k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 148| 41.7k|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 41.7k|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 41.7k|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 41.7k|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 41.7k|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 41.7k|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 41.7k|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ cg_Minus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_NEG, AR_HARD_MSK_NEG, -1 ); ------------------ | | 204| 41.7k|#define AR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 139| 41.7k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 41.7k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 41.7k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 41.7k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 41.7k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 41.7k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 141| 41.7k|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 41.7k|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 41.7k|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 41.7k|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 41.7k|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 41.7k|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 41.7k|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 41.7k|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 41.7k| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 41.7k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 41.7k|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 41.7k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 41.7k|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 41.7k| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 41.7k|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 41.7k|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 41.7k|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 41.7k|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 41.7k| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 41.7k|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 41.7k|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 41.7k|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ 4367| | 4368| 41.7k| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 49| 41.7k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 54| 41.7k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4369| 41.7k| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 41.7k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4370| 41.7k| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 55| 41.7k|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4371| | 4372| | /* Create tautomeric group for non-acidic or negatively charged acidic O */ 4373| 41.7k| tg_H_Other = CreateTGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_HN, AR_HARD_MSK_HN ); ------------------ | | 211| 41.7k|#define AR_HARD_TYP_HN ((ATTYP_N | ATTYP_OS) /*& ~AR_HARD_TYP_HA*/) | | ------------------ | | | | 150| 41.7k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 41.7k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AR_HARD_TYP_HN ((ATTYP_N | ATTYP_OS) /*& ~AR_HARD_TYP_HA*/) | | ------------------ | | | | 148| 41.7k|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 41.7k|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 41.7k|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 41.7k|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 41.7k|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 41.7k|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 41.7k|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ tg_H_Other = CreateTGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_HN, AR_HARD_MSK_HN ); ------------------ | | 210| 41.7k|#define AR_HARD_MSK_HN ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~AR_HARD_MSK_HA) | | ------------------ | | | | 139| 41.7k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 41.7k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 41.7k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 41.7k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 41.7k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 41.7k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AR_HARD_MSK_HN ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~AR_HARD_MSK_HA) | | ------------------ | | | | 141| 41.7k|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 41.7k|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 41.7k|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 41.7k|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 41.7k|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 41.7k|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 41.7k|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 41.7k|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 41.7k| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 41.7k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 41.7k|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 41.7k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 41.7k|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 41.7k| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 41.7k|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 41.7k|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 41.7k|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 41.7k|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 41.7k| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 41.7k|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 41.7k|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 41.7k|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ | | #define AR_HARD_MSK_HN ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~AR_HARD_MSK_HA) | | ------------------ | | | | 207| 41.7k|#define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | | | ------------------ | | | | | | 105| 41.7k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | #define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | | | ------------------ | | | | | | 107| 41.7k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | ------------------ ------------------ 4374| | 4375| | /* Create tautomeric group for possibly acidic O */ 4376| 41.7k| tg_H_Acid = CreateTGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_HA, AR_HARD_MSK_HA ); ------------------ | | 208| 41.7k|#define AR_HARD_TYP_HA (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 31| 41.7k|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define AR_HARD_TYP_HA (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 35| 41.7k|#define ATT_NO 0x0010 | | ------------------ ------------------ tg_H_Acid = CreateTGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_HA, AR_HARD_MSK_HA ); ------------------ | | 207| 41.7k|#define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 105| 41.7k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 107| 41.7k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ 4377| 41.7k| if (tg_H_Other >= num_atoms && tg_H_Acid >= num_atoms) ------------------ | Branch (4377:9): [True: 2.41k, False: 39.3k] | Branch (4377:36): [True: 142, False: 2.27k] ------------------ 4378| 142| { 4379| | /* Find alt path to remove one proton */ 4380| 142| do 4381| 147| { 4382| | /* Remove a proton */ 4383| 147| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4384| | /* djb-rwth: addressing coverity ID #499503 -- tg_H_Other negative values handled properly */ 4385| 147| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4386| 147| at, num_atoms, 4387| 147| tg_H_Other /*nVertDoubleBond*/, 4388| 147| tg_H_Acid /*nVertSingleBond*/, 4389| 147| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 318| 147|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4390| 147| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 147|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 147|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 147|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 147|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 147, False: 0] | | | Branch (67:44): [True: 0, False: 147] | | ------------------ ------------------ 4391| 0| { 4392| 0| return ret; 4393| 0| } 4394| 147| if (ret & 1) ------------------ | Branch (4394:17): [True: 11, False: 136] ------------------ 4395| 11| { 4396| 11| nDelta = ( ret & ~3 ) >> 2; 4397| | /* djb-rwth: removing redundant code */ 4398| 11| if (nDelta) ------------------ | Branch (4398:21): [True: 0, False: 11] ------------------ 4399| 0| { 4400| | /* Radical pair has disappeared */ 4401| 0| ; /* goto quick_exit;*/ 4402| 0| } 4403| 11| nNumMoved2AcidH++; 4404| 11| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + 1) ------------------ | Branch (4404:21): [True: 0, False: 11] ------------------ 4405| 0| { 4406| 0| nNumNeutralized += ( nPrevNumCharges - ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - 1 ) ) / 2; 4407| 0| } 4408| 11| } 4409| 147| } while (( ret & 1 ) && nNumMoved2AcidH < num2remove); ------------------ | Branch (4409:18): [True: 11, False: 136] | Branch (4409:33): [True: 5, False: 6] ------------------ 4410| | 4411| | /* Neutralize: remove ion pairs like >N(+)=-O(-) => >N-=O */ 4412| 142| if (( nNumMoved2AcidH /*|| bCancelChargesAlways*/ ) && cg_Minus >= num_atoms && cg_Plus >= num_atoms && ------------------ | Branch (4412:13): [True: 11, False: 131] | Branch (4412:64): [True: 11, False: 0] | Branch (4412:89): [True: 10, False: 1] ------------------ 4413| 10| pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] > abs( pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] )) ------------------ | Branch (4413:14): [True: 1, False: 9] ------------------ 4414| 1| { 4415| 1| do 4416| 1| { 4417| 1| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4418| 1| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4419| 1| at, num_atoms, 4420| 1| cg_Minus /*nVertDoubleBond*/, 4421| 1| cg_Plus /*nVertSingleBond*/, 4422| 1| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 318| 1|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4423| 1| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 1|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1, False: 0] | | | Branch (67:44): [True: 0, False: 1] | | ------------------ ------------------ 4424| 0| { 4425| 0| return ret; 4426| 0| } 4427| 1| if (ret & 1) ------------------ | Branch (4427:21): [True: 0, False: 1] ------------------ 4428| 0| { 4429| 0| nDelta = ( ret & ~3 ) >> 2; 4430| | /* djb-rwth: removing redundant code */ 4431| 0| if (nDelta) ------------------ | Branch (4431:25): [True: 0, False: 0] ------------------ 4432| 0| { 4433| | /* Radical pair has disappeared */ 4434| 0| ; /* goto quick_exit;*/ 4435| 0| } 4436| 0| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]) ------------------ | Branch (4436:25): [True: 0, False: 0] ------------------ 4437| 0| { 4438| 0| nNumNeutralized += ( nPrevNumCharges - pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] ) / 2; 4439| 0| } 4440| 0| } 4441| 1| } while (ret & 1); ------------------ | Branch (4441:22): [True: 0, False: 1] ------------------ 4442| 1| } 4443| 142| } 4444| | 4445| 41.7k| ret = 0; 4446| 41.7k| if (tg_H_Acid >= num_atoms) ------------------ | Branch (4446:9): [True: 193, False: 41.5k] ------------------ 4447| 193| { 4448| 193| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, tg_H_Acid, pBNS ); 4449| 193| if (!ret && ret2) ------------------ | Branch (4449:13): [True: 193, False: 0] | Branch (4449:21): [True: 0, False: 193] ------------------ 4450| 0| { 4451| 0| ret = ret2; 4452| 0| } 4453| 193| } 4454| 41.7k| if (tg_H_Other >= num_atoms) ------------------ | Branch (4454:9): [True: 2.41k, False: 39.3k] ------------------ 4455| 2.41k| { 4456| 2.41k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, tg_H_Other, pBNS ); 4457| 2.41k| if (!ret && ret2) ------------------ | Branch (4457:13): [True: 2.41k, False: 0] | Branch (4457:21): [True: 0, False: 2.41k] ------------------ 4458| 0| { 4459| 0| ret = ret2; 4460| 0| } 4461| 2.41k| } 4462| 41.7k| if (cg_Minus >= num_atoms) ------------------ | Branch (4462:9): [True: 2.46k, False: 39.3k] ------------------ 4463| 2.46k| { 4464| 2.46k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Minus, pBNS ); 4465| 2.46k| if (!ret && ret2) ------------------ | Branch (4465:13): [True: 2.46k, False: 0] | Branch (4465:21): [True: 0, False: 2.46k] ------------------ 4466| 0| { 4467| 0| ret = ret2; 4468| 0| } 4469| 2.46k| } 4470| 41.7k| if (cg_Plus >= num_atoms) ------------------ | Branch (4470:9): [True: 2.00k, False: 39.7k] ------------------ 4471| 2.00k| { 4472| 2.00k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Plus, pBNS ); 4473| 2.00k| if (!ret && ret2) ------------------ | Branch (4473:13): [True: 2.00k, False: 0] | Branch (4473:21): [True: 0, False: 2.00k] ------------------ 4474| 0| { 4475| 0| ret = ret2; 4476| 0| } 4477| 2.00k| } 4478| | 4479| 41.7k| pBNS->type_CN = 0; 4480| 41.7k| pBNS->type_T = 0; 4481| 41.7k| pBNS->type_TACN = 0; 4482| | 4483| 41.7k| if (ret) ------------------ | Branch (4483:9): [True: 0, False: 41.7k] ------------------ 4484| 0| { 4485| 0| return ret; 4486| 0| } 4487| | 4488| 41.7k| if (pAATG->nAtTypeTotals[ATTOT_NUM_CO_Minus] + pAATG->nAtTypeTotals[ATTOT_NUM_ZO_Minus] && ------------------ | Branch (4488:9): [True: 7, False: 41.7k] ------------------ 4489| 7| pAATG->nAtTypeTotals[ATTOT_NUM_N_Minus]) ------------------ | Branch (4489:10): [True: 0, False: 7] ------------------ 4490| 0| { 4491| 0| } 4492| | 4493| 41.7k| nPosCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4494| 41.7k| nNegCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4495| | /* 4496| | nNumNP_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4497| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4498| | nNumOS_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4499| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4500| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4501| | */ 4502| 41.7k| if (( nPosCharges - nNegCharges ) - ( nPosCharges2 - nNegCharges2 ) != 0) ------------------ | Branch (4502:9): [True: 0, False: 41.7k] ------------------ 4503| 0| { 4504| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4505| 0| } 4506| | 4507| 41.7k| if (nNumCanceledCharges) ------------------ | Branch (4507:9): [True: 41.7k, False: 0] ------------------ 4508| 41.7k| { 4509| |#if ( FIX_CANCEL_CHARGE_COUNT_BUG == 1 ) 4510| | *nNumCanceledCharges += 2 * nNumNeutralized; 4511| |#else 4512| 41.7k| *nNumCanceledCharges = 2 * nNumNeutralized; 4513| 41.7k|#endif 4514| 41.7k| } 4515| | 4516| 41.7k| return nNumMoved2AcidH; 4517| 41.7k|} HardAddAcidicProtons: 4529| 7.15k|{ 4530| 7.15k| int cg_Plus = 0; 4531| 7.15k| int cg_Minus_CO = 0; 4532| 7.15k| int cg_Minus_Other = 0; 4533| 7.15k| int tg_H = 0; 4534| | 4535| 7.15k| int ret = 0, ret2; 4536| 7.15k| int nDelta, nNumChanges = 0, nNumMoved2AcidMinus = 0, nNumNeutralized = 0, nPrevNumCharges; /* djb-rwth: removing redundant variables */ 4537| | 4538| 7.15k| int nPosCharges, nPosCharges2; 4539| 7.15k| int nNegCharges, nNegCharges2; 4540| | /* 4541| | int nNumNP_H, nNumNP_H2; 4542| | int nNumOS_H, nNumOS_H2; 4543| | */ 4544| 7.15k| nPosCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4545| 7.15k| nNegCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4546| | /* 4547| | nNumNP_H = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4548| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4549| | nNumOS_H = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4550| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4551| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4552| | */ 4553| | 4554| | /* Prevent free exchange H <-> (-) */ 4555| 7.15k| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 49| 7.15k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 54| 7.15k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4556| 7.15k| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 7.15k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4557| 7.15k| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 55| 7.15k|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4558| | 4559| | /* Create (+) charge group */ 4560| 7.15k| cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_POS, AA_HARD_MSK_POS, 1 ); ------------------ | | 216| 7.15k|#define AA_HARD_TYP_POS ATTYP_N | | ------------------ | | | | 150| 7.15k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 7.15k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ ------------------ cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_POS, AA_HARD_MSK_POS, 1 ); ------------------ | | 215| 7.15k|#define AA_HARD_MSK_POS ATBIT_MSK_NP | | ------------------ | | | | 139| 7.15k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 7.15k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 7.15k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 7.15k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 7.15k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 7.15k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ ------------------ 4561| | 4562| | /* Create (-) charge group */ 4563| | /* 4564| | if ( nAtTypeTotals[ATTOT_NUM_CO_Minus] + 4565| | nAtTypeTotals[ATTOT_NUM_CS_Minus] + 4566| | nAtTypeTotals[ATTOT_NUM_ZO_Minus] + 4567| | nAtTypeTotals[ATTOT_NUM_N_Minus] ) 4568| | */ 4569| 7.15k| cg_Minus_CO = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_CO, AA_HARD_MSK_CO, -1 ); ------------------ | | 222| 7.15k|#define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 31| 7.15k|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 35| 7.15k|#define ATT_NO 0x0010 | | ------------------ ------------------ cg_Minus_CO = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_CO, AA_HARD_MSK_CO, -1 ); ------------------ | | 221| 7.15k|#define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 105| 7.15k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 107| 7.15k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ 4570| | 4571| 7.15k| cg_Minus_Other = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_NEG, AA_HARD_MSK_NEG, -1 ); ------------------ | | 219| 7.15k|#define AA_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 150| 7.15k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 7.15k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AA_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 148| 7.15k|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 7.15k|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 7.15k|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 7.15k|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 7.15k|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 7.15k|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 7.15k|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ cg_Minus_Other = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_NEG, AA_HARD_MSK_NEG, -1 ); ------------------ | | 218| 7.15k|#define AA_HARD_MSK_NEG ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~(ATBIT_CO | ATBIT_NO )) | | ------------------ | | | | 139| 7.15k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 7.15k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 7.15k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 7.15k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 7.15k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 7.15k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AA_HARD_MSK_NEG ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~(ATBIT_CO | ATBIT_NO )) | | ------------------ | | | | 141| 7.15k|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 7.15k|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 7.15k|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 7.15k|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 7.15k|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 7.15k|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 7.15k|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 7.15k|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 7.15k| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 7.15k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 7.15k|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 7.15k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 7.15k|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 7.15k| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 7.15k|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 7.15k|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 7.15k|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 7.15k|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 7.15k| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 7.15k|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 7.15k|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 7.15k|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ | | #define AA_HARD_MSK_NEG ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~(ATBIT_CO | ATBIT_NO )) | | ------------------ | | | | 105| 7.15k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AA_HARD_MSK_NEG ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~(ATBIT_CO | ATBIT_NO )) | | ------------------ | | | | 107| 7.15k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ 4572| | 4573| 7.15k| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 49| 7.15k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 54| 7.15k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4574| 7.15k| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 7.15k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4575| 7.15k| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 55| 7.15k|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4576| | 4577| | /* Create tautomeric group for all H */ 4578| 7.15k| tg_H = CreateTGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_H, AA_HARD_MSK_H ); ------------------ | | 225| 7.15k|#define AA_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 150| 7.15k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 7.15k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AA_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 148| 7.15k|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 7.15k|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 7.15k|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 7.15k|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 7.15k|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 7.15k|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 7.15k|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ tg_H = CreateTGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_H, AA_HARD_MSK_H ); ------------------ | | 224| 7.15k|#define AA_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 139| 7.15k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 7.15k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 7.15k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 7.15k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 7.15k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 7.15k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AA_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 141| 7.15k|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 7.15k|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 7.15k|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 7.15k|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 7.15k|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 7.15k|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 7.15k|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 7.15k|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 7.15k| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 7.15k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 7.15k|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 7.15k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 7.15k|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 7.15k| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 7.15k|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 7.15k|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 7.15k|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 7.15k|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 7.15k| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 7.15k|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 7.15k|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 7.15k|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ 4579| | 4580| 7.15k| if (cg_Minus_Other >= num_atoms && cg_Minus_CO >= num_atoms) ------------------ | Branch (4580:9): [True: 3.59k, False: 3.56k] | Branch (4580:40): [True: 305, False: 3.28k] ------------------ 4581| 305| { 4582| | /* Find alt path to remove one proton */ 4583| 305| do 4584| 328| { 4585| | /* Add a proton */ 4586| 328| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4587| | /* djb-rwth: addressing coverity ID #499474 -- cg_Minus_CO negative values handled properly */ 4588| 328| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4589| 328| at, num_atoms, 4590| 328| cg_Minus_Other /*nVertDoubleBond*/, 4591| 328| cg_Minus_CO /*nVertSingleBond*/, 4592| 328| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 318| 328|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4593| 328| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 328|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 328|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 328|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 328|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 328, False: 0] | | | Branch (67:44): [True: 2, False: 326] | | ------------------ ------------------ 4594| 2| { 4595| 2| return ret; 4596| 2| } 4597| 326| if (ret & 1) ------------------ | Branch (4597:17): [True: 70, False: 256] ------------------ 4598| 70| { 4599| 70| nDelta = ( ret & ~3 ) >> 2; 4600| 70| nNumChanges += (0 != (ret & 2)); /* djb-rwth: ignoring LLVM warning: variable used */ 4601| 70| if (nDelta) ------------------ | Branch (4601:21): [True: 0, False: 70] ------------------ 4602| 0| { 4603| | /* Radical pair has disappeared */ 4604| 0| ; /* goto quick_exit;*/ 4605| 0| } 4606| 70| nNumMoved2AcidMinus++; 4607| 70| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + 1) ------------------ | Branch (4607:21): [True: 0, False: 70] ------------------ 4608| 0| { 4609| 0| nNumNeutralized += ( nPrevNumCharges - ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - 1 ) ) / 2; 4610| 0| } 4611| 70| } 4612| 326| } while (( ret & 1 ) && nNumMoved2AcidMinus < num2add); ------------------ | Branch (4612:18): [True: 70, False: 256] | Branch (4612:33): [True: 23, False: 47] ------------------ 4613| | 4614| | /* Neutralize: remove ion pairs like >N(+)=-O(-) => >N-=O */ 4615| 303| if (( nNumMoved2AcidMinus /*|| bCancelChargesAlways*/ ) && ------------------ | Branch (4615:13): [True: 70, False: 233] ------------------ 4616| 70| cg_Minus_Other >= num_atoms && cg_Plus >= num_atoms && ------------------ | Branch (4616:14): [True: 70, False: 0] | Branch (4616:45): [True: 51, False: 19] ------------------ 4617| 51| pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] > abs( pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] )) ------------------ | Branch (4617:14): [True: 1, False: 50] ------------------ 4618| 1| { 4619| 1| do 4620| 1| { 4621| 1| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4622| 1| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4623| 1| at, num_atoms, 4624| 1| cg_Minus_Other /*nVertDoubleBond*/, 4625| 1| cg_Plus /*nVertSingleBond*/, 4626| 1| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 318| 1|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4627| 1| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 1|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1, False: 0] | | | Branch (67:44): [True: 0, False: 1] | | ------------------ ------------------ 4628| 0| { 4629| 0| return ret; 4630| 0| } 4631| 1| if (ret & 1) ------------------ | Branch (4631:21): [True: 0, False: 1] ------------------ 4632| 0| { 4633| 0| nDelta = ( ret & ~3 ) >> 2; 4634| 0| nNumChanges += (0 != (ret & 2)); /* djb-rwth: ignoring LLVM warning: variable used */ 4635| 0| if (nDelta) ------------------ | Branch (4635:25): [True: 0, False: 0] ------------------ 4636| 0| { 4637| | /* Radical pair has disappeared */ 4638| 0| ; /* goto quick_exit;*/ 4639| 0| } 4640| 0| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]) ------------------ | Branch (4640:25): [True: 0, False: 0] ------------------ 4641| 0| { 4642| 0| nNumNeutralized += ( nPrevNumCharges - pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] ) / 2; 4643| 0| } 4644| 0| } 4645| 1| } while (ret & 1); ------------------ | Branch (4645:22): [True: 0, False: 1] ------------------ 4646| 1| } 4647| 303| } 4648| | 4649| 7.15k| ret = 0; 4650| 7.15k| if (tg_H >= num_atoms) ------------------ | Branch (4650:9): [True: 3.63k, False: 3.51k] ------------------ 4651| 3.63k| { 4652| 3.63k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, tg_H, pBNS ); 4653| 3.63k| if (!ret && ret2) ------------------ | Branch (4653:13): [True: 3.63k, False: 0] | Branch (4653:21): [True: 0, False: 3.63k] ------------------ 4654| 0| { 4655| 0| ret = ret2; 4656| 0| } 4657| 3.63k| } 4658| 7.15k| if (cg_Minus_Other >= num_atoms) ------------------ | Branch (4658:9): [True: 3.58k, False: 3.56k] ------------------ 4659| 3.58k| { 4660| 3.58k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Minus_Other, pBNS ); 4661| 3.58k| if (!ret && ret2) ------------------ | Branch (4661:13): [True: 3.58k, False: 0] | Branch (4661:21): [True: 0, False: 3.58k] ------------------ 4662| 0| { 4663| 0| ret = ret2; 4664| 0| } 4665| 3.58k| } 4666| 7.15k| if (cg_Minus_CO >= num_atoms) ------------------ | Branch (4666:9): [True: 353, False: 6.80k] ------------------ 4667| 353| { 4668| 353| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Minus_CO, pBNS ); 4669| 353| if (!ret && ret2) ------------------ | Branch (4669:13): [True: 353, False: 0] | Branch (4669:21): [True: 0, False: 353] ------------------ 4670| 0| { 4671| 0| ret = ret2; 4672| 0| } 4673| 353| } 4674| 7.15k| if (cg_Plus >= num_atoms) ------------------ | Branch (4674:9): [True: 2.73k, False: 4.41k] ------------------ 4675| 2.73k| { 4676| 2.73k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Plus, pBNS ); 4677| 2.73k| if (!ret && ret2) ------------------ | Branch (4677:13): [True: 2.73k, False: 0] | Branch (4677:21): [True: 0, False: 2.73k] ------------------ 4678| 0| { 4679| 0| ret = ret2; 4680| 0| } 4681| 2.73k| } 4682| | 4683| 7.15k| pBNS->type_CN = 0; 4684| 7.15k| pBNS->type_T = 0; 4685| 7.15k| pBNS->type_TACN = 0; 4686| | 4687| 7.15k| if (ret) ------------------ | Branch (4687:9): [True: 0, False: 7.15k] ------------------ 4688| 0| { 4689| 0| return ret; 4690| 0| } 4691| | 4692| 7.15k| if (pAATG->nAtTypeTotals[ATTOT_NUM_CO_Minus] + pAATG->nAtTypeTotals[ATTOT_NUM_ZO_Minus] && ------------------ | Branch (4692:9): [True: 757, False: 6.39k] ------------------ 4693| 757| pAATG->nAtTypeTotals[ATTOT_NUM_N_Minus]) ------------------ | Branch (4693:10): [True: 262, False: 495] ------------------ 4694| 262| { 4695| 262| } 4696| | 4697| 7.15k| nPosCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4698| 7.15k| nNegCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4699| | /* 4700| | nNumNP_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4701| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4702| | nNumOS_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4703| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4704| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4705| | */ 4706| | 4707| 7.15k| if (( nPosCharges - nNegCharges ) - ( nPosCharges2 - nNegCharges2 ) != 0) ------------------ | Branch (4707:9): [True: 1, False: 7.15k] ------------------ 4708| 1| { 4709| 1| return BNS_PROGRAM_ERR; ------------------ | | 50| 1|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 1|#define BNS_ERR -9999 | | ------------------ ------------------ 4710| 1| } 4711| | 4712| 7.15k| if (nNumCanceledCharges) ------------------ | Branch (4712:9): [True: 7.15k, False: 0] ------------------ 4713| 7.15k| { 4714| |#if ( FIX_CANCEL_CHARGE_COUNT_BUG == 1 ) 4715| | *nNumCanceledCharges += 2 * nNumNeutralized; 4716| |#else 4717| 7.15k| *nNumCanceledCharges = 2 * nNumNeutralized; 4718| 7.15k|#endif 4719| 7.15k| } 4720| | 4721| 7.15k| return nNumMoved2AcidMinus; 4722| 7.15k|} HardRemoveHplusNP: 4743| 2.88k|{ 4744| | 4745| 2.88k| int cg_Plus = 0; 4746| 2.88k| int cg_Minus = 0; 4747| 2.88k| int tg_H = 0; 4748| |#if ( MOVE_PPLUS_TO_REMOVE_PROTONS == 1 ) 4749| | int cg_PlusP = 0; 4750| |#endif 4751| 2.88k|#if ( FIX_REM_PROTON_COUNT_BUG == 1 ) 4752| 2.88k| int nPrevRemovedProtons, nCurrRemovedProtons; 4753| 2.88k|#endif 4754| 2.88k| int ret = 0, ret2; 4755| 2.88k| int nDelta, nNumChanges = 0, nNumRemovedProtons = 0, nNumNeutralized = 0, nPrevNumCharges; /* djb-rwth: ignoring LLVM warning: variable used */ 4756| | 4757| 2.88k| int nPosCharges, nPosCharges2; 4758| 2.88k| int nNegCharges, nNegCharges2; 4759| | /* 4760| | int nNumNP_H, nNumNP_H2; 4761| | int nNumOS_H, nNumOS_H2; 4762| | */ 4763| | 4764| 2.88k| nPosCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4765| 2.88k| nNegCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4766| | /* 4767| | nNumNP_H = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4768| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4769| | nNumOS_H = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4770| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4771| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4772| | */ 4773| | 4774| | /* Prevent free exchange H <-> (-) */ 4775| 2.88k| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 49| 2.88k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 54| 2.88k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4776| 2.88k| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 2.88k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4777| 2.88k| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 55| 2.88k|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4778| | 4779| | /* Create (+) charge group */ 4780| 2.88k| cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, PR_HARD_TYP_POS, PR_HARD_MSK_POS, 1 ); ------------------ | | 190| 2.88k|#define PR_HARD_TYP_POS ATTYP_N | | ------------------ | | | | 150| 2.88k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 2.88k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ ------------------ cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, PR_HARD_TYP_POS, PR_HARD_MSK_POS, 1 ); ------------------ | | 189| 2.88k|#define PR_HARD_MSK_POS ATBIT_MSK_NP | | ------------------ | | | | 139| 2.88k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 2.88k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 2.88k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 2.88k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 2.88k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 2.88k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ ------------------ 4781| | 4782| | /* Create (-) charge group */ 4783| | /* 4784| | if ( nAtTypeTotals[ATTOT_NUM_CO_Minus] + 4785| | nAtTypeTotals[ATTOT_NUM_CS_Minus] + 4786| | nAtTypeTotals[ATTOT_NUM_ZO_Minus] + 4787| | nAtTypeTotals[ATTOT_NUM_N_Minus] ) 4788| | */ 4789| |#if ( MOVE_PPLUS_TO_REMOVE_PROTONS == 1 ) 4790| | cg_PlusP = CreateCGroupInBnStruct( at, num_atoms, pBNS, PR_HARD_TYP_POSP, PR_HARD_MSK_POS, 1 ); 4791| |#endif 4792| 2.88k| cg_Minus = CreateCGroupInBnStruct( at, num_atoms, pBNS, PR_HARD_TYP_NEG, PR_HARD_MSK_NEG, -1 ); ------------------ | | 194| 2.88k|#define PR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 150| 2.88k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 2.88k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define PR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 148| 2.88k|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 2.88k|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 2.88k|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 2.88k|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 2.88k|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 2.88k|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 2.88k|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ cg_Minus = CreateCGroupInBnStruct( at, num_atoms, pBNS, PR_HARD_TYP_NEG, PR_HARD_MSK_NEG, -1 ); ------------------ | | 193| 2.88k|#define PR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 139| 2.88k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 2.88k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 2.88k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 2.88k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 2.88k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 2.88k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define PR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 141| 2.88k|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 2.88k|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 2.88k|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 2.88k|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 2.88k|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 2.88k|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 2.88k|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 2.88k|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 2.88k| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 2.88k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 2.88k|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 2.88k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 2.88k|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 2.88k| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 2.88k|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 2.88k|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 2.88k|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 2.88k|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 2.88k| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 2.88k|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 2.88k|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 2.88k|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ 4793| | 4794| | /* Create single tautomeric group */ 4795| 2.88k| tg_H = CreateTGroupInBnStruct( at, num_atoms, pBNS, PR_HARD_TYP_H, PR_HARD_MSK_H ); ------------------ | | 197| 2.88k|#define PR_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 150| 2.88k|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 37| 2.88k|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define PR_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 148| 2.88k|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 31| 2.88k|#define ATT_ACIDIC_CO 0x0001 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 32| 2.88k|#define ATT_ACIDIC_S 0x0002 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 33| 2.88k|#define ATT_OO 0x0004 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 34| 2.88k|#define ATT_ZOO 0x0008 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 35| 2.88k|#define ATT_NO 0x0010 | | | | ------------------ | | | | #define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 40| 2.88k|#define ATT_OTHER_ZO 0x0200 /**< -Z=O or =Z=O */ | | | | ------------------ | | ------------------ ------------------ tg_H = CreateTGroupInBnStruct( at, num_atoms, pBNS, PR_HARD_TYP_H, PR_HARD_MSK_H ); ------------------ | | 196| 2.88k|#define PR_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 139| 2.88k|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 92| 2.88k|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 93| 2.88k|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 94| 2.88k|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 95| 2.88k|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) | | | | ------------------ | | | | #define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 96| 2.88k|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define PR_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 141| 2.88k|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 98| 2.88k|#define ATBIT_COH (1 << ATTOT_NUM_COH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 99| 2.88k|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 100| 2.88k|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 101| 2.88k|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 102| 2.88k|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 103| 2.88k|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) | | | | ------------------ | | | | #define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 104| 2.88k|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 142| 2.88k| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 105| 2.88k|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 106| 2.88k|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 107| 2.88k|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 108| 2.88k|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 143| 2.88k| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 109| 2.88k|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 110| 2.88k|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 111| 2.88k|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 112| 2.88k|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 144| 2.88k| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 113| 2.88k|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 114| 2.88k|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 115| 2.88k|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ 4796| | 4797| 2.88k| if (tg_H >= num_atoms && cg_Plus >= num_atoms) ------------------ | Branch (4797:9): [True: 2.52k, False: 358] | Branch (4797:30): [True: 2.45k, False: 71] ------------------ 4798| 2.45k| { 4799| | 4800| |#if ( FIX_N_MINUS_NORN_BUG == 1 ) 4801| | /* neutralize: remove ion pairs like >N(+)=-O(-) => >N-=O; >N(+)=-NH(-) => >N-=NH */ 4802| | if (( nNumRemovedProtons || bCancelChargesAlways ) && cg_Minus >= num_atoms && cg_Plus >= num_atoms && 4803| | pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] > abs( pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] )) 4804| | { 4805| | do 4806| | { 4807| | nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4808| |#if ( FIX_REM_PROTON_COUNT_BUG == 1 ) 4809| | nPrevRemovedProtons = pAATG->t_group_info->tni.nNumRemovedProtons; 4810| |#endif 4811| | ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, at, num_atoms, 4812| | cg_Minus /*nVertDoubleBond*/, cg_Plus /*nVertSingleBond*/, ALT_PATH_MODE_REM_PROTON ); 4813| | if (IS_BNS_ERROR( ret )) 4814| | { 4815| | return ret; 4816| | } 4817| |#if ( FIX_REM_PROTON_COUNT_BUG == 1 ) 4818| | nCurrRemovedProtons = pAATG->t_group_info->tni.nNumRemovedProtons; 4819| | if (nCurrRemovedProtons != nPrevRemovedProtons) 4820| | { 4821| | return BNS_RADICAL_ERR; 4822| | } 4823| |#endif 4824| | if (ret & 1) 4825| | { 4826| | nDelta = ( ret & ~3 ) >> 2; 4827| | nNumChanges += ( 0 != ( ret & 2 ) ); 4828| | if (nDelta) 4829| | { 4830| | /* radical pair has disappeared */ 4831| | ; /* goto quick_exit;*/ 4832| | } 4833| | if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]) 4834| | { 4835| | nNumNeutralized += ( nPrevNumCharges - pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] ) / 2; 4836| | } 4837| | } 4838| | } while (ret & 1); 4839| | } 4840| |#endif 4841| | 4842| | /* Find alt path to remove one proton */ 4843| 2.45k| do 4844| 2.54k| { 4845| | /* Remove a proton */ 4846| 2.54k| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4847| 2.54k|#if ( FIX_REM_PROTON_COUNT_BUG == 1 ) 4848| 2.54k| nPrevRemovedProtons = pAATG->t_group_info->tni.nNumRemovedProtons; 4849| 2.54k|#endif 4850| | /* djb-rwth: addressing coverity ID #499572 -- tg_H negative values handled properly */ 4851| 2.54k| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, at, num_atoms, 4852| 2.54k| tg_H /*nVertDoubleBond*/, 4853| 2.54k| cg_Plus /*nVertSingleBond*/, 4854| 2.54k| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 318| 2.54k|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4855| 2.54k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 2.54k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 2.54k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 2.54k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 2.54k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 2.54k, False: 0] | | | Branch (67:44): [True: 0, False: 2.54k] | | ------------------ ------------------ 4856| 0| { 4857| 0| return ret; 4858| 0| } 4859| 2.54k|#if ( FIX_REM_PROTON_COUNT_BUG == 1 ) 4860| 2.54k| nCurrRemovedProtons = pAATG->t_group_info->tni.nNumRemovedProtons; 4861| 2.54k| if (nCurrRemovedProtons != nPrevRemovedProtons + ( ret & 1 )) ------------------ | Branch (4861:17): [True: 0, False: 2.54k] ------------------ 4862| 0| { 4863| 0| return BNS_RADICAL_ERR; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4864| 0| } 4865| 2.54k|#endif 4866| 2.54k| if (ret & 1) ------------------ | Branch (4866:17): [True: 95, False: 2.45k] ------------------ 4867| 95| { 4868| 95| nDelta = ( ret & ~3 ) >> 2; 4869| 95| nNumChanges += (0 != (ret & 2)); /* djb-rwth: ignoring LLVM warning: variable used */ 4870| 95| if (nDelta) ------------------ | Branch (4870:21): [True: 0, False: 95] ------------------ 4871| 0| { 4872| | /* radical pair has disappeared */ 4873| 0| ; /* goto quick_exit;*/ 4874| 0| } 4875| 95| nNumRemovedProtons++; 4876| 95| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + 1) ------------------ | Branch (4876:21): [True: 0, False: 95] ------------------ 4877| 0| { 4878| 0| nNumNeutralized += ( nPrevNumCharges - ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - 1 ) ) / 2; 4879| 0| } 4880| 95| } 4881| 2.54k| } while (ret & 1); ------------------ | Branch (4881:18): [True: 95, False: 2.45k] ------------------ 4882| | 4883| | /* Neutralize: remove ion pairs like >N(+)=-O(-) => >N-=O */ 4884| 2.45k| if (( nNumRemovedProtons || bCancelChargesAlways ) && cg_Minus >= num_atoms && cg_Plus >= num_atoms && ------------------ | Branch (4884:15): [True: 95, False: 2.35k] | Branch (4884:37): [True: 2.35k, False: 0] | Branch (4884:63): [True: 2.45k, False: 0] | Branch (4884:88): [True: 2.45k, False: 0] ------------------ 4885| 2.45k| pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] > abs( pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] )) ------------------ | Branch (4885:14): [True: 1.33k, False: 1.11k] ------------------ 4886| 1.33k| { 4887| 1.33k| do 4888| 1.35k| { 4889| 1.35k| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4890| 1.35k|#if ( FIX_REM_PROTON_COUNT_BUG == 1 ) 4891| 1.35k| nPrevRemovedProtons = pAATG->t_group_info->tni.nNumRemovedProtons; 4892| 1.35k|#endif 4893| 1.35k| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, at, num_atoms, 4894| 1.35k| cg_Minus /*nVertDoubleBond*/, 4895| 1.35k| cg_Plus /*nVertSingleBond*/, 4896| 1.35k| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 318| 1.35k|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4897| 1.35k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 1.35k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.35k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.35k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.35k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.35k, False: 0] | | | Branch (67:44): [True: 0, False: 1.35k] | | ------------------ ------------------ 4898| 0| { 4899| 0| return ret; 4900| 0| } 4901| 1.35k|#if ( FIX_REM_PROTON_COUNT_BUG == 1 ) 4902| 1.35k| nCurrRemovedProtons = pAATG->t_group_info->tni.nNumRemovedProtons; 4903| 1.35k| if (nCurrRemovedProtons != nPrevRemovedProtons) ------------------ | Branch (4903:21): [True: 0, False: 1.35k] ------------------ 4904| 0| { 4905| 0| return BNS_RADICAL_ERR; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4906| 0| } 4907| 1.35k|#endif 4908| 1.35k| if (ret & 1) ------------------ | Branch (4908:21): [True: 21, False: 1.33k] ------------------ 4909| 21| { 4910| 21| nDelta = ( ret & ~3 ) >> 2; 4911| 21| nNumChanges += (0 != (ret & 2)); /* djb-rwth: ignoring LLVM warning: variable used */ 4912| 21| if (nDelta) ------------------ | Branch (4912:25): [True: 0, False: 21] ------------------ 4913| 0| { 4914| | /* Radical pair has disappeared */ 4915| 0| ; /* goto quick_exit;*/ 4916| 0| } 4917| 21| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]) ------------------ | Branch (4917:25): [True: 21, False: 0] ------------------ 4918| 21| { 4919| 21| nNumNeutralized += ( nPrevNumCharges - pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] ) / 2; 4920| 21| } 4921| 21| } 4922| 1.35k| } while (ret & 1); ------------------ | Branch (4922:22): [True: 21, False: 1.33k] ------------------ 4923| 1.33k| } 4924| 2.45k| } 4925| | 4926| 2.88k| ret = 0; 4927| 2.88k| if (tg_H >= num_atoms) ------------------ | Branch (4927:9): [True: 2.52k, False: 358] ------------------ 4928| 2.52k| { 4929| 2.52k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, tg_H, pBNS ); 4930| 2.52k| if (!ret && ret2) ------------------ | Branch (4930:13): [True: 2.52k, False: 0] | Branch (4930:21): [True: 0, False: 2.52k] ------------------ 4931| 0| { 4932| 0| ret = ret2; 4933| 0| } 4934| 2.52k| } 4935| 2.88k| if (cg_Minus >= num_atoms) ------------------ | Branch (4935:9): [True: 2.52k, False: 358] ------------------ 4936| 2.52k| { 4937| 2.52k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Minus, pBNS ); 4938| 2.52k| if (!ret && ret2) ------------------ | Branch (4938:13): [True: 2.52k, False: 0] | Branch (4938:21): [True: 0, False: 2.52k] ------------------ 4939| 0| { 4940| 0| ret = ret2; 4941| 0| } 4942| 2.52k| } 4943| |#if ( MOVE_PPLUS_TO_REMOVE_PROTONS == 1 ) 4944| | if (cg_PlusP >= num_atoms) 4945| | { 4946| | ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_PlusP, pBNS ); 4947| | if (!ret && ret2) 4948| | { 4949| | ret = ret2; 4950| | } 4951| | } 4952| |#endif 4953| 2.88k| if (cg_Plus >= num_atoms) ------------------ | Branch (4953:9): [True: 2.45k, False: 429] ------------------ 4954| 2.45k| { 4955| 2.45k| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Plus, pBNS ); 4956| 2.45k| if (!ret && ret2) ------------------ | Branch (4956:13): [True: 2.45k, False: 0] | Branch (4956:21): [True: 0, False: 2.45k] ------------------ 4957| 0| { 4958| 0| ret = ret2; 4959| 0| } 4960| 2.45k| } 4961| | 4962| 2.88k| pBNS->type_CN = 0; 4963| 2.88k| pBNS->type_T = 0; 4964| 2.88k| pBNS->type_TACN = 0; 4965| | 4966| 2.88k| if (ret) ------------------ | Branch (4966:9): [True: 0, False: 2.88k] ------------------ 4967| 0| { 4968| 0| return ret; 4969| 0| } 4970| | 4971| 2.88k| if (pAATG->nAtTypeTotals[ATTOT_NUM_CO_Minus] + pAATG->nAtTypeTotals[ATTOT_NUM_ZO_Minus] && ------------------ | Branch (4971:9): [True: 63, False: 2.82k] ------------------ 4972| 63| pAATG->nAtTypeTotals[ATTOT_NUM_N_Minus]) ------------------ | Branch (4972:10): [True: 2, False: 61] ------------------ 4973| 2| { 4974| 2| } 4975| | 4976| 2.88k| nPosCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4977| 2.88k| nNegCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4978| | /* 4979| | nNumNP_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4980| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4981| | nNumOS_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4982| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4983| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4984| | */ 4985| | 4986| 2.88k| if (( nPosCharges - nNegCharges ) - ( nPosCharges2 - nNegCharges2 ) != nNumRemovedProtons) ------------------ | Branch (4986:9): [True: 0, False: 2.88k] ------------------ 4987| 0| { 4988| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4989| 0| } 4990| | 4991| 2.88k| if (nNumCanceledCharges) ------------------ | Branch (4991:9): [True: 2.88k, False: 0] ------------------ 4992| 2.88k| { 4993| |#if ( FIX_CANCEL_CHARGE_COUNT_BUG == 1 ) 4994| | *nNumCanceledCharges += 2 * nNumNeutralized; 4995| |#else 4996| 2.88k| *nNumCanceledCharges = 2 * nNumNeutralized; 4997| 2.88k|#endif 4998| 2.88k| } 4999| | 5000| 2.88k| return nNumRemovedProtons; 5001| 2.88k|} mark_at_type: 5006| 253k|{ 5007| 253k| int i, max_num_ions, mask, type; 5008| | /*int max_protons, max_O_Minus, num_H = 0, num_CO=0;*/ 5009| | 5010| 253k| if (nAtTypeTotals) ------------------ | Branch (5010:9): [True: 253k, False: 0] ------------------ 5011| 253k| { 5012| 253k| memset( nAtTypeTotals, 0, ATTOT_ARRAY_LEN * sizeof( nAtTypeTotals[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5013| 253k| } 5014| | 5015| 1.31M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5015:17): [True: 1.05M, False: 253k] ------------------ 5016| 1.05M| { 5017| 1.05M| type = GetAtomChargeType( atom, i, nAtTypeTotals, &mask, 0 ); 5018| 1.05M| atom[i].at_type = type; 5019| | /* 5020| | num_H += ((type & PR_HARD_TYP_H) && (mask & ATBIT_MSK_H)); 5021| | num_CO += ((type & AR_HARD_TYP_HA) && (mask & AR_HARD_MSK_HA)); 5022| | */ 5023| 1.05M| } 5024| | 5025| 253k| if (nAtTypeTotals) ------------------ | Branch (5025:9): [True: 253k, False: 0] ------------------ 5026| 253k| { 5027| | /* 5028| | max_protons = nAtTypeTotals[ATTOT_NUM_NP_Proton] + 5029| | inchi_min(num_H, nAtTypeTotals[ATTOT_NUM_NP_Plus]); 5030| | max_O_Minus = nAtTypeTotals[ATTOT_NUM_CO_Minus] + nAtTypeTotals[ATTOT_NUM_CS_Minus] + 5031| | nAtTypeTotals[ATTOT_NUM_ZO_Minus] + nAtTypeTotals[ATTOT_NUM_OO_Minus] + 5032| | nAtTypeTotals[ATTOT_NUM_ZOO_Minus] + nAtTypeTotals[ATTOT_NUM_NO_Minus] + 5033| | nAtTypeTotals[ATTOT_NUM_O_Minus] +nAtTypeTotals[ATTOT_NUM_N_Minus]; 5034| | ; 5035| | max_num_ions = max_protons + max_O_Minus + nAtTypeTotals[ATTOT_NUM_CHARGES]; 5036| | */ 5037| 253k| max_num_ions = nAtTypeTotals[ATTOT_NUM_CHARGES]; 5038| 253k| } 5039| 0| else 5040| 0| { 5041| 0| max_num_ions = 0; 5042| 0| } 5043| | 5044| 253k| return max_num_ions; 5045| 253k|} RemoveNPProtonsAndAcidCharges: 5055| 59.9k|{ 5056| | 5057| | /* Prepare data structure */ 5058| 59.9k| int num; 5059| 59.9k| int nNumCanceledCharges = 0; 5060| | /* djb-rwth: removing redundant variables */ 5061| 59.9k| T_GROUP_INFO *t_group_info = pAATG->t_group_info; 5062| 59.9k| int ret = 0, bError = 0; 5063| | 5064| 59.9k| int bAllowHardRemove = ( t_group_info->bTautFlags & TG_FLAG_TEST_TAUT__SALTS ) && ------------------ | | 920| 59.9k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5064:28): [True: 59.9k, False: 0] ------------------ 5065| 59.9k| ( t_group_info->bTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) && ------------------ | | 922| 59.9k|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5065:9): [True: 59.9k, False: 0] ------------------ 5066| 59.9k| ( t_group_info->bTautFlags & TG_FLAG_MOVE_POS_CHARGES ) && ------------------ | | 921| 59.9k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5066:9): [True: 59.9k, False: 0] ------------------ 5067| 59.9k| ( t_group_info->bTautFlags & TG_FLAG_HARD_ADD_REM_PROTONS ); ------------------ | | 936| 59.9k|#define TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */ ------------------ | Branch (5067:9): [True: 59.9k, False: 0] ------------------ 5068| | 5069| 59.9k| if (pAATG->nMarkedAtom && num_atoms < pAATG->nAllocLen) ------------------ | Branch (5069:9): [True: 0, False: 59.9k] | Branch (5069:31): [True: 0, False: 0] ------------------ 5070| 0| { 5071| 0| inchi_free( pAATG->nMarkedAtom ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5072| 0| qzfree( pAATG->nEndPoint ); ------------------ | | 1176| 0|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 0, False: 0] | | | Branch (1176:61): [Folded, False: 0] | | ------------------ ------------------ 5073| 0| memset( pAATG, 0, sizeof( *pAATG ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5074| 0| } 5075| | 5076| 59.9k| if (!pAATG->nMarkedAtom && ( pAATG->nMarkedAtom = (S_CHAR *) inchi_malloc( num_atoms * sizeof( pAATG->nMarkedAtom[0] ) ) )) ------------------ | | 1143| 59.9k|#define inchi_malloc malloc ------------------ | Branch (5076:9): [True: 59.9k, False: 0] | Branch (5076:32): [True: 59.9k, False: 0] ------------------ 5077| 59.9k| { 5078| 59.9k| pAATG->nAllocLen = num_atoms; 5079| 59.9k| pAATG->nNumFound = 0; 5080| 59.9k| } 5081| | 5082| | /* o TECHMAN-5.1. Remove protons from charged heteroatoms */ 5083| | 5084| | /* (TECHMAN-5.1a) Simple remove of protons from N, P, and O,S,Se,Te */ 5085| 59.9k| if ((num = pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton] + pAATG->nAtTypeTotals[ATTOT_NUM_OH_Plus])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5085:9): [True: 665, False: 59.2k] ------------------ 5086| 665| { 5087| 665| ret = SimpleRemoveHplusNPO( at, num_atoms, pAATG->nAtTypeTotals, t_group_info ); 5088| 665| if (ret != num) ------------------ | Branch (5088:13): [True: 0, False: 665] ------------------ 5089| 0| { 5090| 0| bError = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5091| 0| goto exit_function; 5092| 0| } 5093| | /*t_group_info->nNumRemovedProtons += ret;*/ 5094| 665| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_NPO_SIMPLE_REMOVED : 0; ------------------ | | 146| 665|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 ------------------ | Branch (5094:50): [True: 665, False: 0] ------------------ 5095| 665| } 5096| | 5097| 59.9k| if (( num = pAATG->nAtTypeTotals[ATTOT_NUM_NP_Plus] ) && bAllowHardRemove) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | Branch (5097:9): [True: 2.88k, False: 57.0k] | Branch (5097:62): [True: 2.88k, False: 0] ------------------ 5098| 2.88k| { 5099| | /* [TECHMAN-5.1b] Hard removing more protons from cationic N; charges may be canceled */ 5100| 2.88k| ret = HardRemoveHplusNP( pCG, at, num_atoms, 1, &nNumCanceledCharges, pAATG, pBNS, pBD ); 5101| 2.88k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 2.88k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 2.88k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 2.88k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 2.88k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 2.88k, False: 0] | | | Branch (67:44): [True: 0, False: 2.88k] | | ------------------ ------------------ 5102| 0| { 5103| 0| bError = ret; 5104| 0| goto exit_function; 5105| 0| } 5106| | /* djb-rwth: removing redundant code */ 5107| | /*t_group_info->nNumRemovedProtons += ret;*/ 5108| 2.88k| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_NP_HARD_REMOVED : 0; ------------------ | | 147| 95|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 ------------------ | Branch (5108:50): [True: 95, False: 2.78k] ------------------ 5109| 2.88k| } 5110| | 5111| 59.9k| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] > 0) ------------------ | Branch (5111:9): [True: 41.8k, False: 18.0k] ------------------ 5112| 41.8k| { 5113| | /* o TECHMAN-5.2. Remove protons from neutral heteroatoms */ 5114| | 5115| | /* (TECHMAN-5.2a) Simple removal */ 5116| 41.8k| ret = SimpleRemoveAcidicProtons( at, num_atoms, pAATG, pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ); 5117| 41.8k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 41.8k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 41.8k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 41.8k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 41.8k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 41.8k, False: 0] | | | Branch (67:44): [True: 0, False: 41.8k] | | ------------------ ------------------ 5118| 0| { 5119| 0| bError = ret; 5120| 0| goto exit_function; 5121| 0| } 5122| | 5123| | /*t_group_info->nNumRemovedProtons += ret;*/ 5124| 41.8k| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_AC_SIMPLE_REMOVED : 0; ------------------ | | 149| 92|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 ------------------ | Branch (5124:50): [True: 92, False: 41.7k] ------------------ 5125| | 5126| | 5127| 41.8k| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] > 0 && bAllowHardRemove) ------------------ | Branch (5127:13): [True: 41.7k, False: 87] | Branch (5127:59): [True: 41.7k, False: 0] ------------------ 5128| 41.7k| { 5129| | /* (TECHMAN-5.2b) Hard removal */ 5130| 41.7k| ret = HardRemoveAcidicProtons(pCG, at, num_atoms, pAATG, pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE], &nNumCanceledCharges, pBNS, pBD); 5131| 41.7k| if (IS_BNS_ERROR(ret)) ------------------ | | 67| 41.7k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 41.7k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 41.7k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 41.7k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 41.7k, False: 0] | | | Branch (67:44): [True: 0, False: 41.7k] | | ------------------ ------------------ 5132| 0| { 5133| 0| bError = ret; 5134| 0| goto exit_function; 5135| 0| } 5136| 41.7k| if (ret > 0) ------------------ | Branch (5136:17): [True: 11, False: 41.7k] ------------------ 5137| 11| { 5138| 11| int ret2 = SimpleRemoveAcidicProtons(at, num_atoms, pAATG, ret); 5139| 11| if (ret2 != ret) ------------------ | Branch (5139:21): [True: 0, False: 11] ------------------ 5140| 0| { 5141| 0| bError = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5142| 0| goto exit_function; 5143| 0| } 5144| | /*t_group_info->nNumRemovedProtons += ret;*/ 5145| 11| t_group_info->tni.bNormalizationFlags |= (ret > 0) ? FLAG_PROTON_AC_HARD_REMOVED : 0; ------------------ | | 150| 11|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 ------------------ | Branch (5145:58): [True: 11, False: 0] ------------------ 5146| | /* djb-rwth: removing redundant code */ 5147| 11| } 5148| 41.7k| } 5149| | 5150| | 5151| 41.8k| } 5152| 18.0k| else 5153| 18.0k| { 5154| 18.0k| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] < 0) ------------------ | Branch (5154:13): [True: 10.7k, False: 7.27k] ------------------ 5155| 10.7k| { 5156| 10.7k| ret = SimpleAddAcidicProtons( at, num_atoms, pAATG, -pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ); 5157| 10.7k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 10.7k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 10.7k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 10.7k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 10.7k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 10.7k, False: 0] | | | Branch (67:44): [True: 0, False: 10.7k] | | ------------------ ------------------ 5158| 0| { 5159| 0| bError = ret; 5160| 0| goto exit_function; 5161| 0| } 5162| | /*t_group_info->nNumRemovedProtons -= ret;*/ 5163| | /* 5164| | CHECK_TACN == 1 prohibits replacing (-) on N with H unless H can be moved to N 5165| | along an alternating path from another heteroatom (t-group will be detected). 5166| | */ 5167| 10.7k| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_AC_SIMPLE_ADDED : 0; ------------------ | | 148| 3.86k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 ------------------ | Branch (5167:54): [True: 3.86k, False: 6.88k] ------------------ 5168| 10.7k| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] < 0 && bAllowHardRemove) ------------------ | Branch (5168:17): [True: 7.15k, False: 3.60k] | Branch (5168:63): [True: 7.15k, False: 0] ------------------ 5169| 7.15k| { 5170| 7.15k| ret = HardAddAcidicProtons( pCG, at, num_atoms, pAATG, -pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE], &nNumCanceledCharges, pBNS, pBD ); 5171| 7.15k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 7.15k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 7.15k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 7.15k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 7.15k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 7.15k, False: 0] | | | Branch (67:44): [True: 3, False: 7.15k] | | ------------------ ------------------ 5172| 3| { 5173| 3| bError = ret; 5174| 3| goto exit_function; 5175| 3| } 5176| 7.15k| if (ret > 0) ------------------ | Branch (5176:21): [True: 69, False: 7.08k] ------------------ 5177| 69| { 5178| 69| int ret2 = SimpleAddAcidicProtons( at, num_atoms, pAATG, ret ); 5179| 69| if (ret2 != ret) ------------------ | Branch (5179:25): [True: 0, False: 69] ------------------ 5180| 0| { 5181| 0| bError = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5182| 0| goto exit_function; 5183| 0| } 5184| | /*t_group_info->nNumRemovedProtons -= ret;*/ 5185| 69| t_group_info->tni.bNormalizationFlags |= FLAG_PROTON_AC_HARD_ADDED; /* djb-rwth: fixing coverity ID #499527 */ ------------------ | | 151| 69|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 ------------------ 5186| | /* djb-rwth: removing redundant code */ 5187| 69| } 5188| 7.15k| } 5189| 10.7k| } 5190| 18.0k| } 5191| | 5192| 59.8k| t_group_info->tni.bNormalizationFlags |= nNumCanceledCharges ? FLAG_PROTON_CHARGE_CANCEL : 0; ------------------ | | 152| 19|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 ------------------ | Branch (5192:46): [True: 19, False: 59.8k] ------------------ 5193| | 5194| 59.9k|exit_function: 5195| 59.9k| if (bError) ------------------ | Branch (5195:9): [True: 3, False: 59.8k] ------------------ 5196| 3| { 5197| 3| ret = IS_BNS_ERROR( bError ) ? bError : BNS_PROGRAM_ERR; ------------------ | | 67| 3|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 3|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 3|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 3|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 3, False: 0] | | | Branch (67:44): [True: 3, False: 0] | | ------------------ ------------------ ret = IS_BNS_ERROR( bError ) ? bError : BNS_PROGRAM_ERR; ------------------ | | 50| 3|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5198| 3| } 5199| | 5200| 59.9k| return ret; 5201| 59.8k|} mark_alt_bonds_and_taut_groups: 5220| 288k|{ 5221| 288k| BN_STRUCT *pBNS = NULL; 5222| 288k| BN_DATA *pBD = NULL; 5223| 288k| int bError, nChanges, taut_found, salt_found, salt_pass, salt_step, ret, ret2, num, num_changed_bonds; /* djb-rwth: removing redundant variables */ 5224| 288k| int max_altp = BN_MAX_ALTP; ------------------ | | 17| 288k|#define BN_MAX_ALTP 16 ------------------ 5225| 288k| int bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 372| 288k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 288k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 288k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ int bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 374| 288k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ 5226| 288k| BNS_FLOW_CHANGES fcd[BNS_MAX_NUM_FLOW_CHANGES + 1]; 5227| 288k| C_GROUP_INFO CGroupInfo; 5228| 288k| C_GROUP_INFO *c_group_info = &CGroupInfo; 5229| 288k| S_GROUP_INFO SGroupInfo; 5230| 288k| S_GROUP_INFO *s_group_info = &SGroupInfo; 5231| 288k| INCHI_MODE *pbTautFlags = t_group_info ? &t_group_info->bTautFlags : inpbTautFlags; ------------------ | Branch (5231:34): [True: 252k, False: 36.3k] ------------------ 5232| 288k| INCHI_MODE *pbTautFlagsDone = t_group_info ? &t_group_info->bTautFlagsDone : inpbTautFlagsDone; ------------------ | Branch (5232:38): [True: 252k, False: 36.3k] ------------------ 5233| | 5234| 288k| int nAtTypeTotals[ATTOT_ARRAY_LEN]; 5235| 288k| int nNumOrigTotAtoms; 5236| | 5237| 288k| BN_AATG aatg; 5238| 288k| BN_AATG *pAATG = &aatg; 5239| | 5240| 288k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 5241| 288k| int i, n_arom_radicals = 0, *stored_radicals = NULL; 5242| 288k|#endif 5243| 288k| int at_prot; /* moved from below 2024-09-01 DT */ 5244| | 5245| 288k| nChanges = 0; 5246| 288k| bError = 0; 5247| | 5248| 288k| memset( c_group_info, 0, sizeof( *c_group_info ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5249| 288k| memset( s_group_info, 0, sizeof( *s_group_info ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5250| 288k| memset( pAATG, 0, sizeof( *pAATG ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5251| | 5252| | /*(@nnuk : Nauman Ullah Khan) :: Variable for checking (De)protonation status */ 5253| 288k| LOG_NO_ARGS("\n############# Initial state before (De)Protonation (L5373:ichi_bns.c) ###############\n"); 5254| 1.38M| for (at_prot = 0; at_prot < num_atoms; at_prot++) ------------------ | Branch (5254:23): [True: 1.09M, False: 288k] ------------------ 5255| 1.09M| { 5256| 1.09M| LOG_MULT_ARGS("Atom %d: Element: %s, Num_H: %d, Charge: %hhd, Radical: %d\n", at_prot, at[at_prot].elname, at[at_prot].num_H, at[at_prot].charge, at[at_prot].radical); 5257| 1.09M| } 5258| 288k| LOG_NO_ARGS("\n#####################################################################################\n"); 5259| | 5260| | 5261| 288k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 5262| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5262:17): [True: 1.09M, False: 288k] ------------------ 5263| 1.09M| { 5264| 1.09M| if (( at[i].radical == RADICAL_DOUBLET ) && ( at[i].valence == 2 ) && ------------------ | | 76| 1.09M|#define RADICAL_DOUBLET 2 ------------------ | Branch (5264:13): [True: 17.6k, False: 1.07M] | Branch (5264:53): [True: 4.66k, False: 13.0k] ------------------ 5265| 4.66k| ( at[i].bond_type[0] == BOND_ALTERN ) && ( at[i].bond_type[1] == BOND_ALTERN )) ------------------ | | 180| 4.66k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 4.66k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ ( at[i].bond_type[0] == BOND_ALTERN ) && ( at[i].bond_type[1] == BOND_ALTERN )) ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (5265:13): [True: 0, False: 4.66k] | Branch (5265:54): [True: 0, False: 0] ------------------ 5266| 0| { 5267| 0| n_arom_radicals++; 5268| 0| if (!stored_radicals) ------------------ | Branch (5268:17): [True: 0, False: 0] ------------------ 5269| 0| { 5270| 0| stored_radicals = (int *) inchi_calloc( num_atoms, sizeof( int ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 5271| | /* 2011-08-05 explicit cast added due to Evan Bolton */ 5272| 0| if (!stored_radicals) ------------------ | Branch (5272:21): [True: 0, False: 0] ------------------ 5273| 0| { 5274| 0| bError = BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5275| 0| goto exit_function; 5276| 0| } 5277| 0| stored_radicals[i] = RADICAL_DOUBLET; ------------------ | | 76| 0|#define RADICAL_DOUBLET 2 ------------------ 5278| 0| at[i].radical = 0; 5279| 0| at[i].num_H++; 5280| 0| } 5281| 0| } 5282| 1.09M| } 5283| | 5284| 288k|#endif 5285| | 5286| 288k| if (( *pbTautFlags & TG_FLAG_MOVE_POS_CHARGES ) && num_atoms > 1) ------------------ | | 921| 288k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5286:9): [True: 288k, False: 0] | Branch (5286:56): [True: 103k, False: 184k] ------------------ 5287| 103k| { 5288| | /* Charge groups memory allocation */ 5289| 103k| c_group_info->c_group = (C_GROUP *) inchi_calloc( num_atoms / 2, sizeof( c_group_info->c_group[0] ) ); ------------------ | | 1146| 103k|#define inchi_calloc calloc ------------------ 5290| 103k| c_group_info->c_candidate = (C_CANDIDATE*) inchi_calloc( num_atoms, sizeof( c_group_info->c_candidate[0] ) ); ------------------ | | 1146| 103k|#define inchi_calloc calloc ------------------ 5291| 103k| if (c_group_info->c_group && c_group_info->c_candidate) ------------------ | Branch (5291:13): [True: 103k, False: 0] | Branch (5291:38): [True: 103k, False: 0] ------------------ 5292| 103k| { 5293| 103k| c_group_info->max_num_c_groups = num_atoms / 2; 5294| 103k| c_group_info->max_num_candidates = num_atoms; 5295| 103k| } 5296| 0| else 5297| 0| { 5298| 0| bError = BNS_OUT_OF_RAM; /* error: out of RAM */ ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5299| | /*printf("BNS_OUT_OF_RAM-1: num_at=%d, c_gr=%lx c_can=%lx\n", num_atoms, c_group_info->c_group, c_group_info->c_candidate);*/ 5300| 0| goto exit_function; 5301| 0| } 5302| 103k| } 5303| | 5304| 288k| if (*pbTautFlags & TG_FLAG_TEST_TAUT__SALTS) ------------------ | | 920| 288k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5304:9): [True: 252k, False: 36.3k] ------------------ 5305| 252k| { 5306| 252k| if (t_group_info) ------------------ | Branch (5306:13): [True: 252k, False: 0] ------------------ 5307| 252k| { 5308| | /* Salt groups memory allocation */ 5309| 252k| s_group_info->s_candidate = 5310| 252k| (S_CANDIDATE*) inchi_calloc( num_atoms, ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5311| 252k| sizeof( s_group_info->s_candidate[0] ) ); 5312| 252k| if (s_group_info->s_candidate) ------------------ | Branch (5312:17): [True: 252k, False: 0] ------------------ 5313| 252k| { 5314| 252k| s_group_info->max_num_candidates = num_atoms; 5315| 252k| } 5316| 0| else 5317| 0| { 5318| 0| bError = BNS_OUT_OF_RAM; /* error: out of RAM */ ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5319| | /*printf("BNS_OUT_OF_RAM-2\n");*/ 5320| 0| goto exit_function; 5321| 0| } 5322| 252k| } 5323| 252k| } 5324| | 5325| 288k| if (t_group_info) ------------------ | Branch (5325:9): [True: 252k, False: 36.3k] ------------------ 5326| 252k| { 5327| 252k| if (t_group_info->tGroupNumber) ------------------ | Branch (5327:13): [True: 0, False: 252k] ------------------ 5328| 0| { 5329| 0| inchi_free( t_group_info->tGroupNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5330| 0| } 5331| 252k| t_group_info->tGroupNumber = (AT_NUMB *) inchi_calloc( 2 * (long long)num_atoms + 1, sizeof( t_group_info->tGroupNumber[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5332| 252k| if (!t_group_info->tGroupNumber) ------------------ | Branch (5332:13): [True: 0, False: 252k] ------------------ 5333| 0| { 5334| | /*printf("BNS_OUT_OF_RAM-9\n");*/ 5335| 0| bError = BNS_OUT_OF_RAM; /* error: out of RAM */ ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5336| 0| goto exit_function; 5337| 0| } 5338| 252k| num = t_group_info->tni.nNumRemovedExplicitH; 5339| 252k| memset( &t_group_info->tni, 0, sizeof( t_group_info->tni ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5340| 252k| t_group_info->tni.nNumRemovedExplicitH = num; 5341| 252k| } 5342| | 5343| | /* 5344| | again: 5345| | */ 5346| | 5347| | /* Allocate Balanced Network Data Strucures; replace Alternating bonds with Single */ 5348| 288k| if (( pBNS = AllocateAndInitBnStruct( at, num_atoms, ------------------ | Branch (5348:9): [True: 288k, False: 0] ------------------ 5349| 288k| BNS_ADD_ATOMS, BNS_ADD_EDGES, ------------------ | | 88| 288k|#define BNS_ADD_ATOMS 2 /* max. number of fictitious atoms to add (except t-gtoups) */ ------------------ BNS_ADD_ATOMS, BNS_ADD_EDGES, ------------------ | | 89| 288k|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 5350| 288k| max_altp, &num_changed_bonds ) ) 5351| 288k| && 5352| 288k| ( pBD = AllocateAndInitBnData( pBNS->max_vertices ) )) ------------------ | Branch (5352:10): [True: 288k, False: 0] ------------------ 5353| 288k| { 5354| | 5355| | 5356| 288k| pBNS->pbTautFlags = pbTautFlags; /* carry through all functions */ 5357| 288k| pBNS->pbTautFlagsDone = pbTautFlagsDone; /* carry through all functions */ 5358| | 5359| 288k| pBNS->ulTimeOutTime = ulTimeOutTime; /* v. 1.05 */ 5360| 288k| pBNS->ic = ic; /* v. 1.05 */ 5361| | 5362| 288k|#if ( BNS_PROTECT_FROM_TAUT == 1 ) 5363| | /* Protect bonds to acetyl and nitro */ 5364| 288k| SetForbiddenEdges( pBNS, at, num_atoms, BNS_EDGE_FORBIDDEN_MASK, nebend, ebend ); ------------------ | | 39| 288k|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 5365| 288k|#endif 5366| | 5367| | /* Set bonds in case of input "aromatic" bonds or multiple radicals */ 5368| 288k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 5369| 288k| if (n_arom_radicals) ------------------ | Branch (5369:13): [True: 0, False: 288k] ------------------ 5370| 0| { 5371| 0| ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5372| 0| if (stored_radicals) ------------------ | Branch (5372:17): [True: 0, False: 0] ------------------ 5373| 0| { 5374| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5374:29): [True: 0, False: 0] ------------------ 5375| 0| { 5376| 0| if (stored_radicals[i]) ------------------ | Branch (5376:25): [True: 0, False: 0] ------------------ 5377| 0| { 5378| 0| at[i].radical = stored_radicals[i]; 5379| 0| at[i].num_H--; 5380| 0| } 5381| 0| } 5382| 0| } 5383| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 5384| 0| { 5385| 0| bError = ret; 5386| 0| goto exit_function; 5387| 0| } 5388| 0| } 5389| 288k|#endif 5390| | 5391| 288k| ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5392| | 5393| | /* (here pair(s) of radicals could have disappeared from the atoms) */ 5394| 288k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 288k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 288k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 288k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 288k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 288k, False: 0] | | | Branch (67:44): [True: 0, False: 288k] | | ------------------ ------------------ 5395| 0| { 5396| 0| bError = ret; 5397| 0| goto exit_function; 5398| 0| } 5399| 288k| pBNS->tot_st_flow += 2 * ret; 5400| | 5401| | /*return 0;*/ /* debug */ 5402| | /* djb-rwth: removing redundant code */ 5403| | 5404| 288k| if (pBNS->tot_st_cap > pBNS->tot_st_flow) ------------------ | Branch (5404:13): [True: 11.8k, False: 276k] ------------------ 5405| 11.8k| { 5406| | /* has radical */ 5407| 11.8k| bChangeFlow |= BNS_EF_SET_NOSTEREO; ------------------ | | 377| 11.8k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ 5408| 11.8k| } 5409| | 5410| | /******************************************************************** 5411| | * Remove protons from NH(+), but not PH(+) 5412| | * Add protons to COO(-) etc. 5413| | * or remove protons from COOH etc to make the organic part neutral 5414| | * Note: for now (-) from N(-) can be only canceled or moved to -C=O 5415| | ********************************************************************/ 5416| 288k| if (( *pbTautFlags & TG_FLAG_VARIABLE_PROTONS ) && ------------------ | | 935| 288k|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (5416:13): [True: 288k, False: 0] ------------------ 5417| 288k| t_group_info && ------------------ | Branch (5417:14): [True: 252k, False: 36.3k] ------------------ 5418| 252k| mark_at_type( at, num_atoms, nAtTypeTotals ) && ------------------ | Branch (5418:14): [True: 59.9k, False: 192k] ------------------ 5419| 59.9k| nAtTypeTotals[ATTOT_NUM_CHARGES]) ------------------ | Branch (5419:14): [True: 59.9k, False: 0] ------------------ 5420| 59.9k| { 5421| | /* 5422| | the structure is simple to neutralize if it yields exactly 5423| | num[H(+)] = num[N,P H(+)] 5424| | num[N,S,O(-)] = num[=C-O(-)] + num[C-S(-)] + num[N(-)] + num[other O(-), S(-)] 5425| | 5426| | and n(p) = num[H(+)] - num[N,S,O(-)] (no protons, no negative N,O,S condition) 5427| | 5428| | Additional check is needed if: 5429| | min{num[N,PH], num[N,P(+), not onium]} > 0 5430| | => possibility to yield more H(+) 5431| | 5432| | min_charge = orig_charge(P,N,O,S) - n(p) - n(OH,SH) 5433| | max_charge = orig_charge(P,N,O,S) - n(p) + n(O,S,N(-)) 5434| | */ 5435| | 5436| 59.9k| nNumOrigTotAtoms = t_group_info->tni.nNumRemovedExplicitH + num_atoms; 5437| 59.9k| pAATG->nAtTypeTotals = nAtTypeTotals; 5438| 59.9k| pAATG->t_group_info = t_group_info; 5439| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5440| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5441| |#endif 5442| | 5443| | /***********************************************************/ 5444| | /* */ 5445| | /* ( D E ) P R O T O N A T I O N */ 5446| | /* */ 5447| | /***********************************************************/ 5448| | 5449| 59.9k| ret = RemoveNPProtonsAndAcidCharges( pCG, at, num_atoms, pAATG, pBNS, pBD ); 5450| | 5451| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5452| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5453| |#endif 5454| 59.9k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 59.9k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 59.9k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 59.9k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 59.9k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 59.9k, False: 0] | | | Branch (67:44): [True: 3, False: 59.8k] | | ------------------ ------------------ 5455| 3| { 5456| 3| bError = ret; 5457| 3| goto exit_function; 5458| 3| } 5459| | 5460| 59.8k| if (t_group_info->tni.bNormalizationFlags) ------------------ | Branch (5460:17): [True: 4.60k, False: 55.2k] ------------------ 5461| 4.60k| { 5462| 4.60k| SetInitCapFlowToCurrent( pBNS ); 5463| 4.60k| if (at_fixed_bonds_out) ------------------ | Branch (5463:21): [True: 4.60k, False: 0] ------------------ 5464| 4.60k| { 5465| | /* Copy modified initial tautomeric structure for displaying 5466| | Warning: implicit H counts in at_fixed_bonds_out include explicit Hs */ 5467| | 5468| 4.60k| memcpy(at_fixed_bonds_out, at, nNumOrigTotAtoms * sizeof(at_fixed_bonds_out[0])); 5469| | 5470| | /* -- will be done in FillOutInputInfAtom() -- 5471| | RemoveExcessiveImplicitH( num_atoms, t_group_info->tni.nNumRemovedExplicitH, at_fixed_bonds_out ); 5472| | */ 5473| 4.60k| } 5474| 4.60k| } 5475| 59.8k| } 5476| | 5477| | /****************** Initial bonds normalization ***************/ 5478| | 5479| 288k| if (*pbTautFlags & TG_FLAG_MOVE_POS_CHARGES) ------------------ | | 921| 288k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5479:13): [True: 288k, False: 0] ------------------ 5480| 288k| { 5481| | /******************* Find moveable positive charges **********************/ 5482| 288k| do 5483| 289k| { 5484| | /* Cycling while ret>0 added 2004-06-04 */ 5485| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5486| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5487| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5488| |#endif 5489| 289k| ret = MarkChargeGroups( pCG, at, num_atoms, 5490| 289k| c_group_info, t_group_info, 5491| 289k| pBNS, pBD ); 5492| | 5493| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5494| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5495| |#endif 5496| 289k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 289k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 289k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 289k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 289k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 289k, False: 0] | | | Branch (67:44): [True: 1, False: 289k] | | ------------------ ------------------ 5497| 1| { 5498| 1| bError = ret; 5499| 1| goto exit_function; 5500| 1| } 5501| 289k| if (ret) ------------------ | Branch (5501:21): [True: 862, False: 288k] ------------------ 5502| 862| { 5503| 862| nChanges += ret; 5504| 862| ret2 = AddCGroups2BnStruct( pCG, pBNS, at, num_atoms, c_group_info ); 5505| 862| if (IS_BNS_ERROR( ret2 )) ------------------ | | 67| 862|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 862|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 862|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 862|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 862, False: 0] | | | Branch (67:44): [True: 0, False: 862] | | ------------------ ------------------ 5506| 0| { 5507| 0| bError = ret2; 5508| 0| goto exit_function; 5509| 0| } 5510| 862| *pbTautFlagsDone |= TG_FLAG_MOVE_POS_CHARGES_DONE; ------------------ | | 966| 862|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 5511| 862| } 5512| 289k| } while (ret > 0); ------------------ | Branch (5512:22): [True: 862, False: 288k] ------------------ 5513| | 5514| | 5515| 288k|#if ( BNS_RAD_SEARCH == 1 ) 5516| |#else 5517| | /* moveable charges may allow to cancel radicals -- check it */ 5518| | if (pBNS->tot_st_cap > pBNS->tot_st_flow) 5519| | { 5520| | ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5521| | if (IS_BNS_ERROR( ret )) 5522| | { 5523| | bError = ret; 5524| | goto exit_function; 5525| | } 5526| | if (ret > 0) 5527| | { 5528| | /* 5529| | pBNS->tot_st_flow += 2*ret; 5530| | ret = ReInitBnStruct( pBNS, at, num_atoms, 1 ); 5531| | if ( IS_BNS_ERROR( ret ) ) { 5532| | bError = ret; 5533| | goto exit_function; 5534| | } 5535| | */ 5536| | bError = BNS_RADICAL_ERR; 5537| | goto exit_function; 5538| | } 5539| | } 5540| |#endif 5541| 288k| } 5542| | 5543| | /************************************************************************/ 5544| | /******** Test bonds for bond tautomerism **************/ 5545| | /******** replace moveable bonds with "alternating" bonds **************/ 5546| | /************************************************************************/ 5547| 288k| ret = BnsTestAndMarkAltBonds( pBNS, pBD, at, num_atoms, fcd, bChangeFlow, 0 ); 5548| | 5549| 288k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 288k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 288k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 288k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 288k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 288k, False: 0] | | | Branch (67:44): [True: 0, False: 288k] | | ------------------ ------------------ 5550| 0| { 5551| 0| bError = ret; 5552| 0| goto exit_function; 5553| 0| } 5554| | /* djb-rwth: removing redundant code */ 5555| | 5556| | /*********************** End of initial bonds normalization *************/ 5557| | 5558| | /* djb-rwth: removing redundant code */ 5559| | 5560| | /* Check for tautomerism */ 5561| | /* find new tautomer groups */ 5562| 288k| salt_pass = 0; 5563| 288k| salt_step = 0; 5564| 288k| salt_found = 0; 5565| | 5566| | /*************************************************************/ 5567| | /* */ 5568| | /* M A I N C Y C L E B E G I N */ 5569| | /* */ 5570| | /*************************************************************/ 5571| | 5572| 288k| do 5573| 288k| { 5574| | /* djb-rwth: removing redundant code */ 5575| 288k| nChanges = 0; 5576| | /* djb-rwth: removing redundant code */ 5577| | 5578| | /**************** Regular bond/H/(-)/positive charges tautomerism cycle begin **************/ 5579| 288k| do 5580| 294k| { 5581| | /* djb-rwth: removing redundant code */ 5582| 294k| for (taut_found = 0; 5583| 299k| 0 < ( ret = MarkTautomerGroups( pCG, at, num_atoms, ------------------ | Branch (5583:23): [True: 5.55k, False: 294k] ------------------ 5584| 299k| t_group_info, c_group_info, 5585| 299k| pBNS, pBD ) ); 5586| 294k| taut_found++) 5587| 5.55k| { 5588| 5.55k| ; 5589| 5.55k| } 5590| 294k| if (ret < 0) ------------------ | Branch (5590:21): [True: 3, False: 294k] ------------------ 5591| 3| { 5592| 3| bError = ret; 5593| 3| } 5594| 294k| if (taut_found && !salt_pass) ------------------ | Branch (5594:21): [True: 5.38k, False: 288k] | Branch (5594:35): [True: 5.34k, False: 41] ------------------ 5595| 5.34k| { 5596| 5.34k| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT__ATOMS_DONE; ------------------ | | 963| 5.34k|#define TG_FLAG_TEST_TAUT__ATOMS_DONE 0x00000002 ------------------ 5597| 5.34k| } 5598| | 5599| 294k| if (taut_found || salt_found) ------------------ | Branch (5599:21): [True: 5.38k, False: 288k] | Branch (5599:35): [True: 98, False: 288k] ------------------ 5600| 5.48k| { 5601| | /****************** repeat bonds normalization ***************/ 5602| 5.48k| ret = ReInitBnStructAddGroups( pCG, pBNS, at, num_atoms, 5603| 5.48k| t_group_info, c_group_info ); 5604| 5.48k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 5.48k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 5.48k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 5.48k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 5.48k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 5.48k, False: 0] | | | Branch (67:44): [True: 0, False: 5.48k] | | ------------------ ------------------ 5605| 0| { 5606| 0| bError = ret; 5607| 0| goto exit_function; 5608| 0| } 5609| 5.48k|#if ( BNS_RAD_SEARCH == 1 ) 5610| |#else 5611| | /* discovered moveable charges and H-atoms may allow to cancel radicals */ 5612| | if (pBNS->tot_st_cap > pBNS->tot_st_flow) 5613| | { 5614| | ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5615| | if (IS_BNS_ERROR( ret )) 5616| | { 5617| | bError = ret; 5618| | goto exit_function; 5619| | } 5620| | if (ret > 0) 5621| | { 5622| | /* 5623| | pBNS->tot_st_flow += 2*ret; 5624| | ret = ReInitBnStruct( pBNS, at, num_atoms, 1 ); 5625| | if ( IS_BNS_ERROR( ret ) ) { 5626| | bError = ret; 5627| | goto exit_function; 5628| | } 5629| | */ 5630| | bError = BNS_RADICAL_ERR; 5631| | goto exit_function; 5632| | } 5633| | } 5634| |#endif 5635| | /****************** Update bonds normalization ***************/ 5636| 5.48k| if (*pbTautFlags & TG_FLAG_MOVE_POS_CHARGES) ------------------ | | 921| 5.48k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5636:25): [True: 5.48k, False: 0] ------------------ 5637| 5.48k| { 5638| | /******************* Find moveable charges ***************/ 5639| 5.48k| do 5640| 5.55k| { 5641| | /* Cycling while ret>0 added 2004-06-04 */ 5642| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5643| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5644| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5645| |#endif 5646| | 5647| 5.55k| ret = MarkChargeGroups( pCG, at, num_atoms, 5648| 5.55k| c_group_info, t_group_info, 5649| 5.55k| pBNS, pBD ); 5650| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5651| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5652| |#endif 5653| 5.55k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 5.55k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 5.55k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 5.55k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 5.55k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 5.55k, False: 0] | | | Branch (67:44): [True: 0, False: 5.55k] | | ------------------ ------------------ 5654| 0| { 5655| 0| bError = ret; 5656| 0| goto exit_function; 5657| 0| } 5658| 5.55k| nChanges += ret; 5659| 5.55k| if (ret > 0) ------------------ | Branch (5659:33): [True: 63, False: 5.48k] ------------------ 5660| 63| { 5661| 63| ret2 = ReInitBnStructAddGroups( pCG, pBNS, 5662| 63| at, num_atoms, 5663| 63| t_group_info, 5664| 63| c_group_info ); 5665| 63| if (IS_BNS_ERROR( ret2 )) ------------------ | | 67| 63|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 63|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 63|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 63|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 63, False: 0] | | | Branch (67:44): [True: 0, False: 63] | | ------------------ ------------------ 5666| 0| { 5667| 0| bError = ret2; 5668| 0| goto exit_function; 5669| 0| } 5670| 63| *pbTautFlagsDone |= TG_FLAG_MOVE_POS_CHARGES_DONE; ------------------ | | 966| 63|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 5671| 63| } 5672| 5.55k| } while (ret > 0); ------------------ | Branch (5672:34): [True: 63, False: 5.48k] ------------------ 5673| 5.48k| } 5674| | 5675| | /************************************************************************/ 5676| | /******** Find moveable bonds: **************/ 5677| | /******** test bonds for bond tautomerism **************/ 5678| | /******** replace moveable bonds with "alternating" bonds **************/ 5679| | /************************************************************************/ 5680| 5.48k| ret = BnsTestAndMarkAltBonds( pBNS, pBD, at, num_atoms, fcd, bChangeFlow, 0 ); 5681| 5.48k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 5.48k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 5.48k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 5.48k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 5.48k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 5.48k, False: 0] | | | Branch (67:44): [True: 0, False: 5.48k] | | ------------------ ------------------ 5682| 0| { 5683| 0| bError = ret; 5684| 0| goto exit_function; 5685| 0| } 5686| 5.48k| nChanges += ret; 5687| | /****************** End of update bonds normalization ***************/ 5688| | 5689| 5.48k| } 5690| 294k| salt_found = 0; 5691| 294k| } while (taut_found && !bError); ------------------ | Branch (5691:22): [True: 5.38k, False: 288k] | Branch (5691:36): [True: 5.38k, False: 0] ------------------ 5692| | 5693| | 5694| | /**************** Regular bond/H/(-)/positive charges tautomerism cycle end **************/ 5695| | 5696| 288k| if (bError) ------------------ | Branch (5696:17): [True: 3, False: 288k] ------------------ 5697| 3| { 5698| 3| break; 5699| 3| } 5700| | 5701| | 5702| | /******************* 'Salt' tautomerism permitted *************************/ 5703| 288k| if (*pbTautFlags & TG_FLAG_TEST_TAUT__SALTS) ------------------ | | 920| 288k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5703:17): [True: 252k, False: 36.3k] ------------------ 5704| 252k| { 5705| | 5706| 252k| if (*pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS) ------------------ | | 922| 252k|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5706:21): [True: 252k, False: 0] ------------------ 5707| 252k| { 5708| | /*********** Requested one or more "salt" attachement migrartion test ********/ 5709| 252k| if (!nChanges && salt_pass && salt_step) ------------------ | Branch (5709:25): [True: 247k, False: 5.24k] | Branch (5709:38): [True: 125, False: 246k] | Branch (5709:51): [True: 13, False: 112] ------------------ 5710| 13| { 5711| 13| break; /* done */ 5712| 13| } 5713| 252k| if (!salt_step) ------------------ | Branch (5713:25): [True: 252k, False: 4] ------------------ 5714| 252k| { 5715| | /* Salt step 0: process one attachment migrartion */ 5716| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5717| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5718| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5719| |#endif 5720| 252k| salt_found = MarkSaltChargeGroups( pCG, at, num_atoms, 5721| 252k| s_group_info, 5722| 252k| t_group_info, 5723| 252k| c_group_info, 5724| 252k| pBNS, pBD ); 5725| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5726| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5727| |#endif 5728| 252k| if (salt_found < 0) ------------------ | Branch (5728:29): [True: 0, False: 252k] ------------------ 5729| 0| { 5730| 0| bError = salt_found; 5731| 0| break; 5732| 0| } 5733| 252k| else 5734| 252k| { 5735| 252k| if (salt_found > 0) ------------------ | Branch (5735:33): [True: 118, False: 252k] ------------------ 5736| 118| { 5737| 118| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT__SALTS_DONE; ------------------ | | 965| 118|#define TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */ ------------------ 5738| 118| } 5739| 252k| } 5740| 252k| salt_step = !salt_found; 5741| | /* if new 'salt' atoms have been found then repeat regular taut. search 5742| | * MarkTautomerGroups() and do not perform salt step 1 5743| | * if new 'salt' atoms have NOT been found then switch to salt step 1 5744| | * and never repeat salt step 0 for the current structure 5745| | */ 5746| 252k| } 5747| | 5748| 252k| if (salt_step /*|| ------------------ | Branch (5748:25): [True: 252k, False: 118] ------------------ 5749| 252k| (t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT)*/) 5750| 252k| { 5751| | /* Salt step 1: process more than one attachment migration */ 5752| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5753| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5754| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5755| |#endif 5756| 252k| salt_found = MarkSaltChargeGroups2( pCG, at, num_atoms, 5757| 252k| s_group_info, 5758| 252k| t_group_info, 5759| 252k| c_group_info, 5760| 252k| pBNS, pBD ); 5761| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5762| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5763| |#endif 5764| 252k| if (salt_found < 0) ------------------ | Branch (5764:29): [True: 0, False: 252k] ------------------ 5765| 0| { 5766| 0| bError = salt_found; 5767| 0| break; 5768| 0| } 5769| 252k| else 5770| 252k| { 5771| 252k| if (salt_found == 1 || salt_found == 5) ------------------ | Branch (5771:33): [True: 0, False: 252k] | Branch (5771:52): [True: 17, False: 252k] ------------------ 5772| 17| { 5773| 17| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT2_SALTS_DONE; ------------------ | | 967| 17|#define TG_FLAG_TEST_TAUT2_SALTS_DONE 0x00000020 /* merged t-groups */ ------------------ 5774| 17| if (salt_found == 5) ------------------ | Branch (5774:37): [True: 17, False: 0] ------------------ 5775| 17| { 5776| 17| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT3_SALTS_DONE; ------------------ | | 979| 17|#define TG_FLAG_TEST_TAUT3_SALTS_DONE 0x00001000 /* merged t-groups + non-O taut atoms */ ------------------ 5777| 17| } 5778| | /* salt_found == 2 => only negative charges involved */ 5779| 17| } 5780| 252k| } 5781| 252k| } 5782| | 5783| 252k| salt_pass++; 5784| 252k| } 5785| 0| else 5786| 0| { 5787| | /* !( *pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) */ 5788| | /*************** Requested only one attachement migration test **********/ 5789| 0| if (!nChanges && salt_pass) ------------------ | Branch (5789:25): [True: 0, False: 0] | Branch (5789:38): [True: 0, False: 0] ------------------ 5790| 0| { 5791| | /* One attachment migration */ 5792| 0| break; 5793| 0| } 5794| | /* Salt step 0: process one attachment migration */ 5795| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5796| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5797| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5798| |#endif 5799| 0| salt_found = MarkSaltChargeGroups( pCG, at, num_atoms, 5800| 0| s_group_info, 5801| 0| t_group_info, 5802| 0| c_group_info, 5803| 0| pBNS, pBD ); 5804| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5805| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5806| |#endif 5807| 0| if (salt_found < 0) ------------------ | Branch (5807:25): [True: 0, False: 0] ------------------ 5808| 0| { 5809| 0| bError = salt_found; 5810| 0| break; 5811| 0| } 5812| 0| else 5813| 0| { 5814| 0| if (salt_found > 0) ------------------ | Branch (5814:29): [True: 0, False: 0] ------------------ 5815| 0| { 5816| 0| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT__SALTS_DONE; ------------------ | | 965| 0|#define TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */ ------------------ 5817| 0| } 5818| 0| } 5819| 0| salt_pass++; 5820| 0| } /* ( *pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) */ 5821| 252k| } /* ( *pbTautFlags & TG_FLAG_TEST_TAUT__SALTS ) */ 5822| 288k| } while (salt_found && !bError); ------------------ | Branch (5822:18): [True: 135, False: 288k] | Branch (5822:32): [True: 135, False: 0] ------------------ 5823| | 5824| | /*************************************************************/ 5825| | /* */ 5826| | /* M A I N C Y C L E E N D */ 5827| | /* */ 5828| | /*************************************************************/ 5829| | 5830| | 5831| 288k| if (*pbTautFlags & TG_FLAG_MERGE_TAUT_SALTS) ------------------ | | 924| 288k|#define TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */ ------------------ | Branch (5831:13): [True: 252k, False: 36.3k] ------------------ 5832| 252k| { 5833| 252k| if (!bError && s_group_info /*&& s_group_info->num_candidates > 0*/) ------------------ | Branch (5833:17): [True: 252k, False: 3] | Branch (5833:28): [True: 252k, False: 0] ------------------ 5834| 252k| { 5835| 252k| ret = MergeSaltTautGroups( pCG, at, num_atoms, s_group_info, 5836| 252k| t_group_info, c_group_info, pBNS ); 5837| 252k| if (ret < 0) ------------------ | Branch (5837:21): [True: 5, False: 252k] ------------------ 5838| 5| { 5839| 5| bError = ret; 5840| 5| } 5841| 252k| else 5842| 252k| { 5843| 252k| if (ret > 0) ------------------ | Branch (5843:25): [True: 262, False: 251k] ------------------ 5844| 262| { 5845| 262| *pbTautFlagsDone |= TG_FLAG_MERGE_TAUT_SALTS_DONE; ------------------ | | 969| 262|#define TG_FLAG_MERGE_TAUT_SALTS_DONE 0x00000080 /* added non-taut O to taut groups */ ------------------ 5846| 262| } 5847| 252k| } 5848| 252k| } 5849| 252k| } 5850| | 5851| 288k| if (!bError && t_group_info && ------------------ | Branch (5851:13): [True: 288k, False: 8] | Branch (5851:24): [True: 252k, False: 36.3k] ------------------ 5852| 252k| ( t_group_info->bTautFlags & TG_FLAG_VARIABLE_PROTONS ) && ------------------ | | 935| 252k|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (5852:13): [True: 252k, False: 0] ------------------ 5853| 252k| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE | TG_FLAG_FOUND_ISOTOPIC_H_DONE ) )) ------------------ | | 982| 252k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE | TG_FLAG_FOUND_ISOTOPIC_H_DONE ) )) ------------------ | | 981| 252k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5853:14): [True: 4.89k, False: 247k] ------------------ 5854| 4.89k| { 5855| 4.89k| ret = MakeIsotopicHGroup( at, num_atoms, s_group_info, t_group_info ); 5856| 4.89k| if (ret < 0) ------------------ | Branch (5856:17): [True: 0, False: 4.89k] ------------------ 5857| 0| { 5858| 0| bError = ret; 5859| 0| } 5860| 4.89k| } 5861| | 5862| | /* Success */ 5863| | 5864| 288k| remove_alt_bond_marks( at, num_atoms ); 5865| | 5866| | /************************************************ 5867| | * Temporarily ignore all non-alternating bonds 5868| | * and mark non-ring alt bonds non-stereogenic 5869| | ************************************************/ 5870| | 5871| 288k| ReInitBnStructForAltBns( pBNS, at, num_atoms, 0 ); 5872| 288k| MarkRingSystemsAltBns( pBNS, 0 ); 5873| 288k| MarkNonStereoAltBns( pBNS, at, num_atoms, 0 ); 5874| |#if ( FIX_EITHER_DB_AS_NONSTEREO == 1 ) 5875| | /* second time unknown ("Either") alternating bonds are treated as non-stereogenic */ 5876| | /* stereobonds bonds that lost stereo get "Either" stereo_type */ 5877| | ReInitBnStructForAltBns( pBNS, at, num_atoms, 1 ); 5878| | MarkRingSystemsAltBns( pBNS, 1 ); 5879| | MarkNonStereoAltBns( pBNS, at, num_atoms, 1 ); 5880| |#endif 5881| 288k| } 5882| 0| else 5883| 0| { 5884| 0| bError = BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5885| | /*printf("BNS_OUT_OF_RAM-3\n");*/ 5886| 0| } 5887| | 5888| | /*(@nnuk : Nauman Ullah Khan) */ 5889| 288k| LOG_NO_ARGS("\n################# Modified state after (De)Protonation (L6014:ichi_bns.c) ################\n"); 5890| 1.38M| for (at_prot = 0; at_prot < num_atoms; at_prot++) ------------------ | Branch (5890:23): [True: 1.09M, False: 288k] ------------------ 5891| 1.09M| { 5892| 1.09M| LOG_MULT_ARGS("Atom %d: Element: %s, Num_H: %d, Charge: %hhd, Radical: %d\n", at_prot, at[at_prot].elname, at[at_prot].num_H, at[at_prot].charge, at[at_prot].radical); 5893| 1.09M| } 5894| 288k| LOG_NO_ARGS("\n##########################################################################################\n"); 5895| | 5896| 288k|exit_function: 5897| | 5898| | /* djb-rwth: ignoring LLVM warning: variables used to store functions return values */ 5899| 288k| pBNS = DeAllocateBnStruct(pBNS); 5900| 288k| pBD = DeAllocateBnData(pBD); 5901| | /*#if ( MOVE_CHARGES == 1 )*/ 5902| 288k| if (c_group_info) ------------------ | Branch (5902:9): [True: 288k, False: 0] ------------------ 5903| 288k| { 5904| 288k| if (c_group_info->c_group) ------------------ | Branch (5904:13): [True: 103k, False: 184k] ------------------ 5905| 103k| { 5906| 103k| inchi_free( c_group_info->c_group ); ------------------ | | 1152| 103k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 103k, False: 0] | | | Branch (1152:50): [Folded, False: 103k] | | ------------------ ------------------ 5907| 103k| } 5908| 288k| if (c_group_info->c_candidate) ------------------ | Branch (5908:13): [True: 103k, False: 184k] ------------------ 5909| 103k| { 5910| 103k| inchi_free( c_group_info->c_candidate ); ------------------ | | 1152| 103k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 103k, False: 0] | | | Branch (1152:50): [Folded, False: 103k] | | ------------------ ------------------ 5911| 103k| } 5912| 288k| } 5913| | /*#endif*/ 5914| 288k| if (s_group_info && s_group_info->s_candidate) ------------------ | Branch (5914:9): [True: 288k, False: 0] | Branch (5914:25): [True: 252k, False: 36.3k] ------------------ 5915| 252k| { 5916| 252k| inchi_free( s_group_info->s_candidate ); ------------------ | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 252k, False: 0] | | | Branch (1152:50): [Folded, False: 252k] | | ------------------ ------------------ 5917| 252k| } 5918| 288k| if (pAATG && pAATG->nMarkedAtom) ------------------ | Branch (5918:9): [True: 288k, False: 0] | Branch (5918:18): [True: 59.9k, False: 228k] ------------------ 5919| 59.9k| { 5920| 59.9k| inchi_free( pAATG->nMarkedAtom ); ------------------ | | 1152| 59.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 59.9k, False: 0] | | | Branch (1152:50): [Folded, False: 59.9k] | | ------------------ ------------------ 5921| 59.9k| qzfree( pAATG->nEndPoint ); ------------------ | | 1176| 59.9k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 0, False: 59.9k] | | | Branch (1176:61): [Folded, False: 59.9k] | | ------------------ ------------------ 5922| | /*qzfree( pAATG->nAtTypeTotals );*/ /* nAtTypeTotals is a stack array */ 5923| 59.9k| } 5924| 288k| if (t_group_info && t_group_info->tGroupNumber) ------------------ | Branch (5924:9): [True: 252k, False: 36.3k] | Branch (5924:25): [True: 252k, False: 0] ------------------ 5925| 252k| { 5926| 252k| inchi_free( t_group_info->tGroupNumber ); ------------------ | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 252k, False: 0] | | | Branch (1152:50): [Folded, False: 252k] | | ------------------ ------------------ 5927| 252k| t_group_info->tGroupNumber = NULL; 5928| 252k| } 5929| | 5930| 288k| if (!bError && num_atoms == 1 && at[0].at_type == ATT_PROTON && t_group_info && !t_group_info->tni.nNumRemovedExplicitH) ------------------ | | 43| 473k|#define ATT_PROTON 0x1000 ------------------ | Branch (5930:9): [True: 288k, False: 12] | Branch (5930:20): [True: 184k, False: 103k] | Branch (5930:38): [True: 35.0k, False: 149k] | Branch (5930:69): [True: 35.0k, False: 0] | Branch (5930:85): [True: 35.0k, False: 0] ------------------ 5931| 35.0k| { 5932| | /* remove single isolated proton */ 5933| 35.0k| t_group_info->tni.nNumRemovedProtons = 1; 5934| 35.0k| t_group_info->tni.bNormalizationFlags |= FLAG_PROTON_SINGLE_REMOVED; ------------------ | | 153| 35.0k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 ------------------ 5935| 35.0k| if (at[0].iso_atw_diff) ------------------ | Branch (5935:13): [True: 586, False: 34.4k] ------------------ 5936| 586| { 5937| 586|#if ( FIX_CURE53_ISSUE_NULL_DEREFERENCE_MAKE_A_COPY_OF_T_GROUP_INFO==1 || defined(FIX_IMPOSSIBLE_H_ISOTOPE_BUG) ) 5938| 586| if (0 < at[0].iso_atw_diff && ------------------ | Branch (5938:17): [True: 584, False: 2] ------------------ 5939| 584| at[0].iso_atw_diff <= NUM_H_ISOTOPES) ------------------ | | 25| 584|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5939:17): [True: 584, False: 0] ------------------ 5940| 584| { 5941| 584| t_group_info->tni.nNumRemovedProtonsIsotopic[at[0].iso_atw_diff - 1] ++; 5942| 584| } 5943| |#else 5944| | t_group_info->tni.nNumRemovedProtonsIsotopic[at[0].iso_atw_diff - 1] ++; 5945| |#endif 5946| 586| } 5947| 35.0k| if (at_fixed_bonds_out) ------------------ | Branch (5947:13): [True: 35.0k, False: 0] ------------------ 5948| 35.0k| { 5949| 35.0k| memcpy(at_fixed_bonds_out, at, num_atoms * sizeof(at_fixed_bonds_out[0])); 5950| 35.0k| } 5951| | /*num_atoms --;*/ 5952| 35.0k| } 5953| | 5954| | 5955| | /* 5956| | Additional currently unused info: 5957| | 5958| | nOrigDelta > 0: original structure has been changed 5959| | due to fiund augmenting path(s) 5960| | nChanges > 0: either alt. bonds or taut. groups have been found 5961| | */ 5962| | 5963| 288k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 5964| 288k| if (stored_radicals) ------------------ | Branch (5964:9): [True: 0, False: 288k] ------------------ 5965| 0| { 5966| 0| inchi_free( stored_radicals ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5967| 0| } 5968| 288k|#endif 5969| | 5970| 288k| return bError ? bError : num_atoms; /* ret = 0 => success, any other => error */ ------------------ | Branch (5970:12): [True: 12, False: 288k] ------------------ 5971| 288k|} nMaxFlow2Check: 5976| 261k|{ 5977| 261k| BNS_EDGE *pEdge = pBNS->edge + iedge; 5978| 261k| int nMaxFlow = ( pEdge->cap & EDGE_FLOW_MASK ); /* edge cap */ ------------------ | | 133| 261k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 5979| | 5980| 261k| if (nMaxFlow > MAX_BOND_EDGE_CAP) ------------------ | | 123| 261k|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ | Branch (5980:9): [True: 0, False: 261k] ------------------ 5981| 0| { 5982| 0| nMaxFlow = MAX_BOND_EDGE_CAP; ------------------ | | 123| 0|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ 5983| 0| } 5984| 261k| return nMaxFlow; 5985| 261k|} nCurFlow2Check: 5990| 261k|{ 5991| 261k| BNS_EDGE *pEdge = pBNS->edge + iedge; 5992| 261k| int nCurFlow = ( pEdge->flow & EDGE_FLOW_MASK ); /* edge flow */ ------------------ | | 133| 261k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 5993| 261k| return nCurFlow; 5994| 261k|} nMinFlow2Check: 5999| 261k|{ 6000| 261k| BNS_EDGE *pEdge = pBNS->edge + iedge; 6001| 261k| Vertex v1 = pEdge->neighbor1; 6002| 261k| Vertex v2 = v1 ^ pEdge->neighbor12; 6003| 261k| int f12 = ( pEdge->flow & EDGE_FLOW_MASK ); ------------------ | | 133| 261k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6004| 261k| int rescap1, rescap2, rescap12, i, iedge_i; 6005| | 6006| 261k| if (f12 > 0) ------------------ | Branch (6006:9): [True: 90.7k, False: 170k] ------------------ 6007| 90.7k| { 6008| 262k| for (i = 0, rescap1 = 0; i < pBNS->vert[v1].num_adj_edges; i++) ------------------ | Branch (6008:34): [True: 171k, False: 90.7k] ------------------ 6009| 171k| { 6010| 171k| iedge_i = pBNS->vert[v1].iedge[i]; 6011| 171k| if (iedge_i == iedge) ------------------ | Branch (6011:17): [True: 90.7k, False: 80.5k] ------------------ 6012| 90.7k| { 6013| 90.7k| continue; 6014| 90.7k| } 6015| 80.5k| rescap1 += ( pBNS->edge[iedge_i].cap & EDGE_FLOW_MASK ) - ( pBNS->edge[iedge_i].flow & EDGE_FLOW_MASK ); ------------------ | | 133| 80.5k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ rescap1 += ( pBNS->edge[iedge_i].cap & EDGE_FLOW_MASK ) - ( pBNS->edge[iedge_i].flow & EDGE_FLOW_MASK ); ------------------ | | 133| 80.5k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6016| 80.5k| } 6017| 311k| for (i = 0, rescap2 = 0; i < pBNS->vert[v2].num_adj_edges; i++) ------------------ | Branch (6017:34): [True: 220k, False: 90.7k] ------------------ 6018| 220k| { 6019| 220k| iedge_i = pBNS->vert[v2].iedge[i]; 6020| 220k| if (iedge_i == iedge) ------------------ | Branch (6020:17): [True: 90.7k, False: 130k] ------------------ 6021| 90.7k| { 6022| 90.7k| continue; 6023| 90.7k| } 6024| 130k| rescap2 += ( pBNS->edge[iedge_i].cap & EDGE_FLOW_MASK ) - ( pBNS->edge[iedge_i].flow & EDGE_FLOW_MASK ); ------------------ | | 133| 130k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ rescap2 += ( pBNS->edge[iedge_i].cap & EDGE_FLOW_MASK ) - ( pBNS->edge[iedge_i].flow & EDGE_FLOW_MASK ); ------------------ | | 133| 130k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6025| 130k| } 6026| 90.7k| rescap12 = inchi_min( rescap1, rescap2 ); ------------------ | | 139| 90.7k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 28.9k, False: 61.8k] | | ------------------ ------------------ 6027| 90.7k| rescap12 = inchi_min( rescap12, f12 ); ------------------ | | 139| 90.7k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 72.8k, False: 17.9k] | | ------------------ ------------------ 6028| 90.7k| return f12 - rescap12; 6029| 90.7k| } 6030| | 6031| 170k| return 0; 6032| 261k|} bSetBondsAfterCheckOneBond: 6042| 27.7k|{ 6043| 27.7k| int ifcd, iedge, new_flow, ret_val, nChanges = 0, bError = 0; 6044| 27.7k| int bChangeFlow; 6045| 27.7k| Vertex v1, v2; 6046| 27.7k| int ineigh1, ineigh2; 6047| 27.7k| BNS_EDGE *pEdge; 6048| | 6049| 27.7k| bChangeFlow0 &= ~BNS_EF_CHNG_RSTR; /* do not change pEdge flow in SetBondType */ ------------------ | | 372| 27.7k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 27.7k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 27.7k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 6050| 27.7k| if (!bChangeFlow0) ------------------ | Branch (6050:9): [True: 7.54k, False: 20.1k] ------------------ 6051| 7.54k| { 6052| 7.54k| return 0; 6053| 7.54k| } 6054| | 6055| 20.1k| bChangeFlow = ( bChangeFlow0 & ~BNS_EF_SET_NOSTEREO ); ------------------ | | 377| 20.1k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ 6056| | 6057| | /* Find the next to the last changed */ 6058| 20.1k| if (bChangeFlow0 & BNS_EF_SET_NOSTEREO) ------------------ | | 377| 20.1k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ | Branch (6058:9): [True: 11.0k, False: 9.18k] ------------------ 6059| 11.0k| { 6060| 28.9k| for (ifcd = 0; NO_VERTEX != ( iedge = fcd[ifcd].iedge ); ifcd++) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | | 118| 28.9k|#define NO_VERTEX -2 ------------------ | Branch (6060:24): [True: 17.9k, False: 11.0k] ------------------ 6061| 17.9k| { 6062| 17.9k| iedge = fcd[ifcd].iedge; 6063| 17.9k| pEdge = pBNS->edge + iedge; 6064| 17.9k| if (!pEdge->pass) ------------------ | Branch (6064:17): [True: 0, False: 17.9k] ------------------ 6065| 0| { 6066| 0| continue; 6067| 0| } 6068| | 6069| 17.9k| if (!ifcd && nTestFlow >= 0) ------------------ | Branch (6069:17): [True: 10.8k, False: 7.12k] | Branch (6069:26): [True: 10.8k, False: 0] ------------------ 6070| 10.8k| { 6071| 10.8k| new_flow = nTestFlow; 6072| 10.8k| } 6073| 7.12k| else 6074| 7.12k| { 6075| 7.12k| new_flow = (int) pEdge->flow; 6076| 7.12k| } 6077| | 6078| 17.9k| v1 = pEdge->neighbor1; 6079| 17.9k| v2 = pEdge->neighbor12 ^ v1; 6080| 17.9k| if (v1 < num_atoms && v2 < num_atoms && new_flow != pEdge->flow0) ------------------ | Branch (6080:17): [True: 17.9k, False: 0] | Branch (6080:35): [True: 17.1k, False: 806] | Branch (6080:53): [True: 16.9k, False: 130] ------------------ 6081| 16.9k| { 6082| 16.9k| if (( pBNS->vert[v1].st_edge.cap0 == pBNS->vert[v1].st_edge.flow0 ) != ------------------ | Branch (6082:21): [True: 6.24k, False: 10.7k] ------------------ 6083| 16.9k| ( pBNS->vert[v1].st_edge.cap == pBNS->vert[v1].st_edge.flow ) || 6084| 10.7k| ( pBNS->vert[v2].st_edge.cap0 == pBNS->vert[v2].st_edge.flow0 ) != ------------------ | Branch (6084:22): [True: 2.59k, False: 8.15k] ------------------ 6085| 10.7k| ( pBNS->vert[v2].st_edge.cap == pBNS->vert[v2].st_edge.flow )) 6086| 8.84k| { 6087| 8.84k| bChangeFlow |= BNS_EF_SET_NOSTEREO; ------------------ | | 377| 8.84k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ 6088| 8.84k| nChanges |= BNS_EF_SET_NOSTEREO; ------------------ | | 377| 8.84k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ 6089| 8.84k| } 6090| 16.9k| } 6091| 17.9k| } 6092| 11.0k| } 6093| 9.18k| else 6094| 9.18k| { 6095| 23.7k| for (ifcd = 0; NO_VERTEX != ( iedge = fcd[ifcd].iedge ); ifcd++) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | | 118| 23.7k|#define NO_VERTEX -2 ------------------ | Branch (6095:24): [True: 14.5k, False: 9.18k] ------------------ 6096| 14.5k| { 6097| 14.5k| ; 6098| 14.5k| } 6099| 9.18k| } 6100| | 6101| | /* restore in reversed order to correctly handle vertex changed more than once */ 6102| 52.6k| for (ifcd -= 1; 0 <= ifcd; ifcd--) ------------------ | Branch (6102:21): [True: 32.4k, False: 20.1k] ------------------ 6103| 32.4k| { 6104| | 6105| 32.4k| iedge = fcd[ifcd].iedge; 6106| 32.4k| pEdge = pBNS->edge + iedge; 6107| 32.4k| if (!pEdge->pass) ------------------ | Branch (6107:13): [True: 1, False: 32.4k] ------------------ 6108| 1| { 6109| 1| continue; 6110| 1| } 6111| | 6112| 32.4k| if (!ifcd && nTestFlow >= 0) ------------------ | Branch (6112:13): [True: 18.5k, False: 13.8k] | Branch (6112:22): [True: 18.5k, False: 87] ------------------ 6113| 18.5k| { 6114| 18.5k| new_flow = nTestFlow; 6115| 18.5k| } 6116| 13.9k| else 6117| 13.9k| { 6118| 13.9k| new_flow = (int) pEdge->flow; 6119| 13.9k| } 6120| | 6121| 32.4k| v1 = pEdge->neighbor1; 6122| 32.4k| v2 = pEdge->neighbor12 ^ v1; 6123| 32.4k| if (v1 < num_atoms && v2 < num_atoms && bChangeFlow && new_flow != pEdge->flow0) ------------------ | Branch (6123:13): [True: 32.4k, False: 0] | Branch (6123:31): [True: 28.9k, False: 3.48k] | Branch (6123:49): [True: 28.9k, False: 0] | Branch (6123:64): [True: 28.6k, False: 298] ------------------ 6124| 28.6k| { 6125| 28.6k| ineigh1 = pEdge->neigh_ord[0]; 6126| 28.6k| ineigh2 = pEdge->neigh_ord[1]; 6127| 28.6k| ret_val = SetAtomBondType( pEdge, &at[v1].bond_type[ineigh1], &at[v2].bond_type[ineigh2], new_flow - pEdge->flow0, bChangeFlow ); 6128| 28.6k| if (!IS_BNS_ERROR( ret_val )) ------------------ | | 67| 28.6k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 28.6k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 28.6k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 28.6k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 28.6k, False: 0] | | | Branch (67:44): [True: 0, False: 28.6k] | | ------------------ ------------------ 6129| 28.6k| { 6130| 28.6k| nChanges |= ( ret_val > 0 ); 6131| 28.6k| } 6132| 0| else 6133| 0| { 6134| 0| bError = ret_val; 6135| 0| } 6136| 28.6k| } 6137| 32.4k| pEdge->pass = 0; 6138| 32.4k| } 6139| | 6140| 20.1k| return bError ? bError : nChanges; ------------------ | Branch (6140:12): [True: 0, False: 20.1k] ------------------ 6141| 27.7k|} bRestoreFlowAfterCheckOneBond: 6146| 86.8k|{ 6147| 86.8k| int ifcd, iedge; 6148| 86.8k| Vertex v1, v2; 6149| 86.8k| BNS_EDGE *pEdge; 6150| | 6151| | /* Find the next to the last changed */ 6152| 228k| for (ifcd = 0; NO_VERTEX != ( iedge = fcd[ifcd].iedge ); ifcd++) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | | 118| 228k|#define NO_VERTEX -2 ------------------ | Branch (6152:20): [True: 141k, False: 86.8k] ------------------ 6153| 141k| { 6154| 141k| ; 6155| 141k| } 6156| | 6157| | /* Restore in reversed order to correctly handle vertex changed more than once */ 6158| 228k| for (ifcd -= 1; 0 <= ifcd; ifcd--) ------------------ | Branch (6158:21): [True: 141k, False: 86.8k] ------------------ 6159| 141k| { 6160| | /* Restore edge flow & cap */ 6161| 141k| iedge = fcd[ifcd].iedge; 6162| 141k| pEdge = pBNS->edge + iedge; 6163| 141k| pEdge->flow = fcd[ifcd].flow; 6164| 141k| pEdge->cap = fcd[ifcd].cap; 6165| 141k| pEdge->pass = 0; 6166| | 6167| | /* Restore st-flow, cap */ 6168| 141k| if (NO_VERTEX != ( v1 = fcd[ifcd].v1 )) ------------------ | | 118| 141k|#define NO_VERTEX -2 ------------------ | Branch (6168:13): [True: 141k, False: 0] ------------------ 6169| 141k| { 6170| 141k| pBNS->vert[v1].st_edge.flow = fcd[ifcd].flow_st1; 6171| 141k| pBNS->vert[v1].st_edge.cap = fcd[ifcd].cap_st1; 6172| 141k| pBNS->vert[v1].st_edge.pass = 0; 6173| 141k| } 6174| 141k| if (NO_VERTEX != ( v2 = fcd[ifcd].v2 )) ------------------ | | 118| 141k|#define NO_VERTEX -2 ------------------ | Branch (6174:13): [True: 66.2k, False: 75.2k] ------------------ 6175| 66.2k| { 6176| 66.2k| pBNS->vert[v2].st_edge.flow = fcd[ifcd].flow_st2; 6177| 66.2k| pBNS->vert[v2].st_edge.cap = fcd[ifcd].cap_st2; 6178| 66.2k| pBNS->vert[v2].st_edge.pass = 0; 6179| 66.2k| } 6180| 141k| } 6181| | 6182| 86.8k| return 0; 6183| 86.8k|} bSetFlowToCheckOneBond: 6191| 69.5k|{ 6192| 69.5k| BNS_EDGE *pEdge = pBNS->edge + iedge; 6193| 69.5k| int f12 = ( pEdge->flow & EDGE_FLOW_MASK ); /* the original flow */ ------------------ | | 133| 69.5k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6194| 69.5k| int ifcd = 0; 6195| 69.5k| int nDots = 0; 6196| 69.5k| int i, iedge_i; 6197| | 6198| 69.5k| fcd[ifcd].iedge = NO_VERTEX; ------------------ | | 118| 69.5k|#define NO_VERTEX -2 ------------------ 6199| | 6200| 69.5k| if (f12 < flow) ------------------ | Branch (6200:9): [True: 42.0k, False: 27.4k] ------------------ 6201| 42.0k| { 6202| | /* Increase edge flow: Grab flow from the neighbors and delete it: set flow12=cap12 = 0 */ 6203| | /************************************************************************************/ 6204| | /* For example, simulate a new fixed double bond in place of a single bond and */ 6205| | /* creates ONE or NONE (in case of a radical on adjacent atom) augmenting paths and */ 6206| | /* makes it impossible for the BNS to set same flow as it originally was */ 6207| | /************************************************************************************/ 6208| 42.0k| Vertex v1 = pEdge->neighbor1; 6209| 42.0k| Vertex v2 = v1 ^ pEdge->neighbor12; 6210| 42.0k| Vertex v_i; /* neighbor of v1 or v2 */ 6211| 42.0k| BNS_EDGE *pEdge_i; 6212| 42.0k| int delta1, delta2, f, st_edge_rescap; 6213| | 6214| 42.0k| if (( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow || ------------------ | | 128| 42.0k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6214:13): [True: 1.72k, False: 40.3k] ------------------ 6215| 40.3k| ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow) ------------------ | | 128| 40.3k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6215:13): [True: 1.53k, False: 38.8k] ------------------ 6216| 3.25k| { 6217| 3.25k| return BNS_CANT_SET_BOND; ------------------ | | 57| 3.25k|#define BNS_CANT_SET_BOND (BNS_ERR + 9) /*(-9990)*/ | | ------------------ | | | | 47| 3.25k|#define BNS_ERR -9999 | | ------------------ ------------------ 6218| 3.25k| } 6219| 38.8k| if (( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12 || ------------------ | | 128| 38.8k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6219:13): [True: 0, False: 38.8k] ------------------ 6220| 38.8k| ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12) ------------------ | | 128| 38.8k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6220:13): [True: 0, False: 38.8k] ------------------ 6221| 0| { 6222| 0| return BNS_CAP_FLOW_ERR; ------------------ | | 58| 0|#define BNS_CAP_FLOW_ERR (BNS_ERR + 10) /*(-9989)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6223| 0| } 6224| | 6225| 38.8k| fcd[ifcd].iedge = iedge; 6226| 38.8k| fcd[ifcd].flow = pEdge->flow; 6227| 38.8k| fcd[ifcd].cap = pEdge->cap; 6228| | 6229| 38.8k| fcd[ifcd].v1 = v1; 6230| 38.8k| fcd[ifcd].flow_st1 = pBNS->vert[v1].st_edge.flow; 6231| 38.8k| fcd[ifcd].cap_st1 = pBNS->vert[v1].st_edge.cap; 6232| | 6233| 38.8k| fcd[ifcd].v2 = v2; 6234| 38.8k| fcd[ifcd].flow_st2 = pBNS->vert[v2].st_edge.flow; 6235| 38.8k| fcd[ifcd].cap_st2 = pBNS->vert[v2].st_edge.cap; 6236| | 6237| 38.8k| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 118| 38.8k|#define NO_VERTEX -2 ------------------ 6238| 38.8k| pEdge->pass |= 64; 6239| | 6240| 38.8k| delta1 = delta2 = flow - f12; 6241| | 6242| 38.8k| if (f12 > 0) ------------------ | Branch (6242:13): [True: 3.37k, False: 35.4k] ------------------ 6243| 3.37k| { 6244| | /* Remove old edge flow from the flow and cap of the adjacent vertices' st-edges */ 6245| 3.37k| pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6246| 3.37k| pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6247| 3.37k| pBNS->vert[v1].st_edge.flow = ( ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v1].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v1].st_edge.flow = ( ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v1].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6248| 3.37k| pBNS->vert[v2].st_edge.flow = ( ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v2].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v2].st_edge.flow = ( ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v2].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 3.37k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6249| | /* Delete current edge flow and capacity */ 6250| 3.37k| pEdge->flow = ( pEdge->flow & ~EDGE_FLOW_MASK ); ------------------ | | 133| 3.37k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6251| 3.37k| } 6252| 38.8k| pEdge->cap = ( pEdge->cap & ~EDGE_FLOW_MASK ); ------------------ | | 133| 38.8k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6253| | 6254| | /* Grab the adjacent vertex1 radical (st_edge_rescap) if it exists */ 6255| 38.8k| st_edge_rescap = ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 38.8k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ st_edge_rescap = ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 38.8k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6256| 39.6k| while (st_edge_rescap && delta1) ------------------ | Branch (6256:16): [True: 855, False: 38.8k] | Branch (6256:34): [True: 855, False: 0] ------------------ 6257| 855| { 6258| 855| st_edge_rescap--; /* grab the radical */ 6259| 855| delta1--; 6260| 855| pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 855|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 855|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6261| 855| nDots--; 6262| 855| } 6263| | 6264| | /* Grab the adjacent vertex2 radical (st_edge_rescap) if it exists */ 6265| 38.8k| st_edge_rescap = ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 38.8k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ st_edge_rescap = ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 38.8k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6266| 39.8k| while (st_edge_rescap && delta2) ------------------ | Branch (6266:16): [True: 1.05k, False: 38.8k] | Branch (6266:34): [True: 1.05k, False: 0] ------------------ 6267| 1.05k| { 6268| 1.05k| st_edge_rescap--; /* grab the radical */ 6269| 1.05k| delta2--; 6270| 1.05k| pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 1.05k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 1.05k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6271| 1.05k| nDots--; 6272| 1.05k| } 6273| | 6274| | /* Grab flows from v1 neighbors */ 6275| 96.3k| for (i = 0; delta1 && i < pBNS->vert[v1].num_adj_edges; i++) ------------------ | Branch (6275:21): [True: 58.3k, False: 37.9k] | Branch (6275:31): [True: 57.5k, False: 868] ------------------ 6276| 57.5k| { 6277| 57.5k| iedge_i = pBNS->vert[v1].iedge[i]; 6278| 57.5k| if (iedge_i == iedge) ------------------ | Branch (6278:17): [True: 12.6k, False: 44.9k] ------------------ 6279| 12.6k| { 6280| 12.6k| continue; 6281| 12.6k| } 6282| 44.9k| pEdge_i = pBNS->edge + iedge_i; 6283| 44.9k| if (IS_FORBIDDEN( pEdge_i->forbidden, pBNS )) ------------------ | | 41| 44.9k|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (41:48): [True: 941, False: 43.9k] | | ------------------ ------------------ 6284| 941| { 6285| 941| continue; 6286| 941| } 6287| 43.9k| f = ( pEdge_i->flow & EDGE_FLOW_MASK ); ------------------ | | 133| 43.9k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6288| 43.9k| if (f) ------------------ | Branch (6288:17): [True: 37.4k, False: 6.49k] ------------------ 6289| 37.4k| { 6290| 37.4k| v_i = pEdge_i->neighbor12 ^ v1; 6291| | 6292| 37.4k| fcd[ifcd].iedge = iedge_i; 6293| 37.4k| fcd[ifcd].flow = pEdge_i->flow; 6294| 37.4k| fcd[ifcd].cap = pEdge_i->cap; 6295| | 6296| 37.4k| fcd[ifcd].v1 = v_i; 6297| 37.4k| fcd[ifcd].flow_st1 = pBNS->vert[v_i].st_edge.flow; 6298| 37.4k| fcd[ifcd].cap_st1 = pBNS->vert[v_i].st_edge.cap; 6299| | 6300| 37.4k| fcd[ifcd].v2 = NO_VERTEX; ------------------ | | 118| 37.4k|#define NO_VERTEX -2 ------------------ 6301| 37.4k| fcd[ifcd].flow_st2 = 0; 6302| 37.4k| fcd[ifcd].cap_st2 = 0; 6303| | 6304| 37.4k| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 118| 37.4k|#define NO_VERTEX -2 ------------------ 6305| 37.4k| pEdge_i->pass |= 64; 6306| | 6307| 79.2k| while (f && delta1) ------------------ | Branch (6307:24): [True: 50.4k, False: 28.8k] | Branch (6307:29): [True: 41.7k, False: 8.64k] ------------------ 6308| 41.7k| { 6309| 41.7k| f--; 6310| 41.7k| delta1--; 6311| 41.7k| pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 133| 41.7k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 133| 41.7k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6312| 41.7k| pBNS->vert[v_i].st_edge.flow = ( ( pBNS->vert[v_i].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v_i].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.7k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v_i].st_edge.flow = ( ( pBNS->vert[v_i].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v_i].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.7k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6313| | /* next 2 lines added 01-22-2002 */ 6314| 41.7k| pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.7k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.7k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6315| 41.7k| pBNS->vert[v1].st_edge.flow = ( ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v1].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.7k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v1].st_edge.flow = ( ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v1].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.7k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6316| | 6317| 41.7k| nDots++; 6318| 41.7k| } 6319| 37.4k| } 6320| 43.9k| } 6321| | 6322| | /* Grab flows from v2 neighbors */ 6323| 109k| for (i = 0; delta2 && i < pBNS->vert[v2].num_adj_edges; i++) ------------------ | Branch (6323:21): [True: 72.1k, False: 37.6k] | Branch (6323:31): [True: 70.9k, False: 1.18k] ------------------ 6324| 70.9k| { 6325| 70.9k| iedge_i = pBNS->vert[v2].iedge[i]; 6326| 70.9k| if (iedge_i == iedge) ------------------ | Branch (6326:17): [True: 21.1k, False: 49.8k] ------------------ 6327| 21.1k| { 6328| 21.1k| continue; 6329| 21.1k| } 6330| 49.8k| pEdge_i = pBNS->edge + iedge_i; 6331| 49.8k| if (IS_FORBIDDEN( pEdge_i->forbidden, pBNS )) ------------------ | | 41| 49.8k|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (41:48): [True: 1.37k, False: 48.4k] | | ------------------ ------------------ 6332| 1.37k| { 6333| 1.37k| continue; 6334| 1.37k| } 6335| 48.4k| f = ( pEdge_i->flow & EDGE_FLOW_MASK ); ------------------ | | 133| 48.4k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6336| 48.4k| if (f) ------------------ | Branch (6336:17): [True: 37.8k, False: 10.6k] ------------------ 6337| 37.8k| { 6338| 37.8k| v_i = pEdge_i->neighbor12 ^ v2; 6339| | 6340| 37.8k| fcd[ifcd].iedge = iedge_i; 6341| 37.8k| fcd[ifcd].flow = pEdge_i->flow; 6342| 37.8k| fcd[ifcd].cap = pEdge_i->cap; 6343| | 6344| 37.8k| fcd[ifcd].v1 = v_i; 6345| 37.8k| fcd[ifcd].flow_st1 = pBNS->vert[v_i].st_edge.flow; 6346| 37.8k| fcd[ifcd].cap_st1 = pBNS->vert[v_i].st_edge.cap; 6347| | 6348| 37.8k| fcd[ifcd].v2 = NO_VERTEX; ------------------ | | 118| 37.8k|#define NO_VERTEX -2 ------------------ 6349| 37.8k| fcd[ifcd].flow_st2 = 0; 6350| 37.8k| fcd[ifcd].cap_st2 = 0; 6351| | 6352| 37.8k| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 118| 37.8k|#define NO_VERTEX -2 ------------------ 6353| 37.8k| pEdge_i->pass |= 64; 6354| | 6355| 79.0k| while (f && delta2) ------------------ | Branch (6355:24): [True: 49.1k, False: 29.9k] | Branch (6355:29): [True: 41.2k, False: 7.90k] ------------------ 6356| 41.2k| { 6357| 41.2k| f--; 6358| 41.2k| delta2--; 6359| 41.2k| pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 133| 41.2k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 133| 41.2k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6360| 41.2k| pBNS->vert[v_i].st_edge.flow = ( ( pBNS->vert[v_i].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v_i].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v_i].st_edge.flow = ( ( pBNS->vert[v_i].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v_i].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6361| | /* next 2 lines added 01-22-2002 */ 6362| 41.2k| pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6363| 41.2k| pBNS->vert[v2].st_edge.flow = ( ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v2].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v2].st_edge.flow = ( ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) - 1 ) | ( pBNS->vert[v2].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 41.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6364| | 6365| 41.2k| nDots++; 6366| 41.2k| } 6367| 37.8k| } 6368| 48.4k| } 6369| 38.8k| if (delta1 || delta2) ------------------ | Branch (6369:13): [True: 868, False: 37.9k] | Branch (6369:23): [True: 1.04k, False: 36.9k] ------------------ 6370| 1.91k| { 6371| 1.91k| return BNS_CANT_SET_BOND; ------------------ | | 57| 1.91k|#define BNS_CANT_SET_BOND (BNS_ERR + 9) /*(-9990)*/ | | ------------------ | | | | 47| 1.91k|#define BNS_ERR -9999 | | ------------------ ------------------ 6372| 1.91k| } 6373| 38.8k| } 6374| | 6375| 64.3k| if (f12 >= flow) ------------------ | Branch (6375:9): [True: 27.4k, False: 36.9k] ------------------ 6376| 27.4k| { 6377| | /* Decrease edge flow: Redirect flow to the neighbors and delete it on the edge: set flow12=cap12 = 0 */ 6378| | /* f12==flow fixes flow through the edge so that BNS cannot change it */ 6379| | /**********************************************************************************************/ 6380| | /* For example, simulate a removal of a double bond and create ONE or NONE augmenting path */ 6381| | /* Make it impossible for BNS to set same flow as it originally was */ 6382| | /**********************************************************************************************/ 6383| 27.4k| Vertex v1 = pEdge->neighbor1; 6384| 27.4k| Vertex v2 = ( v1 ^ pEdge->neighbor12 ); 6385| 27.4k| int delta; 6386| | /* if NOT (st-cap >= st-flow >= f12 >= flow) then error in the BN structure */ 6387| 27.4k| if (( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12 || ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6387:13): [True: 0, False: 27.4k] ------------------ 6388| 27.4k| ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12 || ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6388:13): [True: 0, False: 27.4k] ------------------ 6389| 27.4k| ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow || ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6389:14): [True: 0, False: 27.4k] ------------------ 6390| 27.4k| ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow) ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6390:14): [True: 0, False: 27.4k] ------------------ 6391| 0| { 6392| 0| return BNS_CAP_FLOW_ERR; ------------------ | | 58| 0|#define BNS_CAP_FLOW_ERR (BNS_ERR + 10) /*(-9989)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6393| 0| } 6394| 27.4k| fcd[ifcd].iedge = iedge; 6395| 27.4k| fcd[ifcd].flow = pEdge->flow; 6396| 27.4k| fcd[ifcd].cap = pEdge->cap; 6397| | 6398| 27.4k| fcd[ifcd].v1 = v1; 6399| 27.4k| fcd[ifcd].flow_st1 = pBNS->vert[v1].st_edge.flow; 6400| 27.4k| fcd[ifcd].cap_st1 = pBNS->vert[v1].st_edge.cap; 6401| | 6402| 27.4k| fcd[ifcd].v2 = v2; 6403| 27.4k| fcd[ifcd].flow_st2 = pBNS->vert[v2].st_edge.flow; 6404| 27.4k| fcd[ifcd].cap_st2 = pBNS->vert[v2].st_edge.cap; 6405| | 6406| 27.4k| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 118| 27.4k|#define NO_VERTEX -2 ------------------ 6407| 27.4k| pEdge->pass |= 64; 6408| | 6409| 27.4k| delta = f12 - flow; 6410| | 6411| | /* Remove current edge flow from st-edges */ 6412| | /* -- seem to be a bug -- 6413| | pBNS->vert[v1].st_edge.flow = ((pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK)-delta) | (pBNS->vert[v1].st_edge.flow & ~EDGE_FLOW_ST_MASK); 6414| | pBNS->vert[v2].st_edge.flow = ((pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK)-delta) | (pBNS->vert[v2].st_edge.flow & ~EDGE_FLOW_ST_MASK); 6415| | */ 6416| | 6417| | /* Replacement to the above 2 lines 01-16-2002 */ 6418| | /* Remove old edge flow from the flow of the adjacent vertices' st-edges */ 6419| | 6420| 27.4k| pBNS->vert[v1].st_edge.flow = ( ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v1].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v1].st_edge.flow = ( ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v1].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6421| 27.4k| pBNS->vert[v2].st_edge.flow = ( ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v2].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v2].st_edge.flow = ( ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) - f12 ) | ( pBNS->vert[v2].st_edge.flow & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6422| | 6423| | /* Sdded 01-16-2002: reduce st-cap if new flow > 0 */ 6424| | /* Remove new edge flow from the cap of the adjacent vertices' st-edges */ 6425| 27.4k| pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - flow ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v1].st_edge.cap = ( ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - flow ) | ( pBNS->vert[v1].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6426| 27.4k| pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - flow ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ pBNS->vert[v2].st_edge.cap = ( ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - flow ) | ( pBNS->vert[v2].st_edge.cap & ~EDGE_FLOW_ST_MASK ); ------------------ | | 128| 27.4k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6427| | 6428| | /* delete current edge flow and capacity */ 6429| 27.4k| pEdge->flow = ( pEdge->flow & ~EDGE_FLOW_MASK ); ------------------ | | 133| 27.4k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6430| 27.4k| pEdge->cap = ( pEdge->cap & ~EDGE_FLOW_MASK ); ------------------ | | 133| 27.4k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6431| 27.4k| nDots = 2 * delta; 6432| 27.4k| } 6433| | 6434| 64.3k| return nDots; 6435| 64.3k|} bAddNewVertex: 6453| 29.3k|{ 6454| 29.3k| Vertex vlast = pBNS->num_vertices - 1; 6455| 29.3k| Vertex vnew = pBNS->num_vertices; 6456| 29.3k| Vertex v2 = nVertDoubleBond; 6457| 29.3k| BNS_VERTEX *pVert2 = pBNS->vert + v2; /* pointer to an old vertex */ 6458| 29.3k| BNS_VERTEX *pNewVert = pBNS->vert + vnew; /* pointer to a new vertex */ 6459| | 6460| 29.3k| EdgeIndex iedge = pBNS->num_edges; 6461| 29.3k| BNS_EDGE *pEdge = pBNS->edge + iedge; /* pointer to a new edge */ 6462| | 6463| 29.3k| if (iedge >= pBNS->max_edges || vnew >= pBNS->max_vertices) ------------------ | Branch (6463:9): [True: 0, False: 29.3k] | Branch (6463:37): [True: 0, False: 29.3k] ------------------ 6464| 0| { 6465| 0| return BNS_VERT_EDGE_OVFL; /* edges or vertices overflow */ ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6466| 0| } 6467| 29.3k| if (( pBNS->vert[vlast].iedge - pBNS->iedge ) + pBNS->vert[vlast].max_adj_edges + nMaxAdjEdges >= pBNS->max_iedges) ------------------ | Branch (6467:9): [True: 0, False: 29.3k] ------------------ 6468| 0| { 6469| 0| return BNS_VERT_EDGE_OVFL; /* iedges overflow */ ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6470| 0| } 6471| 29.3k| if (pVert2->num_adj_edges >= pVert2->max_adj_edges || nMaxAdjEdges <= 0) ------------------ | Branch (6471:9): [True: 4, False: 29.3k] | Branch (6471:59): [True: 0, False: 29.3k] ------------------ 6472| 4| { 6473| 4| return BNS_VERT_EDGE_OVFL; /* neighbors overflow */ ------------------ | | 54| 4|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 4|#define BNS_ERR -9999 | | ------------------ ------------------ 6474| 4| } 6475| | 6476| | /* Fill out the new edge, set its cap and flow, connect */ 6477| | /* memset( pEdge, 0, sizeof(*pEdge) ); */ 6478| 29.3k| pEdge->cap = pEdge->cap0 = nCap; 6479| 29.3k| pEdge->flow = pEdge->flow0 = nFlow; 6480| 29.3k| pEdge->pass = 0; 6481| 29.3k| pEdge->neighbor1 = v2; 6482| 29.3k| pEdge->neighbor12 = v2 ^ vnew; 6483| 29.3k| pEdge->forbidden = 0; 6484| | 6485| | /* Fill out the new vertex */ 6486| | /* memset( pNewVert, 0, sizeof(*pNewVert) ); */ 6487| 29.3k| pNewVert->max_adj_edges = nMaxAdjEdges; 6488| 29.3k| pNewVert->num_adj_edges = 0; 6489| 29.3k| pNewVert->st_edge.cap0 = pNewVert->st_edge.cap = nCap; 6490| 29.3k| pNewVert->st_edge.flow0 = pNewVert->st_edge.flow = nFlow; 6491| 29.3k| pNewVert->st_edge.pass = 0; /* add initialization; added 2006-03-25 */ 6492| 29.3k| pNewVert->iedge = pBNS->vert[vlast].iedge + pBNS->vert[vlast].max_adj_edges; 6493| 29.3k| pNewVert->type = BNS_VERT_TYPE_TEMP; ------------------ | | 51| 29.3k|#define BNS_VERT_TYPE_TEMP 0x0040 ------------------ 6494| 29.3k| *nDots += nCap - nFlow; 6495| | 6496| 29.3k| pEdge->neigh_ord[v2 > vnew] = pVert2->num_adj_edges; 6497| 29.3k| pEdge->neigh_ord[v2 < vnew] = pNewVert->num_adj_edges; 6498| | 6499| | /* Connect new edge to v2 */ 6500| 29.3k| pVert2->iedge[pVert2->num_adj_edges++] = iedge; 6501| | /* Connect new edge to vnew */ 6502| 29.3k| pNewVert->iedge[pNewVert->num_adj_edges++] = iedge; 6503| | 6504| | /* Fix v2 flow and cap */ 6505| 29.3k| *nDots -= (int) pVert2->st_edge.cap - (int) pVert2->st_edge.flow; 6506| 29.3k| pVert2->st_edge.flow += nFlow; 6507| 29.3k| if (pVert2->st_edge.cap < pVert2->st_edge.flow) ------------------ | Branch (6507:9): [True: 0, False: 29.3k] ------------------ 6508| 0| { 6509| 0| pVert2->st_edge.cap = pVert2->st_edge.flow; 6510| 0| } 6511| 29.3k| *nDots += (int) pVert2->st_edge.cap - (int) pVert2->st_edge.flow; 6512| | 6513| 29.3k| pBNS->num_edges++; 6514| 29.3k| pBNS->num_vertices++; 6515| | 6516| 29.3k| return vnew; 6517| 29.3k|} AddNewEdge: 6526| 9.17k|{ 6527| 9.17k| int ip1 = (int) ( p1 - pBNS->vert ); 6528| 9.17k| int ip2 = (int) ( p2 - pBNS->vert ); 6529| 9.17k| int ie = pBNS->num_edges; 6530| 9.17k| BNS_EDGE *e = pBNS->edge + ie; 6531| | 6532| | /* Debug: check bounds */ 6533| 9.17k| if (ip1 >= pBNS->max_vertices || ip1 < 0 || ------------------ | Branch (6533:9): [True: 0, False: 9.17k] | Branch (6533:38): [True: 0, False: 9.17k] ------------------ 6534| 9.17k| ip2 >= pBNS->max_vertices || ip2 < 0 || ------------------ | Branch (6534:10): [True: 0, False: 9.17k] | Branch (6534:39): [True: 0, False: 9.17k] ------------------ 6535| 9.17k| ie >= pBNS->max_edges || ie < 0 || ------------------ | Branch (6535:10): [True: 0, False: 9.17k] | Branch (6535:35): [True: 0, False: 9.17k] ------------------ 6536| 9.17k| ( p1->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (6536:10): [True: 0, False: 9.17k] ------------------ 6537| 9.17k| ( p1->iedge - pBNS->iedge ) + p1->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (6537:10): [True: 0, False: 9.17k] ------------------ 6538| 9.17k| ( p2->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (6538:10): [True: 0, False: 9.17k] ------------------ 6539| 9.17k| ( p2->iedge - pBNS->iedge ) + p2->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (6539:10): [True: 0, False: 9.17k] ------------------ 6540| 9.17k| p1->num_adj_edges >= p1->max_adj_edges || ------------------ | Branch (6540:10): [True: 0, False: 9.17k] ------------------ 6541| 9.17k| p2->num_adj_edges >= p2->max_adj_edges) ------------------ | Branch (6541:10): [True: 0, False: 9.17k] ------------------ 6542| 0| { 6543| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6544| 0| } 6545| | 6546| | /* Clear the edge */ 6547| 9.17k| memset( e, 0, sizeof( *e ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6548| | 6549| | /* Connect */ 6550| 9.17k| e->neighbor1 = inchi_min( ip1, ip2 ); ------------------ | | 139| 9.17k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 9.17k] | | ------------------ ------------------ 6551| 9.17k| e->neighbor12 = ip1 ^ ip2; 6552| 9.17k| p1->iedge[p1->num_adj_edges] = ie; 6553| 9.17k| p2->iedge[p2->num_adj_edges] = ie; 6554| 9.17k| e->neigh_ord[ip1 > ip2] = p1->num_adj_edges++; 6555| 9.17k| e->neigh_ord[ip1 < ip2] = p2->num_adj_edges++; 6556| 9.17k| e->cap = e->cap0 = nEdgeCap; 6557| 9.17k| e->flow = e->flow0 = nEdgeFlow; 6558| 9.17k| p1->st_edge.flow += nEdgeFlow; 6559| 9.17k| p2->st_edge.flow += nEdgeFlow; 6560| 9.17k| if (p1->st_edge.cap < p1->st_edge.flow) ------------------ | Branch (6560:9): [True: 610, False: 8.56k] ------------------ 6561| 610| { 6562| 610| p1->st_edge.cap = p1->st_edge.flow; 6563| 610| } 6564| 9.17k| if (p2->st_edge.cap < p2->st_edge.flow) ------------------ | Branch (6564:9): [True: 0, False: 9.17k] ------------------ 6565| 0| { 6566| 0| p2->st_edge.cap = p2->st_edge.flow; 6567| 0| } 6568| 9.17k| pBNS->num_edges++; 6569| | 6570| 9.17k| return ie; 6571| 9.17k|} GetEdgeToGroupVertex: 6576| 35.6k|{ 6577| 35.6k| if (v1 < pBNS->num_atoms) ------------------ | Branch (6577:9): [True: 35.6k, False: 0] ------------------ 6578| 35.6k| { 6579| 35.6k| Vertex v2; 6580| 35.6k| BNS_EDGE *pEdge1; 6581| 35.6k| BNS_VERTEX *pVert1 = pBNS->vert + v1; 6582| 35.6k| int i = pVert1->num_adj_edges - 1; 6583| | 6584| 82.0k| while (0 <= i) ------------------ | Branch (6584:16): [True: 49.7k, False: 32.2k] ------------------ 6585| 49.7k| { 6586| 49.7k| pEdge1 = pBNS->edge + pVert1->iedge[i]; 6587| 49.7k| v2 = pEdge1->neighbor12 ^ v1; 6588| 49.7k| if (pBNS->vert[v2].type == type) ------------------ | Branch (6588:17): [True: 3.39k, False: 46.3k] ------------------ 6589| 3.39k| { 6590| 3.39k| return IS_FORBIDDEN( pEdge1->forbidden, pBNS ) ? NO_VERTEX : pVert1->iedge[i]; ------------------ | | 41| 3.39k|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (41:48): [True: 0, False: 3.39k] | | ------------------ ------------------ return IS_FORBIDDEN( pEdge1->forbidden, pBNS ) ? NO_VERTEX : pVert1->iedge[i]; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 6591| 3.39k| } 6592| 46.3k| i--; 6593| 46.3k| } 6594| 32.2k| return NO_VERTEX; /* not found t-group */ ------------------ | | 118| 32.2k|#define NO_VERTEX -2 ------------------ 6595| 35.6k| } 6596| 0| else 6597| 0| { 6598| 0| if (v1 < pBNS->num_vertices) ------------------ | Branch (6598:13): [True: 0, False: 0] ------------------ 6599| 0| { 6600| 0| return NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 6601| 0| } 6602| 0| } 6603| | 6604| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6605| 35.6k|} GetGroupVertex: 6610| 2.95k|{ 6611| 2.95k| if (v1 < pBNS->num_atoms) ------------------ | Branch (6611:9): [True: 2.95k, False: 0] ------------------ 6612| 2.95k| { 6613| 2.95k| Vertex v2; 6614| 2.95k| BNS_EDGE *pEdge1; 6615| 2.95k| BNS_VERTEX *pVert1 = pBNS->vert + v1; 6616| 2.95k| int i = pVert1->num_adj_edges - 1; 6617| | 6618| 2.95k| AT_NUMB type2; 6619| | 6620| 2.95k| if (type == BNS_VERT_TYPE_ENDPOINT) ------------------ | | 46| 2.95k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6620:13): [True: 2.95k, False: 0] ------------------ 6621| 2.95k| { 6622| 2.95k| type2 = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 2.95k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 6623| 2.95k| } 6624| 0| else 6625| 0| { 6626| 0| if (type == BNS_VERT_TYPE_C_POINT) ------------------ | | 48| 0|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ | Branch (6626:17): [True: 0, False: 0] ------------------ 6627| 0| { 6628| 0| type2 = BNS_VERT_TYPE_C_GROUP; ------------------ | | 49| 0|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ 6629| 0| } 6630| 0| else 6631| 0| { 6632| 0| type2 = 0; 6633| 0| } 6634| 0| } 6635| | 6636| 2.95k| if (( pVert1->type & type ) == type) ------------------ | Branch (6636:13): [True: 2.95k, False: 0] ------------------ 6637| 2.95k| { 6638| 4.32k| while (0 <= i) ------------------ | Branch (6638:20): [True: 3.63k, False: 695] ------------------ 6639| 3.63k| { 6640| 3.63k| pEdge1 = pBNS->edge + pVert1->iedge[i]; 6641| 3.63k| v2 = pEdge1->neighbor12 ^ v1; 6642| 3.63k| if (pBNS->vert[v2].type == type2) ------------------ | Branch (6642:21): [True: 2.26k, False: 1.36k] ------------------ 6643| 2.26k| { 6644| 2.26k| if (IS_FORBIDDEN( pEdge1->forbidden, pBNS )) ------------------ | | 41| 2.26k|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (41:48): [True: 0, False: 2.26k] | | ------------------ ------------------ 6645| 0| { 6646| 0| return NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 6647| 0| } 6648| 2.26k| return v2; 6649| 2.26k| } 6650| 1.36k| i--; 6651| 1.36k| } 6652| 2.95k| } 6653| 695| return BNS_BOND_ERR; /* not found t-group */ ------------------ | | 52| 695|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 695|#define BNS_ERR -9999 | | ------------------ ------------------ 6654| 2.95k| } 6655| 0| else 6656| 0| { 6657| 0| if (v1 < pBNS->num_vertices) ------------------ | Branch (6657:13): [True: 0, False: 0] ------------------ 6658| 0| { 6659| 0| return NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 6660| 0| } 6661| 0| } 6662| | 6663| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6664| 2.95k|} bAddStCapToAVertex: 6674| 20.3k|{ 6675| 20.3k| BNS_VERTEX *pVert1 = pBNS->vert + v1; 6676| 20.3k| BNS_VERTEX *pVert; 6677| 20.3k| BNS_EDGE *pEdge; 6678| 20.3k| Vertex v; 6679| 20.3k| int i, n; 6680| 20.3k| VertexFlow nNewCap; 6681| | 6682| | /* Change v1: increment its st-cap */ 6683| 20.3k| n = 0; 6684| 20.3k| nOldCapVertSingleBond[n++] = pVert1->st_edge.cap; 6685| | /*if ( pVert1->st_edge.cap == pVert1->st_edge.flow ) {*/ 6686| 20.3k| pVert1->st_edge.cap++; 6687| 20.3k| *nDots += 1; 6688| | 6689| | /*}*/ 6690| | /* increment caps of adjacent edges if 6691| | (1) the neighbor has st-cap != 0 and 6692| | (2) (edge cap==0) OR (nSumEdgeCap < pVert1->st_edge.cap && pVert->st_edge.flow > pVert1->st_edge.cap) 6693| | */ 6694| 20.3k| if (!( pVert1->type & BNS_VERT_TYPE_ANY_GROUP )) ------------------ | | 59| 20.3k|#define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 47| 20.3k|#define BNS_VERT_TYPE_TGROUP 0x0004 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 49| 20.3k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 50| 20.3k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ ------------------ | Branch (6694:9): [True: 17.7k, False: 2.65k] ------------------ 6695| 17.7k| { 6696| | /* 6697| | AT_NUMB nSumEdgeCap = 0; 6698| | for ( i = 0; i < pVert1->num_adj_edges; i ++ ) { 6699| | pEdge = pBNS->edge + pVert1->iedge[i]; 6700| | nSumEdgeCap += pEdge->cap; 6701| | } 6702| | */ 6703| | /* do not increment caps of t-group or c-group edges */ 6704| 50.1k| for (i = 0; i < pVert1->num_adj_edges; i++) ------------------ | Branch (6704:21): [True: 32.4k, False: 17.7k] ------------------ 6705| 32.4k| { 6706| 32.4k| pEdge = pBNS->edge + pVert1->iedge[i]; 6707| 32.4k| nOldCapVertSingleBond[n++] = pEdge->cap; /* save edge cap */ 6708| 32.4k| v = pEdge->neighbor12 ^ v1; 6709| 32.4k| if (v == v2 && !bAdjacentDonors) ------------------ | Branch (6709:17): [True: 3.97k, False: 28.4k] | Branch (6709:28): [True: 3.92k, False: 48] ------------------ 6710| 3.92k| { 6711| 3.92k| continue; 6712| 3.92k| } 6713| 28.5k| pVert = pBNS->vert + v; 6714| 28.5k| if (pVert->type & BNS_VERT_TYPE_ANY_GROUP) ------------------ | | 59| 28.5k|#define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 47| 28.5k|#define BNS_VERT_TYPE_TGROUP 0x0004 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 49| 28.5k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 50| 28.5k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ ------------------ | Branch (6714:17): [True: 3.33k, False: 25.1k] ------------------ 6715| 3.33k| continue; 6716| 25.1k| nNewCap = inchi_min( pVert->st_edge.cap, pVert1->st_edge.cap ); ------------------ | | 139| 25.1k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 10.4k, False: 14.6k] | | ------------------ ------------------ 6717| 25.1k| nNewCap = inchi_min( nNewCap, MAX_BOND_EDGE_CAP ); ------------------ | | 139| 25.1k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 22.2k, False: 2.94k] | | ------------------ ------------------ 6718| 25.1k| pEdge->cap = nNewCap; /* change edge cap */ 6719| | /* 6720| | if ( pVert->st_edge.cap > 0 && !pEdge->cap ) { 6721| | pEdge->cap ++; 6722| | } else 6723| | if ( pVert->st_edge.flow > pVert1->st_edge.cap && 6724| | pEdge->cap < MAX_BOND_EDGE_CAP && 6725| | nSumEdgeCap < pVert1->st_edge.cap ) { 6726| | pEdge->cap ++; 6727| | } 6728| | */ 6729| 25.1k| } 6730| 17.7k| } 6731| | 6732| 20.3k| return n; /* number of elements in nOldCapVertSingleBond[*] */ 6733| 20.3k|} bSetBnsToCheckAltPath: 6751| 23.6k|{ 6752| | 6753| 23.6k| if (!pBNS->vert[nVertDoubleBond].st_edge.flow && ------------------ | Branch (6753:9): [True: 3.01k, False: 20.6k] ------------------ 6754| | 6755| 3.01k| !( path_type == ALT_PATH_MODE_REM2H_CHG || ------------------ | | 314| 6.02k|#define ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */ ------------------ | Branch (6755:13): [True: 22, False: 2.98k] ------------------ 6756| 2.98k| path_type == ALT_PATH_MODE_ADD2H_CHG || ------------------ | | 315| 6.00k|#define ALT_PATH_MODE_ADD2H_CHG 6 /* add 2 H along alt. path A=-=B => AH-=-BH and change bonds to alternating */ ------------------ | Branch (6756:13): [True: 0, False: 2.98k] ------------------ 6757| 2.98k| path_type == ALT_PATH_MODE_REM2H_TST || ------------------ | | 316| 6.00k|#define ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */ ------------------ | Branch (6757:13): [True: 77, False: 2.91k] ------------------ 6758| 2.91k| path_type == ALT_PATH_MODE_ADD2H_TST ) ------------------ | | 317| 2.91k|#define ALT_PATH_MODE_ADD2H_TST 8 /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */ ------------------ | Branch (6758:13): [True: 0, False: 2.91k] ------------------ 6759| 23.6k| ) 6760| 2.91k| { 6761| 2.91k| return BNS_CHK_ALTP_NO_ALTPATH; ------------------ | | 6736| 2.91k|#define BNS_CHK_ALTP_NO_ALTPATH 0 ------------------ 6762| 2.91k| } 6763| 20.7k| else 6764| 20.7k| { 6765| 20.7k| Vertex vNew; 6766| 20.7k| Vertex v1 = nVertSingleBond; 6767| 20.7k| Vertex v2 = nVertDoubleBond; 6768| | 6769| 20.7k| BNS_VERTEX *pVert1 = pBNS->vert + v1; 6770| 20.7k| BNS_VERTEX *pVert2 = pBNS->vert + v2; 6771| 20.7k| int n, bAdjacentDonors = 0; 6772| 20.7k| int ifcd = 0; 6773| | 6774| 20.7k| Vertex t1 = NO_VERTEX; ------------------ | | 118| 20.7k|#define NO_VERTEX -2 ------------------ 6775| 20.7k| Vertex t2 = NO_VERTEX; ------------------ | | 118| 20.7k|#define NO_VERTEX -2 ------------------ 6776| 20.7k| int iapc; 6777| | 6778| | /*#if ( TEST_REMOVE_S_ATOMS == 1 )*/ /* && ALT_PATH_MODE_4_SALT == path_type */ 6779| 20.7k| if (( *pBNS->pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) && ------------------ | | 922| 20.7k|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (6779:13): [True: 19.9k, False: 851] ------------------ 6780| 19.9k| ALT_PATH_MODE_4_SALT2 == path_type && ------------------ | | 313| 19.9k|#define ALT_PATH_MODE_4_SALT2 4 /* mark alt bonds along the path, path to taut. group fict. vertex if exists */ ------------------ | Branch (6780:14): [True: 0, False: 19.9k] ------------------ 6781| 0| ( BNS_VERT_TYPE_ENDPOINT & type )) ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6781:14): [True: 0, False: 0] ------------------ 6782| 0| { 6783| | /* 6784| | --------------------------------------------------------- 6785| | \ action | DB action (v2) | SB action (v1) | 6786| | vertex \ | accept H @ vertex | donate H @ vertex | 6787| | type \ | nVertDoubleBond | nVertSingleBond | 6788| | ----------------+-------------------+-------------------+ 6789| | -ZH (v1) | error | -ZH(.) | 6790| | (cap>0 on edge | | increment | 6791| | except v1-v2) | | st-cap on Z | 6792| | ----------------+-------------------+-------------------+ 6793| | =Z (v2) | =Z-(.) | error | 6794| | (st-flow>0) | add fict vertex | | 6795| | | with st-cap=1 | | 6796| | ----------------+-------------------+-------------------+ 6797| | endpoint | T(.) | T-(.) | 6798| | of t-group | increment | add fict vertex | 6799| | represented | st-cap on T | with st-cap=1 | 6800| | by fictitious | | | 6801| | vertex T | | | 6802| | --------------------------------------------------------- 6803| | */ 6804| | 6805| 0| int bSet_v1; /* indicator: v1 has been set */ 6806| 0| int bSet_v2; /* indicator: v2 has been set */ 6807| 0| int i; 6808| | 6809| 0| Vertex v1t = NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 6810| 0| Vertex v2t = NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 6811| 0| Vertex v1Act, v2Act; 6812| 0| Vertex v; 6813| | 6814| 0| memset( apc, 0, sizeof( *apc ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6815| 0| fcd[ifcd].iedge = NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 6816| 0| *nDots = 0; 6817| | 6818| 0| if (v1 == v2) ------------------ | Branch (6818:17): [True: 0, False: 0] ------------------ 6819| 0| { 6820| 0| return BNS_CHK_ALTP_SAME_VERTEX; ------------------ | | 6738| 0|#define BNS_CHK_ALTP_SAME_VERTEX 2 ------------------ 6821| 0| } 6822| | 6823| | /* Check whether v1 has neighbors adjacent to multiple bonds */ 6824| 0| for (i = 0, n = 0; i < pVert1->num_adj_edges; i++) ------------------ | Branch (6824:32): [True: 0, False: 0] ------------------ 6825| 0| { 6826| 0| v = ( pBNS->edge + pVert1->iedge[i] )->neighbor12 ^ v1; /* v is adjacent to v1 */ 6827| 0| if (v == v2) ------------------ | Branch (6827:21): [True: 0, False: 0] ------------------ 6828| 0| { 6829| 0| continue; /* ignore connection to v2 */ 6830| 0| } 6831| 0| n += ( pBNS->vert[v].st_edge.cap > 0 ); 6832| 0| } 6833| 0| if (!n) ------------------ | Branch (6833:17): [True: 0, False: 0] ------------------ 6834| 0| { 6835| 0| return BNS_CHK_ALTP_NO_ALTPATH; /* the vertex cannot have flow */ ------------------ | | 6736| 0|#define BNS_CHK_ALTP_NO_ALTPATH 0 ------------------ 6836| 0| } 6837| | 6838| 0| v1Act = v1; 6839| 0| v2Act = v2; 6840| | 6841| | /* find t-group that contains v1 */ 6842| 0| if (( pVert1->type & type ) == type) ------------------ | Branch (6842:17): [True: 0, False: 0] ------------------ 6843| 0| { 6844| 0| v1t = GetGroupVertex( pBNS, v1, type ); 6845| 0| if (IS_BNS_ERROR( v1t )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 6846| 0| { 6847| 0| return v1t; 6848| 0| } 6849| 0| if (v1t != NO_VERTEX) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (6849:21): [True: 0, False: 0] ------------------ 6850| 0| { 6851| 0| v1Act = v1t; 6852| 0| } 6853| 0| } 6854| | /* Find t-group that contains v2 */ 6855| 0| if (( pVert2->type & type ) == type) ------------------ | Branch (6855:17): [True: 0, False: 0] ------------------ 6856| 0| { 6857| 0| v2t = GetGroupVertex( pBNS, v2, type ); 6858| 0| if (IS_BNS_ERROR( v2t )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 6859| 0| { 6860| 0| return v2t; 6861| 0| } 6862| 0| if (v2t != NO_VERTEX) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (6862:21): [True: 0, False: 0] ------------------ 6863| 0| { 6864| 0| v2Act = v2t; 6865| 0| } 6866| 0| } 6867| 0| if (v1t != NO_VERTEX && v1t == v2t) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (6867:17): [True: 0, False: 0] | Branch (6867:37): [True: 0, False: 0] ------------------ 6868| 0| { 6869| 0| return BNS_CHK_ALTP_SAME_TGROUP; ------------------ | | 6737| 0|#define BNS_CHK_ALTP_SAME_TGROUP 1 ------------------ 6870| 0| } 6871| | 6872| 0| bSet_v1 = bSet_v2 = 0; 6873| | /* create new edges adjacent to v1t or v2 */ 6874| 0| iapc = 0; 6875| 0| if (v1t != NO_VERTEX) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (6875:17): [True: 0, False: 0] ------------------ 6876| 0| { 6877| | /* Create new edge and vertex, connect to v1t */ 6878| 0| vNew = bAddNewVertex( pBNS, v1t, 1, 0, 1, nDots ); 6879| 0| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 6880| 0| { 6881| 0| return vNew; 6882| 0| } 6883| 0| apc->vNewVertex[iapc] = vNew; 6884| 0| apc->bSetNew[iapc] = 1; 6885| 0| bSet_v1 = 1; 6886| 0| iapc++; 6887| 0| } 6888| 0| if (v2t == NO_VERTEX) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (6888:17): [True: 0, False: 0] ------------------ 6889| 0| { 6890| | /* Create new edge and vertex, connect to v2 */ 6891| 0| vNew = bAddNewVertex( pBNS, v2, 1, 0, 1, nDots ); 6892| 0| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 6893| 0| { 6894| 0| return vNew; 6895| 0| } 6896| 0| apc->vNewVertex[iapc] = vNew; 6897| 0| apc->bSetNew[iapc] = 1; 6898| 0| bSet_v2 = 1; 6899| 0| iapc++; 6900| 0| } 6901| | 6902| | /* Add st-cap to v1 and/or v2t */ 6903| 0| iapc = 0; 6904| 0| if (!bSet_v1) ------------------ | Branch (6904:17): [True: 0, False: 0] ------------------ 6905| 0| { 6906| | /* Add st-cap to v1 */ 6907| 0| if (v1t != NO_VERTEX) /* djb-rwth: addressing coverity ID #499551 -- condition properly written */ ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (6907:21): [True: 0, False: 0] ------------------ 6908| 0| { 6909| 0| return BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6910| 0| } 6911| 0| n = bAddStCapToAVertex( pBNS, v1, v2Act, apc->nOldCapsVert[iapc], nDots, 0 ); 6912| 0| apc->bSetOldCapsVert[iapc] = n; 6913| 0| apc->vOldVert[iapc] = v1; 6914| 0| iapc++; 6915| 0| } 6916| 0| if (!bSet_v2) ------------------ | Branch (6916:17): [True: 0, False: 0] ------------------ 6917| 0| { 6918| | /* Add st-cap to v2t */ 6919| 0| if (v2t == NO_VERTEX) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (6919:21): [True: 0, False: 0] ------------------ 6920| 0| { 6921| 0| return BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6922| 0| } 6923| 0| n = bAddStCapToAVertex( pBNS, v2t, v1Act, apc->nOldCapsVert[iapc], nDots, 0 ); 6924| 0| apc->bSetOldCapsVert[iapc] = n; 6925| 0| apc->vOldVert[iapc] = v2t; 6926| 0| iapc++; 6927| 0| } 6928| 0| if (*nDots < 0 || *nDots % 2) ------------------ | Branch (6928:17): [True: 0, False: 0] | Branch (6928:31): [True: 0, False: 0] ------------------ 6929| 0| { 6930| 0| return BNS_SET_ALTP_ERR; ------------------ | | 55| 0|#define BNS_SET_ALTP_ERR (BNS_ERR + 7) /*(-9992)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6931| 0| } 6932| 0| return BNS_CHK_ALTP_SET_SUCCESS; ------------------ | | 6739| 0|#define BNS_CHK_ALTP_SET_SUCCESS 4 ------------------ 6933| 0| } 6934| | 6935| | /* ( *pBNS->pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) */ 6936| | 6937| | /*#endif*/ 6938| | 6939| | /* ( TEST_REMOVE_S_ATOMS == 1 && ALT_PATH_MODE_4_SALT == path_type ) */ 6940| | 6941| 20.7k| if (path_type == ALT_PATH_MODE_REM2H_CHG || ------------------ | | 314| 41.5k|#define ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */ ------------------ | Branch (6941:13): [True: 32, False: 20.7k] ------------------ 6942| 20.7k| path_type == ALT_PATH_MODE_ADD2H_CHG || ------------------ | | 315| 41.4k|#define ALT_PATH_MODE_ADD2H_CHG 6 /* add 2 H along alt. path A=-=B => AH-=-BH and change bonds to alternating */ ------------------ | Branch (6942:14): [True: 69, False: 20.6k] ------------------ 6943| 20.6k| path_type == ALT_PATH_MODE_REM2H_TST || ------------------ | | 316| 41.4k|#define ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */ ------------------ | Branch (6943:14): [True: 593, False: 20.0k] ------------------ 6944| 20.0k| path_type == ALT_PATH_MODE_ADD2H_TST) ------------------ | | 317| 20.0k|#define ALT_PATH_MODE_ADD2H_TST 8 /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */ ------------------ | Branch (6944:14): [True: 919, False: 19.1k] ------------------ 6945| 1.61k| { 6946| | /* added 2004-03-18 */ 6947| | 6948| 1.61k| int bDonors = ( path_type == ALT_PATH_MODE_REM2H_CHG ) || ( path_type == ALT_PATH_MODE_REM2H_TST ); ------------------ | | 314| 1.61k|#define ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */ ------------------ int bDonors = ( path_type == ALT_PATH_MODE_REM2H_CHG ) || ( path_type == ALT_PATH_MODE_REM2H_TST ); ------------------ | | 316| 1.58k|#define ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */ ------------------ | Branch (6948:27): [True: 32, False: 1.58k] | Branch (6948:71): [True: 593, False: 988] ------------------ 6949| | 6950| 1.61k| int bSet_v1; /* indicator: v1 has been set */ 6951| 1.61k| int bSet_v2; /* indicator: v2 has been set */ 6952| 1.61k| int i, cap = 1; 6953| 1.61k| Vertex v1t = NO_VERTEX; ------------------ | | 118| 1.61k|#define NO_VERTEX -2 ------------------ 6954| 1.61k| Vertex v2t = NO_VERTEX; ------------------ | | 118| 1.61k|#define NO_VERTEX -2 ------------------ 6955| 1.61k| Vertex v1Act, v2Act; 6956| 1.61k| Vertex v; 6957| | 6958| 1.61k| memset( apc, 0, sizeof( *apc ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6959| 1.61k| fcd[ifcd].iedge = NO_VERTEX; ------------------ | | 118| 1.61k|#define NO_VERTEX -2 ------------------ 6960| 1.61k| *nDots = 0; 6961| | /* 6962| | if ( v1 == v2 ) { 6963| | return BNS_CHK_ALTP_SAME_VERTEX; 6964| | } 6965| | */ 6966| | 6967| | /* Check whether v1 and v2 have proper neighbors */ 6968| 5.49k| for (i = 0, n = bAdjacentDonors = 0; i < pVert1->num_adj_edges; i++) ------------------ | Branch (6968:50): [True: 3.87k, False: 1.61k] ------------------ 6969| 3.87k| { 6970| 3.87k| v = ( pBNS->edge + pVert1->iedge[i] )->neighbor12 ^ v1; /* v is adjacent to v1 */ 6971| | /* do not ignore connection to v2 6972| | if ( v == v2 ) 6973| | continue; 6974| | */ 6975| 3.87k| n += bDonors ? ( pBNS->vert[v].st_edge.cap > 0 ) ------------------ | Branch (6975:22): [True: 1.53k, False: 2.34k] ------------------ 6976| 3.87k| : ( ( pBNS->edge + pVert1->iedge[i] )->flow > 0 ); 6977| 3.87k| bAdjacentDonors += bDonors ? ( v == v2 ) && ( ( pBNS->edge + pVert1->iedge[i] )->flow < MAX_BOND_EDGE_CAP ) : 0; ------------------ | | 123| 62|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ | Branch (6977:36): [True: 1.53k, False: 2.34k] | Branch (6977:46): [True: 62, False: 1.47k] | Branch (6977:61): [True: 62, False: 0] ------------------ 6978| | /* two donors connected by a single or double bond */ 6979| 3.87k| } 6980| | 6981| 1.61k| if (!n && !bAdjacentDonors) ------------------ | Branch (6981:17): [True: 26, False: 1.58k] | Branch (6981:23): [True: 9, False: 17] ------------------ 6982| 9| { 6983| 9| return BNS_CHK_ALTP_NO_ALTPATH; /* the vertex cannot have flow */ ------------------ | | 6736| 9|#define BNS_CHK_ALTP_NO_ALTPATH 0 ------------------ 6984| 9| } 6985| 5.19k| for (i = 0, n = bAdjacentDonors = 0; i < pVert2->num_adj_edges; i++) ------------------ | Branch (6985:50): [True: 3.58k, False: 1.60k] ------------------ 6986| 3.58k| { 6987| 3.58k| v = ( pBNS->edge + pVert2->iedge[i] )->neighbor12 ^ v2; /* v is adjacent to v2 */ 6988| | /* do not ignore connection to v1 6989| | if ( v == v1 ) 6990| | continue; 6991| | */ 6992| 3.58k| n += bDonors ? ( pBNS->vert[v].st_edge.cap > 0 ) : ( ( pBNS->edge + pVert2->iedge[i] )->flow > 0 ); ------------------ | Branch (6992:22): [True: 1.45k, False: 2.13k] ------------------ 6993| 3.58k| bAdjacentDonors += bDonors ? ( v == v1 ) && ( ( pBNS->edge + pVert2->iedge[i] )->flow < MAX_BOND_EDGE_CAP ) : 0; ------------------ | | 123| 62|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ | Branch (6993:36): [True: 1.45k, False: 2.13k] | Branch (6993:46): [True: 62, False: 1.39k] | Branch (6993:61): [True: 62, False: 0] ------------------ 6994| | /* two donors connected by a single or double bond */ 6995| 3.58k| } 6996| | 6997| 1.60k| if (!n && !bAdjacentDonors) ------------------ | Branch (6997:17): [True: 25, False: 1.57k] | Branch (6997:23): [True: 4, False: 21] ------------------ 6998| 4| { 6999| 4| return BNS_CHK_ALTP_NO_ALTPATH; /* the vertex cannot have flow */ ------------------ | | 6736| 4|#define BNS_CHK_ALTP_NO_ALTPATH 0 ------------------ 7000| 4| } 7001| | 7002| 1.60k| v1Act = v1; 7003| 1.60k| v2Act = v2; 7004| | 7005| | /* Find t-group that contains v1 */ 7006| 1.60k| if (( pVert1->type & type ) == type) ------------------ | Branch (7006:17): [True: 1.52k, False: 79] ------------------ 7007| 1.52k| { 7008| 1.52k| v1t = GetGroupVertex( pBNS, v1, type ); 7009| 1.52k| if (BNS_BOND_ERR == v1t) ------------------ | | 52| 1.52k|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 1.52k|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (7009:21): [True: 290, False: 1.23k] ------------------ 7010| 290| { 7011| 290| v1t = NO_VERTEX; ------------------ | | 118| 290|#define NO_VERTEX -2 ------------------ 7012| 290| } 7013| 1.23k| else 7014| 1.23k| { 7015| 1.23k| if (IS_BNS_ERROR( v1t )) ------------------ | | 67| 1.23k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.23k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.23k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.23k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.23k, False: 0] | | | Branch (67:44): [True: 0, False: 1.23k] | | ------------------ ------------------ 7016| 0| { 7017| 0| return v1t; 7018| 0| } 7019| 1.23k| else 7020| 1.23k| { 7021| 1.23k| if (v1t != NO_VERTEX) ------------------ | | 118| 1.23k|#define NO_VERTEX -2 ------------------ | Branch (7021:29): [True: 1.23k, False: 0] ------------------ 7022| 1.23k| { 7023| 1.23k| v1Act = v1t; 7024| 1.23k| } 7025| 1.23k| } 7026| 1.23k| } 7027| 1.52k| } 7028| | 7029| | /* Find t-group that contains v2 */ 7030| 1.60k| if (( pVert2->type & type ) == type) ------------------ | Branch (7030:17): [True: 1.43k, False: 163] ------------------ 7031| 1.43k| { 7032| 1.43k| v2t = GetGroupVertex( pBNS, v2, type ); 7033| 1.43k| if (BNS_BOND_ERR == v2t) ------------------ | | 52| 1.43k|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 1.43k|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (7033:21): [True: 405, False: 1.03k] ------------------ 7034| 405| { 7035| 405| v2t = NO_VERTEX; ------------------ | | 118| 405|#define NO_VERTEX -2 ------------------ 7036| 405| } 7037| 1.03k| else 7038| 1.03k| { 7039| 1.03k| if (IS_BNS_ERROR( v2t )) ------------------ | | 67| 1.03k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.03k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.03k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.03k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.03k, False: 0] | | | Branch (67:44): [True: 0, False: 1.03k] | | ------------------ ------------------ 7040| 0| { 7041| 0| return v2t; 7042| 0| } 7043| 1.03k| else 7044| 1.03k| { 7045| 1.03k| if (v2t != NO_VERTEX) ------------------ | | 118| 1.03k|#define NO_VERTEX -2 ------------------ | Branch (7045:29): [True: 1.03k, False: 0] ------------------ 7046| 1.03k| { 7047| 1.03k| v2Act = v2t; 7048| 1.03k| } 7049| 1.03k| } 7050| 1.03k| } 7051| 1.43k| } 7052| | 7053| 1.60k| if (v1t != NO_VERTEX && v1t == v2t) ------------------ | | 118| 3.20k|#define NO_VERTEX -2 ------------------ | Branch (7053:17): [True: 1.23k, False: 369] | Branch (7053:37): [True: 934, False: 297] ------------------ 7054| 934| { 7055| 934| cap = 2; /* same t-group */ 7056| 934| } 7057| | 7058| | /* bAddNewVertex: (bDonors != 0) == (vit != NO_VERTEX), i=1,2 */ 7059| 1.60k| bSet_v1 = bSet_v2 = 0; 7060| | /* create new edges adjacent to v1t or v2 */ 7061| 1.60k| iapc = 0; 7062| 1.60k| if (( bDonors != 0 ) == ( v1t != NO_VERTEX )) ------------------ | | 118| 1.60k|#define NO_VERTEX -2 ------------------ | Branch (7062:17): [True: 891, False: 709] ------------------ 7063| 891| { 7064| | /* Create new edge and vertex, connect to v1Act */ 7065| 891| vNew = bAddNewVertex( pBNS, v1Act, cap, 0, 1, nDots ); 7066| 891| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 891|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 891|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 891|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 891|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 891, False: 0] | | | Branch (67:44): [True: 0, False: 891] | | ------------------ ------------------ 7067| 0| { 7068| 0| return vNew; 7069| 0| } 7070| 891| apc->vNewVertex[iapc] = vNew; 7071| 891| apc->bSetNew[iapc] = 1; 7072| 891| bSet_v1 = 1; 7073| 891| iapc++; 7074| 891| } 7075| 1.60k| if (( bDonors != 0 ) == ( v2t != NO_VERTEX ) && cap == 1) ------------------ | | 118| 1.60k|#define NO_VERTEX -2 ------------------ | Branch (7075:17): [True: 988, False: 612] | Branch (7075:61): [True: 521, False: 467] ------------------ 7076| 521| { 7077| | /* Create new edge and vertex, connect to v2Act; do not do it if cap==2 */ 7078| 521| vNew = bAddNewVertex( pBNS, v2Act, cap, 0, 1, nDots ); 7079| 521| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 521|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 521|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 521|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 521|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 521, False: 0] | | | Branch (67:44): [True: 0, False: 521] | | ------------------ ------------------ 7080| 0| { 7081| 0| return vNew; 7082| 0| } 7083| 521| apc->vNewVertex[iapc] = vNew; 7084| 521| apc->bSetNew[iapc] = 1; 7085| 521| bSet_v2 = 1; 7086| 521| iapc++; 7087| 521| } 7088| 1.07k| else 7089| 1.07k| { 7090| 1.07k| if (( bDonors != 0 ) == ( v2t != NO_VERTEX )) ------------------ | | 118| 1.07k|#define NO_VERTEX -2 ------------------ | Branch (7090:21): [True: 467, False: 612] ------------------ 7091| 467| { 7092| 467| bSet_v2 = 1; 7093| 467| } 7094| 1.07k| } 7095| | 7096| | /* Add st-cap to v1 and/or v2t */ 7097| 1.60k| iapc = 0; 7098| | /* If cap=2 then just increment st_cap 2 times */ 7099| 1.60k| if (!bSet_v1) ------------------ | Branch (7099:17): [True: 709, False: 891] ------------------ 7100| 709| { 7101| | /* Add st-cap to v1 */ 7102| 709| if (( bDonors != 0 ) == ( v1t != NO_VERTEX )) ------------------ | | 118| 709|#define NO_VERTEX -2 ------------------ | Branch (7102:21): [True: 0, False: 709] ------------------ 7103| 0| { 7104| 0| return BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7105| 0| } 7106| 709| n = bAddStCapToAVertex( pBNS, v1Act, v2Act, apc->nOldCapsVert[iapc], nDots, bAdjacentDonors ); 7107| 709| apc->bSetOldCapsVert[iapc] = n; 7108| 709| apc->vOldVert[iapc] = v1Act; 7109| 709| iapc++; 7110| 709| } 7111| 1.60k| if (!bSet_v2) ------------------ | Branch (7111:17): [True: 612, False: 988] ------------------ 7112| 612| { 7113| | /* Add st-cap to v2t */ 7114| 612| if (( bDonors != 0 ) == ( v2t != NO_VERTEX )) ------------------ | | 118| 612|#define NO_VERTEX -2 ------------------ | Branch (7114:21): [True: 0, False: 612] ------------------ 7115| 0| { 7116| 0| return BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7117| 0| } 7118| 612| n = bAddStCapToAVertex( pBNS, v2Act, v1Act, apc->nOldCapsVert[iapc], nDots, bAdjacentDonors ); 7119| 612| apc->bSetOldCapsVert[iapc] = n; 7120| 612| apc->vOldVert[iapc] = v2Act; 7121| 612| iapc++; 7122| 612| } 7123| 1.60k| if (*nDots < 0 || *nDots % 2) ------------------ | Branch (7123:17): [True: 0, False: 1.60k] | Branch (7123:31): [True: 0, False: 1.60k] ------------------ 7124| 0| { 7125| 0| return BNS_SET_ALTP_ERR; ------------------ | | 55| 0|#define BNS_SET_ALTP_ERR (BNS_ERR + 7) /*(-9992)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7126| 0| } 7127| 1.60k| return BNS_CHK_ALTP_SET_SUCCESS; ------------------ | | 6739| 1.60k|#define BNS_CHK_ALTP_SET_SUCCESS 4 ------------------ 7128| 1.60k| } 7129| | 7130| 19.1k| if (path_type == ALT_PATH_MODE_REM_PROTON) ------------------ | | 318| 19.1k|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ | Branch (7130:13): [True: 1.47k, False: 17.6k] ------------------ 7131| 1.47k| { 7132| | /* added 2004-03-05 */ 7133| 1.47k| if (v1 >= 0 && v2 >= 0 && ------------------ | Branch (7133:17): [True: 1.47k, False: 0] | Branch (7133:28): [True: 1.47k, False: 0] ------------------ 7134| 1.47k| ( pVert1->type & BNS_VERT_TYPE_ANY_GROUP ) && ------------------ | | 59| 1.47k|#define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 47| 1.47k|#define BNS_VERT_TYPE_TGROUP 0x0004 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 49| 1.47k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 50| 1.47k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ ------------------ | Branch (7134:17): [True: 1.47k, False: 0] ------------------ 7135| 1.47k| ( pVert2->type & BNS_VERT_TYPE_ANY_GROUP )) ------------------ | | 59| 1.47k|#define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 47| 1.47k|#define BNS_VERT_TYPE_TGROUP 0x0004 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 49| 1.47k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | #define BNS_VERT_TYPE_ANY_GROUP (BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_SUPER_TGROUP) | | ------------------ | | | | 50| 1.47k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ ------------------ | Branch (7135:18): [True: 1.47k, False: 0] ------------------ 7136| 1.47k| { 7137| | /* Create new edge and vertex, connect to v2 */ 7138| 1.47k| if (( pBNS->vert[v1].type & BNS_VERT_TYPE_C_GROUP ) && ------------------ | | 49| 1.47k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (7138:21): [True: 1.45k, False: 13] ------------------ 7139| 1.45k| ( pBNS->vert[v1].st_edge.flow == 2 * pBNS->vert[v1].num_adj_edges )) ------------------ | Branch (7139:21): [True: 0, False: 1.45k] ------------------ 7140| 0| { 7141| | /* so far in a charge group max edge flow = 1 2004-03-08 */ 7142| 0| return BNS_CHK_ALTP_NO_ALTPATH; ------------------ | | 6736| 0|#define BNS_CHK_ALTP_NO_ALTPATH 0 ------------------ 7143| 0| } 7144| 1.47k| memset( apc, 0, sizeof( *apc ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7145| 1.47k| fcd[ifcd].iedge = NO_VERTEX; ------------------ | | 118| 1.47k|#define NO_VERTEX -2 ------------------ 7146| 1.47k| *nDots = 0; 7147| 1.47k| iapc = 0; 7148| | 7149| 1.47k| vNew = bAddNewVertex( pBNS, v2, 1, 0, 1, nDots ); 7150| 1.47k| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 1.47k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.47k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.47k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.47k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.47k, False: 0] | | | Branch (67:44): [True: 0, False: 1.47k] | | ------------------ ------------------ 7151| 0| { 7152| 0| return vNew; 7153| 0| } 7154| 1.47k| apc->vNewVertex[iapc] = vNew; 7155| 1.47k| apc->bSetNew[iapc] = 1; 7156| | /*iapc ++;*/ 7157| | /* add st-cap (dot) to v1 */ 7158| 1.47k| n = bAddStCapToAVertex( pBNS, v1, v2, apc->nOldCapsVert[iapc], nDots, 0 ); 7159| 1.47k| apc->bSetOldCapsVert[iapc] = n; 7160| 1.47k| apc->vOldVert[iapc] = v1; 7161| 1.47k| iapc++; 7162| 1.47k| return BNS_CHK_ALTP_SET_SUCCESS; ------------------ | | 6739| 1.47k|#define BNS_CHK_ALTP_SET_SUCCESS 4 ------------------ 7163| 1.47k| } 7164| 1.47k| } 7165| | 7166| 17.6k|#if ( NEUTRALIZE_ENDPOINTS == 1 ) /* { */ 7167| | 7168| 17.6k| *nDots = 0; 7169| 17.6k| memset( apc, 0, sizeof( *apc ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7170| 17.6k| fcd[ifcd].iedge = NO_VERTEX; ------------------ | | 118| 17.6k|#define NO_VERTEX -2 ------------------ 7171| | 7172| 17.6k| if (type & BNS_VERT_TYPE_ENDPOINT) ------------------ | | 46| 17.6k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (7172:13): [True: 8.94k, False: 8.72k] ------------------ 7173| 8.94k| { 7174| 8.94k| BNS_IEDGE iedge; 7175| 8.94k| AT_NUMB type2; 7176| 8.94k| int ret2; 7177| | /* prohibit charge movement */ 7178| 8.94k| type2 = BNS_VERT_TYPE_C_GROUP; ------------------ | | 49| 8.94k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ 7179| 8.94k| iedge = GetEdgeToGroupVertex( pBNS, v1, type2 ); 7180| 8.94k| if (iedge != NO_VERTEX) ------------------ | | 118| 8.94k|#define NO_VERTEX -2 ------------------ | Branch (7180:17): [True: 395, False: 8.55k] ------------------ 7181| 395| { 7182| | /* Set flow=1 on an edge to a c-group vertex to make sure 7183| | there is no positive charge when moving tautomeric H-atoms */ 7184| 395| ret2 = bSetFlowToCheckOneBond( pBNS, iedge, 1, fcd + ifcd ); 7185| 395| if (IS_BNS_ERROR( ret2 )) ------------------ | | 67| 395|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 395|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 395|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 395|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 395, False: 0] | | | Branch (67:44): [True: 0, False: 395] | | ------------------ ------------------ 7186| 0| { 7187| 0| return ret2; 7188| 0| } 7189| 395| *nDots += ret2; 7190| 940| while (fcd[ifcd].iedge != NO_VERTEX) ------------------ | | 118| 940|#define NO_VERTEX -2 ------------------ | Branch (7190:24): [True: 545, False: 395] ------------------ 7191| 545| { 7192| 545| ifcd++; 7193| 545| } 7194| 395| } 7195| | 7196| 8.94k| iedge = GetEdgeToGroupVertex( pBNS, v2, type2 ); 7197| | 7198| 8.94k| if (iedge != NO_VERTEX) ------------------ | | 118| 8.94k|#define NO_VERTEX -2 ------------------ | Branch (7198:17): [True: 427, False: 8.52k] ------------------ 7199| 427| { 7200| | /* Set flow=1 on an edge to a c-group vertex to make sure 7201| | there is no positive charge when moving tautomeric H-atoms */ 7202| | 7203| 427| ret2 = bSetFlowToCheckOneBond( pBNS, iedge, 1, fcd + ifcd ); 7204| | 7205| 427| if (IS_BNS_ERROR( ret2 )) ------------------ | | 67| 427|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 427|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 427|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 427|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 427, False: 0] | | | Branch (67:44): [True: 82, False: 345] | | ------------------ ------------------ 7206| 82| { 7207| 82| return ret2; 7208| 82| } 7209| 345| *nDots += ret2; 7210| 990| while (fcd[ifcd].iedge != NO_VERTEX) ------------------ | | 118| 990|#define NO_VERTEX -2 ------------------ | Branch (7210:24): [True: 645, False: 345] ------------------ 7211| 645| { 7212| 645| ifcd++; 7213| 645| } 7214| 345| } 7215| | 7216| | /* Set hydrogen counts */ 7217| 8.86k| type2 = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 8.86k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 7218| 8.86k| iedge = GetEdgeToGroupVertex( pBNS, v1, type2 ); 7219| 8.86k| if (iedge != NO_VERTEX) ------------------ | | 118| 8.86k|#define NO_VERTEX -2 ------------------ | Branch (7219:17): [True: 1.76k, False: 7.09k] ------------------ 7220| 1.76k| { 7221| | /* Set flow=1 on an edge to a t-group vertex to make sure there is 7222| | a moveable hydrogen atom or (-) on v1 when moving tautomeric H-atoms */ 7223| 1.76k|#if ( FIX_H_CHECKING_TAUT == 1 ) 7224| 1.76k| ret2 = bSetFlowToCheckOneBond( pBNS, iedge, 1, fcd + ifcd ); 7225| 1.76k| if (IS_BNS_ERROR( ret2 )) ------------------ | | 67| 1.76k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.76k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.76k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.76k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.76k, False: 0] | | | Branch (67:44): [True: 0, False: 1.76k] | | ------------------ ------------------ 7226| 0| { 7227| 0| return ret2; 7228| 0| } 7229| 1.76k| *nDots += ret2; 7230| 5.50k| while (fcd[ifcd].iedge != NO_VERTEX) ------------------ | | 118| 5.50k|#define NO_VERTEX -2 ------------------ | Branch (7230:24): [True: 3.73k, False: 1.76k] ------------------ 7231| 3.73k| { 7232| 3.73k| ifcd++; 7233| 3.73k| } 7234| |#else 7235| | t1 = pBNS->edge[iedge].neighbor12 ^ v1; 7236| |#endif 7237| 1.76k| } 7238| | 7239| 8.86k| iedge = GetEdgeToGroupVertex( pBNS, v2, type2 ); 7240| 8.86k| if (iedge != NO_VERTEX) ------------------ | | 118| 8.86k|#define NO_VERTEX -2 ------------------ | Branch (7240:17): [True: 808, False: 8.05k] ------------------ 7241| 808| { 7242| | /* Set flow=0 on an edge to a t-group vertex to make sure there is 7243| | no moveable hydrogen atom or (-) on v2 when moving tautomeric H-atoms */ 7244| 808|#if ( FIX_H_CHECKING_TAUT == 1 ) 7245| 808| ret2 = bSetFlowToCheckOneBond( pBNS, iedge, 0, fcd + ifcd ); 7246| 808| if (IS_BNS_ERROR( ret2 )) ------------------ | | 67| 808|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 808|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 808|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 808|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 808, False: 0] | | | Branch (67:44): [True: 0, False: 808] | | ------------------ ------------------ 7247| 0| { 7248| 0| return ret2; 7249| 0| } 7250| 808| *nDots += ret2; 7251| 1.61k| while (fcd[ifcd].iedge != NO_VERTEX) ------------------ | | 118| 1.61k|#define NO_VERTEX -2 ------------------ | Branch (7251:24): [True: 808, False: 808] ------------------ 7252| 808| { 7253| 808| ifcd++; 7254| 808| } 7255| |#else 7256| | t2 = pBNS->edge[iedge].neighbor12 ^ v2; 7257| |#endif 7258| 808| } 7259| | 7260| 8.86k|#if ( FIX_H_CHECKING_TAUT == 1 ) 7261| |#else 7262| | if (t1 == t2 && t1 != NO_VERTEX) 7263| | { 7264| | return BNS_CHK_ALTP_SAME_TGROUP; 7265| | } 7266| |#endif 7267| | 7268| 8.86k| iapc = 0; 7269| | /* Create new edge and vertex with cap=1 at v2 and/or t1 */ 7270| 8.86k| if (t1 != NO_VERTEX) ------------------ | | 118| 8.86k|#define NO_VERTEX -2 ------------------ | Branch (7270:17): [True: 0, False: 8.86k] ------------------ 7271| 0| { 7272| | /* Create new edge and vertex, connect to t1 */ 7273| 0| vNew = bAddNewVertex( pBNS, t1, 1/*cap*/, 0/*flow*/, 1/*max_adj_edges*/, nDots ); /* djb-rwth: addressing coverity ID #499581 -- condition works as expected for t1 == -2 */ 7274| 0| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 7275| 0| { 7276| 0| return vNew; 7277| 0| } 7278| 0| apc->vNewVertex[iapc] = vNew; 7279| 0| apc->bSetNew[iapc] = 1; 7280| 0| iapc++; 7281| 0| } 7282| 8.86k| if (t2 == NO_VERTEX) ------------------ | | 118| 8.86k|#define NO_VERTEX -2 ------------------ | Branch (7282:17): [True: 8.86k, False: 0] ------------------ 7283| 8.86k| { 7284| | /* Create new edge and vertex, connect to v2 */ 7285| 8.86k| vNew = bAddNewVertex( pBNS, v2, 1/*cap*/, 0/*flow*/, 1/*max_adj_edges*/, nDots ); 7286| 8.86k| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 8.86k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 8.86k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 8.86k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 8.86k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 8.86k, False: 0] | | | Branch (67:44): [True: 3, False: 8.86k] | | ------------------ ------------------ 7287| 3| { 7288| 3| return vNew; 7289| 3| } 7290| 8.86k| apc->vNewVertex[iapc] = vNew; 7291| 8.86k| apc->bSetNew[iapc] = 1; 7292| 8.86k| iapc++; 7293| 8.86k| } 7294| | 7295| | /* Add st-cap to v1 and/or v2t */ 7296| 8.86k| iapc = 0; 7297| 8.86k| if (t1 == NO_VERTEX) ------------------ | | 118| 8.86k|#define NO_VERTEX -2 ------------------ | Branch (7297:17): [True: 8.86k, False: 0] ------------------ 7298| 8.86k| { 7299| | /* Add st-cap to v1 */ 7300| 8.86k| n = bAddStCapToAVertex(pBNS, v1, (Vertex)(t2 == NO_VERTEX ? v2 : t2), apc->nOldCapsVert[iapc], nDots, 0); /* djb-rwth: addressing coverity ID #499501 -- condition works as expected for t2 == -2 */ ------------------ | | 118| 8.86k|#define NO_VERTEX -2 ------------------ | Branch (7300:59): [True: 8.86k, False: 0] ------------------ 7301| 8.86k| apc->bSetOldCapsVert[iapc] = n; 7302| 8.86k| apc->vOldVert[iapc] = v1; 7303| 8.86k| iapc++; 7304| 8.86k| } 7305| 8.86k| if (t2 != NO_VERTEX) ------------------ | | 118| 8.86k|#define NO_VERTEX -2 ------------------ | Branch (7305:17): [True: 0, False: 8.86k] ------------------ 7306| 0| { 7307| | /* Add st-cap to t2 */ 7308| 0| n = bAddStCapToAVertex( pBNS, t2, (Vertex) ( t1 == NO_VERTEX ? v1 : t1 ), apc->nOldCapsVert[iapc], nDots, 0 ); ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (7308:62): [True: 0, False: 0] ------------------ 7309| 0| apc->bSetOldCapsVert[iapc] = n; 7310| 0| apc->vOldVert[iapc] = t2; 7311| 0| iapc++; 7312| 0| } 7313| 8.86k| } 7314| 8.72k| else 7315| 8.72k| { 7316| | /* Create new edge and vertex, connect to v2 */ 7317| 8.72k| vNew = bAddNewVertex( pBNS, v2, 1 /* cap*/, 0 /* flow */, 1 /* max_adj_edges */, nDots ); 7318| 8.72k| if (IS_BNS_ERROR( vNew )) ------------------ | | 67| 8.72k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 8.72k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 8.72k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 8.72k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 8.72k, False: 0] | | | Branch (67:44): [True: 1, False: 8.72k] | | ------------------ ------------------ 7319| 1| { 7320| 1| return vNew; 7321| 1| } 7322| 8.72k| apc->vNewVertex[0] = vNew; 7323| 8.72k| apc->bSetNew[0] = 1; 7324| | 7325| | /* add st-cap to v1 */ 7326| 8.72k| n = bAddStCapToAVertex( pBNS, v1, v2, apc->nOldCapsVert[0], nDots, 0 ); 7327| 8.72k| apc->bSetOldCapsVert[0] = n; 7328| 8.72k| apc->vOldVert[0] = v1; 7329| 8.72k| } 7330| |#else /* } NEUTRALIZE_ENDPOINTS == 0 {*/ 7331| | 7332| | *nDots = 0; 7333| | memset( apc, 0, sizeof( *apc ) ); 7334| | fcd[ifcd].iedge = NO_VERTEX; 7335| | 7336| | /* Create new edge and vertex, connect to v2 */ 7337| | vNew = bAddNewVertex( pBNS, v2, 1 /* cap*/, 0 /* flow */, 1 /* max_adj_edges */, nDots, 0 ); 7338| | if (IS_BNS_ERROR( vNew )) 7339| | { 7340| | return vNew; 7341| | } 7342| | apc->vNewVertex[0] = vNew; 7343| | apc->bSetNew[0] = 1; 7344| | 7345| | /* Add st-cap to v1 */ 7346| | n = bAddStCapToAVertex( pBNS, v1, v2, apc->nOldCapsVert[0], nDots ); 7347| | apc->bSetOldCapsVert[0] = n; 7348| | apc->vOldVert[0] = v1; 7349| |#endif /* } NEUTRALIZE_ENDPOINTS */ 7350| | 7351| 17.5k| if (*nDots < 0 || *nDots % 2) ------------------ | Branch (7351:13): [True: 0, False: 17.5k] | Branch (7351:27): [True: 0, False: 17.5k] ------------------ 7352| 0| { 7353| 0| return BNS_SET_ALTP_ERR; ------------------ | | 55| 0|#define BNS_SET_ALTP_ERR (BNS_ERR + 7) /*(-9992)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7354| 0| } 7355| 17.5k| return BNS_CHK_ALTP_SET_SUCCESS; ------------------ | | 6739| 17.5k|#define BNS_CHK_ALTP_SET_SUCCESS 4 ------------------ 7356| 17.5k| } 7357| | 7358| | /*return BNS_CHK_ALTP_NO_ALTPATH;*/ 7359| 23.6k|} bRestoreBnsAfterCheckAltPath: 7367| 20.7k|{ 7368| 20.7k| BNS_EDGE *pEdge; 7369| 20.7k| Vertex vNew; 7370| 20.7k| Vertex vOld; 7371| 20.7k| BNS_VERTEX *pOldVert; 7372| 20.7k| BNS_VERTEX *pNewVert; 7373| 20.7k| int i, j, n; /* djb-rwth: removing redundant variables */ 7374| | 7375| | /* djb-rwth: removing redundant code */ 7376| | 7377| 20.7k| if (bChangeFlow & BNS_EF_UPD_H_CHARGE) ------------------ | | 379| 20.7k|#define BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */ ------------------ | Branch (7377:9): [True: 1.47k, False: 19.2k] ------------------ 7378| 1.47k| { 7379| | /* Remove new temp. vertices and edges connectong them to the structure */ 7380| 4.41k| for (i = sizeof( apc->bSetNew ) / sizeof( apc->bSetNew[0] ) - 1; 0 <= i; i--) ------------------ | Branch (7380:74): [True: 2.94k, False: 1.47k] ------------------ 7381| 2.94k| { 7382| 2.94k| if (apc->bSetNew[i]) ------------------ | Branch (7382:17): [True: 1.47k, False: 1.47k] ------------------ 7383| 1.47k| { 7384| 1.47k| vNew = apc->vNewVertex[i]; 7385| 1.47k| pNewVert = pBNS->vert + vNew; 7386| 2.94k| for (j = 0; j < pNewVert->num_adj_edges; j++) ------------------ | Branch (7386:29): [True: 1.47k, False: 1.47k] ------------------ 7387| 1.47k| { 7388| 1.47k| pEdge = pBNS->edge + pNewVert->iedge[j]; 7389| 1.47k| vOld = pEdge->neighbor12 ^ vNew; 7390| 1.47k| pOldVert = pBNS->vert + vOld; 7391| 1.47k| pOldVert->st_edge.flow -= pEdge->flow; 7392| 1.47k| pOldVert->st_edge.cap -= pEdge->flow; 7393| | /* disconnect new edge from pOldVert */ 7394| 1.47k| pOldVert->iedge[--pOldVert->num_adj_edges] = 0; 7395| | /* clear the new edge */ 7396| 1.47k| memset( pEdge, 0, sizeof( *pEdge ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7397| | /* and decrement the total number of edges */ 7398| 1.47k| pBNS->num_edges--; 7399| 1.47k| } 7400| | /* Clear the new vertex */ 7401| 1.47k| memset( pNewVert, 0, sizeof( *pNewVert ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7402| | /* and decrement the total number of vertices 7403| | (new vertice ids are contiguous) */ 7404| 1.47k| pBNS->num_vertices--; 7405| | /* djb-rwth: removing redundant code */ 7406| 1.47k| } 7407| 2.94k| } 7408| | 7409| | /* Restore changed caps of old vertices */ 7410| 1.47k| for (i = sizeof( apc->bSetOldCapsVert ) / sizeof( apc->bSetOldCapsVert[0] ) - 1; 7411| 4.41k| 0 <= i; ------------------ | Branch (7411:15): [True: 2.94k, False: 1.47k] ------------------ 7412| 2.94k| i--) 7413| 2.94k| { 7414| 2.94k| if ((n = apc->bSetOldCapsVert[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7414:17): [True: 1.47k, False: 1.47k] ------------------ 7415| 1.47k| { 7416| 1.47k| pOldVert = pBNS->vert + apc->vOldVert[i]; 7417| 1.47k| if (pOldVert->st_edge.flow <= apc->nOldCapsVert[i][0]) ------------------ | Branch (7417:21): [True: 1.27k, False: 199] ------------------ 7418| 1.27k| { 7419| 1.27k| pOldVert->st_edge.cap = apc->nOldCapsVert[i][0]; 7420| 1.27k| n--; 7421| | /* djb-rwth: removing redundant code */ 7422| 1.27k| for (j = 0; j < n && j < pOldVert->num_adj_edges; j++) ------------------ | Branch (7422:33): [True: 0, False: 1.27k] | Branch (7422:42): [True: 0, False: 0] ------------------ 7423| 0| { 7424| 0| pEdge = pBNS->edge + pOldVert->iedge[j]; 7425| 0| pEdge->cap = apc->nOldCapsVert[i][j + 1]; 7426| 0| } 7427| 1.27k| } 7428| 1.47k| } 7429| 2.94k| } 7430| 1.47k| } 7431| 19.2k| else 7432| 19.2k| { 7433| | /* Restore changed caps of old vertices */ 7434| 57.8k| for (i = sizeof( apc->bSetOldCapsVert ) / sizeof( apc->bSetOldCapsVert[0] ) - 1; 0 <= i; i--) ------------------ | Branch (7434:90): [True: 38.5k, False: 19.2k] ------------------ 7435| 38.5k| { 7436| 38.5k| if ((n = apc->bSetOldCapsVert[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7436:17): [True: 18.9k, False: 19.6k] ------------------ 7437| 18.9k| { 7438| 18.9k| pOldVert = pBNS->vert + apc->vOldVert[i]; 7439| 18.9k| pOldVert->st_edge.cap = apc->nOldCapsVert[i][0]; 7440| 18.9k| n--; 7441| | /* djb-rwth: removing redundant code */ 7442| 51.3k| for (j = 0; j < n && j < pOldVert->num_adj_edges; j++) ------------------ | Branch (7442:29): [True: 32.4k, False: 18.9k] | Branch (7442:38): [True: 32.4k, False: 0] ------------------ 7443| 32.4k| { 7444| 32.4k| pEdge = pBNS->edge + pOldVert->iedge[j]; 7445| 32.4k| pEdge->cap = apc->nOldCapsVert[i][j + 1]; 7446| 32.4k| } 7447| 18.9k| } 7448| 38.5k| } 7449| | 7450| | /* Remove new temp. vertices and edges connectong them to the structure */ 7451| 57.8k| for (i = sizeof( apc->bSetNew ) / sizeof( apc->bSetNew[0] ) - 1; 0 <= i; i--) ------------------ | Branch (7451:74): [True: 38.5k, False: 19.2k] ------------------ 7452| 38.5k| { 7453| 38.5k| if (apc->bSetNew[i]) ------------------ | Branch (7453:17): [True: 18.9k, False: 19.5k] ------------------ 7454| 18.9k| { 7455| 18.9k| vNew = apc->vNewVertex[i]; 7456| 18.9k| pNewVert = pBNS->vert + vNew; 7457| 37.9k| for (j = 0; j < pNewVert->num_adj_edges; j++) ------------------ | Branch (7457:29): [True: 18.9k, False: 18.9k] ------------------ 7458| 18.9k| { 7459| 18.9k| pEdge = pBNS->edge + pNewVert->iedge[j]; 7460| 18.9k| vOld = pEdge->neighbor12 ^ vNew; 7461| 18.9k| pOldVert = pBNS->vert + vOld; 7462| | /* disconnect new edge from pOldVert */ 7463| 18.9k| pOldVert->iedge[--pOldVert->num_adj_edges] = 0; 7464| | /* clear the new edge */ 7465| 18.9k| memset( pEdge, 0, sizeof( *pEdge ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7466| | /* and decrement the total number of edges */ 7467| 18.9k| pBNS->num_edges--; 7468| 18.9k| } 7469| | /* Clear the new vertex */ 7470| 18.9k| memset( pNewVert, 0, sizeof( *pNewVert ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7471| | /* and decrement the total number of vertices (new vertice ids are contiguous */ 7472| 18.9k| pBNS->num_vertices--; 7473| | /* djb-rwth: removing redundant code */ 7474| 18.9k| } 7475| 38.5k| } 7476| 19.2k| } 7477| | 7478| 20.7k| return 0; 7479| 20.7k|} bExistsAnyAltPath: 7491| 8.13k|{ 7492| 8.13k| int nRet1, nRet2; 7493| | 7494| 8.13k| nRet1 = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, nVert2, nVert1, path_type ); 7495| | 7496| 8.13k| if (nRet1 > 0) ------------------ | Branch (7496:9): [True: 4.45k, False: 3.68k] ------------------ 7497| 4.45k| { 7498| 4.45k| return nRet1; 7499| 4.45k| } 7500| | 7501| 3.68k| nRet2 = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, nVert1, nVert2, path_type ); 7502| | 7503| 3.68k| if (nRet2 > 0) ------------------ | Branch (7503:9): [True: 2.78k, False: 898] ------------------ 7504| 2.78k| { 7505| 2.78k| return nRet2; 7506| 2.78k| } 7507| 898| if (IS_BNS_ERROR( nRet1 )) ------------------ | | 67| 898|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 898|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 898|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 898|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 898, False: 0] | | | Branch (67:44): [True: 1, False: 897] | | ------------------ ------------------ 7508| 1| { 7509| 1| return nRet1; 7510| 1| } 7511| 897| if (IS_BNS_ERROR( nRet2 )) ------------------ | | 67| 897|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 897|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 897|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 897|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 897, False: 0] | | | Branch (67:44): [True: 2, False: 895] | | ------------------ ------------------ 7512| 2| { 7513| 2| return nRet2; 7514| 2| } 7515| | 7516| 895| return 0; 7517| 897|} bIsBnsEndpoint: 7527| 6.30k|{ 7528| 6.30k| int i, vt; 7529| 6.30k| BNS_VERTEX *pVert; /* vertices */ 7530| 6.30k| BNS_EDGE *pEdge; /* edges */ 7531| | 7532| 6.30k| if (0 <= v && v < pBNS->num_atoms && ( pVert = pBNS->vert + v ) && ( pVert->type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 46| 6.30k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (7532:9): [True: 6.30k, False: 0] | Branch (7532:19): [True: 6.30k, False: 0] | Branch (7532:42): [True: 6.30k, False: 0] | Branch (7532:72): [True: 5.52k, False: 789] ------------------ 7533| 5.52k| { 7534| 8.13k| for (i = pVert->num_adj_edges - 1; 0 <= i; i--) ------------------ | Branch (7534:44): [True: 6.62k, False: 1.51k] ------------------ 7535| 6.62k| { 7536| 6.62k| pEdge = pBNS->edge + pVert->iedge[i]; 7537| 6.62k| vt = pEdge->neighbor12 ^ v; 7538| 6.62k| if (pBNS->vert[vt].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 6.62k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (7538:17): [True: 4.00k, False: 2.61k] ------------------ 7539| 4.00k| { 7540| 4.00k| return !IS_FORBIDDEN( pEdge->forbidden, pBNS ); ------------------ | | 41| 4.00k|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) ------------------ 7541| 4.00k| } 7542| 6.62k| } 7543| 5.52k| } 7544| | 7545| 2.30k| return 0; 7546| 6.30k|} bRadChangesAtomType: 7558| 1.48k|{ 7559| | 7560| 1.48k| EdgeIndex iuv; 7561| 1.48k| Vertex v_O, v_ChgOrH; 7562| | 7563| | /* The previous atom along the path: should be a terminal atom */ 7564| 1.48k| if (v_1 == NO_VERTEX) ------------------ | | 118| 1.48k|#define NO_VERTEX -2 ------------------ | Branch (7564:9): [True: 1.48k, False: 0] ------------------ 7565| 1.48k| { 7566| 1.48k| v_1 = GetPrevVertex( pBNS, v, pBD->SwitchEdge, &iuv ); 7567| 1.48k| } 7568| 1.48k| v_O = v_1 / 2 - 1; 7569| | 7570| 1.48k| if (v_O < 0 || v_O >= pBNS->num_atoms) ------------------ | Branch (7570:9): [True: 0, False: 1.48k] | Branch (7570:20): [True: 0, False: 1.48k] ------------------ 7571| 0| { 7572| 0| return 0; 7573| 0| } 7574| | 7575| | /* Make sure v_O is a terminal atom: its second neighbor is not an atom */ 7576| 1.48k| if (pBNS->vert[pBNS->edge[pBNS->vert[v_O].iedge[1]].neighbor12 ^ v_O].type & BNS_VERT_TYPE_ATOM) ------------------ | | 45| 1.48k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (7576:9): [True: 1.48k, False: 0] ------------------ 7577| 1.48k| { 7578| 1.48k| return 0; 7579| 1.48k| } 7580| | 7581| | /* The next to previous vertex vertex along the path: should be a Charge or Taut group vertex */ 7582| 0| if (v_2 == NO_VERTEX) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (7582:9): [True: 0, False: 0] ------------------ 7583| 0| { 7584| 0| v_2 = GetPrevVertex( pBNS, v_1, pBD->SwitchEdge, &iuv ); 7585| 0| } 7586| | 7587| 0| v_ChgOrH = v_2 / 2 - 1; 7588| 0| if (v_ChgOrH < pBNS->num_atoms) ------------------ | Branch (7588:9): [True: 0, False: 0] ------------------ 7589| 0| { 7590| 0| return 0; 7591| 0| } 7592| | 7593| | /* Make sure v_ChgOrH is a charge or taut_group */ 7594| 0| if (pBNS->vert[v_ChgOrH].type & ( BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP )) ------------------ | | 47| 0|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ if (pBNS->vert[v_ChgOrH].type & ( BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP )) ------------------ | | 49| 0|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (7594:9): [True: 0, False: 0] ------------------ 7595| 0| { 7596| 0| return 1; 7597| 0| } 7598| | 7599| 0| return 0; 7600| 0|} RegisterRadEndpoint: 7605| 25.7k|{ 7606| 25.7k| EdgeIndex iuv; 7607| 25.7k| int i, num_found; 7608| 25.7k| Vertex v, w; 7609| 25.7k| Vertex u_last, v2; 7610| 25.7k| switch (pBD->bRadSrchMode) ------------------ | Branch (7610:13): [True: 25.7k, False: 0] ------------------ 7611| 25.7k| { 7612| 10.6k| case RAD_SRCH_NORM: ------------------ | Branch (7612:9): [True: 10.6k, False: 15.0k] ------------------ 7613| | /* Go backwards along alt path and stop at the 1st found atom (not a fictitious vertex) */ 7614| | /* we need only vertices where a radical may be moved, therefore exclude u%2=1 (odd) vertices */ 7615| | /* atom number = u/2-1; u = 0 or 1 is 's' or 't' vertices, respectively, they are not atoms */ 7616| 10.6k| num_found = 0; 7617| 14.1k| while (u > Vertex_t && ( u % 2 || u / 2 > pBNS->num_atoms )) ------------------ | | 116| 28.2k|#define Vertex_t 1 ------------------ | Branch (7617:20): [True: 14.1k, False: 0] | Branch (7617:38): [True: 2.70k, False: 11.4k] | Branch (7617:47): [True: 729, False: 10.6k] ------------------ 7618| 3.43k| { 7619| 3.43k| u = GetPrevVertex( pBNS, u, pBD->SwitchEdge, &iuv ); 7620| 3.43k| } 7621| 10.6k| w = u / 2 - 1; /* Check whether u is a radical endpoint */ 7622| 10.6k| if (Vertex_t < u && w < pBNS->num_atoms && ------------------ | | 116| 10.6k|#define Vertex_t 1 ------------------ | Branch (7622:17): [True: 10.6k, False: 0] | Branch (7622:33): [True: 10.6k, False: 0] ------------------ 7623| 10.6k| pBNS->vert[w].st_edge.cap == ( pBNS->vert[w].st_edge.flow & EDGE_FLOW_ST_MASK )) ------------------ | | 128| 10.6k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (7623:18): [True: 5.83k, False: 4.86k] ------------------ 7624| 5.83k| { 7625| | /* u is an atom; it is not a radical atom */ 7626| | /* now search for the starting radical atom by following the path back from u */ 7627| 5.83k| v = u_last = u; 7628| 31.0k| while (v > Vertex_t) ------------------ | | 116| 31.0k|#define Vertex_t 1 ------------------ | Branch (7628:24): [True: 25.2k, False: 5.83k] ------------------ 7629| 25.2k| { 7630| 25.2k| u = v; 7631| 25.2k| v = GetPrevVertex( pBNS, u, pBD->SwitchEdge, &iuv ); /* Radical endpoint */ 7632| 25.2k| } 7633| | /* Check whether u is a radical atom */ 7634| 5.83k| if (!( u % 2 ) && Vertex_t < u && ------------------ | | 116| 5.83k|#define Vertex_t 1 ------------------ | Branch (7634:21): [True: 5.83k, False: 0] | Branch (7634:35): [True: 5.83k, False: 0] ------------------ 7635| 5.83k| ( u = u / 2 - 1 ) < pBNS->num_atoms && ------------------ | Branch (7635:21): [True: 5.83k, False: 0] ------------------ 7636| 5.83k| pBNS->vert[u].st_edge.cap > ( pBNS->vert[u].st_edge.flow & EDGE_FLOW_ST_MASK )) ------------------ | | 128| 5.83k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (7636:22): [True: 5.83k, False: 0] ------------------ 7637| 5.83k| { 7638| | /* at pBNS->vert[u] we have found the radical that originated the path */ 7639| | /* pBD->RadEndpoints[2k] is the radical, pBD->RadEndpoints[2k+1] is the farthest atom */ 7640| | /* to which the radical may be moved (farthest reachable atom) */ 7641| | 7642| | /* add *all* atoms that may receive radical from u_rad */ 7643| | /* exception: at2 in: ==(+/-/H)---at1==at2(possible rad endpoint) if pBNS->type_TACN */ 7644| 31.0k| for (v = u_last; v > Vertex_t; v = GetPrevVertex( pBNS, v, pBD->SwitchEdge, &iuv )) ------------------ | | 116| 31.0k|#define Vertex_t 1 ------------------ | Branch (7644:38): [True: 25.2k, False: 5.83k] ------------------ 7645| 25.2k| { 7646| 25.2k| if (!( v % 2 ) && ( v2 = v / 2 - 1 ) < pBNS->num_atoms && ------------------ | Branch (7646:29): [True: 15.5k, False: 9.70k] | Branch (7646:43): [True: 14.2k, False: 1.25k] ------------------ 7647| 14.2k| pBNS->vert[v2].st_edge.cap == ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK )) ------------------ | | 128| 14.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (7647:30): [True: 8.44k, False: 5.83k] ------------------ 7648| 8.44k| { 7649| | /* Check exception */ 7650| 8.44k| if (pBNS->type_TACN && ------------------ | Branch (7650:33): [True: 1.48k, False: 6.95k] ------------------ 7651| 1.48k| bRadChangesAtomType( pBNS, pBD, v, NO_VERTEX, NO_VERTEX )) ------------------ | | 118| 1.48k|#define NO_VERTEX -2 ------------------ bRadChangesAtomType( pBNS, pBD, v, NO_VERTEX, NO_VERTEX )) ------------------ | | 118| 1.48k|#define NO_VERTEX -2 ------------------ | Branch (7651:34): [True: 0, False: 1.48k] ------------------ 7652| 0| { 7653| 0| continue; 7654| 0| } 7655| | /* Add */ 7656| 15.8k| for (i = 0; i < pBD->nNumRadEndpoints; i += 2) ------------------ | Branch (7656:41): [True: 9.28k, False: 6.58k] ------------------ 7657| 9.28k| { 7658| | /* Check whether this pair, (u,w), has already been saved */ 7659| 9.28k| if (u == pBD->RadEndpoints[i] && ------------------ | Branch (7659:37): [True: 9.28k, False: 0] ------------------ 7660| 9.28k| v2 == pBD->RadEndpoints[i + 1]) ------------------ | Branch (7660:38): [True: 1.85k, False: 7.42k] ------------------ 7661| 1.85k| { 7662| 1.85k| break; 7663| 1.85k| } 7664| 9.28k| } 7665| 8.44k| if (i >= pBD->nNumRadEndpoints) ------------------ | Branch (7665:33): [True: 6.58k, False: 1.85k] ------------------ 7666| 6.58k| { 7667| | /* Add new (u,w) pair */ 7668| 6.58k| if (pBD->nNumRadEndpoints + 2 <= pBD->max_num_vertices) ------------------ | Branch (7668:37): [True: 6.58k, False: 0] ------------------ 7669| 6.58k| { 7670| | /* add */ 7671| 6.58k| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = u; /* radical */ 7672| 6.58k| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = v2; /* endpoint */ 7673| 6.58k| num_found++; 7674| | /*return 1;*/ /* registered */ 7675| 6.58k| } 7676| 0| else 7677| 0| { 7678| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7679| 0| } 7680| 6.58k| } 7681| 8.44k| } 7682| 25.2k| } 7683| 5.83k| if (num_found) ------------------ | Branch (7683:25): [True: 5.20k, False: 621] ------------------ 7684| 5.20k| { 7685| 5.20k| return 1; 7686| 5.20k| } 7687| 5.83k| } 7688| 5.83k| } 7689| 5.48k| break; 7690| | 7691| 15.0k| case RAD_SRCH_FROM_FICT: ------------------ | Branch (7691:9): [True: 15.0k, False: 10.6k] ------------------ 7692| | /* Find the nearest atom accessible from a fictitious vertex */ 7693| | /* go backwards along alt path and stop at the 1st found atom (not a fictitious vertex) */ 7694| | 7695| 15.0k| v = u; 7696| 15.0k| w = NO_VERTEX; /* the nearest atom -- radical-endpoint */ ------------------ | | 118| 15.0k|#define NO_VERTEX -2 ------------------ 7697| 15.0k| u = NO_VERTEX; /* fictitious vertex carrying a radical */ ------------------ | | 118| 15.0k|#define NO_VERTEX -2 ------------------ 7698| | 7699| 149k| while (v > Vertex_t) ------------------ | | 116| 149k|#define Vertex_t 1 ------------------ | Branch (7699:20): [True: 134k, False: 15.0k] ------------------ 7700| 134k| { 7701| 134k| u = v; 7702| 134k| if (!( v % 2 ) && v / 2 <= pBNS->num_atoms && ------------------ | Branch (7702:21): [True: 70.7k, False: 64.1k] | Branch (7702:35): [True: 14.6k, False: 56.0k] ------------------ 7703| 14.6k| pBNS->vert[v / 2 - 1].st_edge.cap - pBNS->vert[v / 2 - 1].st_edge.flow < 2) ------------------ | Branch (7703:22): [True: 14.6k, False: 0] ------------------ 7704| 14.6k| { 7705| 14.6k| w = v; /* vertex w is atom that may be singlet or doublet but not triplet */ 7706| 14.6k| } 7707| 134k| v = GetPrevVertex( pBNS, u, pBD->SwitchEdge, &iuv ); 7708| 134k| } 7709| 15.0k| v = u / 2 - 1; /* vertex u may be the radical from which the path originated; w is the nearest atom */ 7710| 15.0k| if (w == NO_VERTEX || u == NO_VERTEX || w % 2 || u == w || v < pBNS->num_atoms || ------------------ | | 118| 30.1k|#define NO_VERTEX -2 ------------------ if (w == NO_VERTEX || u == NO_VERTEX || w % 2 || u == w || v < pBNS->num_atoms || ------------------ | | 118| 25.5k|#define NO_VERTEX -2 ------------------ | Branch (7710:17): [True: 4.62k, False: 10.4k] | Branch (7710:35): [True: 0, False: 10.4k] | Branch (7710:53): [True: 0, False: 10.4k] | Branch (7710:62): [True: 0, False: 10.4k] | Branch (7710:72): [True: 0, False: 10.4k] ------------------ 7711| 10.4k| pBNS->vert[v].st_edge.cap == pBNS->vert[v].st_edge.flow || ------------------ | Branch (7711:18): [True: 0, False: 10.4k] ------------------ 7712| 10.4k| ( w = w / 2 - 1 ) >= pBNS->num_atoms) ------------------ | Branch (7712:18): [True: 0, False: 10.4k] ------------------ 7713| 4.62k| { 7714| 4.62k| break; /* reject */ 7715| 4.62k| } 7716| 10.4k| u = v; 7717| | /* At pBNS->vert[u] we have found the radical that originated the path, w is the nearest atom */ 7718| 18.0k| for (i = 0; i < pBD->nNumRadEndpoints; i += 2) ------------------ | Branch (7718:25): [True: 15.1k, False: 2.92k] ------------------ 7719| 15.1k| { 7720| 15.1k| if (u == pBD->RadEndpoints[i] && ------------------ | Branch (7720:21): [True: 15.0k, False: 62] ------------------ 7721| 15.0k| w == pBD->RadEndpoints[i + 1]) ------------------ | Branch (7721:22): [True: 7.54k, False: 7.50k] ------------------ 7722| 7.54k| { 7723| 7.54k| break; /* this pair has already been stored */ 7724| 7.54k| } 7725| 15.1k| } 7726| 10.4k| if (i >= pBD->nNumRadEndpoints) ------------------ | Branch (7726:17): [True: 2.92k, False: 7.54k] ------------------ 7727| 2.92k| { 7728| | /* A new pair has been found */ 7729| 2.92k| if (pBD->nNumRadEndpoints + 2 <= pBD->max_num_vertices) ------------------ | Branch (7729:21): [True: 2.92k, False: 0] ------------------ 7730| 2.92k| { 7731| | /* Add */ 7732| 2.92k| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = u; /* radical */ 7733| 2.92k| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = w; /* endpoint */ 7734| 2.92k| return 1; /* registered */ 7735| 2.92k| } 7736| 0| else 7737| 0| { 7738| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7739| 0| } 7740| 2.92k| } 7741| 7.54k| break; 7742| 25.7k| } 7743| | 7744| 17.6k| return 0; /* rejected */ 7745| 25.7k|} cmp_rad_endpoints: 7750| 6.07k|{ 7751| | /* Vertex radical_vertex, radical_endpoint */ 7752| 6.07k| const Vertex *p1 = (const Vertex *) a1; 7753| 6.07k| const Vertex *p2 = (const Vertex *) a2; 7754| | 7755| 6.07k| if (p1[0] < p2[0]) ------------------ | Branch (7755:9): [True: 18, False: 6.05k] ------------------ 7756| 18| { 7757| 18| return -1; 7758| 18| } 7759| 6.05k| if (p1[0] > p2[0]) ------------------ | Branch (7759:9): [True: 6, False: 6.04k] ------------------ 7760| 6| { 7761| 6| return 1; 7762| 6| } 7763| 6.04k| if (p1[1] < p2[1]) ------------------ | Branch (7763:9): [True: 3.01k, False: 3.02k] ------------------ 7764| 3.01k| { 7765| 3.01k| return -1; 7766| 3.01k| } 7767| 3.02k| if (p1[1] > p2[1]) ------------------ | Branch (7767:9): [True: 3.02k, False: 0] ------------------ 7768| 3.02k| { 7769| 3.02k| return 1; 7770| 3.02k| } 7771| | 7772| 0| return 0; 7773| 3.02k|} RemoveRadEndpoints: 7778| 25.1k|{ 7779| 25.1k| BNS_EDGE *e; 7780| 25.1k| EdgeIndex ie; 7781| 25.1k| BNS_VERTEX *p1, *p2; 7782| 25.1k| Vertex v1, v2; 7783| 25.1k| int i, delta, rad; 7784| | 7785| 43.1k| for (i = pBD->nNumRadEdges - 1; 0 <= i; i--) ------------------ | Branch (7785:37): [True: 18.0k, False: 25.1k] ------------------ 7786| 18.0k| { 7787| 18.0k| ie = pBD->RadEdges[i]; 7788| 18.0k| if (ie < 0 || ie >= pBNS->num_edges) ------------------ | Branch (7788:13): [True: 0, False: 18.0k] | Branch (7788:23): [True: 0, False: 18.0k] ------------------ 7789| 0| { 7790| 0| goto error_exit; 7791| 0| } 7792| 18.0k| e = pBNS->edge + ie; 7793| 18.0k| v1 = e->neighbor1; 7794| 18.0k| v2 = e->neighbor12 ^ v1; /* v2 > v1 <=> v2 was added later */ 7795| 18.0k| if (ie + 1 != pBNS->num_edges || ------------------ | Branch (7795:13): [True: 0, False: 18.0k] ------------------ 7796| 18.0k| v1 < 0 || v1 >= pBNS->num_vertices || ------------------ | Branch (7796:14): [True: 0, False: 18.0k] | Branch (7796:24): [True: 0, False: 18.0k] ------------------ 7797| 18.0k| v2 < 0 || v2 >= pBNS->num_vertices) ------------------ | Branch (7797:14): [True: 0, False: 18.0k] | Branch (7797:24): [True: 0, False: 18.0k] ------------------ 7798| 0| { 7799| 0| goto error_exit; 7800| 0| } 7801| 18.0k| p1 = pBNS->vert + v1; 7802| 18.0k| p2 = pBNS->vert + v2; 7803| | 7804| 18.0k| if (p2->iedge[p2->num_adj_edges - 1] != ie || ------------------ | Branch (7804:13): [True: 0, False: 18.0k] ------------------ 7805| 18.0k| p1->iedge[p1->num_adj_edges - 1] != ie) ------------------ | Branch (7805:14): [True: 0, False: 18.0k] ------------------ 7806| 0| { 7807| 0| goto error_exit; 7808| 0| } 7809| | 7810| 18.0k| p2->num_adj_edges--; 7811| 18.0k| p1->num_adj_edges--; 7812| 18.0k| p2->iedge[p2->num_adj_edges] = 0; 7813| 18.0k| p1->iedge[p1->num_adj_edges] = 0; 7814| 18.0k| p2->st_edge.flow -= e->flow; 7815| 18.0k| p1->st_edge.flow -= e->flow; 7816| | 7817| 18.0k| if (!p2->num_adj_edges && v2 >= pBNS->num_atoms) ------------------ | Branch (7817:13): [True: 8.84k, False: 9.17k] | Branch (7817:35): [True: 8.84k, False: 0] ------------------ 7818| 8.84k| { 7819| 8.84k| if (v2 + 1 != pBNS->num_vertices) ------------------ | Branch (7819:17): [True: 0, False: 8.84k] ------------------ 7820| 0| { 7821| 0| goto error_exit; 7822| 0| } 7823| 8.84k| memset( p2, 0, sizeof( *p2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7824| 8.84k| pBNS->num_vertices--; 7825| 8.84k| } 7826| | 7827| 18.0k| if (!p1->num_adj_edges && v1 >= pBNS->num_atoms) ------------------ | Branch (7827:13): [True: 0, False: 18.0k] | Branch (7827:35): [True: 0, False: 0] ------------------ 7828| 0| { 7829| 0| if (v1 + 1 != pBNS->num_vertices) ------------------ | Branch (7829:17): [True: 0, False: 0] ------------------ 7830| 0| { 7831| 0| goto error_exit; 7832| 0| } 7833| 0| memset( p1, 0, sizeof( *p1 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7834| 0| pBNS->num_vertices--; 7835| 0| } 7836| | 7837| 18.0k| if (at && v1 < pBNS->num_atoms) ------------------ | Branch (7837:13): [True: 833, False: 17.1k] | Branch (7837:19): [True: 833, False: 0] ------------------ 7838| 833| { 7839| 833| delta = p1->st_edge.cap - p1->st_edge.flow; 7840| 833| rad = at[v1].radical; 7841| 833| switch (delta) ------------------ | Branch (7841:21): [True: 833, False: 0] ------------------ 7842| 833| { 7843| 334| case 0: ------------------ | Branch (7843:17): [True: 334, False: 499] ------------------ 7844| 334| if (rad == RADICAL_DOUBLET) ------------------ | | 76| 334|#define RADICAL_DOUBLET 2 ------------------ | Branch (7844:25): [True: 1, False: 333] ------------------ 7845| 1| { 7846| 1| rad = 0; 7847| 1| } 7848| 334| break; 7849| 499| case 1: ------------------ | Branch (7849:17): [True: 499, False: 334] ------------------ 7850| 499| if (rad != RADICAL_DOUBLET) ------------------ | | 76| 499|#define RADICAL_DOUBLET 2 ------------------ | Branch (7850:25): [True: 0, False: 499] ------------------ 7851| 0| { 7852| 0| rad = RADICAL_DOUBLET; ------------------ | | 76| 0|#define RADICAL_DOUBLET 2 ------------------ 7853| 0| } 7854| 833| } 7855| 833| at[v1].radical = rad; 7856| 833| } 7857| 18.0k| memset( e, 0, sizeof( *e ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 7858| 18.0k| pBNS->num_edges--; 7859| 18.0k| } 7860| 25.1k| pBD->nNumRadEdges = 0; 7861| 25.1k| pBD->nNumRadicals = 0; 7862| 25.1k| pBD->bRadSrchMode = RAD_SRCH_NORM; 7863| 25.1k| return 0; 7864| | 7865| 0|error_exit: 7866| | 7867| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7868| 25.1k|} RestoreRadicalsOnly: 7873| 197|{ 7874| 197| BNS_EDGE *e; 7875| 197| EdgeIndex ie; 7876| 197| BNS_VERTEX *p1, *p2; 7877| 197| Vertex v1, v2; 7878| 197| int i, delta, rad; 7879| 197| int p1_num_adj_edges, p2_num_adj_edges; 7880| | 7881| 290| for (i = pBD->nNumRadEdges - 1; 0 <= i; i--) ------------------ | Branch (7881:37): [True: 93, False: 197] ------------------ 7882| 93| { 7883| 93| ie = pBD->RadEdges[i]; 7884| 93| if (ie < 0 || ie >= pBNS->num_edges) ------------------ | Branch (7884:13): [True: 0, False: 93] | Branch (7884:23): [True: 0, False: 93] ------------------ 7885| 0| { 7886| 0| goto error_exit; 7887| 0| } 7888| 93| e = pBNS->edge + ie; 7889| 93| v1 = e->neighbor1; /* atom */ 7890| 93| v2 = e->neighbor12 ^ v1; /* v2 > v1 <=> v2 was added later */ 7891| 93| if (v1 < 0 || v1 >= pBNS->num_atoms || ------------------ | Branch (7891:13): [True: 0, False: 93] | Branch (7891:23): [True: 0, False: 93] ------------------ 7892| 93| v2 < pBNS->num_atoms || v2 >= pBNS->num_vertices) ------------------ | Branch (7892:14): [True: 0, False: 93] | Branch (7892:38): [True: 0, False: 93] ------------------ 7893| 0| { 7894| 0| goto error_exit; 7895| 0| } 7896| 93| p1 = pBNS->vert + v1; 7897| 93| p2 = pBNS->vert + v2; 7898| | 7899| 93| p1_num_adj_edges = e->neigh_ord[0]; 7900| 93| p2_num_adj_edges = e->neigh_ord[1]; 7901| | 7902| 93| if (p2->iedge[p2_num_adj_edges] != ie || ------------------ | Branch (7902:13): [True: 0, False: 93] ------------------ 7903| 93| p1->iedge[p1_num_adj_edges] != ie) ------------------ | Branch (7903:14): [True: 0, False: 93] ------------------ 7904| 0| { 7905| 0| goto error_exit; 7906| 0| } 7907| | 7908| 93| if (at && v1 < pBNS->num_atoms) ------------------ | Branch (7908:13): [True: 93, False: 0] | Branch (7908:19): [True: 93, False: 0] ------------------ 7909| 93| { 7910| 93| delta = p1->st_edge.cap - p1->st_edge.flow + e->flow; 7911| 93| rad = at[v1].radical; 7912| 93| switch (delta) ------------------ | Branch (7912:21): [True: 93, False: 0] ------------------ 7913| 93| { 7914| 41| case 0: ------------------ | Branch (7914:17): [True: 41, False: 52] ------------------ 7915| 41| if (rad == RADICAL_DOUBLET) ------------------ | | 76| 41|#define RADICAL_DOUBLET 2 ------------------ | Branch (7915:25): [True: 11, False: 30] ------------------ 7916| 11| rad = 0; 7917| 41| break; 7918| 52| case 1: ------------------ | Branch (7918:17): [True: 52, False: 41] ------------------ 7919| 52| if (rad != RADICAL_DOUBLET) ------------------ | | 76| 52|#define RADICAL_DOUBLET 2 ------------------ | Branch (7919:25): [True: 11, False: 41] ------------------ 7920| 11| rad = RADICAL_DOUBLET; ------------------ | | 76| 11|#define RADICAL_DOUBLET 2 ------------------ 7921| 93| } 7922| 93| at[v1].radical = rad; 7923| 93| } 7924| 93| } 7925| 197| return 0; 7926| | 7927| 0|error_exit: 7928| | 7929| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7930| 197|} SetRadEndpoints: 7935| 3.08k|{ 7936| 3.08k| int ret, i, j, k, delta; /* djb-rwth: removing redundant variables */ 7937| 3.08k| BNS_VERTEX *pRad, *pEndp; 7938| 3.08k| Vertex wRad, vRad, vEndp, nNumRadicals; 7939| 3.08k| int nDots = 0 /* added initialization, 2006-03 */, nNumEdges; 7940| | 7941| 3.08k| if (pBNS->tot_st_cap <= pBNS->tot_st_flow) ------------------ | Branch (7941:9): [True: 0, False: 3.08k] ------------------ 7942| 0| { 7943| 0| return 0; 7944| 0| } 7945| | 7946| 3.08k| pBD->nNumRadEndpoints = 0; 7947| 3.08k| pBD->nNumRadEdges = 0; 7948| 3.08k| pBD->bRadSrchMode = bRadSrchMode; 7949| 3.08k| pBNS->alt_path = pBNS->altp[0]; 7950| 3.08k| pBNS->bChangeFlow = 0; 7951| 3.08k| ret = BalancedNetworkSearch( pBNS, pBD, BNS_EF_RAD_SRCH ); ------------------ | | 384| 3.08k|#define BNS_EF_RAD_SRCH 128 /* search for rafical paths closures */ ------------------ 7952| 3.08k| ReInitBnData( pBD ); 7953| 3.08k| ReInitBnStructAltPaths( pBNS ); 7954| 3.08k| if (!ret && pBD->nNumRadEndpoints >= 2) ------------------ | Branch (7954:9): [True: 3.08k, False: 0] | Branch (7954:17): [True: 1.43k, False: 1.65k] ------------------ 7955| 1.43k| { 7956| | /* Sort by radical locations */ 7957| 1.43k| qsort( pBD->RadEndpoints, pBD->nNumRadEndpoints / 2, 2 * sizeof( pBD->RadEndpoints[0] ), cmp_rad_endpoints ); 7958| | /* djb-rwth: removing redundant code */ 7959| 1.43k| nNumRadicals = 0; 7960| | 7961| | /* Create new vertices (type=BNS_VERT_TYPE_TEMP) and edges with flow=cap=1 */ 7962| | /* connecting the new vertices radical vertices */ 7963| 2.89k| for (i = 0; i < pBD->nNumRadEndpoints; i = j) ------------------ | Branch (7963:21): [True: 1.45k, False: 1.43k] ------------------ 7964| 1.45k| { 7965| 1.45k| wRad = pBD->RadEndpoints[i]; 7966| 1.45k| pRad = pBNS->vert + wRad; 7967| 1.45k| delta = pRad->st_edge.cap - ( pRad->st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 1.45k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 7968| 1.45k| if (delta <= 0) ------------------ | Branch (7968:17): [True: 0, False: 1.45k] ------------------ 7969| 0| { 7970| 0| delta = 1; 7971| 0| } 7972| 1.45k| nNumEdges = 0; 7973| 4.37k| for (j = i; j < pBD->nNumRadEndpoints && wRad == pBD->RadEndpoints[j]; j += 2) ------------------ | Branch (7973:25): [True: 2.93k, False: 1.43k] | Branch (7973:54): [True: 2.92k, False: 15] ------------------ 7974| 2.92k| { 7975| 2.92k| nNumEdges++; 7976| 2.92k| } 7977| | /* Add new aux vertex to the radical atom/vertex */ 7978| 1.45k| vRad = bAddNewVertex( pBNS, wRad, delta, delta, nNumEdges + 1, &nDots ); 7979| 1.45k| if (IS_BNS_ERROR( vRad )) ------------------ | | 67| 1.45k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.45k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.45k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.45k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.45k, False: 0] | | | Branch (67:44): [True: 0, False: 1.45k] | | ------------------ ------------------ 7980| 0| { 7981| 0| ret = vRad; 7982| 0| goto error_exit; 7983| 0| } 7984| 1.45k| pRad = pBNS->vert + vRad; 7985| 1.45k| pBD->RadEdges[pBD->nNumRadEdges++] = pRad->iedge[pRad->num_adj_edges - 1]; 7986| | /* Replace references to vertex wRad with vRad */ 7987| 4.37k| for (k = i, nNumEdges = 0; k < j; k += 2) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | Branch (7987:40): [True: 2.92k, False: 1.45k] ------------------ 7988| 2.92k| { 7989| 2.92k| pBD->RadEndpoints[k] = vRad; 7990| 2.92k| } 7991| 1.45k| nNumRadicals++; 7992| 1.45k| } 7993| | /* All vRad vertex indices should be in the range vFirstNewVertex...vFirstNewVertex+nNumRadicals-1 */ 7994| | /* connect new vertices to the radical endpoints thus replacing radicals with even-length alternating cycles */ 7995| 2.89k| for (i = 0; i < pBD->nNumRadEndpoints; i = j) ------------------ | Branch (7995:21): [True: 1.45k, False: 1.43k] ------------------ 7996| 1.45k| { 7997| 1.45k| vRad = pBD->RadEndpoints[i]; 7998| 1.45k| pRad = pBNS->vert + vRad; 7999| 4.37k| for (j = i; j < pBD->nNumRadEndpoints && vRad == pBD->RadEndpoints[j]; j += 2) ------------------ | Branch (7999:25): [True: 2.93k, False: 1.43k] | Branch (7999:54): [True: 2.92k, False: 15] ------------------ 8000| 2.92k| { 8001| | /* Connect vew vertex pRad to radical endpoints */ 8002| 2.92k| vEndp = pBD->RadEndpoints[j + 1]; 8003| 2.92k| pEndp = pBNS->vert + vEndp; 8004| 2.92k| ret = AddNewEdge( pRad, pEndp, pBNS, 1, 0 ); 8005| 2.92k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 2.92k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 2.92k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 2.92k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 2.92k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 2.92k, False: 0] | | | Branch (67:44): [True: 0, False: 2.92k] | | ------------------ ------------------ 8006| 0| { 8007| 0| goto error_exit; 8008| 0| } 8009| 2.92k| pBD->RadEdges[pBD->nNumRadEdges++] = ret; 8010| 2.92k| } 8011| 1.45k| } 8012| 1.43k| pBD->nNumRadicals = nNumRadicals; 8013| 1.43k| return nNumRadicals; /* done */ 8014| 1.43k| } 8015| | 8016| 1.65k| return 0; /* nothing to do */ 8017| | 8018| 0|error_exit: 8019| 0| RemoveRadEndpoints( pBNS, pBD, NULL ); 8020| | 8021| 0| return ret; 8022| 3.08k|} SetRadEndpoints2: 8033| 23.6k|{ 8034| 23.6k| int ret = 0, i, j, k, n, delta = 1; /* djb-rwth: removing redundant variables */ 8035| 23.6k| BNS_VERTEX *pRad, *pEndp; 8036| 23.6k| Vertex wRad, vRad, vEndp, nNumRadicals; 8037| 23.6k| Vertex vRadList[MAX_NUM_RAD], vRadEqul[MAX_NUM_RAD]; 8038| 23.6k| int nNumRad = 0; 8039| 23.6k| int edge_flow; 8040| 23.6k| int nDots = 0 /* added initialization, 2006-03 */, nNumEdges; 8041| 23.6k| NodeSet VertSet; 8042| | 8043| 23.6k| if (pBNS->tot_st_cap <= pBNS->tot_st_flow) ------------------ | Branch (8043:9): [True: 17.2k, False: 6.40k] ------------------ 8044| 17.2k| { 8045| 17.2k| return 0; 8046| 17.2k| } 8047| | 8048| | /* Find all radicals: their vertices have st_cap-st_flow=delta */ 8049| | /* save radical atom numbers in vRadList[] and remove radical by making st_cap=st_flow */ 8050| 45.6k| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (8050:17): [True: 39.2k, False: 6.40k] ------------------ 8051| 39.2k| { 8052| 39.2k| if (pBNS->vert[i].st_edge.cap - delta == ( pBNS->vert[i].st_edge.flow & EDGE_FLOW_ST_MASK )) ------------------ | | 128| 39.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (8052:13): [True: 8.00k, False: 31.2k] ------------------ 8053| 8.00k| { 8054| 8.00k| if (nNumRad < MAX_NUM_RAD) ------------------ | | 8025| 8.00k|#define MAX_NUM_RAD 256 ------------------ | Branch (8054:17): [True: 8.00k, False: 0] ------------------ 8055| 8.00k| { 8056| 8.00k| pBNS->vert[i].st_edge.cap -= delta; 8057| 8.00k| pBNS->tot_st_cap -= delta; 8058| 8.00k| vRadList[nNumRad] = i; /* radical position; i > j <=> vRadList[i] > vRadList[j] */ 8059| 8.00k| vRadEqul[nNumRad] = nNumRad; /* the smallest radical atom that has reachable 8060| | * atoms in common with this radical atom 8061| | * always keep vRadEqul[nNumRad] <= nNumRad */ 8062| 8.00k| nNumRad++; 8063| 8.00k| } 8064| 8.00k| } 8065| 39.2k| } 8066| | 8067| 6.40k| if (pBNS->tot_st_cap - pBNS->tot_st_flow > nNumRad) ------------------ | Branch (8067:9): [True: 0, False: 6.40k] ------------------ 8068| 0| { 8069| 0| return BNS_CAP_FLOW_ERR; /* extra st_cap on non-atoms or program error */ ------------------ | | 58| 0|#define BNS_CAP_FLOW_ERR (BNS_ERR + 10) /*(-9989)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8070| 0| } 8071| | 8072| 6.40k| memset( &VertSet, 0, sizeof( VertSet ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 8073| | 8074| | /* Find reachable atoms by enabling each radical separately */ 8075| 14.4k| for (j = 0; j < nNumRad; j++) ------------------ | Branch (8075:17): [True: 8.00k, False: 6.40k] ------------------ 8076| 8.00k| { 8077| 8.00k| i = vRadList[j]; 8078| 8.00k| pBD->nNumRadEndpoints = 0; 8079| 8.00k| pBD->nNumRadEdges = 0; 8080| 8.00k| pBD->bRadSrchMode = bRadSrchMode; 8081| 8.00k| pBNS->alt_path = pBNS->altp[0]; 8082| 8.00k| pBNS->bChangeFlow = 0; 8083| 8.00k| pBNS->vert[i].st_edge.cap += delta; /* enable single radical */ 8084| 8.00k| pBNS->tot_st_cap += delta; 8085| 8.00k| ret = BalancedNetworkSearch( pBNS, pBD, BNS_EF_RAD_SRCH ); /* find reachable atoms */ ------------------ | | 384| 8.00k|#define BNS_EF_RAD_SRCH 128 /* search for rafical paths closures */ ------------------ 8086| 8.00k| ReInitBnData( pBD ); 8087| 8.00k| ReInitBnStructAltPaths( pBNS ); 8088| 8.00k| pBD->bRadSrchMode = RAD_SRCH_NORM; 8089| 8.00k| pBNS->vert[i].st_edge.cap -= delta; /* disable single radical */ 8090| 8.00k| pBNS->tot_st_cap -= delta; 8091| 8.00k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 8.00k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 8.00k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 8.00k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 8.00k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 8.00k, False: 0] | | | Branch (67:44): [True: 0, False: 8.00k] | | ------------------ ------------------ 8092| 0| { 8093| 0| goto error_exit; 8094| 0| } 8095| 8.00k| else 8096| 8.00k| { 8097| 8.00k| if (ret) ------------------ | Branch (8097:17): [True: 0, False: 8.00k] ------------------ 8098| 0| { 8099| 0| ret = BNS_RADICAL_ERR; /* found augmenting path: should not happen since only one radical was enabled */ ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8100| 0| goto error_exit; 8101| 0| } 8102| 8.00k| } 8103| 8.00k| if (!ret && pBD->nNumRadEndpoints >= 2) ------------------ | Branch (8103:13): [True: 8.00k, False: 0] | Branch (8103:21): [True: 3.63k, False: 4.36k] ------------------ 8104| 3.63k| { 8105| | /* Sort by: primary_key=radical locations, secondary_key=radical endoint */ 8106| | 8107| 3.63k| qsort( pBD->RadEndpoints, pBD->nNumRadEndpoints / 2, 2 * sizeof( pBD->RadEndpoints[0] ), cmp_rad_endpoints ); 8108| | 8109| 3.63k| if (pBD->RadEndpoints[0] != i || pBD->RadEndpoints[pBD->nNumRadEndpoints - 2] != i) ------------------ | Branch (8109:17): [True: 0, False: 3.63k] | Branch (8109:46): [True: 0, False: 3.63k] ------------------ 8110| 0| { 8111| 0| ret = BNS_RADICAL_ERR; /* more than one radical vertex */ ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8112| 0| goto error_exit; 8113| 0| } 8114| 3.63k| if (nNumRad > 1) ------------------ | Branch (8114:17): [True: 1.76k, False: 1.87k] ------------------ 8115| 1.76k| { 8116| | /* If more than one radical then save reachable atoms in bitmaps to allow */ 8117| | /* faster finding whether same atoms are reachable by two or more radicals */ 8118| | /* Later merge such sets */ 8119| 1.76k| if (NULL == VertSet.bitword) ------------------ | Branch (8119:21): [True: 1.10k, False: 655] ------------------ 8120| 1.10k| { 8121| 1.10k| SetBitCreate( pCG ); 8122| 1.10k| if (!NodeSetCreate( pCG, &VertSet, pBNS->num_atoms, nNumRad )) ------------------ | Branch (8122:25): [True: 0, False: 1.10k] ------------------ 8123| 0| { 8124| 0| ret = BNS_OUT_OF_RAM; /* out of RAM */ ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8125| 0| goto error_exit; 8126| 0| } 8127| 1.10k| } 8128| | 8129| 1.76k| NodeSetFromRadEndpoints( pCG, &VertSet, j, pBD->RadEndpoints, pBD->nNumRadEndpoints ); 8130| | 8131| | /* Do not allow any radical center be treated as a reachable atom: */ 8132| | 8133| 1.76k| RemoveFromNodeSet( pCG, &VertSet, j, vRadList, nNumRad ); 8134| 1.76k| } 8135| 3.63k| } 8136| 8.00k| } 8137| | 8138| | /* Restore radical st_cap so that st_cap-st_flow=delta */ 8139| 14.4k| for (j = 0; j < nNumRad; j++) ------------------ | Branch (8139:17): [True: 8.00k, False: 6.40k] ------------------ 8140| 8.00k| { 8141| 8.00k| i = vRadList[j]; 8142| 8.00k| pBNS->vert[i].st_edge.cap += delta; 8143| 8.00k| pBNS->tot_st_cap += delta; 8144| 8.00k| } 8145| | 8146| | /* Merge lists that have common radical endpoints */ 8147| | /* defect: if vertex sets i and j do not intersect they will be compared 2 times */ 8148| | /* total up to nNumRad*(nNumRad-1)/2 calls to DoNodeSetsIntersect() */ 8149| 6.40k| if (nNumRad > 1) ------------------ | Branch (8149:9): [True: 1.48k, False: 4.92k] ------------------ 8150| 1.48k| { 8151| 4.56k| for (i = 0; i < nNumRad; i++) ------------------ | Branch (8151:21): [True: 3.07k, False: 1.48k] ------------------ 8152| 3.07k| { 8153| 3.07k| if (vRadEqul[i] != i) ------------------ | Branch (8153:17): [True: 610, False: 2.46k] ------------------ 8154| 610| { 8155| 610| continue; 8156| 610| } 8157| 2.46k| do 8158| 3.06k| { 8159| 3.06k| n = 0; 8160| 5.36k| for (j = i + 1; j < nNumRad; j++) ------------------ | Branch (8160:33): [True: 2.30k, False: 3.06k] ------------------ 8161| 2.30k| { 8162| 2.30k| if (vRadEqul[j] != j) ------------------ | Branch (8162:25): [True: 611, False: 1.69k] ------------------ 8163| 611| { 8164| 611| continue; 8165| 611| } 8166| 1.69k| if (DoNodeSetsIntersect( &VertSet, i, j )) ------------------ | Branch (8166:25): [True: 610, False: 1.08k] ------------------ 8167| 610| { 8168| 610| AddNodeSet2ToNodeSet1( &VertSet, i, j ); 8169| 610| vRadEqul[j] = i; /* Set j was copied to set i; i < j */ 8170| 610| n++; 8171| 610| } 8172| 1.69k| } 8173| 3.06k| } while (n); ------------------ | Branch (8173:22): [True: 595, False: 2.46k] ------------------ 8174| 2.46k| } 8175| | /* Fill out pBD->RadEndpoints[] */ 8176| 4.56k| for (i = 0, n = 0; i < nNumRad; i++) ------------------ | Branch (8176:28): [True: 3.07k, False: 1.48k] ------------------ 8177| 3.07k| { 8178| 3.07k| if (i == vRadEqul[i]) ------------------ | Branch (8178:17): [True: 2.46k, False: 610] ------------------ 8179| 2.46k| { 8180| 2.46k| if (!IsNodeSetEmpty( &VertSet, i )) ------------------ | Branch (8180:21): [True: 1.08k, False: 1.38k] ------------------ 8181| 1.08k| { 8182| | /* Store equivalent radicals */ 8183| 1.77k| for (j = i + 1; j < nNumRad; j++) ------------------ | Branch (8183:37): [True: 694, False: 1.08k] ------------------ 8184| 694| { 8185| 694| if (i == vRadEqul[j]) ------------------ | Branch (8185:29): [True: 610, False: 84] ------------------ 8186| 610| { 8187| 610| pBD->RadEndpoints[n++] = vRadList[i]; 8188| 610| pBD->RadEndpoints[n++] = -vRadList[j] - 2; /* equivalent radical, alvays not zero */ 8189| 610| } 8190| 694| } 8191| | /* Store endpoints */ 8192| 1.08k| n = AddNodesToRadEndpoints( pCG, &VertSet, i, pBD->RadEndpoints, vRadList[i], n, pBD->max_len_Pu_Pv ); 8193| 1.08k| if (n < 0) ------------------ | Branch (8193:25): [True: 0, False: 1.08k] ------------------ 8194| 0| { 8195| 0| ret = BNS_RADICAL_ERR; /* pBD->RadEndpoints overflow */ ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8196| 0| goto error_exit; 8197| 0| } 8198| 1.08k| } 8199| 1.38k| else 8200| 1.38k| { 8201| 1.38k| pBD->RadEndpoints[n++] = vRadList[i]; 8202| 1.38k| pBD->RadEndpoints[n++] = -1; /* immobile radical, only one edge to add */ 8203| 1.38k| } 8204| 2.46k| } 8205| 3.07k| } 8206| 1.48k| pBD->nNumRadEndpoints = n; 8207| 1.48k| NodeSetFree( pCG, &VertSet ); 8208| 1.48k| } 8209| 4.92k| else 8210| 4.92k| { 8211| 4.92k| if (nNumRad == 1 && !pBD->nNumRadEndpoints) ------------------ | Branch (8211:13): [True: 4.92k, False: 0] | Branch (8211:29): [True: 3.04k, False: 1.87k] ------------------ 8212| 3.04k| { 8213| | /* 2006-07-30: a single radical; no possible endpoint found */ 8214| 6.08k| for (i = 0, n = 0; i < nNumRad; i++) ------------------ | Branch (8214:32): [True: 3.04k, False: 3.04k] ------------------ 8215| 3.04k| { 8216| 3.04k| pBD->RadEndpoints[n++] = vRadList[i]; 8217| 3.04k| pBD->RadEndpoints[n++] = -1; /* immobile radical, only one edge to add */ 8218| 3.04k| } 8219| 3.04k| pBD->nNumRadEndpoints = n; 8220| 3.04k| } 8221| 4.92k| } 8222| | 8223| 6.40k| if (!ret && pBD->nNumRadEndpoints >= 2) ------------------ | Branch (8223:9): [True: 6.40k, False: 0] | Branch (8223:17): [True: 6.40k, False: 0] ------------------ 8224| 6.40k| { 8225| | /* Already sorted by radical locations */ 8226| | /* djb-rwth: removing redundant code */ 8227| 6.40k| nNumRadicals = 0; 8228| | /************************************************************************** 8229| | * Create new vertices (type=BNS_VERT_TYPE_TEMP) and edges with flow=cap=1 8230| | * connecting the new vertices radical vertices 8231| | * 8232| | * 8233| | * Original structure: atom A is a radical center A==B--C*--D==E 8234| | * A*--B==C--D==E atoms C and E are reachable: A==B--C===D--E* 8235| | * 8236| | * Resultant temporary structure: 8237| | * A---B==C--D==E 8238| | * || / / 8239| | * || / / The additional new vertex (*) and its 8240| | * || / / 3 edges replace the radical with alternating 8241| | * || / / circuits that allow same bond changes 8242| | * || / / as moving the radical to atoms C or E. 8243| | * ||// "Double bonds" here have edge cap=1, flow=1 8244| | * (*) "Single bonds" have edge cap=1, flow=0 8245| | * 8246| | * The "equivalent radical centers" (which have at least one reachable atom 8247| | * in common) are connected to (*) with "double bonds" (edge cap=1, flow=1). 8248| | * Reachable non-radical atoms are connected by edges with cap=1, flow=0 8249| | * After running BNS to find alt.path a "double bond" from (*) may move 8250| | * to another atom thus muving the radical. 8251| | * 8252| | * Number of additional (*) vertices = number of sets of 8253| | * "equivalent radical centers". 8254| | * Each such a set may include one or more radical centers. 8255| | * 8256| | * The radicals will be re-created in RemoveRadEndpoints() 8257| | ***************************************************************************/ 8258| 13.7k| for (i = 0; i < pBD->nNumRadEndpoints; i = j) ------------------ | Branch (8258:21): [True: 7.39k, False: 6.40k] ------------------ 8259| 7.39k| { 8260| 7.39k| wRad = pBD->RadEndpoints[i]; 8261| 7.39k| pRad = pBNS->vert + wRad; 8262| 7.39k| delta = pRad->st_edge.cap - ( pRad->st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 7.39k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 8263| 7.39k| if (delta <= 0) ------------------ | Branch (8263:17): [True: 0, False: 7.39k] ------------------ 8264| 0| { 8265| 0| delta = 1; 8266| 0| } 8267| 7.39k| nNumEdges = 0; 8268| 18.0k| for (j = i; j < pBD->nNumRadEndpoints && wRad == pBD->RadEndpoints[j]; j += 2) ------------------ | Branch (8268:25): [True: 11.6k, False: 6.40k] | Branch (8268:54): [True: 10.6k, False: 983] ------------------ 8269| 10.6k| { 8270| 10.6k| nNumEdges += ( pBD->RadEndpoints[j + 1] != -1 ); /* immobile radicals have one edge only */ 8271| 10.6k| } 8272| | /* Add new aux vertex to the radical atom/vertex making st_cap-st_flow=0 */ 8273| | /* in case of immobile radical there will be no additional eddges since nNumEdges=0 */ 8274| 7.39k| vRad = bAddNewVertex( pBNS, wRad, delta, delta, nNumEdges + 1, &nDots ); 8275| 7.39k| if (IS_BNS_ERROR( vRad )) ------------------ | | 67| 7.39k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 7.39k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 7.39k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 7.39k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 7.39k, False: 0] | | | Branch (67:44): [True: 0, False: 7.39k] | | ------------------ ------------------ 8276| 0| { 8277| 0| ret = vRad; 8278| 0| goto error_exit; 8279| 0| } 8280| 7.39k| pRad = pBNS->vert + vRad; 8281| 7.39k| pBD->RadEdges[pBD->nNumRadEdges++] = pRad->iedge[pRad->num_adj_edges - 1]; 8282| | /* replace references to vertex wRad with vRad */ 8283| 18.0k| for (k = i, nNumEdges = 0; k < j; k += 2) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | Branch (8283:40): [True: 10.6k, False: 7.39k] ------------------ 8284| 10.6k| { 8285| 10.6k| pBD->RadEndpoints[k] = vRad; 8286| 10.6k| } 8287| 7.39k| nNumRadicals++; 8288| 7.39k| } 8289| | /* All vRad vertex indices should be in the range vFirstNewVertex...vFirstNewVertex+nNumRadicals-1 */ 8290| | /* connect new vertices to the radical endpoints thus replacing radicals with even-length alternating cycles */ 8291| 13.7k| for (i = 0; i < pBD->nNumRadEndpoints; i = j) ------------------ | Branch (8291:21): [True: 7.39k, False: 6.40k] ------------------ 8292| 7.39k| { 8293| 7.39k| vRad = pBD->RadEndpoints[i]; 8294| 7.39k| pRad = pBNS->vert + vRad; 8295| 18.0k| for (j = i; j < pBD->nNumRadEndpoints && vRad == pBD->RadEndpoints[j]; j += 2) ------------------ | Branch (8295:25): [True: 11.6k, False: 6.40k] | Branch (8295:54): [True: 10.6k, False: 983] ------------------ 8296| 10.6k| { 8297| | /* connect vew vertex pRad to radical endpoints */ 8298| 10.6k| vEndp = pBD->RadEndpoints[j + 1]; 8299| 10.6k| if (vEndp == -1) ------------------ | Branch (8299:21): [True: 4.42k, False: 6.24k] ------------------ 8300| 4.42k| continue; 8301| 6.24k| if (vEndp < 0) ------------------ | Branch (8301:21): [True: 610, False: 5.63k] ------------------ 8302| 610| { 8303| 610| edge_flow = 1; 8304| 610| vEndp = -vEndp - 2; /* equivalent radical centers */ 8305| 610| } 8306| 5.63k| else 8307| 5.63k| { 8308| 5.63k| edge_flow = 0; 8309| 5.63k| } 8310| 6.24k| pEndp = pBNS->vert + vEndp; 8311| 6.24k| ret = AddNewEdge( pRad, pEndp, pBNS, 1, edge_flow ); 8312| 6.24k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 6.24k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 6.24k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 6.24k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 6.24k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 6.24k, False: 0] | | | Branch (67:44): [True: 0, False: 6.24k] | | ------------------ ------------------ 8313| 0| { 8314| 0| goto error_exit; 8315| 0| } 8316| 6.24k| pBD->RadEdges[pBD->nNumRadEdges++] = ret; 8317| 6.24k| } 8318| 7.39k| } 8319| 6.40k| pBD->nNumRadicals = nNumRadicals; 8320| 6.40k| return nNumRadicals; /* done */ 8321| 6.40k| } 8322| 0| return 0; /* nothing to do */ 8323| | 8324| 0|error_exit: 8325| 0| RemoveRadEndpoints( pBNS, pBD, NULL ); 8326| 0| NodeSetFree( pCG, &VertSet ); 8327| | 8328| 0| return ret; 8329| 6.40k|} bExistsAltPath: 8367| 28.1k|{ 8368| 28.1k| ALT_PATH_CHANGES apc; 8369| 28.1k| int ret, ret_val, bError, bSuccess, bChangeFlow = 0, nDots, nDelta, bDoMarkChangedBonds = 1; 8370| 28.1k| int bAdjustRadicals = 0; 8371| 28.1k| AT_NUMB type; 8372| 28.1k| BNS_FLOW_CHANGES fcd[4 * BNS_MAX_NUM_FLOW_CHANGES + 1]; 8373| 28.1k| ENDPOINT_INFO eif; 8374| 28.1k|#if ( KETO_ENOL_TAUT == 1 ) 8375| 28.1k| ENDPOINT_INFO eif2; 8376| 28.1k|#endif 8377| | 8378| | /* Initialize */ 8379| 28.1k| switch (path_type) 8380| 28.1k| { 8381| 11.8k| case ALT_PATH_MODE_TAUTOM: ------------------ | | 310| 11.8k|#define ALT_PATH_MODE_TAUTOM 1 ------------------ | Branch (8381:9): [True: 11.8k, False: 16.2k] ------------------ 8382| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8383| 11.8k| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 11.8k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8384| 11.8k| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 11.8k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 11.8k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 11.8k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8385| 11.8k| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8385:17): [True: 10.9k, False: 829] ------------------ 8386| 10.9k| ( !nGetEndpointInfo( at, nVertSingleBond, &eif ) || !eif.cDonor )) ------------------ | Branch (8386:19): [True: 0, False: 10.9k] | Branch (8386:69): [True: 3.50k, False: 7.48k] ------------------ 8387| 3.50k| { 8388| 3.50k| return 0; 8389| 3.50k| } 8390| 8.31k| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8390:17): [True: 8.20k, False: 112] ------------------ 8391| 8.20k| ( !nGetEndpointInfo( at, nVertDoubleBond, &eif ) || !eif.cAcceptor )) ------------------ | Branch (8391:19): [True: 0, False: 8.20k] | Branch (8391:69): [True: 800, False: 7.40k] ------------------ 8392| 800| { 8393| 800| return 0; 8394| 800| } 8395| 7.51k| break; 8396| | 8397| 7.51k|#if ( TAUT_PT_22_00 == 1 ) 8398| 7.51k| case ALT_PATH_MODE_TAUTOM_PT_22_00: ------------------ | | 324| 0|#define ALT_PATH_MODE_TAUTOM_PT_22_00 11 ------------------ | Branch (8398:9): [True: 0, False: 28.1k] ------------------ 8399| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8400| 0| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8401| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8402| 0| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8402:17): [True: 0, False: 0] ------------------ 8403| 0| (!nGetEndpointInfo_PT_22_00(at, nVertSingleBond, &eif) || !eif.cDonor)) ------------------ | Branch (8403:18): [True: 0, False: 0] | Branch (8403:75): [True: 0, False: 0] ------------------ 8404| 0| return 0; 8405| 0| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8405:17): [True: 0, False: 0] ------------------ 8406| 0| (!nGetEndpointInfo_PT_22_00(at, nVertDoubleBond, &eif) || !eif.cAcceptor)) ------------------ | Branch (8406:18): [True: 0, False: 0] | Branch (8406:75): [True: 0, False: 0] ------------------ 8407| 0| return 0; 8408| 0| break; 8409| 0|#endif 8410| | 8411| 0|#if ( TAUT_PT_16_00 == 1 ) 8412| 0| case ALT_PATH_MODE_TAUTOM_PT_16_00: ------------------ | | 327| 0|#define ALT_PATH_MODE_TAUTOM_PT_16_00 12 ------------------ | Branch (8412:9): [True: 0, False: 28.1k] ------------------ 8413| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8414| 0| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8415| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8416| 0| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8416:17): [True: 0, False: 0] ------------------ 8417| 0| (!nGetEndpointInfo_PT_16_00(at, nVertSingleBond, &eif) || !eif.cDonor)) ------------------ | Branch (8417:18): [True: 0, False: 0] | Branch (8417:75): [True: 0, False: 0] ------------------ 8418| 0| return 0; 8419| 0| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8419:17): [True: 0, False: 0] ------------------ 8420| 0| (!nGetEndpointInfo_PT_16_00(at, nVertDoubleBond, &eif) || !eif.cAcceptor)) ------------------ | Branch (8420:18): [True: 0, False: 0] | Branch (8420:75): [True: 0, False: 0] ------------------ 8421| 0| return 0; 8422| 0| break; 8423| 0|#endif 8424| | 8425| 0|#if ( TAUT_PT_06_00 == 1 ) 8426| 0| case ALT_PATH_MODE_TAUTOM_PT_06_00: ------------------ | | 330| 0|#define ALT_PATH_MODE_TAUTOM_PT_06_00 13 ------------------ | Branch (8426:9): [True: 0, False: 28.1k] ------------------ 8427| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8428| 0| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8429| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8430| 0| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8430:17): [True: 0, False: 0] ------------------ 8431| 0| (!nGetEndpointInfo_PT_06_00(at, nVertSingleBond, &eif) || !eif.cDonor)) ------------------ | Branch (8431:18): [True: 0, False: 0] | Branch (8431:75): [True: 0, False: 0] ------------------ 8432| 0| return 0; 8433| 0| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8433:17): [True: 0, False: 0] ------------------ 8434| 0| (!nGetEndpointInfo_PT_06_00(at, nVertDoubleBond, &eif) || !eif.cAcceptor)) ------------------ | Branch (8434:18): [True: 0, False: 0] | Branch (8434:75): [True: 0, False: 0] ------------------ 8435| 0| return 0; 8436| 0| break; 8437| 0|#endif 8438| | 8439| 0|#if ( TAUT_PT_39_00 == 1 ) 8440| 0| case ALT_PATH_MODE_TAUTOM_PT_39_00: ------------------ | | 333| 0|#define ALT_PATH_MODE_TAUTOM_PT_39_00 14 ------------------ | Branch (8440:9): [True: 0, False: 28.1k] ------------------ 8441| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8442| 0| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8443| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8444| 0| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8444:17): [True: 0, False: 0] ------------------ 8445| 0| (!nGetEndpointInfo_PT_39_00(at, nVertSingleBond, &eif) || !eif.cDonor)) ------------------ | Branch (8445:18): [True: 0, False: 0] | Branch (8445:75): [True: 0, False: 0] ------------------ 8446| 0| return 0; 8447| 0| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8447:17): [True: 0, False: 0] ------------------ 8448| 0| (!nGetEndpointInfo_PT_39_00(at, nVertDoubleBond, &eif) || !eif.cAcceptor)) ------------------ | Branch (8448:18): [True: 0, False: 0] | Branch (8448:75): [True: 0, False: 0] ------------------ 8449| 0| return 0; 8450| 0| break; 8451| 0|#endif 8452| | 8453| 0|#if ( TAUT_PT_13_00 == 1 ) 8454| 0| case ALT_PATH_MODE_TAUTOM_PT_13_00: ------------------ | | 336| 0|#define ALT_PATH_MODE_TAUTOM_PT_13_00 15 ------------------ | Branch (8454:9): [True: 0, False: 28.1k] ------------------ 8455| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8456| 0| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8457| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8458| 0| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8458:17): [True: 0, False: 0] ------------------ 8459| 0| (!nGetEndpointInfo_PT_13_00(at, nVertSingleBond, &eif) || !eif.cDonor)) ------------------ | Branch (8459:18): [True: 0, False: 0] | Branch (8459:75): [True: 0, False: 0] ------------------ 8460| 0| return 0; 8461| 0| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8461:17): [True: 0, False: 0] ------------------ 8462| 0| (!nGetEndpointInfo_PT_13_00(at, nVertDoubleBond, &eif) || !eif.cAcceptor)) ------------------ | Branch (8462:18): [True: 0, False: 0] | Branch (8462:75): [True: 0, False: 0] ------------------ 8463| 0| return 0; 8464| 0| break; 8465| 0|#endif 8466| | 8467| 0|#if ( TAUT_PT_18_00 == 1 ) 8468| 0| case ALT_PATH_MODE_TAUTOM_PT_18_00: ------------------ | | 339| 0|#define ALT_PATH_MODE_TAUTOM_PT_18_00 16 ------------------ | Branch (8468:9): [True: 0, False: 28.1k] ------------------ 8469| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8470| 0| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8471| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8472| 0| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8472:17): [True: 0, False: 0] ------------------ 8473| 0| (!nGetEndpointInfo_PT_18_00(at, nVertSingleBond, &eif) || !eif.cDonor)) ------------------ | Branch (8473:18): [True: 0, False: 0] | Branch (8473:75): [True: 0, False: 0] ------------------ 8474| 0| return 0; 8475| 0| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8475:17): [True: 0, False: 0] ------------------ 8476| 0| (!nGetEndpointInfo_PT_18_00(at, nVertDoubleBond, &eif) || !eif.cAcceptor)) ------------------ | Branch (8476:18): [True: 0, False: 0] | Branch (8476:75): [True: 0, False: 0] ------------------ 8477| 0| return 0; 8478| 0| break; 8479| 0|#endif 8480| | 8481| | 8482| 0|#if ( KETO_ENOL_TAUT == 1 ) 8483| 0| case ALT_PATH_MODE_TAUTOM_KET: ------------------ | | 320| 0|#define ALT_PATH_MODE_TAUTOM_KET 10 /* same as ALT_PATH_MODE_TAUTOM, applies to C=-OH or CH-=O; H may be (-) */ ------------------ | Branch (8483:9): [True: 0, False: 28.1k] ------------------ 8484| | /* Check for alt path allowing to move H and (-). Purpose: confirm possible tautomerism */ 8485| 0| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8486| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8487| | 8488| 0| if (!at[nVertSingleBond].endpoint && ------------------ | Branch (8488:17): [True: 0, False: 0] ------------------ 8489| 0| ( !nGetEndpointInfo_KET( at, nVertSingleBond, &eif ) || !eif.cDonor )) ------------------ | Branch (8489:19): [True: 0, False: 0] | Branch (8489:73): [True: 0, False: 0] ------------------ 8490| 0| { 8491| 0| return 0; 8492| 0| } 8493| 0| if (!at[nVertDoubleBond].endpoint && ------------------ | Branch (8493:17): [True: 0, False: 0] ------------------ 8494| 0| ( !nGetEndpointInfo_KET( at, nVertDoubleBond, &eif2 ) || !eif2.cAcceptor )) ------------------ | Branch (8494:19): [True: 0, False: 0] | Branch (8494:74): [True: 0, False: 0] ------------------ 8495| 0| { 8496| 0| return 0; 8497| 0| } 8498| | /* 8499| | if ( eif.cKetoEnolCode + eif2.cKetoEnolCode != 3 ) 8500| | return 0; 8501| | */ 8502| 0| break; 8503| | 8504| 0|#endif 8505| 8.72k| case ALT_PATH_MODE_CHARGE: ------------------ | | 311| 8.72k|#define ALT_PATH_MODE_CHARGE 2 ------------------ | Branch (8505:9): [True: 8.72k, False: 19.3k] ------------------ 8506| | /* Find alt path allowing to move (+). Purpose: establish "charge groups", 8507| | mark alt. bonds due to (+) charge movement */ 8508| 8.72k| type = BNS_VERT_TYPE_C_POINT; ------------------ | | 48| 8.72k|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ 8509| 8.72k| bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 372| 8.72k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 8.72k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 8.72k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 374| 8.72k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ 8510| 8.72k| break; 8511| | 8512| 1.43k| case ALT_PATH_MODE_4_SALT: ------------------ | | 312| 1.43k|#define ALT_PATH_MODE_4_SALT 3 /* mark alt bonds along the path */ ------------------ | Branch (8512:9): [True: 1.43k, False: 26.6k] ------------------ 8513| 1.43k| case ALT_PATH_MODE_4_SALT2: ------------------ | | 313| 1.43k|#define ALT_PATH_MODE_4_SALT2 4 /* mark alt bonds along the path, path to taut. group fict. vertex if exists */ ------------------ | Branch (8513:9): [True: 0, False: 28.1k] ------------------ 8514| | /* Find alt paths allowing to move (-) and H between "acidic oxygen atoms". 8515| | Purpose: mark alt bonds due to this "long range" tautomerism. */ 8516| 1.43k| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 1.43k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8517| 1.43k| bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 372| 1.43k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 1.43k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 1.43k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 374| 1.43k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ 8518| 1.43k| if (!bIsBnsEndpoint( pBNS, nVertSingleBond ) /* !at[nVertSingleBond].endpoint*/ && ------------------ | Branch (8518:17): [True: 447, False: 992] ------------------ 8519| 447| ( !nGetEndpointInfo( at, nVertSingleBond, &eif ) || !eif.cDonor )) ------------------ | Branch (8519:19): [True: 0, False: 447] | Branch (8519:69): [True: 6, False: 441] ------------------ 8520| 6| { 8521| 6| return 0; 8522| 6| } 8523| 1.43k| if (!bIsBnsEndpoint( pBNS, nVertDoubleBond ) /* !at[nVertDoubleBond].endpoint*/ && ------------------ | Branch (8523:17): [True: 728, False: 705] ------------------ 8524| 728| ( !nGetEndpointInfo( at, nVertDoubleBond, &eif ) || !eif.cAcceptor )) ------------------ | Branch (8524:19): [True: 0, False: 728] | Branch (8524:69): [True: 0, False: 728] ------------------ 8525| 0| { 8526| 0| return 0; 8527| 0| } 8528| 1.43k| memset( &apc, 0, sizeof( apc ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 8529| 1.43k| break; 8530| | 8531| 52| case ALT_PATH_MODE_REM2H_CHG: ------------------ | | 314| 52|#define ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */ ------------------ | Branch (8531:9): [True: 52, False: 28.0k] ------------------ 8532| 52| bChangeFlow |= BNS_EF_ALTR_BONDS; /* fall through */ ------------------ | | 374| 52|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ 8533| 663| case ALT_PATH_MODE_REM2H_TST: ------------------ | | 316| 663|#define ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */ ------------------ | Branch (8533:9): [True: 611, False: 27.4k] ------------------ 8534| 663| bChangeFlow |= BNS_EF_CHNG_RSTR; ------------------ | | 372| 663|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 663|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 663|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8535| 663| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 663|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8536| | /* Allow non-tautomeric donors or any tautomeric atom */ 8537| 663| if (!bIsBnsEndpoint( pBNS, nVertSingleBond ) /* not linked to a t-group or the edge forbidden */ && ------------------ | Branch (8537:17): [True: 78, False: 585] ------------------ 8538| 78| ( !nGetEndpointInfo( at, nVertSingleBond, &eif ) || !eif.cDonor )) /* not a donor */ ------------------ | Branch (8538:19): [True: 3, False: 75] | Branch (8538:69): [True: 8, False: 67] ------------------ 8539| 11| { 8540| 11| return 0; 8541| 11| } 8542| 652| if (!bIsBnsEndpoint( pBNS, nVertDoubleBond ) /* not connected to a t-group */ && ------------------ | Branch (8542:17): [True: 136, False: 516] ------------------ 8543| 136| ( !nGetEndpointInfo( at, nVertDoubleBond, &eif ) || !eif.cDonor )) ------------------ | Branch (8543:19): [True: 7, False: 129] | Branch (8543:69): [True: 20, False: 109] ------------------ 8544| 27| { 8545| 27| return 0; 8546| 27| } 8547| 625| memset( &apc, 0, sizeof( apc ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 8548| 625| break; 8549| | 8550| 74| case ALT_PATH_MODE_ADD2H_CHG: ------------------ | | 315| 74|#define ALT_PATH_MODE_ADD2H_CHG 6 /* add 2 H along alt. path A=-=B => AH-=-BH and change bonds to alternating */ ------------------ | Branch (8550:9): [True: 74, False: 28.0k] ------------------ 8551| 74| bChangeFlow |= BNS_EF_ALTR_BONDS; /* fall through */ ------------------ | | 374| 74|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ 8552| 1.07k| case ALT_PATH_MODE_ADD2H_TST: ------------------ | | 317| 1.07k|#define ALT_PATH_MODE_ADD2H_TST 8 /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */ ------------------ | Branch (8552:9): [True: 1.00k, False: 27.0k] ------------------ 8553| 1.07k| bChangeFlow |= BNS_EF_CHNG_RSTR; ------------------ | | 372| 1.07k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 1.07k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 1.07k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8554| 1.07k| type = BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 1.07k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 8555| | /* Allow non-tautomeric acceptors or any tautomeric atom */ 8556| 1.07k| if (!bIsBnsEndpoint( pBNS, nVertSingleBond ) /* !at[nVertSingleBond].endpoint*/ && ------------------ | Branch (8556:17): [True: 388, False: 689] ------------------ 8557| 388| ( !nGetEndpointInfo( at, nVertSingleBond, &eif ) || !eif.cAcceptor )) ------------------ | Branch (8557:19): [True: 20, False: 368] | Branch (8557:69): [True: 12, False: 356] ------------------ 8558| 32| { 8559| 32| return 0; 8560| 32| } 8561| 1.04k| if (!bIsBnsEndpoint( pBNS, nVertDoubleBond ) /* !at[nVertSingleBond].endpoint*/ && ------------------ | Branch (8561:17): [True: 529, False: 516] ------------------ 8562| 529| ( !nGetEndpointInfo( at, nVertDoubleBond, &eif ) || !eif.cAcceptor )) ------------------ | Branch (8562:19): [True: 42, False: 487] | Branch (8562:69): [True: 15, False: 472] ------------------ 8563| 57| { 8564| 57| return 0; 8565| 57| } 8566| 988| break; 8567| | 8568| 4.38k| case ALT_PATH_MODE_REM_PROTON: ------------------ | | 318| 4.38k|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ | Branch (8568:9): [True: 4.38k, False: 23.7k] ------------------ 8569| | /* alt path is between the t-group (nVertDoubleBond) and 8570| | the (+)-charge group (nVertSingleBond) */ 8571| 4.38k| type = 0; 8572| | /*bDoMarkChangedBonds = 0;*/ 8573| 4.38k| bChangeFlow = ( BNS_EF_SAVE_ALL | BNS_EF_UPD_H_CHARGE ) | BNS_EF_ALTR_NS; /* added BNS_EF_ALTR_NS: set non-stereo altern non-ring bonds 2004-07-02*/ ------------------ | | 381| 4.38k|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 370| 4.38k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 373| 4.38k|#define BNS_EF_CHNG_BONDS 4 /* change bonds in the structure according to the BN flow */ | | ------------------ | | #define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 375| 4.38k|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ bChangeFlow = ( BNS_EF_SAVE_ALL | BNS_EF_UPD_H_CHARGE ) | BNS_EF_ALTR_NS; /* added BNS_EF_ALTR_NS: set non-stereo altern non-ring bonds 2004-07-02*/ ------------------ | | 379| 4.38k|#define BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */ ------------------ bChangeFlow = ( BNS_EF_SAVE_ALL | BNS_EF_UPD_H_CHARGE ) | BNS_EF_ALTR_NS; /* added BNS_EF_ALTR_NS: set non-stereo altern non-ring bonds 2004-07-02*/ ------------------ | | 382| 4.38k|#define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 374| 4.38k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ | | ------------------ | | #define BNS_EF_ALTR_NS (BNS_EF_ALTR_BONDS | BNS_EF_SET_NOSTEREO) | | ------------------ | | | | 377| 4.38k|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: | | ------------------ ------------------ 8574| 4.38k| break; 8575| 0| default: ------------------ | Branch (8575:9): [True: 0, False: 28.1k] ------------------ 8576| 0| type = 0; 8577| 0| bChangeFlow = BNS_EF_CHNG_RSTR; ------------------ | | 372| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 0|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8578| 0| break; 8579| 28.1k| } 8580| | 8581| 23.6k| bError = 0; 8582| 23.6k| bSuccess = 0; 8583| 23.6k| nDelta = 0; 8584| | 8585| 23.6k| ret = SetRadEndpoints2( pCG, pBNS, pBD, RAD_SRCH_NORM ); 8586| 23.6k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 23.6k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 23.6k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 23.6k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 23.6k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 23.6k, False: 0] | | | Branch (67:44): [True: 0, False: 23.6k] | | ------------------ ------------------ 8587| 0| { 8588| 0| return ret; 8589| 0| } 8590| | 8591| | /* Set BNS to check alt path */ 8592| 23.6k| ret = bSetBnsToCheckAltPath( pBNS, nVertDoubleBond, nVertSingleBond, type, path_type, &apc, fcd, &nDots ); 8593| 23.6k| switch (ret) 8594| 23.6k| { 8595| 2.92k| case BNS_CHK_ALTP_NO_ALTPATH: ------------------ | | 6736| 2.92k|#define BNS_CHK_ALTP_NO_ALTPATH 0 ------------------ | Branch (8595:9): [True: 2.92k, False: 20.7k] ------------------ 8596| 2.92k| ret = RemoveRadEndpoints( pBNS, pBD, NULL ); 8597| 2.92k| return ret; 8598| 0| case BNS_CHK_ALTP_SAME_TGROUP: ------------------ | | 6737| 0|#define BNS_CHK_ALTP_SAME_TGROUP 1 ------------------ | Branch (8598:9): [True: 0, False: 23.6k] ------------------ 8599| 0| bSuccess = 1; 8600| 0| goto reinit_BNS; 8601| 0| case BNS_CHK_ALTP_SAME_VERTEX: ------------------ | | 6738| 0|#define BNS_CHK_ALTP_SAME_VERTEX 2 ------------------ | Branch (8601:9): [True: 0, False: 23.6k] ------------------ 8602| 0| ret = RemoveRadEndpoints( pBNS, pBD, NULL ); 8603| 0| return ret ? ret : 1; /* very strange ... set a breakpoint here */ ------------------ | Branch (8603:20): [True: 0, False: 0] ------------------ 8604| 20.6k| case BNS_CHK_ALTP_SET_SUCCESS: ------------------ | | 6739| 20.6k|#define BNS_CHK_ALTP_SET_SUCCESS 4 ------------------ | Branch (8604:9): [True: 20.6k, False: 3.01k] ------------------ 8605| 20.6k| break; /* actually check the existence of the altpath */ 8606| 82| case BNS_CANT_SET_BOND: ------------------ | | 57| 82|#define BNS_CANT_SET_BOND (BNS_ERR + 9) /*(-9990)*/ | | ------------------ | | | | 47| 82|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (8606:9): [True: 82, False: 23.5k] ------------------ 8607| 82| goto reinit_BNS; 8608| 4| default: ------------------ | Branch (8608:9): [True: 4, False: 23.6k] ------------------ 8609| 4| ret_val = RemoveRadEndpoints( pBNS, pBD, NULL ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 8610| 4| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 4|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 4|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 4|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 4|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 4, False: 0] | | | Branch (67:44): [True: 4, False: 0] | | ------------------ ------------------ 8611| 4| { 8612| 4| return ret; 8613| 4| } 8614| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8615| 23.6k| } 8616| | 8617| 20.6k| bAdjustRadicals = ( ( bChangeFlow & BNS_EF_UPD_RAD_ORI ) && !( bChangeFlow & BNS_EF_RSTR_FLOW ) ); ------------------ | | 375| 20.6k|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: ------------------ bAdjustRadicals = ( ( bChangeFlow & BNS_EF_UPD_RAD_ORI ) && !( bChangeFlow & BNS_EF_RSTR_FLOW ) ); ------------------ | | 371| 1.47k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ ------------------ | Branch (8617:25): [True: 1.47k, False: 19.1k] | Branch (8617:65): [True: 1.47k, False: 0] ------------------ 8618| | 8619| | /***************************************************************** 8620| | * nDots = 2 for ALT_PATH_CHARGE (checking moveable positive charges) 8621| | * Now nDots for ALT_PATH_TAUTOM or ALT_PATH_4_SALT can be greater 8622| | * because some of the bonds are effectively removed and dots 8623| | * (vertex st-caps) may be added 8624| | * -- to make sure there is no (+) charge on a tautomeric endpoint 8625| | * -- to fix positions of moveable tautomeric attachements 8626| | * (H and (-)-charges) at the ends of an alt path 8627| | */ 8628| | 8629| | /* Run BNS */ 8630| | 8631| 20.6k| ret = RunBalancedNetworkSearch( pBNS, pBD, bChangeFlow ); 8632| | 8633| 20.6k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 20.6k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 20.6k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 20.6k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 20.6k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 20.6k, False: 0] | | | Branch (67:44): [True: 2, False: 20.6k] | | ------------------ ------------------ 8634| 2| { 8635| 2| bError = ret; 8636| 2| } 8637| 20.6k| else if (ret > 0) ------------------ | Branch (8637:14): [True: 10.1k, False: 10.5k] ------------------ 8638| 10.1k| { 8639| 10.1k| if (2 * ret >= nDots) ------------------ | Branch (8639:13): [True: 9.22k, False: 876] ------------------ 8640| 9.22k| { 8641| 9.22k| nDelta = 2 * ret - nDots; /* non-zero means augmentation created another alt. path -- between radicals */ 8642| 9.22k| if (pAATG && pAATG->nMarkedAtom) ------------------ | Branch (8642:17): [True: 197, False: 9.02k] | Branch (8642:26): [True: 197, False: 0] ------------------ 8643| 197| { 8644| 197| if (pAATG->nAtTypeTotals && ( bChangeFlow & BNS_EF_UPD_H_CHARGE )) ------------------ | | 379| 197|#define BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */ ------------------ | Branch (8644:21): [True: 197, False: 0] | Branch (8644:45): [True: 197, False: 0] ------------------ 8645| 197| { 8646| 197| memset( pAATG->nMarkedAtom, 0, num_atoms * sizeof( pAATG->nMarkedAtom[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 8647| | /* Mark atoms that have charge or H changed, check their input types (that is, before changes), 8648| | and subtract their input charge/H from nAtTypeTotals */ 8649| 197| SubtractOrChangeAtHChargeBNS( pBNS, at, num_atoms, pAATG->nAtTypeTotals, pAATG->nMarkedAtom, NULL, 1 ); 8650| | /* ZChange charges and/or H, update t_group_info, do not check types or change nAtTypeTotals */ 8651| | /* Atom types will be checked and nAtTypeTotals will be changed in 8652| | AddChangedAtHChargeBNS() later */ 8653| 197| SubtractOrChangeAtHChargeBNS( pBNS, at, num_atoms, NULL, NULL, pAATG->t_group_info, 0 ); 8654| 197| } 8655| 0| else 8656| 0| { 8657| 0| if (!pAATG->nAtTypeTotals) ------------------ | Branch (8657:25): [True: 0, False: 0] ------------------ 8658| 0| { 8659| 0| bDoMarkChangedBonds = MarkAtomsAtTautGroups( pBNS, num_atoms, pAATG, nVertSingleBond, nVertDoubleBond ); 8660| 0| if (bDoMarkChangedBonds < 0) ------------------ | Branch (8660:29): [True: 0, False: 0] ------------------ 8661| 0| { 8662| 0| bError = bDoMarkChangedBonds; 8663| 0| bDoMarkChangedBonds = 0; 8664| 0| } 8665| 0| } 8666| 0| } 8667| 197| } 8668| 9.22k| if (bDoMarkChangedBonds) ------------------ | Branch (8668:17): [True: 9.22k, False: 0] ------------------ 8669| 9.22k| { 8670| | /* Mark bonds that were changed to configure bond testing */ 8671| 9.22k| ret_val = bSetBondsAfterCheckOneBond( pBNS, fcd, -1, at, num_atoms, bChangeFlow ); 8672| 9.22k| if (IS_BNS_ERROR( ret_val )) ------------------ | | 67| 9.22k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 9.22k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 9.22k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 9.22k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 9.22k, False: 0] | | | Branch (67:44): [True: 0, False: 9.22k] | | ------------------ ------------------ 8673| 0| { 8674| 0| bError = ret_val; 8675| 0| } 8676| | /*ret = SetBondsRestoreBnStructFlow( pBNS, at, num_atoms, bChangeFlow );*/ 8677| | /* mark all other changed bonds */ 8678| 9.22k| ret = SetBondsFromBnStructFlow( pBNS, at, num_atoms, bChangeFlow ); 8679| 9.22k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 9.22k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 9.22k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 9.22k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 9.22k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 9.22k, False: 0] | | | Branch (67:44): [True: 0, False: 9.22k] | | ------------------ ------------------ 8680| 0| { 8681| 0| bError = ret; 8682| 0| } 8683| 9.22k| else 8684| 9.22k| { 8685| 9.22k| if (!( ret & 1 ) && !( ret_val & 1 )) ------------------ | Branch (8685:25): [True: 7.74k, False: 1.48k] | Branch (8685:41): [True: 7.74k, False: 0] ------------------ 8686| 7.74k| { 8687| 7.74k| bSuccess = 1; 8688| 7.74k| } 8689| 1.48k| else 8690| 1.48k| { 8691| 1.48k| if ((( ( ret & 1 ) || ( ret_val & 1 ) ) && ------------------ | Branch (8691:32): [True: 1.48k, False: 0] | Branch (8691:47): [True: 0, False: 0] ------------------ 8692| 1.48k| ( bChangeFlow & BNS_EF_ALTR_BONDS )) || ( bChangeFlow & BNS_EF_UPD_H_CHARGE )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 374| 1.48k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ ( bChangeFlow & BNS_EF_ALTR_BONDS )) || ( bChangeFlow & BNS_EF_UPD_H_CHARGE )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 379| 0|#define BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */ ------------------ | Branch (8692:29): [True: 1.48k, False: 0] | Branch (8692:69): [True: 0, False: 0] ------------------ 8693| 1.48k| { 8694| | /* Some bonds have been changed to alternating */ 8695| 1.48k| bSuccess = 3; 8696| 1.48k| } 8697| 0| else 8698| 0| { 8699| 0| bError = BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8700| 0| } 8701| 1.48k| } 8702| 9.22k| } 8703| 9.22k| if (!bError && pAATG && pAATG->nMarkedAtom && ( bChangeFlow & BNS_EF_UPD_H_CHARGE )) ------------------ | | 379| 197|#define BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */ ------------------ | Branch (8703:21): [True: 9.22k, False: 0] | Branch (8703:32): [True: 197, False: 9.02k] | Branch (8703:41): [True: 197, False: 0] | Branch (8703:63): [True: 197, False: 0] ------------------ 8704| 197| { 8705| | /* Update radicals to avoid errors in atom type check in AddChangedAtHChargeBNS() */ 8706| 197| if (bAdjustRadicals) ------------------ | Branch (8706:25): [True: 197, False: 0] ------------------ 8707| 197| { 8708| 197| ret_val = RestoreRadicalsOnly( pBNS, pBD, at ); 8709| 197| if (IS_BNS_ERROR( ret_val )) ------------------ | | 67| 197|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 197|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 197|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 197|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 197, False: 0] | | | Branch (67:44): [True: 0, False: 197] | | ------------------ ------------------ 8710| 0| { 8711| 0| bError = ret_val; 8712| 0| } 8713| 197| } 8714| | /* Check atom types of marked atoms and add charge/H changes to nAtTypeTotals */ 8715| | /* Changing atoms were marked in the 1st call to SubtractOrChangeAtHChargeBNS(..., 1) above */ 8716| 197| AddChangedAtHChargeBNS( at, num_atoms, pAATG->nAtTypeTotals, pAATG->nMarkedAtom ); 8717| 197| if (bChangeFlow & BNS_EF_CHNG_FLOW) ------------------ | | 370| 197|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ | Branch (8717:25): [True: 197, False: 0] ------------------ 8718| 197| { 8719| | /* Eliminate ambiguities in already changed flow: 8720| | replace (+)--N==(-) with (+)==N--(-) (both represent neutral N) */ 8721| 197| EliminatePlusMinusChargeAmbiguity( pBNS, num_atoms ); 8722| 197| } 8723| 197| } 8724| 9.22k| } 8725| 9.22k| } 8726| | 8727| 10.1k| ret = RestoreBnStructFlow( pBNS, bChangeFlow & BNS_EF_CHNG_RSTR ); ------------------ | | 372| 10.1k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 370| 10.1k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ | | ------------------ | | #define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 371| 10.1k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 8728| | 8729| 10.1k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 10.1k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 10.1k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 10.1k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 10.1k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 10.1k, False: 0] | | | Branch (67:44): [True: 0, False: 10.1k] | | ------------------ ------------------ 8730| 0| { 8731| 0| bError = ret; 8732| 0| } 8733| 10.1k| } 8734| | 8735| 20.7k|reinit_BNS: 8736| | 8737| | /* --- Reinitialize to repeat the calculations --- */ 8738| 20.7k| bRestoreBnsAfterCheckAltPath( pBNS, &apc, bChangeFlow & BNS_EF_UPD_H_CHARGE ); ------------------ | | 379| 20.7k|#define BNS_EF_UPD_H_CHARGE 64 /* update charges and H-counts according to change flow to c- and t-group vertices */ ------------------ 8739| 20.7k| bRestoreFlowAfterCheckOneBond( pBNS, fcd ); 8740| 20.7k| ret_val = RemoveRadEndpoints( pBNS, pBD, bAdjustRadicals ? at : NULL ); ------------------ | Branch (8740:46): [True: 1.47k, False: 19.2k] ------------------ 8741| 20.7k| ReInitBnStructAltPaths( pBNS ); 8742| | 8743| 20.7k| return bError ? bError : ret_val ? ret_val : ( bSuccess + 4 * nDelta ); ------------------ | Branch (8743:12): [True: 2, False: 20.7k] | Branch (8743:30): [True: 0, False: 20.7k] ------------------ 8744| 20.6k|} AllocateAndInitBnStruct: 8754| 288k|{ 8755| 288k| BN_STRUCT *pBNS = NULL; 8756| 288k| BNS_VERTEX *vert; 8757| | 8758| 288k| int neigh, num_changed_bonds = 0; 8759| 288k| U_CHAR bond_type, bond_mark; 8760| | 8761| 288k| int i, j, k, n_edges, num_bonds, num_edges, f1, f2, edge_cap, edge_flow, st_flow; /* djb-rwth: removing redundant variables */ 8762| 288k| int tot_st_cap, tot_st_flow; 8763| 288k| int max_tg, max_edges, max_vertices, len_alt_path, max_iedges, num_altp; 8764| 288k|#if ( BNS_RAD_SEARCH == 1 ) 8765| 288k| int num_rad = 0; 8766| | 8767| 288k| nMaxAddEdges += 1; 8768| 288k|#endif 8769| |#if ( FIX_NUM_TG == 1 ) 8770| | max_tg = inchi_max( num_atoms / 2, 5 ); 8771| |#else 8772| 288k| max_tg = num_atoms; 8773| 288k|#endif 8774| 288k| num_changed_bonds = 0; 8775| | 8776| 1.38M| for (i = 0, num_bonds = 0; i < num_atoms; i++) ------------------ | Branch (8776:32): [True: 1.09M, False: 288k] ------------------ 8777| 1.09M| { 8778| | /*(@nnuk : Nauman Ullah Khan) */ 8779| 1.09M| LOG_NO_ARGS("\n################# (L8916:ichi_bns.c) ###################\n"); 8780| 1.09M| LOG_MULT_ARGS("Number of changed bonds (Start): %d\n", num_changed_bonds); 8781| 1.09M| LOG_NO_ARGS("\n########################################################\n"); 8782| | 8783| 1.09M| num_bonds += at[i].valence; 8784| 1.09M|#if ( BNS_RAD_SEARCH == 1 ) 8785| 1.09M| num_rad += ( at[i].radical == RADICAL_DOUBLET ); ------------------ | | 76| 1.09M|#define RADICAL_DOUBLET 2 ------------------ 8786| 1.09M|#endif 8787| 1.09M| } 8788| | /* Each atom has enough edges to belong to a tautomeric group + nMaxAddEdges */ 8789| | /* number of atoms is large enough to accommodate max. possible number of t-groups + nMaxAddAtoms */ 8790| | /* max_altp cannot be larger than BN_MAX_ALTP = 16 */ 8791| 288k| num_edges = ( num_bonds /= 2 ); 8792| | /* +1 for a super-tautomeric group */ 8793| 288k| max_vertices = num_atoms + nMaxAddAtoms + max_tg + 1; 8794| | /* +max_tg for edges between t-groups and super-tautomeric group */ 8795| 288k| max_edges = num_edges + ( nMaxAddEdges + NUM_KINDS_OF_GROUPS )*max_vertices + max_tg; ------------------ | | 86| 288k|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 8796| 288k|#if ( BNS_RAD_SEARCH == 1 ) 8797| 288k| if (num_rad) ------------------ | Branch (8797:9): [True: 13.3k, False: 275k] ------------------ 8798| 13.3k| { 8799| 13.3k| max_vertices *= 2; 8800| 13.3k| max_edges *= 2; 8801| 13.3k| } 8802| 288k|#endif 8803| 288k| max_iedges = 2 * max_edges; 8804| 288k| len_alt_path = max_vertices + iALTP_HDR_LEN + 1; /* may overflow if an edge is traversed in 2 directions */ 8805| | 8806| 288k| if (!( pBNS = (BN_STRUCT *) inchi_calloc( 1, sizeof( BN_STRUCT ) ) ) || ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ | Branch (8806:9): [True: 0, False: 288k] ------------------ 8807| 288k| !( pBNS->edge = (BNS_EDGE *) inchi_calloc( max_edges, sizeof( BNS_EDGE ) ) ) || ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ | Branch (8807:10): [True: 0, False: 288k] ------------------ 8808| 288k| !( pBNS->vert = (BNS_VERTEX *) inchi_calloc( max_vertices, sizeof( BNS_VERTEX ) ) ) || ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ | Branch (8808:10): [True: 0, False: 288k] ------------------ 8809| 288k| !( pBNS->iedge = (BNS_IEDGE *) inchi_calloc( max_iedges, sizeof( BNS_IEDGE ) ) )) ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ | Branch (8809:10): [True: 0, False: 288k] ------------------ 8810| 0| { 8811| 0| return DeAllocateBnStruct( pBNS ); 8812| 0| } 8813| | /* Alt path init */ 8814| 4.90M| for (num_altp = 0; num_altp < max_altp && num_altp < BN_MAX_ALTP; num_altp++) ------------------ | | 17| 4.61M|#define BN_MAX_ALTP 16 ------------------ | Branch (8814:24): [True: 4.61M, False: 288k] | Branch (8814:47): [True: 4.61M, False: 0] ------------------ 8815| 4.61M| { 8816| 4.61M| if (!( pBNS->altp[num_altp] = (BNS_ALT_PATH*) inchi_calloc( len_alt_path, sizeof( BNS_ALT_PATH ) ) )) ------------------ | | 1146| 4.61M|#define inchi_calloc calloc ------------------ | Branch (8816:13): [True: 0, False: 4.61M] ------------------ 8817| 0| { 8818| 0| return DeAllocateBnStruct( pBNS ); 8819| 0| } 8820| 4.61M| ALTP_ALLOCATED_LEN( pBNS->altp[num_altp] ) = len_alt_path; ------------------ | | 111| 4.61M|#define ALTP_ALLOCATED_LEN(altp) (altp)[iALTP_MAX_LEN].number ------------------ 8821| 4.61M| pBNS->len_alt_path = len_alt_path; /* ??? duplication ??? */ 8822| | /* re-init */ 8823| 4.61M| ALTP_DELTA( pBNS->altp[num_altp] ) = 0; ------------------ | | 112| 4.61M|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 8824| 4.61M| ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 103| 4.61M|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 118| 4.61M|#define NO_VERTEX -2 ------------------ 8825| 4.61M| ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 102| 4.61M|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 118| 4.61M|#define NO_VERTEX -2 ------------------ 8826| 4.61M| ALTP_PATH_LEN( pBNS->altp[num_altp] ) = 0; ------------------ | | 101| 4.61M|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 8827| 4.61M| } 8828| 288k| pBNS->alt_path = NULL; 8829| 288k| pBNS->num_altp = 0; 8830| 288k| pBNS->max_altp = num_altp; 8831| | 8832| | /* Fill vertices (no connectivity) */ 8833| 288k| pBNS->vert[0].iedge = pBNS->iedge; 8834| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (8834:17): [True: 1.09M, False: 288k] ------------------ 8835| 1.09M| { 8836| 1.09M| k = pBNS->vert[i].max_adj_edges = at[i].valence + ( nMaxAddEdges + NUM_KINDS_OF_GROUPS ); ------------------ | | 86| 1.09M|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 8837| 1.09M| pBNS->vert[i + 1].iedge = pBNS->vert[i].iedge + k; 8838| 1.09M| } 8839| 288k| pBNS->num_atoms = num_atoms; /* number of real atoms */ 8840| 288k| pBNS->num_added_atoms = 0; 8841| 288k| pBNS->num_t_groups = 0; /* number of added t-groups */ 8842| 288k| pBNS->num_c_groups = 0; 8843| 288k| pBNS->nMaxAddAtoms = nMaxAddAtoms; 8844| 288k| pBNS->nMaxAddEdges = nMaxAddEdges; 8845| | 8846| 288k| pBNS->num_vertices = num_atoms; /* current number of vertices, a sum of 8847| | pBNS->num_atoms 8848| | pBNS->num_t_groups 8849| | pBNS->num_added_atoms */ 8850| 288k| pBNS->max_vertices = max_vertices; 8851| | 8852| | 8853| 288k| pBNS->num_bonds = num_bonds; /* number of real edges (bonds) */ 8854| 288k| pBNS->max_edges = max_edges; 8855| 288k| pBNS->max_iedges = max_iedges; 8856| | 8857| | /* 8858| | To remove t-groups and added atoms: 8859| | In atoms i = 0..pBNS->num_atoms-1 8860| | pBNS->vert[i].num_adj_edges = pBNS->vert[i].max_adj_edges - pBNS->nMaxAddEdges - NUM_KINDS_OF_GROUPS; 8861| | pBNS->num_vertices = pBNS->num_atoms; 8862| | pBNS->num_edges = pBNS->num_bonds; 8863| | pBNS->num_added_atoms = 0; 8864| | pBNS->num_t_groups = 0; 8865| | pBNS->num_added_edges = 0; 8866| | 8867| | ALTP_DELTA(pBNS->alt_path) = 0; 8868| | ALTP_START_ATOM(pBNS->alt_path) = NO_VERTEX; 8869| | ALTP_END_ATOM(pBNS->alt_path) = NO_VERTEX; 8870| | ALTP_PATH_LEN(pBNS->alt_path) = 0; 8871| | */ 8872| | 8873| | /* Fill edges and connectivity */ 8874| 288k| tot_st_cap = tot_st_flow = 0; 8875| 1.38M| for (i = 0, n_edges = 0; i < num_atoms; i++) ------------------ | Branch (8875:30): [True: 1.09M, False: 288k] ------------------ 8876| 1.09M| { 8877| 1.09M| vert = &pBNS->vert[i]; 8878| | /* djb-rwth: removing redundant code */ 8879| 1.09M| st_flow = 0; 8880| | /* djb-rwth: removing redundant code */ 8881| 1.57M| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (8881:21): [True: 479k, False: 1.09M] ------------------ 8882| 479k| { 8883| 479k| neigh = at[i].neighbor[j]; 8884| | /* find this bond at the neighbor */ 8885| 780k| for (k = 0; k < at[neigh].valence; k++) ------------------ | Branch (8885:25): [True: 780k, False: 0] ------------------ 8886| 780k| { 8887| 780k| if (at[neigh].neighbor[k] == i) ------------------ | Branch (8887:21): [True: 479k, False: 300k] ------------------ 8888| 479k| { 8889| 479k| break; 8890| 479k| } 8891| 780k| } 8892| 479k| bond_type = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 479k|#define BOND_TYPE_MASK 0x0f ------------------ 8893| 479k| bond_mark = ( at[i].bond_type[j] & ~BOND_TYPE_MASK ); ------------------ | | 189| 479k|#define BOND_TYPE_MASK 0x0f ------------------ 8894| 479k| if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && ------------------ | | 177| 479k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 959k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && ------------------ | | 178| 171k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 650k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (8894:17): [True: 171k, False: 308k] | Branch (8894:45): [True: 53.6k, False: 117k] ------------------ 8895| 53.6k| bond_type != BOND_TRIPLE /*&& bond_type != BOND_ALTERN*/) ------------------ | | 179| 53.6k|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 53.6k|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (8895:18): [True: 0, False: 53.6k] ------------------ 8896| 0| { 8897| | /* Make Unknown or Alternating bonds single */ 8898| 0| bond_type = 1; 8899| 0| at[i].bond_type[j] = bond_mark | bond_type; 8900| 0| num_changed_bonds++; 8901| 0| } 8902| 479k| if (neigh > i) ------------------ | Branch (8902:17): [True: 239k, False: 239k] ------------------ 8903| 239k| { 8904| | /* This is the first time we encounter this bond */ 8905| 239k| f1 = MAX_AT_FLOW( at[i] ); ------------------ | | 143| 239k|#define MAX_AT_FLOW(X) (((X).chem_bonds_valence - (X).valence)+\ | | 144| 239k| ((is_centerpoint_elem((X).el_number)||get_endpoint_valence((X).el_number))?\ | | ------------------ | | | Branch (144:26): [True: 169k, False: 70.6k] | | | Branch (144:62): [True: 22.8k, False: 47.7k] | | ------------------ | | 145| 239k| (((X).radical==RADICAL_DOUBLET)/*+2*((X).radical==RADICAL_TRIPLET)*/):0)) | | ------------------ | | | | 76| 192k|#define RADICAL_DOUBLET 2 | | ------------------ ------------------ 8906| 239k| f2 = MAX_AT_FLOW( at[neigh] ); ------------------ | | 143| 239k|#define MAX_AT_FLOW(X) (((X).chem_bonds_valence - (X).valence)+\ | | 144| 239k| ((is_centerpoint_elem((X).el_number)||get_endpoint_valence((X).el_number))?\ | | ------------------ | | | Branch (144:26): [True: 127k, False: 112k] | | | Branch (144:62): [True: 23.5k, False: 88.7k] | | ------------------ | | 145| 239k| (((X).radical==RADICAL_DOUBLET)/*+2*((X).radical==RADICAL_TRIPLET)*/):0)) | | ------------------ | | | | 76| 151k|#define RADICAL_DOUBLET 2 | | ------------------ ------------------ 8907| 239k| edge_flow = bond_type - 1; 8908| 239k| if (edge_flow > MAX_BOND_EDGE_CAP) ------------------ | | 123| 239k|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ | Branch (8908:21): [True: 0, False: 239k] ------------------ 8909| 0| { 8910| | /* djb-rwth: removing redundant code */ 8911| 0| edge_flow = 0; /* BNS will determine flows (that is, bonds) */ 8912| 0| edge_cap = AROM_BOND_EDGE_CAP; ------------------ | | 124| 0|#define AROM_BOND_EDGE_CAP 1 ------------------ 8913| 0| } 8914| 239k| else 8915| 239k| { 8916| |#if ( 0 && KETO_ENOL_TAUT == 1 ) /* ????? */ 8917| | edge_cap = inchi_max( f1, f2 ); 8918| |#else 8919| 239k| edge_cap = inchi_min( f1, f2 ); ------------------ | | 139| 239k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 55.5k, False: 184k] | | ------------------ ------------------ 8920| 239k|#endif 8921| 239k| edge_cap = inchi_min( edge_cap, MAX_BOND_EDGE_CAP ); /* max capacity = 2 means up to triple bond */ ------------------ | | 139| 239k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 202k, False: 36.8k] | | ------------------ ------------------ 8922| 239k| } 8923| | 8924| 239k| pBNS->edge[n_edges].neighbor1 = (AT_NUMB) i; 8925| 239k| pBNS->edge[n_edges].neighbor12 = (AT_NUMB) ( i ^ neigh ); 8926| 239k| pBNS->edge[n_edges].flow = pBNS->edge[n_edges].flow0 = edge_flow; 8927| 239k| pBNS->edge[n_edges].cap = pBNS->edge[n_edges].cap0 = edge_cap; 8928| 239k| pBNS->edge[n_edges].neigh_ord[0] = j; 8929| 239k| pBNS->edge[n_edges].neigh_ord[1] = k; 8930| 239k| pBNS->edge[n_edges].pass = 0; 8931| 239k| pBNS->edge[n_edges].forbidden = 0; 8932| | 8933| 239k| vert->iedge[j] = pBNS->vert[neigh].iedge[k] = n_edges++; 8934| 239k| } 8935| 239k| else 8936| 239k| { 8937| | /* This is the second time we encounter this bond. It was stored at */ 8938| 239k| int iedge = pBNS->vert[neigh].iedge[k]; 8939| 239k| edge_cap = pBNS->edge[iedge].cap; /* djb-rwth: ignoring LLVM warning: variable used */ 8940| 239k| edge_flow = pBNS->edge[iedge].flow; 8941| 239k| } 8942| 479k| st_flow += edge_flow; 8943| | /* djb-rwth: removing redundant code */ 8944| 479k| } 8945| 1.09M| vert->num_adj_edges = j; 8946| 1.09M| vert->st_edge.cap = 8947| 1.09M| vert->st_edge.cap0 = MAX_AT_FLOW( at[i] ); ------------------ | | 143| 1.09M|#define MAX_AT_FLOW(X) (((X).chem_bonds_valence - (X).valence)+\ | | 144| 1.09M| ((is_centerpoint_elem((X).el_number)||get_endpoint_valence((X).el_number))?\ | | ------------------ | | | Branch (144:26): [True: 305k, False: 789k] | | | Branch (144:62): [True: 195k, False: 593k] | | ------------------ | | 145| 1.09M| (((X).radical==RADICAL_DOUBLET)/*+2*((X).radical==RADICAL_TRIPLET)*/):0)) | | ------------------ | | | | 76| 501k|#define RADICAL_DOUBLET 2 | | ------------------ ------------------ 8948| 1.09M| vert->st_edge.flow = 8949| 1.09M| vert->st_edge.flow0 = st_flow; 8950| 1.09M| vert->type = BNS_VERT_TYPE_ATOM; ------------------ | | 45| 1.09M|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ 8951| 1.09M| tot_st_cap += vert->st_edge.cap; 8952| 1.09M| tot_st_flow += vert->st_edge.flow; 8953| 1.09M| } 8954| 288k| *pNum_changed_bonds = num_changed_bonds / 2; 8955| | 8956| 288k| pBNS->num_edges = n_edges; /* number of edges */ 8957| 288k| pBNS->num_added_edges = 0; 8958| | 8959| | /*(@nnuk : Nauman Ullah Khan) */ 8960| 288k| LOG_NO_ARGS("\n################# (L9108:ichi_bns.c) ################\n"); 8961| 1.38M| for (i = 0, num_bonds = 0; i < num_atoms; i++) { ------------------ | Branch (8961:32): [True: 1.09M, False: 288k] ------------------ 8962| | 8963| 1.09M| LOG_MULT_ARGS("Element : %s, Number of changed bonds (End): %d\n", at[i].elname, *pNum_changed_bonds); 8964| 1.09M| } 8965| 288k| LOG_NO_ARGS("\n#####################################################\n"); 8966| | 8967| 288k| pBNS->tot_st_cap = tot_st_cap; 8968| 288k| pBNS->tot_st_flow = tot_st_flow; 8969| | 8970| 288k| return pBNS; 8971| 288k|} DeAllocateBnStruct: 8976| 376k|{ 8977| 376k| int i; 8978| 376k| if (pBNS) ------------------ | Branch (8978:9): [True: 376k, False: 129] ------------------ 8979| 376k| { 8980| 376k| if (pBNS->edge) ------------------ | Branch (8980:13): [True: 376k, False: 0] ------------------ 8981| 376k| { 8982| 376k| inchi_free( pBNS->edge ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 8983| 376k| } 8984| 6.39M| for (i = 0; i < pBNS->max_altp && i < BN_MAX_ALTP; i++) ------------------ | | 17| 6.02M|#define BN_MAX_ALTP 16 ------------------ | Branch (8984:21): [True: 6.02M, False: 376k] | Branch (8984:43): [True: 6.02M, False: 0] ------------------ 8985| 6.02M| { 8986| 6.02M| if (pBNS->altp[i]) ------------------ | Branch (8986:17): [True: 6.02M, False: 0] ------------------ 8987| 6.02M| { 8988| 6.02M| inchi_free( pBNS->altp[i] ); ------------------ | | 1152| 6.02M|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.02M, False: 0] | | | Branch (1152:50): [Folded, False: 6.02M] | | ------------------ ------------------ 8989| 6.02M| } 8990| 6.02M| } 8991| 376k| if (pBNS->vert) ------------------ | Branch (8991:13): [True: 376k, False: 0] ------------------ 8992| 376k| { 8993| 376k| if (pBNS->vert[0].iedge) ------------------ | Branch (8993:17): [True: 376k, False: 0] ------------------ 8994| 376k| { 8995| 376k| inchi_free( pBNS->vert[0].iedge ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 8996| 376k| } 8997| 376k| inchi_free( pBNS->vert ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 8998| 376k| } 8999| 376k| inchi_free( pBNS ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9000| 376k| } 9001| | 9002| | return NULL; 9003| 376k|} ReInitBnStructAltPaths: 9008| 1.09M|{ 9009| 1.09M| int i; 9010| 18.6M| for (i = 0; i < pBNS->max_altp && i < BN_MAX_ALTP; i++) ------------------ | | 17| 17.5M|#define BN_MAX_ALTP 16 ------------------ | Branch (9010:17): [True: 17.5M, False: 1.09M] | Branch (9010:39): [True: 17.5M, False: 0] ------------------ 9011| 17.5M| { 9012| 17.5M| if (pBNS->altp[i]) ------------------ | Branch (9012:13): [True: 17.5M, False: 0] ------------------ 9013| 17.5M| { 9014| 17.5M| ALTP_DELTA( pBNS->altp[i] ) = 0; ------------------ | | 112| 17.5M|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 9015| 17.5M| ALTP_PATH_LEN( pBNS->altp[i] ) = 0; ------------------ | | 101| 17.5M|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 9016| 17.5M| ALTP_START_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 103| 17.5M|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ ALTP_START_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 118| 17.5M|#define NO_VERTEX -2 ------------------ 9017| 17.5M| ALTP_END_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 102| 17.5M|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ ALTP_END_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 118| 17.5M|#define NO_VERTEX -2 ------------------ 9018| 17.5M| } 9019| 17.5M| } 9020| | pBNS->alt_path = NULL; 9021| 1.09M| pBNS->num_altp = 0; 9022| 1.09M| return i; 9023| 1.09M|} ReInitBnStructAddGroups: 9033| 5.55k|{ 9034| 5.55k| int ret; 9035| | /* strip all t-groups and c-groups */ 9036| 5.55k| ret = ReInitBnStruct( pBNS, at, num_atoms, 0 ); 9037| 5.55k| if (ret) ------------------ | Branch (9037:9): [True: 0, False: 5.55k] ------------------ 9038| 0| { 9039| 0| ret = BNS_REINIT_ERR; ------------------ | | 60| 0|#define BNS_REINIT_ERR (BNS_ERR + 12) /*(-9987)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9040| 0| goto exit_function; 9041| 0| } 9042| | /*#if ( MOVE_CHARGES == 1 )*/ 9043| 5.55k| if (*pBNS->pbTautFlags & TG_FLAG_MOVE_POS_CHARGES) ------------------ | | 921| 5.55k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (9043:9): [True: 5.55k, False: 0] ------------------ 9044| 5.55k| { 9045| | /* Add c-groups */ 9046| 5.55k| ret = AddCGroups2BnStruct( pCG, pBNS, at, num_atoms, cgi ); 9047| 5.55k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 5.55k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 5.55k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 5.55k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 5.55k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 5.55k, False: 0] | | | Branch (67:44): [True: 0, False: 5.55k] | | ------------------ ------------------ 9048| 0| { 9049| 0| goto exit_function; 9050| 0| } 9051| 5.55k| } 9052| | /*#endif*/ 9053| | /* Add t-groups */ 9054| 5.55k| ret = AddTGroups2BnStruct( pCG, pBNS, at, num_atoms, tgi ); 9055| 5.55k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 5.55k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 5.55k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 5.55k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 5.55k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 5.55k, False: 0] | | | Branch (67:44): [True: 0, False: 5.55k] | | ------------------ ------------------ 9056| 0| { 9057| 0| goto exit_function; 9058| 0| } 9059| | 9060| 5.55k|exit_function: 9061| | 9062| 5.55k| return ret; 9063| 5.55k|} ReInitBnStruct: 9071| 300k|{ 9072| 300k| int i, vfict, kfict, iedgefict, endpoint, centerpoint, iedge, k; 9073| 300k| int ret = 0; 9074| 300k| if (pBNS) ------------------ | Branch (9074:9): [True: 300k, False: 0] ------------------ 9075| 300k| { 9076| 300k| if (pBNS->vert && pBNS->edge) ------------------ | Branch (9076:13): [True: 300k, False: 0] | Branch (9076:27): [True: 300k, False: 0] ------------------ 9077| 300k| { 9078| | /* Debug */ 9079| 642k| for (k = 0, i = 0; k < pBNS->num_edges; k++) ------------------ | Branch (9079:32): [True: 341k, False: 300k] ------------------ 9080| 341k| { 9081| 341k| if (pBNS->edge[k].pass) ------------------ | Branch (9081:21): [True: 10, False: 341k] ------------------ 9082| 10| { 9083| 10| i++; 9084| 10| } 9085| 341k| } 9086| 300k| ret += i * 100; 9087| | /* Restore flow and cap on edges to vertices connected to fictitious atoms */ 9088| 314k| for (vfict = pBNS->num_atoms; vfict < pBNS->num_vertices; vfict++) ------------------ | Branch (9088:43): [True: 14.1k, False: 300k] ------------------ 9089| 14.1k| { 9090| 47.9k| for (kfict = 0; kfict < pBNS->vert[vfict].num_adj_edges; kfict++) ------------------ | Branch (9090:33): [True: 33.8k, False: 14.1k] ------------------ 9091| 33.8k| { 9092| 33.8k| iedgefict = pBNS->vert[vfict].iedge[kfict]; /* fictitious edge to the endpoint */ 9093| 33.8k| endpoint = pBNS->edge[iedgefict].neighbor12 ^ vfict; /* the endpoint */ 9094| | /* To simlify restore cap and flow in ALL edges to the endpoint */ 9095| 33.8k| if (bRemoveGroupsFromAtoms && endpoint < num_at) ------------------ | Branch (9095:25): [True: 0, False: 33.8k] | Branch (9095:51): [True: 0, False: 0] ------------------ 9096| 0| { 9097| 0| at[endpoint].c_point = 0; 9098| 0| at[endpoint].endpoint = 0; 9099| 0| } 9100| 117k| for (k = 0; k < pBNS->vert[endpoint].num_adj_edges; k++) ------------------ | Branch (9100:33): [True: 83.7k, False: 33.8k] ------------------ 9101| 83.7k| { 9102| 83.7k| iedge = pBNS->vert[endpoint].iedge[k]; /* edge to endpoint */ 9103| 83.7k| centerpoint = pBNS->edge[iedge].neighbor12 ^ endpoint; 9104| 83.7k| pBNS->edge[iedge].cap = pBNS->edge[iedge].cap0; 9105| 83.7k| pBNS->edge[iedge].flow = pBNS->edge[iedge].flow0; 9106| 83.7k| pBNS->edge[iedge].pass = 0; 9107| 83.7k|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 9108| 83.7k| pBNS->edge[iedge].forbidden &= pBNS->edge_forbidden_mask; 9109| 83.7k|#endif 9110| 83.7k| pBNS->vert[centerpoint].st_edge.cap = pBNS->vert[centerpoint].st_edge.cap0; 9111| 83.7k| pBNS->vert[centerpoint].st_edge.flow = pBNS->vert[centerpoint].st_edge.flow0; 9112| 83.7k| } 9113| 33.8k| pBNS->vert[endpoint].st_edge.cap = pBNS->vert[endpoint].st_edge.cap0; 9114| 33.8k| pBNS->vert[endpoint].st_edge.flow = pBNS->vert[endpoint].st_edge.flow0; 9115| 33.8k| pBNS->vert[endpoint].type &= BNS_VERT_TYPE_ATOM; ------------------ | | 45| 33.8k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ 9116| 33.8k| } 9117| 14.1k| } 9118| | /* Reset number of neighbors */ 9119| 300k| if (pBNS->num_edges > pBNS->num_bonds) ------------------ | Branch (9119:17): [True: 12.8k, False: 287k] ------------------ 9120| 12.8k| { 9121| 94.5k| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (9121:29): [True: 81.6k, False: 12.8k] ------------------ 9122| 81.6k| { 9123| 81.6k| pBNS->vert[i].num_adj_edges = 9124| 81.6k| pBNS->vert[i].max_adj_edges - pBNS->nMaxAddEdges - NUM_KINDS_OF_GROUPS; ------------------ | | 86| 81.6k|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 9125| 81.6k| } 9126| 12.8k| } 9127| 300k| } 9128| 0| else 9129| 0| { 9130| 0| ret += 2; 9131| 0| } 9132| 300k| if (!pBNS->edge) ------------------ | Branch (9132:13): [True: 0, False: 300k] ------------------ 9133| 0| { 9134| 0| ret += 4; 9135| 0| } 9136| 300k| if (!pBNS->iedge) ------------------ | Branch (9136:13): [True: 0, False: 300k] ------------------ 9137| 0| { 9138| 0| ret += 8; 9139| 0| } 9140| | 9141| 300k| ReInitBnStructAltPaths( pBNS ); 9142| | 9143| 300k| pBNS->num_vertices = pBNS->num_atoms; 9144| 300k| pBNS->num_edges = pBNS->num_bonds; 9145| 300k| pBNS->num_added_atoms = 0; 9146| 300k| pBNS->num_t_groups = 0; 9147| 300k| pBNS->num_c_groups = 0; 9148| 300k| pBNS->num_added_edges = 0; 9149| 300k| } 9150| 0| else 9151| 0| { 9152| 0| ret += 1; 9153| 0| } 9154| | 9155| 300k| return ret; 9156| 300k|} AddTGroups2BnStruct: 9179| 12.0k|{ 9180| 12.0k| int ret = 0; 9181| | /* ret = ReInitBnStruct( pBNS ); */ 9182| 12.0k| if (tgi && tgi->num_t_groups && tgi->t_group) ------------------ | Branch (9182:9): [True: 12.0k, False: 0] | Branch (9182:16): [True: 12.0k, False: 0] | Branch (9182:37): [True: 12.0k, False: 0] ------------------ 9183| 12.0k| { 9184| 12.0k| int i, k, endpoint, centerpoint, fictpoint; 9185| 12.0k| int num_tg = tgi->num_t_groups; 9186| 12.0k| int num_edges = pBNS->num_edges; 9187| 12.0k| int num_vertices = pBNS->num_vertices; 9188| 12.0k| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing t-group */ 9189| 12.0k| BNS_VERTEX *vert_endpoint; 9190| 12.0k| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 9191| 12.0k| int nMaxTGroupNumber = 0; 9192| 12.0k| ENDPOINT_INFO eif; 9193| | 9194| | /* Debug: check overflow */ 9195| 12.0k| if (num_vertices + num_tg >= pBNS->max_vertices) ------------------ | Branch (9195:13): [True: 0, False: 12.0k] ------------------ 9196| 0| { 9197| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9198| 0| } 9199| | /* Find the largest t-group ID */ 9200| 24.8k| for (i = 0; i < num_tg; i++) ------------------ | Branch (9200:21): [True: 12.7k, False: 12.0k] ------------------ 9201| 12.7k| { 9202| 12.7k| if (tgi->t_group[i].nGroupNumber > nMaxTGroupNumber) ------------------ | Branch (9202:17): [True: 12.7k, False: 0] ------------------ 9203| 12.7k| { 9204| 12.7k| nMaxTGroupNumber = tgi->t_group[i].nGroupNumber; 9205| 12.7k| } 9206| 12.7k| } 9207| | /* Since t-group IDs may be not contiguous, clear all vertices that will be added. 9208| | all-zeroes-vertex will be ignored by the BNS 9209| | */ 9210| 12.0k| memset( pBNS->vert + num_vertices, 0, nMaxTGroupNumber * sizeof( pBNS->vert[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 9211| | /* Make sure the last t-group has the largest t-group ID: 9212| | this is necessary to correctly add new edges 9213| | and vertices for testing augmenting paths */ 9214| |#if ( bRELEASE_VERSION != 1 ) 9215| | insertions_sort( pCG, tgi->t_group, num_tg, sizeof( tgi->t_group[0] ), CompTGroupNumber ); 9216| | for (i = 1; i < num_tg; i++) 9217| | { 9218| | if (1 != tgi->t_group[i].nGroupNumber - tgi->t_group[i - 1].nGroupNumber) 9219| | { 9220| | return BNS_BOND_ERR; 9221| | } 9222| | } 9223| |#else 9224| 12.0k| if (nMaxTGroupNumber != tgi->t_group[num_tg - 1].nGroupNumber) ------------------ | Branch (9224:13): [True: 0, False: 12.0k] ------------------ 9225| 0| { 9226| 0| insertions_sort( pCG, tgi->t_group, num_tg, sizeof( tgi->t_group[0] ), CompTGroupNumber ); 9227| 0| } 9228| 12.0k|#endif 9229| | /* Initialize new fictitious vertices */ 9230| 12.0k| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 9231| | 9232| 24.8k| for (i = 0; i < num_tg; i++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (9232:21): [True: 12.7k, False: 12.0k] ------------------ 9233| 12.7k| { 9234| | /* 9235| | vert_ficpoint-1 is the last vertex; 9236| | vert_ficpoint is the vertex that is being added 9237| | Note: nGroupNumber are not contiguous 9238| | */ 9239| 12.7k| vert_ficpoint = pBNS->vert + num_vertices + tgi->t_group[i].nGroupNumber - 1; 9240| 12.7k| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 9241| 12.7k| vert_ficpoint->max_adj_edges = tgi->t_group[i].nNumEndpoints + BNS_ADD_EDGES + BNS_ADD_SUPER_TGROUP; ------------------ | | 89| 12.7k|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ vert_ficpoint->max_adj_edges = tgi->t_group[i].nNumEndpoints + BNS_ADD_EDGES + BNS_ADD_SUPER_TGROUP; ------------------ | | 85| 12.7k|#define BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */ ------------------ 9242| 12.7k| vert_ficpoint->num_adj_edges = 0; 9243| 12.7k| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 9244| 12.7k| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 9245| 12.7k| vert_ficpoint->type = BNS_VERT_TYPE_TGROUP; ------------------ | | 47| 12.7k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 9246| 12.7k| } 9247| | 9248| 88.3k| for (endpoint = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (9248:28): [True: 76.2k, False: 12.0k] ------------------ 9249| 76.2k| { 9250| 76.2k| if (!at[endpoint].endpoint) ------------------ | Branch (9250:17): [True: 46.1k, False: 30.0k] ------------------ 9251| 46.1k| { 9252| 46.1k| continue; 9253| 46.1k| } 9254| 30.0k| fictpoint = at[endpoint].endpoint + num_vertices - 1; 9255| 30.0k| vert_ficpoint = pBNS->vert + fictpoint; 9256| 30.0k| vert_endpoint = pBNS->vert + endpoint; 9257| | /* Debug: check overflow */ 9258| 30.0k| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (9258:17): [True: 0, False: 30.0k] ------------------ 9259| 30.0k| num_edges >= pBNS->max_edges || ------------------ | Branch (9259:18): [True: 0, False: 30.0k] ------------------ 9260| 30.0k| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (9260:18): [True: 0, False: 30.0k] ------------------ 9261| 30.0k| vert_endpoint->num_adj_edges >= vert_endpoint->max_adj_edges) ------------------ | Branch (9261:18): [True: 0, False: 30.0k] ------------------ 9262| 0| { 9263| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9264| 0| break; 9265| 0| } 9266| | /* Obtain donor/acceptor info */ 9267| 30.0k| if (!nGetEndpointInfo(at, endpoint, &eif) ------------------ | Branch (9267:17): [True: 5, False: 30.0k] ------------------ 9268| 5|#if ( TAUT_PT_22_00 == 1 ) 9269| 5| && !((tgi->bTautFlags & TG_FLAG_PT_22_00) && nGetEndpointInfo_PT_22_00(at, endpoint, &eif)) ------------------ | | 953| 5|#define TG_FLAG_PT_22_00 0x00800000 ------------------ | Branch (9269:22): [True: 0, False: 5] | Branch (9269:62): [True: 0, False: 0] ------------------ 9270| 5|#endif 9271| 5|#if ( TAUT_PT_16_00 == 1 ) 9272| 5| && !((tgi->bTautFlags & TG_FLAG_PT_16_00) && nGetEndpointInfo_PT_16_00(at, endpoint, &eif)) ------------------ | | 954| 5|#define TG_FLAG_PT_16_00 0x01000000 ------------------ | Branch (9272:22): [True: 0, False: 5] | Branch (9272:62): [True: 0, False: 0] ------------------ 9273| 5|#endif 9274| 5|#if ( TAUT_PT_06_00 == 1 ) 9275| 5| && !((tgi->bTautFlags & TG_FLAG_PT_06_00) && nGetEndpointInfo_PT_06_00(at, endpoint, &eif)) ------------------ | | 955| 5|#define TG_FLAG_PT_06_00 0x02000000 ------------------ | Branch (9275:22): [True: 0, False: 5] | Branch (9275:62): [True: 0, False: 0] ------------------ 9276| 5|#endif 9277| 5|#if ( TAUT_PT_39_00 == 1 ) 9278| 5| && !((tgi->bTautFlags & TG_FLAG_PT_39_00) && nGetEndpointInfo_PT_39_00(at, endpoint, &eif)) ------------------ | | 956| 5|#define TG_FLAG_PT_39_00 0x04000000 ------------------ | Branch (9278:22): [True: 0, False: 5] | Branch (9278:62): [True: 0, False: 0] ------------------ 9279| 5|#endif 9280| 5|#if ( TAUT_PT_13_00 == 1 ) 9281| 5| && !((tgi->bTautFlags & TG_FLAG_PT_13_00) && nGetEndpointInfo_PT_13_00(at, endpoint, &eif)) ------------------ | | 957| 5|#define TG_FLAG_PT_13_00 0x08000000 ------------------ | Branch (9281:22): [True: 0, False: 5] | Branch (9281:62): [True: 0, False: 0] ------------------ 9282| 5|#endif 9283| 5|#if ( TAUT_PT_18_00 == 1 ) 9284| 5| && !((tgi->bTautFlags & TG_FLAG_PT_18_00) && nGetEndpointInfo_PT_18_00(at, endpoint, &eif)) ------------------ | | 958| 5|#define TG_FLAG_PT_18_00 0x10000000 ------------------ | Branch (9284:22): [True: 0, False: 5] | Branch (9284:62): [True: 0, False: 0] ------------------ 9285| 30.0k|#endif 9286| 30.0k| ) { 9287| 5|#if ( KETO_ENOL_TAUT == 1 ) 9288| 5| if (!( ( tgi->bTautFlags & TG_FLAG_KETO_ENOL_TAUT ) && ------------------ | | 946| 5|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (9288:24): [True: 0, False: 5] ------------------ 9289| 0| nGetEndpointInfo_KET( at, endpoint, &eif ) )) ------------------ | Branch (9289:24): [True: 0, False: 0] ------------------ 9290| 5|#endif 9291| 5| { 9292| 5| ret = BNS_BOND_ERR; ------------------ | | 52| 5|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 5|#define BNS_ERR -9999 | | ------------------ ------------------ 9293| 5| break; 9294| 5| } 9295| 5| } 9296| | 9297| 30.0k| vert_endpoint->type |= BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 30.0k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 9298| | 9299| | /* Set capacity = 1 to the edges from the endpoint to the centerpoint(s) */ 9300| 70.5k| for (k = 0; k < vert_endpoint->num_adj_edges; k++) ------------------ | Branch (9300:25): [True: 40.4k, False: 30.0k] ------------------ 9301| 40.4k| { 9302| 40.4k| int iedge = vert_endpoint->iedge[k]; 9303| 40.4k| if (!pBNS->edge[iedge].cap) ------------------ | Branch (9303:21): [True: 18.5k, False: 21.9k] ------------------ 9304| 18.5k| { 9305| | /* Single bond, possibly between endpoint and centerpoint */ 9306| 18.5k| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ endpoint ); 9307| 18.5k| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (9307:25): [True: 18.5k, False: 0] ------------------ 9308| 18.5k| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (9308:26): [True: 13.9k, False: 4.54k] ------------------ 9309| 13.9k| { 9310| 13.9k| int bond_type = ( at[endpoint].bond_type[k] & BOND_TYPE_MASK ); ------------------ | | 189| 13.9k|#define BOND_TYPE_MASK 0x0f ------------------ 9311| 13.9k| if (bond_type == BOND_TAUTOM || ------------------ | | 185| 27.9k|#define BOND_TAUTOM 8 ------------------ | Branch (9311:29): [True: 7.54k, False: 6.44k] ------------------ 9312| 6.44k| bond_type == BOND_ALTERN || ------------------ | | 180| 6.44k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 20.4k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (9312:30): [True: 184, False: 6.26k] ------------------ 9313| 6.26k| bond_type == BOND_ALT12NS || ------------------ | | 186| 20.2k|#define BOND_ALT12NS 9 ------------------ | Branch (9313:30): [True: 58, False: 6.20k] ------------------ 9314| 6.20k| bond_type == BOND_SINGLE) ------------------ | | 177| 6.20k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 6.20k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (9314:30): [True: 6.20k, False: 0] ------------------ 9315| 13.9k| { 9316| 13.9k| pBNS->edge[iedge].cap = 1; 9317| 13.9k| } 9318| 13.9k| } 9319| 18.5k| } 9320| 40.4k| } 9321| | 9322| | /* Create a new edge connecting endpoint to the new fictitious t-group vertex vert_ficpoint */ 9323| 30.0k| edge = pBNS->edge + num_edges; 9324| 30.0k| edge->cap = 1; 9325| 30.0k| edge->flow = 0; 9326| 30.0k| edge->pass = 0; 9327| 30.0k|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 9328| 30.0k| edge->forbidden &= pBNS->edge_forbidden_mask; 9329| 30.0k|#endif 9330| | /* Later include case when the charge change allows the endpoint to become tautomeric */ 9331| | /* mark endoint having moveable H atom with flow=1 */ 9332| | 9333| | /* -- old "no charges" version -- */ 9334| | /* if (at[endpoint].chem_bonds_valence == at[endpoint].valence) */ 9335| | /* -- the following line takes charges into account -- */ 9336| 30.0k| if (eif.cDonor) /* means the endpoint has an H-atom to donate */ ------------------ | Branch (9336:17): [True: 14.8k, False: 15.1k] ------------------ 9337| 14.8k| { 9338| | /* increment edge flow */ 9339| 14.8k| edge->flow++; 9340| | /* increment one vertex st-flow & cap */ 9341| 14.8k| vert_ficpoint->st_edge.flow++; 9342| 14.8k| vert_ficpoint->st_edge.cap++; 9343| | /* increment another vertex st-flow & cap */ 9344| 14.8k| vert_endpoint->st_edge.flow++; 9345| 14.8k| vert_endpoint->st_edge.cap++; 9346| 14.8k| } 9347| | /* Connect edge to endpoint and fictpoint and increment the counters of neighbors and edges */ 9348| 30.0k| edge->neighbor1 = endpoint; /* the smallest out of v1=endopoint and v2=num_vertices */ 9349| 30.0k| edge->neighbor12 = endpoint ^ fictpoint; /* v1 ^ v2 */ 9350| 30.0k| vert_endpoint->iedge[vert_endpoint->num_adj_edges] = num_edges; 9351| 30.0k| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 9352| 30.0k| edge->neigh_ord[0] = vert_endpoint->num_adj_edges++; 9353| 30.0k| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 9354| 30.0k| edge->cap0 = edge->cap; 9355| 30.0k| edge->flow0 = edge->flow; 9356| 30.0k| } 9357| | 9358| 12.0k| pBNS->num_edges = num_edges; 9359| 12.0k| pBNS->num_vertices += nMaxTGroupNumber; 9360| 12.0k| pBNS->num_t_groups = num_tg; 9361| 12.0k| } 9362| | 9363| 12.0k| return ret; 9364| 12.0k|} AddCGroups2BnStruct: 9376| 12.9k|{ 9377| 12.9k| int ret = 0; 9378| | /* ret = ReInitBnStruct( pBNS ); */ 9379| 12.9k| if (cgi && cgi->num_c_groups && cgi->c_group) ------------------ | Branch (9379:9): [True: 12.9k, False: 0] | Branch (9379:16): [True: 1.25k, False: 11.7k] | Branch (9379:37): [True: 1.25k, False: 0] ------------------ 9380| 1.25k| { 9381| 1.25k| int i, k, c_point, centerpoint, fictpoint; 9382| 1.25k| int num_cg = cgi->num_c_groups; 9383| 1.25k| int num_edges = pBNS->num_edges; 9384| 1.25k| int num_vertices = pBNS->num_vertices; 9385| 1.25k| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing charge c-group */ 9386| 1.25k| BNS_VERTEX *vertex_cpoint; 9387| 1.25k| BNS_EDGE *edge; /* edge between that vertex and the tautomeric c_point */ 9388| 1.25k| int nMaxCGroupNumber = 0; 9389| | 9390| | /* Debug: check overflow */ 9391| 1.25k| if (num_vertices + num_cg >= pBNS->max_vertices) ------------------ | Branch (9391:13): [True: 0, False: 1.25k] ------------------ 9392| 0| { 9393| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9394| 0| } 9395| | /* Find the largest t-group ID */ 9396| 2.63k| for (i = 0; i < num_cg; i++) ------------------ | Branch (9396:21): [True: 1.38k, False: 1.25k] ------------------ 9397| 1.38k| { 9398| 1.38k| if (cgi->c_group[i].nGroupNumber > nMaxCGroupNumber) ------------------ | Branch (9398:17): [True: 1.38k, False: 0] ------------------ 9399| 1.38k| { 9400| 1.38k| nMaxCGroupNumber = cgi->c_group[i].nGroupNumber; 9401| 1.38k| } 9402| 1.38k| } 9403| | /* Since t-group IDs may be not contiguous, clear all vertices that will be added. 9404| | all-zeroes-vertex will be ignored by the BNS 9405| | */ 9406| 1.25k| memset( pBNS->vert + num_vertices, 0, nMaxCGroupNumber * sizeof( pBNS->vert[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 9407| | /* Make sure the last t-group has the largest t-group ID: 9408| | this is necessary to correctly add new edges and vertices for testing augmenting paths 9409| | */ 9410| |#if ( bRELEASE_VERSION != 1 ) 9411| | insertions_sort( cgi->c_group, num_cg, sizeof( cgi->c_group[0] ), CompCGroupNumber ); 9412| | for (i = 1; i < num_cg; i++) 9413| | { 9414| | if (1 != cgi->c_group[i].nGroupNumber - cgi->c_group[i - 1].nGroupNumber) 9415| | { 9416| | return BNS_BOND_ERR; 9417| | } 9418| | } 9419| |#else 9420| 1.25k| if (nMaxCGroupNumber != cgi->c_group[num_cg - 1].nGroupNumber) ------------------ | Branch (9420:13): [True: 0, False: 1.25k] ------------------ 9421| 0| { 9422| 0| insertions_sort( pCG, cgi->c_group, num_cg, 9423| 0| sizeof( cgi->c_group[0] ), 9424| 0| CompCGroupNumber ); 9425| 0| } 9426| 1.25k|#endif 9427| | /**************************************/ 9428| | /* initialize new fictitious vertices */ 9429| | /* representing c-point groups */ 9430| | /**************************************/ 9431| 1.25k| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 9432| | 9433| 2.63k| for (i = 0; i < num_cg; i++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (9433:21): [True: 1.38k, False: 1.25k] ------------------ 9434| 1.38k| { 9435| | /* 9436| | vert_ficpoint-1 is the last vertex; 9437| | vert_ficpoint is the being added vertex 9438| | Note: nGroupNumber are not contiguous 9439| | */ 9440| 1.38k| vert_ficpoint = pBNS->vert + num_vertices + cgi->c_group[i].nGroupNumber - 1; 9441| 1.38k| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 9442| 1.38k| vert_ficpoint->max_adj_edges = cgi->c_group[i].num_CPoints + BNS_ADD_EDGES; ------------------ | | 89| 1.38k|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 9443| 1.38k| vert_ficpoint->num_adj_edges = 0; 9444| 1.38k| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 9445| 1.38k| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 9446| 1.38k| vert_ficpoint->type = BNS_VERT_TYPE_C_GROUP; ------------------ | | 49| 1.38k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ 9447| 1.38k| } 9448| | 9449| | /************************************************/ 9450| | /* Connect c-points to the fictitious vertices */ 9451| | /* representing c-point groups; set caps, flows */ 9452| | /************************************************/ 9453| 10.1k| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (9453:27): [True: 8.91k, False: 1.25k] ------------------ 9454| 8.91k| { 9455| 8.91k| if (!at[c_point].c_point) ------------------ | Branch (9455:17): [True: 5.16k, False: 3.74k] ------------------ 9456| 5.16k| { 9457| 5.16k| continue; 9458| 5.16k| } 9459| 3.74k| fictpoint = at[c_point].c_point + num_vertices - 1; /* c-group vertex index */ 9460| 3.74k| vert_ficpoint = pBNS->vert + fictpoint; /* c-group vertex */ 9461| 3.74k| vertex_cpoint = pBNS->vert + c_point; /* c_point vertex */ 9462| | /* Debug: check overflow */ 9463| 3.74k| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (9463:17): [True: 0, False: 3.74k] ------------------ 9464| 3.74k| num_edges >= pBNS->max_edges || ------------------ | Branch (9464:18): [True: 0, False: 3.74k] ------------------ 9465| 3.74k| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (9465:18): [True: 0, False: 3.74k] ------------------ 9466| 3.74k| vertex_cpoint->num_adj_edges >= vertex_cpoint->max_adj_edges) ------------------ | Branch (9466:18): [True: 0, False: 3.74k] ------------------ 9467| 0| { 9468| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9469| 0| break; 9470| 0| } 9471| 3.74k| vertex_cpoint->type |= BNS_VERT_TYPE_C_POINT; ------------------ | | 48| 3.74k|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ 9472| |#if ( FIX_CPOINT_BOND_CAP != 1 ) /* { */ 9473| | /* set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 9474| | /* if their current capacity is zero */ 9475| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 9476| | for (k = 0; k < vertex_cpoint->num_adj_edges; k++) 9477| | { 9478| | int iedge = vertex_cpoint->iedge[k]; 9479| | if (!pBNS->edge[iedge].cap) 9480| | { 9481| | /* single bond, possibly between c_point and centerpoint */ 9482| | centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 9483| | if (centerpoint < pBNS->num_atoms && 9484| | pBNS->vert[centerpoint].st_edge.cap >= 1) 9485| | { 9486| | int bond_type = ( at[c_point].bond_type[k] & BOND_TYPE_MASK ); 9487| | if (bond_type == BOND_TAUTOM || 9488| | bond_type == BOND_ALTERN || 9489| | bond_type == BOND_SINGLE) 9490| | { 9491| | pBNS->edge[iedge].cap = 1; 9492| | } 9493| | } 9494| | } 9495| | } 9496| |#endif /* } FIX_CPOINT_BOND_CAP */ 9497| | 9498| | /* Create a new edge connecting c_point to the new fictitious c-group vertex vert_ficpoint */ 9499| 3.74k| edge = pBNS->edge + num_edges; 9500| 3.74k| edge->cap = 1; 9501| 3.74k| edge->flow = 0; 9502| 3.74k| edge->pass = 0; 9503| 3.74k|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 9504| 3.74k| edge->forbidden &= pBNS->edge_forbidden_mask; 9505| 3.74k|#endif 9506| | /* Mark edge to c-point having NO moveable charge with flow=1 */ 9507| 3.74k| if (!CHARGED_CPOINT( at, c_point )) ------------------ | | 253| 3.74k|#define CHARGED_CPOINT(X,i) ((X)[i].charge==1) ------------------ | Branch (9507:17): [True: 2.07k, False: 1.67k] ------------------ 9508| 2.07k| { 9509| | /* Increment edge flow */ 9510| 2.07k| edge->flow++; 9511| | /* Increment c-group vertex st-flow & cap */ 9512| 2.07k| vert_ficpoint->st_edge.flow++; 9513| 2.07k| vert_ficpoint->st_edge.cap++; 9514| | /* Increment c-point vertex st-flow & cap */ 9515| 2.07k| vertex_cpoint->st_edge.flow++; 9516| 2.07k| vertex_cpoint->st_edge.cap++; 9517| 2.07k| } 9518| | 9519| 3.74k|#if ( FIX_CPOINT_BOND_CAP == 1 ) /* { */ 9520| | 9521| | /* Set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 9522| | /* if their current capacity is zero */ 9523| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 9524| 12.2k| for (k = 0; k < vertex_cpoint->num_adj_edges; k++) ------------------ | Branch (9524:25): [True: 8.52k, False: 3.74k] ------------------ 9525| 8.52k| { 9526| 8.52k| int iedge = vertex_cpoint->iedge[k]; 9527| 8.52k| VertexFlow nNewCap = vertex_cpoint->st_edge.cap; 9528| 8.52k| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 9529| 8.52k| if (!pBNS->edge[iedge].cap) ------------------ | Branch (9529:21): [True: 2.45k, False: 6.07k] ------------------ 9530| 2.45k| { 9531| | /* Single bond, possibly between c_point and centerpoint */ 9532| 2.45k| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (9532:25): [True: 2.45k, False: 0] ------------------ 9533| 2.45k| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (9533:26): [True: 917, False: 1.53k] ------------------ 9534| 917| { 9535| 917| nNewCap = inchi_min( pBNS->vert[centerpoint].st_edge.cap, nNewCap ); ------------------ | | 139| 917|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 917] | | ------------------ ------------------ 9536| 917| nNewCap = inchi_min( nNewCap, MAX_BOND_EDGE_CAP ); ------------------ | | 139| 917|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 917, False: 0] | | ------------------ ------------------ 9537| 917| pBNS->edge[iedge].cap = nNewCap; 9538| 917| } 9539| |#if ( FIX_CPOINT_BOND_CAP2 == 1 ) /* multiple bond */ 9540| | else 9541| | if (centerpoint < pBNS->num_atoms && 9542| | edge->flow && pBNS->edge[iedge].cap < MAX_BOND_EDGE_CAP) 9543| | { 9544| | pBNS->edge[iedge].cap++; 9545| | } 9546| |#endif 9547| 2.45k| } 9548| 8.52k| } 9549| 3.74k|#endif /* } FIX_CPOINT_BOND_CAP */ 9550| | 9551| | /* Connect edge to c_point and fictpoint and increment the counters of neighbors and edges */ 9552| 3.74k| edge->neighbor1 = c_point; /* the smallest out of v1=endopoint and v2=num_vertices */ 9553| 3.74k| edge->neighbor12 = c_point ^ fictpoint; /* v1 ^ v2 */ 9554| 3.74k| vertex_cpoint->iedge[vertex_cpoint->num_adj_edges] = num_edges; 9555| 3.74k| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 9556| 3.74k| edge->neigh_ord[0] = vertex_cpoint->num_adj_edges++; 9557| 3.74k| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 9558| 3.74k| edge->cap0 = edge->cap; 9559| 3.74k| edge->flow0 = edge->flow; 9560| 3.74k| } 9561| | 9562| 1.25k| pBNS->num_edges = num_edges; 9563| 1.25k| pBNS->num_vertices += nMaxCGroupNumber; 9564| 1.25k| pBNS->num_c_groups = num_cg; 9565| 1.25k| } 9566| | 9567| 12.9k| return ret; 9568| 12.9k|} ClearAllBnDataVertices: 9575| 376k|{ 9576| 376k| int i; 9577| 12.6M| for (i = 0; i < size; i++) ------------------ | Branch (9577:17): [True: 12.2M, False: 376k] ------------------ 9578| 12.2M| { 9579| 12.2M| v[i] = value; 9580| 12.2M| } 9581| 376k|} ClearAllBnDataEdges: 9586| 376k|{ 9587| 376k| int i; 9588| 12.6M| for (i = 0; i < size; i++) ------------------ | Branch (9588:17): [True: 12.2M, False: 376k] ------------------ 9589| 12.2M| { 9590| 12.2M| e[i][0] = value; 9591| 12.2M| } 9592| 376k|} DeAllocateBnData: 9597| 376k|{ 9598| 376k| if (pBD) ------------------ | Branch (9598:9): [True: 376k, False: 129] ------------------ 9599| 376k| { 9600| 376k| if (pBD->BasePtr) ------------------ | Branch (9600:13): [True: 376k, False: 0] ------------------ 9601| 376k| { 9602| 376k| inchi_free( pBD->BasePtr ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9603| 376k| } 9604| 376k| if (pBD->SwitchEdge) ------------------ | Branch (9604:13): [True: 376k, False: 0] ------------------ 9605| 376k| { 9606| 376k| inchi_free( pBD->SwitchEdge ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9607| 376k| } 9608| 376k| if (pBD->Tree) ------------------ | Branch (9608:13): [True: 376k, False: 0] ------------------ 9609| 376k| { 9610| 376k| inchi_free( pBD->Tree ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9611| 376k| } 9612| 376k| if (pBD->ScanQ) ------------------ | Branch (9612:13): [True: 376k, False: 0] ------------------ 9613| 376k| { 9614| 376k| inchi_free( pBD->ScanQ ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9615| 376k| } 9616| 376k| if (pBD->Pu) ------------------ | Branch (9616:13): [True: 376k, False: 0] ------------------ 9617| 376k| { 9618| 376k| inchi_free( pBD->Pu ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9619| 376k| } 9620| 376k| if (pBD->Pv) ------------------ | Branch (9620:13): [True: 376k, False: 0] ------------------ 9621| 376k| { 9622| 376k| inchi_free( pBD->Pv ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9623| 376k| } 9624| 376k|#if ( BNS_RAD_SEARCH == 1 ) 9625| 376k| if (pBD->RadEndpoints) ------------------ | Branch (9625:13): [True: 376k, False: 0] ------------------ 9626| 376k| { 9627| 376k| inchi_free( pBD->RadEndpoints ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9628| 376k| } 9629| 376k| if (pBD->RadEdges) ------------------ | Branch (9629:13): [True: 376k, False: 0] ------------------ 9630| 376k| { 9631| 376k| inchi_free( pBD->RadEdges ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9632| 376k| } 9633| 376k|#endif 9634| 376k| inchi_free( pBD ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 9635| 376k| } 9636| | 9637| | return NULL; 9638| 376k|} AllocateAndInitBnData: 9643| 376k|{ 9644| 376k| BN_DATA *pBD = NULL; 9645| 376k| int max_len_Pu_Pv; 9646| 376k| max_num_vertices = 2 * max_num_vertices + 2; 9647| 376k| max_len_Pu_Pv = max_num_vertices / 2 + 1; 9648| 376k| max_len_Pu_Pv += max_len_Pu_Pv % 2; /* even length */ 9649| 376k| if (!( pBD = (BN_DATA *) inchi_calloc( 1, sizeof( BN_DATA ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9649:9): [True: 0, False: 376k] ------------------ 9650| 376k| !( pBD->BasePtr = (Vertex *) inchi_calloc( max_num_vertices, sizeof( Vertex ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9650:10): [True: 0, False: 376k] ------------------ 9651| 376k| !( pBD->SwitchEdge = (Edge *) inchi_calloc( max_num_vertices, sizeof( Edge ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9651:10): [True: 0, False: 376k] ------------------ 9652| 376k| !( pBD->Tree = (S_CHAR *) inchi_calloc( max_num_vertices, sizeof( S_CHAR ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9652:10): [True: 0, False: 376k] ------------------ 9653| 376k| !( pBD->ScanQ = (Vertex *) inchi_calloc( max_num_vertices, sizeof( Vertex ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9653:10): [True: 0, False: 376k] ------------------ 9654| 376k| !( pBD->Pu = (Vertex *) inchi_calloc( max_len_Pu_Pv, sizeof( Vertex ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9654:10): [True: 0, False: 376k] ------------------ 9655| 376k|#if ( BNS_RAD_SEARCH == 1 ) 9656| 376k| !( pBD->RadEndpoints = (Vertex *) inchi_calloc( max_len_Pu_Pv, sizeof( Vertex ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9656:10): [True: 0, False: 376k] ------------------ 9657| 376k| !( pBD->RadEdges = (EdgeIndex*) inchi_calloc( max_len_Pu_Pv, sizeof( EdgeIndex ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9657:10): [True: 0, False: 376k] ------------------ 9658| 376k|#endif 9659| 376k| !( pBD->Pv = (Vertex *) inchi_calloc( max_len_Pu_Pv, sizeof( Vertex ) ) ) ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (9659:10): [True: 0, False: 376k] ------------------ 9660| 376k| ) 9661| 0| { 9662| 0| pBD = DeAllocateBnData( pBD ); 9663| 0| } 9664| 376k| else 9665| 376k| { 9666| | /* Initialize data */ 9667| 376k| ClearAllBnDataEdges( pBD->SwitchEdge, NO_VERTEX, max_num_vertices ); ------------------ | | 118| 376k|#define NO_VERTEX -2 ------------------ 9668| 376k| ClearAllBnDataVertices( pBD->BasePtr, NO_VERTEX, max_num_vertices ); ------------------ | | 118| 376k|#define NO_VERTEX -2 ------------------ 9669| 376k| memset( pBD->Tree, TREE_NOT_IN_M, max_num_vertices ); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 237| 376k|#define TREE_NOT_IN_M 0 /* not in T or T' */ ------------------ 9670| 376k| pBD->QSize = -1; 9671| 376k| pBD->max_len_Pu_Pv = max_len_Pu_Pv; 9672| 376k| pBD->max_num_vertices = max_num_vertices; 9673| 376k|#if ( BNS_RAD_SEARCH == 1 ) 9674| 376k| pBD->nNumRadEndpoints = 0; 9675| 376k|#endif 9676| 376k| } 9677| | 9678| 376k| return pBD; 9679| 376k|} ReInitBnData: 9684| 942k|{ 9685| 942k| int i, ret = 0; 9686| 942k| Vertex u, v; 9687| 942k| if (pBD) ------------------ | Branch (9687:9): [True: 942k, False: 0] ------------------ 9688| 942k| { 9689| 942k| if (!pBD->ScanQ) ------------------ | Branch (9689:13): [True: 0, False: 942k] ------------------ 9690| 0| { 9691| 0| ret += 2; 9692| 0| } 9693| 942k| if (!pBD->BasePtr) ------------------ | Branch (9693:13): [True: 0, False: 942k] ------------------ 9694| 0| { 9695| 0| ret += 4; 9696| 0| } 9697| 942k| if (!pBD->SwitchEdge) ------------------ | Branch (9697:13): [True: 0, False: 942k] ------------------ 9698| 0| { 9699| 0| ret += 8; 9700| 0| } 9701| 942k| if (!pBD->Tree) ------------------ | Branch (9701:13): [True: 0, False: 942k] ------------------ 9702| 0| { 9703| 0| ret += 16; 9704| 0| } 9705| 942k| if (!ret) ------------------ | Branch (9705:13): [True: 942k, False: 0] ------------------ 9706| 942k| { 9707| 6.95M| for (i = 0; i <= pBD->QSize; i++) ------------------ | Branch (9707:25): [True: 6.01M, False: 942k] ------------------ 9708| 6.01M| { 9709| 6.01M| u = pBD->ScanQ[i]; 9710| 6.01M| v = prim( u ); ------------------ | | 392| 6.01M|#define prim(v) (Vertex)((v)^1) ------------------ 9711| 6.01M| pBD->BasePtr[u] = 9712| 6.01M| pBD->BasePtr[v] = 9713| 6.01M| pBD->SwitchEdge_Vert1( u ) = ------------------ | | 395| 6.01M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 9714| 6.01M| pBD->SwitchEdge_Vert1( v ) = NO_VERTEX; ------------------ | | 395| 6.01M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ pBD->SwitchEdge_Vert1( v ) = NO_VERTEX; ------------------ | | 118| 6.01M|#define NO_VERTEX -2 ------------------ 9715| 6.01M| pBD->Tree[u] = 9716| 6.01M| pBD->Tree[v] = TREE_NOT_IN_M; ------------------ | | 237| 6.01M|#define TREE_NOT_IN_M 0 /* not in T or T' */ ------------------ 9717| 6.01M| } 9718| 942k| } 9719| 942k| pBD->QSize = -1; 9720| 942k| if (!pBD->Pu) ------------------ | Branch (9720:13): [True: 0, False: 942k] ------------------ 9721| 0| { 9722| 0| ret += 32; 9723| 0| } 9724| 942k| if (!pBD->Pv) ------------------ | Branch (9724:13): [True: 0, False: 942k] ------------------ 9725| 0| { 9726| 0| ret += 64; 9727| 0| } 9728| 942k| } 9729| 0| else 9730| 0| { 9731| 0| ret += 1; 9732| 0| } 9733| | 9734| 942k| return ret; 9735| 942k|} GetVertexDegree: 9740| 4.64M|{ 9741| 4.64M| int i = v / 2 - 1; 9742| 4.64M| if (i >= 0) ------------------ | Branch (9742:9): [True: 3.89M, False: 742k] ------------------ 9743| 3.89M| { 9744| 3.89M| if (pBNS->vert[i].st_edge.cap > 0) ------------------ | Branch (9744:13): [True: 3.83M, False: 60.0k] ------------------ 9745| 3.83M| { 9746| 3.83M| return pBNS->vert[i].num_adj_edges + 1; /* add 1 neighbor for s or t */ 9747| 3.83M| } 9748| 60.0k| else 9749| 60.0k| { 9750| 60.0k| return 0; /* since the edge s-v has zero capacity, we ignore vertex v */ 9751| 60.0k| } 9752| 3.89M| } 9753| 742k| else 9754| 742k| { 9755| 742k| return pBNS->num_vertices; 9756| 742k| } 9757| 4.64M|} Get2ndEdgeVertex: 9762| 6.93M|{ 9763| | /* 9764| | Vertex ret; 9765| | */ 9766| 6.93M| if (uv[1] >= 0) ------------------ | Branch (9766:9): [True: 5.67M, False: 1.25M] ------------------ 9767| 5.67M| { 9768| | /* -- debug -- 9769| | if ( uv[1] > pBNS->num_edges || uv[0] > 2*pBNS->num_vertices+3 ) { 9770| | int stop = 1; 9771| | } 9772| | ret = ((uv[0]-2) ^ (2*pBNS->edge[uv[1]].neighbor12+1)) + 2; 9773| | if ( ret > 2*pBNS->num_vertices+3 ) { 9774| | int stop = 1; 9775| | } 9776| | return ret; 9777| | -- end debug -- */ 9778| | 9779| 5.67M| return ( ( uv[0] - 2 ) ^ ( 2 * pBNS->edge[uv[1]].neighbor12 + 1 ) ) + 2; 9780| | 9781| | /*short u = uv[0]-FIRST_INDX; */ 9782| | /*short t = 2*(((u / 2 - 1) ^ pBNS->edge[uv[1]].neighbor12) + 1) + ((u+1) & 1) + FIRST_INDX; */ 9783| | /*return t; */ 9784| 5.67M| } 9785| | 9786| 1.25M| if (uv[0] <= 1) ------------------ | Branch (9786:9): [True: 1.25M, False: 16] ------------------ 9787| 1.25M| { 9788| 1.25M| return -( 1 + uv[1] ); /* vertex1 is s or t, return x or y */ 9789| 1.25M| } 9790| 16| else 9791| 16| { 9792| 16| return uv[0] % 2; /* vertex1 is x or y, return s or t; never happens? -- NSC 3737, 7634,... */ 9793| 16| } 9794| | 9795| 1.25M|} GetVertexNeighbor: 9803| 23.6M|{ 9804| | /* neigh = 0 => the neighbor is s or t except case when v is s or t. */ 9805| | /* v= FIRST_INDX or FIRST_INDX+1: v is s or t respectively */ 9806| 23.6M| int i, neighbor; 9807| 23.6M| if (( i = v - 2 ) >= 0) ------------------ | Branch (9807:9): [True: 14.5M, False: 9.04M] ------------------ 9808| 14.5M| { 9809| | /* Neighbor of x or y */ 9810| 14.5M| if (neigh) ------------------ | Branch (9810:13): [True: 10.7M, False: 3.83M] ------------------ 9811| 10.7M| { 9812| 10.7M| neigh--; 9813| | /* x or y */ 9814| 10.7M| *iedge = pBNS->vert[i / 2].iedge[neigh]; 9815| 10.7M| if (!( pBNS->edge[*iedge].cap & EDGE_FLOW_MASK ) || IS_FORBIDDEN( pBNS->edge[*iedge].forbidden, pBNS )) ------------------ | | 133| 10.7M|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ if (!( pBNS->edge[*iedge].cap & EDGE_FLOW_MASK ) || IS_FORBIDDEN( pBNS->edge[*iedge].forbidden, pBNS )) ------------------ | | 41| 10.4M|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (41:48): [True: 598k, False: 9.83M] | | ------------------ ------------------ | Branch (9815:17): [True: 299k, False: 10.4M] ------------------ 9816| 897k| { 9817| 897k| return NO_VERTEX; ------------------ | | 118| 897k|#define NO_VERTEX -2 ------------------ 9818| 897k| } 9819| 9.83M| neighbor = ( i ^ ( 2 * pBNS->edge[*iedge].neighbor12 + 1 ) ) + 2; /* parity opposite to v parity */ 9820| 9.83M| } 9821| 3.83M| else 9822| 3.83M| { 9823| | /* neighbor of x or y is s or t */ 9824| 3.83M| neighbor = ( v & 1 ); /* s or t, same parity as v */ 9825| 3.83M| *iedge = -( neighbor + 1 ); 9826| 3.83M| } 9827| 14.5M| } 9828| 9.04M| else 9829| 9.04M| { 9830| | /* neighbor of s or t: x or y, same parity as v */ 9831| 9.04M| if (!( pBNS->vert[neigh].st_edge.cap & EDGE_FLOW_ST_MASK )) ------------------ | | 128| 9.04M|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (9831:13): [True: 2.02M, False: 7.02M] ------------------ 9832| 2.02M| { 9833| 2.02M| return NO_VERTEX; ------------------ | | 118| 2.02M|#define NO_VERTEX -2 ------------------ 9834| 2.02M| } 9835| 7.02M| neighbor = 2 * neigh + 2 + ( v & 1 ); /* parity same as the parity of v */ 9836| 7.02M| *iedge = -( neighbor + 1 ); 9837| 7.02M| } 9838| | 9839| 20.6M| return neighbor; 9840| 23.6M|} GetEdgePointer: 9850| 20.1M|{ 9851| 20.1M| int i = u / 2 - 1; 9852| 20.1M| int j = v / 2 - 1; 9853| 20.1M| int bBackward = BNS_WRONG_PARMS; ------------------ | | 48| 20.1M|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 20.1M|#define BNS_ERR -9999 | | ------------------ ------------------ 9854| 20.1M| *uv = NULL; 9855| 20.1M| if (i >= 0) ------------------ | Branch (9855:9): [True: 12.3M, False: 7.80M] ------------------ 9856| 12.3M| { 9857| | /* u is an atom */ 9858| 12.3M| if (j >= 0) ------------------ | Branch (9858:13): [True: 9.09M, False: 3.22M] ------------------ 9859| 9.09M| { 9860| | /* v is an atom */ 9861| 9.09M| if (( u + v ) % 2) ------------------ | Branch (9861:17): [True: 9.09M, False: 0] ------------------ 9862| 9.09M| { 9863| 9.09M| *uv = pBNS->edge + iuv; 9864| 9.09M| bBackward = ( u & 1 ); 9865| 9.09M| *s_or_t = 0; 9866| 9.09M| } 9867| 9.09M| } 9868| 3.22M| else 9869| 3.22M| { 9870| | /* v is s or t */ 9871| 3.22M| if (v >= 0 && !( ( u + v ) % 2 )) ------------------ | Branch (9871:17): [True: 3.22M, False: 0] | Branch (9871:27): [True: 3.22M, False: 0] ------------------ 9872| 3.22M| { 9873| 3.22M| *uv = (BNS_EDGE*) &pBNS->vert[i].st_edge; 9874| 3.22M| bBackward = !( v & 1 ); 9875| 3.22M| *s_or_t = v + 3; /* 3=> v=s, 4=> v=t */ 9876| 3.22M| } 9877| 3.22M| } 9878| 12.3M| } 9879| 7.80M| else 9880| 7.80M| { 9881| 7.80M| if (j >= 0) ------------------ | Branch (9881:13): [True: 7.80M, False: 0] ------------------ 9882| 7.80M| { 9883| | /* u is s or t */ 9884| 7.80M| if (u >= 0 && !( ( u + v ) % 2 )) ------------------ | Branch (9884:17): [True: 7.80M, False: 0] | Branch (9884:27): [True: 7.80M, False: 0] ------------------ 9885| 7.80M| { 9886| | /* v is an atom */ 9887| 7.80M| *uv = (BNS_EDGE*) &pBNS->vert[j].st_edge; 9888| 7.80M| bBackward = ( u & 1 ); 9889| 7.80M| *s_or_t = u + 1; /* 1=> u=s, 2=> u=t */ 9890| 7.80M| } 9891| 7.80M| } 9892| 7.80M| } 9893| | 9894| 20.1M| return bBackward; 9895| 20.1M|} AugmentEdge: 9906| 1.19M|{ 9907| 1.19M| int f, flow, ret = 0; 9908| | 9909| 1.19M| BNS_ST_EDGE *pst_edge; 9910| 1.19M| BNS_EDGE *pedge; 9911| 1.19M| S_CHAR s_or_t; 9912| 1.19M| int bBackward = GetEdgePointer( pBNS, u, v, iuv, &pedge, &s_or_t ); 9913| 1.19M| if (!IS_BNS_ERROR( bBackward )) ------------------ | | 67| 1.19M|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.19M|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.19M|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.19M|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.19M, False: 0] | | | Branch (67:44): [True: 0, False: 1.19M] | | ------------------ ------------------ 9914| 1.19M| { 9915| 1.19M| if (bBackward) ------------------ | Branch (9915:13): [True: 384k, False: 810k] ------------------ 9916| 384k| { 9917| 384k| delta = -delta; 9918| 384k| } 9919| | 9920| 1.19M| if (s_or_t) ------------------ | Branch (9920:13): [True: 284k, False: 911k] ------------------ 9921| 284k| { 9922| 284k| pst_edge = (BNS_ST_EDGE *) pedge; 9923| 284k| flow = pst_edge->flow; 9924| 284k| f = ( flow & EDGE_FLOW_ST_MASK ) + delta; /* new flow */ ------------------ | | 128| 284k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 9925| 284k| if (!delta) ------------------ | Branch (9925:17): [True: 0, False: 284k] ------------------ 9926| 0| { 9927| | /*((BNS_ST_EDGE *)pedge)->flow = pst_edge->flow & ~EDGE_FLOW_ST_PATH;*/ 9928| 0| pst_edge->flow = pst_edge->flow & ~EDGE_FLOW_ST_PATH; ------------------ | | 129| 0|#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 9929| 0| } 9930| 284k| else 9931| 284k| { 9932| 284k| int cap = pst_edge->cap; 9933| 284k| if (f < 0 || f > cap) ------------------ | Branch (9933:21): [True: 0, False: 284k] | Branch (9933:30): [True: 0, False: 284k] ------------------ 9934| 0| { 9935| 0| ret = BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9936| 0| } 9937| 284k| else 9938| 284k| { 9939| 284k| if (!( bChangeFlow & BNS_EF_CHNG_FLOW )) ------------------ | | 370| 284k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ | Branch (9939:25): [True: 38.2k, False: 245k] ------------------ 9940| 38.2k| { 9941| 38.2k| f -= delta; /* do not actually change the flow, only find the augmenting path */ 9942| 38.2k| } 9943| 245k| else 9944| 245k| { 9945| 245k| if (delta) ------------------ | Branch (9945:29): [True: 245k, False: 0] ------------------ 9946| 245k| { 9947| | /*((BNS_ST_EDGE *)pedge)->pass ++;*/ 9948| 245k| pst_edge->pass++; 9949| 245k| } 9950| 245k| } 9951| 284k| flow = ( flow & ~( EDGE_FLOW_ST_PATH | EDGE_FLOW_ST_MASK ) ) + f; ------------------ | | 129| 284k|#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ flow = ( flow & ~( EDGE_FLOW_ST_PATH | EDGE_FLOW_ST_MASK ) ) + f; ------------------ | | 128| 284k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 9952| | /*((BNS_ST_EDGE *)pedge)->flow = flow;*/ 9953| 284k| pst_edge->flow = flow; 9954| | /*((BNS_ST_EDGE *)pedge)->delta += delta; */ 9955| 284k| if (bReverse) ------------------ | Branch (9955:25): [True: 142k, False: 142k] ------------------ 9956| 142k| { 9957| | /* u <- v; Note: in case of bReverse s_or_t has actually been determined 9958| | for the u' <- v' pair; therefore s and t should be switched 9959| | in order to correctly determine the 1st or the last atom 9960| | on the augmenting path. 9961| | */ 9962| 142k| switch (s_or_t) 9963| 142k| { 9964| 142k| case 1: /* u = t: t<-v, v is the last vertex */ ------------------ | Branch (9964:29): [True: 142k, False: 0] ------------------ 9965| 142k| ALTP_END_ATOM( pBNS->alt_path ) = v / 2 - 1; ------------------ | | 102| 142k|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 9966| 142k| break; 9967| 0| case 2: /* u = s: s<-v, error */ ------------------ | Branch (9967:29): [True: 0, False: 142k] ------------------ 9968| 0| ret = BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9969| 0| break; 9970| 0| case 3: /* v = t: u<-t, error */ ------------------ | Branch (9970:29): [True: 0, False: 142k] ------------------ 9971| 0| ret = BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9972| 0| break; 9973| 0| case 4: /* v = s: u<-s, u is the first vertex */ ------------------ | Branch (9973:29): [True: 0, False: 142k] ------------------ 9974| 0| ALTP_START_ATOM( pBNS->alt_path ) = u / 2 - 1; ------------------ | | 103| 0|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 9975| 0| ALTP_DELTA( pBNS->alt_path ) = delta; ------------------ | | 112| 0|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 9976| 0| break; 9977| 0| default: ------------------ | Branch (9977:29): [True: 0, False: 142k] ------------------ 9978| 0| ret = BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9979| 0| break; 9980| 142k| } 9981| 142k| } 9982| 142k| else 9983| 142k| { 9984| | /* u -> v */ 9985| 142k| switch (s_or_t) 9986| 142k| { 9987| 142k| case 1: /* u = s: s->v, v is the first vertex */ ------------------ | Branch (9987:29): [True: 142k, False: 8] ------------------ 9988| 142k| ALTP_START_ATOM( pBNS->alt_path ) = v / 2 - 1; ------------------ | | 103| 142k|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 9989| 142k| ALTP_DELTA( pBNS->alt_path ) = delta; ------------------ | | 112| 142k|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 9990| 142k| break; 9991| 0| case 2: /* u = t: t->v, error */ ------------------ | Branch (9991:29): [True: 0, False: 142k] ------------------ 9992| 0| ret = BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9993| 0| break; 9994| 0| case 3: /* v = s: u->s, error */ ------------------ | Branch (9994:29): [True: 0, False: 142k] ------------------ 9995| 0| ret = BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9996| 0| break; 9997| 8| case 4: /* v = t: u->t, u is the last vertex */ ------------------ | Branch (9997:29): [True: 8, False: 142k] ------------------ 9998| 8| ALTP_END_ATOM( pBNS->alt_path ) = u / 2 - 1; ------------------ | | 102| 8|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 9999| 8| break; 10000| 0| default: ------------------ | Branch (10000:29): [True: 0, False: 142k] ------------------ 10001| 0| ret = BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 10002| 0| break; 10003| 142k| } 10004| 142k| } 10005| 284k| } 10006| 284k| } 10007| 284k| } 10008| 911k| else 10009| 911k| { 10010| 911k| f = ( pedge->flow & EDGE_FLOW_MASK ) + delta; ------------------ | | 133| 911k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 10011| 911k| if (!delta) ------------------ | Branch (10011:17): [True: 0, False: 911k] ------------------ 10012| 0| { 10013| 0| pedge->flow &= ~EDGE_FLOW_PATH; ------------------ | | 134| 0|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 10014| 0| } 10015| 911k| else 10016| 911k| { 10017| 911k| if (f < 0 || f > pedge->cap) ------------------ | Branch (10017:21): [True: 0, False: 911k] | Branch (10017:30): [True: 2, False: 911k] ------------------ 10018| 2| { 10019| 2| ret = BNS_WRONG_PARMS; ------------------ | | 48| 2|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 2|#define BNS_ERR -9999 | | ------------------ ------------------ 10020| 2| } 10021| 911k| else 10022| 911k| { 10023| 911k| AT_NUMB iu = u / 2 - 1; 10024| 911k| AT_NUMB iv = v / 2 - 1; 10025| 911k| int indx; 10026| 911k| if (!( bChangeFlow & BNS_EF_CHNG_FLOW )) ------------------ | | 370| 911k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ | Branch (10026:25): [True: 180k, False: 731k] ------------------ 10027| 180k| { 10028| 180k| f -= delta; /* do not actually change the flow, only find the augmenting path */ 10029| 180k| } 10030| 731k| else 10031| 731k| { 10032| 731k| if (delta) ------------------ | Branch (10032:29): [True: 731k, False: 0] ------------------ 10033| 731k| { 10034| 731k| pedge->pass++; 10035| 731k| } 10036| 731k| } 10037| 911k| pedge->flow = ( pedge->flow & ~( EDGE_FLOW_PATH | EDGE_FLOW_MASK ) ) | f; ------------------ | | 134| 911k|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ pedge->flow = ( pedge->flow & ~( EDGE_FLOW_PATH | EDGE_FLOW_MASK ) ) | f; ------------------ | | 133| 911k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 10038| 911k| if (ALTP_MAY_ADD( pBNS->alt_path )) ------------------ | | 110| 911k|#define ALTP_MAY_ADD(altp) (iALTP_NEIGHBOR + (altp)[iALTP_PATH_LEN].number < (altp)[iALTP_MAX_LEN].number) | | ------------------ | | | Branch (110:41): [True: 911k, False: 0] | | ------------------ ------------------ 10039| 911k| { 10040| | /* bReverse? u <- v : u -> v */ 10041| 911k| indx = bReverse ? ( pedge->neighbor1 == iv ) : ( pedge->neighbor1 == iu ); ------------------ | Branch (10041:32): [True: 372k, False: 539k] ------------------ 10042| 911k| ALTP_CUR_THIS_ATOM_NEIGHBOR( pBNS->alt_path ) = pedge->neigh_ord[1 - indx]; ------------------ | | 106| 911k|#define ALTP_CUR_THIS_ATOM_NEIGHBOR(altp) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[0] /* 0 <= X < path_len */ | | ------------------ | | | | 101| 911k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ | | ------------------ ------------------ 10043| 911k| ALTP_CUR_NEXT_ATOM_NEIGHBOR( pBNS->alt_path ) = pedge->neigh_ord[indx]; ------------------ | | 107| 911k|#define ALTP_CUR_NEXT_ATOM_NEIGHBOR(altp) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[1] | | ------------------ | | | | 101| 911k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ | | ------------------ ------------------ 10044| 911k| ALTP_NEXT( pBNS->alt_path ); ------------------ | | 108| 911k|#define ALTP_NEXT(altp) (++ALTP_PATH_LEN(altp)) | | ------------------ | | | | 101| 911k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ | | ------------------ ------------------ 10045| 911k| } 10046| 0| else 10047| 0| { 10048| 0| ALTP_OVERFLOW( pBNS->alt_path ) = 1; ------------------ | | 113| 0|#define ALTP_OVERFLOW(altp) (altp)[iALTP_FLOW].flow[1] ------------------ 10049| 0| ret = BNS_ALTPATH_OVFL; ------------------ | | 51| 0|#define BNS_ALTPATH_OVFL (BNS_ERR + 3) /*(-9996)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 10050| 0| } 10051| 911k| } 10052| 911k| } 10053| 911k| } 10054| 1.19M| return ret ? ret : f; ------------------ | Branch (10054:16): [True: 2, False: 1.19M] ------------------ 10055| 1.19M| } 10056| | 10057| 0| return bBackward; 10058| 1.19M|} rescap_mark: 10068| 1.19M|{ 10069| 1.19M| BNS_ST_EDGE *pst_edge; 10070| 1.19M| BNS_EDGE *pedge; 10071| | 10072| 1.19M| int f, flow; 10073| 1.19M| S_CHAR s_or_t; 10074| 1.19M| int bBackward = GetEdgePointer( pBNS, u, v, iuv, &pedge, &s_or_t ); 10075| | 10076| 1.19M| if (!IS_BNS_ERROR( bBackward )) ------------------ | | 67| 1.19M|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.19M|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.19M|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.19M|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.19M, False: 0] | | | Branch (67:44): [True: 0, False: 1.19M] | | ------------------ ------------------ 10077| 1.19M| { 10078| 1.19M| if (s_or_t) ------------------ | Branch (10078:13): [True: 284k, False: 911k] ------------------ 10079| 284k| { 10080| 284k| pst_edge = (BNS_ST_EDGE *) pedge; 10081| 284k| flow = pst_edge->flow; 10082| 284k| f = ( flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 284k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 10083| 284k| if (!bBackward) ------------------ | Branch (10083:17): [True: 284k, False: 0] ------------------ 10084| 284k| { 10085| 284k| f = (int) pst_edge->cap - f; 10086| 284k| } 10087| 284k| if (flow & EDGE_FLOW_ST_PATH) ------------------ | | 129| 284k|#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ | Branch (10087:17): [True: 14.4k, False: 269k] ------------------ 10088| 14.4k| { 10089| 14.4k| pBNS->bNotASimplePath++; 10090| 14.4k| f /= 2; /* this is the second time we pass the same edge: reduce flow by a factor of 2 */ 10091| 14.4k| } 10092| 269k| else 10093| 269k| { 10094| 269k| pst_edge->flow |= EDGE_FLOW_ST_PATH; /* mark the edge */ ------------------ | | 129| 269k|#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 10095| 269k| } 10096| 284k| } 10097| 911k| else 10098| 911k| { 10099| 911k| flow = pedge->flow; 10100| 911k| f = flow & EDGE_FLOW_MASK; ------------------ | | 133| 911k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 10101| 911k| if (!bBackward) ------------------ | Branch (10101:17): [True: 526k, False: 384k] ------------------ 10102| 526k| { 10103| 526k| f = (int) pedge->cap - f; 10104| 526k| } 10105| 911k| if (flow & EDGE_FLOW_PATH) ------------------ | | 134| 911k|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ | Branch (10105:17): [True: 44.3k, False: 867k] ------------------ 10106| 44.3k| { 10107| 44.3k| f /= 2; /* this is the second time we pass the same edge: reduce flow by a factor of 2 */ 10108| 44.3k| pBNS->bNotASimplePath++; 10109| 44.3k| } 10110| 867k| else 10111| 867k| { 10112| 867k| pedge->flow |= EDGE_FLOW_PATH; /* mark the edge */ ------------------ | | 134| 867k|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 10113| 867k| } 10114| 911k| } 10115| 1.19M| return f; 10116| 1.19M| } 10117| | 10118| 0| return bBackward; 10119| 1.19M|} GetPrevVertex: 10129| 206k|{ 10130| 206k| Vertex w, z, x2, y2; /* djb-rwth: removing redundant variables */ 10131| 206k| EdgeIndex iwy; 10132| | 10133| 206k| w = SwitchEdge_Vert1( y ); ------------------ | | 395| 206k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 10134| 206k| z = SwitchEdge_Vert2( y ); ------------------ | | 396| 206k|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 10135| 206k| iwy = SwitchEdge_IEdge( y ); ------------------ | | 397| 206k|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 10136| 206k| if (z == y) ------------------ | Branch (10136:9): [True: 182k, False: 23.2k] ------------------ 10137| 182k| { 10138| 182k| *iuv = iwy; 10139| 182k| return w; 10140| 182k| } 10141| 23.2k| x2 = prim( y ); ------------------ | | 392| 23.2k|#define prim(v) (Vertex)((v)^1) ------------------ 10142| 23.2k| y2 = prim( z ); ------------------ | | 392| 23.2k|#define prim(v) (Vertex)((v)^1) ------------------ 10143| | /* djb-rwth: removing redundant code */ 10144| 55.6k| while (y2 != NO_VERTEX) ------------------ | | 118| 55.6k|#define NO_VERTEX -2 ------------------ | Branch (10144:12): [True: 55.6k, False: 0] ------------------ 10145| 55.6k| { 10146| 55.6k| w = SwitchEdge_Vert1( y2 ); ------------------ | | 395| 55.6k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 10147| 55.6k| z = SwitchEdge_Vert2( y2 ); ------------------ | | 396| 55.6k|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 10148| 55.6k| iwy = SwitchEdge_IEdge( y2 ); ------------------ | | 397| 55.6k|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 10149| 55.6k| if (w == x2) ------------------ | Branch (10149:13): [True: 23.2k, False: 32.4k] ------------------ 10150| 23.2k| { 10151| 23.2k| *iuv = iwy; 10152| | /*return z; */ 10153| 23.2k| return ( y + z ) % 2 ? z : prim( z ); ------------------ | | 392| 23.2k|#define prim(v) (Vertex)((v)^1) ------------------ | Branch (10153:20): [True: 0, False: 23.2k] ------------------ 10154| 23.2k| } 10155| | /* djb-rwth: removing redundant code */ 10156| | /* 10157| | #ifdef _DEBUG 10158| | if ( n ) { 10159| | int stop = 1; 10160| | } 10161| | #endif 10162| | */ 10163| 32.4k| if (w == y2) ------------------ | Branch (10163:13): [True: 0, False: 32.4k] ------------------ 10164| 0| { 10165| 0| return NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 10166| 0| } 10167| 32.4k| y2 = w; 10168| 32.4k| } 10169| | 10170| 0| return y2; 10171| 23.2k|} bIgnoreVertexNonTACN_atom: 10257| 27.3k|{ 10258| 27.3k| int i, degree, ret, u_is_taut = 0, num_allowed = 0, num_found_groups = 0; 10259| 27.3k| Vertex w; 10260| 27.3k| EdgeIndex ivw; 10261| 27.3k| if (!pBNS->type_TACN || u <= 1 || v <= 1 || ------------------ | Branch (10261:9): [True: 0, False: 27.3k] | Branch (10261:29): [True: 5.17k, False: 22.1k] | Branch (10261:39): [True: 5.13k, False: 17.0k] ------------------ 10262| 17.0k| ( pBNS->vert[v / 2 - 1].type & pBNS->type_TACN )) ------------------ | Branch (10262:9): [True: 541, False: 16.5k] ------------------ 10263| 10.8k| { 10264| 10.8k| return 0; /* add/remove H(+) is allowed for acidic atoms */ 10265| 10.8k| } 10266| 16.5k| if (!pBNS->type_T || !pBNS->type_CN) ------------------ | Branch (10266:9): [True: 0, False: 16.5k] | Branch (10266:26): [True: 0, False: 16.5k] ------------------ 10267| 0| { 10268| 0| return 0; /* should not happen */ 10269| 0| } 10270| 16.5k| if (( u_is_taut = ( pBNS->vert[u / 2 - 1].type & pBNS->type_T ) == pBNS->type_T ) || ------------------ | Branch (10270:9): [True: 470, False: 16.0k] ------------------ 10271| 16.0k| ( ( pBNS->vert[u / 2 - 1].type & pBNS->type_CN ) == pBNS->type_CN )) ------------------ | Branch (10271:9): [True: 1.26k, False: 14.7k] ------------------ 10272| 1.73k| { 10273| | /* u is either t-group vertex or (-) c-group */ 10274| 1.73k| degree = GetVertexDegree( pBNS, v ); 10275| 11.1k| for (i = 0; i < degree; i++) ------------------ | Branch (10275:21): [True: 9.37k, False: 1.73k] ------------------ 10276| 9.37k| { 10277| | /* v = vert[u].neighbor[i]; */ 10278| 9.37k| w = GetVertexNeighbor( pBNS, v, i, &ivw ); 10279| 9.37k| if (w == NO_VERTEX || w <= 1) ------------------ | | 118| 18.7k|#define NO_VERTEX -2 ------------------ | Branch (10279:17): [True: 208, False: 9.16k] | Branch (10279:35): [True: 1.73k, False: 7.43k] ------------------ 10280| 1.94k| { 10281| 1.94k| continue; /* the atom has only single bonds or it is s or t, ignore it */ 10282| 1.94k| } 10283| 7.43k| if (w != u && ( ret = rescap( pBNS, v, w, ivw ) ) > 0) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (10283:17): [True: 5.69k, False: 1.73k] | Branch (10283:27): [True: 2.88k, False: 2.81k] ------------------ 10284| 2.88k| { 10285| 2.88k| num_allowed++; 10286| 2.88k| if (( u_is_taut ? ( ( pBNS->vert[w / 2 - 1].type & pBNS->type_CN ) == pBNS->type_CN ) : ------------------ | Branch (10286:21): [True: 1.52k, False: 1.35k] | Branch (10286:23): [True: 1.04k, False: 1.83k] ------------------ 10287| 2.88k| ( ( pBNS->vert[w / 2 - 1].type & pBNS->type_T ) == pBNS->type_T ) )) 10288| 1.52k| { 10289| 1.52k| num_found_groups++; 10290| 1.52k| } 10291| 2.88k| } 10292| 7.43k| } 10293| 1.73k| if (num_found_groups && num_allowed == 1) ------------------ | Branch (10293:13): [True: 1.52k, False: 213] | Branch (10293:33): [True: 777, False: 745] ------------------ 10294| 777| { 10295| 777| return 1; /* reject */ 10296| 777| } 10297| 1.73k| } 10298| | 10299| 15.7k| return 0; 10300| 16.5k|} bIgnoreVertexNonTACN_group: 10388| 26.9k|{ 10389| 26.9k| int u_is_taut = 0, w_is_taut = 0; 10390| 26.9k| Vertex u; 10391| 26.9k| EdgeIndex iuv; 10392| 26.9k| if (v <= 1 || w <= 1) ------------------ | Branch (10392:9): [True: 5.17k, False: 21.7k] | Branch (10392:19): [True: 5.13k, False: 16.6k] ------------------ 10393| 10.3k| return 0; 10394| 16.6k|#if ( CHECK_TACN == 1 ) 10395| 16.6k| if (!pBNS->type_TACN || ------------------ | Branch (10395:9): [True: 0, False: 16.6k] ------------------ 10396| 16.6k| ( pBNS->vert[v / 2 - 1].type & pBNS->type_TACN )) ------------------ | Branch (10396:9): [True: 683, False: 15.9k] ------------------ 10397| 683| { 10398| 683| return 0; 10399| 683| } 10400| 15.9k| if (!pBNS->type_T || !pBNS->type_CN) ------------------ | Branch (10400:9): [True: 0, False: 15.9k] | Branch (10400:26): [True: 0, False: 15.9k] ------------------ 10401| 0| { 10402| 0| return 0; /* should not happen */ 10403| 0| } 10404| 15.9k|#endif 10405| 15.9k| u = GetPrevVertex( pBNS, v, SwitchEdge, &iuv ); 10406| | /* 10407| | u = SwitchEdge_Vert1(v); 10408| | iuv = SwitchEdge_IEdge(v); 10409| | */ 10410| 15.9k| if (u == NO_VERTEX || iuv < 0) ------------------ | | 118| 31.9k|#define NO_VERTEX -2 ------------------ | Branch (10410:9): [True: 0, False: 15.9k] | Branch (10410:27): [True: 3.94k, False: 12.0k] ------------------ 10411| 3.94k| { 10412| 3.94k| return 0; /* should not happen */ 10413| 3.94k| } 10414| | /* check edge adjacency */ 10415| 12.0k| if ((pBNS->edge[iuv].neighbor1 != ( u / 2 - 1 ) && pBNS->edge[iuv].neighbor1 != v / 2 - 1) || ------------------ | Branch (10415:10): [True: 7.99k, False: 4.00k] | Branch (10415:56): [True: 0, False: 7.99k] ------------------ 10416| 12.0k| (( pBNS->edge[iuv].neighbor12 ^ ( u / 2 - 1 ) ) != ( v / 2 - 1 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (10416:9): [True: 0, False: 12.0k] ------------------ 10417| 0| { 10418| 0| return 0; /* !!! should not happen !!! */ 10419| 0| } 10420| | 10421| 12.0k|#if ( CHECK_TACN == 1 ) 10422| 12.0k| if (( ( u_is_taut = ( pBNS->vert[u / 2 - 1].type & pBNS->type_T ) == pBNS->type_T ) || ------------------ | Branch (10422:11): [True: 832, False: 11.1k] ------------------ 10423| 11.1k| ( ( pBNS->vert[u / 2 - 1].type & pBNS->type_CN ) == pBNS->type_CN ) ) && ------------------ | Branch (10423:9): [True: 818, False: 10.3k] ------------------ 10424| 1.65k| ( ( w_is_taut = ( pBNS->vert[w / 2 - 1].type & pBNS->type_T ) == pBNS->type_T ) || ------------------ | Branch (10424:13): [True: 352, False: 1.29k] ------------------ 10425| 1.29k| ( ( pBNS->vert[w / 2 - 1].type & pBNS->type_CN ) == pBNS->type_CN ) ) && ------------------ | Branch (10425:10): [True: 239, False: 1.05k] ------------------ 10426| 591| u_is_taut + w_is_taut == 1) ------------------ | Branch (10426:10): [True: 589, False: 2] ------------------ 10427| 589| { 10428| | /* rescap must have already been checked */ 10429| 589| return 1; 10430| 589| } 10431| 11.4k|#endif 10432| | 10433| 11.4k| return 0; 10434| 12.0k|} rescap: 10610| 17.7M|{ 10611| 17.7M| BNS_ST_EDGE *pst_edge; 10612| 17.7M| BNS_EDGE *pedge; 10613| | 10614| 17.7M| int f; 10615| 17.7M| S_CHAR s_or_t; 10616| 17.7M| int bBackward = GetEdgePointer( pBNS, u, v, iuv, &pedge, &s_or_t ); 10617| | 10618| 17.7M| if (!IS_BNS_ERROR( bBackward )) ------------------ | | 67| 17.7M|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 17.7M|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 17.7M|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 17.7M|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 17.7M, False: 0] | | | Branch (67:44): [True: 0, False: 17.7M] | | ------------------ ------------------ 10619| 17.7M| { 10620| | 10621| 17.7M| if (s_or_t) ------------------ | Branch (10621:13): [True: 10.4M, False: 7.27M] ------------------ 10622| 10.4M| { 10623| 10.4M| pst_edge = (BNS_ST_EDGE *) pedge; 10624| 10.4M| f = ( pst_edge->flow & EDGE_FLOW_ST_MASK ); ------------------ | | 128| 10.4M|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 10625| 10.4M| if (!bBackward) ------------------ | Branch (10625:17): [True: 9.02M, False: 1.44M] ------------------ 10626| 9.02M| { 10627| 9.02M| f = (int) pst_edge->cap - f; 10628| 9.02M| } 10629| 10.4M| } 10630| 7.27M| else 10631| 7.27M| { 10632| 7.27M| f = ( pedge->flow & EDGE_FLOW_MASK ); ------------------ | | 133| 7.27M|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 10633| 7.27M| if (!bBackward) ------------------ | Branch (10633:17): [True: 3.86M, False: 3.41M] ------------------ 10634| 3.86M| { 10635| 3.86M| f = (int) pedge->cap - f; 10636| 3.86M| } 10637| 7.27M| } 10638| 17.7M| return f; 10639| 17.7M| } 10640| | 10641| 0| return bBackward; /* error */ 10642| 17.7M|} BalancedNetworkSearch: 10746| 742k|{ 10747| 742k| Vertex *BasePtr = pBD->BasePtr; 10748| 742k| Edge *SwitchEdge = pBD->SwitchEdge; 10749| 742k| S_CHAR *Tree = pBD->Tree; 10750| 742k| Vertex *ScanQ = pBD->ScanQ; 10751| 742k| int QSize = pBD->QSize; 10752| 742k| Vertex *Pu = pBD->Pu; 10753| 742k| Vertex *Pv = pBD->Pv; 10754| 742k| int max_len_Pu_Pv = pBD->max_len_Pu_Pv; 10755| | 10756| | /* added to translate into C */ 10757| 742k| int i, k, degree, delta, ret = 0; 10758| 742k| Vertex u, b_u, v, b_v, w; 10759| 742k| EdgeIndex iuv; 10760| 742k|#if ( BNS_RAD_SEARCH == 1 ) 10761| 742k| int n, bRadSearch = ( BNS_EF_RAD_SRCH & bChangeFlow ) && pBD->RadEndpoints; ------------------ | | 384| 742k|#define BNS_EF_RAD_SRCH 128 /* search for rafical paths closures */ ------------------ | Branch (10761:38): [True: 11.0k, False: 731k] | Branch (10761:75): [True: 11.0k, False: 0] ------------------ 10762| 742k| BRS_MODE bRadSrchMode = RAD_SRCH_NORM; 10763| 742k| int bRadSearchPrelim = 0; 10764| 742k| if (bRadSearch) ------------------ | Branch (10764:9): [True: 11.0k, False: 731k] ------------------ 10765| 11.0k| { 10766| 11.0k| pBD->nNumRadEndpoints = 0; 10767| 11.0k| bRadSrchMode = pBD->bRadSrchMode; 10768| 11.0k| bRadSearchPrelim = pBNS->type_TACN && bRadSrchMode == RAD_SRCH_NORM; ------------------ | Branch (10768:28): [True: 2.22k, False: 8.86k] | Branch (10768:47): [True: 2.22k, False: 0] ------------------ 10769| 11.0k| } 10770| 742k|#endif 10771| | 10772| | /* -- Always -- 10773| | Vertex_s = FIRST_INDX; 10774| | Vertex_t = Vertex_s+1; 10775| | */ 10776| 742k| QSize = k = 0; /* put s on ScanQ = set S */ 10777| 742k| ScanQ[QSize] = Vertex_s; ------------------ | | 115| 742k|#define Vertex_s 0 ------------------ 10778| 742k| BasePtr[Vertex_t] = Vertex_s; ------------------ | | 116| 742k|#define Vertex_t 1 ------------------ BasePtr[Vertex_t] = Vertex_s; ------------------ | | 115| 742k|#define Vertex_s 0 ------------------ 10779| 742k| BasePtr[Vertex_s] = BLOSSOM_BASE; /* create initial blossom C(Vertex_s) with base s */ ------------------ | | 115| 742k|#define Vertex_s 0 ------------------ BasePtr[Vertex_s] = BLOSSOM_BASE; /* create initial blossom C(Vertex_s) with base s */ ------------------ | | 119| 742k|#define BLOSSOM_BASE -1 ------------------ 10780| 742k| Tree[Vertex_s] = TREE_IN_1; ------------------ | | 115| 742k|#define Vertex_s 0 ------------------ Tree[Vertex_s] = TREE_IN_1; ------------------ | | 240| 742k|#define TREE_IN_1 3 /* in T and is s-reachable */ ------------------ 10781| | 10782| 742k| do 10783| 4.63M| { 10784| 4.63M| u = ScanQ[k]; /* select u from the head of ScanQ */ 10785| | /* since u is on the queue, it has a blossom C(U) with base b_u */ 10786| 4.63M| b_u = FindBase( u, BasePtr ); 10787| 4.63M| degree = GetVertexDegree( pBNS, u ); 10788| 4.63M|#if ( BNS_RAD_SEARCH == 1 ) 10789| 4.63M| n = 0; 10790| 4.63M|#endif 10791| 28.1M| for (i = 0; i < degree; i++) ------------------ | Branch (10791:21): [True: 23.6M, False: 4.49M] ------------------ 10792| 23.6M| { 10793| | /* v = vert[u].neighbor[i]; */ 10794| 23.6M| v = GetVertexNeighbor( pBNS, u, i, &iuv ); 10795| 23.6M| if (v == NO_VERTEX) ------------------ | | 118| 23.6M|#define NO_VERTEX -2 ------------------ | Branch (10795:17): [True: 2.92M, False: 20.6M] ------------------ 10796| 2.92M| { 10797| 2.92M| continue; /* the atom has only single bonds, ignore it */ 10798| 2.92M| } 10799| 20.6M|#if ( BNS_RAD_SEARCH == 1 ) 10800| 20.6M| if (!k && bRadSrchMode == RAD_SRCH_FROM_FICT && v / 2 <= pBNS->num_atoms) ------------------ | Branch (10800:17): [True: 7.02M, False: 13.6M] | Branch (10800:23): [True: 43.9k, False: 6.97M] | Branch (10800:61): [True: 10.8k, False: 33.1k] ------------------ 10801| 10.8k| { 10802| 10.8k| continue; /* start from fict. vertices only */ 10803| 10.8k| } 10804| 20.6M| if (bRadSearchPrelim && v / 2 > pBNS->num_atoms) ------------------ | Branch (10804:17): [True: 30.6k, False: 20.6M] | Branch (10804:37): [True: 7.19k, False: 23.4k] ------------------ 10805| 7.19k| { 10806| 7.19k| continue; /* during initial add/remove H allow radical movement only through real atoms */ 10807| 7.19k| } 10808| 20.6M|#endif 10809| 20.6M| if ( /* PrevPt[u] != v ** avoid edges of T */ 10810| 20.6M| ( SwitchEdge_Vert1( u ) != v || SwitchEdge_Vert2( u ) != u ) /* avoid edges of T */ ------------------ | | 395| 20.6M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ ( SwitchEdge_Vert1( u ) != v || SwitchEdge_Vert2( u ) != u ) /* avoid edges of T */ ------------------ | | 396| 3.40M|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ | Branch (10810:19): [True: 17.2M, False: 3.40M] | Branch (10810:49): [True: 1.56k, False: 3.40M] ------------------ 10811| 17.2M| && ( ret = rescap( pBNS, u, v, iuv ) ) > 0) ------------------ | Branch (10811:21): [True: 7.32M, False: 9.93M] ------------------ 10812| 7.32M| { 10813| | /* Special treatment to prevent H<->(-) replacement on non-acidic atoms */ 10814| | /*----------------------------------------------------------------------*/ 10815| 7.32M| if (pBNS->type_TACN) ------------------ | Branch (10815:21): [True: 27.3k, False: 7.29M] ------------------ 10816| 27.3k| { 10817| 27.3k| if (bIgnoreVertexNonTACN_atom( pBNS, u, v )) ------------------ | Branch (10817:25): [True: 777, False: 26.5k] ------------------ 10818| 777| { 10819| 777| continue; 10820| 777| } 10821| 26.5k| if (bIgnoreVertexNonTACN_group( pBNS, u, v, SwitchEdge )) ------------------ | Branch (10821:25): [True: 531, False: 26.0k] ------------------ 10822| 531| { 10823| 531| continue; 10824| 531| } 10825| |#if ( FIX_KEEP_H_ON_NH_ANION == 1 ) 10826| | if (bIsRemovedHfromNHaion( pBNS, u, v )) 10827| | { 10828| | continue; 10829| | } 10830| |#endif 10831| |#if ( FIX_AVOID_ADP == 1 ) 10832| | if (bIsAggressiveDeprotonation( pBNS, u, v, SwitchEdge )) 10833| | { 10834| | continue; 10835| | } 10836| |#endif 10837| 26.5k| } 10838| | /*----------------------------------------------------------------------*/ 10839| 7.32M| b_v = FindBase( v, BasePtr ); /* Notation: b_x is a base of x */ 10840| | 10841| 7.32M| if (b_v == NO_VERTEX) ------------------ | | 118| 7.32M|#define NO_VERTEX -2 ------------------ | Branch (10841:21): [True: 3.48M, False: 3.83M] ------------------ 10842| 3.48M| { 10843| | /* Originally 0 instead of NO_VERTEX */ 10844| | 10845| | /* Important note: following "A. Note of Implementing the Algorithm" from the 10846| | article by Kocay and Stone, all references to PrevPt[a] have been 10847| | replaced with SwitchEdge[a][0]=SwitchEdge_Vert1(a); to be on a safe side 10848| | the check whether (SwitchEdge_Vert2(a)==a) has been added. 10849| | */ 10850| | 10851| | /* v is not yet in T or T' -- add it to T and M */ 10852| | /*PrevPt[v] = u; ** this effectively adds v to T and v' to T' */ 10853| | 10854| 3.48M| QSize++; 10855| 3.48M| ScanQ[QSize] = v; 10856| 3.48M| TREE_MARK( v, TREE_IN_1 ); /* mark v s-reachable (in T) */ ------------------ | | 245| 3.48M|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (245:46): [True: 3.48M, False: 0] | | | Branch (245:84): [Folded, False: 3.48M] | | ------------------ ------------------ 10857| 3.48M| TREE_MARK( prim( v ), TREE_IN_2 ); /* mark v' in T' */ ------------------ | | 245| 3.48M|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (245:46): [True: 3.48M, False: 0] | | | Branch (245:84): [Folded, False: 3.48M] | | ------------------ ------------------ 10858| | 10859| | /* Switch Edges: If u in T then Pu (a valid su-path) can be constructed 10860| | by successfully executing u=PrevPt[u] until u=s. 10861| | For vertices in T' the situation is different. 10862| | Suppose uv and v'u' are added to a mirror network M creating a blossom: 10863| | 10864| | s T (Note: in the code v' is prim(v), 10865| | T / \ u' is prim(u), etc.) 10866| | / ... 10867| | w=x1 10868| | / \ u in T, v in T' 10869| | u=y2 v'=y3 10870| | \ / <--- two added edges uv and (uv)'=v'u' 10871| | -------- X ------------intersection of the edges ------------------------ 10872| | / \ <--- (the edges intersection in the picture is shown as X) 10873| | u'=x2 v=x3 u' it T', v' in T 10874| | \ / 10875| | T' w'=y1 10876| | \ ... 10877| | \ / 10878| | t T' 10879| | 10880| | Vertices v and u' now become s-reachable; 10881| | The valid paths to v and u' must use the edges uv and v'u' respectively. 10882| | 10883| | For each vertex z in S we define a switch-edge that allows a valid sz-path 10884| | to be constructed, SwitchEdge[v]=uv and SwitchEdge[u']=v'u'. (We don't 10885| | know the direction of the edge uv, it may be (u,v) or (v,u). In either case, 10886| | the complementary edge is indicated by v'u'). 10887| | 10888| | Vertex w' also becomes s-reachable when uv is added to M, and a valid sw'-path 10889| | must use one of uv and v'u'. Therefore we choose one of them, say uv (see below 10890| | the rule of choosing the switch-edge), and define SwitchEdge[w'] = uv. 10891| | 10892| | When the addition of an edge uv to M causes a vertex z to become s-reachable 10893| | (where z was previously non-reachable), z is placed on the ScanQ, that is, into S. 10894| | The edge uv is said to be a switch-edge for z. 10895| | 10896| | Rule: We choose the the order of the vertices uv to be such that the valid sz-path 10897| | consists of a valid su-path, followed by edge uv, followed by a valid vz-path. 10898| | 10899| | For vertices z in T we can take SwitchEdge[z]=yz where y=PrevPt[z] since 10900| | it is the edge yz that allows z to be s-reachable. 10901| | For vertices z not in S we take SwitchEdge[z]=NONE. 10902| | 10903| | */ 10904| | 10905| | /* v is not yet in T or T' -- add it to T and M */ 10906| 3.48M| SwitchEdge_Vert1( v ) = u; /* this effectively adds uv and v'u' to M */ ------------------ | | 395| 3.48M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 10907| 3.48M| SwitchEdge_IEdge( v ) = iuv; ------------------ | | 397| 3.48M|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 10908| | 10909| 3.48M| BasePtr[prim( v )] = v; ------------------ | | 392| 3.48M|#define prim(v) (Vertex)((v)^1) ------------------ 10910| 3.48M| BasePtr[v] = BLOSSOM_BASE; /* create a trivial blossom C(v) with base v */ ------------------ | | 119| 3.48M|#define BLOSSOM_BASE -1 ------------------ 10911| 3.48M|#if ( BNS_RAD_SEARCH == 1 ) 10912| 3.48M| n++; 10913| 3.48M|#endif 10914| 3.48M| } 10915| | 10916| 3.83M| else if (TREE_IS_S_REACHABLE( prim( v ) ) /*Is_s_Reachable(prim(v)*/ ------------------ | | 242| 7.67M|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | ------------------ | | | | 239| 3.83M|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | ------------------ | | | Branch (242:32): [True: 1.74M, False: 2.08M] | | ------------------ ------------------ 10917| 1.74M| /* if v' is reachable, an st-path is given by P(u)-uv-P'(v') */ 10918| 1.74M| /*&& PrevPt[prim(u)] != prim(v) ** avoid edges of T' */ 10919| 1.74M| && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 395| 1.74M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 392| 3.49M|#define prim(v) (Vertex)((v)^1) ------------------ && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 396| 868k|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 392| 868k|#define prim(v) (Vertex)((v)^1) ------------------ | Branch (10919:32): [True: 879k, False: 868k] | Branch (10919:78): [True: 0, False: 868k] ------------------ 10920| 879k| && b_u != b_v ------------------ | Branch (10920:30): [True: 484k, False: 394k] ------------------ 10921| 484k| && !( pBNS->type_TACN && bIgnoreVertexNonTACN_group( pBNS, prim( v ), u, SwitchEdge ) ) ------------------ | | 392| 363|#define prim(v) (Vertex)((v)^1) ------------------ | Branch (10921:33): [True: 363, False: 484k] | Branch (10921:52): [True: 58, False: 305] ------------------ 10922| |#if ( FIX_KEEP_H_ON_NH_ANION == 1 ) 10923| | && !( pBNS->type_TACN && bIsRemovedHfromNHaion( pBNS, prim( v ), u ) ) 10924| |#endif 10925| 3.83M| ) 10926| 484k| { 10927| 484k|#if ( BNS_RAD_SEARCH == 1 ) 10928| 484k| n++; 10929| 484k|#endif 10930| | /* There is now a valid sv-path via u avoiding b_v (unless v==b_v) 10931| | => u, v, u', and v' now all become part of the same connected component of M[C] */ 10932| | 10933| | /* djb-rwth: addressing coverity ID #499578 -- negative values of b_u handled properly */ 10934| 484k| w = MakeBlossom( pBNS, ScanQ, &QSize, Pu, Pv, max_len_Pu_Pv, SwitchEdge, BasePtr, u, v, iuv, b_u, b_v, Tree ); 10935| | /* this constructed the new blossom and returned its base */ 10936| | 10937| 484k| if (IS_BNS_ERROR( w )) ------------------ | | 67| 484k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 484k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 484k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 484k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 484k, False: 0] | | | Branch (67:44): [True: 0, False: 484k] | | ------------------ ------------------ 10938| 0| { 10939| 0| pBD->QSize = QSize; 10940| 0| return w; /* error */ 10941| 0| } 10942| | 10943| 484k| b_u = w; /* the new base of C(u) */ 10944| 484k| if (prim( w ) == Vertex_t) ------------------ | | 392| 484k|#define prim(v) (Vertex)((v)^1) ------------------ if (prim( w ) == Vertex_t) ------------------ | | 116| 484k|#define Vertex_t 1 ------------------ | Branch (10944:25): [True: 142k, False: 342k] ------------------ 10945| 142k| { 10946| | /* t is now s-reachable, a valid augmenting path P exists in M */ 10947| 142k| delta = FindPathCap( pBNS, SwitchEdge, Vertex_s, Vertex_t, 10000 ); /* compute the residual capacity of P + P' */ ------------------ | | 115| 142k|#define Vertex_s 0 ------------------ delta = FindPathCap( pBNS, SwitchEdge, Vertex_s, Vertex_t, 10000 ); /* compute the residual capacity of P + P' */ ------------------ | | 116| 142k|#define Vertex_t 1 ------------------ 10948| 142k| if (IS_BNS_ERROR( delta )) ------------------ | | 67| 142k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 142k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 142k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 142k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 142k, False: 0] | | | Branch (67:44): [True: 0, False: 142k] | | ------------------ ------------------ 10949| 0| { 10950| 0| pBD->QSize = QSize; 10951| 0| return delta; /* error */ 10952| 0| } 10953| |#if ( ALLOW_ONLY_SIMPLE_ALT_PATH == 1 ) 10954| | if (pBNS->bNotASimplePath || abs( delta ) > 1) 10955| | { 10956| | delta = 0; 10957| | } 10958| |#endif 10959| 142k| if (delta) ------------------ | Branch (10959:29): [True: 142k, False: 0] ------------------ 10960| 142k| { 10961| 142k| pBNS->bChangeFlow |= ( bChangeFlow & BNS_EF_CHNG_FLOW ); ------------------ | | 370| 142k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ 10962| 142k| } 10963| 142k| ret = PullFlow( pBNS, SwitchEdge, Vertex_s, Vertex_t, delta, 0, bChangeFlow ); /* augment on a pair of valid st-paths */ ------------------ | | 115| 142k|#define Vertex_s 0 ------------------ ret = PullFlow( pBNS, SwitchEdge, Vertex_s, Vertex_t, delta, 0, bChangeFlow ); /* augment on a pair of valid st-paths */ ------------------ | | 116| 142k|#define Vertex_t 1 ------------------ 10964| 142k| pBD->QSize = QSize; 10965| 142k| return 10966| 142k| ( IS_BNS_ERROR( ret ) ? ret : delta ); ------------------ | | 67| 142k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 142k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 142k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 142k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 142k, False: 0] | | | Branch (67:44): [True: 2, False: 142k] | | ------------------ ------------------ 10967| 142k| } 10968| 484k| } 10969| 7.32M| } 10970| | 10971| 13.3M| else if (IS_BNS_ERROR( ret )) ------------------ | | 67| 13.3M|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 13.3M|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 13.3M|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 13.3M|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 13.3M, False: 59] | | | Branch (67:44): [True: 0, False: 13.3M] | | ------------------ ------------------ 10972| 0| { 10973| 0| pBD->QSize = QSize; 10974| 0| return ret; /* error */ 10975| 0| } 10976| 20.6M| } 10977| | 10978| 4.49M|#if ( BNS_RAD_SEARCH == 1 ) 10979| 4.49M| if (bRadSearch && !n) ------------------ | Branch (10979:13): [True: 69.3k, False: 4.42M] | Branch (10979:27): [True: 25.7k, False: 43.5k] ------------------ 10980| 25.7k| { 10981| | /* The BNS stopped at u */ 10982| 25.7k| n = RegisterRadEndpoint( pBNS, pBD, u ); 10983| 25.7k| if (IS_BNS_ERROR( n )) ------------------ | | 67| 25.7k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 25.7k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 25.7k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 25.7k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 25.7k, False: 0] | | | Branch (67:44): [True: 0, False: 25.7k] | | ------------------ ------------------ 10984| 0| { 10985| 0| pBD->QSize = QSize; 10986| 0| return n; 10987| 0| } 10988| 25.7k| } 10989| 4.49M|#endif 10990| | 10991| 4.49M| k++; /* advance ScanQ */ 10992| 4.49M| } while (k <= QSize); ------------------ | Branch (10992:14): [True: 3.89M, False: 600k] ------------------ 10993| | 10994| | 10995| | /* if this point is reached, no valid augmenting path exists, ScanQ contains 10996| | the set S of all s-reachable vertices and K=[S,S-] is a minimum balanced edge-cut */ 10997| | /* ClearFlowMarks( vert, num_vert); */ 10998| | 10999| 600k| pBD->QSize = QSize; 11000| | 11001| 600k| return 0; 11002| 742k|} FindBase: 11034| 17.9M|{ 11035| 17.9M| if (BasePtr[u] == NO_VERTEX) ------------------ | | 118| 17.9M|#define NO_VERTEX -2 ------------------ | Branch (11035:9): [True: 3.48M, False: 14.4M] ------------------ 11036| 3.48M| { 11037| 3.48M| return NO_VERTEX; ------------------ | | 118| 3.48M|#define NO_VERTEX -2 ------------------ 11038| 3.48M| } 11039| 14.4M| else if (BasePtr[u] == BLOSSOM_BASE) ------------------ | | 119| 14.4M|#define BLOSSOM_BASE -1 ------------------ | Branch (11039:14): [True: 11.4M, False: 2.99M] ------------------ 11040| 11.4M| { 11041| 11.4M| return u; 11042| 11.4M| } 11043| 2.99M| else 11044| 2.99M| { 11045| 2.99M| Vertex b; 11046| 2.99M| b = FindBase( BasePtr[u], BasePtr ); 11047| 2.99M| BasePtr[u] = b; /* path compression */ 11048| 2.99M| return b; 11049| 2.99M| } 11050| | 11051| 17.9M|} FindPathToVertex_s: 11062| 969k|{ 11063| | /* x is the base of a blossom, construct a valid Path of blossom bases to s */ 11064| 969k| int i = 0; 11065| 969k| Path[i] = x; 11066| 3.99M| while (x != Vertex_s) ------------------ | | 115| 3.99M|#define Vertex_s 0 ------------------ | Branch (11066:12): [True: 3.02M, False: 969k] ------------------ 11067| 3.02M| { 11068| 3.02M| x = FindBase( SwitchEdge_Vert1( x ), BasePtr ); ------------------ | | 395| 3.02M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11069| 3.02M| if (++i < MaxPathLen) ------------------ | Branch (11069:13): [True: 3.02M, False: 0] ------------------ 11070| 3.02M| { 11071| 3.02M| Path[i] = x; 11072| 3.02M| } 11073| 0| else 11074| 0| { 11075| 0| return BNS_WRONG_PARMS; ------------------ | | 48| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 11076| 0| } 11077| 3.02M| } 11078| | 11079| 969k| return i; 11080| 969k|} MakeBlossom: 11101| 484k|{ 11102| | /* In order to find the base of the new blossom, the paths 11103| | P(u) and P(v') are constructed and compared in order to 11104| | find the last blossom base they have in common which 11105| | is reachable on a valid path. 11106| | 11107| | Edge uv connects two blossoms, their bases are b_u and b_v. 11108| | */ 11109| 484k| Vertex w, z; 11110| 484k| int len_Pu, len_Pv; 11111| 484k| int i, j, k; 11112| 484k| EdgeIndex izw; 11113| | 11114| 484k| len_Pu = FindPathToVertex_s( b_u, SwitchEdge, BasePtr, Pu, max_len_Pu_Pv ); 11115| 484k| if (IS_BNS_ERROR( len_Pu )) ------------------ | | 67| 484k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 484k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 484k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 484k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 484k, False: 0] | | | Branch (67:44): [True: 0, False: 484k] | | ------------------ ------------------ 11116| 0| { 11117| 0| return len_Pu; 11118| 0| } 11119| 484k| len_Pv = FindPathToVertex_s( b_v, SwitchEdge, BasePtr, Pv, max_len_Pu_Pv ); 11120| 484k| if (IS_BNS_ERROR( len_Pv )) ------------------ | | 67| 484k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 484k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 484k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 484k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 484k, False: 0] | | | Branch (67:44): [True: 0, False: 484k] | | ------------------ ------------------ 11121| 0| { 11122| 0| return len_Pv; 11123| 0| } 11124| 484k| i = len_Pu; 11125| 484k| j = len_Pv; 11126| | /* Initially Pu[i] and Pv[j] both equal to s, but their first elements are different */ 11127| | /* Find the last blossom base common to Pu and Pv */ 11128| 1.75M| while (i >= 0 && j >= 0 && Pu[i] == Pv[j]) ------------------ | Branch (11128:12): [True: 1.57M, False: 173k] | Branch (11128:22): [True: 1.56M, False: 17.1k] | Branch (11128:32): [True: 1.26M, False: 293k] ------------------ 11129| 1.26M| { 11130| | /* Was (Pu[i]==Pv[j] && i>=0 && j>=0) => tested Pu[-1], Pv[-1] <- pointed by W.Ihlenfeldt 08-26-2004*/ 11131| 1.26M| i--; 11132| 1.26M| j--; 11133| 1.26M| } 11134| 484k| i++; 11135| 484k| w = Pu[i]; /* w is the last common vertex */ 11136| 484k| z = SwitchEdge_Vert1( w ); ------------------ | | 395| 484k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11137| 484k| izw = SwitchEdge_IEdge( w ); ------------------ | | 397| 484k|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11138| | /* now extend the blossom if rescap(zw) >= 2 */ 11139| 619k| while (w != Vertex_s && rescap( pBNS, z, w, izw ) >= 2) ------------------ | | 115| 1.23M|#define Vertex_s 0 ------------------ | Branch (11139:12): [True: 477k, False: 142k] | Branch (11139:29): [True: 134k, False: 342k] ------------------ 11140| 134k| { 11141| 134k| i++; 11142| 134k| w = Pu[i]; 11143| 134k| z = SwitchEdge_Vert1( w ); ------------------ | | 395| 134k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11144| 134k| izw = SwitchEdge_IEdge( w ); ------------------ | | 397| 134k|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11145| 134k| } 11146| | /* w is the base of the new blossom */ 11147| | /* first follow the path Pu from w to b_u */ 11148| 1.24M| for (k = i - 1; k >= 0; k--) ------------------ | Branch (11148:21): [True: 759k, False: 484k] ------------------ 11149| 759k| { 11150| 759k| z = Pu[k]; /* z is the base of the blossom */ 11151| 759k| BasePtr[z] = w; 11152| 759k| BasePtr[prim( z )] = w; /* w is the new base of the blossom */ ------------------ | | 392| 759k|#define prim(v) (Vertex)((v)^1) ------------------ 11153| | /* z and z' may already be part of a blossom that is being 11154| | swallowed into a larger blossom. 11155| | We don't want to change the switch edge in that case. 11156| | */ 11157| | 11158| 759k| if (!TREE_IS_ON_SCANQ( prim( z ) ) /*!IsInScanQ(prim(z)) */) ------------------ | | 243| 759k|#define TREE_IS_ON_SCANQ TREE_IS_S_REACHABLE | | ------------------ | | | | 242| 759k|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | | | ------------------ | | | | | | 239| 759k|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | | | ------------------ | | ------------------ ------------------ | Branch (11158:13): [True: 714k, False: 45.2k] ------------------ 11159| 714k| { 11160| 714k| SwitchEdge_Vert1( prim( z ) ) = prim( v ); /* set the switch edge of z' */ ------------------ | | 395| 714k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ SwitchEdge_Vert1( prim( z ) ) = prim( v ); /* set the switch edge of z' */ ------------------ | | 392| 714k|#define prim(v) (Vertex)((v)^1) ------------------ 11161| | /* SwitchEdge[prim(z)][1] = prim(u); */ 11162| 714k| SwitchEdge_IEdge( prim( z ) ) = iuv; ------------------ | | 397| 714k|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11163| 714k| ( *pQSize )++; 11164| 714k| ScanQ[*pQSize] = prim( z ); /* add z' to ScanQ */ ------------------ | | 392| 714k|#define prim(v) (Vertex)((v)^1) ------------------ 11165| 714k| TREE_MARK( prim( z ), TREE_IN_2BLOSS ); /* mark z' s-reachable */ ------------------ | | 245| 714k|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (245:46): [True: 714k, False: 0] | | | Branch (245:84): [Folded, False: 714k] | | ------------------ ------------------ 11166| 714k| } 11167| 759k| } 11168| | /* Now follow the path Pv */ 11169| 1.31M| for (k = j; k >= 0; k--) /* djb-rwth: converting for loop into while loop to avoid LLVM warning */ ------------------ | Branch (11169:17): [True: 832k, False: 484k] ------------------ 11170| 832k| { 11171| 832k| z = Pv[k]; /* z is the base of the blossom */ 11172| 832k| BasePtr[z] = w; 11173| 832k| BasePtr[prim( z )] = w; /* w is the new base of the blossom */ ------------------ | | 392| 832k|#define prim(v) (Vertex)((v)^1) ------------------ 11174| | /* z and z' may already be part of a blossom that is being 11175| | swallowed into a larger blossom. 11176| | We don't want to change the switch edge in that case. 11177| | */ 11178| | 11179| 832k| if (!TREE_IS_ON_SCANQ( prim( z ) ) /*!IsInScanQ(prim(z)) */) ------------------ | | 243| 832k|#define TREE_IS_ON_SCANQ TREE_IS_S_REACHABLE | | ------------------ | | | | 242| 832k|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | | | ------------------ | | | | | | 239| 832k|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | | | ------------------ | | ------------------ ------------------ | Branch (11179:13): [True: 808k, False: 23.6k] ------------------ 11180| 808k| { 11181| 808k| SwitchEdge_Vert1( prim( z ) ) = u; /* set the switch edge of z' */ ------------------ | | 395| 808k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11182| | /* SwitchEdge[prim(z)][1] = v; */ 11183| 808k| SwitchEdge_IEdge( prim( z ) ) = iuv; ------------------ | | 397| 808k|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11184| 808k| ( *pQSize )++; 11185| 808k| ScanQ[*pQSize] = prim( z ); /* add z' to ScanQ */ ------------------ | | 392| 808k|#define prim(v) (Vertex)((v)^1) ------------------ 11186| 808k| TREE_MARK( prim( z ), TREE_IN_2BLOSS ); /* mark z' s-reachable */ ------------------ | | 245| 808k|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (245:46): [True: 808k, False: 0] | | | Branch (245:84): [Folded, False: 808k] | | ------------------ ------------------ 11187| 808k| } 11188| 832k| } 11189| | 11190| 484k| if (!TREE_IS_ON_SCANQ( prim( w ) ) /* !IsInScanQ(prim(w))*/) ------------------ | | 243| 484k|#define TREE_IS_ON_SCANQ TREE_IS_S_REACHABLE | | ------------------ | | | | 242| 484k|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | | | ------------------ | | | | | | 239| 484k|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | | | ------------------ | | ------------------ ------------------ | Branch (11190:9): [True: 254k, False: 230k] ------------------ 11191| 254k| { /* add w' to the blossom */ 11192| 254k| SwitchEdge_Vert1( prim( w ) ) = u; /* set the switch edge of w' */ ------------------ | | 395| 254k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11193| | /* SwitchEdge[prim(w)][1] = v; */ 11194| 254k| SwitchEdge_IEdge( prim( w ) ) = iuv; ------------------ | | 397| 254k|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11195| 254k| ( *pQSize )++; 11196| 254k| ScanQ[*pQSize] = prim( w ); /* add w' to ScanQ */ ------------------ | | 392| 254k|#define prim(v) (Vertex)((v)^1) ------------------ 11197| 254k| TREE_MARK( prim( w ), TREE_IN_2BLOSS ); /* mark w' s-reachable */ ------------------ | | 245| 254k|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (245:46): [True: 254k, False: 0] | | | Branch (245:84): [Folded, False: 254k] | | ------------------ ------------------ 11198| 254k| } 11199| | 11200| 484k| return w; 11201| 484k|} PullFlow: 11262| 1.19M|{ 11263| 1.19M| Vertex w, z; 11264| 1.19M| EdgeIndex iwz; 11265| 1.19M| int ret = 0; 11266| | 11267| 1.19M| w = SwitchEdge_Vert1( y ); ------------------ | | 395| 1.19M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11268| 1.19M| z = SwitchEdge_Vert2( y ); ------------------ | | 396| 1.19M|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 11269| 1.19M| iwz = SwitchEdge_IEdge( y ); ------------------ | | 397| 1.19M|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11270| 1.19M| if (bReverse) ------------------ | Branch (11270:9): [True: 514k, False: 681k] ------------------ 11271| 514k| { 11272| | /* P consists of a path from x to w, then wz, then a path from z to y. */ 11273| | /* z may equal y, in which case z is just PrevPt[y] */ 11274| 514k| if (z != y) ------------------ | Branch (11274:13): [True: 10.1k, False: 504k] ------------------ 11275| 10.1k| { 11276| 10.1k| ret = PullFlow( pBNS, SwitchEdge, prim( y ), prim( z ), delta, (S_CHAR) ( 1 - bReverse ), bChangeFlow ); /* augment between z and y */ ------------------ | | 392| 10.1k|#define prim(v) (Vertex)((v)^1) ------------------ ret = PullFlow( pBNS, SwitchEdge, prim( y ), prim( z ), delta, (S_CHAR) ( 1 - bReverse ), bChangeFlow ); /* augment between z and y */ ------------------ | | 392| 10.1k|#define prim(v) (Vertex)((v)^1) ------------------ 11277| 10.1k| } 11278| 514k| if (!IS_BNS_ERROR( ret )) ------------------ | | 67| 514k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 514k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 514k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 514k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 514k, False: 0] | | | Branch (67:44): [True: 1, False: 514k] | | ------------------ ------------------ 11279| 514k| { 11280| 514k| ret = AugmentEdge( pBNS, w, z, iwz, delta, bReverse, bChangeFlow ); 11281| 514k| } 11282| | /* Do not augment the complementary path: AugmentEdge( prim(z), prim(w), vert, delta); */ 11283| | /* w may equal x, in which case there is no need to call PullFlow(x, w) */ 11284| 514k| if (w != x && !IS_BNS_ERROR( ret )) ------------------ | | 67| 340k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 340k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 340k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 340k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 340k, False: 0] | | | Branch (67:44): [True: 1, False: 340k] | | ------------------ ------------------ | Branch (11284:13): [True: 340k, False: 173k] ------------------ 11285| 340k| { 11286| 340k| ret = PullFlow( pBNS, SwitchEdge, x, w, delta, bReverse, bChangeFlow ); /* augment between x and w */ 11287| 340k| } 11288| 514k| } 11289| 681k| else 11290| 681k| { 11291| | /* P consists of a path from x to w, then wz, then a path from z to y. */ 11292| | /* w may equal x, in which case there is no need to call PullFlow(x, w) */ 11293| 681k| if (w != x && !IS_BNS_ERROR( ret )) ------------------ | | 67| 529k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 529k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 529k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 529k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 529k, False: 0] | | | Branch (67:44): [True: 0, False: 529k] | | ------------------ ------------------ | Branch (11293:13): [True: 529k, False: 152k] ------------------ 11294| 529k| { 11295| 529k| ret = PullFlow( pBNS, SwitchEdge, x, w, delta, bReverse, bChangeFlow ); /* augment between x and w */ 11296| 529k| } 11297| 681k| if (!IS_BNS_ERROR( ret )) ------------------ | | 67| 681k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 681k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 681k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 681k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 681k, False: 0] | | | Branch (67:44): [True: 1, False: 681k] | | ------------------ ------------------ 11298| 681k| { 11299| 681k| ret = AugmentEdge( pBNS, w, z, iwz, delta, bReverse, bChangeFlow ); 11300| 681k| } 11301| | /* z may equal y, in which case z is just PrevPt[y] */ 11302| 681k| if (z != y && !IS_BNS_ERROR( ret )) ------------------ | | 67| 173k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 173k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 173k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 173k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 173k, False: 0] | | | Branch (67:44): [True: 1, False: 173k] | | ------------------ ------------------ | Branch (11302:13): [True: 173k, False: 507k] ------------------ 11303| 173k| { 11304| 173k| ret = PullFlow( pBNS, SwitchEdge, prim( y ), prim( z ), delta, (S_CHAR) ( 1 - bReverse ), bChangeFlow ); /* augment between z and y */ ------------------ | | 392| 173k|#define prim(v) (Vertex)((v)^1) ------------------ ret = PullFlow( pBNS, SwitchEdge, prim( y ), prim( z ), delta, (S_CHAR) ( 1 - bReverse ), bChangeFlow ); /* augment between z and y */ ------------------ | | 392| 173k|#define prim(v) (Vertex)((v)^1) ------------------ 11305| 173k| } 11306| 681k| } 11307| | 11308| 1.19M| return ret; 11309| 1.19M|} FindPathCap: 11333| 1.19M|{ 11334| | 11335| 1.19M| Vertex w, z, iwz; 11336| 1.19M| int cap, delta2; 11337| | 11338| | /* static int level; 11339| | if ( level ++ > 50 ) 11340| | { 11341| | #ifdef _DEBUG 11342| | int stop = 1; 11343| | #else 11344| | ; 11345| | #endif 11346| | } 11347| | */ 11348| | 11349| 1.19M| w = SwitchEdge_Vert1( y ); ------------------ | | 395| 1.19M|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11350| 1.19M| z = SwitchEdge_Vert2( y ); /* wz is on the path P */ ------------------ | | 396| 1.19M|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 11351| 1.19M| iwz = SwitchEdge_IEdge( y ); /* edge index */ ------------------ | | 397| 1.19M|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11352| | 11353| | /* Rescap_mark() detects edges passed 2 times and reduces rescap */ 11354| 1.19M| cap = rescap_mark( pBNS, w, z, iwz ); 11355| | 11356| 1.19M| if (IS_BNS_ERROR( cap )) ------------------ | | 67| 1.19M|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.19M|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.19M|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.19M|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.19M, False: 0] | | | Branch (67:44): [True: 0, False: 1.19M] | | ------------------ ------------------ 11357| 0| { 11358| | /* level --; */ 11359| 0| return cap; 11360| 0| } 11361| 1.19M| if (cap < delta) ------------------ | Branch (11361:9): [True: 240k, False: 955k] ------------------ 11362| 240k| { 11363| 240k| delta = cap; 11364| 240k| } 11365| | /* P consists of a path from x to w, then wz, then a path from z to y */ 11366| 1.19M| if (w != x) ------------------ | Branch (11366:9): [True: 869k, False: 325k] ------------------ 11367| 869k| { 11368| 869k| delta2 = FindPathCap( pBNS, SwitchEdge, x, w, delta ); 11369| 869k| delta = inchi_min( delta2, delta ); ------------------ | | 139| 869k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 187k, False: 682k] | | ------------------ ------------------ 11370| 869k| } 11371| 1.19M| if (z != y) ------------------ | Branch (11371:9): [True: 183k, False: 1.01M] ------------------ 11372| 183k| { 11373| 183k| delta2 = FindPathCap( pBNS, SwitchEdge, prim( y ), prim( z ), delta ); ------------------ | | 392| 183k|#define prim(v) (Vertex)((v)^1) ------------------ delta2 = FindPathCap( pBNS, SwitchEdge, prim( y ), prim( z ), delta ); ------------------ | | 392| 183k|#define prim(v) (Vertex)((v)^1) ------------------ 11374| 183k| delta = inchi_min( delta2, delta ); ------------------ | | 139| 183k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 11.5k, False: 172k] | | ------------------ ------------------ 11375| 183k| } 11376| | /* level --; */ 11377| | 11378| 1.19M| return delta; 11379| 1.19M|} MarkRingSystemsAltBns: 11425| 288k|{ 11426| 288k| AT_NUMB *nStackAtom = NULL; 11427| 288k| int nTopStackAtom; 11428| 288k| AT_NUMB *nRingStack = NULL; 11429| 288k| int nTopRingStack; /* was AT_NUMB */ 11430| 288k| AT_NUMB *nBondStack = NULL; 11431| 288k| int nTopBondStack; 11432| 288k| AT_NUMB *nDfsNumber = NULL; 11433| 288k| AT_NUMB *nLowNumber = NULL; 11434| 288k| S_CHAR *cNeighNumb = NULL; 11435| 288k| AT_NUMB nDfs; 11436| 288k| AT_NUMB nNumAtInRingSystem; 11437| 288k| int i, j, u, w, start, nNumRingSystems; /* djb-rwth: removing redundant variables */ 11438| 288k| BNS_VERTEX *at = pBNS->vert; 11439| 288k| BNS_EDGE *bond = pBNS->edge; 11440| 288k| int num_atoms = pBNS->num_atoms; 11441| 288k| int num_edges = pBNS->num_bonds; 11442| | 11443| | /* Allocate arrays */ 11444| 288k| nStackAtom = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nStackAtom[0] ) ); ------------------ | | 1143| 288k|#define inchi_malloc malloc ------------------ 11445| 288k| nRingStack = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nRingStack[0] ) ); ------------------ | | 1143| 288k|#define inchi_malloc malloc ------------------ 11446| 288k| nDfsNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nDfsNumber[0] ) ); ------------------ | | 1143| 288k|#define inchi_malloc malloc ------------------ 11447| 288k| nLowNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nLowNumber[0] ) ); ------------------ | | 1143| 288k|#define inchi_malloc malloc ------------------ 11448| 288k| nBondStack = num_edges ? ( (AT_NUMB *) inchi_malloc( num_edges * sizeof( nBondStack[0] ) ) ) : (AT_NUMB *) ( NULL ); /* special case: no bonds 2006-03 */ ------------------ | | 1143| 49.9k|#define inchi_malloc malloc ------------------ | Branch (11448:18): [True: 49.9k, False: 238k] ------------------ 11449| 288k| cNeighNumb = (S_CHAR *) inchi_malloc( num_atoms * sizeof( cNeighNumb[0] ) ); ------------------ | | 1143| 288k|#define inchi_malloc malloc ------------------ 11450| | 11451| | /* Check allocation */ 11452| 288k| if (!nStackAtom || !nRingStack || !nDfsNumber || !nLowNumber || (!nBondStack && num_edges) || !cNeighNumb ------------------ | Branch (11452:9): [True: 0, False: 288k] | Branch (11452:24): [True: 0, False: 288k] | Branch (11452:39): [True: 0, False: 288k] | Branch (11452:54): [True: 0, False: 288k] | Branch (11452:70): [True: 238k, False: 49.9k] | Branch (11452:85): [True: 0, False: 238k] | Branch (11452:99): [True: 0, False: 288k] ------------------ 11453| 288k| ) /* djb-rwth: addressing LLVM warning */ 11454| 0| { 11455| 0| nNumRingSystems = CT_OUT_OF_RAM; /* program error */ /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 11456| 0| goto exit_function; 11457| 0| } 11458| | 11459| | /******************************************** 11460| | * 11461| | * Find Cut-vertices & Blocks 11462| | * 11463| | * 1\ /5 has 3 blocks (maximal subgraphs that 11464| | * Example: | >3--4< | are nonseparable by deleting a single vertex): 11465| | * 2/ \6 (1,2,3, has 3 bonds), (3,4, has 1 bond), and (4,5,6, has 3 bonds) 11466| | * 11467| | * Cut-vertices or articulation points are 11468| | * intersections of the blocks: points 3 and 4. 11469| | ********************************************/ 11470| | 11471| | /******************************************************** 11472| | 11473| | RingSystemAlt are atoms connected by alternating bonds 11474| | (as must be indicated in bIsAltBond()): 11475| | 11476| | BOND_ALTERN 11477| | BOND_ALT_123 11478| | BOND_ALT_13 11479| | BOND_ALT_23 11480| | 11481| | Since other bonds may be present, we possibly need 11482| | to restart to move to another component 11483| | *********************************************************/ 11484| | 11485| 288k| nNumRingSystems = 0; 11486| 288k| memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 11487| | 11488| 1.38M| for (start = 0; start < num_atoms; start++) ------------------ | Branch (11488:21): [True: 1.09M, False: 288k] ------------------ 11489| 1.09M| { 11490| 1.09M| if (nDfsNumber[start]) ------------------ | Branch (11490:13): [True: 7.52k, False: 1.08M] ------------------ 11491| 7.52k| { 11492| 7.52k| continue; 11493| 7.52k| } 11494| 1.54M| for (i = 0; i < at[start].valenceAltBns; i++) ------------------ | |11420| 1.54M|#define valenceAltBns num_adj_edges ------------------ | Branch (11494:21): [True: 459k, False: 1.08M] ------------------ 11495| 459k| { 11496| 459k| if (bond[at[start].iedge[i]].nBondTypeInpAltBns & BT_ALTERN_BOND) ------------------ | |11408| 459k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ if (bond[at[start].iedge[i]].nBondTypeInpAltBns & BT_ALTERN_BOND) ------------------ | |11387| 459k|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ | Branch (11496:17): [True: 2.90k, False: 456k] ------------------ 11497| 2.90k| goto found_alt; 11498| 459k| } 11499| 1.08M| continue; 11500| | 11501| 1.08M| found_alt: 11502| | 11503| | /* Initiation */ 11504| 2.90k| u = start; /* start atom */ 11505| 2.90k| nDfs = 0; 11506| 2.90k| nTopStackAtom = -1; 11507| 2.90k| nTopRingStack = -1; 11508| 2.90k| nTopBondStack = -1; 11509| 2.90k| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 11510| | /* Push the start atom on the stack */ 11511| 2.90k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11512| 2.90k| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11513| 2.90k| nRingStack[++nTopRingStack] = (AT_NUMB) u; 11514| | 11515| | /* djb-rwth: removing redundant code */ 11516| | 11517| 2.90k| do 11518| 10.6k| { 11519| | /* advance */ 11520| | /*while ( (int)at[i=nStackAtom[nTopStackAtom]].valenceAltBns > (j = (int)cNeighNumb[i]) )*/ 11521| | /* replaced due to missing sequence point */ 11522| 35.3k| while (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valenceAltBns > j) ------------------ | |11420| 35.3k|#define valenceAltBns num_adj_edges ------------------ | Branch (11522:20): [True: 24.6k, False: 10.6k] ------------------ 11523| 24.6k| { 11524| 24.6k| cNeighNumb[i] ++; 11525| 24.6k| if (!( bond[w = at[i].iedge[j]].nBondTypeInpAltBns & BT_ALT_BOND_MASK )) ------------------ | |11408| 24.6k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ if (!( bond[w = at[i].iedge[j]].nBondTypeInpAltBns & BT_ALT_BOND_MASK )) ------------------ | |11400| 24.6k|#define BT_ALT_BOND_MASK (BT_ALTERN_BOND|BT_OTHER_ALTERN_BOND) | | ------------------ | | | |11387| 24.6k|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ | | ------------------ | | #define BT_ALT_BOND_MASK (BT_ALTERN_BOND|BT_OTHER_ALTERN_BOND) | | ------------------ | | | |11388| 24.6k|#define BT_OTHER_ALTERN_BOND 2 /* 1-3, 2-3, 1-2-3 alternating non-stereo non-taut bonds */ | | ------------------ ------------------ | Branch (11525:21): [True: 6.09k, False: 18.5k] ------------------ 11526| 6.09k| { 11527| 6.09k| continue; 11528| 6.09k| } 11529| 18.5k| u = (int) ( bond[at[i].iedge[j]].neighbor12 ^ i ); 11530| 18.5k| if (!nDfsNumber[u] && nBondStack) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (11530:21): [True: 7.77k, False: 10.8k] | Branch (11530:39): [True: 7.77k, False: 0] ------------------ 11531| 7.77k| { 11532| | /* tree edge, 1st visit -- advance */ 11533| 7.77k| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11534| 7.77k| nRingStack[++nTopRingStack] = (AT_NUMB) u; 11535| 7.77k| nBondStack[++nTopBondStack] = (AT_NUMB) w; 11536| 7.77k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11537| | /* djb-rwth: removing redundant code */ 11538| 7.77k| } 11539| 10.8k| else 11540| 10.8k| { 11541| 10.8k| if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) ------------------ | Branch (11541:25): [True: 1.38k, False: 9.42k] | Branch (11541:43): [True: 1.64k, False: 7.77k] ------------------ 11542| 3.02k| { /* may comment out ? */ 11543| | /* back edge: u is not a predecessor of i */ 11544| 3.02k| if ((nDfsNumber[u] < nDfsNumber[i]) && nBondStack) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (11544:29): [True: 1.51k, False: 1.51k] | Branch (11544:64): [True: 1.51k, False: 0] ------------------ 11545| 1.51k| { 11546| | /* Back edge, 1st visit: u is ancestor of i. Save and compare */ 11547| 1.51k| nBondStack[++nTopBondStack] = (AT_NUMB) w; 11548| 1.51k| if (nLowNumber[i] > nDfsNumber[u]) ------------------ | Branch (11548:33): [True: 1.39k, False: 117] ------------------ 11549| 1.39k| { 11550| 1.39k| nLowNumber[i] = nDfsNumber[u]; 11551| 1.39k| } 11552| 1.51k| } 11553| 3.02k| } 11554| 10.8k| } 11555| 18.5k| } 11556| 10.6k| cNeighNumb[i] = 0; 11557| | 11558| | /* Back up */ 11559| 10.6k| if (i != start) ------------------ | Branch (11559:17): [True: 7.77k, False: 2.90k] ------------------ 11560| 7.77k| { 11561| 7.77k| u = (int) nStackAtom[nTopStackAtom - 1]; /* predecessor of i */ 11562| 7.77k| if (nLowNumber[i] >= nDfsNumber[u]) ------------------ | Branch (11562:21): [True: 4.32k, False: 3.45k] ------------------ 11563| 4.32k| { 11564| | /* Output the block; the block was entered through its first bond u->i */ 11565| 4.32k| nNumRingSystems++; 11566| | /*at[u].nBlockSystemAltBns = nNumRingSystems;*/ /* mark the atom */ 11567| 4.32k| nNumAtInRingSystem = 1; 11568| | /* 11569| | if ( u != start || nNumStartChildren > 1 ) { 11570| | at[u].bCutVertexAltBns += 1; // mark cut-vertex (articulation point) 11571| | } 11572| | */ 11573| 7.77k| while (nTopRingStack >= 0) ------------------ | Branch (11573:28): [True: 7.77k, False: 0] ------------------ 11574| 7.77k| { 11575| 7.77k| j = nRingStack[nTopRingStack--]; 11576| | /*at[j].nBlockSystemAltBns = nNumRingSystems;*/ /* mark the atom */ 11577| 7.77k| nNumAtInRingSystem++; 11578| 7.77k| if (i == j) ------------------ | Branch (11578:29): [True: 4.32k, False: 3.45k] ------------------ 11579| 4.32k| { 11580| 4.32k| break; 11581| 4.32k| } 11582| 7.77k| } 11583| 9.29k| while (nTopBondStack >= 0) ------------------ | Branch (11583:28): [True: 9.29k, False: 0] ------------------ 11584| 9.29k| { 11585| 9.29k| w = nBondStack[nTopBondStack--]; 11586| 9.29k| bond[w].nBlockNumberAltBns = nNumRingSystems; /* mark the bond */ ------------------ | |11406| 9.29k|#define nBlockNumberAltBns flow /* internal variable of the DFS traversal: mark traversed bonds */ ------------------ 11587| 9.29k| bond[w].nNumAtInBlockAltBns = nNumAtInRingSystem; ------------------ | |11407| 9.29k|#define nNumAtInBlockAltBns cap ------------------ 11588| 9.29k| if ((i == bond[w].neighbor1 && u == ( i ^ bond[w].neighbor12 )) || ------------------ | Branch (11588:30): [True: 1.46k, False: 7.83k] | Branch (11588:56): [True: 425, False: 1.03k] ------------------ 11589| 8.86k| (u == bond[w].neighbor1 && i == ( u ^ bond[w].neighbor12 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (11589:31): [True: 5.28k, False: 3.58k] | Branch (11589:57): [True: 3.89k, False: 1.38k] ------------------ 11590| 4.32k| { 11591| 4.32k| break; 11592| 4.32k| } 11593| 9.29k| } 11594| 4.32k| } 11595| 3.45k| else 11596| 3.45k| { 11597| 3.45k| if (nLowNumber[u] > nLowNumber[i]) ------------------ | Branch (11597:25): [True: 3.33k, False: 120] ------------------ 11598| 3.33k| { 11599| | /* inherit */ 11600| 3.33k| nLowNumber[u] = nLowNumber[i]; 11601| 3.33k| } 11602| 3.45k| } 11603| 7.77k| } 11604| 10.6k| } while (--nTopStackAtom >= 0); ------------------ | Branch (11604:18): [True: 7.77k, False: 2.90k] ------------------ 11605| 2.90k| } 11606| | 11607| |#if ( BNS_MARK_ONLY_BLOCKS != 1 ) /* { */ 11608| | 11609| | /******************************************** 11610| | * 11611| | * Find Ring Systems 11612| | * Including chain atoms X: A-X-B, where the bonds (of any kind) are bridges. 11613| | * 11614| | ********************************************/ 11615| | 11616| | /* Initiation */ 11617| | nNumRingSystems = 0; 11618| | for (start = 0; start < num_atoms; start++) 11619| | { 11620| | if (at[start].nRingSystemAltBns) 11621| | { 11622| | continue; 11623| | } 11624| | for (i = 0; i < at[start].valenceAltBns; i++) 11625| | { 11626| | if (bond[at[start].iedge[i]].nBondTypeInpAltBns & BT_ALT_BOND_MASK) 11627| | { 11628| | goto found_alt2; 11629| | } 11630| | } 11631| | continue; 11632| | 11633| | found_alt2: 11634| | u = start; /* start atom */ 11635| | nDfs = 0; 11636| | nTopStackAtom = -1; 11637| | nTopRingStack = -1; 11638| | memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); 11639| | memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); 11640| | /* push the start atom on the stack */ 11641| | nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11642| | nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11643| | nRingStack[++nTopRingStack] = (AT_NUMB) u; 11644| | 11645| | do 11646| | { 11647| | /* advance */ 11648| | advance_ring: 11649| | /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valenceAltBns > (j = (int)cNeighNumb[i]) )*/ 11650| | /* replaced due to missing sequence point */ 11651| | if (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valenceAltBns > j) 11652| | { 11653| | cNeighNumb[i] ++; 11654| | if (!( bond[at[i].iedge[j]].nBondTypeInpAltBns & BT_ALTERN_BOND )) 11655| | { 11656| | goto advance_ring; 11657| | } 11658| | u = (int) ( bond[at[i].iedge[j]].neighbor12 ^ i ); 11659| | if (!nDfsNumber[u]) 11660| | { 11661| | /* tree edge, 1st visit -- advance */ 11662| | nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11663| | nRingStack[++nTopRingStack] = (AT_NUMB) u; 11664| | nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11665| | } 11666| | else 11667| | { 11668| | if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) 11669| | { 11670| | /* back edge: u is not a predecessor of i */ 11671| | if (nDfsNumber[u] < nDfsNumber[i]) 11672| | { 11673| | /* Back edge, 1st visit: u is ancestor of i. Compare */ 11674| | if (nLowNumber[i] > nDfsNumber[u]) 11675| | { 11676| | nLowNumber[i] = nDfsNumber[u]; 11677| | } 11678| | } 11679| | } 11680| | } 11681| | goto advance_ring; 11682| | } 11683| | else 11684| | { 11685| | cNeighNumb[i] = 0; 11686| | } 11687| | 11688| | /* Back up */ 11689| | if (nDfsNumber[i] == nLowNumber[i]) 11690| | { 11691| | /* Found a ring system */ 11692| | nNumRingSystems++; 11693| | 11694| | /* Unwind nRingStack[] down to i */ 11695| | 11696| | /* Count atoms in a ring system */ 11697| | for (nNumAtInRingSystem = 0, j = nTopRingStack; 0 <= j; j--) 11698| | { 11699| | nNumAtInRingSystem++; 11700| | if (i == (int) nRingStack[j]) 11701| | { 11702| | break; 11703| | } 11704| | } 11705| | while (nTopRingStack >= 0) 11706| | { 11707| | j = (int) nRingStack[nTopRingStack--]; 11708| | at[j].nRingSystemAltBns = (AT_NUMB) nNumRingSystems; /* ring system id */ 11709| | at[j].nNumAtInRingSystemAltBns = nNumAtInRingSystem; 11710| | if (i == j) 11711| | { 11712| | /* Reached atom on the top of nStackAtom[] stack */ 11713| | break; 11714| | } 11715| | } 11716| | } 11717| | else 11718| | { 11719| | if (nTopStackAtom > 0) 11720| | { 11721| | j = (int) nStackAtom[nTopStackAtom - 1]; 11722| | /* inherit nLowNumber */ 11723| | if (nLowNumber[j] > nLowNumber[i]) 11724| | { 11725| | nLowNumber[j] = nLowNumber[i]; 11726| | } 11727| | } 11728| | } 11729| | } while (--nTopStackAtom >= 0); 11730| | } 11731| | 11732| |#endif /* } BNS_MARK_ONLY_BLOCKS != 1 */ 11733| | 11734| 288k|exit_function: 11735| 288k| if (nStackAtom) ------------------ | Branch (11735:9): [True: 288k, False: 0] ------------------ 11736| 288k| { 11737| 288k| inchi_free( nStackAtom ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 11738| 288k| } 11739| 288k| if (nRingStack) ------------------ | Branch (11739:9): [True: 288k, False: 0] ------------------ 11740| 288k| { 11741| 288k| inchi_free( nRingStack ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 11742| 288k| } 11743| 288k| if (nDfsNumber) ------------------ | Branch (11743:9): [True: 288k, False: 0] ------------------ 11744| 288k| { 11745| 288k| inchi_free( nDfsNumber ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 11746| 288k| } 11747| 288k| if (nLowNumber) ------------------ | Branch (11747:9): [True: 288k, False: 0] ------------------ 11748| 288k| { 11749| 288k| inchi_free( nLowNumber ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 11750| 288k| } 11751| 288k| if (nBondStack) ------------------ | Branch (11751:9): [True: 49.9k, False: 238k] ------------------ 11752| 49.9k| { 11753| 49.9k| inchi_free( nBondStack ); ------------------ | | 1152| 49.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 49.9k, False: 0] | | | Branch (1152:50): [Folded, False: 49.9k] | | ------------------ ------------------ 11754| 49.9k| } 11755| 288k| if (cNeighNumb) ------------------ | Branch (11755:9): [True: 288k, False: 0] ------------------ 11756| 288k| { 11757| 288k| inchi_free( cNeighNumb ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 11758| 288k| } 11759| | 11760| 288k| return nNumRingSystems; 11761| 288k|} ReInitBnStructForAltBns: 11769| 288k|{ 11770| 288k| Vertex v, v2; 11771| 288k| int ret, bond_type, num_to_test, j; 11772| 288k| BNS_EDGE *pBond; 11773| 288k| BNS_VERTEX *pAtom; 11774| | 11775| | /* Strip all t-groups and c-groups */ 11776| 288k| num_to_test = 0; 11777| 288k| if (bUnknAltAsNoStereo) ------------------ | Branch (11777:9): [True: 0, False: 288k] ------------------ 11778| 0| { 11779| 0| for (j = 0; j < pBNS->num_edges; j++) ------------------ | Branch (11779:21): [True: 0, False: 0] ------------------ 11780| 0| { 11781| 0| pBNS->edge[j].pass = 0; 11782| 0| } 11783| 0| } 11784| | 11785| 288k| ret = ReInitBnStruct( pBNS, at, num_atoms, 0 ); 11786| | 11787| 288k| if (ret || pBNS->num_atoms != num_atoms || pBNS->num_vertices != num_atoms || pBNS->num_bonds != pBNS->num_edges) ------------------ | Branch (11787:9): [True: 3, False: 288k] | Branch (11787:16): [True: 0, False: 288k] | Branch (11787:48): [True: 0, False: 288k] | Branch (11787:83): [True: 0, False: 288k] ------------------ 11788| 3| { 11789| 3| ret = BNS_REINIT_ERR; ------------------ | | 60| 3|#define BNS_REINIT_ERR (BNS_ERR + 12) /*(-9987)*/ | | ------------------ | | | | 47| 3|#define BNS_ERR -9999 | | ------------------ ------------------ 11790| 3| goto exit_function; 11791| 3| } 11792| | 11793| | /* Eliminate bonds and fix st-caps */ 11794| 1.38M| for (v = 0; v < num_atoms; v++) ------------------ | Branch (11794:17): [True: 1.09M, False: 288k] ------------------ 11795| 1.09M| { 11796| 1.09M| pAtom = pBNS->vert + v; 11797| 1.57M| for (j = 0; j < pAtom->valenceAltBns; j++) ------------------ | |11420| 1.57M|#define valenceAltBns num_adj_edges ------------------ | Branch (11797:21): [True: 479k, False: 1.09M] ------------------ 11798| 479k| { 11799| 479k| pBond = pBNS->edge + pAtom->iedge[j]; 11800| 479k| if (pBond->neighbor1 == v) ------------------ | Branch (11800:17): [True: 239k, False: 239k] ------------------ 11801| 239k| { 11802| 239k| bond_type = ( at[v].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 239k|#define BOND_TYPE_MASK 0x0f ------------------ 11803| 239k| v2 = pBond->neighbor12 ^ v; 11804| 239k| if (at[v].endpoint || at[v2].endpoint) ------------------ | Branch (11804:21): [True: 9.09k, False: 230k] | Branch (11804:39): [True: 6.91k, False: 223k] ------------------ 11805| 16.0k| { 11806| 16.0k| bond_type = 0; /* any bond to an endpoint considered non-stereogenic */ 11807| 16.0k| } 11808| |#if ( FIX_EITHER_DB_AS_NONSTEREO == 1 ) 11809| | if (bUnknAltAsNoStereo) 11810| | { 11811| | if (bond_type == BOND_ALTERN && at[v].bond_stereo[j] == STEREO_DBLE_EITHER) 11812| | { 11813| | bond_type = 0; /* treat unknown (Either) ALT bond as non-stereo */ 11814| | } 11815| | } 11816| |#endif 11817| 239k| switch (bond_type) 11818| 239k| { 11819| | 11820| 7.94k| case BOND_ALTERN: ------------------ | | 180| 7.94k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 7.94k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11820:21): [True: 7.94k, False: 231k] ------------------ 11821| 7.94k| pBond->nBondTypeInpAltBns = BT_ALTERN_BOND; ------------------ | |11408| 7.94k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_ALTERN_BOND; ------------------ | |11387| 7.94k|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ 11822| 7.94k| num_to_test++; 11823| 7.94k| break; 11824| | 11825| 2.06k| case BOND_ALT_123: ------------------ | | 182| 2.06k|#define BOND_ALT_123 5 /* single/double/triple */ ------------------ | Branch (11825:21): [True: 2.06k, False: 237k] ------------------ 11826| 2.06k| case BOND_ALT_13: ------------------ | | 183| 2.06k|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (11826:21): [True: 0, False: 239k] ------------------ 11827| 6.00k| case BOND_ALT_23: ------------------ | | 184| 6.00k|#define BOND_ALT_23 7 /* double/triple */ ------------------ | Branch (11827:21): [True: 3.94k, False: 235k] ------------------ 11828| 6.00k| pBond->nBondTypeInpAltBns = BT_OTHER_ALTERN_BOND; ------------------ | |11408| 6.00k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_OTHER_ALTERN_BOND; ------------------ | |11388| 6.00k|#define BT_OTHER_ALTERN_BOND 2 /* 1-3, 2-3, 1-2-3 alternating non-stereo non-taut bonds */ ------------------ 11829| 6.00k| break; 11830| | 11831| 195| case BOND_TAUTOM: ------------------ | | 185| 195|#define BOND_TAUTOM 8 ------------------ | Branch (11831:21): [True: 195, False: 239k] ------------------ 11832| 195| pBond->nBondTypeInpAltBns = BT_TAUTOM_BOND; ------------------ | |11408| 195|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_TAUTOM_BOND; ------------------ | |11392| 195|#define BT_TAUTOM_BOND 8 ------------------ 11833| 195| break; 11834| | 11835| 10.2k| case BOND_ALT12NS: ------------------ | | 186| 10.2k|#define BOND_ALT12NS 9 ------------------ | Branch (11835:21): [True: 10.2k, False: 229k] ------------------ 11836| 10.2k| pBond->nBondTypeInpAltBns = BT_ALTERN_NS_BOND; ------------------ | |11408| 10.2k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_ALTERN_NS_BOND; ------------------ | |11390| 10.2k|#define BT_ALTERN_NS_BOND 4 ------------------ 11837| 10.2k| break; 11838| | 11839| 16.0k| case 0: ------------------ | Branch (11839:21): [True: 16.0k, False: 223k] ------------------ 11840| 149k| case BOND_SINGLE: ------------------ | | 177| 149k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 149k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (11840:21): [True: 133k, False: 106k] ------------------ 11841| 191k| case BOND_DOUBLE: ------------------ | | 178| 191k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 191k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (11841:21): [True: 42.3k, False: 197k] ------------------ 11842| 215k| case BOND_TRIPLE: ------------------ | | 179| 215k|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 215k|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (11842:21): [True: 23.6k, False: 216k] ------------------ 11843| 215k| pBond->nBondTypeInpAltBns = BT_IGNORE_BOND; ------------------ | |11408| 215k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_IGNORE_BOND; ------------------ | |11396| 215k|#define BT_IGNORE_BOND 0 ------------------ 11844| 215k| break; 11845| | 11846| 0| default: ------------------ | Branch (11846:21): [True: 0, False: 239k] ------------------ 11847| 0| pBond->nBondTypeInpAltBns = BT_IGNORE_BOND; ------------------ | |11408| 0|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_IGNORE_BOND; ------------------ | |11396| 0|#define BT_IGNORE_BOND 0 ------------------ 11848| 0| break; 11849| 239k| } 11850| 239k| pBond->nBondNonStereoAltBns = 0; /* djb-rwth: addressing GCC warning -- operations on pBond->cap might be undefined */ ------------------ | |11409| 239k|#define nBondNonStereoAltBns cap /* 1=>found to be non-stereogenic although BondTypeInp=2; 0=>as in BondTypeInp */ ------------------ 11851| 239k| pBond->nBlockNumberAltBns = 0; ------------------ | |11406| 239k|#define nBlockNumberAltBns flow /* internal variable of the DFS traversal: mark traversed bonds */ ------------------ 11852| 239k| pBond->nNumAtInBlockAltBns = 0; ------------------ | |11407| 239k|#define nNumAtInBlockAltBns cap ------------------ 11853| | 11854| 239k|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 11855| 239k| pBond->forbidden &= pBNS->edge_forbidden_mask; 11856| 239k|#endif 11857| 239k| } 11858| 479k| } 11859| 1.09M| pAtom->bCutVertexAltBns = ------------------ | |11413| 1.09M|#define bCutVertexAltBns st_edge.cap0 /* cut-vertex flag */ ------------------ 11860| 1.09M| pAtom->nRingSystemAltBns = ------------------ | |11414| 1.09M|#define nRingSystemAltBns st_edge.cap /* ordering number of a ring system */ ------------------ 11861| 1.09M| pAtom->nNumAtInRingSystemAltBns = ------------------ | |11415| 1.09M|#define nNumAtInRingSystemAltBns st_edge.flow0 /* number of vertices in a ring system */ ------------------ 11862| 1.09M| pAtom->nBlockSystemAltBns = 0; ------------------ | |11416| 1.09M|#define nBlockSystemAltBns st_edge.flow /* result of the DFS traversal: even cirquit must be within one block */ ------------------ 11863| 1.09M| } 11864| | 11865| 288k| return num_to_test; 11866| | 11867| 3|exit_function: 11868| | 11869| 3| return ret; 11870| 288k|} MarkNonStereoAltBns: 11878| 288k|{ 11879| 288k| int num_bonds = pBNS->num_bonds; 11880| 288k| int ret; 11881| 288k| int ibond, ib1, ib2; 11882| 288k| BNS_EDGE *pBond; 11883| 288k| Vertex iat1, iat2; 11884| | 11885| 288k| ret = 0; 11886| | 11887| 288k| if (pBNS->num_atoms != num_atoms || pBNS->num_vertices != num_atoms || pBNS->num_bonds != pBNS->num_edges) ------------------ | Branch (11887:9): [True: 0, False: 288k] | Branch (11887:41): [True: 0, False: 288k] | Branch (11887:76): [True: 0, False: 288k] ------------------ 11888| 0| { 11889| 0| ret = BNS_REINIT_ERR; ------------------ | | 60| 0|#define BNS_REINIT_ERR (BNS_ERR + 12) /*(-9987)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 11890| 0| goto exit_function; 11891| 0| } 11892| 288k| if (bUnknAltAsNoStereo) ------------------ | Branch (11892:9): [True: 0, False: 288k] ------------------ 11893| 0| { 11894| 0| for (ibond = 0; ibond < num_bonds; ibond++) ------------------ | Branch (11894:25): [True: 0, False: 0] ------------------ 11895| 0| { 11896| 0| pBond = pBNS->edge + ibond; 11897| 0| if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11408| 0|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11387| 0|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11408| 0|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11396| 0|#define BT_IGNORE_BOND 0 ------------------ | Branch (11897:17): [True: 0, False: 0] | Branch (11897:64): [True: 0, False: 0] ------------------ 11898| 0| { 11899| 0| continue; 11900| 0| } 11901| 0| iat1 = pBond->neighbor1; 11902| 0| iat2 = pBond->neighbor12 ^ iat1; 11903| 0| ib1 = pBond->neigh_ord[0]; 11904| 0| ib2 = pBond->neigh_ord[1]; 11905| 0| if ( /* alt bond non-adjacent to a taut. endpoint: */ 11906| 0| ( pBond->nBondTypeInpAltBns == BT_ALTERN_BOND && ------------------ | |11408| 0|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ ( pBond->nBondTypeInpAltBns == BT_ALTERN_BOND && ------------------ | |11387| 0|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ | Branch (11906:19): [True: 0, False: 0] ------------------ 11907| 0| pBond->nNumAtInBlockAltBns <= 3 ) /* non-ring bond */ || ------------------ | |11407| 0|#define nNumAtInBlockAltBns cap ------------------ | Branch (11907:19): [True: 0, False: 0] ------------------ 11908| | /* alt bond adjacent to a taut. endpoint: */ 11909| 0| ( pBond->nBondTypeInpAltBns == BT_IGNORE_BOND && ------------------ | |11408| 0|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ ( pBond->nBondTypeInpAltBns == BT_IGNORE_BOND && ------------------ | |11396| 0|#define BT_IGNORE_BOND 0 ------------------ | Branch (11909:21): [True: 0, False: 0] ------------------ 11910| 0| ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 189| 0|#define BOND_TYPE_MASK 0x0f ------------------ ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11910:18): [True: 0, False: 0] ------------------ 11911| 0| ) 11912| 0| { 11913| 0| if (( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN) ------------------ | | 189| 0|#define BOND_TYPE_MASK 0x0f ------------------ if (( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN) ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11913:21): [True: 0, False: 0] ------------------ 11914| 0| { 11915| | /* bond_type = BOND_ALT12NS; */ 11916| 0| at[iat1].bond_stereo[ib1] = 11917| 0| at[iat2].bond_stereo[ib2] = STEREO_DBLE_EITHER; ------------------ | | 40| 0|#define STEREO_DBLE_EITHER 3 ------------------ 11918| 0| ret++; 11919| 0| } 11920| 0| } 11921| 0| } 11922| 0| } 11923| 288k| else 11924| 288k| { 11925| 528k| for (ibond = 0; ibond < num_bonds; ibond++) ------------------ | Branch (11925:25): [True: 239k, False: 288k] ------------------ 11926| 239k| { 11927| 239k| pBond = pBNS->edge + ibond; 11928| 239k| if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11408| 239k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11387| 479k|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11408| 231k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11396| 231k|#define BT_IGNORE_BOND 0 ------------------ | Branch (11928:17): [True: 231k, False: 7.94k] | Branch (11928:64): [True: 16.4k, False: 215k] ------------------ 11929| 16.4k| { 11930| 16.4k| continue; 11931| 16.4k| } 11932| 223k| iat1 = pBond->neighbor1; 11933| 223k| iat2 = pBond->neighbor12 ^ iat1; 11934| 223k| ib1 = pBond->neigh_ord[0]; 11935| 223k| ib2 = pBond->neigh_ord[1]; 11936| 223k| if ( /* alt bond non-adjacent to a taut. endpoint: */ 11937| 223k| ( pBond->nBondTypeInpAltBns == BT_ALTERN_BOND && ------------------ | |11408| 223k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ ( pBond->nBondTypeInpAltBns == BT_ALTERN_BOND && ------------------ | |11387| 446k|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ | Branch (11937:19): [True: 7.94k, False: 215k] ------------------ 11938| 7.94k| pBond->nNumAtInBlockAltBns <= 3 ) /* non-ring bond */ || ------------------ | |11407| 7.94k|#define nNumAtInBlockAltBns cap ------------------ | Branch (11938:19): [True: 2.29k, False: 5.65k] ------------------ 11939| | /* alt bond adjacent to a taut. endpoint: */ 11940| 221k| ( pBond->nBondTypeInpAltBns == BT_IGNORE_BOND && ------------------ | |11408| 221k|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ ( pBond->nBondTypeInpAltBns == BT_IGNORE_BOND && ------------------ | |11396| 442k|#define BT_IGNORE_BOND 0 ------------------ | Branch (11940:21): [True: 215k, False: 5.65k] ------------------ 11941| 215k| ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 189| 215k|#define BOND_TYPE_MASK 0x0f ------------------ ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 180| 215k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 215k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11941:18): [True: 271, False: 215k] ------------------ 11942| 223k| ) 11943| 2.56k| { 11944| 2.56k| at[iat1].bond_type[ib1] = 11945| 2.56k| at[iat2].bond_type[ib2] = BOND_ALT12NS; ------------------ | | 186| 2.56k|#define BOND_ALT12NS 9 ------------------ 11946| 2.56k| ret++; 11947| 2.56k| } 11948| 223k| } 11949| 288k| } 11950| | 11951| 288k|exit_function: 11952| | 11953| 288k| return ret; 11954| 288k|} bHasChargedNeighbor: 11971| 2.60k|{ 11972| 2.60k| int i; 11973| 4.72k| for (i = 0; i < at[iat].valence; i++) ------------------ | Branch (11973:17): [True: 3.65k, False: 1.06k] ------------------ 11974| 3.65k| { 11975| 3.65k| if (at[(int) at[iat].neighbor[i]].charge) ------------------ | Branch (11975:13): [True: 1.53k, False: 2.12k] ------------------ 11976| 1.53k| { 11977| 1.53k| return 1; 11978| 1.53k| } 11979| 3.65k| } 11980| | 11981| 1.06k| return 0; 11982| 2.60k|} AddRemoveProtonsRestr: 12029| 1.16k|{ 12030| 1.16k| int i, j, ret = 0; 12031| 1.16k| int nAtTypeTotals[ATTOT_ARRAY_LEN]; 12032| 1.16k| int num_prot = *num_protons_to_add; 12033| 1.16k| int type, mask, bSuccess, nTotCharge, nNumSuccess = 0; 12034| 1.16k| int max_j_Aa = -1, max_j_Ar = -1; 12035| | 12036| | /* for the reference: 12037| | 12038| | #define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ 12039| | FLAG_PROTON_NP_HARD_REMOVED | \ 12040| | FLAG_PROTON_AC_SIMPLE_ADDED | \ 12041| | FLAG_PROTON_AC_SIMPLE_REMOVED | \ 12042| | FLAG_PROTON_AC_HARD_REMOVED | \ 12043| | FLAG_PROTON_AC_HARD_ADDED | \ 12044| | FLAG_PROTON_SINGLE_REMOVED | \ 12045| | FLAG_PROTON_CHARGE_CANCEL ) 12046| | 12047| | #define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ 12048| | FLAG_PROTON_AC_HARD_REMOVED | \ 12049| | FLAG_PROTON_AC_HARD_ADDED ) 12050| | 12051| | */ 12052| | 12053| | /* if ChargeRevrs > nChargeInChI then we should prevent proton addition or facilitate proton removal 12054| | a typical case is (=) on N or O instead of C(-) 12055| | 12056| | if ChargeRevrs < nChargeInChI then we should prevent proton removal or facilitate proton addition 12057| | */ 12058| | 12059| 1.16k| mark_at_type( at, num_atoms, nAtTypeTotals ); 12060| 7.09k| for (i = nTotCharge = 0; i < num_atoms; i++) ------------------ | Branch (12060:30): [True: 5.93k, False: 1.16k] ------------------ 12061| 5.93k| { 12062| 5.93k| nTotCharge += at[i].charge; 12063| 5.93k| } 12064| | /* Size for SimpleAddAcidicProtons() */ 12065| 3.50k| for (max_j_Aa = 0; AaTypMask[2 * max_j_Aa]; max_j_Aa++) ------------------ | Branch (12065:24): [True: 2.33k, False: 1.16k] ------------------ 12066| 2.33k| { 12067| 2.33k| ; 12068| 2.33k| } 12069| | /* Size for SimpleRemoveAcidicProtons */ 12070| 2.33k| for (max_j_Ar = 0; ArTypMask[2 * max_j_Ar]; max_j_Ar++) ------------------ | Branch (12070:24): [True: 1.16k, False: 1.16k] ------------------ 12071| 1.16k| { 12072| 1.16k| ; 12073| 1.16k| } 12074| 1.16k| if (num_prot < 0 && nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr <= 0) ------------------ | Branch (12074:9): [True: 393, False: 774] | Branch (12074:25): [True: 326, False: 67] ------------------ 12075| 326| { 12076| | /* Remove proton(s) */ 12077| | /* use test from SimpleAddAcidicProtons() to test whether removal of H(+) from =C-OH, etc. is correct */ 12078| 1.42k| for (i = 0; i < num_atoms && num_prot; i++) ------------------ | Branch (12078:21): [True: 1.10k, False: 322] | Branch (12078:38): [True: 1.10k, False: 4] ------------------ 12079| 1.10k| { 12080| | /* Choose an atom */ 12081| 1.10k| if (at[i].sb_parity[0] || at[i].p_parity || at[i].charge || ------------------ | Branch (12081:17): [True: 6, False: 1.09k] | Branch (12081:39): [True: 28, False: 1.06k] | Branch (12081:57): [True: 256, False: 813] ------------------ 12082| 813| !at[i].num_H || at[i].radical || bHasChargedNeighbor( at, i )) ------------------ | Branch (12082:18): [True: 784, False: 29] | Branch (12082:34): [True: 1, False: 28] | Branch (12082:51): [True: 13, False: 15] ------------------ 12083| 1.08k| { 12084| 1.08k| continue; 12085| 1.08k| } 12086| | /* try to remove a proton and check whether InChI would add it back */ 12087| 15| at[i].charge--; 12088| 15| at[i].num_H--; 12089| 15| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12090| 15| at[i].charge++; 12091| 15| at[i].num_H++; 12092| | 12093| 15| if (type) ------------------ | Branch (12093:17): [True: 10, False: 5] ------------------ 12094| 10| { 12095| 16| for (bSuccess = 0, j = 0; j < max_j_Aa; j++) ------------------ | Branch (12095:43): [True: 13, False: 3] ------------------ 12096| 13| { 12097| 13| if ((bSuccess = ( type & AaTypMask[2 * j] ) && ( mask && AaTypMask[2 * j + 1] ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (12097:25): [True: 7, False: 6] | Branch (12097:37): [True: 7, False: 6] | Branch (12097:70): [True: 7, False: 0] | Branch (12097:78): [True: 7, False: 0] ------------------ 12098| 7| { 12099| 7| break; /* the proton may be added to this atom */ 12100| 7| } 12101| 13| } 12102| 10| if (bSuccess) ------------------ | Branch (12102:21): [True: 7, False: 3] ------------------ 12103| 7| { 12104| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 12105| 7| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12106| 7| at[i].charge--; 12107| 7| at[i].num_H--; 12108| 7| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12109| 7| num_prot++; /* success */ 12110| 7| nNumSuccess++; 12111| 7| } 12112| 10| } 12113| 15| } 12114| 326| } 12115| | 12116| 1.16k| if (num_prot < 0 && num_tg && nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr <= 0) ------------------ | Branch (12116:9): [True: 389, False: 778] | Branch (12116:25): [True: 29, False: 360] | Branch (12116:35): [True: 22, False: 7] ------------------ 12117| 22| { 12118| | /* Alternative proton removal: O=C-NH => (-)O-C=N, O and N are taut. endpoints */ 12119| 22| int endp2, centp, k, i0, k0; 12120| 182| for (i = 0; i < num_atoms; i++) ------------------ | Branch (12120:21): [True: 160, False: 22] ------------------ 12121| 160| { 12122| | /* Choose an atom */ 12123| 160| if (!at[i].endpoint || at[i].sb_parity[0] || at[i].p_parity || ------------------ | Branch (12123:17): [True: 119, False: 41] | Branch (12123:36): [True: 0, False: 41] | Branch (12123:58): [True: 0, False: 41] ------------------ 12124| 41| at[i].radical || at[i].charge || bHasChargedNeighbor( at, i )) ------------------ | Branch (12124:18): [True: 2, False: 39] | Branch (12124:35): [True: 3, False: 36] | Branch (12124:51): [True: 17, False: 19] ------------------ 12125| 141| { 12126| 141| continue; 12127| 141| } 12128| | /* Looking for tautomeric =O */ 12129| 19| if (1 != at[i].valence || BOND_TYPE_DOUBLE != at[i].bond_type[0] || at[i].num_H || ------------------ | | 33| 17|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (12129:17): [True: 2, False: 17] | Branch (12129:39): [True: 3, False: 14] | Branch (12129:81): [True: 0, False: 14] ------------------ 12130| 14| 2 != get_endpoint_valence( at[i].el_number )) ------------------ | Branch (12130:18): [True: 0, False: 14] ------------------ 12131| 5| { 12132| 5| continue; 12133| 5| } 12134| 14| centp = at[i].neighbor[0]; 12135| 14| if (at[centp].sb_parity[0] || at[centp].p_parity || !is_centerpoint_elem( at[centp].el_number )) ------------------ | Branch (12135:17): [True: 0, False: 14] | Branch (12135:43): [True: 0, False: 14] | Branch (12135:65): [True: 3, False: 11] ------------------ 12136| 3| { 12137| 3| continue; 12138| 3| } 12139| | /* Found a possible centerpoint, looking for -NH endpoint */ 12140| 55| for (k = 0; k < at[centp].valence; k++) ------------------ | Branch (12140:25): [True: 44, False: 11] ------------------ 12141| 44| { 12142| 44| if (at[centp].bond_type[k] != BOND_TYPE_SINGLE) ------------------ | | 32| 44|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (12142:21): [True: 17, False: 27] ------------------ 12143| 17| { 12144| 17| continue; 12145| 17| } 12146| 27| endp2 = at[centp].neighbor[k]; 12147| 27| if (at[endp2].endpoint != at[i].endpoint || ------------------ | Branch (12147:21): [True: 20, False: 7] ------------------ 12148| 7| !at[endp2].num_H || at[endp2].charge || ------------------ | Branch (12148:22): [True: 3, False: 4] | Branch (12148:42): [True: 0, False: 4] ------------------ 12149| 4| at[endp2].sb_parity[0] || at[endp2].p_parity || ------------------ | Branch (12149:22): [True: 0, False: 4] | Branch (12149:48): [True: 0, False: 4] ------------------ 12150| 4| at[endp2].valence != at[endp2].chem_bonds_valence || ------------------ | Branch (12150:22): [True: 0, False: 4] ------------------ 12151| 4| 3 != at[endp2].chem_bonds_valence + at[endp2].num_H || ------------------ | Branch (12151:22): [True: 2, False: 2] ------------------ 12152| 2| 3 != get_endpoint_valence( at[endp2].el_number )) ------------------ | Branch (12152:22): [True: 0, False: 2] ------------------ 12153| 25| { 12154| 25| continue; 12155| 25| } 12156| | /* Find bonds in reciprocal ajacency lists */ 12157| 5| for (i0 = 0; i0 < at[centp].valence && i != at[centp].neighbor[i0]; i0++) ------------------ | Branch (12157:30): [True: 5, False: 0] | Branch (12157:56): [True: 3, False: 2] ------------------ 12158| 3| { 12159| 3| ; 12160| 3| } 12161| 2| for (k0 = 0; k0 < at[endp2].valence && centp != at[endp2].neighbor[k0]; k0++) ------------------ | Branch (12161:30): [True: 2, False: 0] | Branch (12161:56): [True: 0, False: 2] ------------------ 12162| 0| { 12163| 0| ; 12164| 0| } 12165| 2| if (i0 == at[centp].valence || k0 == at[endp2].valence) ------------------ | Branch (12165:21): [True: 0, False: 2] | Branch (12165:48): [True: 0, False: 2] ------------------ 12166| 0| { 12167| 0| return RI_ERR_PROGR; ------------------ | |11963| 0|#define RI_ERR_PROGR (-3) ------------------ 12168| 0| } 12169| | /* -NH has been found */ 12170| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 12171| 2| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12172| 2| type = GetAtomChargeType( at, endp2, nAtTypeTotals, &mask, 1 ); /* subtract at[endp2] */ 12173| | 12174| 2| at[i].bond_type[0] --; 12175| 2| at[centp].bond_type[i0] --; 12176| 2| at[i].chem_bonds_valence--; 12177| 2| at[i].charge--; 12178| | 12179| 2| at[endp2].bond_type[k0] ++; 12180| 2| at[centp].bond_type[k] ++; 12181| 2| at[endp2].chem_bonds_valence++; 12182| 2| at[endp2].num_H--; 12183| | 12184| 2| num_prot++; 12185| 2| nNumSuccess++; 12186| | 12187| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 12188| 2| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add at[i] */ 12189| 2| type = GetAtomChargeType( at, endp2, nAtTypeTotals, &mask, 0 ); /* add at[endp2] */ 12190| 2| } 12191| 11| } 12192| 22| } 12193| | 12194| 1.16k| if (num_prot > 0) ------------------ | Branch (12194:9): [True: 774, False: 393] ------------------ 12195| 774| { 12196| | /* Add protons */ 12197| | /* 1. Use test from SimpleRemoveAcidicProtons() to test whether addition of H(+) to =C-O(-), etc. is correct */ 12198| 2.51k| for (i = 0; i < num_atoms && num_prot && nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr >= 0; i++) ------------------ | Branch (12198:21): [True: 2.22k, False: 297] | Branch (12198:38): [True: 2.22k, False: 1] | Branch (12198:50): [True: 1.74k, False: 476] ------------------ 12199| 1.74k| { 12200| | /* Choose an atom */ 12201| 1.74k| if (at[i].sb_parity[0] || at[i].p_parity || at[i].num_H || ------------------ | Branch (12201:17): [True: 10, False: 1.73k] | Branch (12201:39): [True: 14, False: 1.72k] | Branch (12201:57): [True: 7, False: 1.71k] ------------------ 12202| 1.71k| at[i].charge != -1 || at[i].radical || bHasChargedNeighbor( at, i )) ------------------ | Branch (12202:18): [True: 1.41k, False: 302] | Branch (12202:40): [True: 31, False: 271] | Branch (12202:57): [True: 81, False: 190] ------------------ 12203| 1.55k| { 12204| 1.55k| continue; 12205| 1.55k| } 12206| | /* Try to add a proton and check whether InChI would remove it back */ 12207| 190| at[i].charge++; 12208| 190| at[i].num_H++; 12209| 190| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12210| 190| at[i].charge--; 12211| 190| at[i].num_H--; 12212| 190| if (type) ------------------ | Branch (12212:17): [True: 120, False: 70] ------------------ 12213| 120| { 12214| 197| for (bSuccess = 0, j = 0; j < max_j_Ar; j++) ------------------ | Branch (12214:43): [True: 120, False: 77] ------------------ 12215| 120| { 12216| 120| if ((bSuccess = ( type & ArTypMask[2 * j] ) && ( mask && ArTypMask[2 * j + 1] ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (12216:25): [True: 43, False: 77] | Branch (12216:37): [True: 43, False: 77] | Branch (12216:70): [True: 43, False: 0] | Branch (12216:78): [True: 43, False: 0] ------------------ 12217| 43| { 12218| 43| break; 12219| 43| } 12220| 120| } 12221| 120| if (bSuccess) ------------------ | Branch (12221:21): [True: 43, False: 77] ------------------ 12222| 43| { 12223| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 12224| 43| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12225| 43| at[i].charge++; 12226| 43| at[i].num_H++; 12227| 43| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12228| 43| num_prot--; /* success */ 12229| 43| nNumSuccess++; 12230| 43| } 12231| 120| } 12232| 190| } 12233| | /* 2. Use test from SimpleRemoveHplusNPO() */ 12234| 4.95k| for (i = 0; i < num_atoms && num_prot; i++) ------------------ | Branch (12234:21): [True: 4.24k, False: 704] | Branch (12234:38): [True: 4.17k, False: 70] ------------------ 12235| 4.17k| { 12236| | /* Choose an atom */ 12237| 4.17k| if (at[i].sb_parity[0] || at[i].p_parity || ------------------ | Branch (12237:17): [True: 24, False: 4.15k] | Branch (12237:39): [True: 17, False: 4.13k] ------------------ 12238| 4.13k| at[i].charge || at[i].radical || bHasChargedNeighbor( at, i )) ------------------ | Branch (12238:18): [True: 1.72k, False: 2.41k] | Branch (12238:34): [True: 144, False: 2.26k] | Branch (12238:51): [True: 1.42k, False: 844] ------------------ 12239| 3.33k| { 12240| 3.33k| continue; 12241| 3.33k| } 12242| | /* Try to add a proton and check whether InChI would remove it back */ 12243| 844| at[i].num_H++; 12244| 844| at[i].charge++; 12245| 844| bSuccess = ( PR_SIMPLE_TYP & ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) ) ) && ------------------ | | 137| 844|#define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 37| 844|#define ATT_ATOM_N 0x0040 | | ------------------ | | #define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 38| 844|#define ATT_ATOM_P 0x0080 | | ------------------ | | #define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 42| 844|#define ATT_O_PLUS 0x0800 /**< -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */ | | ------------------ ------------------ | Branch (12245:24): [True: 298, False: 546] ------------------ 12246| 298| ( PR_SIMPLE_MSK & mask ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | | 136| 298|#define PR_SIMPLE_MSK (ATBIT_NP_Proton | ATBIT_OH_Plus) | | ------------------ | | | | 93| 298|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | ------------------ | | #define PR_SIMPLE_MSK (ATBIT_NP_Proton | ATBIT_OH_Plus) | | ------------------ | | | | 117| 298|#define ATBIT_OH_Plus (1 << ATTOT_NUM_OH_Plus) | | ------------------ ------------------ | Branch (12246:17): [True: 298, False: 0] ------------------ 12247| 844| at[i].num_H--; /* failed */ 12248| 844| at[i].charge--; 12249| 844| if (bSuccess) ------------------ | Branch (12249:17): [True: 298, False: 546] ------------------ 12250| 298| { 12251| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 12252| 298| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12253| 298| at[i].num_H++; 12254| 298| at[i].charge++; 12255| 298| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12256| 298| num_prot--; /* succeeded */ 12257| 298| nNumSuccess++; 12258| 298| } 12259| 844| } 12260| 774| } 12261| | 12262| 1.16k| if (num_prot < 0 && ( bNormalizationFlags & FLAG_PROTON_AC_HARD_ADDED ) && 1 == num_tg && ------------------ | | 151| 388|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 ------------------ | Branch (12262:9): [True: 388, False: 779] | Branch (12262:25): [True: 0, False: 388] | Branch (12262:80): [True: 0, False: 0] ------------------ 12263| 0| nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr <= 0) ------------------ | Branch (12263:10): [True: 0, False: 0] ------------------ 12264| 0| { 12265| | /* Try to remove protons from tautomeric N (specific ADP must be present) */ 12266| 0| int nNumAcceptors_DB_O = 0, nNumDonors_SB_NH = 0, num_max, num_success; 12267| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (12267:21): [True: 0, False: 0] ------------------ 12268| 0| { 12269| | /* Choose an atom */ 12270| 0| if (!at[i].endpoint || at[i].radical || ------------------ | Branch (12270:17): [True: 0, False: 0] | Branch (12270:36): [True: 0, False: 0] ------------------ 12271| 0| at[i].sb_parity[0] || at[i].p_parity || bHasChargedNeighbor( at, i )) ------------------ | Branch (12271:18): [True: 0, False: 0] | Branch (12271:40): [True: 0, False: 0] | Branch (12271:58): [True: 0, False: 0] ------------------ 12272| 0| { 12273| 0| continue; 12274| 0| } 12275| 0| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12276| 0| if (( type & AA_HARD_TYP_CO ) && ( mask & AA_HARD_MSK_CO )) ------------------ | | 222| 0|#define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 31| 0|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 35| 0|#define ATT_NO 0x0010 | | ------------------ ------------------ if (( type & AA_HARD_TYP_CO ) && ( mask & AA_HARD_MSK_CO )) ------------------ | | 221| 0|#define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 105| 0|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 107| 0|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ | Branch (12276:17): [True: 0, False: 0] | Branch (12276:46): [True: 0, False: 0] ------------------ 12277| 0| { 12278| 0| nNumAcceptors_DB_O++; 12279| 0| } 12280| 0| else 12281| 0| { 12282| 0| if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 37| 0|#define ATT_ATOM_N 0x0040 ------------------ if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 94| 0|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ | Branch (12282:21): [True: 0, False: 0] | Branch (12282:47): [True: 0, False: 0] | Branch (12282:73): [True: 0, False: 0] ------------------ 12283| 0| at[i].valence == at[i].chem_bonds_valence) ------------------ | Branch (12283:22): [True: 0, False: 0] ------------------ 12284| 0| { 12285| 0| nNumDonors_SB_NH++; 12286| 0| } 12287| 0| } 12288| 0| } 12289| 0| num_max = inchi_min( nNumAcceptors_DB_O, nNumDonors_SB_NH ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 12290| 0| for (i = 0, num_success = 0; i < num_atoms && num_success < num_max && num_prot < 0; i++) ------------------ | Branch (12290:38): [True: 0, False: 0] | Branch (12290:55): [True: 0, False: 0] | Branch (12290:80): [True: 0, False: 0] ------------------ 12291| 0| { 12292| | /* Choose an atom */ 12293| 0| if (!at[i].endpoint || at[i].radical || at[i].sb_parity[0] || ------------------ | Branch (12293:17): [True: 0, False: 0] | Branch (12293:36): [True: 0, False: 0] | Branch (12293:53): [True: 0, False: 0] ------------------ 12294| 0| at[i].p_parity || bHasChargedNeighbor( at, i )) ------------------ | Branch (12294:18): [True: 0, False: 0] | Branch (12294:36): [True: 0, False: 0] ------------------ 12295| 0| { 12296| 0| continue; 12297| 0| } 12298| 0| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12299| 0| if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 37| 0|#define ATT_ATOM_N 0x0040 ------------------ if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 94| 0|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ | Branch (12299:17): [True: 0, False: 0] | Branch (12299:43): [True: 0, False: 0] | Branch (12299:69): [True: 0, False: 0] ------------------ 12300| 0| at[i].valence == at[i].chem_bonds_valence) ------------------ | Branch (12300:18): [True: 0, False: 0] ------------------ 12301| 0| { 12302| | /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 12303| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12304| 0| at[i].num_H--; 12305| 0| at[i].charge--; 12306| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12307| 0| num_prot++; 12308| 0| num_success++; 12309| 0| nNumSuccess++; 12310| 0| } 12311| 0| } 12312| 0| } 12313| | 12314| | /*exit_function:*/ 12315| | 12316| 1.16k| *num_protons_to_add = num_prot; 12317| | 12318| 1.16k| return ret < 0 ? ret : nNumSuccess; ------------------ | Branch (12318:12): [True: 0, False: 1.16k] ------------------ 12319| 1.16k|} AddRemoveIsoProtonsRestr: 12329| 1.53k|{ 12330| 1.53k| int i, j, k, n, ret = 0; 12331| 1.53k| int nNumSuccess = 0, min_at, max_at, num_H, num_iso_H, num_expl_H, num_expl_iso_H; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 12332| 1.53k| int iCurIso; /* 0=> 1H, 1=> D, 2=> T */ 12333| 1.53k| int iCurMode, iCurMode1, iCurMode2; /* 0=> Not Endpoints, 1=> Endpoints */ 12334| | 12335| | /* Distribute isotopes from heaviest to lightest; pick up atoms in order 1. Not endpoints; 2. Endpoints */ 12336| 1.53k| iCurMode1 = 0; 12337| 1.53k| iCurMode2 = num_tg ? 1 : 0; ------------------ | Branch (12337:17): [True: 3, False: 1.52k] ------------------ 12338| 3.05k| for (iCurMode = iCurMode1; iCurMode <= iCurMode2; iCurMode++) ------------------ | Branch (12338:32): [True: 1.53k, False: 1.52k] ------------------ 12339| 1.53k| { 12340| 6.11k| for (iCurIso = 2; 0 <= iCurIso; iCurIso--) ------------------ | Branch (12340:27): [True: 4.58k, False: 1.52k] ------------------ 12341| 4.58k| { 12342| | /* check for isotopic H to add */ 12343| 4.58k| if (!num_protons_to_add[iCurIso]) ------------------ | Branch (12343:17): [True: 3.02k, False: 1.56k] ------------------ 12344| 3.02k| { 12345| 3.02k| continue; 12346| 3.02k| } 12347| 1.56k| if (0 > num_protons_to_add[iCurIso]) ------------------ | Branch (12347:17): [True: 5, False: 1.55k] ------------------ 12348| 5| { 12349| 5| ret = RI_ERR_PROGR; ------------------ | |11963| 5|#define RI_ERR_PROGR (-3) ------------------ 12350| 5| goto exit_function; 12351| 5| } 12352| | 12353| | /* Limits for atom scanning */ 12354| 1.55k| min_at = 0; 12355| 1.55k| max_at = num_atoms; 12356| | 12357| | /* Cycle withio the limits */ 12358| 4.95k| for (i = min_at; i < max_at && 0 < num_protons_to_add[iCurIso]; i++) ------------------ | Branch (12358:30): [True: 3.43k, False: 1.52k] | Branch (12358:44): [True: 3.40k, False: 32] ------------------ 12359| 3.40k| { 12360| | /* Pick an atom */ 12361| 3.40k| if (iCurMode) ------------------ | Branch (12361:21): [True: 12, False: 3.38k] ------------------ 12362| 12| { 12363| 12| if (at[i].endpoint) ------------------ | Branch (12363:25): [True: 3, False: 9] ------------------ 12364| 3| { 12365| 3| j = i; /* atom number */ 12366| 3| } 12367| 9| else 12368| 9| { 12369| 9| continue; 12370| 9| } 12371| 12| } 12372| 3.38k| else 12373| 3.38k| { 12374| 3.38k| if (!at[i].endpoint && 1 == bHeteroAtomMayHaveXchgIsoH( at, i )) ------------------ | Branch (12374:25): [True: 3.38k, False: 4] | Branch (12374:44): [True: 249, False: 3.13k] ------------------ 12375| 249| { /* atom number */ 12376| 249| j = i; 12377| 249| } 12378| 3.14k| else 12379| 3.14k| { 12380| 3.14k| if (at[i].el_number == EL_NUMBER_H && at[i].charge == 1 && ------------------ | | 11| 6.28k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (12380:29): [True: 1.41k, False: 1.72k] | Branch (12380:63): [True: 651, False: 763] ------------------ 12381| 651| !at[i].valence && !at[i].radical && !at[i].iso_atw_diff) ------------------ | Branch (12381:30): [True: 651, False: 0] | Branch (12381:48): [True: 651, False: 0] | Branch (12381:66): [True: 584, False: 67] ------------------ 12382| 584| { 12383| | /* proton, not isotopic; make it isotopic */ 12384| 584| at[i].iso_atw_diff = 1 + iCurIso; 12385| 584| num_protons_to_add[iCurIso] --; 12386| 584| nNumSuccess++; 12387| 584| continue; 12388| 584| } 12389| 2.55k| else 12390| 2.55k| { 12391| 2.55k| continue; 12392| 2.55k| } 12393| 3.14k| } 12394| 3.38k| } 12395| | 12396| | /* j is the atom number */ 12397| | /* count implicit H */ 12398| 252| num_H = at[j].num_H; 12399| 252| num_iso_H = NUM_ISO_H(at, j); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 55| 252|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) ------------------ 12400| | 12401| 456| while (num_H > 0 && num_protons_to_add[iCurIso] > 0) ------------------ | Branch (12401:24): [True: 215, False: 241] | Branch (12401:37): [True: 204, False: 11] ------------------ 12402| 204| { 12403| | /* Substitute one implicit H with an isotopic atom H */ 12404| 204| at[j].num_iso_H[iCurIso] ++; 12405| 204| at[j].num_H--; 12406| 204| num_protons_to_add[iCurIso] --; 12407| 204| num_H--; 12408| 204| num_iso_H++; 12409| 204| nNumSuccess++; 12410| 204| } 12411| | /* Count explicit H */ 12412| 252| num_expl_H = num_expl_iso_H = 0; 12413| 252| for (k = 0; k < at[j].valence && num_atoms <= ( n = at[j].neighbor[k] ); k++) ------------------ | Branch (12413:29): [True: 252, False: 0] | Branch (12413:50): [True: 0, False: 252] ------------------ 12414| 0| { 12415| 0| num_expl_H += ( 0 == at[n].iso_atw_diff ); 12416| 0| num_expl_iso_H += ( 0 != at[n].iso_atw_diff ); 12417| 0| } 12418| 252| while (num_expl_H > 0 && num_protons_to_add[iCurIso] > 0) ------------------ | Branch (12418:24): [True: 0, False: 252] | Branch (12418:42): [True: 0, False: 0] ------------------ 12419| 0| { 12420| | /* Substitute one explicit H with an isotopic atom H */ 12421| 0| n = at[j].neighbor[num_expl_H]; 12422| 0| if (at[n].iso_atw_diff) ------------------ | Branch (12422:25): [True: 0, False: 0] ------------------ 12423| 0| { 12424| 0| ret = RI_ERR_PROGR; ------------------ | |11963| 0|#define RI_ERR_PROGR (-3) ------------------ 12425| 0| goto exit_function; 12426| 0| } 12427| 0| at[n].iso_atw_diff = 1 + iCurIso; 12428| 0| num_expl_H--; 12429| 0| num_expl_iso_H++; 12430| 0| num_protons_to_add[iCurIso] --; 12431| 0| nNumSuccess++; 12432| 0| } 12433| 252| } 12434| 1.55k| } 12435| 1.53k| } 12436| | 12437| 1.53k|exit_function: 12438| | 12439| 1.53k| return ret < 0 ? ret : nNumSuccess; ------------------ | Branch (12439:12): [True: 5, False: 1.52k] ------------------ 12440| 1.53k|} ichi_bns.c:remove_alt_bond_marks: 1953| 288k|{ 1954| 288k| int i, j, val; 1955| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1955:17): [True: 1.09M, False: 288k] ------------------ 1956| 1.09M| { 1957| 1.57M| for (val = at[i].valence, j = 0; j < val; j++) ------------------ | Branch (1957:42): [True: 479k, False: 1.09M] ------------------ 1958| 479k| { 1959| 479k| at[i].bond_type[j] &= BOND_TYPE_MASK; ------------------ | | 189| 479k|#define BOND_TYPE_MASK 0x0f ------------------ 1960| 479k| } 1961| 1.09M| } 1962| | 1963| 288k|} inchi_ios_init: 51| 44.5k|{ 52| 44.5k| memset(ios, 0, sizeof(*ios)); /* djb-rwth: memset_s C11/Annex K variant? */ 53| 44.5k| switch (io_type) 54| 44.5k| { 55| 0| case INCHI_IOS_TYPE_FILE: ------------------ | | 1017| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (55:5): [True: 0, False: 44.5k] ------------------ 56| 0| ios->type = INCHI_IOS_TYPE_FILE; ------------------ | | 1017| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ 57| 0| break; 58| 44.5k| case INCHI_IOS_TYPE_STRING: ------------------ | | 1016| 44.5k|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (58:5): [True: 44.5k, False: 0] ------------------ 59| 44.5k| default: ------------------ | Branch (59:5): [True: 0, False: 44.5k] ------------------ 60| 44.5k| ios->type = INCHI_IOS_TYPE_STRING; ------------------ | | 1016| 44.5k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 61| 44.5k| break; 62| 44.5k| } 63| 44.5k| ios->f = f; 64| 44.5k| return; 65| 44.5k|} inchi_ios_close: 195| 31.8k|{ 196| 31.8k| if (NULL == ios) ------------------ | Branch (196:9): [True: 0, False: 31.8k] ------------------ 197| 0| { 198| 0| return; 199| 0| } 200| 31.8k| if (ios->s.pStr) ------------------ | Branch (200:9): [True: 6.28k, False: 25.5k] ------------------ 201| 6.28k| { 202| 6.28k| inchi_free(ios->s.pStr); ------------------ | | 1152| 6.28k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.28k, False: 0] | | | Branch (1152:50): [Folded, False: 6.28k] | | ------------------ ------------------ 203| 6.28k| } 204| 31.8k| ios->s.pStr = NULL; 205| 31.8k| ios->s.nUsedLength = ios->s.nAllocatedLength = ios->s.nPtr = 0; 206| | 207| 31.8k| if (NULL != ios->f && stdout != ios->f && stderr != ios->f && stdin != ios->f) ------------------ | Branch (207:9): [True: 0, False: 31.8k] | Branch (207:27): [True: 0, False: 0] | Branch (207:47): [True: 0, False: 0] | Branch (207:67): [True: 0, False: 0] ------------------ 208| 0| { 209| 0| fclose(ios->f); 210| 0| } 211| | 212| 31.8k| return; 213| 31.8k|} inchi_ios_reset: 221| 6.37k|{ 222| 6.37k| ios->s.pStr = NULL; 223| 6.37k| ios->s.nUsedLength = ios->s.nAllocatedLength = ios->s.nPtr = 0; 224| 6.37k| if (NULL != ios->f && stdout != ios->f && stderr != ios->f && stdin != ios->f) ------------------ | Branch (224:9): [True: 0, False: 6.37k] | Branch (224:27): [True: 0, False: 0] | Branch (224:47): [True: 0, False: 0] | Branch (224:67): [True: 0, False: 0] ------------------ 225| 0| { 226| 0| fclose(ios->f); 227| 0| } 228| | 229| 6.37k| return; 230| 6.37k|} inchi_ios_print: 443| 487|{ 444| 487| int ret = 0, ret2 = 0; 445| 487| va_list argList; 446| | 447| 487| if (!ios) ------------------ | Branch (447:9): [True: 0, False: 487] ------------------ 448| 0| { 449| 0| return -1; 450| 0| } 451| | 452| 487| if (ios->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1016| 487|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (452:9): [True: 487, False: 0] ------------------ 453| 487| { 454| | /* output to string buffer */ 455| 487| int max_len; 456| 487| my_va_start(argList, lpszFormat); ------------------ | | 22| 487|#define my_va_start va_start ------------------ 457| 487| max_len = GetMaxPrintfLength(lpszFormat, argList); 458| 487| va_end(argList); 459| 487| if (max_len >= 0) ------------------ | Branch (459:13): [True: 487, False: 0] ------------------ 460| 487| { 461| | /* djb-rwth: fixing oss-fuzz issue #30152 */ 462| 487| int nAddLength = inchi_max(INCHI_ADD_STR_LEN, max_len); ------------------ | | 138| 487|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 469, False: 18] | | ------------------ ------------------ 463| 487| long long new_str_len = (long long)ios->s.nAllocatedLength + (long long)nAddLength; 464| 487| if (ios->s.nAllocatedLength - ios->s.nUsedLength <= max_len) ------------------ | Branch (464:17): [True: 487, False: 0] ------------------ 465| 487| { 466| | /* enlarge output string */ 467| 487| char* new_str = (char*)inchi_calloc(new_str_len, sizeof(char)); /* djb-rwth: cast operators added */ ------------------ | | 1146| 487|#define inchi_calloc calloc ------------------ 468| 487| if (new_str) ------------------ | Branch (468:21): [True: 487, False: 0] ------------------ 469| 487| { 470| 487| if (ios->s.pStr) ------------------ | Branch (470:25): [True: 0, False: 487] ------------------ 471| 0| { 472| 0| if (ios->s.nUsedLength > 0) ------------------ | Branch (472:29): [True: 0, False: 0] ------------------ 473| 0| { 474| 0| memcpy(new_str, ios->s.pStr, sizeof(new_str[0]) * ios->s.nUsedLength); 475| 0| } 476| 0| inchi_free(ios->s.pStr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 477| 0| } 478| 487| ios->s.pStr = new_str; 479| 487| ios->s.nAllocatedLength += nAddLength; 480| 487| } 481| 0| else 482| 0| { 483| 0| return -1; /* failed */ 484| 0| } 485| 487| } 486| | /* output */ 487| 487| my_va_start(argList, lpszFormat); ------------------ | | 22| 487|#define my_va_start va_start ------------------ 488| 487| ret = vsprintf(ios->s.pStr + ios->s.nUsedLength, lpszFormat, argList); /* djb-rwth: not using vsnprintf due to variable length argument */ 489| 487| va_end(argList); 490| 487| if (ret >= 0) ------------------ | Branch (490:17): [True: 487, False: 0] ------------------ 491| 487| { 492| 487| ios->s.nUsedLength += ret; 493| 487| } 494| |#ifdef TARGET_LIB_FOR_WINCHI 495| |#if 0 496| | if (FWPRINT) 497| | { 498| | my_va_start(argList, lpszFormat); 499| | FWPRINT(lpszFormat, argList); 500| | va_end(argList); 501| | } 502| |#endif 503| |#endif 504| 487| return ret; 505| 487| } 506| 0| return -1; 507| 487| } 508| | 509| 0| else if (ios->type == INCHI_IOS_TYPE_FILE) ------------------ | | 1017| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (509:14): [True: 0, False: 0] ------------------ 510| 0| { 511| | /* output to file */ 512| 0| if (ios->f) ------------------ | Branch (512:13): [True: 0, False: 0] ------------------ 513| 0| { 514| 0| my_va_start(argList, lpszFormat); ------------------ | | 22| 0|#define my_va_start va_start ------------------ 515| 0| ret = vfprintf(ios->f, lpszFormat, argList); 516| 0| va_end(argList); 517| 0| } 518| 0| else 519| 0| { 520| 0| my_va_start(argList, lpszFormat); ------------------ | | 22| 0|#define my_va_start va_start ------------------ 521| 0| ret2 = vfprintf(stdout, lpszFormat, argList); 522| 0| va_end(argList); 523| 0| } 524| |#ifdef TARGET_LIB_FOR_WINCHI 525| | if (FWPRINT) 526| | { 527| | my_va_start(argList, lpszFormat); 528| | FWPRINT(lpszFormat, argList); 529| | va_end(argList); 530| | } 531| |#endif 532| 0| return ret ? ret : ret2; ------------------ | Branch (532:16): [True: 0, False: 0] ------------------ 533| 0| } 534| | 535| | /* no output */ 536| 0| return 0; 537| 487|} inchi_ios_print_nodisplay: 572| 34.4k|{ 573| 34.4k| va_list argList; 574| | 575| 34.4k| if (!ios) ------------------ | Branch (575:9): [True: 0, False: 34.4k] ------------------ 576| 0| { 577| 0| return -1; 578| 0| } 579| | 580| 34.4k| if (ios->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1016| 34.4k|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (580:9): [True: 34.4k, False: 0] ------------------ 581| 34.4k| { 582| | /* output to string buffer */ 583| 34.4k| int ret = 0, max_len; 584| 34.4k| my_va_start( argList, lpszFormat ); ------------------ | | 22| 34.4k|#define my_va_start va_start ------------------ 585| 34.4k| max_len = GetMaxPrintfLength( lpszFormat, argList ); 586| 34.4k| va_end( argList ); 587| 34.4k| if (max_len >= 0) ------------------ | Branch (587:13): [True: 34.4k, False: 0] ------------------ 588| 34.4k| { 589| | /* djb-rwth: fixing oss-fuzz issue #30163 */ 590| 34.4k| int nAddLength = inchi_max(INCHI_ADD_STR_LEN, max_len); ------------------ | | 138| 34.4k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 34.3k, False: 23] | | ------------------ ------------------ 591| 34.4k| long long new_str_len = (long long)ios->s.nAllocatedLength + (long long)nAddLength; 592| 34.4k| if (ios->s.nAllocatedLength - ios->s.nUsedLength <= max_len) ------------------ | Branch (592:17): [True: 11.3k, False: 23.1k] ------------------ 593| 11.3k| { 594| | /* enlarge output string */ 595| 11.3k| char* new_str = (char*)inchi_calloc(new_str_len, sizeof(new_str[0])); /* djb-rwth: cast operators added */ ------------------ | | 1146| 11.3k|#define inchi_calloc calloc ------------------ 596| 11.3k| if (new_str) ------------------ | Branch (596:21): [True: 11.3k, False: 0] ------------------ 597| 11.3k| { 598| 11.3k| if (ios->s.pStr) ------------------ | Branch (598:25): [True: 0, False: 11.3k] ------------------ 599| 0| { 600| 0| if (ios->s.nUsedLength > 0) ------------------ | Branch (600:29): [True: 0, False: 0] ------------------ 601| 0| { 602| 0| memcpy( new_str, ios->s.pStr, sizeof( new_str[0] )*ios->s.nUsedLength ); 603| 0| } 604| 0| inchi_free( ios->s.pStr ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 605| 0| } 606| 11.3k| ios->s.pStr = new_str; 607| 11.3k| ios->s.nAllocatedLength += nAddLength; 608| 11.3k| } 609| 0| else 610| 0| { 611| 0| return -1; /* failed */ 612| 0| } 613| 11.3k| } 614| | /* output */ 615| | /* djb-rwth: fixing oss-fuzz issue #67676 */ 616| 34.4k| my_va_start(argList, lpszFormat); ------------------ | | 22| 34.4k|#define my_va_start va_start ------------------ 617| 34.4k| size_t remaining_length = (size_t)(ios->s.nAllocatedLength - ios->s.nUsedLength); 618| 34.4k| ret = vsnprintf(ios->s.pStr + ios->s.nUsedLength, remaining_length, lpszFormat, argList); 619| 34.4k| va_end(argList); 620| | 621| | /* djb-rwth: if vsnprintf fails, try again with + 1 */ 622| 34.4k| if (ret < 0 || (size_t)ret >= remaining_length) ------------------ | Branch (622:17): [True: 0, False: 34.4k] | Branch (622:28): [True: 23, False: 34.3k] ------------------ 623| 23| { 624| 23| long long str_length_extension; 625| 23| if (ret >= 0) ------------------ | Branch (625:21): [True: 23, False: 0] ------------------ 626| 23| { 627| 23| str_length_extension = (long long)ret + 1; 628| 23| } 629| 0| else 630| 0| { 631| 0| str_length_extension = (long long)max_len + 1; 632| 0| } 633| 23| long long new_str_length = (long long)ios->s.nAllocatedLength + str_length_extension; 634| 23| char* new_str = (char*)inchi_calloc(new_str_length, sizeof(new_str[0])); ------------------ | | 1146| 23|#define inchi_calloc calloc ------------------ 635| 23| if (!new_str) ------------------ | Branch (635:21): [True: 0, False: 23] ------------------ 636| 0| { 637| 0| return -1; 638| 0| } 639| 23| if (ios->s.pStr) ------------------ | Branch (639:21): [True: 23, False: 0] ------------------ 640| 23| { 641| 23| if (ios->s.nUsedLength > 0) ------------------ | Branch (641:25): [True: 0, False: 23] ------------------ 642| 0| { 643| 0| memcpy(new_str, ios->s.pStr, sizeof(new_str[0]) * ios->s.nUsedLength); 644| 0| } 645| 23| inchi_free(ios->s.pStr); ------------------ | | 1152| 23|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 23, False: 0] | | | Branch (1152:50): [Folded, False: 23] | | ------------------ ------------------ 646| 23| } 647| 23| ios->s.pStr = new_str; 648| 23| ios->s.nAllocatedLength += (int)str_length_extension; 649| | 650| | // try printing again 651| 23| my_va_start(argList, lpszFormat); ------------------ | | 22| 23|#define my_va_start va_start ------------------ 652| 23| size_t remainingLength2 = (size_t)(ios->s.nAllocatedLength - ios->s.nUsedLength); 653| 23| ret = vsnprintf(ios->s.pStr + ios->s.nUsedLength, remainingLength2, lpszFormat, argList); 654| 23| va_end(argList); 655| 23| } 656| | 657| 34.4k| if (ret >= 0) ------------------ | Branch (657:17): [True: 34.4k, False: 0] ------------------ 658| 34.4k| { 659| 34.4k| ios->s.nUsedLength += ret; 660| 34.4k| } 661| 34.4k| return ret; 662| 34.4k| } 663| 0| return -1; 664| 34.4k| } 665| | 666| 0| else if (ios->type == INCHI_IOS_TYPE_FILE) ------------------ | | 1017| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (666:14): [True: 0, False: 0] ------------------ 667| 0| { 668| 0| my_va_start( argList, lpszFormat ); ------------------ | | 22| 0|#define my_va_start va_start ------------------ 669| 0| inchi_print_nodisplay( ios->f, lpszFormat, argList ); 670| 0| va_end( argList ); 671| 0| } 672| | 673| | /* no output */ 674| 0| return 0; 675| 34.4k|} inchi_ios_eprint: 712| 148k|{ 713| 148k| int ret = 0, ret2 = 0; 714| 148k| va_list argList; 715| | 716| 148k| if (!ios) ------------------ | Branch (716:9): [True: 9.46k, False: 139k] ------------------ 717| 9.46k| { 718| 9.46k| return -1; 719| 9.46k| } 720| | 721| 139k| if (ios->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1016| 139k|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (721:9): [True: 139k, False: 0] ------------------ 722| | /* was #if ( defined(TARGET_API_LIB) || defined(INCHI_STANDALONE_EXE) ) */ 723| 139k| { 724| | /* output to string buffer */ 725| 139k| int max_len, nAddLength = 0; 726| 139k| char* new_str = NULL; 727| | 728| 139k| my_va_start(argList, lpszFormat); ------------------ | | 22| 139k|#define my_va_start va_start ------------------ 729| 139k| max_len = GetMaxPrintfLength(lpszFormat, argList); 730| 139k| va_end(argList); 731| | 732| 139k| if (max_len >= 0) ------------------ | Branch (732:13): [True: 139k, False: 0] ------------------ 733| 139k| { 734| 139k| if (ios->s.nAllocatedLength - ios->s.nUsedLength <= max_len) ------------------ | Branch (734:17): [True: 12.5k, False: 126k] ------------------ 735| 12.5k| { 736| | /* enlarge output string */ 737| 12.5k| nAddLength = inchi_max(INCHI_ADD_STR_LEN, max_len); ------------------ | | 138| 12.5k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 12.5k, False: 0] | | ------------------ ------------------ 738| 12.5k| new_str = (char*)inchi_calloc((long long)ios->s.nAllocatedLength + (long long)nAddLength, sizeof(new_str[0])); /* djb-rwth: cast operators added */ ------------------ | | 1146| 12.5k|#define inchi_calloc calloc ------------------ 739| 12.5k| if (new_str) ------------------ | Branch (739:21): [True: 12.5k, False: 0] ------------------ 740| 12.5k| { 741| 12.5k| if (ios->s.pStr) ------------------ | Branch (741:25): [True: 0, False: 12.5k] ------------------ 742| 0| { 743| 0| if (ios->s.nUsedLength > 0) ------------------ | Branch (743:29): [True: 0, False: 0] ------------------ 744| 0| { 745| 0| memcpy(new_str, ios->s.pStr, sizeof(new_str[0]) * ios->s.nUsedLength); 746| 0| } 747| 0| inchi_free(ios->s.pStr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 748| 0| } 749| 12.5k| ios->s.pStr = new_str; 750| 12.5k| ios->s.nAllocatedLength += nAddLength; 751| 12.5k| } 752| 0| else 753| 0| { 754| 0| return -1; /* failed */ 755| 0| } 756| 12.5k| } 757| | 758| | /* output */ 759| 139k| my_va_start(argList, lpszFormat); ------------------ | | 22| 139k|#define my_va_start va_start ------------------ 760| 139k| ret = vsprintf(ios->s.pStr + ios->s.nUsedLength, lpszFormat, argList); 761| 139k| va_end(argList); 762| 139k| if (ret >= 0) ------------------ | Branch (762:17): [True: 139k, False: 0] ------------------ 763| 139k| { 764| 139k| ios->s.nUsedLength += ret; 765| 139k| } 766| 139k| return ret; 767| 139k| } 768| 0| return -1; 769| 139k| } 770| | 771| 0| else if (ios->type == INCHI_IOS_TYPE_FILE) ------------------ | | 1017| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (771:14): [True: 0, False: 0] ------------------ 772| 0| { 773| 0| if (ios->f) ------------------ | Branch (773:13): [True: 0, False: 0] ------------------ 774| 0| { 775| | /* output to plain file */ 776| 0| my_va_start(argList, lpszFormat); ------------------ | | 22| 0|#define my_va_start va_start ------------------ 777| 0| ret = inchi_vfprintf(ios->f, lpszFormat, argList); 778| 0| va_end(argList); 779| | /* No output to stderr from within dll or GUI program */ 780| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) 781| | if (ios->f != stderr) 782| | { 783| | my_va_start(argList, lpszFormat); 784| | ret2 = vfprintf(stderr, lpszFormat, argList); 785| | va_end(argList); 786| | } 787| |#endif 788| 0| return ret ? ret : ret2; ------------------ | Branch (788:20): [True: 0, False: 0] ------------------ 789| 0| } 790| 0| } 791| | 792| | /* no output */ 793| 0| return 0; 794| 139k|} GetMaxPrintfLength: 1069| 347k|{ 1070| | /*ASSERT(AfxIsValidString(lpszFormat, FALSE));*/ 1071| 347k| const char* lpsz; 1072| 347k| int nMaxLen, nWidth, nPrecision, nModifier, nItemLen; 1073| | 1074| 347k| nMaxLen = 0; 1075| | /* make a guess at the maximum length of the resulting string */ 1076| 5.27M| for (lpsz = lpszFormat; *lpsz; lpsz++) ------------------ | Branch (1076:29): [True: 4.92M, False: 347k] ------------------ 1077| 4.92M| { 1078| | /* moved from below for C syntax reason - 2024-09-01 DT */ 1079| | /* djb-rwth: return values needed for va_arg; djb-rwth: ignoring LLVM warnings: function returning value */ 1080| 4.92M| int ivarg; 1081| 4.92M| double dvarg; 1082| 4.92M| void* ivvarg; 1083| 4.92M| int* ipvarg; 1084| | 1085| | /* handle '%' character, but watch out for '%%' */ 1086| 4.92M| if (*lpsz != '%' || *(++lpsz) == '%') ------------------ | Branch (1086:13): [True: 4.72M, False: 195k] | Branch (1086:29): [True: 0, False: 195k] ------------------ 1087| 4.72M| { 1088| 4.72M| nMaxLen += 1; 1089| 4.72M| continue; 1090| 4.72M| } 1091| | 1092| 195k| nItemLen = 0; 1093| | 1094| | /* handle '%' character with format */ 1095| 195k| nWidth = 0; 1096| 198k| for (; *lpsz; lpsz++) ------------------ | Branch (1096:16): [True: 198k, False: 0] ------------------ 1097| 198k| { 1098| | /* check for valid flags */ 1099| 198k| if (*lpsz == '#') ------------------ | Branch (1099:17): [True: 0, False: 198k] ------------------ 1100| 0| { 1101| 0| nMaxLen += 2; /* for '0x' */ 1102| 0| } 1103| 198k| else if (*lpsz == '*') ------------------ | Branch (1103:22): [True: 0, False: 198k] ------------------ 1104| 0| { 1105| 0| nWidth = va_arg(argList, int); 1106| 0| } 1107| 198k| else if (*lpsz == '-' || *lpsz == '+' || *lpsz == '0' ------------------ | Branch (1107:22): [True: 1.77k, False: 196k] | Branch (1107:38): [True: 393, False: 195k] | Branch (1107:54): [True: 0, False: 195k] ------------------ 1108| 195k| || *lpsz == ' ') ------------------ | Branch (1108:20): [True: 0, False: 195k] ------------------ 1109| 2.16k| { 1110| 2.16k| ; 1111| 2.16k| } 1112| 195k| else /* hit non-flag character */ 1113| 195k| { 1114| 195k| break; 1115| 195k| } 1116| 198k| } 1117| | /* get width and skip it */ 1118| 195k| if (nWidth == 0) ------------------ | Branch (1118:13): [True: 195k, False: 0] ------------------ 1119| 195k| { 1120| | /* width indicated by */ 1121| 195k| nWidth = atoi(lpsz); 1122| 195k| for (; *lpsz && isdigit(*lpsz); lpsz++) ------------------ | Branch (1122:20): [True: 195k, False: 0] | Branch (1122:29): [True: 0, False: 195k] ------------------ 1123| 0| { 1124| 0| ; 1125| 0| } 1126| 195k| } 1127| | /*ASSERT(nWidth >= 0);*/ 1128| 195k| if (nWidth < 0) ------------------ | Branch (1128:13): [True: 0, False: 195k] ------------------ 1129| 0| { 1130| 0| goto exit_error; /* instead of exception */ 1131| 0| } 1132| | 1133| 195k| nPrecision = 0; 1134| 195k| if (*lpsz == '.') ------------------ | Branch (1134:13): [True: 0, False: 195k] ------------------ 1135| 0| { 1136| | /* skip past '.' separator (width.precision)*/ 1137| 0| lpsz++; 1138| | 1139| | /* get precision and skip it*/ 1140| 0| if (*lpsz == '*') ------------------ | Branch (1140:17): [True: 0, False: 0] ------------------ 1141| 0| { 1142| 0| nPrecision = va_arg(argList, int); 1143| 0| lpsz++; 1144| 0| } 1145| 0| else 1146| 0| { 1147| 0| nPrecision = atoi(lpsz); 1148| 0| for (; *lpsz && isdigit(*lpsz); lpsz++) ------------------ | Branch (1148:24): [True: 0, False: 0] | Branch (1148:33): [True: 0, False: 0] ------------------ 1149| 0| { 1150| 0| ; 1151| 0| } 1152| 0| } 1153| 0| if (nPrecision < 0) ------------------ | Branch (1153:17): [True: 0, False: 0] ------------------ 1154| 0| { 1155| 0| goto exit_error; /* instead of exception */ 1156| 0| } 1157| 0| } 1158| | 1159| | /* should be on type modifier or specifier */ 1160| 195k| nModifier = 0; 1161| 195k| switch (*lpsz) ------------------ | Branch (1161:17): [True: 0, False: 195k] ------------------ 1162| 195k| { 1163| | /* modifiers that affect size */ 1164| 0| case 'h': ------------------ | Branch (1164:9): [True: 0, False: 195k] ------------------ 1165| 0| switch (lpsz[1]) 1166| 0| { 1167| 0| case 'd': ------------------ | Branch (1167:13): [True: 0, False: 0] ------------------ 1168| 0| case 'i': ------------------ | Branch (1168:13): [True: 0, False: 0] ------------------ 1169| 0| case 'o': ------------------ | Branch (1169:13): [True: 0, False: 0] ------------------ 1170| 0| case 'x': ------------------ | Branch (1170:13): [True: 0, False: 0] ------------------ 1171| 0| case 'X': ------------------ | Branch (1171:13): [True: 0, False: 0] ------------------ 1172| 0| case 'u': ------------------ | Branch (1172:13): [True: 0, False: 0] ------------------ 1173| | /* short unsigned, short double, etc. -- added to the original MS example */ 1174| | /* ignore the fact that these modifiers do affect size */ 1175| 0| lpsz++; 1176| 0| break; 1177| 0| default: ------------------ | Branch (1177:13): [True: 0, False: 0] ------------------ 1178| 0| nModifier = FORCE_ANSI; ------------------ | | 1062| 0|#define FORCE_ANSI 0x10000 ------------------ 1179| 0| lpsz++; 1180| 0| break; 1181| 0| } 1182| 0| break; 1183| 0| case 'l': ------------------ | Branch (1183:9): [True: 0, False: 195k] ------------------ 1184| 0| switch (lpsz[1]) 1185| 0| { 1186| 0| case 'd': ------------------ | Branch (1186:13): [True: 0, False: 0] ------------------ 1187| 0| case 'i': ------------------ | Branch (1187:13): [True: 0, False: 0] ------------------ 1188| 0| case 'o': ------------------ | Branch (1188:13): [True: 0, False: 0] ------------------ 1189| 0| case 'x': ------------------ | Branch (1189:13): [True: 0, False: 0] ------------------ 1190| 0| case 'X': ------------------ | Branch (1190:13): [True: 0, False: 0] ------------------ 1191| 0| case 'u': ------------------ | Branch (1191:13): [True: 0, False: 0] ------------------ 1192| 0| case 'f': /* long float -- post ANSI C */ ------------------ | Branch (1192:13): [True: 0, False: 0] ------------------ 1193| | /* long unsigned, long double, etc. -- added to the original MS example */ 1194| | /* ignore the fact that these modifiers do affect size */ 1195| 0| lpsz++; 1196| 0| break; 1197| 0| default: ------------------ | Branch (1197:13): [True: 0, False: 0] ------------------ 1198| | /* 1199| | nModifier = FORCE_UNICODE; 1200| | lpsz ++; 1201| | break; 1202| | */ 1203| 0| goto exit_error; /* no UNICODE, please */ 1204| 0| } 1205| 0| break; 1206| | /* modifiers that do not affect size */ 1207| 0| case 'F': ------------------ | Branch (1207:9): [True: 0, False: 195k] ------------------ 1208| 0| case 'N': ------------------ | Branch (1208:9): [True: 0, False: 195k] ------------------ 1209| 0| case 'L': ------------------ | Branch (1209:9): [True: 0, False: 195k] ------------------ 1210| 0| lpsz++; 1211| 0| break; 1212| 195k| } 1213| | 1214| | /* now should be on specifier */ 1215| | 1216| 195k| switch (*lpsz | nModifier) ------------------ | Branch (1216:17): [True: 179k, False: 16.8k] ------------------ 1217| 195k| { 1218| | /* single characters*/ 1219| 0| case 'c': ------------------ | Branch (1219:9): [True: 0, False: 195k] ------------------ 1220| 0| case 'C': ------------------ | Branch (1220:9): [True: 0, False: 195k] ------------------ 1221| 0| nItemLen = 2; 1222| 0| ivarg = va_arg(argList, int); /* djb-rwth: int return value; ignoring LLVM warning */ 1223| 0| break; 1224| 0| case 'c' | FORCE_ANSI: ------------------ | | 1062| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1224:9): [True: 0, False: 195k] ------------------ 1225| 0| case 'C' | FORCE_ANSI: ------------------ | | 1062| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1225:9): [True: 0, False: 195k] ------------------ 1226| 0| nItemLen = 2; 1227| 0| ivarg = va_arg(argList, int); /* djb-rwth: int return value; ignoring LLVM warning */ 1228| 0| break; 1229| 0| case 'c' | FORCE_UNICODE: ------------------ | | 1063| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1229:9): [True: 0, False: 195k] ------------------ 1230| 0| case 'C' | FORCE_UNICODE: ------------------ | | 1063| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1230:9): [True: 0, False: 195k] ------------------ 1231| 0| goto exit_error; /* no UNICODE, please */ 1232| | /* 1233| | nItemLen = 2; 1234| | va_arg(argList, wchar_t); 1235| | break; 1236| | */ 1237| | 1238| | /* strings*/ 1239| 179k| case 's': ------------------ | Branch (1239:9): [True: 179k, False: 16.8k] ------------------ 1240| 179k| case 'S': ------------------ | Branch (1240:9): [True: 0, False: 195k] ------------------ 1241| 179k| nItemLen = (int)strlen(va_arg(argList, char*)); 1242| 179k| nItemLen = inchi_max(1, nItemLen); ------------------ | | 138| 179k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 46.5k, False: 132k] | | ------------------ ------------------ 1243| 179k| break; 1244| 0| case 's' | FORCE_ANSI: ------------------ | | 1062| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1244:9): [True: 0, False: 195k] ------------------ 1245| 0| case 'S' | FORCE_ANSI: ------------------ | | 1062| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1245:9): [True: 0, False: 195k] ------------------ 1246| 0| nItemLen = (int)strlen(va_arg(argList, char*)); 1247| 0| nItemLen = inchi_max(1, nItemLen); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 1248| 0| break; 1249| | 1250| 0| case 's' | FORCE_UNICODE: ------------------ | | 1063| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1250:9): [True: 0, False: 195k] ------------------ 1251| 0| case 'S' | FORCE_UNICODE: ------------------ | | 1063| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1251:9): [True: 0, False: 195k] ------------------ 1252| 0| goto exit_error; /* no UNICODE, please */ 1253| | /* 1254| | nItemLen = wcslen(va_arg(argList, wchar_t*)); 1255| | nItemLen = inchi_max(1, nItemLen); 1256| | break; 1257| | */ 1258| 195k| } 1259| | 1260| | /* adjust nItemLen for strings */ 1261| 195k| if (nItemLen != 0) ------------------ | Branch (1261:13): [True: 179k, False: 16.8k] ------------------ 1262| 179k| { 1263| 179k| nItemLen = inchi_max(nItemLen, nWidth); ------------------ | | 138| 179k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 179k, False: 0] | | ------------------ ------------------ 1264| 179k| if (nPrecision != 0) ------------------ | Branch (1264:17): [True: 0, False: 179k] ------------------ 1265| 0| { 1266| 0| nItemLen = inchi_min(nItemLen, nPrecision); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 1267| 0| } 1268| 179k| } 1269| 16.8k| else 1270| 16.8k| { 1271| 16.8k| switch (*lpsz) 1272| 16.8k| { 1273| | /* integers */ 1274| 16.8k| case 'd': ------------------ | Branch (1274:13): [True: 16.8k, False: 0] ------------------ 1275| 16.8k| case 'i': ------------------ | Branch (1275:13): [True: 0, False: 16.8k] ------------------ 1276| 16.8k| case 'u': ------------------ | Branch (1276:13): [True: 0, False: 16.8k] ------------------ 1277| 16.8k| case 'x': ------------------ | Branch (1277:13): [True: 0, False: 16.8k] ------------------ 1278| 16.8k| case 'X': ------------------ | Branch (1278:13): [True: 0, False: 16.8k] ------------------ 1279| 16.8k| case 'o': ------------------ | Branch (1279:13): [True: 0, False: 16.8k] ------------------ 1280| 16.8k| ivarg = va_arg(argList, int); /* djb-rwth: int return value; ignoring LLVM warning */ 1281| 16.8k| nItemLen = 32; 1282| 16.8k| nItemLen = inchi_max(nItemLen, nWidth + nPrecision); ------------------ | | 138| 16.8k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 16.8k, False: 0] | | ------------------ ------------------ 1283| 16.8k| break; 1284| | 1285| 0| case 'e': ------------------ | Branch (1285:13): [True: 0, False: 16.8k] ------------------ 1286| 0| case 'f': ------------------ | Branch (1286:13): [True: 0, False: 16.8k] ------------------ 1287| 0| case 'g': ------------------ | Branch (1287:13): [True: 0, False: 16.8k] ------------------ 1288| 0| case 'G': ------------------ | Branch (1288:13): [True: 0, False: 16.8k] ------------------ 1289| 0| dvarg = va_arg(argList, double); /* djb-rwth: double return value; ignoring LLVM warning */ 1290| 0| nItemLen = 32; 1291| 0| nItemLen = inchi_max(nItemLen, nWidth + nPrecision); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 1292| 0| break; 1293| | 1294| 0| case 'p': ------------------ | Branch (1294:13): [True: 0, False: 16.8k] ------------------ 1295| 0| ivvarg = va_arg(argList, void*); /* djb-rwth: void* return value; ignoring LLVM warning */ 1296| 0| nItemLen = 32; 1297| 0| nItemLen = inchi_max(nItemLen, nWidth + nPrecision); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 1298| 0| break; 1299| | 1300| | /* no output */ 1301| 0| case 'n': ------------------ | Branch (1301:13): [True: 0, False: 16.8k] ------------------ 1302| 0| ipvarg = va_arg(argList, int*); /* djb-rwth: int* return value; ignoring LLVM warning */ 1303| 0| break; 1304| | 1305| 0| default: ------------------ | Branch (1305:13): [True: 0, False: 16.8k] ------------------ 1306| | /*ASSERT(FALSE);*/ /* unknown formatting option*/ 1307| 0| goto exit_error; /* instead of exception */ 1308| 16.8k| } 1309| 16.8k| } 1310| | 1311| | /* adjust nMaxLen for output nItemLen */ 1312| 195k| nMaxLen += nItemLen; 1313| 195k| } 1314| 347k| return nMaxLen; 1315| | 1316| 0|exit_error: 1317| 0| return -1; /* wrong format */ 1318| 347k|} inchi_strbuf_init: 1374| 75.8k|{ 1375| 75.8k| char* new_str = NULL; 1376| 75.8k| memset(buf, 0, sizeof(*buf)); /* djb-rwth: memset_s C11/Annex K variant? */ 1377| | 1378| 75.8k| if (start_size <= 0) ------------------ | Branch (1378:9): [True: 0, False: 75.8k] ------------------ 1379| 0| { 1380| 0| start_size = INCHI_STRBUF_INITIAL_SIZE; ------------------ | | 65| 0|#define INCHI_STRBUF_INITIAL_SIZE 262144 ------------------ 1381| 0| } 1382| 75.8k| if (incr_size <= 0) ------------------ | Branch (1382:9): [True: 0, False: 75.8k] ------------------ 1383| 0| { 1384| 0| incr_size = INCHI_STRBUF_SIZE_INCREMENT; ------------------ | | 66| 0|#define INCHI_STRBUF_SIZE_INCREMENT 262144 ------------------ 1385| 0| } 1386| | 1387| 75.8k| new_str = (char*)inchi_calloc(start_size, sizeof(char)); ------------------ | | 1146| 75.8k|#define inchi_calloc calloc ------------------ 1388| | 1389| 75.8k| if (!new_str) ------------------ | Branch (1389:9): [True: 0, False: 75.8k] ------------------ 1390| 0| { 1391| 0| return -1; 1392| 0| } 1393| | 1394| 75.8k| buf->pStr = new_str; 1395| 75.8k| buf->nAllocatedLength = start_size; 1396| 75.8k| buf->nPtr = incr_size; 1397| | 1398| 75.8k| return start_size; 1399| 75.8k|} inchi_strbuf_reset: 1407| 23.8k|{ 1408| 23.8k| if (!buf) ------------------ | Branch (1408:9): [True: 0, False: 23.8k] ------------------ 1409| 0| { 1410| 0| return; 1411| 0| } 1412| 23.8k| if (buf->pStr) ------------------ | Branch (1412:9): [True: 23.8k, False: 0] ------------------ 1413| 23.8k| { 1414| 23.8k| buf->pStr[0] = '\0'; 1415| 23.8k| } 1416| | 1417| 23.8k| buf->nUsedLength = buf->nPtr = 0; 1418| 23.8k|} inchi_strbuf_close: 1426| 76.3k|{ 1427| 76.3k| if (!buf) ------------------ | Branch (1427:9): [True: 0, False: 76.3k] ------------------ 1428| 0| { 1429| 0| return; 1430| 0| } 1431| 76.3k| if (buf->pStr) ------------------ | Branch (1431:9): [True: 76.3k, False: 0] ------------------ 1432| 76.3k| { 1433| 76.3k| inchi_free(buf->pStr); ------------------ | | 1152| 76.3k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 76.3k, False: 0] | | | Branch (1152:50): [Folded, False: 76.3k] | | ------------------ ------------------ 1434| 76.3k| } 1435| | 1436| 76.3k| memset(buf, 0, sizeof(*buf)); /* djb-rwth: memset_s C11/Annex K variant? */ 1437| 76.3k|} inchi_strbuf_update: 1463| 185k|{ 1464| 185k| int requsted_len; 1465| | 1466| 185k| if (!buf) ------------------ | Branch (1466:9): [True: 0, False: 185k] ------------------ 1467| 0| { 1468| 0| return -1; 1469| 0| } 1470| | 1471| 185k| if (new_addition_size <= 0) ------------------ | Branch (1471:9): [True: 0, False: 185k] ------------------ 1472| 0| { 1473| 0| return buf->nAllocatedLength; 1474| 0| } 1475| | 1476| 185k| requsted_len = buf->nUsedLength + new_addition_size; 1477| | 1478| 185k| if (requsted_len >= buf->nAllocatedLength) ------------------ | Branch (1478:9): [True: 0, False: 185k] ------------------ 1479| 0| { 1480| | /* Expand */ 1481| 0| int nAddLength = inchi_max(buf->nPtr, new_addition_size); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 1482| | /* buf->nPtr stores size increment for this buffer */ 1483| 0| char* new_str = 1484| 0| (char*)inchi_calloc((long long)buf->nAllocatedLength + (long long)nAddLength, ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 1485| 0| sizeof(new_str[0])); /* djb-rwth: cast operators added */ 1486| 0| if (!new_str) ------------------ | Branch (1486:13): [True: 0, False: 0] ------------------ 1487| 0| { 1488| 0| return -1; /* failed */ 1489| 0| } 1490| 0| if (buf->pStr) ------------------ | Branch (1490:13): [True: 0, False: 0] ------------------ 1491| 0| { 1492| 0| if (buf->nUsedLength > 0) ------------------ | Branch (1492:17): [True: 0, False: 0] ------------------ 1493| 0| { 1494| 0| memcpy(new_str, buf->pStr, sizeof(new_str[0]) * buf->nUsedLength); 1495| 0| } 1496| 0| inchi_free(buf->pStr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1497| 0| } 1498| 0| buf->pStr = new_str; 1499| 0| buf->nAllocatedLength += nAddLength; 1500| 0| } 1501| | 1502| 185k| return buf->nAllocatedLength; 1503| 185k|} inchi_strbuf_printf: 1511| 173k|{ 1512| 173k| int ret = 0, max_len; 1513| 173k| va_list argList; 1514| | 1515| 173k| if (!buf) ------------------ | Branch (1515:9): [True: 0, False: 173k] ------------------ 1516| 0| { 1517| 0| return -1; 1518| 0| } 1519| | 1520| 173k| my_va_start(argList, lpszFormat); ------------------ | | 22| 173k|#define my_va_start va_start ------------------ 1521| 173k| max_len = GetMaxPrintfLength(lpszFormat, argList); 1522| 173k| va_end(argList); 1523| 173k| if (max_len < 0) ------------------ | Branch (1523:9): [True: 0, False: 173k] ------------------ 1524| 0| { 1525| 0| return 0; 1526| 0| } 1527| | 1528| 173k| inchi_strbuf_update(buf, max_len); 1529| | 1530| 173k| my_va_start(argList, lpszFormat); ------------------ | | 22| 173k|#define my_va_start va_start ------------------ 1531| 173k| ret = vsprintf(buf->pStr + buf->nUsedLength, lpszFormat, argList); 1532| 173k| va_end(argList); 1533| 173k| if (ret >= 0) ------------------ | Branch (1533:9): [True: 173k, False: 0] ------------------ 1534| 173k| { 1535| 173k| buf->nUsedLength += ret; 1536| 173k| } 1537| | 1538| 173k| return ret; 1539| 173k|} TranspositionCreate: 660| 330k|{ 661| 330k| p->nAtNumb = (AT_NUMB*) inchi_calloc( n, sizeof( p->nAtNumb[0] ) ); ------------------ | | 1146| 330k|#define inchi_calloc calloc ------------------ 662| 330k| if (p->nAtNumb) ------------------ | Branch (662:9): [True: 330k, False: 0] ------------------ 663| 330k| { 664| 330k| return 1; 665| 330k| } 666| | 667| 0| return 0; 668| 330k|} TranspositionFree: 673| 330k|{ 674| 330k| if (p && p->nAtNumb) ------------------ | Branch (674:9): [True: 330k, False: 0] | Branch (674:14): [True: 330k, False: 0] ------------------ 675| 330k| { 676| 330k| inchi_free( p->nAtNumb ); ------------------ | | 1152| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 330k, False: 0] | | | Branch (1152:50): [Folded, False: 330k] | | ------------------ ------------------ 677| | p->nAtNumb = NULL; 678| 330k| } 679| 330k|} NodeSetCreate: 687| 993k|{ 688| 993k| int i, len; 689| | 690| 993k| len = ( n + pCG->m_num_bit - 1 ) / pCG->m_num_bit; 691| | 692| 993k| pSet->bitword = (bitWord**) inchi_calloc( L, sizeof( pSet->bitword[0] ) ); ------------------ | | 1146| 993k|#define inchi_calloc calloc ------------------ 693| | 694| 993k| if (!pSet->bitword) ------------------ | Branch (694:9): [True: 0, False: 993k] ------------------ 695| 0| { 696| 0| return 0; 697| 0| } 698| 993k| pSet->bitword[0] = (bitWord*) inchi_calloc( (long long)len * (long long)L, sizeof( pSet->bitword[0][0] ) ); /* djb-rwth: cast operators added */ ------------------ | | 1146| 993k|#define inchi_calloc calloc ------------------ 699| 993k| if (!pSet->bitword[0]) ------------------ | Branch (699:9): [True: 0, False: 993k] ------------------ 700| 0| { 701| | /* Cleanup */ 702| 0| inchi_free( pSet->bitword ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 703| 0| pSet->bitword = NULL; 704| 0| return 0; /* failed */ 705| 0| } 706| 1.35G| for (i = 1; i < L; i++) ------------------ | Branch (706:17): [True: 1.35G, False: 993k] ------------------ 707| 1.35G| { 708| 1.35G| pSet->bitword[i] = pSet->bitword[i - 1] + len; 709| 1.35G| } 710| | 711| 993k| pSet->len_set = len; 712| 993k| pSet->num_set = L; 713| | 714| 993k| return 1; 715| 993k|} NodeSetFree: 720| 993k|{ 721| 993k| if (pSet && pSet->bitword) ------------------ | Branch (721:9): [True: 993k, False: 0] | Branch (721:17): [True: 993k, False: 380] ------------------ 722| 993k| { 723| 993k| if (pSet->bitword[0]) ------------------ | Branch (723:13): [True: 993k, False: 0] ------------------ 724| 993k| { 725| 993k| inchi_free( pSet->bitword[0] ); ------------------ | | 1152| 993k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 993k, False: 0] | | | Branch (1152:50): [Folded, False: 993k] | | ------------------ ------------------ 726| 993k| } 727| 993k| inchi_free( pSet->bitword ); ------------------ | | 1152| 993k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 993k, False: 0] | | | Branch (1152:50): [Folded, False: 993k] | | ------------------ ------------------ 728| | pSet->bitword = NULL; 729| 993k| } 730| 993k|} CTableCreate: 735| 1.24M|{ 736| 1.24M| int maxlenCt = pCD->nMaxLenLinearCT + 1; /* add one element for CtPartINCHI_CANON_INFINITY() */ 737| 1.24M| int maxlenNumH = pCD->NumH ? ( pCD->maxlenNumH + 1 ) : 0; ------------------ | Branch (737:22): [True: 488k, False: 756k] ------------------ 738| 1.24M| int maxlenNumHfixed = pCD->NumHfixed ? ( pCD->maxlenNumHfixed + 1 ) : 0; ------------------ | Branch (738:27): [True: 109k, False: 1.13M] ------------------ 739| 1.24M| int maxlenIso = pCD->maxlen_iso_sort_key ? ( pCD->maxlen_iso_sort_key + 1 ) : 0; ------------------ | Branch (739:21): [True: 2.97k, False: 1.24M] ------------------ 740| 1.24M| int maxlenIsoExchg = pCD->iso_exchg_atnos ? ( pCD->maxlen_iso_exchg_atnos + 1 ) : 0; ------------------ | Branch (740:26): [True: 277, False: 1.24M] ------------------ 741| | 742| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 743| | int maxlenIsoHfixed = pCD->maxlen_iso_sort_key_Hfixed ? ( pCD->maxlen_iso_sort_key_Hfixed + 1 ) : 0; 744| |#endif 745| | 746| 1.24M| memset( Ct, 0, sizeof( Ct[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 747| | 748| 1.24M| Ct->maxVert = n; 749| | 750| 1.24M| n++; 751| | 752| 1.24M| Ct->Ctbl = (AT_RANK*) inchi_calloc( maxlenCt, sizeof( Ct->Ctbl[0] ) ); ------------------ | | 1146| 1.24M|#define inchi_calloc calloc ------------------ 753| 1.24M| Ct->nextCtblPos = (AT_NUMB*) inchi_calloc( n, sizeof( Ct->nextCtblPos[0] ) ); ------------------ | | 1146| 1.24M|#define inchi_calloc calloc ------------------ 754| 1.24M| Ct->nextAtRank = (AT_RANK*) inchi_calloc( n, sizeof( Ct->nextAtRank[0] ) ); ------------------ | | 1146| 1.24M|#define inchi_calloc calloc ------------------ 755| 1.24M| if (maxlenNumH) ------------------ | Branch (755:9): [True: 488k, False: 756k] ------------------ 756| 488k| { 757| 488k| Ct->NumH = (NUM_H *) inchi_calloc( maxlenNumH, sizeof( Ct->NumH[0] ) ); ------------------ | | 1146| 488k|#define inchi_calloc calloc ------------------ 758| 488k| } 759| 1.24M| if (maxlenNumHfixed) ------------------ | Branch (759:9): [True: 109k, False: 1.13M] ------------------ 760| 109k| { 761| 109k| Ct->NumHfixed = (NUM_H *) inchi_calloc( maxlenNumHfixed, sizeof( Ct->NumH[0] ) ); ------------------ | | 1146| 109k|#define inchi_calloc calloc ------------------ 762| 109k| } 763| 1.24M| if (maxlenIso) ------------------ | Branch (763:9): [True: 2.97k, False: 1.24M] ------------------ 764| 2.97k| { 765| 2.97k| Ct->iso_sort_key = (AT_ISO_SORT_KEY *) inchi_calloc( maxlenIso, sizeof( Ct->iso_sort_key[0] ) ); ------------------ | | 1146| 2.97k|#define inchi_calloc calloc ------------------ 766| 2.97k| } 767| 1.24M| if (maxlenIsoExchg) ------------------ | Branch (767:9): [True: 277, False: 1.24M] ------------------ 768| 277| { 769| 277| Ct->iso_exchg_atnos = (S_CHAR *) inchi_calloc( maxlenIsoExchg, sizeof( Ct->iso_exchg_atnos[0] ) ); ------------------ | | 1146| 277|#define inchi_calloc calloc ------------------ 770| 277| } 771| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 772| | if (maxlenIsoHfixed) 773| | { 774| | Ct->iso_sort_key_Hfixed = (AT_ISO_SORT_KEY *) inchi_calloc( maxlenIsoHfixed, sizeof( Ct->iso_sort_key_Hfixed[0] ) ); 775| | } 776| |#endif 777| |#ifdef INCHI_CANON_USE_HASH 778| | Ct->hash = (CtHash*) inchi_calloc( n, sizeof( Ct->hash[0] ) ); 779| |#endif 780| | 781| 1.24M| Ct->lenCt = 0; 782| 1.24M| Ct->nLenCTAtOnly = pCD->nLenCTAtOnly; 783| 1.24M| Ct->maxlenCt = maxlenCt; 784| 1.24M| Ct->lenNumH = 0; 785| 1.24M| Ct->maxlenNumH = maxlenNumH; 786| 1.24M| Ct->len_iso_sort_key = 0; 787| 1.24M| Ct->maxlen_iso_sort_key = maxlenIso; 788| 1.24M| Ct->len_iso_exchg_atnos = 0; 789| 1.24M| Ct->maxlen_iso_exchg_atnos = maxlenIso; 790| | 791| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 792| | Ct->len_iso_sort_key_Hfixed = 0; 793| | Ct->maxlen_iso_sort_key_Hfixed = maxlenIsoHfixed; 794| |#endif 795| | 796| 1.24M| Ct->maxPos = n; 797| 1.24M| Ct->lenPos = 0; 798| | /* djb-rwth: fixing a NULL pointer dereferences */ 799| 1.24M| if (Ct->nextAtRank) ------------------ | Branch (799:9): [True: 1.24M, False: 0] ------------------ 800| 1.24M| Ct->nextAtRank[0] = 0; 801| 1.24M| if (Ct->nextCtblPos) ------------------ | Branch (801:9): [True: 1.24M, False: 0] ------------------ 802| 1.24M| Ct->nextCtblPos[0] = 0; 803| | 804| 1.24M| if (Ct->Ctbl && Ct->nextCtblPos && ------------------ | Branch (804:9): [True: 1.24M, False: 0] | Branch (804:21): [True: 1.24M, False: 0] ------------------ 805| 1.24M| ( !maxlenNumH || Ct->NumH ) && ------------------ | Branch (805:11): [True: 756k, False: 488k] | Branch (805:26): [True: 488k, False: 0] ------------------ 806| 1.24M| ( !maxlenNumHfixed || Ct->NumHfixed )) ------------------ | Branch (806:11): [True: 1.13M, False: 109k] | Branch (806:31): [True: 109k, False: 0] ------------------ 807| 1.24M| { 808| 1.24M| return 1; 809| 1.24M| } 810| | 811| 0| return 0; 812| 1.24M|} CTableFree: 817| 1.24M|{ 818| 1.24M| if (Ct) ------------------ | Branch (818:9): [True: 1.24M, False: 0] ------------------ 819| 1.24M| { 820| 1.24M| if (Ct->Ctbl) ------------------ | Branch (820:13): [True: 956k, False: 288k] ------------------ 821| 956k| { 822| 956k| inchi_free( Ct->Ctbl ); ------------------ | | 1152| 956k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 956k, False: 0] | | | Branch (1152:50): [Folded, False: 956k] | | ------------------ ------------------ 823| 956k| } 824| 1.24M| if (Ct->nextCtblPos) ------------------ | Branch (824:13): [True: 1.24M, False: 0] ------------------ 825| 1.24M| { 826| 1.24M| inchi_free( Ct->nextCtblPos ); ------------------ | | 1152| 1.24M|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.24M, False: 0] | | | Branch (1152:50): [Folded, False: 1.24M] | | ------------------ ------------------ 827| 1.24M| } 828| 1.24M| if (Ct->nextAtRank) ------------------ | Branch (828:13): [True: 1.24M, False: 0] ------------------ 829| 1.24M| { 830| 1.24M| inchi_free( Ct->nextAtRank ); ------------------ | | 1152| 1.24M|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.24M, False: 0] | | | Branch (1152:50): [Folded, False: 1.24M] | | ------------------ ------------------ 831| 1.24M| } 832| 1.24M| if (Ct->NumH) ------------------ | Branch (832:13): [True: 200k, False: 1.04M] ------------------ 833| 200k| { 834| 200k| inchi_free( Ct->NumH ); ------------------ | | 1152| 200k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 200k, False: 0] | | | Branch (1152:50): [Folded, False: 200k] | | ------------------ ------------------ 835| 200k| } 836| 1.24M| if (Ct->NumHfixed) ------------------ | Branch (836:13): [True: 73.4k, False: 1.17M] ------------------ 837| 73.4k| { 838| 73.4k| inchi_free( Ct->NumHfixed ); ------------------ | | 1152| 73.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 73.4k, False: 0] | | | Branch (1152:50): [Folded, False: 73.4k] | | ------------------ ------------------ 839| 73.4k| } 840| 1.24M| if (Ct->iso_sort_key) ------------------ | Branch (840:13): [True: 916, False: 1.24M] ------------------ 841| 916| { 842| 916| inchi_free( Ct->iso_sort_key ); ------------------ | | 1152| 916|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 916, False: 0] | | | Branch (1152:50): [Folded, False: 916] | | ------------------ ------------------ 843| 916| } 844| 1.24M| if (Ct->iso_exchg_atnos) ------------------ | Branch (844:13): [True: 120, False: 1.24M] ------------------ 845| 120| { 846| 120| inchi_free( Ct->iso_exchg_atnos ); ------------------ | | 1152| 120|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 120, False: 0] | | | Branch (1152:50): [Folded, False: 120] | | ------------------ ------------------ 847| 120| } 848| | 849| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 850| | if (Ct->iso_sort_key_Hfixed) 851| | { 852| | inchi_free( Ct->iso_sort_key_Hfixed ); 853| | } 854| |#endif 855| | 856| |#ifdef INCHI_CANON_USE_HASH 857| | if (Ct->hash) 858| | { 859| | inchi_free( Ct->hash ); 860| | } 861| |#endif 862| | 863| 1.24M| memset( Ct, 0, sizeof( Ct[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 864| 1.24M| } 865| 1.24M|} UnorderedPartitionCreate: 870| 661k|{ 871| 661k| p->equ2 = (AT_NUMB*) inchi_calloc( n, sizeof( p->equ2[0] ) ); ------------------ | | 1146| 661k|#define inchi_calloc calloc ------------------ 872| | /* p->next = (AT_NUMB*)inchi_calloc( n, sizeof(p->next[0])); */ 873| | 874| 661k| if (p->equ2 /*&& p->next*/) ------------------ | Branch (874:9): [True: 661k, False: 0] ------------------ 875| 661k| { 876| 661k| return 1; 877| 661k| } 878| | 879| 0| return 0; 880| 661k|} UnorderedPartitionFree: 885| 661k|{ 886| 661k| if (p->equ2) ------------------ | Branch (886:9): [True: 661k, False: 0] ------------------ 887| 661k| { 888| 661k| inchi_free( p->equ2 ); ------------------ | | 1152| 661k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 661k, False: 0] | | | Branch (1152:50): [Folded, False: 661k] | | ------------------ ------------------ 889| 661k| } 890| | 891| | /* if (p->next) inchi_free( p->next); */ 892| 661k| p->equ2 = NULL; 893| | /* p->next = NULL; */ 894| 661k|} UnorderedPartitionMakeDiscrete: 899| 330k|{ 900| 330k| int i; 901| 1.52M| for (i = 0; i < n; i++) ------------------ | Branch (901:17): [True: 1.19M, False: 330k] ------------------ 902| 1.19M| { 903| 1.19M| p->equ2[i] = (AT_NUMB) i; 904| | /* p->next[i] = INCHI_CANON_INFINITY; */ 905| 1.19M| } 906| 330k| INCHI_HEAPCHK 907| 330k|} PartitionCreate: 912| 661k|{ 913| 661k| p->AtNumber = (AT_NUMB*) inchi_calloc( n, sizeof( p->AtNumber[0] ) ); ------------------ | | 1146| 661k|#define inchi_calloc calloc ------------------ 914| 661k| p->Rank = (AT_RANK*) inchi_calloc( n, sizeof( p->Rank[0] ) ); ------------------ | | 1146| 661k|#define inchi_calloc calloc ------------------ 915| 661k| if (p->AtNumber && p->Rank) ------------------ | Branch (915:9): [True: 661k, False: 0] | Branch (915:24): [True: 661k, False: 0] ------------------ 916| 661k| { 917| 661k| return 1; 918| 661k| } 919| 0| return 0; 920| 661k|} PartitionFree: 925| 1.66M|{ 926| 1.66M| if (p) ------------------ | Branch (926:9): [True: 1.66M, False: 0] ------------------ 927| 1.66M| { 928| 1.66M| if (p->AtNumber) ------------------ | Branch (928:13): [True: 951k, False: 717k] ------------------ 929| 951k| { 930| 951k| inchi_free( p->AtNumber ); ------------------ | | 1152| 951k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 951k, False: 0] | | | Branch (1152:50): [Folded, False: 951k] | | ------------------ ------------------ 931| 951k| p->AtNumber = NULL; 932| 951k| } 933| 1.66M| if (p->Rank) ------------------ | Branch (933:13): [True: 951k, False: 717k] ------------------ 934| 951k| { 935| 951k| inchi_free( p->Rank ); ------------------ | | 1152| 951k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 951k, False: 0] | | | Branch (1152:50): [Folded, False: 951k] | | ------------------ ------------------ 936| | p->Rank = NULL; 937| 951k| } 938| 1.66M| } 939| 1.66M|} PartitionIsDiscrete: 944| 6.52M|{ 945| 6.52M| int i; 946| 6.52M| AT_RANK r; 947| 636M| for (i = 0, r = 1; i < n; i++, r++) ------------------ | Branch (947:24): [True: 635M, False: 717k] ------------------ 948| 635M| { 949| 635M| if (r != ( rank_mask_bit & p->Rank[p->AtNumber[i]] )) ------------------ | Branch (949:13): [True: 5.80M, False: 630M] ------------------ 950| 5.80M| { 951| 5.80M| INCHI_HEAPCHK 952| 5.80M| return 0; 953| 5.80M| } 954| 635M| } 955| | 956| | INCHI_HEAPCHK 957| | 958| 717k| return 1; 959| 6.52M|} PartitionGetFirstCell: 964| 5.80M|{ 965| 5.80M| int i; 966| 5.80M| AT_RANK r; 967| 5.80M| Cell *W = baseW + k - 1; 968| | 969| 5.80M| i = ( k > 1 ) ? baseW[k - 2].first + 1 : 0; ------------------ | Branch (969:9): [True: 5.72M, False: 76.5k] ------------------ 970| | 971| 5.80M| if (i < n) ------------------ | Branch (971:9): [True: 5.80M, False: 0] ------------------ 972| 5.80M| { 973| | /* bypass single vertex cells */ 974| 6.69M| for (r = (AT_RANK) ( i + 1 ); i < n && r == ( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ); i++, r++) ------------------ | Branch (974:39): [True: 6.69M, False: 0] | Branch (974:48): [True: 894k, False: 5.80M] ------------------ 975| 894k| { 976| 894k| ; 977| 894k| } 978| 5.80M| } 979| 5.80M| if (i < n) ------------------ | Branch (979:9): [True: 5.80M, False: 0] ------------------ 980| 5.80M| { 981| 5.80M| W->first = i; 982| 5.80M| for (r = ( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ), i++; 983| 235M| i < n && r == ( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ); ------------------ | Branch (983:15): [True: 234M, False: 855k] | Branch (983:24): [True: 229M, False: 4.94M] ------------------ 984| 229M| i++) 985| 229M| { 986| 229M| ; 987| 229M| } 988| 5.80M| W->next = i; 989| | 990| | INCHI_HEAPCHK 991| | 992| 5.80M| return ( W->next - W->first ); 993| 5.80M| } 994| | 995| 0| W->first = INCHI_CANON_INFINITY; ------------------ | | 31| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 996| 0| W->next = 0; 997| | 998| | INCHI_HEAPCHK 999| | 1000| 0| return 0; 1001| 5.80M|} CellMakeEmpty: 1006| 5.89M|{ 1007| 5.89M| k--; 1008| 5.89M| baseW[k].first = INCHI_CANON_INFINITY; ------------------ | | 31| 5.89M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1009| 5.89M| baseW[k].next = 0; 1010| 5.89M| baseW[k].prev = -1; 1011| | 1012| 5.89M| INCHI_HEAPCHK 1013| 5.89M|} NodeSetFromVertices: 1018| 121k|{ 1019| 121k| bitWord *Bits = cur_nodes->bitword[l - 1]; 1020| 121k| int len = cur_nodes->len_set * sizeof( bitWord ); 1021| 121k| int i, j; 1022| | 1023| 121k| memset( Bits, 0, len ); /* djb-rwth: memset_s C11/Annex K variant? */ 1024| | 1025| 7.91M| for (i = 0; i < num_v; i++) ------------------ | Branch (1025:17): [True: 7.79M, False: 121k] ------------------ 1026| 7.79M| { 1027| 7.79M| j = (int) v[i] - 1; 1028| 7.79M| Bits[j / pCG->m_num_bit] |= pCG->m_bBit[j % pCG->m_num_bit]; 1029| 7.79M| } 1030| | 1031| 121k| INCHI_HEAPCHK 1032| 121k|} AllNodesAreInSet: 1037| 8.95M|{ 1038| 8.95M| int i; 1039| 8.95M| int n = cur_nodes->len_set; 1040| | 1041| 8.95M| bitWord *BitsNode = cur_nodes->bitword[lcur_nodes - 1]; 1042| 8.95M| bitWord *BitsSet = set->bitword[lset - 1]; 1043| | 1044| | /* find any BitsNode[i] bit not in BitsSet[i] */ 1045| 43.6M| for (i = 0; i < n; i++) ------------------ | Branch (1045:17): [True: 40.6M, False: 2.97M] ------------------ 1046| 40.6M| { 1047| 40.6M| if (BitsNode[i] & ~BitsSet[i]) ------------------ | Branch (1047:13): [True: 5.97M, False: 34.7M] ------------------ 1048| 5.97M| { 1049| | 1050| | INCHI_HEAPCHK 1051| | 1052| 5.97M| return 0; 1053| 5.97M| } 1054| 40.6M| } 1055| | 1056| | INCHI_HEAPCHK 1057| | 1058| 2.97M| return 1; 1059| 8.95M|} PartitionGetMcrAndFixSet: 1069| 4|{ 1070| 4| int i, j1, j2; 1071| 4| AT_RANK r, r1; 1072| 4| bitWord *McrBits = Mcr->bitword[l - 1]; 1073| 4| bitWord *FixBits = Fix->bitword[l - 1]; 1074| 4| int len = Mcr->len_set * sizeof( bitWord ); 1075| | 1076| 4| memset( McrBits, 0, len ); /* djb-rwth: memset_s C11/Annex K variant? */ 1077| 4| memset( FixBits, 0, len ); /* djb-rwth: memset_s C11/Annex K variant? */ 1078| 30| for (i = 0, r = 1; i < n; i++, r++) ------------------ | Branch (1078:24): [True: 26, False: 4] ------------------ 1079| 26| { 1080| 26| if (r == ( r1 = ( rank_mask_bit&p->Rank[j1 = (int) p->AtNumber[i]] ) )) ------------------ | Branch (1080:13): [True: 20, False: 6] ------------------ 1081| 20| { 1082| 20| FixBits[j1 / pCG->m_num_bit] |= pCG->m_bBit[j1 % pCG->m_num_bit]; 1083| 20| McrBits[j1 / pCG->m_num_bit] |= pCG->m_bBit[j1 % pCG->m_num_bit]; 1084| 20| } 1085| 6| else 1086| 6| { 1087| 12| for (r = r1; i + 1 < n && r == ( rank_mask_bit&p->Rank[j2 = (int) p->AtNumber[i + 1]] ); i++) ------------------ | Branch (1087:26): [True: 11, False: 1] | Branch (1087:39): [True: 6, False: 5] ------------------ 1088| 6| { 1089| 6| if (j1 > j2) ------------------ | Branch (1089:21): [True: 0, False: 6] ------------------ 1090| 0| { 1091| 0| j1 = j2; 1092| 0| } 1093| 6| } 1094| 6| McrBits[j1 / pCG->m_num_bit] |= pCG->m_bBit[j1 % pCG->m_num_bit]; 1095| 6| } 1096| 26| } 1097| | 1098| 4| INCHI_HEAPCHK 1099| 4|} NodeSetFromRadEndpoints: 1108| 1.76k|{ 1109| 1.76k| bitWord *Bits = cur_nodes->bitword[k]; 1110| 1.76k| int len = cur_nodes->len_set * sizeof( bitWord ); 1111| 1.76k| int i, j; 1112| | 1113| 1.76k| memset( Bits, 0, len ); /* djb-rwth: memset_s C11/Annex K variant? */ 1114| | 1115| 4.32k| for (i = 1; i < num_v; i += 2) ------------------ | Branch (1115:17): [True: 2.56k, False: 1.76k] ------------------ 1116| 2.56k| { 1117| 2.56k| j = (int) RadEndpoints[i]; 1118| 2.56k| Bits[j / pCG->m_num_bit] |= pCG->m_bBit[j % pCG->m_num_bit]; 1119| 2.56k| } 1120| 1.76k|} RemoveFromNodeSet: 1126| 1.76k|{ 1127| 1.76k| if (cur_nodes->bitword) ------------------ | Branch (1127:9): [True: 1.76k, False: 0] ------------------ 1128| 1.76k| { 1129| 1.76k| bitWord *Bits = cur_nodes->bitword[k]; 1130| | /*int len = cur_nodes->len_set*sizeof(bitWord);*/ 1131| 1.76k| int i, j; 1132| | 1133| 5.49k| for (i = 0; i < num_v; i++) ------------------ | Branch (1133:21): [True: 3.73k, False: 1.76k] ------------------ 1134| 3.73k| { 1135| 3.73k| j = (int) v[i]; 1136| 3.73k| Bits[j / pCG->m_num_bit] &= ~pCG->m_bBit[j % pCG->m_num_bit]; 1137| 3.73k| } 1138| 1.76k| } 1139| 1.76k|} DoNodeSetsIntersect: 1144| 1.69k|{ 1145| 1.69k| if (cur_nodes->bitword) ------------------ | Branch (1145:9): [True: 1.29k, False: 398] ------------------ 1146| 1.29k| { 1147| 1.29k| bitWord *Bits1 = cur_nodes->bitword[k1]; 1148| 1.29k| bitWord *Bits2 = cur_nodes->bitword[k2]; 1149| 1.29k| int len = cur_nodes->len_set; 1150| 1.29k| int i; 1151| | 1152| 1.98k| for (i = 0; i < len; i++) ------------------ | Branch (1152:21): [True: 1.29k, False: 687] ------------------ 1153| 1.29k| { 1154| 1.29k| if (Bits1[i] & Bits2[i]) ------------------ | Branch (1154:17): [True: 610, False: 687] ------------------ 1155| 610| { 1156| 610| return 1; 1157| 610| } 1158| 1.29k| } 1159| 1.29k| } 1160| | 1161| 1.08k| return 0; 1162| 1.69k|} IsNodeSetEmpty: 1167| 2.46k|{ 1168| 2.46k| if (cur_nodes->bitword) ------------------ | Branch (1168:9): [True: 1.69k, False: 769] ------------------ 1169| 1.69k| { 1170| 1.69k| bitWord *Bits = cur_nodes->bitword[k]; 1171| 1.69k| int len = cur_nodes->len_set; 1172| 1.69k| int i; 1173| | 1174| 2.31k| for (i = 0; i < len; i++) ------------------ | Branch (1174:21): [True: 1.69k, False: 616] ------------------ 1175| 1.69k| { 1176| 1.69k| if (Bits[i]) ------------------ | Branch (1176:17): [True: 1.08k, False: 616] ------------------ 1177| 1.08k| { 1178| 1.08k| return 0; 1179| 1.08k| } 1180| 1.69k| } 1181| 1.69k| } 1182| | 1183| 1.38k| return 1; 1184| 2.46k|} AddNodeSet2ToNodeSet1: 1189| 610|{ 1190| 610| if (cur_nodes->bitword) ------------------ | Branch (1190:9): [True: 610, False: 0] ------------------ 1191| 610| { 1192| 610| bitWord *Bits1 = cur_nodes->bitword[k1]; 1193| 610| bitWord *Bits2 = cur_nodes->bitword[k2]; 1194| 610| int len = cur_nodes->len_set; 1195| 610| int i; 1196| | 1197| 1.22k| for (i = 0; i < len; i++) ------------------ | Branch (1197:21): [True: 610, False: 610] ------------------ 1198| 610| { 1199| 610| Bits1[i] |= Bits2[i]; 1200| 610| } 1201| 610| } 1202| 610|} AddNodesToRadEndpoints: 1212| 1.08k|{ 1213| 1.08k| int n = nStart; 1214| 1.08k| if (cur_nodes->bitword) ------------------ | Branch (1214:9): [True: 1.08k, False: 0] ------------------ 1215| 1.08k| { 1216| 1.08k| bitWord *Bits = cur_nodes->bitword[k]; 1217| 1.08k| int len = cur_nodes->len_set; 1218| 1.08k| int i, j; 1219| 1.08k| Vertex v; 1220| | 1221| 2.16k| for (i = 0, v = 0; i < len; i++) ------------------ | Branch (1221:28): [True: 1.08k, False: 1.08k] ------------------ 1222| 1.08k| { 1223| 1.08k| if (Bits[i]) ------------------ | Branch (1223:17): [True: 1.08k, False: 0] ------------------ 1224| 1.08k| { 1225| 18.4k| for (j = 0; j < pCG->m_num_bit; j++, v++) ------------------ | Branch (1225:29): [True: 17.3k, False: 1.08k] ------------------ 1226| 17.3k| { 1227| 17.3k| if (Bits[i] & pCG->m_bBit[j]) ------------------ | Branch (1227:25): [True: 1.61k, False: 15.7k] ------------------ 1228| 1.61k| { 1229| 1.61k| if (n >= nLen) ------------------ | Branch (1229:29): [True: 0, False: 1.61k] ------------------ 1230| 0| { 1231| 0| return -1; /* overflow */ 1232| 0| } 1233| 1.61k| RadEndpoints[n++] = vRad; 1234| 1.61k| RadEndpoints[n++] = v; 1235| 1.61k| } 1236| 17.3k| } 1237| 1.08k| } 1238| 0| else 1239| 0| { 1240| 0| v += pCG->m_num_bit; 1241| 0| } 1242| 1.08k| } 1243| 1.08k| } 1244| | 1245| 1.08k| return n; 1246| 1.08k|} PartitionGetTransposition: 1254| 386k|{ 1255| 386k| int i; 1256| | 1257| 13.6M| for (i = 0; i < n; i++) ------------------ | Branch (1257:17): [True: 13.2M, False: 386k] ------------------ 1258| 13.2M| { 1259| 13.2M| gamma->nAtNumb[(int) pFrom->AtNumber[i]] = pTo->AtNumber[i]; 1260| 13.2M| } 1261| | 1262| 386k| INCHI_HEAPCHK 1263| 386k|} nGetMcr2: 1271| 15.4M|{ 1272| 15.4M| AT_RANK n1, n2, mcr; /* recursive version is much shorter. */ 1273| | 1274| | INCHI_HEAPCHK 1275| | 1276| 15.4M| n1 = nEqArray[(int) n]; 1277| | 1278| 15.4M| if (n == n1) ------------------ | Branch (1278:9): [True: 7.65M, False: 7.80M] ------------------ 1279| 7.65M| { 1280| 7.65M| return n; 1281| 7.65M| } 1282| | 1283| | /* 1st pass: find mcr */ 1284| 11.0M| while (n1 != ( n2 = nEqArray[(int) n1] )) ------------------ | Branch (1284:12): [True: 3.23M, False: 7.80M] ------------------ 1285| 3.23M| { 1286| 3.23M| n1 = n2; 1287| 3.23M| } 1288| | 1289| | /* 2nd pass: copy mcr to each element of the set starting from nEqArray[n] */ 1290| 7.80M| mcr = n1; 1291| 7.80M| n1 = n; 1292| 11.0M| while ( /*n1*/ mcr != ( n2 = nEqArray[(int) n1] )) ------------------ | Branch (1292:20): [True: 3.23M, False: 7.80M] ------------------ 1293| 3.23M| { 1294| 3.23M| nEqArray[(int) n1] = mcr; 1295| 3.23M| n1 = n2; 1296| 3.23M| } 1297| | 1298| | INCHI_HEAPCHK 1299| | 1300| 7.80M| return ( mcr ); 1301| 15.4M|} nJoin2Mcrs2: 1308| 391k|{ 1309| 391k| n1 = nGetMcr2( nEqArray, n1 ); 1310| 391k| n2 = nGetMcr2( nEqArray, n2 ); 1311| | 1312| 391k| if (n1 < n2) ------------------ | Branch (1312:9): [True: 80, False: 391k] ------------------ 1313| 80| { 1314| 80| nEqArray[n2] = n1; 1315| | 1316| | INCHI_HEAPCHK 1317| | 1318| 80| return 1; /* a change has been made */ 1319| 80| } 1320| | 1321| 391k| if (n2 < n1) ------------------ | Branch (1321:9): [True: 391k, False: 340] ------------------ 1322| 391k| { 1323| 391k| nEqArray[n1] = n2; 1324| | 1325| | INCHI_HEAPCHK 1326| | 1327| 391k| return 1; /* a change has been made */ 1328| 391k| } 1329| | 1330| | INCHI_HEAPCHK 1331| | 1332| 340| return 0; /* no changes */ 1333| 391k|} GetUnorderedPartitionMcrNode: 1338| 14.6M|{ 1339| 14.6M| Node ret = (Node) ( 1 + nGetMcr2( p1->equ2, (AT_RANK) ( v - 1 ) ) ); 1340| | 1341| | INCHI_HEAPCHK 1342| | 1343| 14.6M| return ret; 1344| 14.6M|} UnorderedPartitionJoin: 1353| 386k|{ 1354| 386k| int i, j; 1355| 386k| int nNumChanges = 0; 1356| 13.6M| for (i = 0; i < n; i++) ------------------ | Branch (1356:17): [True: 13.2M, False: 386k] ------------------ 1357| 13.2M| { 1358| 13.2M| if (( j = (int) p1->equ2[i] ) == i || p2->equ2[(int) i] == p2->equ2[(int) j]) ------------------ | Branch (1358:13): [True: 12.8M, False: 391k] | Branch (1358:47): [True: 44, False: 391k] ------------------ 1359| 12.8M| { 1360| 12.8M| continue; 1361| 12.8M| } 1362| 391k| nNumChanges += nJoin2Mcrs2( p2->equ2, (AT_NUMB) i, (AT_NUMB) j ); 1363| 391k| } 1364| | 1365| | INCHI_HEAPCHK 1366| | 1367| 386k| return nNumChanges; 1368| 386k|} PartitionSatisfiesLemma_2_25: 1373| 4.68M|{ 1374| 4.68M| int nPartitionSize = 0; 1375| 4.68M| int nNumNonTrivialCells = 0; 1376| 4.68M| AT_RANK r; 1377| 4.68M| int i, num; 1378| | 1379| 756M| for (i = num = 0, r = 1; i < n; i++, r++) ------------------ | Branch (1379:30): [True: 752M, False: 4.68M] ------------------ 1380| 752M| { 1381| 752M| if (( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ) == r) ------------------ | Branch (1381:13): [True: 507M, False: 244M] ------------------ 1382| 507M| { 1383| 507M| nPartitionSize++; 1384| 507M| if (num) ------------------ | Branch (1384:17): [True: 10.8M, False: 496M] ------------------ 1385| 10.8M| { 1386| | /* num+1 = cell size > 1 */ 1387| 10.8M| nNumNonTrivialCells++; 1388| 10.8M| num = 0; 1389| 10.8M| } 1390| 507M| } 1391| 244M| else 1392| 244M| { 1393| 244M| num++; 1394| 244M| } 1395| 752M| } 1396| | 1397| | /* check Lemma_2_25 conditions */ 1398| 4.68M| if (n <= nPartitionSize + 4 || ------------------ | Branch (1398:9): [True: 1.12M, False: 3.55M] ------------------ 1399| 3.55M| n == nPartitionSize + nNumNonTrivialCells || ------------------ | Branch (1399:10): [True: 2.50k, False: 3.55M] ------------------ 1400| 3.55M| n == nPartitionSize + nNumNonTrivialCells + 1) ------------------ | Branch (1400:10): [True: 15.1k, False: 3.53M] ------------------ 1401| 1.14M| { 1402| 1.14M| return 1; 1403| 1.14M| } 1404| | 1405| 3.53M| return 0; 1406| 4.68M|} PartitionCopy: 1411| 6.61M|{ 1412| 6.61M| int i; 1413| 6.61M| memcpy(To->AtNumber, From->AtNumber, n * sizeof(To->AtNumber[0])); 1414| 6.61M| memcpy(To->Rank, From->Rank, n * sizeof(To->AtNumber[0])); 1415| | 1416| 960M| for (i = 0; i < n; i++) ------------------ | Branch (1416:17): [True: 953M, False: 6.61M] ------------------ 1417| 953M| { 1418| 953M| To->Rank[i] &= rank_mask_bit; 1419| 953M| } 1420| | 1421| 6.61M| INCHI_HEAPCHK 1422| 6.61M|} PartitionColorVertex: 1438| 6.20M|{ 1439| 6.20M| int nNumNewRanks, i, j; 1440| 6.20M| long lNumNeighListIter = 0; 1441| 6.20M| AT_RANK rv, r; 1442| 6.20M| AT_NUMB s, sv; 1443| | 1444| 18.6M| for (i = 1; i <= 2; i++) ------------------ | Branch (1444:17): [True: 12.4M, False: 6.20M] ------------------ 1445| 12.4M| { 1446| 12.4M| if (!p[i].AtNumber) ------------------ | Branch (1446:13): [True: 434k, False: 11.9M] ------------------ 1447| 434k| { 1448| 434k| p[i].AtNumber = (AT_NUMB *) inchi_malloc( n_max * sizeof( p[0].AtNumber[0] ) ); ------------------ | | 1143| 434k|#define inchi_malloc malloc ------------------ 1449| 434k| } 1450| 12.4M| if (!p[i].Rank) ------------------ | Branch (1450:13): [True: 434k, False: 11.9M] ------------------ 1451| 434k| { 1452| 434k| p[i].Rank = (AT_RANK *) inchi_malloc( n_max * sizeof( p[0].Rank[0] ) ); ------------------ | | 1143| 434k|#define inchi_malloc malloc ------------------ 1453| 434k| } 1454| 12.4M| if (!p[i].AtNumber || !p[i].Rank) ------------------ | Branch (1454:13): [True: 0, False: 12.4M] | Branch (1454:31): [True: 0, False: 12.4M] ------------------ 1455| 0| { 1456| | 1457| | INCHI_HEAPCHK 1458| | 1459| 0| return CT_OUT_OF_RAM; ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1460| 0| } 1461| 12.4M| } 1462| | 1463| 6.20M| PartitionCopy( p + 1, p, n_tg ); 1464| | 1465| 6.20M| sv = v - 1; /* atom number we are looking for */ 1466| 6.20M| if (sv >= (AT_NUMB) n_tg) ------------------ | Branch (1466:9): [True: 0, False: 6.20M] ------------------ 1467| 0| { 1468| | 1469| | INCHI_HEAPCHK 1470| | 1471| 0| return CT_CANON_ERR; /* !!! severe program error: sv not found !!! */ ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1472| 0| } 1473| | 1474| 6.20M| rv = p[1].Rank[(int) sv]; /* rank of this atom */ 1475| | 1476| | /* second, locate sv among all vertices that have same rank as v */ 1477| 6.20M| s = n_max + 1; /* always greater than sv; this initialization is needed only to keep the compiler happy */ 1478| 239M| for (j = (int) rv - 1; 0 <= j && rv == ( p[1].Rank[(int) ( s = p[1].AtNumber[j] )] ) && s != sv; j--) /* djb-rwth: removing redundant code */ ------------------ | Branch (1478:28): [True: 239M, False: 0] | Branch (1478:38): [True: 239M, False: 0] | Branch (1478:93): [True: 232M, False: 6.20M] ------------------ 1479| 232M| { 1480| 232M| ; 1481| 232M| } 1482| | 1483| 6.20M| if (s != sv) ------------------ | Branch (1483:9): [True: 0, False: 6.20M] ------------------ 1484| 0| { 1485| 0| INCHI_HEAPCHK 1486| 0| return CT_CANON_ERR; /* !!! severe program error: sv not found !!! */ ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1487| 0| } 1488| | 1489| | /* shift preceding atom numbers to the right to fill the gap after removing sv */ 1490| 6.20M| r = rv - 1; /* initialization only to keep compiler happy */ 1491| 6.68M| for (i = j--; 0 <= j && rv == ( r = p[1].Rank[(int) ( s = p[1].AtNumber[j] )] ); i = j, j--) ------------------ | Branch (1491:19): [True: 6.59M, False: 88.6k] | Branch (1491:29): [True: 477k, False: 6.11M] ------------------ 1492| 477k| { 1493| 477k| p[1].AtNumber[i] = s; 1494| 477k| } 1495| | 1496| 6.20M| r = ( i > 0 ) ? ( r + 1 ) : 1; /* new reduced rank = (next lower rank)+1 or 1 */ ------------------ | Branch (1496:9): [True: 6.11M, False: 88.6k] ------------------ 1497| | /* insert sv and adjust its rank */ 1498| 6.20M| p[1].AtNumber[i] = sv; 1499| 6.20M| p[1].Rank[(int) sv] = r; 1500| | 1501| | 1502| | /* make equitable partition */ 1503| 6.20M| if (bDigraph) ------------------ | Branch (1503:9): [True: 1.22M, False: 4.98M] ------------------ 1504| 1.22M| { 1505| | /* 1506| | nNumNewRanks = DifferentiateRanks2( pCG, n_tg, G, 1507| | nNumPrevRanks+1, p[1].Rank, p[2].Rank, 1508| | p[1].AtNumber, &lNumNeighListIter, 1 ); 1509| | */ 1510| 1.22M| nNumNewRanks = DifferentiateRanks4( pCG, n_tg, G, 1511| 1.22M| nNumPrevRanks + 1, p[1].Rank, p[2].Rank /* temp array */, 1512| 1.22M| p[1].AtNumber, (AT_RANK) n, &lNumNeighListIter ); 1513| 1.22M| } 1514| 4.98M| else 1515| 4.98M| { 1516| | /* 1517| | nNumNewRanks = DifferentiateRanks2( pCG, n_tg, G, 1518| | nNumPrevRanks+1, p[1].Rank, p[2].Rank, 1519| | p[1].AtNumber, &lNumNeighListIter, 1 ); 1520| | */ 1521| 4.98M| nNumNewRanks = DifferentiateRanks3( pCG, n_tg, G, 1522| 4.98M| nNumPrevRanks + 1, p[1].Rank, p[2].Rank /* temp array */, 1523| 4.98M| p[1].AtNumber, &lNumNeighListIter ); 1524| 4.98M| } 1525| 6.20M| INCHI_HEAPCHK 1526| | 1527| 6.20M| return nNumNewRanks; 1528| 6.20M|} CellGetMinNode: 1552| 10.4M|{ 1553| 10.4M| AT_NUMB i; 1554| 10.4M| AT_NUMB uCurAtNumb, uMinAtNumb = INCHI_CANON_INFINITY; ------------------ | | 31| 10.4M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1555| | 1556| | /* in case of emty cell: (W->first=INCHI_CANON_INFINITY) > (W->next=0); returns INCHI_CANON_INFINITY */ 1557| 10.4M| if (W->first > W->next) ------------------ | Branch (1557:9): [True: 0, False: 10.4M] ------------------ 1558| 0| { 1559| 0| return INCHI_CANON_INFINITY; ------------------ | | 31| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1560| 0| } 1561| | 1562| 10.4M|#if ( USE_AUX_RANKING == 1 ) 1563| 10.4M| if (pCD && pCD->nAuxRank) ------------------ | Branch (1563:9): [True: 10.4M, False: 0] | Branch (1563:16): [True: 2.21M, False: 8.21M] ------------------ 1564| 2.21M| { 1565| 2.21M| AT_RANK uMinAuxRank, uCurAuxRank; 1566| 2.21M| int nCurAtNumb; 1567| | 1568| 2.21M|#if ( USE_AUX_RANKING_ALL == 1 ) 1569| 2.21M| AT_RANK uInpAuxRank; 1570| 2.21M| int nInpAtNumb, nMinAtNumb; 1571| 2.21M|#endif 1572| | 1573| 2.21M| for (i = W->first; i < W->next; i++) ------------------ | Branch (1573:28): [True: 2.21M, False: 0] ------------------ 1574| 2.21M| { 1575| 2.21M| uCurAtNumb = p->AtNumber[(int) i]; 1576| 2.21M| if (!( p->Rank[(int) uCurAtNumb] & rank_mark_bit )) ------------------ | Branch (1576:17): [True: 2.21M, False: 0] ------------------ 1577| 2.21M| { 1578| 2.21M| break; /* found the first unmarked yet node */ 1579| 2.21M| } 1580| 2.21M| } 1581| 2.21M| if (i == W->next) ------------------ | Branch (1581:13): [True: 0, False: 2.21M] ------------------ 1582| 0| { 1583| 0| return INCHI_CANON_INFINITY; ------------------ | | 31| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1584| 0| } 1585| | 1586| 2.21M|#if ( USE_AUX_RANKING_ALL == 1 ) 1587| | /*==== vertex ordering definition === 1588| | * vertex v1 < v2 <=> (AuxRank(v1)==AuxRank(v2) && AtNumb(v1) < AtNumb(v2)) || (AuxRank(v1) < AuxRank(v2)) 1589| | * vertex v1 > v2 <=> (AuxRank(v1)==AuxRank(v2) && AtNumb(v1) > AtNumb(v2)) || (AuxRank(v1) > AuxRank(v2)) 1590| | * vertex v1 = v2 <=> (AuxRank(v1)==AuxRank(v2) && AtNumb(v1) == AtNumb(v2)) 1591| | */ 1592| | 1593| | /* set initial vMin so that vMin > any vertex */ 1594| 2.21M| uMinAuxRank = INCHI_CANON_INFINITY; ------------------ | | 31| 2.21M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1595| 2.21M| nMinAtNumb = INCHI_CANON_INFINITY; ------------------ | | 31| 2.21M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1596| | /* set vInp */ 1597| 2.21M| if (v) ------------------ | Branch (1597:13): [True: 999k, False: 1.21M] ------------------ 1598| 999k| { 1599| 999k| nInpAtNumb = (int) v - 1; /* previous vertex */ 1600| 999k| uInpAuxRank = pCD->nAuxRank[nInpAtNumb]; 1601| 999k| } 1602| 1.21M| else 1603| 1.21M| { 1604| 1.21M| nInpAtNumb = -1; /* less than any vertex */ 1605| 1.21M| uInpAuxRank = 0; 1606| 1.21M| } 1607| | /* find vMin = min { vCur : (vCur > vInp) && (vCur in W) } */ 1608| 142M| for (; i < W->next; i++) ------------------ | Branch (1608:16): [True: 140M, False: 2.21M] ------------------ 1609| 140M| { 1610| 140M| nCurAtNumb = (int) p->AtNumber[(int) i]; 1611| 140M| if (!( p->Rank[nCurAtNumb] & rank_mark_bit )) ------------------ | Branch (1611:17): [True: 137M, False: 3.00M] ------------------ 1612| 137M| { 1613| | /* vertex nCurAtNumb is not marked, find whether it fits the conditions */ 1614| 137M| uCurAuxRank = pCD->nAuxRank[nCurAtNumb]; 1615| 137M| if ((uCurAuxRank == uInpAuxRank && nCurAtNumb > nInpAtNumb) || uCurAuxRank > uInpAuxRank) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1615:22): [True: 82.2M, False: 54.9M] | Branch (1615:52): [True: 40.6M, False: 41.6M] | Branch (1615:80): [True: 53.3M, False: 43.1M] ------------------ 1616| 93.9M| { 1617| | /* here vCur > vInp */ 1618| 93.9M| if (uCurAuxRank == uMinAuxRank && nCurAtNumb < nMinAtNumb) ------------------ | Branch (1618:25): [True: 88.4M, False: 5.52M] | Branch (1618:55): [True: 0, False: 88.4M] ------------------ 1619| 0| { 1620| | /* vCur < vMin (1) */ 1621| 0| nMinAtNumb = nCurAtNumb; 1622| 0| } 1623| 93.9M| else if (uCurAuxRank < uMinAuxRank) ------------------ | Branch (1623:30): [True: 2.09M, False: 91.8M] ------------------ 1624| 2.09M| { 1625| | /* vCur < vMin (2) */ 1626| 2.09M| uMinAuxRank = uCurAuxRank; 1627| 2.09M| nMinAtNumb = nCurAtNumb; 1628| 2.09M| } 1629| 93.9M| } 1630| 137M| } 1631| 140M| } 1632| | 1633| 2.21M| uMinAtNumb = ( nMinAtNumb == INCHI_CANON_INFINITY ) ? INCHI_CANON_INFINITY : (AT_NUMB) nMinAtNumb; ------------------ | | 31| 2.21M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ uMinAtNumb = ( nMinAtNumb == INCHI_CANON_INFINITY ) ? INCHI_CANON_INFINITY : (AT_NUMB) nMinAtNumb; ------------------ | | 31| 146k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (1633:22): [True: 146k, False: 2.06M] ------------------ 1634| | 1635| |#else 1636| | 1637| | if (v) 1638| | { 1639| | nCurAtNumb = (int) v - 1; 1640| | /* any valid found node must have nAuxRank == uMinAuxRank */ 1641| | uMinAuxRank = pCD->nAuxRank[nCurAtNumb]; 1642| | } 1643| | else 1644| | { 1645| | /* any valid found node must have minimal uMinAuxRank from pCD->nAuxRank[] */ 1646| | uMinAuxRank = INCHI_CANON_INFINITY; /* undefined */ 1647| | } 1648| | 1649| | for (; i < W->next; i++) 1650| | { 1651| | uCurAtNumb = p->AtNumber[(int) i]; 1652| | nCurAtNumb = (int) uCurAtNumb; 1653| | if (uCurAtNumb >= v && !( p->Rank[nCurAtNumb] & rank_mark_bit )) 1654| | { 1655| | uCurAuxRank = pCD->nAuxRank[nCurAtNumb]; 1656| | if (v) 1657| | { 1658| | /* get next node */ 1659| | /* find node with smallest uCurAtNumb among nodes with aux. ranks equal to uMinAuxRank */ 1660| | if (uCurAuxRank == uMinAuxRank && uCurAtNumb < uMinAtNumb) 1661| | { 1662| | uMinAtNumb = uCurAtNumb; 1663| | } 1664| | } 1665| | else 1666| | { 1667| | /* get first node */ 1668| | /* find node with smallest smallest uCurAtNumb among nodes with smallest aux. ranks */ 1669| | if (uMinAuxRank > uCurAuxRank) 1670| | { 1671| | uMinAuxRank = uCurAuxRank; 1672| | uMinAtNumb = uCurAtNumb; 1673| | } 1674| | else 1675| | { 1676| | if (uMinAuxRank == uCurAuxRank && uCurAtNumb < uMinAtNumb) 1677| | { 1678| | uMinAtNumb = uCurAtNumb; 1679| | } 1680| | } 1681| | } 1682| | } 1683| | } 1684| |#endif 1685| 2.21M| } 1686| | 1687| 8.21M| else 1688| 8.21M|#endif /* } USE_AUX_RANKING */ 1689| | 1690| 8.21M| { 1691| 503M| for (i = W->first; i < W->next; i++) ------------------ | Branch (1691:28): [True: 495M, False: 8.21M] ------------------ 1692| 495M| { 1693| 495M| uCurAtNumb = p->AtNumber[(int) i]; 1694| 495M| if (uCurAtNumb >= v && !( p->Rank[(int) uCurAtNumb] & rank_mark_bit ) && uCurAtNumb < uMinAtNumb) ------------------ | Branch (1694:17): [True: 339M, False: 155M] | Branch (1694:36): [True: 339M, False: 0] | Branch (1694:86): [True: 7.84M, False: 331M] ------------------ 1695| 7.84M| { 1696| 7.84M| uMinAtNumb = uCurAtNumb; 1697| 7.84M| } 1698| 495M| } 1699| 8.21M| } 1700| | 1701| 10.4M| if (uMinAtNumb != INCHI_CANON_INFINITY) ------------------ | | 31| 10.4M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (1701:9): [True: 9.91M, False: 510k] ------------------ 1702| 9.91M| { 1703| 9.91M| uMinAtNumb++; 1704| 9.91M| } 1705| | 1706| | INCHI_HEAPCHK 1707| | 1708| 10.4M| return uMinAtNumb; 1709| 10.4M|} CellGetNumberOfNodes: 1714| 380k|{ 1715| 380k| int first = W->first; 1716| 380k| int next = W->next; 1717| 380k| int i, num; 1718| 4.05M| for (i = first, num = 0; i < next; i++) ------------------ | Branch (1718:30): [True: 3.67M, False: 380k] ------------------ 1719| 3.67M| { 1720| 3.67M| if (!( rank_mark_bit & p->Rank[(int) p->AtNumber[i]] )) ------------------ | Branch (1720:13): [True: 3.67M, False: 0] ------------------ 1721| 3.67M| { 1722| 3.67M| num++; 1723| 3.67M| } 1724| 3.67M| } 1725| | 1726| | INCHI_HEAPCHK 1727| | 1728| 380k| return num; 1729| 380k|} CellIntersectWithSet: 1735| 2.97M|{ 1736| 2.97M| bitWord *McrBits = Mcr->bitword[l - 1]; 1737| 2.97M| int first = W->first; 1738| 2.97M| int next = W->next; 1739| 2.97M| int i, j, k; 1740| | 1741| 2.97M| if (first >= next) ------------------ | Branch (1741:9): [True: 0, False: 2.97M] ------------------ 1742| 0| { 1743| | /* for testing only */ 1744| 0| return 0; 1745| 0| } 1746| 136M| for (i = first, k = 0; i < next; i++) ------------------ | Branch (1746:28): [True: 133M, False: 2.97M] ------------------ 1747| 133M| { 1748| 133M| j = (int) p->AtNumber[i]; 1749| 133M| if (!( McrBits[j / pCG->m_num_bit] & pCG->m_bBit[j % pCG->m_num_bit] )) ------------------ | Branch (1749:13): [True: 2.86M, False: 130M] ------------------ 1750| 2.86M| { 1751| | /* BC: reading uninit memory ???-not examined yet */ 1752| 2.86M| k += !( p->Rank[j] & rank_mark_bit ); /* for testing only */ 1753| 2.86M| p->Rank[j] |= rank_mark_bit; 1754| 2.86M| } 1755| 133M| } 1756| 2.97M| INCHI_HEAPCHK 1757| | 1758| 2.97M| return k; 1759| 2.97M|} CtPartClear: 1764| 76.5k|{ 1765| 76.5k| int start; 1766| 76.5k| int len; 1767| | /* connection table */ 1768| 76.5k| start = k > 1 ? Ct->nextCtblPos[k - 1] : 0; ------------------ | Branch (1768:13): [True: 0, False: 76.5k] ------------------ 1769| 76.5k| len = Ct->lenCt - start; 1770| 76.5k| if (len > 0) ------------------ | Branch (1770:9): [True: 0, False: 76.5k] ------------------ 1771| 0| { 1772| 0| memset( Ct->Ctbl + start, 0, ( (long long)Ct->lenCt - (long long)start ) * sizeof( Ct->Ctbl[0] ) ); /* djb-rwth: cast operators added; memset_s C11/Annex K variant? */ 1773| 0| } 1774| 76.5k| Ct->lenCt = start; 1775| 76.5k| Ct->lenPos = k; 1776| | 1777| 76.5k| INCHI_HEAPCHK 1778| 76.5k|} insertions_sort_NeighList_AT_NUMBERS2: 1787| 8.43M|{ 1788| 8.43M| AT_NUMB *i, *j, *pk, tmp, rj; 1789| 8.43M| int k, num = (int) *base++; 1790| 8.86M| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (1790:28): [True: 427k, False: 8.43M] ------------------ 1791| 427k| { 1792| 427k| i = pk; 1793| 427k| j = i + 1; 1794| 427k| rj = ( rank_mask_bit & nRank[(int) *j] ); 1795| 427k| if (rj < max_rj) ------------------ | Branch (1795:13): [True: 186k, False: 241k] ------------------ 1796| 186k| { 1797| 217k| while (j > base && rj < ( rank_mask_bit & nRank[(int) *i] )) ------------------ | Branch (1797:20): [True: 202k, False: 14.7k] | Branch (1797:32): [True: 31.0k, False: 171k] ------------------ 1798| 31.0k| { 1799| 31.0k| tmp = *i; 1800| 31.0k| *i = *j; 1801| 31.0k| *j = tmp; 1802| 31.0k| j = i--; 1803| 31.0k| } 1804| 186k| } 1805| 427k| } 1806| | 1807| 8.43M| INCHI_HEAPCHK 1808| 8.43M|} CtPartFill: 1823| 6.46M|{ 1824| | /* k = (new index in Ct->nextAtRank[] and Ct->nextCtblPos[]) + 1 */ 1825| | 1826| 6.46M| int startCtbl; 1827| 6.46M| int startAtOrd; 1828| 6.46M| AT_RANK r, rj, nn, j, rj_prev; /* djb-rwth: ignoring LLVM warning as the variable is used */ 1829| 6.46M| int i, m, an_sao; 1830| | 1831| |#ifdef INCHI_CANON_USE_HASH 1832| | CtHash hash = 0; 1833| |#endif 1834| | 1835| | /* djb-rwth: removing redundant code */ 1836| | 1837| | INCHI_HEAPCHK 1838| | 1839| 6.46M| k--; 1840| 6.46M| if (Ct && k) /* djb-rwth: fixing oss-fuzz issue #69612 */ ------------------ | Branch (1840:9): [True: 6.46M, False: 0] | Branch (1840:15): [True: 6.05M, False: 408k] ------------------ 1841| 6.05M| { 1842| 6.05M| startCtbl = Ct->nextCtblPos[k - 1]; 1843| 6.05M| startAtOrd = Ct->nextAtRank[k - 1] - 1; /* here p->Rank[p->AtNumber[r-1]] = r */ 1844| 6.05M| } 1845| 408k| else 1846| 408k| { 1847| 408k| startCtbl = 0; 1848| 408k| startAtOrd = 0; 1849| 408k| } 1850| | 1851| | /******* Well-defined (by fixed ranks) part of the connection table ************/ 1852| | /* djb-rwth: fixing oss-fuzz issue #69612 */ 1853| 6.46M| if (startAtOrd < 0) ------------------ | Branch (1853:9): [True: 0, False: 6.46M] ------------------ 1854| 0| { 1855| 0| return; 1856| 0| } 1857| | /* djb-rwth: fixing oss-fuzz issue #391043585 */ 1858| 6.46M| if (startAtOrd < n_max && Ct) ------------------ | Branch (1858:9): [True: 6.46M, False: 0] | Branch (1858:31): [True: 6.46M, False: 0] ------------------ 1859| 6.46M| { 1860| 6.46M| an_sao = (int)p->AtNumber[startAtOrd]; 1861| 6.46M| r = (rank_mask_bit & p->Rank[an_sao]); 1862| | 1863| 14.8M| for (i = startAtOrd; i < n_tg && r == (rank_mask_bit & p->Rank[m = (int)p->AtNumber[i]]); i++, r++) ------------------ | Branch (1863:30): [True: 14.1M, False: 730k] | Branch (1863:42): [True: 8.43M, False: 5.73M] ------------------ 1864| 8.43M| { 1865| 8.43M| Ct->Ctbl[startCtbl++] = r; 1866| 8.43M| insertions_sort_NeighList_AT_NUMBERS2(G[m], p->Rank, r); 1867| 8.43M| nn = G[m][0]; /* number of neighbors */ 1868| 8.43M| rj_prev = 0; /* debug only */ /* djb-rwth: ignoring LLVM warning as the variable is used */ 1869| | 1870| |#ifdef INCHI_CANON_USE_HASH 1871| | hash = add2crc32(hash, (AT_NUMB)(r + n)); 1872| |#endif 1873| | 1874| 8.90M| for (j = 1; j <= nn && (rj = (rank_mask_bit & p->Rank[(int)G[m][j]])) < r; j++) ------------------ | Branch (1874:25): [True: 797k, False: 8.11M] | Branch (1874:36): [True: 471k, False: 325k] ------------------ 1875| 471k| { 1876| 471k| Ct->Ctbl[startCtbl++] = rj; 1877| | 1878| |#ifdef INCHI_CANON_USE_HASH 1879| | hash = add2crc32(hash, rj); 1880| |#endif 1881| | 1882| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 1883| | /* debug only */ 1884| | if (rj < rj_prev) 1885| | { 1886| | int stop = 1; /* */ 1887| | } 1888| |#endif 1889| | 1890| 471k| rj_prev = rj; /* djb-rwth: ignoring LLVM warning as the variable is used */ 1891| 471k| } 1892| 8.43M| } 1893| 6.46M| } 1894| 0| else 1895| 0| { 1896| 0| return; 1897| 0| } 1898| | 1899| | INCHI_HEAPCHK 1900| | 1901| | /****************** Well-defined part of base hydrogen atoms *******************/ 1902| 6.46M| if (Ct) ------------------ | Branch (1902:9): [True: 6.46M, False: 0] ------------------ 1903| 6.46M| { 1904| 6.46M| if (pCD->NumH && Ct->NumH) ------------------ | Branch (1904:13): [True: 1.30M, False: 5.16M] | Branch (1904:26): [True: 1.30M, False: 0] ------------------ 1905| 1.30M| { 1906| 1.30M| nn = inchi_min(n, i); ------------------ | | 139| 1.30M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 20.1k, False: 1.28M] | | ------------------ ------------------ 1907| 2.76M| for (j = startAtOrd; j < nn; j++) ------------------ | Branch (1907:34): [True: 1.46M, False: 1.30M] ------------------ 1908| 1.46M| { 1909| | /* atoms */ 1910| 1.46M| Ct->NumH[j] = pCD->NumH[p->AtNumber[j]]; 1911| 1.46M| } 1912| 1.32M| for (; j < i; j++) ------------------ | Branch (1912:20): [True: 20.3k, False: 1.30M] ------------------ 1913| 20.3k| { 1914| | /* t-groups */ 1915| 20.3k| int data_pos = n + T_NUM_NO_ISOTOPIC * ((int)p->AtNumber[j] - n); ------------------ | | 69| 20.3k|#define T_NUM_NO_ISOTOPIC 2 ------------------ 1916| 60.9k| for (m = 0; m < T_NUM_NO_ISOTOPIC; m++) ------------------ | | 69| 60.9k|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (1916:29): [True: 40.6k, False: 20.3k] ------------------ 1917| 40.6k| { 1918| 40.6k| Ct->NumH[nn++] = pCD->NumH[data_pos++]; 1919| 40.6k| } 1920| 20.3k| } 1921| 1.30M| Ct->lenNumH = nn; 1922| 1.30M| } 1923| 5.16M| else 1924| 5.16M| { 1925| 5.16M| Ct->lenNumH = 0; 1926| 5.16M| } 1927| | 1928| | INCHI_HEAPCHK 1929| | 1930| | /****************** Well-defined part of fixed hydrogen atoms *******************/ 1931| 6.46M| if (pCD->NumHfixed && Ct->NumHfixed) ------------------ | Branch (1931:17): [True: 43.4k, False: 6.41M] | Branch (1931:35): [True: 43.4k, False: 0] ------------------ 1932| 43.4k| { 1933| 43.4k| nn = inchi_min(n, i); ------------------ | | 139| 43.4k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 43.4k] | | ------------------ ------------------ 1934| 102k| for (j = startAtOrd; j < nn; j++) ------------------ | Branch (1934:38): [True: 58.8k, False: 43.4k] ------------------ 1935| 58.8k| { 1936| 58.8k| Ct->NumHfixed[j] = pCD->NumHfixed[p->AtNumber[j]]; 1937| | 1938| 58.8k| INCHI_HEAPCHK 1939| 58.8k| } 1940| | /* Ct->lenNumHfixed = nn; */ 1941| 43.4k| } 1942| 6.41M| else 1943| 6.41M| { 1944| 6.41M| ;/* Ct->lenNumHfixed = 0; */ 1945| 6.41M| } 1946| | 1947| | INCHI_HEAPCHK 1948| | 1949| | /****************** Well-defined part of isotopic keys ***************************/ 1950| 6.46M| if (pCD->iso_sort_key && Ct->iso_sort_key) ------------------ | Branch (1950:17): [True: 360k, False: 6.10M] | Branch (1950:38): [True: 360k, False: 0] ------------------ 1951| 360k| { 1952| 772k| for (j = startAtOrd; j < i; j++) ------------------ | Branch (1952:38): [True: 411k, False: 360k] ------------------ 1953| 411k| { 1954| 411k| Ct->iso_sort_key[j] = pCD->iso_sort_key[p->AtNumber[j]]; 1955| 411k| } 1956| 360k| Ct->len_iso_sort_key = i; 1957| 360k| } 1958| 6.10M| else 1959| 6.10M| { 1960| 6.10M| Ct->len_iso_sort_key = 0; 1961| 6.10M| } 1962| | 1963| | INCHI_HEAPCHK 1964| | 1965| | /****************** Well-defined part of isotopic iso_exchg_atnos ***************************/ 1966| 6.46M| if (pCD->iso_exchg_atnos && Ct->iso_exchg_atnos) ------------------ | Branch (1966:17): [True: 140k, False: 6.32M] | Branch (1966:41): [True: 140k, False: 0] ------------------ 1967| 140k| { 1968| 291k| for (j = startAtOrd; j < i; j++) ------------------ | Branch (1968:38): [True: 151k, False: 140k] ------------------ 1969| 151k| { 1970| 151k| Ct->iso_exchg_atnos[j] = pCD->iso_exchg_atnos[p->AtNumber[j]]; 1971| 151k| } 1972| 140k| Ct->len_iso_exchg_atnos = i; 1973| 140k| } 1974| 6.32M| else 1975| 6.32M| { 1976| 6.32M| Ct->len_iso_exchg_atnos = 0; 1977| 6.32M| } 1978| | 1979| | INCHI_HEAPCHK 1980| | 1981| | /******** Well-defined part of isotopic keys for fixed hydrogen atoms ************/ 1982| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 1983| | if (pCD->iso_sort_key_Hfixed && Ct->iso_sort_key_Hfixed) 1984| | { 1985| | nn = inchi_min(n, i); 1986| | for (j = startAtOrd; j < nn; j++) 1987| | { 1988| | Ct->iso_sort_key_Hfixed[j] = pCD->iso_sort_key_Hfixed[p->AtNumber[j]]; 1989| | } 1990| | Ct->len_iso_sort_key_Hfixed = nn; 1991| | } 1992| | else 1993| | { 1994| | Ct->len_iso_sort_key_Hfixed = 0; 1995| | } 1996| |#endif 1997| | 1998| | INCHI_HEAPCHK 1999| | 2000| 6.46M| Ct->lenCt = startCtbl; /* not aways increases */ 2001| 6.46M| Ct->nextCtblPos[k] = startCtbl; 2002| 6.46M| Ct->nextAtRank[k] = r; 2003| 6.46M| Ct->lenPos = k + 1; 2004| | 2005| | /* The rest of the CTable */ 2006| | 2007| |#ifdef INCHI_CANON_USE_HASH 2008| | while (i < n) 2009| | { 2010| | r = (rank_mask_bit & p->Rank[m = (int)p->AtNumber[i]]); 2011| | hash = add2crc32(hash, (AT_NUMB)(r + n)); 2012| | r++; 2013| | insertions_sort_NeighList_AT_NUMBERS2(G[m], p->Rank, r); 2014| | nn = G[m][0]; 2015| | rj_prev = 0; /* debug only */ 2016| | for (j = 1; j <= nn && (rj = (rank_mask_bit & p->Rank[(int)G[m][j]])) < r; j++) 2017| | { 2018| | hash = add2crc32(hash, rj); 2019| | } 2020| | i++; 2021| | } 2022| | Ct->hash[k] = hash; 2023| |#endif 2024| 6.46M| } 2025| 6.46M| INCHI_HEAPCHK 2026| 6.46M|} CtPartINCHI_CANON_INFINITY: 2031| 407k|{ 2032| 407k| int startCtbl; 2033| | /*int startAtOrd;*/ 2034| 407k| k--; 2035| 407k| if (k) ------------------ | Branch (2035:9): [True: 407k, False: 0] ------------------ 2036| 407k| { 2037| 407k| startCtbl = Ct->nextCtblPos[k - 1]; 2038| | /*startAtOrd = Ct->nextAtRank[k-1]-1;*/ /* here p->Rank[p->AtNumber[r-1]] = r */ 2039| 407k| if (cmp) ------------------ | Branch (2039:13): [True: 0, False: 407k] ------------------ 2040| 0| { 2041| 0| memset( cmp, 0, k * sizeof( cmp[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2042| 0| } 2043| 407k| } 2044| 0| else 2045| 0| { 2046| 0| startCtbl = 0; 2047| | /*startAtOrd = 0;*/ 2048| 0| } 2049| 407k| if (!startCtbl || Ct->Ctbl[startCtbl - 1] != EMPTY_CT) ------------------ | | 35| 407k|#define EMPTY_CT 0 ------------------ | Branch (2049:9): [True: 0, False: 407k] | Branch (2049:23): [True: 407k, False: 0] ------------------ 2050| 407k| { 2051| 407k| Ct->Ctbl[startCtbl] = EMPTY_CT; ------------------ | | 35| 407k|#define EMPTY_CT 0 ------------------ 2052| 407k| } 2053| | 2054| 407k| INCHI_HEAPCHK 2055| 407k|} CtPartCompare: 2095| 12.7M|{ 2096| 12.7M| int startCt1, endCt1, startCt2, endCt2; /*endCt,*/ 2097| 12.7M| int startAt1, endAt1, startAt2, endAt2; /*endCt,*/ 2098| 12.7M| int midCt /* end of atoms only Ct */, midNumH = 0 /* end of atoms only NumH */, maxVert; 2099| 12.7M| int diff, i, k1, k2, lenNumH, /*mid_iso_sort_key,*/ midAt; /* djb-rwth: ignoring LLVM warning: variables used */ 2100| 12.7M| int nLayer = 0; 2101| | 2102| 12.7M| k--; 2103| 12.7M| i = -1; 2104| | 2105| | /* set kLeastForLayer[nLayer].k = (k+1) or -(k+1) 2106| | kLeastForLayer[nLayer].i = iDiff 2107| | if all the conditions are met: 2108| | 1) kLeastForLayer[nLayer].k = 0 2109| | 2) diff==0 for all layers < nLayer 2110| | 2111| | sign: 2112| | if the final diff < 0 then kLeastForLayer[nLayer].k = -(k+1) else 2113| | if the final diff > 0 then kLeastForLayer[nLayer].k = +(k+1) 2114| | 2115| | k+1 instead of k takes into account k--; statememt above) 2116| | 2117| | meaning: 2118| | ======== 2119| | abs(kLeastForLayer[nLayer].k) is the greatest level k at which 2120| | difference at layer nLayer are zeroes of hidden by differences in smaller nLayer. 2121| | 2122| | "Hidden by difference in smaller level" means that nLayer of comparison 2123| | has not been reached because the difference was discovered at a previous layer. 2124| | 2125| | 2126| | Lambda vs zf_zeta comparison 2127| | ============================================= 2128| | accept only diff == 0 2129| | 2130| | Lambda vs pzb_rho and pzb_rho_fix comparison 2131| | ============================================= 2132| | Maintain kLeastForLayer[] and kLeastForLayerFix[] 2133| | 2134| | The algorithm provides that pzb_rho(m-1) < pzb_rho(m) <= pzb_rho_fix 2135| | 2136| | Definition: pzb_rho(m-1) < pzb_rho(m) means that 2137| | ----------------------------------------------- 2138| | pzb_rho(m-1)[nLayerCurr] == pzb_rho(m)[nLayerCurr] for nLayerCurr = 0..nLayerDiff-1 2139| | pzb_rho(m-1)[nLayerDiff] < pzb_rho(m)[nLayerDiff] 2140| | 2141| | Definition: pzb_rho(m-1)[nLayerDiff] < pzb_rho(m)[nLayerDiff] means that 2142| | ------------------------------------------------------------------------- 2143| | pzb_rho(m-1)[nLayerDiff][i] == pzb_rho(m)[nLayerDiff][i] for i=0..iDdiff-1 2144| | pzb_rho(m-1)[nLayerDiff][iDdiff] < pzb_rho(m)[nLayerDiff][iDdiff] 2145| | 2146| | This defines nLayerDiff(pzb1, pzb2) where pszb1 = pzb_rho(a), pzb2=pzb_rho(b) (a= 0 *) && 2163| | ((L_fix < L_rho) || (L_fix == L_rho && I_fix < I_rho)) 2164| | => 2165| | qzb_rho_fix = kLeastForLayerFix[L_fix].k if prevoiusly qzb_rho_fix == 0 2166| | 2167| | b) otherwise do not change qzb_rho_fix, except the following: 2168| | 2169| | c) Special case L_rho == L_fix && I_rho == I_fix. Let L=L_rho, I = I_rho. 2170| | 2171| | Compare 3 valirs: Lambda[L][I], pzb_rho(m)[L][I], pzb_rho_fix[L][I] 2172| | The algorithm provides pzb_rho(m)[L][I] < pzb_rho_fix[L][I] 2173| | (pzb_rho(m)[L][I]==pzb_rho_fix[L][I] <=> pzb_rho(m)[L][I]==pzb_rho_fix[L][I] 2174| | is impossible by construction) 2175| | There are 3 possibilities: 2176| | c1) Lambda[L][I] < pzb_rho(m)[L][I] < pzb_rho_fix[L][I] <=> 2177| | kLeastForLayer[L].k < 0 && kLeastForLayerFix[L].k < 0 2178| | => qzb_rho := kLeastForLayer[L].k, reject too small Lambda 2179| | c2) pzb_rho(m)[L][I] < Lambda[L][I] < pzb_rho_fix[L][I] 2180| | kLeastForLayer[L].k > 0 && kLeastForLayerFix[L].k < 0 2181| | => qzb_rho := kLeastForLayer[L].k, accept Lambda, rho:=nu 2182| | c3) pzb_rho(m)[L][I] < pzb_rho_fix[L][I] < Lambda[L][I] 2183| | kLeastForLayer[L].k > 0 && kLeastForLayerFix[L].k > 0 2184| | => qzb_rho_fix := kLeastForLayerFix[L].k, reject too big Lambda 2185| | 2186| | Case 2187| | kLeastForLayer[L].k < 0 && kLeastForLayerFix[L].k > 0 is impossible 2188| | because it means 2189| | pzb_rho_fix < Lambda < pzb_rho(m) <=> pzb_rho_fix < pzb_rho(m) 2190| | 2191| | 2192| | Case (c3) occurs in case of (a) 2193| | Case (c1) 2194| | 2195| | 2. Comparison Lambda vs pzb_rho before reaching discrete partition 2196| | ---------------------------------------------------------------------- 2197| | a) (L_rho < L_fix) || (L_rho == L_fix && I_rho < I_fix) => 2198| | 2199| | Lambda differs from pzb_rho(m) in the part of pzb_rho(m) that will never change 2200| | qzb_rho = kLeastForLayer[L_rho].k; reject Labmda or accept pzb_rho(m+1):=Labmda 2201| | 2202| | b) (L_rho == L_fix && I_rho > I_fix) && kLeastForLayer[L_rho].k < 0 2203| | Lambda < pzb_rho(m), therefore 2204| | qzb_rho = kLeastForLayer[L_rho].k; reject Labmda 2205| | 2206| | c) (L_rho > L_fix) => 2207| | qzb_rho := 0 because more significant difference may be discovered 2208| | in layer < L_rho later. The final comparison may be needed at the 2209| | level of discrete partition. 2210| | 2211| | 2212| | */ 2213| | 2214| 12.7M| if (cmp) ------------------ | Branch (2214:9): [True: 0, False: 12.7M] ------------------ 2215| 0| { 2216| 0| for (i = 0; i <= k && !cmp[i]; i++) ------------------ | Branch (2216:21): [True: 0, False: 0] | Branch (2216:31): [True: 0, False: 0] ------------------ 2217| 0| { 2218| 0| ; 2219| 0| } 2220| 0| if (i < k) ------------------ | Branch (2220:13): [True: 0, False: 0] ------------------ 2221| 0| { 2222| 0| cmp[k] = cmp[i]; 2223| 0| return (int) cmp[i]; 2224| 0| } 2225| 0| } 2226| | 2227| 12.7M| k1 = Ct1->lenPos - 1; /* djb-rwth: ignoring LLVM warning: variable used */ 2228| 12.7M| k2 = Ct2->lenPos - 1; /* djb-rwth: ignoring LLVM warning: variable used */ 2229| | 2230| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2231| | if (k > k1 || k > k2) 2232| | { 2233| | int stop = 1; 2234| | } 2235| |#endif 2236| | 2237| 12.7M| diff = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 2238| | 2239| 12.7M| if (k) ------------------ | Branch (2239:9): [True: 12.6M, False: 167k] ------------------ 2240| 12.6M| { 2241| 12.6M| startCt1 = Ct1->nextCtblPos[k - 1]; 2242| 12.6M| startCt2 = Ct2->nextCtblPos[k - 1]; 2243| 12.6M| startAt1 = Ct1->nextAtRank[k - 1] - 1; 2244| 12.6M| startAt2 = Ct2->nextAtRank[k - 1] - 1; 2245| 12.6M| } 2246| 167k| else 2247| 167k| { 2248| 167k| startCt1 = startCt2 = 0; 2249| 167k| startAt1 = startAt2 = 0; 2250| 167k| } 2251| | 2252| 12.7M| endCt1 = Ct1->nextCtblPos[k]; 2253| 12.7M| endCt2 = Ct2->nextCtblPos[k]; 2254| 12.7M| endAt1 = (int) Ct1->nextAtRank[k] - 1; 2255| 12.7M| endAt2 = (int) Ct2->nextAtRank[k] - 1; 2256| | 2257| 12.7M| maxVert = inchi_min( Ct1->maxVert, Ct2->maxVert ); ------------------ | | 139| 12.7M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 12.7M] | | ------------------ ------------------ 2258| | 2259| |#ifdef INCHI_CANON_USE_HASH 2260| | if (!diff) 2261| | { 2262| | if (Ct1->hash[k] > Ct2->hash[k]) 2263| | diff = 1; 2264| | else 2265| | if (Ct1->hash[k] < Ct2->hash[k]) 2266| | diff = -1; 2267| | } 2268| | if (diff) 2269| | { 2270| | goto done; 2271| | } 2272| |#endif 2273| | 2274| | /************************** lengths **************************************************/ 2275| 12.7M| if ((diff = -( startCt1 - startCt2 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2275:9): [True: 0, False: 12.7M] ------------------ 2276| 0| { 2277| | /* comparing two INCHI_CANON_INFINITY terminations */ 2278| 0| if (bOnlyCommon && ------------------ | Branch (2278:13): [True: 0, False: 0] ------------------ 2279| 0| startCt1 >= Ct1->nLenCTAtOnly && startCt2 >= Ct2->nLenCTAtOnly && ------------------ | Branch (2279:14): [True: 0, False: 0] | Branch (2279:47): [True: 0, False: 0] ------------------ 2280| 0| Ct1->Ctbl[startCt1] == EMPTY_CT && Ct2->Ctbl[startCt2] == EMPTY_CT) ------------------ | | 35| 0|#define EMPTY_CT 0 ------------------ Ct1->Ctbl[startCt1] == EMPTY_CT && Ct2->Ctbl[startCt2] == EMPTY_CT) ------------------ | | 35| 0|#define EMPTY_CT 0 ------------------ | Branch (2280:14): [True: 0, False: 0] | Branch (2280:49): [True: 0, False: 0] ------------------ 2281| 0| { 2282| 0| return 0; 2283| 0| } 2284| 0| if (bOnlyCommon) ------------------ | Branch (2284:13): [True: 0, False: 0] ------------------ 2285| 0| { 2286| 0| startCt1 = inchi_min( startCt1, startCt2 ); /* djb-rwth: removing redundant code */ ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2287| 0| startAt1 = startAt2 = inchi_min( startAt1, startAt2 ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2288| 0| if (Ct1->lenCt == Ct2->lenCt) ------------------ | Branch (2288:17): [True: 0, False: 0] ------------------ 2289| 0| { 2290| 0| endCt1 = endCt2 = inchi_max( endCt1, endCt2 ); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 2291| 0| endAt1 = endAt2 = inchi_max( endAt1, endAt2 ); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 2292| 0| } 2293| | 2294| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2295| | else 2296| | { 2297| | int stop = 1; 2298| | } 2299| |#endif 2300| 0| } 2301| 0| else 2302| | /* comparing (taut tail) vs INCHI_CANON_INFINITY termination -- ??? */ 2303| 0| if (startCt1 > startCt2 && ------------------ | Branch (2303:17): [True: 0, False: 0] ------------------ 2304| 0| Ct1->maxVert > Ct2->maxVert && ------------------ | Branch (2304:18): [True: 0, False: 0] ------------------ 2305| 0| startAt2 == Ct2->maxVert) ------------------ | Branch (2305:18): [True: 0, False: 0] ------------------ 2306| 0| { 2307| 0| return 0; 2308| 0| } 2309| 0| else 2310| 0| { 2311| 0| goto done; 2312| 0| } 2313| 0| } 2314| | 2315| 12.7M| lenNumH = Ct1->lenNumH; 2316| | /* djb-rwth: removing redundant code */ 2317| | 2318| 12.7M| if ((diff = -( endCt1 - endCt2 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2318:9): [True: 10.1k, False: 12.7M] ------------------ 2319| 10.1k| { 2320| | /* negative sign reproduces results for NSC=28393 */ 2321| 10.1k| if (bOnlyCommon) ------------------ | Branch (2321:13): [True: 10.1k, False: 12] ------------------ 2322| 10.1k| { 2323| 10.1k| endCt1 = inchi_min( endCt1, endCt2 ); /* djb-rwth: removing redundant code */ ------------------ | | 139| 10.1k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 10.1k] | | ------------------ ------------------ 2324| 10.1k| endAt1 = endAt2 = inchi_min( endAt1, endAt2 ); ------------------ | | 139| 10.1k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 10.1k] | | ------------------ ------------------ 2325| 10.1k| lenNumH = inchi_min( Ct1->lenNumH, Ct2->lenNumH ); ------------------ | | 139| 10.1k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 10.1k] | | ------------------ ------------------ 2326| | /* djb-rwth: removing redundant code */ 2327| 10.1k| } 2328| 12| else 2329| 12| { 2330| | /* take care of case when comparing tautomeric vs non-tautomeric: 2331| | since (taut)->maxVert > (non-taut)->maxVert, --??? 2332| | (taut)->maxlenCt > (non-taut)->maxlenCt --!!! 2333| | compare up to min out of the two, ignoring INCHI_CANON_INFINITY in the last position */ 2334| 12| if (endCt1 > endCt2 && Ct1->maxlenCt > Ct2->maxlenCt) ------------------ | Branch (2334:17): [True: 5, False: 7] | Branch (2334:36): [True: 0, False: 5] ------------------ 2335| 0| { 2336| 0| if (endAt2 == Ct2->maxVert + 1) ------------------ | Branch (2336:21): [True: 0, False: 0] ------------------ 2337| 0| { 2338| | /* remove INCHI_CANON_INFINITY termination of the shorter CT */ 2339| | /* should never happen */ 2340| 0| endAt2--; 2341| 0| lenNumH = endAt1 = endAt2; /* djb-rwth: removing redundant code */ 2342| 0| endCt2--; 2343| 0| endCt1 = endCt2; 2344| 0| diff = 0; /* djb-rwth: ignoring LLVM warning: value used? */ 2345| 0| } 2346| 0| else if (endAt2 == Ct2->maxVert) ------------------ | Branch (2346:26): [True: 0, False: 0] ------------------ 2347| 0| { 2348| | /* remove INCHI_CANON_INFINITY termination of CT */ 2349| 0| lenNumH = endAt1 = endAt2; /* djb-rwth: removing redundant code */ 2350| 0| endCt1 = endCt2; 2351| 0| diff = 0; /* djb-rwth: ignoring LLVM warning: value used? */ 2352| 0| } 2353| 0| else 2354| 0| { 2355| 0| goto done; 2356| 0| } 2357| 0| } 2358| 12| else 2359| 12| { 2360| 12| goto done; 2361| 12| } 2362| 12| } 2363| 10.1k| } 2364| | 2365| 12.7M| if (bSplitTautCompare) ------------------ | Branch (2365:9): [True: 3.53M, False: 9.23M] ------------------ 2366| 3.53M| { 2367| 3.53M| midCt = inchi_min( Ct1->nLenCTAtOnly, Ct2->nLenCTAtOnly ); ------------------ | | 139| 3.53M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 3.53M] | | ------------------ ------------------ 2368| 3.53M| if (midCt > endCt1) ------------------ | Branch (2368:13): [True: 3.44M, False: 97.3k] ------------------ 2369| 3.44M| { 2370| 3.44M| midCt = endCt1; 2371| 3.44M| } 2372| 3.53M| midAt = inchi_min( maxVert, endAt1 ); ------------------ | | 139| 3.53M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 28.1k, False: 3.51M] | | ------------------ ------------------ 2373| 3.53M| } 2374| 9.23M| else 2375| 9.23M| { 2376| 9.23M| midCt = endCt1; 2377| 9.23M| midAt = endAt1; 2378| 9.23M| } 2379| | 2380| | 2381| | /*endCt = min(endCt1, endCt2);*/ 2382| | /*************************************************************************/ 2383| | /************ layer 0: connection table without tautomeric groups ********/ 2384| | /*************************************************************************/ 2385| | 2386| 28.8M| for (i = startCt1; i < midCt && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2386:24): [True: 16.0M, False: 12.7M] | Branch (2386:37): [True: 16.0M, False: 8] ------------------ 2387| | /*for ( i = startCt1; i < endCt && !(diff = (int)Ct1->Ctbl[i] - (int)Ct2->Ctbl[i]); i ++ )*/ 2388| 16.0M| { 2389| 16.0M| ; 2390| 16.0M| } 2391| | 2392| 12.7M| if (i < midCt) ------------------ | Branch (2392:9): [True: 8, False: 12.7M] ------------------ 2393| 8| { 2394| 8| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2395| 8| goto done; 2396| 8| } 2397| | 2398| | /*************************************************************************/ 2399| | /******** layer 1 NumH: H atoms without tautomeric H *********************/ 2400| | /*************************************************************************/ 2401| | 2402| 12.7M| nLayer++; 2403| | 2404| | /*============= check limits for consistency ==========*/ 2405| 12.7M| if ((diff = -( startAt1 - startAt2 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2405:9): [True: 0, False: 12.7M] ------------------ 2406| 0| { 2407| 0| goto done; /* should not happen */ 2408| 0| } 2409| 12.7M| if ((diff = -( endAt1 - endAt2 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2409:9): [True: 0, False: 12.7M] ------------------ 2410| 0| { 2411| 0| goto done; /* should not happen */ 2412| 0| } 2413| | 2414| | /*============= comparison =============================*/ 2415| 12.7M| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2415:9): [True: 3.53M, False: 9.23M] | Branch (2415:22): [True: 3.09M, False: 443k] ------------------ 2416| 3.09M| { 2417| 3.09M| if (endAt1 < maxVert) ------------------ | Branch (2417:13): [True: 3.00M, False: 89.0k] ------------------ 2418| 3.00M| { 2419| 3.00M| midNumH = lenNumH = endAt1; 2420| 3.00M| } 2421| 89.0k| else if (bSplitTautCompare) ------------------ | Branch (2421:18): [True: 89.0k, False: 0] ------------------ 2422| 89.0k| { 2423| 89.0k| midNumH = maxVert; 2424| 89.0k| } 2425| 0| else 2426| 0| { 2427| 0| midNumH = lenNumH; 2428| 0| } 2429| | 2430| | /* lenNumH = (endAt2 >= maxVert)? lenNumH : endAt2; */ 2431| | /* endAt1 = (endAt2 == n)? lenNumH : endAt2; */ 2432| | 2433| 6.52M| for (i = startAt1; i < midNumH && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2433:28): [True: 3.43M, False: 3.08M] | Branch (2433:43): [True: 3.42M, False: 7.39k] ------------------ 2434| 3.42M| { 2435| 3.42M| ; 2436| 3.42M| } 2437| 3.09M| if (i < midNumH) ------------------ | Branch (2437:13): [True: 7.39k, False: 3.08M] ------------------ 2438| 7.39k| { 2439| 7.39k| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2440| 7.39k| goto done; 2441| 7.39k| } 2442| 3.09M| } 2443| | 2444| | 2445| | /*************************************************************************/ 2446| | /************** layer 2: tautomeric part of CT and tautomeric H **********/ 2447| | /*************************************************************************/ 2448| 12.7M| nLayer++; 2449| 12.8M| for (i = midCt; i < endCt1 && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2449:21): [True: 73.2k, False: 12.7M] | Branch (2449:35): [True: 55.4k, False: 17.7k] ------------------ 2450| 55.4k| { 2451| 55.4k| ; /* compare tautomeric groups part of CT */ 2452| 55.4k| } 2453| 12.7M| if (i < endCt1) ------------------ | Branch (2453:9): [True: 17.7k, False: 12.7M] ------------------ 2454| 17.7k| { 2455| 17.7k| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2456| 17.7k| goto done; 2457| 17.7k| } 2458| 12.7M| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2458:9): [True: 3.51M, False: 9.23M] | Branch (2458:22): [True: 3.07M, False: 443k] ------------------ 2459| 3.07M| { 2460| 3.09M| for (i = midNumH; i < lenNumH && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2460:27): [True: 20.9k, False: 3.07M] | Branch (2460:42): [True: 20.9k, False: 2] ------------------ 2461| 20.9k| { 2462| 20.9k| ; /* compare tautomeric H */ 2463| 20.9k| } 2464| 3.07M| if (i < lenNumH) ------------------ | Branch (2464:13): [True: 2, False: 3.07M] ------------------ 2465| 2| { 2466| 2| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2467| 2| i += endCt1 - midCt; 2468| 2| goto done; 2469| 2| } 2470| 3.07M| } 2471| | 2472| | 2473| | /*************************************************************************/ 2474| | /************** layer 3: Fixed H atoms ***********************************/ 2475| | /*************************************************************************/ 2476| 12.7M| nLayer++; 2477| 12.7M| if (Ct1->NumHfixed && Ct2->NumHfixed) ------------------ | Branch (2477:9): [True: 20.6k, False: 12.7M] | Branch (2477:27): [True: 15.7k, False: 4.88k] ------------------ 2478| 15.7k| { 2479| 42.8k| for (i = startAt1; i < midAt && Ct1->NumHfixed[i] == Ct2->NumHfixed[i]; i++) ------------------ | Branch (2479:28): [True: 27.8k, False: 15.0k] | Branch (2479:41): [True: 27.0k, False: 742] ------------------ 2480| 27.0k| { 2481| 27.0k| ; 2482| 27.0k| } 2483| 15.7k| if (i < midAt) ------------------ | Branch (2483:13): [True: 742, False: 15.0k] ------------------ 2484| 742| { 2485| 742| diff = (int) Ct1->NumHfixed[i] - (int) Ct2->NumHfixed[i]; 2486| 742| goto done; 2487| 742| } 2488| 15.7k| } 2489| | 2490| | 2491| | /*************************************************************************/ 2492| | /************** layer 4: isotopic atoms H, incl. tautomeric **************/ 2493| | /*************************************************************************/ 2494| 12.7M| nLayer++; 2495| 12.7M| if (Ct1->iso_sort_key && Ct2->iso_sort_key) ------------------ | Branch (2495:9): [True: 962k, False: 11.7M] | Branch (2495:30): [True: 610k, False: 351k] ------------------ 2496| 610k| { 2497| 1.27M| for (i = startAt1; i < endAt1 && Ct1->iso_sort_key[i] == Ct2->iso_sort_key[i]; i++) ------------------ | Branch (2497:28): [True: 665k, False: 607k] | Branch (2497:42): [True: 661k, False: 3.65k] ------------------ 2498| 661k| ; 2499| 610k| if (i < endAt1) ------------------ | Branch (2499:13): [True: 3.65k, False: 607k] ------------------ 2500| 3.65k| { 2501| 3.65k| diff = Ct1->iso_sort_key[i] > Ct2->iso_sort_key[i] ? 1 : -1; ------------------ | Branch (2501:20): [True: 3.31k, False: 338] ------------------ 2502| 3.65k| goto done; 2503| 3.65k| } 2504| 610k| } 2505| 12.7M| if (Ct1->iso_exchg_atnos && Ct2->len_iso_exchg_atnos) ------------------ | Branch (2505:9): [True: 406k, False: 12.3M] | Branch (2505:33): [True: 267k, False: 139k] ------------------ 2506| 267k| { 2507| 554k| for (i = startAt1; i < endAt1 && Ct1->iso_exchg_atnos[i] == Ct2->iso_exchg_atnos[i]; i++) ------------------ | Branch (2507:28): [True: 287k, False: 266k] | Branch (2507:42): [True: 287k, False: 353] ------------------ 2508| 287k| { 2509| 287k| ; 2510| 287k| } 2511| 267k| if (i < endAt1) ------------------ | Branch (2511:13): [True: 353, False: 266k] ------------------ 2512| 353| { 2513| 353| diff = Ct1->iso_exchg_atnos[i] > Ct2->iso_exchg_atnos[i] ? 1 : -1; ------------------ | Branch (2513:20): [True: 212, False: 141] ------------------ 2514| 353| goto done; 2515| 353| } 2516| 267k| } 2517| | 2518| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 2519| | 2520| | /*************************************************************************/ 2521| | /************** layer 6: Fixed isotopic H atoms **************************/ 2522| | /*************************************************************************/ 2523| | nLayer++; 2524| | if (Ct1->iso_sort_key_Hfixed && Ct2->iso_sort_key_Hfixed) 2525| | { 2526| | for (i = startAt1; i < midAt && Ct1->iso_sort_key_Hfixed[i] == Ct2->iso_sort_key_Hfixed[i]; i++) 2527| | { 2528| | ; 2529| | } 2530| | if (i < midAt) 2531| | { 2532| | diff = Ct1->iso_sort_key_Hfixed[i] > Ct2->iso_sort_key_Hfixed[i] ? 1 : -1; 2533| | goto done; 2534| | } 2535| | } 2536| |#endif 2537| | 2538| | 2539| | 2540| 12.7M|done: 2541| | 2542| 12.7M|#ifdef INCHI_CANON_MIN 2543| 12.7M| diff = -diff; 2544| 12.7M|#endif 2545| | 2546| 12.7M| if (diff) ------------------ | Branch (2546:9): [True: 29.9k, False: 12.7M] ------------------ 2547| 29.9k| { 2548| 29.9k| diff = ( diff > 0 ) ? ( nLayer + 1 ) : -( nLayer + 1 ); /* return the discovered difference layer number >= 1 */ ------------------ | Branch (2548:16): [True: 1.50k, False: 28.4k] ------------------ 2549| 29.9k| if (kLeastForLayer) ------------------ | Branch (2549:13): [True: 18.5k, False: 11.3k] ------------------ 2550| 18.5k| { 2551| | 2552| |#if ( bRELEASE_VERSION != 1 ) 2553| | if (abs( kLeastForLayer[nLayer].k ) > k + 1) 2554| | { /* for debug only */ 2555| | int stop = 1; /* */ 2556| | } 2557| |#endif 2558| | 2559| 18.5k| if (!kLeastForLayer[nLayer].k) ------------------ | Branch (2559:17): [True: 18.5k, False: 0] ------------------ 2560| 18.5k| { 2561| 18.5k| kLeastForLayer[nLayer].k = ( diff > 0 ) ? ( k + 1 ) : -( k + 1 ); ------------------ | Branch (2561:44): [True: 524, False: 18.0k] ------------------ 2562| 18.5k| kLeastForLayer[nLayer].i = i; 2563| 18.5k| } 2564| 18.5k| if (nLayer /* && !bOnlyCommon */) ------------------ | Branch (2564:17): [True: 18.5k, False: 10] ------------------ 2565| 18.5k| { 2566| 18.5k| diff = 0; 2567| 18.5k| } 2568| 18.5k| } 2569| 29.9k| } 2570| | 2571| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2572| | else 2573| | { 2574| | int stop = 1; /* for debug only */ 2575| | } 2576| |#endif 2577| | 2578| 12.7M| if (cmp) ------------------ | Branch (2578:9): [True: 0, False: 12.7M] ------------------ 2579| 0| { 2580| 0| cmp[k] = ( diff > 0 ) ? 1 : ( diff < 0 ) ? -1 : 0; ------------------ | Branch (2580:18): [True: 0, False: 0] | Branch (2580:37): [True: 0, False: 0] ------------------ 2581| 0| } 2582| | 2583| 12.7M| return diff; 2584| 12.7M|} CtFullCompare: 2592| 471k|{ 2593| 471k| int startCt1, endCt1, endCt2; /*endCt,*/ 2594| 471k| int startAt1, endAt1, endAt2; /*endCt,*/ 2595| 471k| int midCt /* end of atoms only in Ctbl */, 2596| 471k| midNumH = 0 /* end of atoms only NumH */, 2597| 471k| midAt /* end of atoms only */; /* djb-rwth: ignoring LLVM warning: variable used */ 2598| 471k| int diff = 0, i, k1, k2, lenNumH1, lenNumH2, maxVert /* min num atoms */; 2599| 471k| int len_iso_sort_key1, len_iso_sort_key2 /*, mid_iso_sort_key*/; 2600| 471k| int nLayer = 0; 2601| | 2602| 471k| k1 = Ct1->lenPos - 1; 2603| 471k| k2 = Ct2->lenPos - 1; 2604| | 2605| | /* djb-rwth: removing redundant code */ 2606| | 2607| 471k| startCt1 = 0; /* djb-rwth: removing redundant code */ 2608| 471k| startAt1 = 0; /* djb-rwth: removing redundant code */ 2609| | 2610| 471k| endCt1 = Ct1->nextCtblPos[k1]; 2611| 471k| endCt2 = Ct2->nextCtblPos[k2]; 2612| 471k| endAt1 = (int) Ct1->nextAtRank[k1] - 1; 2613| 471k| endAt2 = (int) Ct2->nextAtRank[k2] - 1; 2614| | 2615| 471k| maxVert = inchi_min( Ct1->maxVert, Ct2->maxVert ); ------------------ | | 139| 471k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 471k] | | ------------------ ------------------ 2616| | 2617| 471k| if (bOnlyCommon) ------------------ | Branch (2617:9): [True: 84.9k, False: 386k] ------------------ 2618| 84.9k| { 2619| 84.9k| endCt1 = inchi_min( endCt1, endCt2 ); ------------------ | | 139| 84.9k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 3.46k, False: 81.4k] | | ------------------ ------------------ 2620| 84.9k| endCt1 = endCt2 = inchi_min( endCt1, Ct1->lenCt ); ------------------ | | 139| 84.9k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 2.94k, False: 82.0k] | | ------------------ ------------------ 2621| 84.9k| endAt1 = inchi_min( endAt1, endAt2 ); /* djb-rwth: removing redundant code */ ------------------ | | 139| 84.9k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 3.46k, False: 81.4k] | | ------------------ ------------------ 2622| | 2623| 84.9k| if (Ct1->Ctbl[endCt1] == EMPTY_CT || Ct2->Ctbl[endCt1] == EMPTY_CT) /* djb-rwth: redundant conditions removed */ ------------------ | | 35| 169k|#define EMPTY_CT 0 ------------------ if (Ct1->Ctbl[endCt1] == EMPTY_CT || Ct2->Ctbl[endCt1] == EMPTY_CT) /* djb-rwth: redundant conditions removed */ ------------------ | | 35| 2.94k|#define EMPTY_CT 0 ------------------ | Branch (2623:13): [True: 82.0k, False: 2.94k] | Branch (2623:46): [True: 2.94k, False: 0] ------------------ 2624| 84.9k| { 2625| 84.9k| endCt1 = endCt2 = endCt1 - 1; 2626| 84.9k| } 2627| | /* djb-rwth: removing redundant code */ 2628| 84.9k| lenNumH1 = 2629| 84.9k| lenNumH2 = inchi_min( Ct1->lenNumH, Ct2->lenNumH ); ------------------ | | 139| 84.9k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 4.33k, False: 80.6k] | | ------------------ ------------------ 2630| | 2631| | /* djb-rwth: removing redundant code */ 2632| 84.9k| len_iso_sort_key1 = 2633| 84.9k| len_iso_sort_key2 = inchi_min( Ct1->len_iso_sort_key, Ct1->len_iso_sort_key ); ------------------ | | 139| 84.9k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 84.9k] | | ------------------ ------------------ 2634| 84.9k| } 2635| 386k| else 2636| 386k| { 2637| 386k| if (Ct1->Ctbl[endCt1 - 1] == EMPTY_CT) ------------------ | | 35| 386k|#define EMPTY_CT 0 ------------------ | Branch (2637:13): [True: 0, False: 386k] ------------------ 2638| 0| { 2639| 0| endCt1--; 2640| 0| } 2641| 386k| if (Ct2->Ctbl[endCt2 - 1] == EMPTY_CT) ------------------ | | 35| 386k|#define EMPTY_CT 0 ------------------ | Branch (2641:13): [True: 0, False: 386k] ------------------ 2642| 0| { 2643| 0| endCt2--; 2644| 0| } 2645| 386k| lenNumH1 = Ct1->lenNumH; 2646| 386k| lenNumH2 = Ct2->lenNumH; 2647| | /* djb-rwth: removing redundant code */ 2648| | 2649| 386k| len_iso_sort_key1 = Ct1->len_iso_sort_key; 2650| 386k| len_iso_sort_key2 = Ct2->len_iso_sort_key; 2651| | /* djb-rwth: removing redundant code */ 2652| 386k| } 2653| | 2654| 471k| if ((diff = -( endCt1 - endCt2 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2654:9): [True: 0, False: 471k] ------------------ 2655| 0| { 2656| | /* negative sign reproduces results for NSC=28393 */ 2657| 0| goto done; 2658| 0| } 2659| | 2660| 471k| if (bSplitTautCompare) ------------------ | Branch (2660:9): [True: 107k, False: 364k] ------------------ 2661| 107k| { 2662| 107k| midCt = inchi_min( Ct1->nLenCTAtOnly, Ct2->nLenCTAtOnly ); ------------------ | | 139| 107k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 107k] | | ------------------ ------------------ 2663| 107k| if (midCt > endCt1) ------------------ | Branch (2663:13): [True: 84.8k, False: 22.2k] ------------------ 2664| 84.8k| { 2665| 84.8k| midCt = endCt1; 2666| 84.8k| } 2667| 107k| midAt = inchi_min( maxVert, endAt1 ); /* djb-rwth: ignoring LLVM warning: variable used? */ ------------------ | | 139| 107k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 5.04k, False: 102k] | | ------------------ ------------------ 2668| 107k| } 2669| 364k| else 2670| 364k| { 2671| 364k| midCt = endCt1; 2672| 364k| midAt = endAt1; /* djb-rwth: ignoring LLVM warning: variable used? */ 2673| 364k| } 2674| | 2675| | 2676| | /*************************************************************************/ 2677| | /************ layer 0: connection table without tautomeric groups ********/ 2678| | /*************************************************************************/ 2679| 14.0M| for (i = startCt1; i < midCt && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2679:24): [True: 13.5M, False: 471k] | Branch (2679:37): [True: 13.5M, False: 0] ------------------ 2680| 13.5M| { 2681| 13.5M| ; 2682| 13.5M| } 2683| 471k| if (i < midCt) ------------------ | Branch (2683:9): [True: 0, False: 471k] ------------------ 2684| 0| { 2685| 0| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2686| 0| goto done; 2687| 0| } 2688| | 2689| | 2690| | /*************************************************************************/ 2691| | /************* layer 1: H atoms without tautomeric H *********************/ 2692| | /*************************************************************************/ 2693| 471k| nLayer++; 2694| 471k| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2694:9): [True: 106k, False: 365k] | Branch (2694:22): [True: 105k, False: 868] ------------------ 2695| 105k| { 2696| 105k| if ((diff = -( lenNumH1 - lenNumH2 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2696:13): [True: 0, False: 105k] ------------------ 2697| 0| { 2698| | /* negative sign reproduces results for NSC=28393 */ 2699| 0| goto done; 2700| 0| } 2701| 105k| if (endAt1 < maxVert) ------------------ | Branch (2701:13): [True: 0, False: 105k] ------------------ 2702| 0| { 2703| 0| midNumH = lenNumH1 = endAt1; 2704| 0| } 2705| 105k| else if (bSplitTautCompare) ------------------ | Branch (2705:18): [True: 105k, False: 0] ------------------ 2706| 105k| { 2707| 105k| midNumH = maxVert; 2708| 105k| } 2709| 0| else 2710| 0| { 2711| 0| midNumH = lenNumH1; 2712| 0| } 2713| | 2714| 2.46M| for (i = startAt1; i < midNumH && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2714:28): [True: 2.35M, False: 105k] | Branch (2714:43): [True: 2.35M, False: 0] ------------------ 2715| 2.35M| { 2716| 2.35M| ; 2717| 2.35M| } 2718| 105k| if (i < midNumH) ------------------ | Branch (2718:13): [True: 0, False: 105k] ------------------ 2719| 0| { 2720| 0| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2721| 0| goto done; 2722| 0| } 2723| 105k| } 2724| | 2725| | 2726| | /*************************************************************************/ 2727| | /************** layer 2: tautomeric part of CT and tautomeric H **********/ 2728| | /*************************************************************************/ 2729| 471k| nLayer++; 2730| 488k| for (i = midCt; i < endCt1 && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2730:21): [True: 16.8k, False: 471k] | Branch (2730:35): [True: 16.8k, False: 0] ------------------ 2731| 16.8k| { 2732| 16.8k| ; /* compare tautomeric groups part of CT */ 2733| 16.8k| } 2734| 471k| if (i < endCt1) ------------------ | Branch (2734:9): [True: 0, False: 471k] ------------------ 2735| 0| { 2736| 0| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2737| 0| goto done; 2738| 0| } 2739| 471k| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2739:9): [True: 106k, False: 365k] | Branch (2739:22): [True: 105k, False: 868] ------------------ 2740| 105k| { 2741| 115k| for (i = midNumH; i < lenNumH1 && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2741:27): [True: 10.2k, False: 105k] | Branch (2741:43): [True: 10.2k, False: 0] ------------------ 2742| 10.2k| { 2743| 10.2k| ; /* compare tautomeric H */ 2744| 10.2k| } 2745| 105k| if (i < lenNumH1) ------------------ | Branch (2745:13): [True: 0, False: 105k] ------------------ 2746| 0| { 2747| 0| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2748| 0| goto done; 2749| 0| } 2750| 105k| } 2751| | 2752| | /*************************************************************************/ 2753| | /************** layer 3: Fixed H atoms ***********************************/ 2754| | /*************************************************************************/ 2755| 471k| nLayer++; 2756| 471k| if (Ct1->NumHfixed && Ct2->NumHfixed) ------------------ | Branch (2756:9): [True: 1.86k, False: 469k] | Branch (2756:27): [True: 919, False: 942] ------------------ 2757| 919| { 2758| 19.1k| for (i = startAt1; i < endAt1 && Ct1->NumHfixed[i] == Ct2->NumHfixed[i]; i++) ------------------ | Branch (2758:28): [True: 18.2k, False: 919] | Branch (2758:42): [True: 18.2k, False: 0] ------------------ 2759| 18.2k| { 2760| 18.2k| ; 2761| 18.2k| } 2762| 919| if (i < endAt1) ------------------ | Branch (2762:13): [True: 0, False: 919] ------------------ 2763| 0| { 2764| 0| diff = (int) Ct1->NumHfixed[i] - (int) Ct2->NumHfixed[i]; 2765| 0| goto done; 2766| 0| } 2767| 919| } 2768| | 2769| | 2770| | /*************************************************************************/ 2771| | /************** layer 4: isotopic atoms, H and isotopic taut H ***********/ 2772| | /*************************************************************************/ 2773| 471k| nLayer++; 2774| 471k| if (Ct1->iso_sort_key && Ct2->iso_sort_key) ------------------ | Branch (2774:9): [True: 6.22k, False: 465k] | Branch (2774:30): [True: 5.68k, False: 546] ------------------ 2775| 5.68k| { 2776| 5.68k| if ((diff = -( len_iso_sort_key1 - len_iso_sort_key2 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2776:13): [True: 0, False: 5.68k] ------------------ 2777| 0| { 2778| | /* negative sign reproduces results for NSC=28393 */ 2779| 0| goto done; 2780| 0| } 2781| 550k| for (i = startAt1; i < endAt1 && Ct1->iso_sort_key[i] == Ct2->iso_sort_key[i]; i++) ------------------ | Branch (2781:28): [True: 545k, False: 5.68k] | Branch (2781:42): [True: 545k, False: 0] ------------------ 2782| 545k| { 2783| 545k| ; 2784| 545k| } 2785| 5.68k| if (i < endAt1) ------------------ | Branch (2785:13): [True: 0, False: 5.68k] ------------------ 2786| 0| { 2787| 0| diff = Ct1->iso_sort_key[i] > Ct2->iso_sort_key[i] ? 1 : -1; ------------------ | Branch (2787:20): [True: 0, False: 0] ------------------ 2788| 0| goto done; 2789| 0| } 2790| 5.68k| } 2791| | 2792| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 2793| | 2794| | 2795| | /*************************************************************************/ 2796| | /************** layer 6: Fixed isotopic H atoms **************************/ 2797| | /*************************************************************************/ 2798| | nLayer++; 2799| | if (Ct1->iso_sort_key_Hfixed && Ct2->iso_sort_key_Hfixed) 2800| | { 2801| | for (i = startAt1; i < midAt && Ct1->iso_sort_key_Hfixed[i] == Ct2->iso_sort_key_Hfixed[i]; i++) 2802| | ; 2803| | if (i < midAt) 2804| | { 2805| | diff = Ct1->iso_sort_key_Hfixed[i] > Ct2->iso_sort_key_Hfixed[i] ? 1 : -1; 2806| | goto done; 2807| | } 2808| | } 2809| |#endif 2810| | 2811| | 2812| 471k|done: 2813| | 2814| 471k|#ifdef INCHI_CANON_MIN 2815| 471k| diff = -diff; 2816| 471k|#endif 2817| | 2818| 471k| if (diff) ------------------ | Branch (2818:9): [True: 0, False: 471k] ------------------ 2819| 0| { 2820| 0| diff = ( diff > 0 ) ? ( nLayer + 1 ) : -( nLayer + 1 ); /* return the discovered difference layer number >= 1 */ ------------------ | Branch (2820:16): [True: 0, False: 0] ------------------ 2821| 0| } 2822| | 2823| 471k| return diff; 2824| 471k|} CtFullCompareLayers: 2829| 460|{ 2830| 460| int iLayer; 2831| | /* check for the rejection condition: Lambda > zb_rho_fix */ 2832| 46.4k| for (iLayer = 0; iLayer < MAX_LAYERS; iLayer++) ------------------ | | 27| 46.4k|#define MAX_LAYERS 100 ------------------ | Branch (2832:22): [True: 46.0k, False: 460] ------------------ 2833| 46.0k| { 2834| 46.0k| if (kLeastForLayer[iLayer].k) ------------------ | Branch (2834:13): [True: 0, False: 46.0k] ------------------ 2835| 0| { 2836| 0| return ( kLeastForLayer[iLayer].k > 0 ) ? ( iLayer + 1 ) : -( iLayer + 1 ); ------------------ | Branch (2836:20): [True: 0, False: 0] ------------------ 2837| 0| } 2838| 46.0k| } 2839| | 2840| 460| return 0; 2841| 460|} CtCompareLayersGetFirstDiff: 2850| 6.97M|{ 2851| 6.97M| int iLayer; 2852| 6.97M| if (kLeast_rho) ------------------ | Branch (2852:9): [True: 6.97M, False: 0] ------------------ 2853| 6.97M| { 2854| 702M| for (iLayer = 0; iLayer < MAX_LAYERS; iLayer++) ------------------ | | 27| 702M|#define MAX_LAYERS 100 ------------------ | Branch (2854:26): [True: 695M, False: 6.95M] ------------------ 2855| 695M| { 2856| 695M| if (kLeast_rho[iLayer].k) ------------------ | Branch (2856:17): [True: 18.5k, False: 695M] ------------------ 2857| 18.5k| { 2858| 18.5k| *L_rho = iLayer; 2859| 18.5k| *I_rho = kLeast_rho[iLayer].i; 2860| 18.5k| *k_rho = kLeast_rho[iLayer].k; 2861| 18.5k| break; 2862| 18.5k| } 2863| 695M| } 2864| 6.97M| if (iLayer == MAX_LAYERS) ------------------ | | 27| 6.97M|#define MAX_LAYERS 100 ------------------ | Branch (2864:13): [True: 6.95M, False: 18.5k] ------------------ 2865| 6.95M| { 2866| 6.95M| if (nOneAdditionalLayer) ------------------ | Branch (2866:17): [True: 934k, False: 6.02M] ------------------ 2867| 934k| { 2868| 934k| *L_rho = nOneAdditionalLayer; /* ??? subtract 1 ??? */ 2869| 934k| *I_rho = -1; 2870| 934k| *k_rho = 0; 2871| 934k| return 0; /* difference may be in the first additional layer */ 2872| 934k| } 2873| 6.02M| else 2874| 6.02M| { 2875| 6.02M| *L_rho = INCHI_CANON_INFINITY; ------------------ | | 31| 6.02M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 2876| 6.02M| *I_rho = -1; 2877| 6.02M| *k_rho = 0; 2878| 6.02M| return 0; /* no difference found */ 2879| 6.02M| } 2880| 6.95M| } 2881| 18.5k| else 2882| 18.5k| { 2883| 18.5k| return 1; /* difference in a real layer */ 2884| 18.5k| } 2885| 6.97M| } 2886| 0| else 2887| 0| { 2888| 0| return -1; /* no input, should not happen */ 2889| 0| } 2890| 6.97M|} CtPartCompareLayers: 2897| 6.97M|{ 2898| 6.97M| int L_rho, I_rho, k_rho; 2899| 6.97M| if (0 < CtCompareLayersGetFirstDiff( kLeast_rho, nOneAdditionalLayer, &L_rho, &I_rho, &k_rho ) && ------------------ | Branch (2899:9): [True: 18.5k, False: 6.95M] ------------------ 2900| | /* differences has been found in a real layer or all real layers are identical */ 2901| 18.5k| L_rho <= L_rho_fix_prev) ------------------ | Branch (2901:10): [True: 18.5k, False: 0] ------------------ 2902| 18.5k| { 2903| | /* in this layer pzb_rho == pzb_rho_fix or in the previous real layer */ 2904| 18.5k| return k_rho > 0 ? ( L_rho + 1 ) : -( L_rho + 1 ); ------------------ | Branch (2904:16): [True: 522, False: 17.9k] ------------------ 2905| 18.5k| } 2906| | 2907| 6.95M| return 0; 2908| 6.97M|} UpdateCompareLayers: 2913| 443k|{ 2914| 443k| int i; 2915| 443k| if (kLeastForLayer) ------------------ | Branch (2915:9): [True: 443k, False: 0] ------------------ 2916| 443k| { 2917| 44.8M| for (i = 0; i < MAX_LAYERS; i++) ------------------ | | 27| 44.8M|#define MAX_LAYERS 100 ------------------ | Branch (2917:21): [True: 44.3M, False: 443k] ------------------ 2918| 44.3M| { 2919| 44.3M| if (abs( kLeastForLayer[i].k ) >= hzz) ------------------ | Branch (2919:17): [True: 15.9k, False: 44.3M] ------------------ 2920| 15.9k| { 2921| 15.9k| kLeastForLayer[i].k = 0; 2922| 15.9k| kLeastForLayer[i].i = 0; 2923| 15.9k| } 2924| 44.3M| } 2925| 443k| } 2926| 443k|} CtPartCopy: 2933| 1.32M|{ 2934| 1.32M| int startCt1, startCt2, endCt2; 2935| 1.32M| int len2, len2H, len2Hfixed = 0, len2iso_sort_key, len2iso_exchg_atnos, i; 2936| 1.32M| int startAt1, startAt2, endAt2; /*endCt,*/ 2937| | 2938| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 2939| | int len2iso_sort_key_Hfixed; 2940| |#endif 2941| | 2942| 1.32M| k--; 2943| | 2944| 1.32M| if (k) ------------------ | Branch (2944:9): [True: 923k, False: 406k] ------------------ 2945| 923k| { 2946| 923k| startCt1 = Ct1->nextCtblPos[k - 1]; 2947| 923k| startCt2 = Ct2->nextCtblPos[k - 1]; 2948| 923k| startAt1 = Ct1->nextAtRank[k - 1] - 1; 2949| 923k| startAt2 = Ct2->nextAtRank[k - 1] - 1; 2950| 923k| } 2951| 406k| else 2952| 406k| { 2953| 406k| startCt1 = startCt2 = 0; 2954| 406k| startAt1 = startAt2 = 0; 2955| 406k| } 2956| | 2957| | /* djb-rwth: removing redundant code */ 2958| 1.32M| endCt2 = Ct2->nextCtblPos[k]; 2959| | /* djb-rwth: removing redundant code */ 2960| 1.32M| endAt2 = (int) Ct2->nextAtRank[k] - 1; 2961| | 2962| 1.32M| len2 = endCt2 - startCt2; 2963| | /* len = min(len1, len2); */ 2964| | 2965| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2966| | if (startCt1 != startCt2 || startAt1 != startAt2) 2967| | { 2968| | int stop = 1; 2969| | } 2970| |#endif 2971| | 2972| | /* copy connection table: Ctbl */ 2973| 4.49M| for (i = 0; i < len2; i++) ------------------ | Branch (2973:17): [True: 3.16M, False: 1.32M] ------------------ 2974| 3.16M| { 2975| 3.16M| Ct1->Ctbl[startCt1 + i] = Ct2->Ctbl[startCt2 + i]; 2976| 3.16M| } 2977| | 2978| | /* copy number of H: NumH */ 2979| 1.32M| len2H = 0; 2980| 1.32M| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2980:9): [True: 601k, False: 728k] | Branch (2980:22): [True: 63.3k, False: 538k] ------------------ 2981| 63.3k| { 2982| 63.3k| len2H = endAt2 - startAt2; 2983| 63.3k| if (endAt2 > Ct2->maxVert) ------------------ | Branch (2983:13): [True: 5.68k, False: 57.7k] ------------------ 2984| 5.68k| { 2985| 5.68k| len2H = Ct2->lenNumH - startAt2; 2986| 5.68k| } 2987| 203k| for (i = 0; i < len2H; i++) ------------------ | Branch (2987:21): [True: 140k, False: 63.3k] ------------------ 2988| 140k| { 2989| 140k| Ct1->NumH[startAt1 + i] = Ct2->NumH[startAt2 + i]; 2990| 140k| } 2991| 63.3k| } 2992| | 2993| | /* copy number of fixed H */ 2994| | /* djb-rwth: removing redundant code */ 2995| 1.32M| if (Ct1->NumHfixed && Ct2->NumHfixed) ------------------ | Branch (2995:9): [True: 3.46k, False: 1.32M] | Branch (2995:27): [True: 3.46k, False: 0] ------------------ 2996| 3.46k| { 2997| 3.46k| len2Hfixed = endAt2 - startAt2; 2998| 19.1k| for (i = 0; i < len2Hfixed; i++) ------------------ | Branch (2998:21): [True: 15.6k, False: 3.46k] ------------------ 2999| 15.6k| { 3000| 15.6k| Ct1->NumHfixed[startAt1 + i] = Ct2->NumHfixed[startAt2 + i]; 3001| 15.6k| } 3002| 3.46k| } 3003| | 3004| | /* copy isotopic keys */ 3005| 1.32M| len2iso_sort_key = 0; 3006| 1.32M| if (Ct1->iso_sort_key && Ct2->iso_sort_key) ------------------ | Branch (3006:9): [True: 18.6k, False: 1.31M] | Branch (3006:30): [True: 16.5k, False: 2.08k] ------------------ 3007| 16.5k| { 3008| 16.5k| len2iso_sort_key = endAt2 - startAt2; 3009| 36.9k| for (i = 0; i < len2iso_sort_key; i++) ------------------ | Branch (3009:21): [True: 20.3k, False: 16.5k] ------------------ 3010| 20.3k| { 3011| 20.3k| Ct1->iso_sort_key[startAt1 + i] = Ct2->iso_sort_key[startAt2 + i]; 3012| 20.3k| } 3013| 16.5k| } 3014| | 3015| 1.32M| len2iso_exchg_atnos = 0; 3016| 1.32M| if (Ct1->iso_exchg_atnos && Ct2->iso_exchg_atnos) ------------------ | Branch (3016:9): [True: 8.74k, False: 1.32M] | Branch (3016:33): [True: 8.22k, False: 516] ------------------ 3017| 8.22k| { 3018| 8.22k| len2iso_exchg_atnos = endAt2 - startAt2; 3019| 17.3k| for (i = 0; i < len2iso_exchg_atnos; i++) ------------------ | Branch (3019:21): [True: 9.17k, False: 8.22k] ------------------ 3020| 9.17k| { 3021| 9.17k| Ct1->iso_exchg_atnos[startAt1 + i] = Ct2->iso_exchg_atnos[startAt2 + i]; 3022| 9.17k| } 3023| 8.22k| } 3024| | 3025| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3026| | len2iso_sort_key_Hfixed = 0; 3027| | if (Ct1->iso_sort_key_Hfixed && Ct2->iso_sort_key_Hfixed) 3028| | { 3029| | len2iso_sort_key_Hfixed = endAt2 - startAt2; 3030| | for (i = 0; i < len2iso_sort_key; i++) 3031| | { 3032| | Ct1->iso_sort_key_Hfixed[startAt1 + i] = Ct2->iso_sort_key_Hfixed[startAt2 + i]; 3033| | } 3034| | } 3035| |#endif 3036| | 3037| 1.32M| Ct1->lenCt = startCt1 + len2; 3038| 1.32M| Ct1->nextCtblPos[k] = startCt1 + len2; 3039| 1.32M| Ct1->nextAtRank[k] = Ct2->nextAtRank[k]; 3040| 1.32M| if (len2H) ------------------ | Branch (3040:9): [True: 63.3k, False: 1.26M] ------------------ 3041| 63.3k| { 3042| 63.3k| Ct1->lenNumH = startAt1 + len2H; 3043| 63.3k| } 3044| | 3045| | /* 3046| | if ( len2Hfixed ) 3047| | { 3048| | Ct1->lenNumHfixed = startAt1 + len2Hfixed; 3049| | } 3050| | */ 3051| | 3052| 1.32M| if (len2iso_sort_key) ------------------ | Branch (3052:9): [True: 16.5k, False: 1.31M] ------------------ 3053| 16.5k| { 3054| 16.5k| Ct1->len_iso_sort_key = startAt1 + len2iso_sort_key; 3055| 16.5k| } 3056| 1.32M| if (len2iso_exchg_atnos) ------------------ | Branch (3056:9): [True: 8.22k, False: 1.32M] ------------------ 3057| 8.22k| { 3058| 8.22k| Ct1->len_iso_exchg_atnos = startAt1 + len2iso_exchg_atnos; 3059| 8.22k| } 3060| | 3061| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3062| | if (len2iso_sort_key_Hfixed) 3063| | { 3064| | Ct1->len_iso_sort_key_Hfixed = startAt1 + len2iso_sort_key_Hfixed; 3065| | } 3066| |#endif 3067| | 3068| |#ifdef INCHI_CANON_USE_HASH 3069| | Ct1->hash[k] = Ct2->hash[k]; 3070| |#endif 3071| | 3072| 1.32M| Ct1->lenPos = k + 1; 3073| 1.32M| INCHI_HEAPCHK 3074| 1.32M|} CtFullCopy: 3079| 253k|{ 3080| | /* Ct1 does not have INCHI_CANON_INFINITY termination */ 3081| 253k| int k; 3082| 804k| for (k = 0; k < Ct2->lenPos; k++) ------------------ | Branch (3082:17): [True: 551k, False: 253k] ------------------ 3083| 551k| { 3084| 551k| CtPartCopy( Ct1 /* to */, Ct2 /* from */, k + 1 ); 3085| 551k| } 3086| 253k|} TranspositionGetMcrAndFixSetAndUnorderedPartition: 3097| 386k|{ 3098| 386k| int i, j, k, mcr; 3099| 386k| AT_RANK next; 3100| 386k| bitWord *McrBits = McrSet->bitword[l - 1]; 3101| 386k| bitWord *FixBits = FixSet->bitword[l - 1]; 3102| 386k| int len = McrSet->len_set * sizeof( bitWord ); 3103| | 3104| 386k| memset( McrBits, 0, len ); /* djb-rwth: memset_s C11/Annex K variant? */ 3105| 386k| memset( FixBits, 0, len ); /* djb-rwth: memset_s C11/Annex K variant? */ 3106| 13.6M| for (i = 0; i < n; i++) ------------------ | Branch (3106:17): [True: 13.2M, False: 386k] ------------------ 3107| 13.2M| { 3108| 13.2M| p->equ2[i] = INCHI_CANON_INFINITY; /* for debug only */ ------------------ | | 31| 13.2M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 3109| 13.2M| } 3110| | 3111| 13.6M| for (i = 0; i < n; i++) ------------------ | Branch (3111:17): [True: 13.2M, False: 386k] ------------------ 3112| 13.2M| { 3113| 13.2M| j = (int) ( next = gamma->nAtNumb[i] ); 3114| | 3115| 13.2M| if (j == i) ------------------ | Branch (3115:13): [True: 12.4M, False: 783k] ------------------ 3116| 12.4M| { 3117| 12.4M| FixBits[i / pCG->m_num_bit] |= pCG->m_bBit[i % pCG->m_num_bit]; 3118| 12.4M| McrBits[i / pCG->m_num_bit] |= pCG->m_bBit[i % pCG->m_num_bit]; 3119| | /* p->next[i] = INCHI_CANON_INFINITY; */ /* no link to same orbit points */ 3120| 12.4M| p->equ2[i] = next; /* fixed point */ 3121| 12.4M| } 3122| 783k| else if (!( rank_mark_bit & next )) ------------------ | Branch (3122:18): [True: 391k, False: 391k] ------------------ 3123| 391k| { 3124| 391k| gamma->nAtNumb[i] |= rank_mark_bit; 3125| 391k| mcr = inchi_min( j, i ); ------------------ | | 139| 391k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 391k] | | ------------------ ------------------ 3126| | /* djb-rwth: removing redundant code */ 3127| | /* mark all nodes in the cycle to ignore later; find mcr */ 3128| 783k| while (!( rank_mark_bit & ( next = gamma->nAtNumb[j] ) )) ------------------ | Branch (3128:20): [True: 391k, False: 391k] ------------------ 3129| 391k| { 3130| 391k| gamma->nAtNumb[j] |= rank_mark_bit; 3131| 391k| j = (int) next; 3132| 391k| if (mcr > j) ------------------ | Branch (3132:21): [True: 0, False: 391k] ------------------ 3133| 0| { 3134| 0| mcr = j; 3135| 0| } 3136| | /* djb-rwth: removing redundant code */ 3137| 391k| } 3138| 391k| McrBits[mcr / pCG->m_num_bit] |= pCG->m_bBit[mcr % pCG->m_num_bit]; /* save mcr */ 3139| | /* fill out the unordered partition, the mcr first, other in the cycle after that */ 3140| 391k| p->equ2[mcr] = mcr; 3141| 783k| for (k = mcr; mcr != ( j = (int) ( rank_mask_bit & gamma->nAtNumb[k] ) ); k = j) ------------------ | Branch (3141:27): [True: 391k, False: 391k] ------------------ 3142| 391k| { 3143| 391k| p->equ2[j] = mcr; 3144| 391k| } 3145| 391k| } 3146| 13.2M| } 3147| | 3148| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 3149| | /* for debug only */ 3150| | for (i = 0; i < n; i++) 3151| | { 3152| | if (p->equ2[i] >= n) 3153| | { 3154| | int stop = 1; 3155| | } 3156| | } 3157| |#endif 3158| | 3159| | /* remove the marks */ 3160| 13.6M| for (i = 0; i < n; i++) ------------------ | Branch (3160:17): [True: 13.2M, False: 386k] ------------------ 3161| 13.2M| { 3162| 13.2M| gamma->nAtNumb[i] &= rank_mask_bit; 3163| 13.2M| } 3164| | 3165| 386k| INCHI_HEAPCHK 3166| 386k|} SetBitCreate: 3171| 331k|{ 3172| 331k| bitWord b1 = 1, b2; 3173| 331k| AT_NUMB n1, n2; 3174| |#ifdef INCHI_CANON_USE_HASH 3175| | CtHash h1, h2; 3176| |#endif 3177| 331k| int i; 3178| | 3179| 331k| if (pCG->m_bBitInitialized) ------------------ | Branch (3179:9): [True: 326k, False: 4.87k] ------------------ 3180| 326k| { 3181| 326k| INCHI_HEAPCHK 3182| 326k| return 0; /* already created */ 3183| 326k| } 3184| | 3185| | /* djb-rwth: removing redundant code */ 3186| 4.87k| pCG->m_num_bit = 1; 3187| 77.9k| for (b1 = 1, pCG->m_num_bit = 1; b1 < ( b2 = (bitWord) ( ( b1 << 1 )& BIT_WORD_MASK ) ); b1 = b2, pCG->m_num_bit++) ------------------ | | 343| 77.9k|#define BIT_WORD_MASK ((bitWord)~0) ------------------ | Branch (3187:38): [True: 73.1k, False: 4.87k] ------------------ 3188| 73.1k| { 3189| 73.1k| ; 3190| 73.1k| } 3191| 4.87k| pCG->m_bBit = (bitWord*) inchi_calloc( pCG->m_num_bit, sizeof( bitWord ) ); ------------------ | | 1146| 4.87k|#define inchi_calloc calloc ------------------ 3192| 4.87k| if (!pCG->m_bBit) ------------------ | Branch (3192:9): [True: 0, False: 4.87k] ------------------ 3193| 0| { 3194| 0| INCHI_HEAPCHK 3195| 0| return -1; /* failed */ 3196| 0| } 3197| 82.8k| for (i = 0, b1 = 1; i < pCG->m_num_bit; i++, b1 <<= 1) ------------------ | Branch (3197:25): [True: 77.9k, False: 4.87k] ------------------ 3198| 77.9k| { 3199| 77.9k| pCG->m_bBit[i] = b1; 3200| 77.9k| } 3201| | 3202| 77.9k| for (n1 = 1; n1 < ( n2 = (AT_RANK) ( ( n1 << 1 )& AT_RANK_MASK ) ); n1 = n2) ------------------ | | 12| 77.9k|#define AT_RANK_MASK ((AT_RANK)~0) ------------------ | Branch (3202:18): [True: 73.1k, False: 4.87k] ------------------ 3203| 73.1k| { 3204| 73.1k| ; 3205| 73.1k| } 3206| 4.87k| rank_mark_bit = n1; 3207| 4.87k| rank_mask_bit = ~n1; 3208| | 3209| |#ifdef INCHI_CANON_USE_HASH 3210| | for (h1 = 1; h1 < ( h2 = ( h1 << 1 ) ); h1 = h2) 3211| | { 3212| | ; 3213| | } 3214| | hash_mark_bit = h1; 3215| |#endif 3216| 4.87k| pCG->m_bBitInitialized = 1; 3217| 4.87k| INCHI_HEAPCHK 3218| | 3219| 4.87k| return 1; 3220| 4.87k|} SetBitFree: 3225| 12.7k|{ 3226| 12.7k| if (pCG->m_bBit) ------------------ | Branch (3226:9): [True: 4.87k, False: 7.86k] ------------------ 3227| 4.87k| { 3228| 4.87k| inchi_free( pCG->m_bBit ); ------------------ | | 1152| 4.87k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 4.87k, False: 0] | | | Branch (1152:50): [Folded, False: 4.87k] | | ------------------ ------------------ 3229| 4.87k| pCG->m_bBit = NULL; 3230| 4.87k| INCHI_HEAPCHK 3231| 4.87k| return 1; /* success */ 3232| 4.87k| } 3233| | 3234| | INCHI_HEAPCHK 3235| | 3236| 7.86k| return 0; /* already destroyed */ 3237| 12.7k|} GetOneAdditionalLayer: 3532| 330k|{ 3533| 330k| int nLastLayer = -1, nNumLast = 0, nLayer = 0; 3534| | 3535| 330k| if (!pCD || !pzb_rho_fix) ------------------ | Branch (3535:9): [True: 0, False: 330k] | Branch (3535:17): [True: 252k, False: 78.5k] ------------------ 3536| 252k| { 3537| 252k| return 0; 3538| 252k| } 3539| | 3540| 78.5k| nLayer++; /* 1 */ 3541| 78.5k| if (pCD->NumH && !pzb_rho_fix->NumH) ------------------ | Branch (3541:9): [True: 78.5k, False: 0] | Branch (3541:22): [True: 868, False: 77.7k] ------------------ 3542| 868| { 3543| 868| nLastLayer = nLayer; 3544| 868| nNumLast++; 3545| 868| } 3546| | 3547| 78.5k| nLayer++; /* 2 */ 3548| 78.5k| if (pCD->nLenCTAtOnly < pCD->nLenLinearCT && pzb_rho_fix->nLenCTAtOnly == pzb_rho_fix->lenCt) ------------------ | Branch (3548:9): [True: 3.50k, False: 75.0k] | Branch (3548:50): [True: 3.46k, False: 36] ------------------ 3549| 3.46k| { 3550| 3.46k| nLastLayer = nLayer; 3551| 3.46k| nNumLast++; 3552| 3.46k| } 3553| | 3554| 78.5k| nLayer++; /* 3 */ 3555| 78.5k| if (pCD->NumHfixed && !pzb_rho_fix->NumHfixed) ------------------ | Branch (3555:9): [True: 36.4k, False: 42.1k] | Branch (3555:27): [True: 36.3k, False: 37] ------------------ 3556| 36.3k| { 3557| 36.3k| nLastLayer = nLayer; 3558| 36.3k| nNumLast++; 3559| 36.3k| } 3560| | 3561| 78.5k| nLayer++; /* 4 */ 3562| 78.5k| if (pCD->iso_sort_key && !pzb_rho_fix->iso_sort_key) ------------------ | Branch (3562:9): [True: 458, False: 78.1k] | Branch (3562:30): [True: 458, False: 0] ------------------ 3563| 458| { 3564| 458| nLastLayer = nLayer; 3565| 458| nNumLast++; 3566| 458| } 3567| | 3568| | /* 3569| | nLayer ++; // 5 3570| | if ( pCD->nLenCTAtOnly < pCD->nLenLinearCT && pCD->iso_sort_key && 3571| | (pzb_rho_fix->nLenCTAtOnly == pzb_rho_fix->lenCt || !pzb_rho_fix->iso_sort_key ) ) 3572| | { 3573| | nLastLayer = nLayer; 3574| | nNumLast ++; 3575| | } 3576| | */ 3577| | 3578| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3579| | 3580| | nLayer++; /* 6 */ 3581| | if (pCD->iso_sort_key_Hfixed && !pzb_rho_fix->iso_sort_key_Hfixed) 3582| | { 3583| | nLastLayer = nLayer; 3584| | nNumLast++; 3585| | } 3586| |#endif 3587| 78.5k| if (1 == nNumLast) ------------------ | Branch (3587:9): [True: 41.1k, False: 37.4k] ------------------ 3588| 41.1k| { 3589| 41.1k| return nLastLayer; 3590| 41.1k| } 3591| | 3592| 37.4k| return 0; 3593| 78.5k|} CanonGraph: 3643| 330k|{ 3644| | 3645| | /* bDigraph != 0 3646| | means consider edges from atoms to t-groups 3647| | as directed, that is, do not include 3648| | t-group ranks in comparing neighbors 3649| | when refining partition 3650| | */ 3651| | 3652| | /* Always set 3653| | lab = true 3654| | dig = true 3655| | */ 3656| | 3657| | /* in the comments: 3658| | m = |zeta| 3659| | r = |rho| 3660| | 3661| | m < n or r < n in case pi[k] in P (i.e. satisfies Lemma 2.25) 3662| | 3663| | Just after passing point B: 3664| | =========================== 3665| | K = k-1 3666| | wi = v[i], i = 1..K 3667| | Gamma(0) = Gamma = Aut(G)pi 3668| | Gamma(i) = Gamma(w1,w2,...,wi) pointwise stabilizer for i=1..K 3669| | zeta is a terminal node => 3670| | the coarsest equitable partition that fixes w1,...,wK is discrete => 3671| | Gamma(K)=1 3672| | At point A only: 3673| | index = |Gamma(k-1)|/|Gamma(k)| 3674| | At points A and B: 3675| | size = |Gamma(k-1)| 3676| | theta = theta(Gamma(k-1)); 3677| | Gamma(k-1) = , where Y is the set of all automprhisms output up 3678| | to the present stage (in Step 10 = L10 ) 3679| | |Y| <= n - |theta| 3680| | */ 3681| | 3682| 330k| AT_RANK *pCt = pCD->LinearCT; 3683| | /*int nMaxLenCt = pCD->nMaxLenLinearCT;*/ 3684| 330k| int *nLenCt = &pCD->nLenLinearCT; 3685| 330k| CANON_DATA *pCD1 = pCD; 3686| | 3687| 330k| int i, k, k2, index, l, ok, ret = 0, res; 3688| 330k| int t_Lemma; /* hh: if pi[k-1] satisfies Lemma 2-25 then 3689| | t_Lemma = min{i| i=1..k && pi[i-1] satisfies Lemma 2-25}*/ 3690| | /* otherwise t_Lemma = k --> here this is always the case */ 3691| 330k| int t_eq_zeta; /* ht: min{i|i=1..m && all terminal modes descended from or equal 3692| | to zeta(i) have been shown to be equivalent}. */ 3693| 330k| int h_zeta; /* h: the longest common ancestor of zeta and nu is nu(h_zeta) */ 3694| 330k| int h_rho; /* hb: the longest common ancestor of rho and nu is nu(h_rho) */ 3695| 330k| int hz_rho; /* hzb: max{i|i=1..min(k,r) && Lambda(G,pi,nu(i)) == Lambda(G,pi,rho(i))} */ 3696| 330k| int hz_zeta; /* hzf: max{i|i=1..min(k,m) && Lambda(G,pi,nu(i)) == Lambda(G,pi,zeta(i))} */ 3697| 330k| int qzb_rho; /* Ct(Lambda[k]) - Ct(rho[k]) */ 3698| 330k| double size; /* |Aut(G)| */ 3699| | 3700| | 3701| 330k| int nNumLayers = ( NULL != pCD->NumH ) + ( NULL != pCD->NumHfixed ) + 3702| | /* (bDigraph && pCD->nLenLinearCT > pCD->nLenCTAtOnly)*/ /* ??? tautomeric */ 3703| 330k| ( NULL != pCD->iso_sort_key ) 3704| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3705| | + ( NULL != pCD->iso_sort_key_Hfixed ) 3706| |#endif 3707| 330k| ; 3708| | 3709| | 3710| 330k| int dig = ( bDigraph || nNumLayers ); ------------------ | Branch (3710:18): [True: 42.2k, False: 288k] | Branch (3710:30): [True: 36.3k, False: 252k] ------------------ 3711| 330k| int bSplitTautCompare = ( bDigraph || nNumLayers ); /* compare taut. H and tgroups connections after H */ ------------------ | Branch (3711:32): [True: 42.2k, False: 288k] | Branch (3711:44): [True: 36.3k, False: 252k] ------------------ 3712| | /* digraph: 1=>do not use Lemma 2.25, 0 => use */ 3713| 330k| int lab = 1; /* label: 1=>find canonical numbering; 3714| | 0=>do not find canonical numbering, do not use rho */ 3715| 330k| int r; /* |rho| */ 3716| 330k| int bZetaEqRho = lab; 3717| 330k| int bZetaIsomorph; 3718| | 3719| | /*const int L = MAX_SET_SIZE;*/ 3720| 330k| int L_curr_max_set_size = MAX_SET_SIZE; ------------------ | | 25| 330k|#define MAX_SET_SIZE 32766 /*16384*/ ------------------ 3721| | 3722| 330k| UnorderedPartition theta, theta_from_gamma; 3723| | 3724| 330k| Cell *W; /* W[i] is the first non-trivial cell of pi[i+1] */ 3725| 330k| Node *v; /* v[i] is in W[i] to create T(G,pi,nu[i+1]) */ 3726| 330k| Node tvc, tvh; 3727| 330k| S_CHAR *e, *qzb = NULL; /* qzb = NULL always */ 3728| | 3729| | /* current node CT */ 3730| 330k| ConTable Lambda; 3731| | /* first leaf CT */ 3732| 330k| ConTable zf_zeta; /* Ct for zeta, the first discovered terminal node */ 3733| | /* best leaf/node CT: find the greatest pzb_rho possibly subject to pzb_rho[k] <= pzb_rho_fix[k] condition */ 3734| 330k| ConTable *pzb_rho = NULL; /* Ct for rho, the best discovered terminal node */ 3735| | /* fixed input CT: for all k pzb_rho[k] <= pzb_rho_fix[k]; at the end pzb_rho == pzb_rho_fix */ 3736| 330k| ConTable *pzb_rho_fix = ( pp_zb_rho_inp && *pp_zb_rho_inp ) ? *pp_zb_rho_inp : NULL; ------------------ | Branch (3736:31): [True: 78.5k, False: 252k] | Branch (3736:48): [True: 78.5k, False: 0] ------------------ 3737| | 3738| 330k| NodeSet Omega; /* MAX_SET_SIZE */ 3739| 330k| NodeSet Phi; /* MAX_SET_SIZE */ 3740| 330k| NodeSet cur_nodes; /* 1 each */ 3741| | 3742| 330k| Transposition gamma; 3743| | 3744| 330k| Partition zeta; /* the first discovered terminal node */ 3745| 330k| Partition rho; /* the best discovered terminal node */ 3746| | 3747| 330k| int nNumFoundGenerators = 0; 3748| 330k| int qzb_rho_fix = 0; 3749| 330k| int hzb_rho_fix = 0; 3750| 330k| int bRhoIsDiscrete = 1; 3751| 330k| kLeast kLeast_rho[MAX_LAYERS]; 3752| 330k| kLeast kLeast_rho_fix[MAX_LAYERS]; 3753| 330k| int nOneAdditionalLayer; 3754| 330k| int pzb_rho_fix_reached = 0; 3755| 330k| int L_rho_fix_prev = 0, I_rho_fix_prev = -1, k_rho_fix_prev = 0; 3756| | 3757| 330k| if (!LargeMolecules) ------------------ | Branch (3757:9): [True: 330k, False: 0] ------------------ 3758| 330k| { 3759| 330k| L_curr_max_set_size = NORMALLY_ALLOWED_MAX_SET_SIZE; ------------------ | | 26| 330k|#define NORMALLY_ALLOWED_MAX_SET_SIZE 2048 ------------------ 3760| 330k| } 3761| | 3762| | 3763| | /* Note: Layered comparison should be consistent, especially in layer numbers. 3764| | Layered comparison is implemented in: 3765| | CtFullCompare() 3766| | CtPartCompare() 3767| | GetOneAdditionalLayer() 3768| | 3769| | The partial comparison results in kLeast[] are used in 3770| | CtFullCompareLayers() 3771| | CtPartCompareLayers() 3772| | CtCompareLayersGetFirstDiff() 3773| | UpdateCompareLayers() 3774| | */ 3775| | 3776| | 3777| 330k| nOneAdditionalLayer = GetOneAdditionalLayer( pCD1, pzb_rho_fix ); 3778| | 3779| | 3780| | /* next 2 lines for debug only */ 3781| | /* num_g++; */ 3782| | /* WriteGraph( G, n_tg, num_g, "V:\\IChI_v10\\Gordon-Graphs\\hard\\k06g08v312-alt.dre", "a+" ); */ 3783| | 3784| | /* memory allocation */ 3785| | 3786| 330k| if (0 > SetBitCreate( pCG )) ------------------ | Branch (3786:9): [True: 0, False: 330k] ------------------ 3787| 0| { 3788| 0| return -1; 3789| 0| } 3790| 330k| if (pzb_rho_fix && pzb_rho_fix->nLenCTAtOnly != pCD->nLenCTAtOnly) ------------------ | Branch (3790:9): [True: 78.5k, False: 252k] | Branch (3790:24): [True: 0, False: 78.5k] ------------------ 3791| 0| { 3792| | /* consistency check */ 3793| 0| return -2; 3794| 0| } 3795| 330k| ok = 1; 3796| | 3797| 330k| ok &= UnorderedPartitionCreate( &theta, n_tg ); 3798| 330k| ok &= UnorderedPartitionCreate( &theta_from_gamma, n_tg ); 3799| | 3800| | /* djb-rwth: fixing dereferencing NULL pointer and buffer overflows */ 3801| 330k| W = (Cell*) inchi_calloc( n_tg, sizeof( W[0] ) ); ------------------ | | 1146| 330k|#define inchi_calloc calloc ------------------ 3802| 330k| v = (Node*) inchi_calloc( n_tg, sizeof( v[0] ) ); ------------------ | | 1146| 330k|#define inchi_calloc calloc ------------------ 3803| 330k| e = (S_CHAR*) inchi_calloc( n_tg, sizeof( e[0] ) ); ------------------ | | 1146| 330k|#define inchi_calloc calloc ------------------ 3804| | 3805| 330k| if (!W || !v || !e) ------------------ | Branch (3805:9): [True: 0, False: 330k] | Branch (3805:15): [True: 0, False: 330k] | Branch (3805:21): [True: 0, False: 330k] ------------------ 3806| 0| { 3807| 0| ok &= 0; 3808| 0| } 3809| | 3810| |/* 3811| | ok &= ( NULL != ( W = (Cell*) inchi_calloc( n_tg, sizeof( W[0] ) ) ) ); 3812| | ok &= ( NULL != ( v = (Node*) inchi_calloc( n_tg, sizeof( v[0] ) ) ) ); 3813| | ok &= ( NULL != ( e = (S_CHAR*) inchi_calloc( n_tg, sizeof( e[0] ) ) ) ); 3814| |*/ 3815| | /* 3816| | ok &= (NULL != (v = (Node*)inchi_calloc( n_tg, sizeof(W[0])))); 3817| | ok &= (NULL != (e = (S_CHAR*)inchi_calloc( n_tg, sizeof(W[0])))); 3818| | */ 3819| | 3820| | /* ok &= (NULL != (qzb = (S_CHAR*)inchi_calloc( n_tg, sizeof(W[0])))); */ 3821| 330k| ok &= CTableCreate( &Lambda, n, pCD ); 3822| 330k| ok &= CTableCreate( &zf_zeta, n, pCD ); 3823| 330k| ok &= ( ( pzb_rho = (ConTable *) inchi_calloc( 1, sizeof( *pzb_rho ) ) ) && ------------------ | | 1146| 330k|#define inchi_calloc calloc ------------------ | Branch (3823:13): [True: 330k, False: 0] ------------------ 3824| 330k| CTableCreate( pzb_rho, n, pCD ) ); ------------------ | Branch (3824:13): [True: 330k, False: 0] ------------------ 3825| | 3826| 330k| ok &= NodeSetCreate( pCG, &Omega, n_tg, L_curr_max_set_size ); 3827| 330k| ok &= NodeSetCreate( pCG, &Phi, n_tg, L_curr_max_set_size ); 3828| 330k| ok &= NodeSetCreate( pCG, &cur_nodes, n_tg, 1 ); 3829| | 3830| 330k| ok &= PartitionCreate( &zeta, n_tg ); 3831| 330k| ok &= PartitionCreate( &rho, n_tg ); 3832| 330k| ok &= TranspositionCreate( &gamma, n_tg ); 3833| | 3834| | INCHI_HEAPCHK 3835| | 3836| |/*L1:*/ 3837| 330k| k = 1; 3838| 330k| size = 1.0; 3839| 330k| hz_rho = index = l = 0; /* djb-rwth: removing redundant code */ 3840| | 3841| 330k| if (!ok) ------------------ | Branch (3841:9): [True: 0, False: 330k] ------------------ 3842| 0| { 3843| 0| goto exit_function; /* initialization failed */ 3844| 0| } 3845| | 3846| 330k| UnorderedPartitionMakeDiscrete( &theta, n_tg ); 3847| 330k| t_Lemma = 2; 3848| | 3849| 330k| pCC->lNumBreakTies = 0; 3850| 330k| pCC->lNumDecreasedCT = 0; 3851| 330k| pCC->lNumRejectedCT = 0; 3852| 330k| pCC->lNumEqualCT = 1; 3853| 330k| pCC->lNumTotCT = 0; 3854| | /* djb-rwth: removing redundant code */ 3855| | 3856| 330k| hzb_rho_fix = 1; 3857| | 3858| 330k| memset( kLeast_rho, 0, sizeof( kLeast_rho ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3859| 330k| memset( kLeast_rho_fix, 0, sizeof( kLeast_rho_fix ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3860| | 3861| 330k| if (PartitionIsDiscrete( &pi[k - 1], n_tg )) ------------------ | Branch (3861:9): [True: 254k, False: 76.5k] ------------------ 3862| 254k| { 3863| | /* added the following 3 lines to the original to create Ct */ 3864| 254k| PartitionCopy( &rho, &pi[k - 1], n_tg ); 3865| 254k| CtPartFill( G, pCD, &pi[k - 1], pzb_rho, 1, n, n_tg, n_max ); 3866| 254k| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, 2 ); 3867| 254k| pCC->lNumTotCT++; 3868| | /* djb-rwth: removing redundant code */ 3869| | /* goto L18; */ 3870| 254k| goto exit_function; 3871| 254k| } 3872| | 3873| 76.5k| if (!dig && PartitionSatisfiesLemma_2_25( &pi[0], n )) ------------------ | Branch (3873:9): [True: 70.6k, False: 5.96k] | Branch (3873:17): [True: 36.7k, False: 33.8k] ------------------ 3874| 36.7k| { 3875| 36.7k| t_Lemma = 1; 3876| 36.7k| } 3877| | 3878| | /* 3879| | PartitionGetFirstCell( &pi[k-1], &W[k-1], k, n ); 3880| | v[k-1] = CellGetMinNode( &pi[k-1], &W[k-1], 0, pCD1 ); 3881| | CtPartClear( &Lambda, 1 ); 3882| | e[k-1] = 0; 3883| | */ 3884| 76.5k| CtPartClear( &Lambda, 1 ); 3885| 76.5k| INCHI_HEAPCHK 3886| | 3887| |/* L2: reach the first leaf and save it in zeta and rho */ 3888| 389k| while (k) ------------------ | Branch (3888:12): [True: 389k, False: 0] ------------------ 3889| 389k| { 3890| | /* the two next lines intentionally switched */ 3891| | /* Create equitable partition in pi[k] */ 3892| 389k| PartitionGetFirstCell( &pi[k - 1], W, k, n ); 3893| 389k| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], 0, pCD1 ); 3894| 389k| e[k - 1] = 0; 3895| 389k| if (dig || !PartitionSatisfiesLemma_2_25( &pi[k - 1], n )) ------------------ | Branch (3895:13): [True: 25.1k, False: 364k] | Branch (3895:20): [True: 146k, False: 217k] ------------------ 3896| 172k| { 3897| 172k| t_Lemma = k + 1; 3898| 172k| } 3899| | /* e[k-1] = 0; */ 3900| 389k| { 3901| 389k| Node vv = v[k - 1]; 3902| 389k| if (0 > ( ret = PartitionColorVertex( pCG, G, &pi[k - 1], vv /*v[k-1]*/, n, n_tg, n_max, bDigraph, 0 ) )) ------------------ | Branch (3902:17): [True: 0, False: 389k] ------------------ 3903| 0| { 3904| 0| goto exit_error; 3905| 0| } 3906| 389k| } 3907| 389k| pCC->lNumBreakTies++; 3908| 389k| k++; 3909| | 3910| 389k| CtPartFill( G, pCD, &pi[k - 1], &Lambda, k - 1, n, n_tg, n_max); 3911| | 3912| | /* return -1; *//* debug only */ 3913| | /* if(h_zeta==0)goto L5; L5: */ 3914| | /* the first terminal node has not been reached yet */ 3915| | /* search for the predefined numbering */ 3916| 389k| if (pzb_rho_fix && QZFIX_OK( qzb_rho_fix )) ------------------ | | 3527| 25.1k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3527:21): [True: 25.1k, False: 0] | | ------------------ ------------------ | Branch (3916:13): [True: 25.1k, False: 364k] ------------------ 3917| 25.1k| { 3918| 25.1k| qzb_rho_fix = CtPartCompare( &Lambda, pzb_rho_fix, qzb, kLeast_rho_fix, k - 1, 1, bSplitTautCompare ); 3919| 25.1k| if (QZFIX_OK( qzb_rho_fix )) ------------------ | | 3527| 25.1k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3527:21): [True: 25.1k, False: 0] | | ------------------ ------------------ 3920| 25.1k| { 3921| 25.1k| hzb_rho_fix = k; 3922| 25.1k| } 3923| 25.1k| } 3924| | 3925| 389k| if (lab && QZFIX_OK( qzb_rho_fix )) /* DCh */ ------------------ | | 3527| 389k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3527:21): [True: 389k, False: 0] | | ------------------ ------------------ | Branch (3925:13): [True: 389k, False: 0] ------------------ 3926| 389k| CtPartCopy( pzb_rho, &Lambda, k - 1 ); 3927| 389k| CtPartCopy( &zf_zeta, &Lambda, k - 1 ); 3928| | /*goto L4; L4:*/ 3929| 389k| if (PartitionIsDiscrete( &pi[k - 1], n )) ------------------ | Branch (3929:13): [True: 76.5k, False: 312k] ------------------ 3930| 76.5k| { 3931| 76.5k| break; /* goto L7; */ 3932| 76.5k| } 3933| | /* goto L2; */ 3934| 389k| } 3935| | 3936| 76.5k| pCC->lNumTotCT++; 3937| | 3938| | /* L7; L7: */ 3939| | /* if ( h_zeta == 0 ) goto L18; L18:*/ 3940| 76.5k| h_zeta = t_eq_zeta = hz_zeta = k; 3941| 76.5k| CtPartINCHI_CANON_INFINITY( &zf_zeta, NULL, k ); 3942| | /******************** <<<===== B **************************/ 3943| 76.5k| PartitionCopy( &zeta, &pi[k - 1], n_tg ); 3944| 76.5k| if (lab) ------------------ | Branch (3944:9): [True: 76.5k, False: 0] ------------------ 3945| 76.5k| { 3946| 76.5k| if (pzb_rho_fix) ------------------ | Branch (3946:13): [True: 5.96k, False: 70.6k] ------------------ 3947| 5.96k| { 3948| 5.96k| if (0 == qzb_rho_fix) ------------------ | Branch (3948:17): [True: 5.96k, False: 0] ------------------ 3949| 5.96k| { 3950| 5.96k| qzb_rho_fix = CtFullCompare( &Lambda, pzb_rho_fix, 1, bSplitTautCompare ); 3951| 5.96k| if (qzb_rho_fix > 0) ------------------ | Branch (3951:21): [True: 0, False: 5.96k] ------------------ 3952| 0| { 3953| 0| hzb_rho_fix = 1; 3954| 0| } 3955| 5.96k| } 3956| 5.96k| if (hzb_rho_fix > 1) ------------------ | Branch (3956:17): [True: 5.96k, False: 0] ------------------ 3957| 5.96k| { 3958| 5.96k| PartitionCopy( &rho, &pi[hzb_rho_fix - 1], n_tg ); 3959| | /*CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k );*/ 3960| 5.96k| } 3961| 5.96k| hz_rho = h_rho = hzb_rho_fix; 3962| 5.96k| bRhoIsDiscrete = ( hzb_rho_fix == k ); 3963| 5.96k| if (bRhoIsDiscrete) ------------------ | Branch (3963:17): [True: 5.96k, False: 0] ------------------ 3964| 5.96k| { 3965| 5.96k| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k ); 3966| 5.96k| pzb_rho_fix_reached = !qzb_rho_fix; 3967| 5.96k| CtCompareLayersGetFirstDiff( kLeast_rho_fix, nOneAdditionalLayer, 3968| 5.96k| &L_rho_fix_prev, &I_rho_fix_prev, &k_rho_fix_prev ); 3969| 5.96k| } 3970| | 3971| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 3972| | else 3973| | { 3974| | int stop = 1; 3975| | } 3976| |#endif 3977| 5.96k| } 3978| 70.6k| else 3979| 70.6k| { 3980| 70.6k| PartitionCopy( &rho, &pi[k - 1], n_tg ); 3981| 70.6k| hz_rho = h_rho = k; 3982| 70.6k| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k ); 3983| 70.6k| } 3984| 76.5k| qzb_rho = 0; 3985| 76.5k| } 3986| | 3987| 76.5k| r = k; 3988| 76.5k| v[k - 1] = INCHI_CANON_INFINITY; /* DCh */ ------------------ | | 31| 76.5k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 3989| 76.5k| CellMakeEmpty( W, k ); /* DCh */ 3990| 76.5k| k--; 3991| 76.5k| goto L13; 3992| | 3993| | 3994| 5.81M|L2: 3995| | /* the two next lines intentionally switched */ 3996| | /* Create equitable partition in pi[k] */ 3997| 5.81M| if (0 > ( ret = PartitionColorVertex( pCG, G, &pi[k - 1], v[k - 1], ------------------ | Branch (3997:9): [True: 0, False: 5.81M] ------------------ 3998| 5.81M| n, n_tg, n_max, bDigraph, 0 ) )) 3999| 0| { 4000| 0| goto exit_error; 4001| 0| } 4002| 5.81M| pCC->lNumBreakTies++; 4003| 5.81M| k++; 4004| 5.81M| CtPartFill( G, pCD, &pi[k - 1], &Lambda, k - 1, n, n_tg, n_max ); 4005| 5.81M| e[k - 1] = 0; /* moved */ 4006| 5.81M| v[k - 1] = INCHI_CANON_INFINITY; /* added by DCh. */ ------------------ | | 31| 5.81M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 4007| 5.81M| CellMakeEmpty( W, k ); /* DCh */ 4008| | 4009| 5.81M| if (hz_zeta == k - 1 && ------------------ | Branch (4009:9): [True: 5.77M, False: 45.3k] ------------------ 4010| 5.77M| 0 == CtPartCompare( &Lambda, &zf_zeta, NULL, NULL, k - 1, 0, bSplitTautCompare )) ------------------ | Branch (4010:10): [True: 5.76M, False: 11.3k] ------------------ 4011| 5.76M| { 4012| 5.76M| hz_zeta = k; /* max{k|Lambda(G,pi,nu(k))==Lambda(G,pi,zeta) } */ 4013| 5.76M| } /* added */ 4014| | 4015| | 4016| | /* -- old code --- 4017| | if ( pzb_rho_fix && QZFIX_OK(qzb_rho_fix) ) { 4018| | qzb_rho_fix = CtPartCompare( &Lambda, pzb_rho_fix, qzb, kLeast_rho_fix, k-1, 1, bSplitTautCompare ); 4019| | if ( QZFIX_OK(qzb_rho_fix) ) { 4020| | hzb_rho_fix = k; 4021| | } else { 4022| | pCC->lNumRejectedCT ++; 4023| | } 4024| | } 4025| | */ 4026| | 4027| | /* --- new code ---*/ 4028| 5.81M| if (pzb_rho_fix && !qzb_rho_fix) ------------------ | Branch (4028:9): [True: 1.20M, False: 4.61M] | Branch (4028:24): [True: 1.20M, False: 0] ------------------ 4029| 1.20M| { 4030| 1.20M| qzb_rho_fix = CtPartCompare( &Lambda, pzb_rho_fix, qzb, kLeast_rho_fix, k - 1, 1, bSplitTautCompare ); 4031| 1.20M| if (!qzb_rho_fix && bRhoIsDiscrete) ------------------ | Branch (4031:13): [True: 1.20M, False: 0] | Branch (4031:29): [True: 1.20M, False: 0] ------------------ 4032| 1.20M| { 4033| 1.20M| qzb_rho_fix = CtPartCompareLayers( kLeast_rho_fix, L_rho_fix_prev, nOneAdditionalLayer ); 4034| | 4035| 1.20M|#if ( FIX_ChCh_CONSTIT_CANON_BUG == 1 ) 4036| 1.20M| if (qzb_rho_fix) ------------------ | Branch (4036:17): [True: 9.92k, False: 1.19M] ------------------ 4037| 9.92k| { 4038| 9.92k| int L_rho_fix_diff = abs( qzb_rho_fix ) - 1; 4039| 9.92k| if (L_rho_fix_diff < L_rho_fix_prev || ------------------ | Branch (4039:21): [True: 9.92k, False: 0] ------------------ 4040| 0| (L_rho_fix_diff == (L_rho_fix_prev && kLeast_rho_fix[L_rho_fix_diff].i < I_rho_fix_prev))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4040:22): [True: 0, False: 0] | Branch (4040:42): [True: 0, False: 0] | Branch (4040:60): [True: 0, False: 0] ------------------ 4041| 9.92k| { 4042| 9.92k| qzb_rho_fix = L_rho_fix_diff + 1; /* positive difference will be rejected */ 4043| 9.92k| } 4044| 9.92k| } 4045| 1.20M|#endif 4046| | 4047| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4048| | if (qzb_rho_fix) 4049| | { 4050| | int stop = 1; /* debug only */ 4051| | } 4052| |#endif 4053| 1.20M| } 4054| 1.20M| if (!QZFIX_OK( qzb_rho_fix )) ------------------ | | 3527| 1.20M|#define QZFIX_OK(X) ((X)<=0) ------------------ | Branch (4054:13): [True: 9.92k, False: 1.19M] ------------------ 4055| 9.92k| { 4056| 9.92k| pCC->lNumRejectedCT++; 4057| 9.92k| } 4058| 1.20M| } 4059| 5.81M| if (pzb_rho_fix && QZFIX_OK( qzb_rho_fix )) ------------------ | | 3527| 1.20M|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3527:21): [True: 1.19M, False: 9.92k] | | ------------------ ------------------ | Branch (4059:9): [True: 1.20M, False: 4.61M] ------------------ 4060| 1.19M| { 4061| 1.19M| hzb_rho_fix = k; 4062| 1.19M| } 4063| | /* if (!lab) goto L3; */ 4064| 5.81M| if (lab && QZFIX_OK( qzb_rho_fix )) ------------------ | | 3527| 5.81M|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3527:21): [True: 5.80M, False: 9.92k] | | ------------------ ------------------ | Branch (4064:9): [True: 5.81M, False: 0] ------------------ 4065| 5.80M| { 4066| | /* once the difference has been found it is meaningful as long as k increments */ 4067| | /* cur_qzb2 = CtPartCompare( &Lambda, pzb_rho, qzb, k-1 ); */ /* rho compare */ 4068| 5.80M| if (hz_rho == k - 1 && !qzb_rho && bRhoIsDiscrete) ------------------ | Branch (4068:13): [True: 5.76M, False: 40.6k] | Branch (4068:32): [True: 5.76M, False: 0] | Branch (4068:44): [True: 5.76M, False: 0] ------------------ 4069| 5.76M| { 4070| 5.76M| int qzb_rho_temp = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 4071| 5.76M| qzb_rho = CtPartCompare( &Lambda, pzb_rho, qzb, kLeast_rho, k - 1, 0, bSplitTautCompare ); 4072| | /* old code */ 4073| 5.76M| if (!qzb_rho && pzb_rho_fix_reached && ------------------ | Branch (4073:17): [True: 5.76M, False: 10] | Branch (4073:29): [True: 1.15M, False: 4.61M] ------------------ 4074| 1.15M| nOneAdditionalLayer && 0 > kLeast_rho[nOneAdditionalLayer].k) ------------------ | Branch (4074:19): [True: 888k, False: 264k] | Branch (4074:42): [True: 8.07k, False: 880k] ------------------ 4075| 8.07k| { 4076| 8.07k| qzb_rho_temp = -( nOneAdditionalLayer + 1 ); /* djb-rwth: ignoring LLVM warning: variable used */ 4077| | /* qzb_rho = -(nOneAdditionalLayer+1); *//* early rejection */ 4078| 8.07k| } 4079| | /* new code */ 4080| 5.76M| if (!qzb_rho && bRhoIsDiscrete) ------------------ | Branch (4080:17): [True: 5.76M, False: 10] | Branch (4080:29): [True: 5.76M, False: 0] ------------------ 4081| 5.76M| { 4082| 5.76M| qzb_rho = CtPartCompareLayers( kLeast_rho, L_rho_fix_prev, 0 ); 4083| 5.76M|#if ( FIX_ChCh_CONSTIT_CANON_BUG == 1 ) 4084| 5.76M| if (qzb_rho) ------------------ | Branch (4084:21): [True: 8.59k, False: 5.75M] ------------------ 4085| 8.59k| { 4086| 8.59k| int L_rho_diff = abs( qzb_rho ) - 1; 4087| 8.59k| if (L_rho_diff < L_rho_fix_prev || ------------------ | Branch (4087:25): [True: 7, False: 8.58k] ------------------ 4088| 8.58k| (L_rho_diff == (L_rho_fix_prev && kLeast_rho[L_rho_diff].i < I_rho_fix_prev))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4088:26): [True: 0, False: 8.58k] | Branch (4088:42): [True: 8.58k, False: 0] | Branch (4088:60): [True: 0, False: 8.58k] ------------------ 4089| 7| { 4090| 7| qzb_rho = -( L_rho_diff + 1 ); /* negative difference will be rejected */ 4091| 7| } 4092| 8.59k| } 4093| 5.76M|#endif 4094| 5.76M| } 4095| | /* compare old results to new */ 4096| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4097| | if (qzb_rho_temp && qzb_rho_temp != qzb_rho) 4098| | { 4099| | int stop = 1; /* */ 4100| | } 4101| |#endif 4102| 5.76M| if (!qzb_rho) ------------------ | Branch (4102:17): [True: 5.75M, False: 8.60k] ------------------ 4103| 5.75M| { 4104| 5.75M| hz_rho = k; 4105| 5.75M| } 4106| 8.60k| else 4107| 8.60k| { 4108| 8.60k| if (qzb_rho < 0) ------------------ | Branch (4108:21): [True: 8.08k, False: 517] ------------------ 4109| 8.08k| { 4110| 8.08k| pCC->lNumRejectedCT++; 4111| 8.08k| } 4112| 8.60k| } 4113| 5.76M| } 4114| 5.80M| if (qzb_rho > 0 || (!qzb_rho && !bRhoIsDiscrete)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4114:13): [True: 39.4k, False: 5.76M] | Branch (4114:29): [True: 5.75M, False: 9.72k] | Branch (4114:41): [True: 0, False: 5.75M] ------------------ 4115| 39.4k| { 4116| | /* found better rho */ 4117| 39.4k| if (!nNumLayers) ------------------ | Branch (4117:17): [True: 4, False: 39.4k] ------------------ 4118| 4| { 4119| 4| CtPartCopy( pzb_rho, &Lambda, k - 1 ); 4120| 4| } 4121| 39.4k| } 4122| 5.80M| } 4123| | 4124| | 4125| |/*L3:*/ 4126| | /*if ( hz_rho == k || (lab && qzb_rho >= 0 ) )*/ 4127| | /*if ( hz_zeta == k || hz_rho == k || (lab && qzb_rho >= 0 ) ) goto L4; else goto L6;*/ 4128| 5.81M| if (hz_zeta == k || hz_rho == k || ------------------ | Branch (4128:9): [True: 5.76M, False: 56.7k] | Branch (4128:25): [True: 64, False: 56.6k] ------------------ 4129| 56.6k| ( lab && qzb_rho >= 0 && QZFIX_OK( qzb_rho_fix ) )) ------------------ | | 3527| 49.4k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3527:21): [True: 39.4k, False: 9.92k] | | ------------------ ------------------ | Branch (4129:11): [True: 56.6k, False: 0] | Branch (4129:18): [True: 49.4k, False: 7.24k] ------------------ 4130| 5.80M| { 4131| | /*L4: check for possible isomorphism or found a better rho */ 4132| 5.80M| if (PartitionIsDiscrete( &pi[k - 1], n )) ------------------ | Branch (4132:13): [True: 386k, False: 5.41M] ------------------ 4133| 386k| { 4134| 386k| pCC->lNumTotCT++; 4135| 386k| goto L7; 4136| 386k| } 4137| 5.41M| PartitionGetFirstCell( &pi[k - 1], W, k, n ); 4138| 5.41M| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], 0, pCD1 ); 4139| 5.41M| if (!dig && PartitionSatisfiesLemma_2_25( &pi[k - 1], n )) ------------------ | Branch (4139:13): [True: 4.25M, False: 1.16M] | Branch (4139:21): [True: 891k, False: 3.35M] ------------------ 4140| 891k| { 4141| 891k| ; /* found additional isomprphism */ 4142| 891k| } 4143| 4.52M| else 4144| 4.52M| { 4145| 4.52M| t_Lemma = k + 1; 4146| 4.52M| } 4147| 5.41M| e[k - 1] = 0; /* created new cell W[k-1] */ 4148| 5.41M| goto L2; 4149| 5.80M| } 4150| | 4151| | 4152| 17.5k|L6: 4153| | /* a better rho or no good node was found at this level; return to smaller k */ 4154| 17.5k| k2 = k; 4155| 17.5k| k = inchi_min( t_Lemma - 1, inchi_max( t_eq_zeta - 1, hz_rho ) ); ------------------ | | 139| 35.0k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 3.78k, False: 13.7k] | | | Branch (139:32): [True: 9.45k, False: 8.06k] | | | Branch (139:41): [True: 6.02k, False: 7.71k] | | ------------------ ------------------ 4156| 17.5k| if (k2 == t_Lemma) ------------------ | Branch (4156:9): [True: 17.5k, False: 4] ------------------ 4157| 17.5k| { 4158| 17.5k| goto L13; 4159| 17.5k| } 4160| | 4161| | /* store isomorphism found from Lemma 2.25. should be dig=0 !!! */ 4162| 4| if (dig) ------------------ | Branch (4162:9): [True: 0, False: 4] ------------------ 4163| 0| { 4164| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4165| | int stop = 1; 4166| |#endif 4167| 0| goto L13; 4168| 0| } 4169| | 4170| 4| l = inchi_min( l + 1, L_curr_max_set_size ); ------------------ | | 139| 4|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 4, False: 0] | | ------------------ ------------------ 4171| 4| PartitionGetMcrAndFixSet( pCG, &pi[t_Lemma - 1], &Omega, &Phi, n_tg, l ); 4172| 4| goto L12; 4173| | 4174| | 4175| | 4176| 386k|L7: 4177| | /* from L4: pi[k-1] is discrete */ 4178| 386k| if (h_zeta == 0) ------------------ | Branch (4178:9): [True: 0, False: 386k] ------------------ 4179| 0| { 4180| | /*goto L18;*/ /* error. the first T(nu) leaf was found */ 4181| 0| ret = CT_CANON_ERR; ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4182| 0| goto exit_error; 4183| 0| } 4184| 386k| if (k != hz_zeta) ------------------ | Branch (4184:9): [True: 406, False: 386k] ------------------ 4185| 406| { 4186| 406| goto L8; 4187| 406| } 4188| | /* here zeta^gamma == nu */ 4189| | /* if ( G^gamma == G ) goto L10; */ 4190| 386k| if (0 == ( res = CtFullCompare( &Lambda, &zf_zeta, 0, bSplitTautCompare ) )) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4190:9): [True: 386k, False: 0] ------------------ 4191| 386k| { 4192| 386k| PartitionGetTransposition( &zeta, &pi[k - 1], n_tg, &gamma ); 4193| 386k| bZetaIsomorph = 1; /* for testing only */ 4194| | /* djb-rwth: removing redundant code */ 4195| 386k| goto L10; 4196| 386k| } 4197| 0| else 4198| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4199| | { 4200| | int stop = 1; 4201| | } 4202| |#endif 4203| | /* !!! we should never come here !!! */ 4204| 0| if (!nNumLayers) ------------------ | Branch (4204:9): [True: 0, False: 0] ------------------ 4205| 0| { 4206| 0| ret = -2; 4207| 0| goto exit_error; 4208| 0| } 4209| | 4210| | 4211| 406|L8: /* here nu is discrete: check rho for being a bettere leaf or isomorphism */ 4212| | /*if ( !lab || qzb_rho < 0 || !QZFIX_OK(qzb_rho_fix) )*/ 4213| 406| if (!lab || (qzb_rho < 0 && ( !pzb_rho_fix || qzb_rho_fix > 0 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4213:9): [True: 0, False: 406] | Branch (4213:18): [True: 0, False: 406] | Branch (4213:35): [True: 0, False: 0] | Branch (4213:51): [True: 0, False: 0] ------------------ 4214| 0| { 4215| 0| goto L6; 4216| 0| } 4217| 406| if (pzb_rho_fix && kLeast_rho_fix && 0 == qzb_rho_fix) /* djb-rwth: addressing of array kLeast_rho_fix will always evaluate to true? */ ------------------ | Branch (4217:9): [True: 403, False: 3] | Branch (4217:24): [True: 403, False: 0] | Branch (4217:42): [True: 403, False: 0] ------------------ 4218| 403| { 4219| | /* check for the rejection condition: Lambda > zb_rho_fix */ 4220| 403| if (kLeast_rho_fix) /* djb-rwth: addressing of array kLeast_rho_fix will always evaluate to true? */ ------------------ | Branch (4220:13): [True: 403, False: 0] ------------------ 4221| 403| { 4222| 403| int qzb_rho_fix_alt; 4223| 403| qzb_rho_fix = CtFullCompareLayers( kLeast_rho_fix ); 4224| | /* for debug only */ 4225| 403| qzb_rho_fix_alt = CtFullCompare( &Lambda, pzb_rho_fix, 1, bSplitTautCompare ); 4226| 403| if (qzb_rho_fix != qzb_rho_fix_alt) ------------------ | Branch (4226:17): [True: 0, False: 403] ------------------ 4227| 0| { 4228| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4229| | int stop = 1; 4230| |#endif 4231| 0| qzb_rho_fix = qzb_rho_fix_alt; 4232| 0| } 4233| | /* end debug */ 4234| 403| } 4235| 0| else 4236| 0| { 4237| 0| qzb_rho_fix = CtFullCompare( &Lambda, pzb_rho_fix, 1, bSplitTautCompare ); 4238| 0| } 4239| 403| if (!pzb_rho_fix_reached) ------------------ | Branch (4239:13): [True: 0, False: 403] ------------------ 4240| 0| { 4241| 0| pzb_rho_fix_reached = !qzb_rho_fix; 4242| 0| } 4243| 403| if (0 < qzb_rho_fix) ------------------ | Branch (4243:13): [True: 0, False: 403] ------------------ 4244| 0| { 4245| | /* Lambda > pzb_rho_fix, ignore this node */ 4246| | /* hzb_rho_fix = min( hzb_rho_fix, hz_rho ); */ /* ??? */ 4247| 0| qzb_rho_fix = 0; 4248| 0| goto L6; 4249| 0| } 4250| 403| qzb_rho_fix = 0; 4251| 403| } 4252| | 4253| 406| if (qzb_rho < 0) ------------------ | Branch (4253:9): [True: 0, False: 406] ------------------ 4254| 0| { 4255| 0| goto L6; 4256| 0| } 4257| 406| if (qzb_rho > 0 || !bRhoIsDiscrete) ------------------ | Branch (4257:9): [True: 348, False: 58] | Branch (4257:24): [True: 0, False: 58] ------------------ 4258| 348| { 4259| 348| goto L9; /* note: p67 says k > PartitionSize( &rho, n ) */ 4260| 348| } 4261| 58| if (k < r) ------------------ | Branch (4261:9): [True: 1, False: 57] ------------------ 4262| 1| { 4263| 1| goto L9; /* cannot understand it... */ 4264| 1| } 4265| | 4266| | /* !!! we should never come here if G(nu) != G(rho): CtPartCompare must be enough !!! */ 4267| | 4268| | /* if ( G(nu) > G(rho) ) goto L9; */ 4269| 57| if (kLeast_rho) /* djb-rwth: addressing of array kLeast_rho will always evaluate to true? */ ------------------ | Branch (4269:9): [True: 57, False: 0] ------------------ 4270| 57| { 4271| 57| int cur_qzb_alt; 4272| 57| qzb_rho = CtFullCompareLayers( kLeast_rho ); 4273| | /* for debug only */ 4274| 57| cur_qzb_alt = CtFullCompare( &Lambda, pzb_rho, 0, bSplitTautCompare ); 4275| 57| if (qzb_rho != cur_qzb_alt) ------------------ | Branch (4275:13): [True: 0, False: 57] ------------------ 4276| 0| { 4277| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4278| | int stop = 1; 4279| |#endif 4280| 0| qzb_rho = cur_qzb_alt; 4281| 0| } 4282| | /* end debug */ 4283| 57| } 4284| 0| else 4285| 0| { 4286| 0| qzb_rho = CtFullCompare( &Lambda, pzb_rho, 0, bSplitTautCompare ); 4287| 0| } 4288| | /* qzb_rho difference can be due to layers 1..MAX_LAYERS-1 only */ 4289| 57| if (0 < qzb_rho) ------------------ | Branch (4289:9): [True: 0, False: 57] ------------------ 4290| 0| { 4291| | /* CtFullCompare( &Lambda, pzb_rho, 0, bSplitTautCompare ); */ 4292| | /* djb-rwth: removing redundant code */ 4293| 0| goto L9; 4294| 0| } 4295| | /* if ( G(nu) < G(rho) ) goto L6; */ 4296| 57| if (0 > qzb_rho) ------------------ | Branch (4296:9): [True: 0, False: 57] ------------------ 4297| 0| { 4298| 0| qzb_rho = 0; 4299| 0| goto L6; 4300| 0| } 4301| | /* nu^gamma == rho */ 4302| 57| if (r != k) ------------------ | Branch (4302:9): [True: 0, False: 57] ------------------ 4303| 0| { /* if() is for debug only */ 4304| 0| r = k; 4305| 0| } 4306| | 4307| 57| PartitionGetTransposition( &pi[k - 1], &rho, n_tg, &gamma ); 4308| 57| bZetaIsomorph = 0; /* DCh */ 4309| 57| pCC->lNumEqualCT++; 4310| 57| goto L10; 4311| | 4312| 349|L9: 4313| | /* rho := nu; */ 4314| 349| PartitionCopy( &rho, &pi[k - 1], n_tg ); 4315| 349| if (nNumLayers) ------------------ | Branch (4315:9): [True: 346, False: 3] ------------------ 4316| 346| { 4317| 346| CtFullCopy( pzb_rho, &Lambda ); 4318| 346| } 4319| 349| bZetaEqRho = 0; 4320| 349| qzb_rho = 0; 4321| 349| CtCompareLayersGetFirstDiff( kLeast_rho_fix, nOneAdditionalLayer, 4322| 349| &L_rho_fix_prev, &I_rho_fix_prev, 4323| 349| &k_rho_fix_prev ); 4324| 349| memset( kLeast_rho, 0, sizeof( kLeast_rho ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4325| 349| h_rho = hz_rho = k; 4326| 349| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k ); 4327| 349| pCC->lNumDecreasedCT++; 4328| 349| pCC->lNumEqualCT = 1; 4329| 349| bRhoIsDiscrete = 1; 4330| 349| goto L6; 4331| | 4332| 386k|L10: /* discrete pi[k-1] && G^gamma == G */ 4333| 386k| pCC->lNumEqualCT += bZetaEqRho || !( bZetaIsomorph || qzb_rho ); ------------------ | Branch (4333:25): [True: 385k, False: 908] | Branch (4333:42): [True: 851, False: 57] | Branch (4333:59): [True: 0, False: 57] ------------------ 4334| 386k| l = inchi_min( l + 1, L_curr_max_set_size ); ------------------ | | 139| 386k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 386k, False: 0] | | ------------------ ------------------ 4335| | /* Omega[l] := mcr(gamma); 4336| | Phi[l] := fix(gamma); 4337| | */ 4338| | 4339| 386k| TranspositionGetMcrAndFixSetAndUnorderedPartition( pCG, &gamma, &Omega, &Phi, 4340| 386k| n_tg, l, &theta_from_gamma ); 4341| | /* 4342| | if ( theta(gamma) <= theta ) goto L11; 4343| | theta := theta v theta(gamma); 4344| | UnorderedPartitionJoin() returns 0 if theta_from_gamma is finer than theta, 4345| | which means no changes in theta: theta_from_gamma ^ theta == theta. 4346| | */ 4347| 386k| if (!UnorderedPartitionJoin( &theta_from_gamma, &theta, n_tg )) ------------------ | Branch (4347:9): [True: 2, False: 386k] ------------------ 4348| 2| { 4349| 2| goto L11; /* no new isomorphism found */ 4350| 2| } 4351| | 4352| | /* Output gamma (it is the Aut(G) generator) -- omitted -- */ 4353| 386k| nNumFoundGenerators++; 4354| | /* if ( tvc in mcr(theta) ) goto L11; */ 4355| 386k| if (tvc == GetUnorderedPartitionMcrNode( &theta, tvc )) ------------------ | Branch (4355:9): [True: 386k, False: 6] ------------------ 4356| 386k| { 4357| 386k| goto L11; 4358| 386k| } 4359| 6| k = h_zeta; 4360| 6| goto L13; 4361| | 4362| 386k|L11: 4363| 386k| k = lab ? h_rho : h_zeta; /***Changed*** originally was k = h_rho; */ ------------------ | Branch (4363:9): [True: 386k, False: 0] ------------------ 4364| | 4365| 386k|L12: 4366| | /* if ( e[k-1] == 1 ) */ 4367| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4368| | if (e[k - 1] == 1 && v[k - 1] == INCHI_CANON_INFINITY) 4369| | { 4370| | int stop = 1; /* testing only */ 4371| | } 4372| |#endif 4373| 386k| if (e[k - 1] == 1 && v[k - 1] != INCHI_CANON_INFINITY) ------------------ | | 31| 31|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4373:9): [True: 31, False: 386k] | Branch (4373:26): [True: 31, False: 0] ------------------ 4374| 31| { 4375| | /* INCHI_CANON_INFINITY for testing only */ 4376| 31| CellIntersectWithSet( pCG, &pi[k - 1], &W[k - 1], &Omega, l ); 4377| 31| } 4378| | 4379| 991k|L13: 4380| | 4381| 991k| if ((UserAction && USER_ACTION_QUIT == ( *UserAction )( )) || ------------------ | | 124| 0|#define USER_ACTION_QUIT 1 ------------------ | Branch (4381:10): [True: 0, False: 991k] | Branch (4381:24): [True: 0, False: 0] ------------------ 4382| 991k| (ConsoleQuit && ( *ConsoleQuit )( ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4382:11): [True: 0, False: 991k] | Branch (4382:26): [True: 0, False: 0] ------------------ 4383| 0| { 4384| 0| ret = CT_USER_QUIT_ERR; ------------------ | | 32| 0|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4385| 0| goto exit_error; 4386| 0| } 4387| | 4388| 991k| if (bInchiTimeIsOver( ic, pCD->ulTimeOutTime )) ------------------ | Branch (4388:9): [True: 0, False: 991k] ------------------ 4389| 0| { 4390| 0| ret = CT_TIMEOUT_ERR; ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4391| 0| goto exit_error; 4392| 0| } 4393| | 4394| 991k| if (k == 0) ------------------ | Branch (4394:9): [True: 76.5k, False: 914k] ------------------ 4395| 76.5k| { 4396| 76.5k| goto exit_function; /* stop */ 4397| 76.5k| } 4398| | 4399| 914k| if (lab && k < h_rho) ------------------ | Branch (4399:9): [True: 914k, False: 0] | Branch (4399:16): [True: 397k, False: 517k] ------------------ 4400| 397k| { 4401| | /***Added***/ 4402| 397k| h_rho = k; 4403| 397k| } 4404| | 4405| 914k| if (k > h_zeta) ------------------ | Branch (4405:9): [True: 132k, False: 781k] ------------------ 4406| 132k| { 4407| 132k| if (v[k - 1] == INCHI_CANON_INFINITY) ------------------ | | 31| 132k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4407:13): [True: 0, False: 132k] ------------------ 4408| 0| { 4409| | /*** Added by DCh for testing only ****/ 4410| 0| k--; 4411| 0| goto L13; 4412| 0| } 4413| 132k| goto L17; 4414| 132k| } 4415| 781k| if (k == h_zeta) ------------------ | Branch (4415:9): [True: 392k, False: 389k] ------------------ 4416| 392k| { 4417| 392k| goto L14; 4418| 392k| } 4419| 389k| h_zeta = k; 4420| 389k| tvc = tvh = CellGetMinNode( &pi[k - 1], &W[k - 1], 0, pCD1 ); 4421| | 4422| 4.10M|L14: 4423| | /* if v[k] and tvh are in the same cell of theta then index ++ */ 4424| 4.10M| if (GetUnorderedPartitionMcrNode( &theta, v[k - 1] ) == ------------------ | Branch (4424:9): [True: 4.01M, False: 87.1k] ------------------ 4425| 4.10M| GetUnorderedPartitionMcrNode( &theta, tvh )) 4426| 4.01M| { 4427| 4.01M| index++; 4428| 4.01M| } 4429| 4.10M| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], v[k - 1], pCD1 ); 4430| | 4431| 4.10M| if (v[k - 1] == INCHI_CANON_INFINITY) ------------------ | | 31| 4.10M|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4431:9): [True: 389k, False: 3.71M] ------------------ 4432| 389k| { 4433| 389k| goto L16; 4434| 389k| } 4435| 3.71M| if (v[k - 1] != GetUnorderedPartitionMcrNode( &theta, v[k - 1] )) ------------------ | Branch (4435:9): [True: 3.31M, False: 392k] ------------------ 4436| 3.31M| { 4437| 3.31M| goto L14; 4438| 3.31M| } 4439| | 4440| 404k|L15: 4441| 404k| t_Lemma = inchi_min( t_Lemma, k + 1 ); ------------------ | | 139| 404k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 217k, False: 186k] | | ------------------ ------------------ 4442| 404k| hz_zeta = inchi_min( hz_zeta, k ); ------------------ | | 139| 404k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 6.17k, False: 397k] | | ------------------ ------------------ 4443| | /* 4444| | if ( lab && hz_rho >= k ) { 4445| | hz_rho = k; 4446| | qzb_rho = 0; 4447| | } 4448| | */ 4449| 404k| if (lab) ------------------ | Branch (4449:9): [True: 404k, False: 0] ------------------ 4450| 404k| { 4451| 404k| if (hz_rho >= k /*-1*/) ------------------ | Branch (4451:13): [True: 398k, False: 5.84k] ------------------ 4452| 398k| { 4453| 398k| qzb_rho = 0; 4454| 398k| } 4455| 404k| if (hz_rho > k) ------------------ | Branch (4455:13): [True: 396k, False: 7.32k] ------------------ 4456| 396k| { 4457| 396k| hz_rho = k; 4458| 396k| } 4459| 404k| UpdateCompareLayers( kLeast_rho, hz_rho ); 4460| 404k| } 4461| 404k| if (pzb_rho_fix) ------------------ | Branch (4461:9): [True: 39.6k, False: 364k] ------------------ 4462| 39.6k| { 4463| 39.6k| if (hzb_rho_fix >= k /*-1*/) ------------------ | Branch (4463:13): [True: 39.6k, False: 0] ------------------ 4464| 39.6k| { 4465| 39.6k| qzb_rho_fix = 0; 4466| 39.6k| } 4467| 39.6k| if (hzb_rho_fix > k) ------------------ | Branch (4467:13): [True: 36.6k, False: 2.99k] ------------------ 4468| 36.6k| { 4469| 36.6k| hzb_rho_fix = k; 4470| 36.6k| } 4471| 39.6k| UpdateCompareLayers( kLeast_rho_fix, hzb_rho_fix ); 4472| 39.6k| } 4473| | 4474| 404k| goto L2; 4475| | 4476| 389k|L16: 4477| 389k| if (t_eq_zeta == k + 1 && index == CellGetNumberOfNodes( &pi[k - 1], &W[k - 1] )) ------------------ | Branch (4477:9): [True: 380k, False: 9.19k] | Branch (4477:31): [True: 377k, False: 2.51k] ------------------ 4478| 377k| { 4479| 377k| t_eq_zeta = k; 4480| 377k| } 4481| | 4482| 389k| size *= (double) index; 4483| | /******************** <<<===== A **************************/ 4484| | /* passed K times after passing point A. At these passes 4485| | k = K, K-1, ..., 1 in this order 4486| | */ 4487| 389k| index = 0; 4488| 389k| k--; 4489| 389k| goto L13; 4490| | 4491| 132k|L17: 4492| | /* if ( e[k-1] == 0 ) */ 4493| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4494| | if (e[k - 1] == 0 && v[k - 1] == INCHI_CANON_INFINITY) 4495| | { 4496| | /* testing only */ 4497| | int stop = 1; /* */ 4498| | } 4499| |#endif 4500| | /* 4501| | if ( e[k] == 0 set W[k] = Intersection(W[k], Omega[i]) for each i = 1..l, 4502| | such that {v[1]..v[k-1]} in Phi[i] 4503| | */ 4504| 132k| if (e[k - 1] == 0 && v[k - 1] != INCHI_CANON_INFINITY) /* Added v[k-1]!=... DCh */ ------------------ | | 31| 121k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4504:9): [True: 121k, False: 11.5k] | Branch (4504:26): [True: 121k, False: 0] ------------------ 4505| 121k| { 4506| 121k| NodeSetFromVertices( pCG, &cur_nodes, 1, v, k - 1 ); 4507| 9.07M| for (i = 1; i <= l; i++) ------------------ | Branch (4507:21): [True: 8.95M, False: 121k] ------------------ 4508| 8.95M| { 4509| 8.95M| if (AllNodesAreInSet( &cur_nodes, 1, &Phi, i )) ------------------ | Branch (4509:17): [True: 2.97M, False: 5.97M] ------------------ 4510| 2.97M| { 4511| 2.97M| CellIntersectWithSet( pCG, &pi[k - 1], &W[k - 1], &Omega, i ); 4512| 2.97M| } 4513| 8.95M| } 4514| 121k| } 4515| | 4516| 132k| e[k - 1] = 1; 4517| 132k| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], v[k - 1], pCD1 ); 4518| 132k| if (v[k - 1] != INCHI_CANON_INFINITY) ------------------ | | 31| 132k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4518:9): [True: 11.5k, False: 121k] ------------------ 4519| 11.5k| { 4520| 11.5k| goto L15; 4521| 11.5k| } 4522| 121k| k--; 4523| 121k| goto L13; 4524| |/* L18: see above */ 4525| | 4526| 330k|exit_function: 4527| | /* CtPartFill( G, pCD, &rho, pzb_rho, 1, n, n_tg ); */ 4528| 330k| if (!bRhoIsDiscrete) ------------------ | Branch (4528:9): [True: 0, False: 330k] ------------------ 4529| 0| { 4530| 0| ret = CT_CANON_ERR; ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4531| 0| goto exit_error; 4532| 0| } 4533| | 4534| 330k| if (pzb_rho_fix) ------------------ | Branch (4534:9): [True: 78.5k, False: 252k] ------------------ 4535| 78.5k| { 4536| 78.5k| qzb_rho_fix = CtFullCompare( pzb_rho_fix, pzb_rho, 1, bSplitTautCompare ); 4537| 78.5k| if (qzb_rho_fix) ------------------ | Branch (4537:13): [True: 0, False: 78.5k] ------------------ 4538| 0| { 4539| 0| ret = CT_CANON_ERR; ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4540| 0| goto exit_error; 4541| 0| } 4542| 78.5k| } 4543| | 4544| | /* SymmRank */ 4545| 330k| memset( nSymmRank, 0, n_tg * sizeof( nSymmRank[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4546| 1.52M| for (i = 0; i < n_tg; i++) ------------------ | Branch (4546:17): [True: 1.19M, False: 330k] ------------------ 4547| 1.19M| { 4548| 1.19M| k = rho.AtNumber[i]; 4549| 1.19M| k2 = (int) GetUnorderedPartitionMcrNode( &theta, (AT_NUMB) ( k + 1 ) ) - 1; 4550| 1.19M| if (!nSymmRank[k2] || nSymmRank[k2] > rho.Rank[k]) ------------------ | Branch (4550:13): [True: 800k, False: 391k] | Branch (4550:31): [True: 0, False: 391k] ------------------ 4551| 800k| { 4552| 800k| nSymmRank[k2] = rho.Rank[k]; 4553| 800k| } 4554| 1.19M| } 4555| 1.52M| for (i = 0; i < n_tg; i++) ------------------ | Branch (4555:17): [True: 1.19M, False: 330k] ------------------ 4556| 1.19M| { 4557| 1.19M| k = rho.AtNumber[i]; 4558| 1.19M| k2 = (int) GetUnorderedPartitionMcrNode( &theta, (AT_NUMB) ( k + 1 ) ) - 1; 4559| 1.19M| nSymmRank[k] = nSymmRank[k2]; 4560| 1.19M| } 4561| | /* CanonRank, nAtomNumberCanon */ 4562| 330k| memcpy(nCanonRank, rho.Rank, n_tg * sizeof(nCanonRank[0])); 4563| 330k| memcpy(nAtomNumberCanon, rho.AtNumber, n_tg * sizeof(nAtomNumberCanon[0])); 4564| | /* LinearCT */ 4565| 330k| if (pzb_rho) ------------------ | Branch (4565:9): [True: 330k, False: 0] ------------------ 4566| 330k| { 4567| 330k| *nLenCt = pzb_rho->lenCt - 1; 4568| 330k| } 4569| 330k| if (pCt && pzb_rho && (*nLenCt > 0)) /* djb-rwth: GHI #164 fix */ ------------------ | Branch (4569:9): [True: 0, False: 330k] | Branch (4569:16): [True: 0, False: 0] | Branch (4569:27): [True: 0, False: 0] ------------------ 4570| 0| { 4571| 0| memcpy(pCt, pzb_rho->Ctbl, *nLenCt * sizeof(pCt[0])); 4572| 0| } 4573| 330k| pCC->lNumTotCT = pCC->lNumDecreasedCT + pCC->lNumRejectedCT + pCC->lNumEqualCT; 4574| 330k| pCC->dGroupSize = size; 4575| 330k| pCC->lNumGenerators = nNumFoundGenerators; 4576| 330k| pCC->lNumStoredIsomorphisms = l; 4577| | /* Note: check nNumFoundGenerators */ 4578| | 4579| 330k| if (pp_zb_rho_out && !*pp_zb_rho_out) ------------------ | Branch (4579:9): [True: 330k, False: 0] | Branch (4579:26): [True: 330k, False: 0] ------------------ 4580| 330k| { 4581| 330k| *pp_zb_rho_out = pzb_rho; 4582| 330k| pzb_rho = NULL; 4583| 330k| } 4584| | 4585| | 4586| | 4587| 330k|exit_error: 4588| 330k| INCHI_HEAPCHK 4589| | 4590| 330k| UnorderedPartitionFree( &theta ); 4591| 330k| UnorderedPartitionFree( &theta_from_gamma ); 4592| 330k| if (W) ------------------ | Branch (4592:9): [True: 330k, False: 0] ------------------ 4593| 330k| { 4594| 330k| inchi_free( W ); ------------------ | | 1152| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 330k, False: 0] | | | Branch (1152:50): [Folded, False: 330k] | | ------------------ ------------------ 4595| 330k| } 4596| 330k| if (v) ------------------ | Branch (4596:9): [True: 330k, False: 0] ------------------ 4597| 330k| { 4598| 330k| inchi_free( v ); ------------------ | | 1152| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 330k, False: 0] | | | Branch (1152:50): [Folded, False: 330k] | | ------------------ ------------------ 4599| 330k| } 4600| 330k| if (e) ------------------ | Branch (4600:9): [True: 330k, False: 0] ------------------ 4601| 330k| { 4602| 330k| inchi_free( e ); ------------------ | | 1152| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 330k, False: 0] | | | Branch (1152:50): [Folded, False: 330k] | | ------------------ ------------------ 4603| 330k| } 4604| 330k| if (qzb) ------------------ | Branch (4604:9): [True: 0, False: 330k] ------------------ 4605| 0| { 4606| 0| inchi_free( qzb ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4607| 0| } 4608| 330k| CTableFree( &Lambda ); 4609| 330k| CTableFree( &zf_zeta ); 4610| 330k| if (pzb_rho) ------------------ | Branch (4610:9): [True: 0, False: 330k] ------------------ 4611| 0| { 4612| 0| CTableFree( pzb_rho ); 4613| 0| inchi_free( pzb_rho ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4614| 0| pzb_rho = NULL; 4615| 0| } 4616| | /* CTableFree( &zf_zeta2 ); */ 4617| 330k| NodeSetFree( pCG, &Omega ); 4618| 330k| NodeSetFree( pCG, &Phi ); 4619| | /* NodeSetFree( &mcr_theta, n, 1 ); */ 4620| 330k| NodeSetFree( pCG, &cur_nodes ); 4621| 330k| PartitionFree( &zeta ); 4622| | /* PartitionFree( &zeta2 ); */ 4623| 330k| PartitionFree( &rho ); 4624| 330k| TranspositionFree( &gamma ); 4625| | 4626| 330k| return ret; 4627| 330k|} SetInitialRanks2: 4644| 371k|{ 4645| 371k| int i, nNumDiffRanks; 4646| 371k| AT_RANK nCurrentRank; 4647| | 4648| 1.64M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4648:17): [True: 1.27M, False: 371k] ------------------ 4649| 1.27M| { 4650| 1.27M| nAtomNumber[i] = (AT_RANK) i; 4651| 1.27M| } 4652| | 4653| | /* global for qsort */ 4654| 371k| pCG->m_pAtomInvariant2ForSort = pAtomInvariant2; 4655| | 4656| 371k| inchi_qsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompAtomInvariants2 ); 4657| | 4658| | /* nNewRank[i]: non-decreading order; do not increment nCurrentRank */ 4659| | /* if consecutive sorted atom invariants are identical */ 4660| | 4661| | /* djb-rwth: fixing oss-fuzz issue #69315 */ 4662| 371k| nNumDiffRanks = 1; 4663| 371k| if (num_atoms > 0) ------------------ | Branch (4663:9): [True: 371k, False: 0] ------------------ 4664| 371k| { 4665| 371k| nCurrentRank = (AT_RANK)num_atoms; 4666| 371k| nNewRank[nAtomNumber[num_atoms - 1]] = nCurrentRank; 4667| 1.27M| for (i = num_atoms - 1; i > 0; i--) ------------------ | Branch (4667:33): [True: 898k, False: 371k] ------------------ 4668| 898k| { 4669| | /* Note: CompAtomInvariants2Only() in following line implicitly reads pAtomInvariant2 pointed by pAtomInvariant2ForSort */ 4670| 898k| if (CompAtomInvariants2Only(&nAtomNumber[i - 1], &nAtomNumber[i], pCG)) ------------------ | Branch (4670:17): [True: 471k, False: 426k] ------------------ 4671| 471k| { 4672| 471k| nNumDiffRanks++; 4673| 471k| nCurrentRank = (AT_RANK)i; 4674| 471k| } 4675| 898k| nNewRank[nAtomNumber[i - 1]] = nCurrentRank; 4676| 898k| } 4677| 371k| } 4678| | 4679| 371k| return nNumDiffRanks; 4680| 371k|} FillOutAtomInvariant2: 4694| 292k|{ 4695| 292k| int i, k, j, i_t_group; 4696| | /* tautomers */ 4697| 292k| T_GROUP *t_group = NULL; 4698| 292k| int num_t_groups = 0; 4699| 292k| int num_tautomer_iso = 0; 4700| 292k|#define ELEM_NAME_LEN 2 4701| 292k| char ChemElements[ELEM_NAME_LEN*NUM_CHEM_ELEMENTS + ELEM_NAME_LEN]; 4702| 292k| char CurElement[ELEM_NAME_LEN + ELEM_NAME_LEN], *pCurElem; 4703| 292k| int nNumChemElements = 0; 4704| 292k| int nNumHydrogenAtoms = 0; 4705| 292k| int nNumCarbonAtoms = 0; 4706| | 4707| 292k| ChemElements[0] = '\0'; /* djb-rwth: initialisation prevents empty string comparison */ 4708| 292k| memset( ChemElements, 0, sizeof( ChemElements ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4709| 292k| memset( CurElement, 0, sizeof( CurElement ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4710| 292k| nNumChemElements = 0; 4711| | 4712| 292k| if (num_at_tg > num_atoms && t_group_info) ------------------ | Branch (4712:9): [True: 3.46k, False: 289k] | Branch (4712:34): [True: 3.46k, False: 0] ------------------ 4713| 3.46k| { 4714| 3.46k| t_group = t_group_info->t_group; 4715| 3.46k| num_t_groups = t_group_info->num_t_groups; 4716| 3.46k| num_tautomer_iso = t_group_info->bIgnoreIsotopic ? 0 : T_NUM_ISOTOPIC; ------------------ | | 70| 0|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 25| 3.46k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (4716:28): [True: 3.46k, False: 0] ------------------ 4717| 3.46k| } 4718| | 4719| 292k| if (!bTautGroupsOnly) ------------------ | Branch (4719:9): [True: 252k, False: 40.8k] ------------------ 4720| 252k| { 4721| | 4722| 1.30M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4722:21): [True: 1.04M, False: 252k] ------------------ 4723| 1.04M| { 4724| 1.04M| if (!strcmp( at[i].elname, "C" )) ------------------ | Branch (4724:17): [True: 106k, False: 943k] ------------------ 4725| 106k| { 4726| 106k| nNumCarbonAtoms++; 4727| 106k| } 4728| 943k| else if (!strcmp( at[i].elname, "H" ) || ------------------ | Branch (4728:22): [True: 101k, False: 841k] ------------------ 4729| 841k| !strcmp( at[i].elname, "D" ) || ------------------ | Branch (4729:18): [True: 0, False: 841k] ------------------ 4730| 841k| !strcmp( at[i].elname, "T" )) ------------------ | Branch (4730:18): [True: 0, False: 841k] ------------------ 4731| 101k| { 4732| 101k| nNumHydrogenAtoms++; 4733| 101k| } 4734| 841k| else 4735| 841k| { 4736| 841k| CurElement[0] = at[i].elname[0]; 4737| 841k| CurElement[1] = at[i].elname[1] ? at[i].elname[1] : ' '; ------------------ | Branch (4737:33): [True: 175k, False: 665k] ------------------ 4738| 841k| if (!( pCurElem = strstr( ChemElements, CurElement ) )) /* djb-rwth: ignoring LLVM warning: variable used for function return value */ ------------------ | Branch (4738:21): [True: 471k, False: 370k] ------------------ 4739| 471k| { 4740| 471k| strcat(ChemElements, CurElement); 4741| 471k| nNumChemElements++; 4742| 471k| } 4743| 841k| } 4744| 1.04M| } 4745| 252k| if (nNumChemElements > 1) ------------------ | Branch (4745:13): [True: 84.9k, False: 167k] ------------------ 4746| 84.9k| { 4747| 84.9k| qsort( ChemElements, nNumChemElements, ELEM_NAME_LEN, CompChemElemLex ); ------------------ | | 4700| 84.9k|#define ELEM_NAME_LEN 2 ------------------ 4748| 84.9k| } 4749| 252k| if (nNumCarbonAtoms) ------------------ | Branch (4749:13): [True: 63.2k, False: 188k] ------------------ 4750| 63.2k| { 4751| 63.2k| if (nNumChemElements) ------------------ | Branch (4751:17): [True: 55.1k, False: 8.13k] ------------------ 4752| 55.1k| { 4753| 55.1k| memmove(ChemElements + ELEM_NAME_LEN, ChemElements, (long long)ELEM_NAME_LEN * (long long)nNumChemElements); /* djb-rwth: cast operators added */ ------------------ | | 4700| 55.1k|#define ELEM_NAME_LEN 2 ------------------ memmove(ChemElements + ELEM_NAME_LEN, ChemElements, (long long)ELEM_NAME_LEN * (long long)nNumChemElements); /* djb-rwth: cast operators added */ ------------------ | | 4700| 55.1k|#define ELEM_NAME_LEN 2 ------------------ 4754| 55.1k| } 4755| 63.2k| ChemElements[0] = 'C'; 4756| 63.2k| ChemElements[1] = ' '; 4757| 63.2k| nNumChemElements++; 4758| 63.2k| } 4759| 252k| if (nNumHydrogenAtoms) ------------------ | Branch (4759:13): [True: 79.9k, False: 172k] ------------------ 4760| 79.9k| { 4761| 79.9k| ChemElements[ELEM_NAME_LEN*nNumChemElements] = 'H'; ------------------ | | 4700| 79.9k|#define ELEM_NAME_LEN 2 ------------------ 4762| 79.9k| ChemElements[ELEM_NAME_LEN*nNumChemElements + 1] = ' '; ------------------ | | 4700| 79.9k|#define ELEM_NAME_LEN 2 ------------------ 4763| 79.9k| nNumChemElements++; 4764| 79.9k| } 4765| | 4766| | /* general */ 4767| 1.30M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4767:21): [True: 1.04M, False: 252k] ------------------ 4768| 1.04M| { 4769| 1.04M| memset( &pAtomInvariant[i], 0, sizeof( pAtomInvariant[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4770| 1.04M| CurElement[0] = at[i].elname[0]; 4771| 1.04M| CurElement[1] = at[i].elname[1] ? at[i].elname[1] : ' '; ------------------ | Branch (4771:29): [True: 175k, False: 873k] ------------------ 4772| 1.04M| pCurElem = strstr( ChemElements, CurElement ); 4773| 1.04M| if (pCurElem) ------------------ | Branch (4773:17): [True: 1.04M, False: 0] ------------------ 4774| 1.04M| { 4775| 1.04M| j = (int) ( pCurElem - ChemElements ) / ELEM_NAME_LEN + 1; ------------------ | | 4700| 1.04M|#define ELEM_NAME_LEN 2 ------------------ 4776| 1.04M| } 4777| 0| else 4778| 0| { 4779| 0| j = nNumChemElements; /* must be D or T */ 4780| 0| } 4781| | /* at[i].hill_type = (U_CHAR) j; */ 4782| 1.04M| pAtomInvariant[i].val[AT_INV_HILL_ORDER] = j; 4783| | 4784| 1.04M| pAtomInvariant[i].val[AT_INV_NUM_CONNECTIONS] = at[i].valence; 4785| 1.04M| if (bHydrogensInRanks) ------------------ | Branch (4785:17): [True: 0, False: 1.04M] ------------------ 4786| 0| { 4787| 0| pAtomInvariant[i].val[AT_INV_NUM_H] = ( ( t_group && at[i].endpoint > 0 ) ? 0 : at[i].num_H ); ------------------ | Branch (4787:59): [True: 0, False: 0] | Branch (4787:70): [True: 0, False: 0] ------------------ 4788| 0| } 4789| 1.04M| if (bHydrogensFixedInRanks) ------------------ | Branch (4789:17): [True: 0, False: 1.04M] ------------------ 4790| 0| { 4791| 0| pAtomInvariant[i].val[AT_INV_NUM_H_FIX] = ( ( t_group && at[i].endpoint > 0 ) ? at[i].num_H : 0 ); ------------------ | Branch (4791:63): [True: 0, False: 0] | Branch (4791:74): [True: 0, False: 0] ------------------ 4792| 0| } 4793| 1.04M| if (!bDigraph && t_group && ( i_t_group = (int) at[i].endpoint - 1 ) >= 0 && i_t_group < num_t_groups) ------------------ | Branch (4793:17): [True: 1.04M, False: 0] | Branch (4793:31): [True: 0, False: 1.04M] | Branch (4793:42): [True: 0, False: 0] | Branch (4793:91): [True: 0, False: 0] ------------------ 4794| 0| { 4795| 0| pAtomInvariant[i].val[AT_INV_NUM_TG_ENDPOINTS] = t_group[i_t_group].nNumEndpoints; 4796| 0| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 69| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (4796:29): [True: 0, False: 0] ------------------ 4797| 0| { 4798| 0| pAtomInvariant[i].val[AT_INV_TG_NUMBERS + j] = t_group[i_t_group].num[j]; 4799| 0| } 4800| 0| for (j = 0; j < num_tautomer_iso; j++) ------------------ | Branch (4800:29): [True: 0, False: 0] ------------------ 4801| 0| { 4802| 0| pAtomInvariant[i].val[AT_INV_TAUT_ISO + j] = t_group[i_t_group].num[j + T_NUM_NO_ISOTOPIC]; ------------------ | | 69| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ 4803| 0| } 4804| 0| } 4805| 1.04M| pAtomInvariant[i].iso_sort_key = bIgnoreIsotopic ? 0 : at[i].iso_sort_key; ------------------ | Branch (4805:46): [True: 1.04M, False: 0] ------------------ 4806| 1.04M| } 4807| 252k| } 4808| 40.8k| else 4809| 40.8k| { 4810| | /* fill tautomeric groups only */ 4811| 40.8k| memset( pAtomInvariant, 0, num_at_tg * sizeof( pAtomInvariant[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4812| 40.8k| } 4813| | 4814| | /**************************************/ 4815| | /* tautomeric groups */ 4816| | /**************************************/ 4817| 296k| for (i = num_atoms; i < num_at_tg; i++) ------------------ | Branch (4817:25): [True: 3.56k, False: 292k] ------------------ 4818| 3.56k| { 4819| | 4820| 3.56k| k = i - num_atoms; 4821| 3.56k| memset( &pAtomInvariant[i], 0, sizeof( pAtomInvariant[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4822| 3.56k| if (!t_group) ------------------ | Branch (4822:13): [True: 0, False: 3.56k] ------------------ 4823| 0| continue; 4824| | /* make sure ranks of t-groups are larger than that of any atom */ 4825| | /* greater than for any real atom */ 4826| 3.56k| pAtomInvariant[i].val[AT_INV_HILL_ORDER] = bTautGroupsOnly ? num_at_tg : nNumChemElements + 1; ------------------ | Branch (4826:52): [True: 3.56k, False: 0] ------------------ 4827| | /* greater than for any real atom */ 4828| 3.56k| pAtomInvariant[i].val[AT_INV_NUM_CONNECTIONS] = MAXVAL + 1; ------------------ | | 60| 3.56k|#define MAXVAL 50 /* maximum valence */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ 4829| 3.56k| if (k < num_t_groups) ------------------ | Branch (4829:13): [True: 3.56k, False: 0] ------------------ 4830| 3.56k| { 4831| 3.56k| pAtomInvariant[i].val[AT_INV_NUM_TG_ENDPOINTS] = t_group[k].nNumEndpoints; 4832| 10.7k| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 69| 10.7k|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (4832:25): [True: 7.13k, False: 3.56k] ------------------ 4833| 7.13k| { 4834| 7.13k| pAtomInvariant[i].val[AT_INV_TAUT_ISO + j] = t_group[k].num[j]; 4835| 7.13k| } 4836| 3.56k| for (j = 0; j < num_tautomer_iso; j++) ------------------ | Branch (4836:25): [True: 0, False: 3.56k] ------------------ 4837| 0| { 4838| 0| pAtomInvariant[i].val[AT_INV_TAUT_ISO + j] = t_group[k].num[j + T_NUM_NO_ISOTOPIC]; ------------------ | | 69| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ 4839| 0| } 4840| 3.56k| } 4841| 3.56k| } 4842| 292k|} CleanNumH: 4847| 1.07M|{ 4848| 1.07M| int i; 4849| 1.07M| if (NumH) ------------------ | Branch (4849:9): [True: 649k, False: 422k] ------------------ 4850| 649k| { 4851| 3.58M| for (i = 0; i < len; i++) ------------------ | Branch (4851:21): [True: 2.93M, False: 649k] ------------------ 4852| 2.93M| { 4853| 2.93M| if (NumH[i] == EMPTY_H_NUMBER) ------------------ | | 36| 2.93M|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 31| 2.93M|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (4853:17): [True: 2.25M, False: 685k] ------------------ 4854| 2.25M| { 4855| 2.25M| NumH[i] = 0; 4856| 2.25M| } 4857| 685k| else 4858| 685k| { 4859| 685k| NumH[i] -= BASE_H_NUMBER; ------------------ | | 37| 685k|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 31| 685k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ 4860| 685k| } 4861| 2.93M| } 4862| 649k| } 4863| 1.07M|} CleanCt: 4868| 288k|{ 4869| 288k| if (Ct && Ct[len] == EMPTY_CT) ------------------ | | 35| 288k|#define EMPTY_CT 0 ------------------ | Branch (4869:9): [True: 288k, False: 0] | Branch (4869:15): [True: 288k, False: 0] ------------------ 4870| 288k| { 4871| 288k| Ct[len] = 0; 4872| 288k| return 1; 4873| 288k| } 4874| | 4875| 0| return 0; 4876| 288k|} CleanIsoSortKeys: 4881| 4.24k|{ 4882| 4.24k| int i; 4883| 4.24k| if (isk) ------------------ | Branch (4883:9): [True: 4.12k, False: 122] ------------------ 4884| 4.12k| { 4885| 28.0k| for (i = 0; i < len; i++) ------------------ | Branch (4885:21): [True: 23.9k, False: 4.12k] ------------------ 4886| 23.9k| { 4887| 23.9k| if (isk[i] == EMPTY_ISO_SORT_KEY) ------------------ | | 38| 23.9k|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ | Branch (4887:17): [True: 19.0k, False: 4.82k] ------------------ 4888| 19.0k| { 4889| 19.0k| isk[i] = 0; 4890| 19.0k| } 4891| 23.9k| } 4892| 4.12k| } 4893| 4.24k|} DeAllocBCN: 4926| 252k|{ 4927| 252k| int i, k; 4928| 252k| FTCN *ftcn; 4929| 252k| if (!pBCN) ------------------ | Branch (4929:9): [True: 0, False: 252k] ------------------ 4930| 0| { 4931| 0| return; 4932| 0| } 4933| 252k| if (pBCN->pRankStack) ------------------ | Branch (4933:9): [True: 252k, False: 38] ------------------ 4934| 252k| { 4935| 3.01M| for (i = 0; i < pBCN->nMaxLenRankStack; i++) ------------------ | Branch (4935:21): [True: 2.76M, False: 252k] ------------------ 4936| 2.76M| { 4937| 2.76M| FREE_ARRAY( pBCN->pRankStack[i] ) ------------------ | | 4921| 2.76M|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 871k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 871k, False: 0] | | | | | Branch (1152:50): [Folded, False: 871k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 871k, False: 1.88M] | | ------------------ ------------------ 4938| 2.76M| } 4939| 252k| FREE_ARRAY( pBCN->pRankStack ) ------------------ | | 4921| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 252k, False: 0] | | ------------------ ------------------ 4940| 252k| } 4941| 756k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 756k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (4941:17): [True: 504k, False: 252k] ------------------ 4942| 504k| { 4943| 504k| ftcn = pBCN->ftcn + k; 4944| 504k| FreeNeighList( ftcn->NeighList ); 4945| | 4946| 504k| FREE_ARRAY( ftcn->LinearCt ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 288k, False: 215k] | | ------------------ ------------------ 4947| | 4948| 504k| PartitionFree( &ftcn->PartitionCt ); 4949| | 4950| 504k| FREE_ARRAY( ftcn->nSymmRankCt ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 288k, False: 215k] | | ------------------ ------------------ 4951| 504k| FREE_ARRAY( ftcn->nNumHOrig ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 288k, False: 215k] | | ------------------ ------------------ 4952| 504k| FREE_ARRAY( ftcn->nNumH ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 288k, False: 215k] | | ------------------ ------------------ 4953| 504k| FREE_ARRAY( ftcn->nNumHOrigFixH ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 36.3k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 36.3k, False: 0] | | | | | Branch (1152:50): [Folded, False: 36.3k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 36.3k, False: 467k] | | ------------------ ------------------ 4954| 504k| FREE_ARRAY( ftcn->nNumHFixH ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 36.3k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 36.3k, False: 0] | | | | | Branch (1152:50): [Folded, False: 36.3k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 36.3k, False: 467k] | | ------------------ ------------------ 4955| | 4956| 504k| PartitionFree( &ftcn->PartitionCtIso ); 4957| | 4958| 504k| FREE_ARRAY( ftcn->nSymmRankCtIso ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 2.12k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 2.12k, False: 0] | | | | | Branch (1152:50): [Folded, False: 2.12k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 2.12k, False: 502k] | | ------------------ ------------------ 4959| 504k| FREE_ARRAY( ftcn->iso_sort_keys ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 2.06k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 2.06k, False: 0] | | | | | Branch (1152:50): [Folded, False: 2.06k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 2.06k, False: 502k] | | ------------------ ------------------ 4960| 504k| FREE_ARRAY( ftcn->iso_sort_keysOrig ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 2.06k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 2.06k, False: 0] | | | | | Branch (1152:50): [Folded, False: 2.06k] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 2.06k, False: 502k] | | ------------------ ------------------ 4961| 504k| FREE_ARRAY( ftcn->iso_exchg_atnos ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 157|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 157, False: 0] | | | | | Branch (1152:50): [Folded, False: 157] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 157, False: 504k] | | ------------------ ------------------ 4962| 504k| FREE_ARRAY( ftcn->iso_exchg_atnosOrig ) ------------------ | | 4921| 504k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 157|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 157, False: 0] | | | | | Branch (1152:50): [Folded, False: 157] | | | | ------------------ | | ------------------ | | | Branch (4921:28): [True: 157, False: 504k] | | ------------------ ------------------ 4963| 504k| } 4964| 252k|} GetBaseCanonRanking: 5081| 252k|{ 5082| 252k| int ret = 0; 5083| 252k| int iBase; /* base structure index, always valid; = TAUT_YES except special fully non-taut mode */ 5084| 252k| int iOther; /* other than basic structure index, usually non-taut; may be = iBase */ 5085| 252k| int bReqNonTaut; /* 1 => requested non-tautomeric results */ 5086| 252k| int bReqTaut; /* 1 => requested tautomeric results and the base structure is tautomeric */ 5087| 252k| int bChanged; 5088| | 5089| 252k| sp_ATOM *at_base = NULL; 5090| 252k| sp_ATOM *at_other = NULL; 5091| | 5092| 252k| int bTautIgnoreIsotopic = 0; 5093| | /*int bIgnoreIsotopic = 0;*/ 5094| 252k| int nNumCurrRanks = 0; 5095| 252k| int nMaxLenRankStack = 0; 5096| 252k| int num_max = num_at_tg; 5097| 252k| long lCount; 5098| | 5099| | /* local allocations */ 5100| 252k| ATOM_INVARIANT2 *pAtomInvariant = NULL; 5101| 252k| NEIGH_LIST *NeighList[TAUT_NUM]; 5102| 252k| ConTable *Ct_Temp = NULL; 5103| | 5104| | /* initial partition for canonicalization */ 5105| 252k| AT_RANK *nRank = NULL; 5106| 252k| AT_NUMB *nAtomNumber = NULL; 5107| | 5108| | /* canonicalization output */ 5109| | 5110| 252k| ConTable *Ct_NoH = NULL; 5111| 252k| AT_RANK *nCanonRankNoH = NULL; 5112| 252k| AT_NUMB *nAtomNumberCanonNoH = NULL; 5113| 252k| AT_RANK *nSymmRankNoH = NULL; 5114| | 5115| 252k| ConTable *Ct_NoTautH = NULL; 5116| 252k| AT_RANK *nSymmRankNoTautH = NULL; 5117| 252k| AT_RANK *nCanonRankNoTautH = NULL; 5118| 252k| AT_NUMB *nAtomNumberCanonNoTautH = NULL; 5119| 252k| NUM_H *numHNoTautH = NULL; 5120| 252k| int lenNumHNoTautH; 5121| 252k| int maxlenNumHNoTautH; 5122| | 5123| 252k| ConTable *Ct_Base = NULL; 5124| 252k| AT_RANK *nSymmRankBase = NULL; 5125| 252k| AT_RANK *nCanonRankBase = NULL; 5126| 252k| AT_NUMB *nAtomNumberCanonBase = NULL; 5127| 252k| NUM_H *numH = NULL; 5128| 252k| int lenNumH = num_atoms; 5129| 252k| int maxlenNumH = 0; 5130| | 5131| 252k|#if ( USE_AUX_RANKING == 1 ) 5132| 252k| AT_RANK *nRankAux = NULL; 5133| 252k| AT_NUMB *nAtomNumberAux = NULL; 5134| 252k| ATOM_INVARIANT2 *pAtomInvariantAux = NULL; 5135| 252k|#endif 5136| | 5137| 252k| ConTable *Ct_FixH = NULL; 5138| 252k| AT_RANK *nSymmRankFixH = NULL; 5139| 252k| AT_RANK *nCanonRankFixH = NULL; 5140| 252k| AT_NUMB *nAtomNumberCanonFixH = NULL; 5141| 252k| NUM_H *NumHfixed = NULL; 5142| 252k| int maxlenNumHfixed; 5143| | 5144| | /* isotopic canonicalization */ 5145| | 5146| 252k| ConTable *Ct_NoTautHIso = NULL; 5147| 252k| AT_RANK *nSymmRankNoTautHIso = NULL; 5148| 252k| AT_RANK *nCanonRankNoTautHIso = NULL; 5149| 252k| AT_NUMB *nAtomNumberCanonNoTautHIso = NULL; 5150| 252k| AT_ISO_SORT_KEY *iso_sort_key_NoTautH = NULL; 5151| 252k| int maxlen_iso_sort_key_NoTautH = 0; 5152| 252k| int len_iso_sort_key_NoTautH = 0; 5153| 252k| int num_iso_NoTautH = 0, num_iso_NoAuxBase; 5154| | 5155| 252k| ConTable *Ct_BaseIso = NULL; 5156| 252k| AT_RANK *nSymmRankBaseIso = NULL; 5157| 252k| AT_RANK *nCanonRankBaseIso = NULL; 5158| 252k| AT_NUMB *nAtomNumberCanonBaseIso = NULL; 5159| | 5160| 252k| AT_ISO_SORT_KEY *iso_sort_keyBase = NULL; 5161| 252k| int maxlen_iso_sort_keyBase = 0; 5162| 252k| int len_iso_sort_keyBase = 0; 5163| | 5164| 252k| int bUseIsoAuxBase[TAUT_NUM]; 5165| 252k| S_CHAR *iso_exchg_atnos = NULL; 5166| 252k| int len_iso_exchg_atnos = 0; 5167| 252k| int maxlen_iso_exchg_atnos = 0; 5168| 252k| int num_iso_Base = 0; 5169| | 5170| 252k| AT_ISO_SORT_KEY iso_sort_key; 5171| | 5172| 252k| ConTable *Ct_FixHIso = NULL; 5173| 252k| AT_RANK *nSymmRankFixHIso = NULL; 5174| 252k| AT_RANK *nCanonRankFixHIso = NULL; 5175| 252k| AT_NUMB *nAtomNumberCanonFixHIso = NULL; 5176| | 5177| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5178| | AT_ISO_SORT_KEY iso_sort_key2; 5179| | AT_ISO_SORT_KEY *iso_sort_key_Hfixed = NULL; 5180| | int maxlen_iso_sort_key_Hfixed; 5181| | int len_iso_sort_key_Hfixed; 5182| | int num_iso_Hfixed; 5183| |#endif 5184| | 5185| 252k| AT_RANK *nTempRank = NULL; 5186| | 5187| 252k| CANON_DATA pCD[3]; /* = &CanonData; */ 5188| 252k| CANON_COUNTS CanonCounts; 5189| 252k| CANON_COUNTS *pCC = &CanonCounts; 5190| | 5191| 252k| int i, j, k, m; 5192| 252k| int nCanonFlags[2]; 5193| | 5194| | /* */ 5195| 252k| int iflag; 5196| | 5197| 252k| memset( pCD, 0, sizeof( pCD ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5198| 252k| memset( pCC, 0, sizeof( pCC[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5199| 252k| memset( bUseIsoAuxBase, 0, sizeof( bUseIsoAuxBase ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5200| 252k| memset( nCanonFlags, 0, sizeof( nCanonFlags ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5201| 252k| NeighList[TAUT_NON] = NULL; ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5202| 252k| NeighList[TAUT_YES] = NULL; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5203| | 5204| | /* select base structure, find whether it is tautomeric or not */ 5205| | /* djb-rwth: addressing LLVM warning */ 5206| 252k| if (at[TAUT_YES] && s[TAUT_YES].nLenCT && ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (at[TAUT_YES] && s[TAUT_YES].nLenCT && ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5206:9): [True: 252k, False: 0] | Branch (5206:25): [True: 252k, False: 0] ------------------ 5207| 252k| t_group_info && ( s[TAUT_YES].nLenLinearCTTautomer > 0 && /* ordinary tautomerism */ ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5207:10): [True: 252k, False: 0] | Branch (5207:28): [True: 40.8k, False: 211k] ------------------ 5208| 40.8k| ((t_group_info->t_group && t_group_info->num_t_groups > 0) || ------------------ | Branch (5208:16): [True: 40.8k, False: 0] | Branch (5208:41): [True: 3.46k, False: 37.4k] ------------------ 5209| | /* protons have been moved */ 5210| 37.4k| ( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) || ------------------ | | 156| 37.4k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 146| 37.4k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 157| 37.4k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 37.4k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 158| 37.4k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 148| 37.4k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 159| 37.4k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 149| 37.4k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 160| 37.4k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 37.4k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 161| 37.4k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 151| 37.4k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 162| 37.4k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 153| 37.4k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 163| 37.4k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 152| 37.4k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (5210:14): [True: 37.2k, False: 122] ------------------ 5211| | /* tautomerism due to possible isotopic proton exchange */ 5212| 122| (t_group_info->nNumIsotopicEndpoints > 1 && ------------------ | Branch (5212:15): [True: 122, False: 0] ------------------ 5213| 122| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ))) )) ------------------ | | 981| 122|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ))) )) ------------------ | | 982| 122|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5213:14): [True: 122, False: 0] ------------------ 5214| 40.8k| { 5215| | /* tautomeric: (1) has tautomeric atoms OR 5216| | (2) H-atoms have been rearranged due to proton addition/removal OR 5217| | (3) Found isotopic H-atoms on tautomeric or hetero atoms 5218| | */ 5219| 40.8k| iBase = TAUT_YES; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5220| 40.8k| bReqTaut = 1; 5221| 40.8k| bUseIsoAuxBase[iBase] = ( s[iBase].nLenIsotopicEndpoints > 1 ) && ------------------ | Branch (5221:33): [True: 157, False: 40.7k] ------------------ 5222| 157| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ); ------------------ | | 981| 157|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ); ------------------ | | 982| 157|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5222:13): [True: 157, False: 0] ------------------ 5223| 40.8k| if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 574| 40.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5223:13): [True: 36.3k, False: 4.50k] | Branch (5223:29): [True: 36.3k, False: 0] ------------------ 5224| 36.3k| { 5225| 36.3k| iOther = TAUT_NON; /* tautomeric and non-tautomeric */ ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5226| 36.3k| bReqNonTaut = 1; 5227| 36.3k| } 5228| 4.50k| else 5229| 4.50k| { 5230| 4.50k| iOther = iBase; /* tautomeric only */ 5231| 4.50k| bReqNonTaut = 0; 5232| 4.50k| } 5233| 40.8k| } 5234| | 5235| 211k| else if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 574| 211k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ else if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5235:14): [True: 0, False: 211k] | Branch (5235:30): [True: 0, False: 0] ------------------ 5236| 0| { 5237| | /* force pure non-tautomeric processing; happens for testing only */ 5238| 0| iBase = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5239| 0| bReqTaut = 0; 5240| 0| iOther = iBase; 5241| 0| bReqNonTaut = 1; 5242| 0| num_at_tg = num_atoms; 5243| 0| } 5244| | 5245| 211k| else if (at[TAUT_YES] && s[TAUT_YES].nLenCT) ------------------ | | 575| 211k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ else if (at[TAUT_YES] && s[TAUT_YES].nLenCT) ------------------ | | 575| 211k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5245:14): [True: 211k, False: 0] | Branch (5245:30): [True: 211k, False: 0] ------------------ 5246| 211k| { 5247| | /* although the user requested tautomeric processing, tautomerism has not been found */ 5248| | /* however, the results should be saved in the TAUT_YES elements of the arrays */ 5249| 211k| iBase = TAUT_YES; ------------------ | | 575| 211k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5250| 211k| bReqTaut = 0; 5251| 211k| bUseIsoAuxBase[iBase] = ( s[iBase].nLenIsotopicEndpoints > 1 ); 5252| 211k| iOther = iBase; 5253| 211k| bReqNonTaut = 1; 5254| 211k| num_at_tg = num_atoms; 5255| 211k| } 5256| 0| else 5257| 0| { 5258| 0| ret = CT_UNKNOWN_ERR; ------------------ | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5259| 0| goto exit_error; 5260| 0| } 5261| | 5262| | 5263| 252k| if (bReqTaut) ------------------ | Branch (5263:9): [True: 40.8k, False: 211k] ------------------ 5264| 40.8k| { 5265| | /* save "process isotopic" mark; temporarily set it to NO */ 5266| 40.8k| bTautIgnoreIsotopic = t_group_info->bIgnoreIsotopic; 5267| 40.8k| t_group_info->bIgnoreIsotopic = 1; 5268| 40.8k| } 5269| | 5270| | /* djb-rwth: removing redundant code */ 5271| | 5272| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5273| | num_iso_Hfixed = 5274| | len_iso_sort_key_Hfixed = 5275| | maxlen_iso_sort_key_Hfixed = 0; 5276| |#endif 5277| | 5278| | /* prepare initial data */ 5279| 252k| at_base = at[iBase]; 5280| 252k| at_other = at[iOther]; 5281| 252k| pAtomInvariant = (ATOM_INVARIANT2 *) inchi_calloc( num_max, sizeof( pAtomInvariant[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5282| 252k| nSymmRankNoH = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankNoH[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5283| 252k| nCanonRankNoH = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankNoH[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5284| 252k| nAtomNumberCanonNoH = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonNoH[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5285| 252k| nRank = (AT_RANK *) inchi_calloc( num_max, sizeof( nRank[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5286| 252k| nAtomNumber = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumber[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5287| 252k| nTempRank = (AT_RANK *) inchi_calloc( num_max, sizeof( nTempRank[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5288| | 5289| 252k| if (!pAtomInvariant || ------------------ | Branch (5289:9): [True: 0, False: 252k] ------------------ 5290| 252k| !nSymmRankNoH || !nCanonRankNoH || !nAtomNumberCanonNoH || ------------------ | Branch (5290:10): [True: 0, False: 252k] | Branch (5290:27): [True: 0, False: 252k] | Branch (5290:45): [True: 0, False: 252k] ------------------ 5291| 252k| !nRank || !nAtomNumber || !nTempRank) ------------------ | Branch (5291:10): [True: 0, False: 252k] | Branch (5291:20): [True: 0, False: 252k] | Branch (5291:36): [True: 0, False: 252k] ------------------ 5292| 0| { 5293| 0| goto exit_error_alloc; 5294| 0| } 5295| | 5296| 252k|#if ( USE_AUX_RANKING == 1 ) 5297| 252k| nRankAux = (AT_RANK *) inchi_calloc( num_max, sizeof( nRankAux[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5298| 252k| nAtomNumberAux = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberAux[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5299| 252k| pAtomInvariantAux = (ATOM_INVARIANT2 *) inchi_malloc( num_max * sizeof( pAtomInvariantAux[0] ) ); ------------------ | | 1143| 252k|#define inchi_malloc malloc ------------------ 5300| 252k| if (!nRankAux || !nAtomNumberAux || !pAtomInvariantAux) ------------------ | Branch (5300:9): [True: 0, False: 252k] | Branch (5300:22): [True: 0, False: 252k] | Branch (5300:41): [True: 0, False: 252k] ------------------ 5301| 0| { 5302| 0| goto exit_error_alloc; 5303| 0| } 5304| 252k|#endif 5305| | 5306| 252k| if (bReqTaut) ------------------ | Branch (5306:9): [True: 40.8k, False: 211k] ------------------ 5307| 40.8k| { 5308| 40.8k| if (!( NeighList[TAUT_YES] = ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5308:13): [True: 0, False: 40.8k] ------------------ 5309| 40.8k| CreateNeighList( num_atoms, num_at_tg, at_base, 0, t_group_info ) )) 5310| 0| { 5311| 0| goto exit_error_alloc; 5312| 0| } 5313| | /* needed for the hydrogenless structure */ 5314| 40.8k| if (!( NeighList[TAUT_NON] = ------------------ | | 574| 40.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5314:13): [True: 0, False: 40.8k] ------------------ 5315| 40.8k| CreateNeighList( num_atoms, num_atoms, at_base, 0, NULL ) )) 5316| 0| { 5317| 0| goto exit_error_alloc; 5318| 0| } 5319| 40.8k| } 5320| 211k| else 5321| 211k| { 5322| 211k| if (!( NeighList[TAUT_NON] = ------------------ | | 574| 211k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5322:13): [True: 0, False: 211k] ------------------ 5323| 211k| CreateNeighList( num_atoms, num_atoms, at_base, 0, NULL ) )) 5324| 0| { 5325| 0| goto exit_error_alloc; 5326| 0| } 5327| 211k| NeighList[TAUT_YES] = NULL; ------------------ | | 575| 211k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5328| | 5329| 211k| INCHI_HEAPCHK 5330| 211k| } 5331| | 5332| | 5333| | /* avoid memory leaks in case of error */ 5334| | /* 5335| | pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; 5336| | pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; 5337| | */ 5338| 252k| pBCN->nMaxLenRankStack = 0; 5339| 252k| pBCN->num_max = num_max; /* allocated nRank[] arrays lengths in pRankStack */ 5340| 252k| pBCN->num_at_tg = num_at_tg; /* all of the following arrays have this length */ 5341| 252k| pBCN->num_atoms = num_atoms; 5342| 252k| pBCN->ulTimeOutTime = ulTimeOutTime; 5343| | 5344| | /* initial partitioning of a hydrogenless skeleton: fill out the inveriant */ 5345| 252k| FillOutAtomInvariant2( at_base, 5346| 252k| num_atoms, 5347| 252k| num_atoms, 5348| 252k| pAtomInvariant, 5349| 252k| 1 /*bIgnoreIsotopic*/, 5350| 252k| 0 /*bHydrogensInRanks*/, 5351| 252k| 0 /*bHydrogensFixedInRanks*/, 5352| 252k| 0 /*bTaut=bDigraph*/, 5353| 252k| 0 /* bTautGroupsOnly */, 5354| 252k| NULL /*t_group_info*/ ); 5355| | 5356| | /* initial partitioning of a hydrogenless skeleton: create equitable partition (assign initial ranks) */ 5357| 252k| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariant, nRank, nAtomNumber, pCG ); 5358| | 5359| 252k| lCount = 0; 5360| | 5361| | /* make equitable partition in pBCN->pRankStack[0,1] */ 5362| 252k| nNumCurrRanks = DifferentiateRanks2( pCG, 5363| 252k| num_atoms, 5364| 252k| NeighList[TAUT_NON], ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5365| 252k| nNumCurrRanks, nRank, 5366| 252k| nTempRank, 5367| 252k| nAtomNumber, 5368| 252k| &lCount, 5369| 252k| 0 /* 0 means use qsort */ ); 5370| | 5371| | /* allocate partition stack */ 5372| 252k| nMaxLenRankStack = 2 * ( num_at_tg - nNumCurrRanks ) + 8; /* was 2*(...) + 6 */ 5373| 252k| pBCN->pRankStack = (AT_RANK **) inchi_calloc( nMaxLenRankStack, sizeof( pBCN->pRankStack[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5374| 252k| if (!pBCN->pRankStack) ------------------ | Branch (5374:9): [True: 0, False: 252k] ------------------ 5375| 0| { 5376| 0| pBCN->nMaxLenRankStack = 0; /* avoid memory leaks in case of error */ 5377| 0| goto exit_error_alloc; 5378| 0| } 5379| 252k| pBCN->nMaxLenRankStack = nMaxLenRankStack; /* avoid memory leaks in case of error */ 5380| | /* init partition stack */ 5381| 252k| pBCN->pRankStack[0] = nRank; 5382| 252k| pBCN->pRankStack[1] = nAtomNumber; 5383| | 5384| | /********************************************************************************************/ 5385| | /* get NoH/no taut groups canonical numbering, connection table, and equivalence partition */ 5386| | /********************************************************************************************/ 5387| | 5388| | /* pointers */ 5389| 252k| pCD[iOther].LinearCT = NULL; 5390| 252k| pCD[iOther].NumH = NULL; 5391| 252k| pCD[iOther].NumHfixed = NULL; 5392| 252k| pCD[iOther].iso_sort_key = NULL; 5393| 252k| pCD[iOther].iso_exchg_atnos = NULL; 5394| | 5395| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5396| | pCD[iOther].iso_sort_key_Hfixed = NULL; 5397| |#endif 5398| | 5399| | /* variables - unchanged */ 5400| 252k| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 5401| 252k| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 5402| | /* return values & input/output */ 5403| 252k| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 5404| 252k| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 5405| 252k| pCD[iOther].lenNumH = 0; 5406| 252k| pCD[iOther].lenNumHfixed = 0; 5407| 252k| pCD[iOther].len_iso_sort_key = 0; 5408| 252k| pCD[iOther].maxlen_iso_sort_key = 0; 5409| 252k| pCD[iOther].len_iso_exchg_atnos = 0; 5410| 252k| pCD[iOther].maxlen_iso_exchg_atnos = 0; 5411| | 5412| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5413| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 5414| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 5415| |#endif 5416| | 5417| 252k| ret = CanonGraph01( ic, pCG, num_atoms, num_atoms, num_max, 0, ------------------ | | 598| 252k|#define CanonGraph01 CanonGraph ------------------ 5418| 252k| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5419| 252k| nSymmRankNoH, nCanonRankNoH, nAtomNumberCanonNoH, 5420| 252k| pCD + iOther, pCC, NULL, &Ct_NoH, LargeMolecules ); 5421| | 5422| 252k| if (ret < 0) ------------------ | Branch (5422:9): [True: 0, False: 252k] ------------------ 5423| 0| { 5424| 0| goto exit_error; 5425| 0| } 5426| | 5427| | /* update initial partitioning */ 5428| 252k| nNumCurrRanks = FixCanonEquivalenceInfo( pCG, num_atoms, nSymmRankNoH, nRank, nTempRank, nAtomNumber, &bChanged ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 5429| | 5430| | /* repartition if necessary */ 5431| 252k| if (bChanged & 3) ------------------ | Branch (5431:9): [True: 7, False: 252k] ------------------ 5432| 7| { 5433| 7| if (Ct_NoH) ------------------ | Branch (5433:13): [True: 7, False: 0] ------------------ 5434| 7| { 5435| 7| CTableFree( Ct_NoH ); 5436| 7| inchi_free( Ct_NoH ); ------------------ | | 1152| 7|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 7, False: 0] | | | Branch (1152:50): [Folded, False: 7] | | ------------------ ------------------ 5437| 7| Ct_NoH = NULL; 5438| 7| } 5439| 7| pCD[iOther].nCanonFlags |= CANON_FLAG_NO_H_RECANON; ------------------ | | 206| 7|#define CANON_FLAG_NO_H_RECANON 0x0001 /* iOther: second canonicalization of the no H structure */ ------------------ 5440| | 5441| 7| ret = CanonGraph02( ic, pCG, num_atoms, num_atoms, num_max, 0, ------------------ | | 599| 7|#define CanonGraph02 CanonGraph ------------------ 5442| 7| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 574| 7|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5443| 7| nSymmRankNoH, nCanonRankNoH, nAtomNumberCanonNoH, 5444| 7| pCD + iOther, pCC, NULL, &Ct_NoH, LargeMolecules ); 5445| | 5446| 7| if (ret < 0) ------------------ | Branch (5446:13): [True: 0, False: 7] ------------------ 5447| 0| { 5448| 0| goto exit_error; 5449| 0| } 5450| 7| } 5451| | 5452| | 5453| | /********************************************************************************/ 5454| | /* get NoTautH canonical numbering, connection table, and equivalence partition */ 5455| | /********************************************************************************/ 5456| 252k| maxlenNumHNoTautH = num_atoms + 1; 5457| 252k| nSymmRankNoTautH = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankNoTautH[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5458| 252k| nCanonRankNoTautH = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankNoTautH[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5459| 252k| nAtomNumberCanonNoTautH = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonNoTautH[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5460| 252k| numHNoTautH = (NUM_H *) inchi_calloc( maxlenNumHNoTautH, sizeof( numHNoTautH[0] ) ); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 5461| 252k| if (!numHNoTautH || !nSymmRankNoTautH || !nCanonRankNoTautH || !nAtomNumberCanonNoTautH) ------------------ | Branch (5461:9): [True: 0, False: 252k] | Branch (5461:25): [True: 0, False: 252k] | Branch (5461:46): [True: 0, False: 252k] | Branch (5461:68): [True: 0, False: 252k] ------------------ 5462| 0| { 5463| 0| goto exit_error_alloc; 5464| 0| } 5465| | 5466| | /* find number of H atoms attached to not-a-tautomeric-endpoint atoms */ 5467| 1.30M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5467:17): [True: 1.04M, False: 252k] ------------------ 5468| 1.04M| { 5469| 1.04M| numHNoTautH[i] = ( !at_base[i].endpoint && at_base[i].num_H ) ? at_base[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 37| 10.7k|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 31| 10.7k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ numHNoTautH[i] = ( !at_base[i].endpoint && at_base[i].num_H ) ? at_base[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 36| 2.08M|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 31| 1.03M|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (5469:28): [True: 1.03M, False: 13.2k] | Branch (5469:52): [True: 10.7k, False: 1.02M] ------------------ 5470| 1.04M| } 5471| | 5472| | /* pointers */ 5473| 252k| pCD[iOther].LinearCT = NULL; 5474| 252k| pCD[iOther].NumH = numHNoTautH; 5475| 252k| pCD[iOther].NumHfixed = NULL; 5476| 252k| pCD[iOther].iso_sort_key = NULL; 5477| 252k| pCD[iOther].iso_exchg_atnos = NULL; 5478| | 5479| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5480| | pCD[iOther].iso_sort_key_Hfixed = NULL; 5481| |#endif 5482| | 5483| | /* variables - unchanged */ 5484| 252k| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 5485| 252k| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 5486| 252k| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 5487| | /* return values & input/output */ 5488| 252k| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 5489| 252k| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 5490| 252k| pCD[iOther].lenNumH = lenNumHNoTautH = num_atoms; 5491| 252k| pCD[iOther].lenNumHfixed = 0; 5492| 252k| pCD[iOther].len_iso_sort_key = 0; 5493| 252k| pCD[iOther].maxlen_iso_sort_key = 0; 5494| 252k| pCD[iOther].len_iso_exchg_atnos = 0; 5495| 252k| pCD[iOther].maxlen_iso_exchg_atnos = 0; 5496| | 5497| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5498| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 5499| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 5500| |#endif 5501| | 5502| 252k| pCD[iOther].nAuxRank = NULL; 5503| | 5504| | /* check whether we need NoTautH cononicalization */ 5505| 252k| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5506| 1.30M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5506:17): [True: 1.04M, False: 252k] ------------------ 5507| 1.04M| { 5508| 1.04M| if (nTempRank[nSymmRankNoH[i] - 1] < i) ------------------ | Branch (5508:13): [True: 797k, False: 252k] ------------------ 5509| 797k| { 5510| 797k| nTempRank[nSymmRankNoH[i] - 1] = i; /* greatest class representative */ 5511| 797k| } 5512| 1.04M| } 5513| 1.29M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5513:17): [True: 1.04M, False: 251k] ------------------ 5514| 1.04M| { 5515| 1.04M| if (numHNoTautH[i] != numHNoTautH[nTempRank[nSymmRankNoH[i] - 1]]) ------------------ | Branch (5515:13): [True: 868, False: 1.03M] ------------------ 5516| 868| { 5517| 868| pCD[iOther].nCanonFlags |= CANON_FLAG_NO_TAUT_H_DIFF; ------------------ | | 207| 868|#define CANON_FLAG_NO_TAUT_H_DIFF 0x0002 /* iOther: NoTautH eq. partition differs from NoH */ ------------------ 5518| 868| break; /* atoms so far found to be equivalent have different number of H; the canonicalization is needed */ 5519| 868| } 5520| 1.04M| } 5521| | 5522| | /* i = 0; *//* debug: force to call the canonicalization */ 5523| 252k| if (i < num_atoms) ------------------ | Branch (5523:9): [True: 868, False: 251k] ------------------ 5524| 868| { 5525| | /* needs canonicalization */ 5526| | /* get aux canonical ranking of the structure with attached H */ 5527| | 5528| 868|#if ( USE_AUX_RANKING == 1 ) 5529| | /* refine no-H partition according to not-a-taut-H distribution */ 5530| 868| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5531| 12.7k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5531:21): [True: 11.8k, False: 868] ------------------ 5532| 11.8k| { 5533| 11.8k| pAtomInvariantAux[i].val[0] = nSymmRankNoH[i]; 5534| 11.8k| pAtomInvariantAux[i].val[1] = numHNoTautH[i]; /* additional differentiation: not-a-taut-H distribution */ 5535| 11.8k| } 5536| | 5537| | /* initial partitioning */ 5538| 868| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 5539| | 5540| | /* make equitable partition */ 5541| 868| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 574| 868|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5542| 868| nNumCurrRanks, nRankAux, 5543| 868| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 5544| | 5545| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 5546| 868| pCD[iOther].nAuxRank = nRankAux; 5547| 868|#endif 5548| | 5549| 868| ret = CanonGraph03( ic, pCG, num_atoms, num_atoms, num_max, 1 /* digraph?? was 0 */, ------------------ | | 600| 868|#define CanonGraph03 CanonGraph ------------------ 5550| 868| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 574| 868|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5551| 868| nSymmRankNoTautH, nCanonRankNoTautH, nAtomNumberCanonNoTautH, 5552| 868| pCD + iOther, pCC, &Ct_NoH, &Ct_NoTautH, LargeMolecules ); 5553| | 5554| 868| if (ret < 0) ------------------ | Branch (5554:13): [True: 0, False: 868] ------------------ 5555| 0| { 5556| 0| goto exit_error; 5557| 0| } 5558| | 5559| | /* in case of non-tautomeric structure the final results are in: 5560| | 5561| | nSymmRankNoTautH 5562| | nCanonRankNoTautH 5563| | nAtomNumberCanonNoTautH 5564| | Ct_NoTautH 5565| | numHNoTautH (original H positions) 5566| | */ 5567| 868| } /* if ( i < num_atoms ) */ 5568| | 5569| 251k| else 5570| | 5571| 251k| { 5572| | 5573| | /* copy the results of the previous (no H) canonicalization */ 5574| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 5575| 251k| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1146| 251k|#define inchi_calloc calloc ------------------ | Branch (5575:13): [True: 251k, False: 0] ------------------ 5576| 251k| CTableCreate( Ct_Temp, num_atoms, pCD + iOther )) ------------------ | Branch (5576:14): [True: 251k, False: 0] ------------------ 5577| 251k| { 5578| 251k| CtFullCopy( Ct_Temp, Ct_NoH ); 5579| | /* since Ct_NoH does not have Ct_NoH->NumH we have to fill out Ct_Temp->NumH separately */ 5580| 1.28M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5580:25): [True: 1.03M, False: 251k] ------------------ 5581| 1.03M| { 5582| 1.03M| Ct_Temp->NumH[nCanonRankNoH[i] - 1] = numHNoTautH[i]; 5583| | /*Ct_Temp->NumH[i] = numHNoTautH[nAtomNumberCanonNoH[i]]; -- alternative */ 5584| 1.03M| } 5585| 251k| Ct_Temp->lenNumH = num_atoms; 5586| 251k| } 5587| 0| else 5588| 0| { 5589| 0| goto exit_error_alloc; 5590| 0| } 5591| | 5592| 251k| Ct_NoTautH = Ct_Temp; 5593| 251k| Ct_Temp = NULL; 5594| | /* djb-rwth: functions replaced with their safe C11 variants */ 5595| 251k| memcpy(nSymmRankNoTautH, nSymmRankNoH, num_atoms * sizeof(nSymmRankNoTautH[0])); 5596| 251k| memcpy(nCanonRankNoTautH, nCanonRankNoH, num_atoms * sizeof(nCanonRankNoTautH[0])); 5597| 251k| memcpy(nAtomNumberCanonNoTautH, nAtomNumberCanonNoH, num_atoms * sizeof(nAtomNumberCanonNoTautH[0])); 5598| 251k| } 5599| | 5600| | /* in case of non-tautomeric component this is the final result */ 5601| | /* i = CtFullCompare( Ct_NoTautH, Ct_Temp, num_atoms, 0, 0 );*/ 5602| | 5603| | /*******************************************************************************************/ 5604| | /* If only Isotopic atoms and isotopic H, tautomerism has not been found: */ 5605| | /* get isotopic canonical numbering, connection table, and equivalence partition */ 5606| | /*******************************************************************************************/ 5607| | 5608| 252k| if (s[iOther].num_isotopic_atoms && !s[iOther].bIgnoreIsotopic && !bReqTaut && bReqNonTaut) ------------------ | Branch (5608:9): [True: 1.41k, False: 250k] | Branch (5608:41): [True: 1.41k, False: 0] | Branch (5608:71): [True: 594, False: 823] | Branch (5608:84): [True: 594, False: 0] ------------------ 5609| 594| { 5610| | 5611| 594| maxlen_iso_sort_key_NoTautH = num_atoms + 1; 5612| 594| nSymmRankNoTautHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankNoTautHIso[0] ) ); ------------------ | | 1146| 594|#define inchi_calloc calloc ------------------ 5613| 594| nCanonRankNoTautHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankNoTautHIso[0] ) ); ------------------ | | 1146| 594|#define inchi_calloc calloc ------------------ 5614| 594| nAtomNumberCanonNoTautHIso = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonNoTautHIso[0] ) ); ------------------ | | 1146| 594|#define inchi_calloc calloc ------------------ 5615| 594| iso_sort_key_NoTautH = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_key_NoTautH, sizeof( iso_sort_key_NoTautH[0] ) ); ------------------ | | 1146| 594|#define inchi_calloc calloc ------------------ 5616| | 5617| 594| if (!nSymmRankNoTautHIso || !nCanonRankNoTautHIso || !nAtomNumberCanonNoTautHIso || !iso_sort_key_NoTautH) ------------------ | Branch (5617:13): [True: 0, False: 594] | Branch (5617:37): [True: 0, False: 594] | Branch (5617:62): [True: 0, False: 594] | Branch (5617:93): [True: 0, False: 594] ------------------ 5618| 0| { 5619| 0| goto exit_error_alloc; 5620| 0| } 5621| | 5622| | /* fill out isotopic non-tautomeric keys */ 5623| 594| num_iso_NoTautH = 0; 5624| 5.84k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5624:21): [True: 5.24k, False: 594] ------------------ 5625| 5.24k| { 5626| 5.24k| if (at_base[i].endpoint) ------------------ | Branch (5626:17): [True: 25, False: 5.22k] ------------------ 5627| 25| { 5628| | /* should not happen */ 5629| 25| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, 0, 0, 0 ); 5630| 25| } 5631| 5.22k| else 5632| 5.22k| { 5633| 5.22k| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, at_base[i].num_iso_H[0], at_base[i].num_iso_H[1], at_base[i].num_iso_H[2] ); 5634| 5.22k| } 5635| 5.24k| if (iso_sort_key) ------------------ | Branch (5635:17): [True: 850, False: 4.39k] ------------------ 5636| 850| { 5637| 850| iso_sort_key_NoTautH[i] = iso_sort_key; 5638| 850| num_iso_NoTautH++; 5639| 850| } 5640| 4.39k| else 5641| 4.39k| { 5642| 4.39k| iso_sort_key_NoTautH[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 38| 4.39k|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 5643| 4.39k| } 5644| 5.24k| } 5645| | 5646| | /* pointers */ 5647| 594| pCD[iOther].LinearCT = NULL; /* LinearCT; */ 5648| 594| pCD[iOther].NumH = numHNoTautH; 5649| 594| pCD[iOther].NumHfixed = NULL; 5650| 594| pCD[iOther].iso_sort_key = iso_sort_key_NoTautH; 5651| 594| pCD[iOther].iso_exchg_atnos = NULL; 5652| | 5653| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5654| | pCD[iOther].iso_sort_key_Hfixed = NULL; 5655| |#endif 5656| | 5657| | /* variables - unchanged */ 5658| 594| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 5659| 594| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 5660| 594| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 5661| | /* return values & input/output */ 5662| 594| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 5663| 594| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 5664| 594| pCD[iOther].lenNumH = lenNumHNoTautH /*= num_atoms*/; 5665| 594| pCD[iOther].lenNumHfixed = 0; 5666| 594| pCD[iOther].len_iso_sort_key = len_iso_sort_key_NoTautH = num_atoms; 5667| 594| pCD[iOther].maxlen_iso_sort_key = maxlen_iso_sort_key_NoTautH; 5668| 594| pCD[iOther].len_iso_exchg_atnos = 0; 5669| 594| pCD[iOther].maxlen_iso_exchg_atnos = 0; 5670| | 5671| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5672| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 5673| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 5674| |#endif 5675| | 5676| 594| pCD[iOther].nAuxRank = NULL; 5677| | 5678| 594| if (num_iso_NoTautH) ------------------ | Branch (5678:13): [True: 594, False: 0] ------------------ 5679| 594| { 5680| | /* check whether we need NoTautH cononicalization */ 5681| 594| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5682| 5.84k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5682:25): [True: 5.24k, False: 594] ------------------ 5683| 5.24k| { 5684| 5.24k| if (nTempRank[nSymmRankNoTautH[i] - 1] < i) ------------------ | Branch (5684:21): [True: 4.65k, False: 594] ------------------ 5685| 4.65k| { 5686| 4.65k| nTempRank[nSymmRankNoTautH[i] - 1] = i; /* greatest class representative */ 5687| 4.65k| } 5688| 5.24k| } 5689| 2.25k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5689:25): [True: 1.97k, False: 275] ------------------ 5690| 1.97k| { 5691| 1.97k| if (iso_sort_key_NoTautH[i] != iso_sort_key_NoTautH[nTempRank[nSymmRankNoTautH[i] - 1]]) ------------------ | Branch (5691:21): [True: 319, False: 1.66k] ------------------ 5692| 319| { 5693| 319| pCD[iOther].nCanonFlags |= CANON_FLAG_ISO_ONLY_NON_TAUT_DIFF; ------------------ | | 208| 319|#define CANON_FLAG_ISO_ONLY_NON_TAUT_DIFF 0x0004 /* iOther: eq. partition in isotopic only non-taut differs from non-isotopic */ ------------------ 5694| 319| break; /* atoms so far found to be equivalent differ in isotopes; the canonicalization is needed */ 5695| 319| } 5696| 1.97k| } 5697| 594| } 5698| 0| else 5699| 0| { 5700| 0| i = num_atoms; 5701| 0| } 5702| | /* i = 0; *//* debug: force to call the canonicalization */ 5703| 594| if (i < num_atoms) ------------------ | Branch (5703:13): [True: 319, False: 275] ------------------ 5704| 319| { 5705| | /* we need canonicalization */ 5706| | /* get aux canonical ranking of the structure with isotopic non-tautomeric H */ 5707| | 5708| 319|#if ( USE_AUX_RANKING == 1 ) 5709| | /* refine no-taut-H partition according to non-taut H isotopic distribution */ 5710| 319| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5711| 4.33k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5711:25): [True: 4.01k, False: 319] ------------------ 5712| 4.01k| { 5713| 4.01k| pAtomInvariantAux[i].val[0] = nSymmRankNoTautH[i]; 5714| 4.01k| pAtomInvariantAux[i].iso_sort_key = iso_sort_key_NoTautH[i]; /* additional differentiation */ 5715| 4.01k| } 5716| | /* initial ranks for non-taut H isotopic distribution */ 5717| 319| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 5718| | /* make equitable */ 5719| 319| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 574| 319|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5720| 319| nNumCurrRanks, nRankAux, 5721| 319| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 5722| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 5723| 319| pCD[iOther].nAuxRank = nRankAux; 5724| 319|#endif 5725| | 5726| 319| ret = CanonGraph04( ic, pCG, ------------------ | | 601| 319|#define CanonGraph04 CanonGraph ------------------ 5727| 319| num_atoms, num_atoms, num_max, 1 /* digraph?? was 0 */, 5728| 319| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 574| 319|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5729| 319| nSymmRankNoTautHIso, nCanonRankNoTautHIso, nAtomNumberCanonNoTautHIso, 5730| 319| pCD + iOther, pCC, &Ct_NoTautH, &Ct_NoTautHIso, LargeMolecules ); 5731| 319| if (ret < 0) ------------------ | Branch (5731:17): [True: 0, False: 319] ------------------ 5732| 0| { 5733| 0| goto exit_error; 5734| 0| } 5735| | 5736| | /* in case of non-tautomeric structure the final results are in: 5737| | 5738| | nSymmRankNoTautHIso 5739| | nCanonRankNoTautHIso 5740| | nAtomNumberCanonNoTautHIso 5741| | Ct_NoTautHIso 5742| | iso_sort_key_NoTautH (original isotopic atom positions) 5743| | */ 5744| 319| } 5745| 275| else 5746| 275| { 5747| | /* copy the results of the previous (no taut H) canonicalization */ 5748| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 5749| 275| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1146| 275|#define inchi_calloc calloc ------------------ | Branch (5749:17): [True: 275, False: 0] ------------------ 5750| 275| CTableCreate( Ct_Temp, num_atoms, pCD + iOther )) ------------------ | Branch (5750:18): [True: 275, False: 0] ------------------ 5751| 275| { 5752| 275| CtFullCopy( Ct_Temp, Ct_NoTautH ); 5753| | /* since Ct_NoTautH does not have Ct_NoTautH->iso_sort_key we have to fill out Ct_Temp->iso_sort_key separately */ 5754| 1.50k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5754:29): [True: 1.23k, False: 275] ------------------ 5755| 1.23k| { 5756| 1.23k| Ct_Temp->iso_sort_key[nCanonRankNoTautH[i] - 1] = iso_sort_key_NoTautH[i]; 5757| 1.23k| } 5758| 275| Ct_Temp->len_iso_sort_key = num_atoms; 5759| 275| } 5760| 0| else 5761| 0| { 5762| 0| goto exit_error_alloc; 5763| 0| } 5764| 275| Ct_NoTautHIso = Ct_Temp; 5765| 275| Ct_Temp = NULL; 5766| 275| memcpy(nSymmRankNoTautHIso, nSymmRankNoTautH, num_atoms * sizeof(nSymmRankNoTautHIso[0])); 5767| 275| memcpy(nCanonRankNoTautHIso, nCanonRankNoTautH, num_atoms * sizeof(nCanonRankNoTautHIso[0])); 5768| 275| memcpy(nAtomNumberCanonNoTautHIso, nAtomNumberCanonNoTautH, num_atoms * sizeof(nAtomNumberCanonNoTautHIso[0])); 5769| 275| } 5770| | /* in case of non-tautomeric component this is the final result */ 5771| | /* i = CtFullCompare( Ct_NoTautHIso, Ct_Temp, num_atoms, 0, 0 );*/ 5772| 594| } 5773| | 5774| | 5775| 252k| if (bReqTaut) ------------------ | Branch (5775:9): [True: 40.8k, False: 211k] ------------------ 5776| 40.8k| { 5777| | /*****************************************************************************/ 5778| | /* Tautomeric Structure Canonicalizaton: */ 5779| | /* get base canonical numbering, connection table, and equivalence partition */ 5780| | /*****************************************************************************/ 5781| | /* find H atoms attached to non-tautomeric-endpoints and to tautomeric endpoints */ 5782| 40.8k| maxlenNumH = num_atoms + T_NUM_NO_ISOTOPIC*( num_at_tg - num_atoms ) + 1; /* including negative charges */ ------------------ | | 69| 40.8k|#define T_NUM_NO_ISOTOPIC 2 ------------------ 5783| 40.8k| nSymmRankBase = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankBase[0] ) ); ------------------ | | 1146| 40.8k|#define inchi_calloc calloc ------------------ 5784| 40.8k| nCanonRankBase = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankBase[0] ) ); ------------------ | | 1146| 40.8k|#define inchi_calloc calloc ------------------ 5785| 40.8k| nAtomNumberCanonBase = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonBase[0] ) ); ------------------ | | 1146| 40.8k|#define inchi_calloc calloc ------------------ 5786| 40.8k| numH = (NUM_H *) inchi_calloc( maxlenNumH, sizeof( numH[0] ) ); ------------------ | | 1146| 40.8k|#define inchi_calloc calloc ------------------ 5787| | 5788| 40.8k| if (!numH || !nSymmRankBase || !nCanonRankBase || !nAtomNumberCanonBase) ------------------ | Branch (5788:13): [True: 0, False: 40.8k] | Branch (5788:22): [True: 0, False: 40.8k] | Branch (5788:40): [True: 0, False: 40.8k] | Branch (5788:59): [True: 0, False: 40.8k] ------------------ 5789| 0| { 5790| 0| goto exit_error_alloc; 5791| 0| } 5792| | 5793| | /* non-tautomeric H counts */ 5794| 115k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5794:21): [True: 74.5k, False: 40.8k] ------------------ 5795| 74.5k| { 5796| 74.5k| numH[i] = ( !at_base[i].endpoint && at_base[i].num_H ) ? at_base[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 37| 3.90k|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 31| 3.90k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ numH[i] = ( !at_base[i].endpoint && at_base[i].num_H ) ? at_base[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 36| 145k|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 31| 70.6k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (5796:25): [True: 65.7k, False: 8.78k] | Branch (5796:49): [True: 3.90k, False: 61.8k] ------------------ 5797| 74.5k| } 5798| | 5799| | /* tautomeric H and negative charge counts */ 5800| 44.4k| for (i = k = num_atoms; i < num_at_tg; i++) ------------------ | Branch (5800:33): [True: 3.56k, False: 40.8k] ------------------ 5801| 3.56k| { 5802| 3.56k| m = i - num_atoms; 5803| 10.7k| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 69| 10.7k|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (5803:25): [True: 7.13k, False: 3.56k] ------------------ 5804| 7.13k| { 5805| | /* non-zeroes for j=1 are negative charge counts; T_NUM_NO_ISOTOPIC=2 entry per t-group */ 5806| 7.13k| numH[k++] = t_group_info->t_group[m].num[j] ? t_group_info->t_group[m].num[j] + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 37| 4.61k|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 31| 4.61k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ numH[k++] = t_group_info->t_group[m].num[j] ? t_group_info->t_group[m].num[j] + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 36| 9.65k|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 31| 2.51k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (5806:29): [True: 4.61k, False: 2.51k] ------------------ 5807| 7.13k| } 5808| 3.56k| } 5809| | 5810| | /* pointers */ 5811| 40.8k| pCD[iBase].LinearCT = NULL; 5812| 40.8k| pCD[iBase].NumH = numH; /* num_atoms non-tautomeric H; num_tg pairs of H and (-) in t-groups */ 5813| 40.8k| pCD[iBase].NumHfixed = NULL; 5814| 40.8k| pCD[iBase].iso_sort_key = NULL; 5815| 40.8k| pCD[iBase].iso_exchg_atnos = NULL; 5816| | 5817| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5818| | pCD[iBase].iso_sort_key_Hfixed = NULL; 5819| |#endif 5820| | 5821| | /* variables - unchanged */ 5822| 40.8k| pCD[iBase].ulTimeOutTime = pBCN->ulTimeOutTime; 5823| 40.8k| pCD[iBase].nMaxLenLinearCT = s[iBase].nLenCT + 1; 5824| 40.8k| pCD[iBase].maxlenNumH = maxlenNumH; 5825| | /* return values & input/output */ 5826| 40.8k| pCD[iBase].nLenLinearCT = s[iBase].nLenCT; 5827| 40.8k| pCD[iBase].nLenCTAtOnly = s[iBase].nLenCTAtOnly; 5828| 40.8k| pCD[iBase].lenNumH = lenNumH = k; 5829| 40.8k| pCD[iBase].lenNumHfixed = 0; 5830| 40.8k| pCD[iBase].len_iso_sort_key = 0; 5831| 40.8k| pCD[iBase].maxlen_iso_sort_key = 0; 5832| 40.8k| pCD[iBase].len_iso_exchg_atnos = 0; 5833| 40.8k| pCD[iBase].maxlen_iso_exchg_atnos = 0; 5834| | 5835| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5836| | pCD[iBase].len_iso_sort_key_Hfixed = 0; 5837| | pCD[iBase].maxlen_iso_sort_key_Hfixed = 0; 5838| |#endif 5839| | 5840| 40.8k| pCD[iBase].nAuxRank = NULL; 5841| | 5842| | /* make sure the initial partition is equitable (at this point t-groups do not have ranks yet) */ 5843| 40.8k| FillOutAtomInvariant2( at_base, 5844| 40.8k| num_atoms, 5845| 40.8k| num_at_tg, 5846| 40.8k| pAtomInvariant, 5847| 40.8k| 1 /*bIgnoreIsotopic*/, 5848| 40.8k| 0 /*bHydrogensInRanks*/, 5849| 40.8k| 0 /*bHydrogensFixedInRanks*/, 5850| 40.8k| 1 /*bTaut=bDigraph*/, 5851| 40.8k| 1 /* bTautGroupsOnly */, 5852| 40.8k| t_group_info ); 5853| | 5854| 115k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5854:21): [True: 74.5k, False: 40.8k] ------------------ 5855| 74.5k| { 5856| 74.5k| pAtomInvariant[i].val[0] = pBCN->pRankStack[0][i]; 5857| 74.5k| } 5858| | 5859| | /* initial ranks for t-group(s) only */ 5860| 40.8k| nNumCurrRanks = SetInitialRanks2( num_at_tg, pAtomInvariant, nRank, nAtomNumber, pCG ); 5861| | 5862| | /* make equitable, call digraph procedure; 5863| | pBCN->pRankStack[0] is nRank, pBCN->pRankStack[1] is nAtomNumber 5864| | This should only split ranks of tautomeric groups */ 5865| 40.8k| nNumCurrRanks = DifferentiateRanks4( pCG, num_at_tg, NeighList[TAUT_YES], ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5866| 40.8k| nNumCurrRanks, pBCN->pRankStack[0], nTempRank /* temp array */, 5867| 40.8k| pBCN->pRankStack[1], (AT_RANK) num_atoms, &lCount ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 5868| | 5869| 40.8k|#if ( USE_AUX_RANKING == 1 ) 5870| | /* refine no-H partition according to non-taut H distribution */ 5871| 40.8k| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5872| 115k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5872:21): [True: 74.5k, False: 40.8k] ------------------ 5873| 74.5k| { 5874| 74.5k| pAtomInvariantAux[i].val[0] = nSymmRankNoTautH[i]; 5875| 74.5k| pAtomInvariantAux[i].val[1] = numH[i]; /* additional differentiation */ 5876| 74.5k| } 5877| | /* 5878| | * djb-rwth: original badly written loop 5879| | for (j = i; i < num_at_tg; i++) 5880| | { 5881| | pAtomInvariantAux[i].val[0] = nRank[i]; 5882| | } 5883| | */ 5884| 44.4k| for (j = i; j < num_at_tg; j++) /* djb-rwth: corrected loop */ ------------------ | Branch (5884:21): [True: 3.56k, False: 40.8k] ------------------ 5885| 3.56k| { 5886| 3.56k| pAtomInvariantAux[j].val[0] = nRank[j]; 5887| 3.56k| } 5888| | /* initial ranks for t-group(s) */ 5889| 40.8k| nNumCurrRanks = SetInitialRanks2( num_at_tg, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 5890| | /* make equitable, call digraph procedure */ 5891| 40.8k| nNumCurrRanks = DifferentiateRanks4( pCG, num_at_tg, NeighList[TAUT_YES], ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5892| 40.8k| nNumCurrRanks, nRankAux, nTempRank /* temp array */, 5893| 40.8k| nAtomNumberAux, (AT_RANK) num_atoms, &lCount ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 5894| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 5895| 40.8k| pCD[iBase].nAuxRank = nRankAux; 5896| 40.8k|#endif 5897| | 5898| 40.8k| ret = CanonGraph05( ic, pCG, num_atoms, num_at_tg, num_max, 1 /* digraph*/, ------------------ | | 602| 40.8k|#define CanonGraph05 CanonGraph ------------------ 5899| 40.8k| NeighList[TAUT_YES], (Partition *) pBCN->pRankStack, ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5900| 40.8k| nSymmRankBase, nCanonRankBase, nAtomNumberCanonBase, 5901| 40.8k| pCD + iBase, pCC, &Ct_NoTautH, &Ct_Base, LargeMolecules ); 5902| 40.8k| if (ret < 0) ------------------ | Branch (5902:13): [True: 0, False: 40.8k] ------------------ 5903| 0| { 5904| 0| goto exit_error; 5905| 0| } 5906| | 5907| | /* tautomeric isotopic structure */ 5908| | /**************************************************************************************/ 5909| | /* Isotopic atoms and isotopic H atoms and isotopic tautomeric groups */ 5910| | /* get isotopic canonical numbering, connection table, and equivalence partition */ 5911| | /**************************************************************************************/ 5912| 40.8k| if ((s[iBase].num_isotopic_atoms && !s[iBase].bIgnoreIsotopic) || ------------------ | Branch (5912:14): [True: 800, False: 40.0k] | Branch (5912:45): [True: 800, False: 0] ------------------ 5913| 40.0k| (s[iBase].bHasIsotopicTautGroups && !bTautIgnoreIsotopic) || ------------------ | Branch (5913:15): [True: 91, False: 39.9k] | Branch (5913:50): [True: 91, False: 0] ------------------ 5914| 39.9k| (bUseIsoAuxBase[iBase] && !bTautIgnoreIsotopic)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5914:15): [True: 0, False: 39.9k] | Branch (5914:40): [True: 0, False: 0] ------------------ 5915| 891| { 5916| | 5917| 891| t_group_info->bIgnoreIsotopic = bTautIgnoreIsotopic; 5918| | 5919| 891| nSymmRankBaseIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankBaseIso[0] ) ); ------------------ | | 1146| 891|#define inchi_calloc calloc ------------------ 5920| 891| nCanonRankBaseIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankBaseIso[0] ) ); ------------------ | | 1146| 891|#define inchi_calloc calloc ------------------ 5921| 891| nAtomNumberCanonBaseIso = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonBaseIso[0] ) ); ------------------ | | 1146| 891|#define inchi_calloc calloc ------------------ 5922| 891| if (bUseIsoAuxBase[iBase]) ------------------ | Branch (5922:17): [True: 157, False: 734] ------------------ 5923| 157| { 5924| 157| maxlen_iso_exchg_atnos = num_max + 1; 5925| 157| iso_exchg_atnos = (S_CHAR *) inchi_calloc( maxlen_iso_exchg_atnos, sizeof( iso_exchg_atnos[0] ) ); ------------------ | | 1146| 157|#define inchi_calloc calloc ------------------ 5926| 157| } 5927| 891| maxlen_iso_sort_keyBase = num_max + 1; /* num_at_tg+1;*/ 5928| 891| iso_sort_keyBase = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_keyBase, sizeof( iso_sort_keyBase[0] ) ); ------------------ | | 1146| 891|#define inchi_calloc calloc ------------------ 5929| 891| if (!nSymmRankBaseIso || !nCanonRankBaseIso || !nAtomNumberCanonBaseIso || ------------------ | Branch (5929:17): [True: 0, False: 891] | Branch (5929:38): [True: 0, False: 891] | Branch (5929:60): [True: 0, False: 891] ------------------ 5930| 891| !iso_sort_keyBase || ------------------ | Branch (5930:18): [True: 0, False: 891] ------------------ 5931| 891| (maxlen_iso_exchg_atnos && !iso_exchg_atnos)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5931:19): [True: 157, False: 734] | Branch (5931:45): [True: 0, False: 157] ------------------ 5932| 0| { 5933| 0| goto exit_error_alloc; 5934| 0| } 5935| | /* atoms */ 5936| 891| num_iso_NoTautH = 0; 5937| 891| num_iso_NoAuxBase = 0; 5938| 891| if (iso_exchg_atnos) ------------------ | Branch (5938:17): [True: 157, False: 734] ------------------ 5939| 157| { 5940| 157| len_iso_exchg_atnos = num_at_tg; 5941| 157| } 5942| 7.03k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5942:25): [True: 6.14k, False: 891] ------------------ 5943| 6.14k| { 5944| 6.14k| if (at_base[i].endpoint || (iso_exchg_atnos && ( at_base[i].cFlags & AT_FLAG_ISO_H_POINT ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 50| 3.43k|#define AT_FLAG_ISO_H_POINT 0x01 /**< may have isotopic H */ ------------------ | Branch (5944:21): [True: 309, False: 5.83k] | Branch (5944:45): [True: 3.43k, False: 2.39k] | Branch (5944:64): [True: 241, False: 3.19k] ------------------ 5945| 550| { 5946| | /* tautomeric or may have exchangeable isotopic H */ 5947| 550| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, 0, 0, 0 ); 5948| 550| if (iso_exchg_atnos) ------------------ | Branch (5948:25): [True: 254, False: 296] ------------------ 5949| 254| { 5950| 254| num_iso_NoAuxBase += !at_base[i].endpoint; /* these non-taut atom may exchange isotopic H as tautomeric atoms do */ 5951| 254| } 5952| 550| } 5953| 5.59k| else 5954| 5.59k| { 5955| | /* non-mobile H */ 5956| 5.59k| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, at_base[i].num_iso_H[0], at_base[i].num_iso_H[1], at_base[i].num_iso_H[2] ); 5957| 5.59k| if (iso_exchg_atnos) ------------------ | Branch (5957:25): [True: 3.19k, False: 2.39k] ------------------ 5958| 3.19k| { 5959| 3.19k| iso_exchg_atnos[i] = 1; /* atom cannot have exchangable isotopic H atom(s) */ 5960| 3.19k| } 5961| 5.59k| } 5962| 6.14k| if (iso_sort_key) ------------------ | Branch (5962:21): [True: 886, False: 5.25k] ------------------ 5963| 886| { 5964| 886| num_iso_NoTautH++; 5965| 886| iso_sort_keyBase[i] = iso_sort_key; 5966| 886| } 5967| 5.25k| else 5968| 5.25k| { 5969| 5.25k| iso_sort_keyBase[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 38| 5.25k|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 5970| 5.25k| } 5971| 6.14k| } 5972| | 5973| | /* check marking and count of non-taut atoms that may exchange isotopic H -- debug only */ 5974| 891| if (iso_exchg_atnos) ------------------ | Branch (5974:17): [True: 157, False: 734] ------------------ 5975| 157| { 5976| 157| if (num_iso_NoAuxBase != t_group_info->nIsotopicEndpointAtomNumber[0]) ------------------ | Branch (5976:21): [True: 0, False: 157] ------------------ 5977| 0| { 5978| 0| ret = CT_ISOCOUNT_ERR; ------------------ | | 23| 0|#define CT_ISOCOUNT_ERR (CT_ERR_FIRST- 4) /*(-30004) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5979| 0| goto exit_error; 5980| 0| } 5981| 398| for (i = 1; i <= num_iso_NoAuxBase; i++) ------------------ | Branch (5981:29): [True: 241, False: 157] ------------------ 5982| 241| { 5983| 241| j = t_group_info->nIsotopicEndpointAtomNumber[i]; 5984| 241| if (at_base[j].endpoint || !( at_base[j].cFlags & AT_FLAG_ISO_H_POINT )) ------------------ | | 50| 241|#define AT_FLAG_ISO_H_POINT 0x01 /**< may have isotopic H */ ------------------ | Branch (5984:25): [True: 0, False: 241] | Branch (5984:48): [True: 0, False: 241] ------------------ 5985| 0| { 5986| 0| ret = CT_ISOCOUNT_ERR; ------------------ | | 23| 0|#define CT_ISOCOUNT_ERR (CT_ERR_FIRST- 4) /*(-30004) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5987| 0| goto exit_error; 5988| 0| } 5989| 241| } 5990| 157| } 5991| | 5992| | /* t-groups */ 5993| 891| num_iso_Base = 0; 5994| 891| if (iso_exchg_atnos) ------------------ | Branch (5994:17): [True: 157, False: 734] ------------------ 5995| 157| { 5996| 161| for (i = num_atoms; i < num_at_tg; i++) ------------------ | Branch (5996:37): [True: 4, False: 157] ------------------ 5997| 4| { 5998| 4| iso_sort_keyBase[i] = EMPTY_ISO_SORT_KEY; /* new mode: do not provide info about isotopic tautomeric H */ ------------------ | | 38| 4|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 5999| 4| } 6000| 157| } 6001| 734| else 6002| 734| { 6003| 878| for (i = num_atoms; i < num_at_tg; i++) ------------------ | Branch (6003:37): [True: 144, False: 734] ------------------ 6004| 144| { 6005| | /* should not happen anymore */ 6006| 144| m = i - num_atoms; 6007| 144| if ((iso_sort_key = t_group_info->t_group[m].iWeight)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6007:25): [True: 0, False: 144] ------------------ 6008| 0| { 6009| | /* old approach: each t-group has its own isotopic "weight" */ 6010| 0| num_iso_Base++; 6011| 0| iso_sort_keyBase[i] = iso_sort_key; 6012| 0| } 6013| 144| else 6014| 144| { 6015| 144| iso_sort_keyBase[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 38| 144|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 6016| 144| } 6017| 144| } 6018| 734| } 6019| | 6020| 891| if (!num_iso_NoAuxBase && iso_exchg_atnos) ------------------ | Branch (6020:17): [True: 734, False: 157] | Branch (6020:39): [True: 0, False: 734] ------------------ 6021| 0| { 6022| | /* all atoms that may exchange isotopic H are either tautomeric or not present */ 6023| 0| inchi_free( iso_exchg_atnos ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6024| 0| iso_exchg_atnos = NULL; 6025| 0| len_iso_exchg_atnos = 0; 6026| 0| maxlen_iso_exchg_atnos = 0; 6027| 0| } 6028| | 6029| 891| if (!num_iso_NoTautH && !num_iso_Base && iso_sort_keyBase) ------------------ | Branch (6029:17): [True: 91, False: 800] | Branch (6029:37): [True: 91, False: 0] | Branch (6029:54): [True: 91, False: 0] ------------------ 6030| 91| { 6031| | /* no isotopic atoms present */ 6032| 91| inchi_free( iso_sort_keyBase ); ------------------ | | 1152| 91|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 91, False: 0] | | | Branch (1152:50): [Folded, False: 91] | | ------------------ ------------------ 6033| 91| iso_sort_keyBase = NULL; 6034| 91| maxlen_iso_sort_keyBase = 0; 6035| 91| } 6036| 800| else 6037| 800| { 6038| 800| len_iso_sort_keyBase = num_at_tg; 6039| 800| } 6040| | 6041| 891| if (!iso_exchg_atnos && !iso_sort_keyBase) ------------------ | Branch (6041:17): [True: 734, False: 157] | Branch (6041:37): [True: 30, False: 704] ------------------ 6042| 30| { 6043| | /* no isotopic part at all or only tautomeric groups */ 6044| 30| inchi_free( nSymmRankBaseIso ); nSymmRankBaseIso = NULL; ------------------ | | 1152| 30|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 30, False: 0] | | | Branch (1152:50): [Folded, False: 30] | | ------------------ ------------------ 6045| 30| inchi_free( nCanonRankBaseIso ); nCanonRankBaseIso = NULL; ------------------ | | 1152| 30|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 30, False: 0] | | | Branch (1152:50): [Folded, False: 30] | | ------------------ ------------------ 6046| 30| inchi_free( nAtomNumberCanonBaseIso ); nAtomNumberCanonBaseIso = NULL; ------------------ | | 1152| 30|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 30, False: 0] | | | Branch (1152:50): [Folded, False: 30] | | ------------------ ------------------ 6047| 30| } 6048| 861| else 6049| 861| { 6050| | /* proceed with tautomeric isotopic canonicalization */ 6051| | /* pointers */ 6052| 861| pCD[iBase].LinearCT = NULL; 6053| 861| pCD[iBase].NumH = numH; /* num_atoms non-tautomeric H; num_tg pairs of H and (-) in t-groups */ 6054| 861| pCD[iBase].NumHfixed = NULL; 6055| 861| pCD[iBase].iso_sort_key = iso_sort_keyBase; 6056| 861| pCD[iBase].iso_exchg_atnos = iso_exchg_atnos; 6057| | 6058| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6059| | pCD[iBase].iso_sort_key_Hfixed = NULL; 6060| |#endif 6061| | 6062| | /* variables - unchanged */ 6063| 861| pCD[iBase].ulTimeOutTime = pBCN->ulTimeOutTime; 6064| 861| pCD[iBase].nMaxLenLinearCT = s[iBase].nLenCT + 1; 6065| 861| pCD[iBase].maxlenNumH = maxlenNumH; 6066| | /* return values & input/output */ 6067| 861| pCD[iBase].nLenLinearCT = s[iBase].nLenCT; 6068| 861| pCD[iBase].nLenCTAtOnly = s[iBase].nLenCTAtOnly; 6069| 861| pCD[iBase].lenNumH = lenNumH /* = k */; 6070| 861| pCD[iBase].lenNumHfixed = 0; 6071| 861| pCD[iBase].len_iso_sort_key = len_iso_sort_keyBase; 6072| 861| pCD[iBase].maxlen_iso_sort_key = maxlen_iso_sort_keyBase; 6073| 861| pCD[iBase].len_iso_exchg_atnos = len_iso_exchg_atnos; 6074| 861| pCD[iBase].maxlen_iso_exchg_atnos = maxlen_iso_exchg_atnos; 6075| | 6076| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6077| | pCD[iBase].len_iso_sort_key_Hfixed = 0; 6078| | pCD[iBase].maxlen_iso_sort_key_Hfixed = 0; 6079| |#endif 6080| | 6081| 861| pCD[iBase].nAuxRank = NULL; 6082| | 6083| 861| if (num_iso_NoTautH || num_iso_Base || num_iso_NoAuxBase) ------------------ | Branch (6083:21): [True: 800, False: 61] | Branch (6083:40): [True: 0, False: 61] | Branch (6083:56): [True: 61, False: 0] ------------------ 6084| 861| { 6085| | /* check whether we need actual canonicalization */ 6086| 861| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6087| 6.90k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6087:33): [True: 6.04k, False: 861] ------------------ 6088| 6.04k| { 6089| 6.04k| if (nTempRank[nSymmRankBase[i] - 1] < i) ------------------ | Branch (6089:29): [True: 5.18k, False: 861] ------------------ 6090| 5.18k| { 6091| 5.18k| nTempRank[nSymmRankBase[i] - 1] = i; /* greatest class representative */ 6092| 5.18k| } 6093| 6.04k| } 6094| 2.99k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6094:33): [True: 2.24k, False: 754] ------------------ 6095| 2.24k| { 6096| 2.24k| if (( iso_sort_keyBase ? ( iso_sort_keyBase[i] != iso_sort_keyBase[nTempRank[nSymmRankBase[i] - 1]] ) : 0 ) || ------------------ | Branch (6096:29): [True: 75, False: 2.16k] | Branch (6096:31): [True: 1.83k, False: 404] ------------------ 6097| 2.16k| ( iso_exchg_atnos ? ( iso_exchg_atnos[i] != iso_exchg_atnos[nTempRank[nSymmRankBase[i] - 1]] ) : 0 )) ------------------ | Branch (6097:29): [True: 32, False: 2.13k] | Branch (6097:31): [True: 933, False: 1.23k] ------------------ 6098| 107| { 6099| 107| pCD[iBase].nCanonFlags |= CANON_FLAG_ISO_TAUT_DIFF; ------------------ | | 209| 107|#define CANON_FLAG_ISO_TAUT_DIFF 0x0008 /* iBase: isotopic eq. partition in isotopic taut differs from non-isotopic taut */ ------------------ 6100| 107| break; /* atoms so far found to be equivalent have different number of H; the canonicalization is needed */ 6101| 107| } 6102| 2.24k| } 6103| 861| } 6104| 0| else 6105| 0| { 6106| 0| i = num_at_tg; /* should not happen */ 6107| 0| } 6108| | 6109| | /* i = 0; *//* debug: force to call the canonicalization */ 6110| | 6111| 861| if (i < num_at_tg) ------------------ | Branch (6111:21): [True: 107, False: 754] ------------------ 6112| 107| { 6113| | /* we need canonicalization */ 6114| | /* get aux canonical ranking of the structure with isotopic non-tautomeric H */ 6115| | 6116| 107|#if ( USE_AUX_RANKING == 1 ) 6117| | /* refine no-taut-H partition according to non-taut H + t-groups isotopic distribution */ 6118| 107| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6119| 4.18k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6119:33): [True: 4.08k, False: 107] ------------------ 6120| 4.08k| { 6121| 4.08k| pAtomInvariantAux[i].val[0] = nSymmRankBase[i]; 6122| 4.08k| pAtomInvariantAux[i].iso_sort_key = iso_sort_keyBase ? iso_sort_keyBase[i] : 0; /* additional differentiation */ ------------------ | Branch (6122:61): [True: 3.81k, False: 269] ------------------ 6123| 4.08k| pAtomInvariantAux[i].iso_aux_key = iso_exchg_atnos ? iso_exchg_atnos[i] : 0; ------------------ | Branch (6123:60): [True: 2.65k, False: 1.42k] ------------------ 6124| 4.08k| } 6125| | /* initial ranks for non-taut H isotopic distribution */ 6126| 107| nNumCurrRanks = SetInitialRanks2( num_at_tg, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 6127| | /* make equitable, not a digraph procedure */ 6128| 107| nNumCurrRanks = DifferentiateRanks2( pCG, num_at_tg, NeighList[TAUT_YES], ------------------ | | 575| 107|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6129| 107| nNumCurrRanks, nRankAux, 6130| 107| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means first use qsort */ ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 6131| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 6132| 107| pCD[iBase].nAuxRank = nRankAux; 6133| 107|#endif 6134| | 6135| 107| ret = CanonGraph06( ic, pCG, num_atoms, num_at_tg, num_max, 1 /* digraph */, ------------------ | | 603| 107|#define CanonGraph06 CanonGraph ------------------ 6136| 107| NeighList[TAUT_YES], (Partition *) pBCN->pRankStack, ------------------ | | 575| 107|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6137| 107| nSymmRankBaseIso, nCanonRankBaseIso, nAtomNumberCanonBaseIso, 6138| 107| pCD + iBase, pCC, &Ct_Base, &Ct_BaseIso, LargeMolecules ); 6139| 107| if (ret < 0) ------------------ | Branch (6139:25): [True: 0, False: 107] ------------------ 6140| 0| { 6141| 0| goto exit_error; 6142| 0| } 6143| | /* in case of a tautomeric structure the final results are in: 6144| | 6145| | nSymmRankBaseIso 6146| | nCanonRankBaseIso 6147| | nAtomNumberCanonBaseIso 6148| | Ct_BaseIso 6149| | iso_sort_keyBase (original isotopic atom & t-group positions) 6150| | Ct_BaseIso->iso_exchg_atnos: 0=>can exchange isotopic H, including tautomeric atoms 6151| | iso_exchg_atnos : same, in order of t_group_info->nIsotopicEndpointAtomNumber[] 6152| | */ 6153| 107| } 6154| 754| else 6155| 754| { 6156| | /* copy the results of the previous (no taut H) canonicalization */ 6157| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 6158| 754| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1146| 754|#define inchi_calloc calloc ------------------ | Branch (6158:25): [True: 754, False: 0] ------------------ 6159| 754| CTableCreate( Ct_Temp, num_atoms, pCD + iBase )) ------------------ | Branch (6159:26): [True: 754, False: 0] ------------------ 6160| 754| { 6161| 754| CtFullCopy( Ct_Temp, Ct_Base ); 6162| | /* since Ct_Base does not have Ct_Base->iso_sort_key we 6163| | have to fill out Ct_Temp->iso_sort_key separately */ 6164| 754| if (iso_sort_keyBase) ------------------ | Branch (6164:29): [True: 698, False: 56] ------------------ 6165| 698| { 6166| 2.26k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6166:41): [True: 1.57k, False: 698] ------------------ 6167| 1.57k| { 6168| 1.57k| Ct_Temp->iso_sort_key[nCanonRankBase[i] - 1] = iso_sort_keyBase[i]; 6169| 1.57k| } 6170| 698| Ct_Temp->len_iso_sort_key = num_at_tg; 6171| 698| } 6172| 56| else 6173| 56| { 6174| 56| Ct_Temp->len_iso_sort_key = 0; 6175| 56| } 6176| 754| if (iso_exchg_atnos) ------------------ | Branch (6176:29): [True: 97, False: 657] ------------------ 6177| 97| { 6178| 894| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6178:41): [True: 797, False: 97] ------------------ 6179| 797| { 6180| 797| Ct_Temp->iso_exchg_atnos[nCanonRankBase[i] - 1] = iso_exchg_atnos[i]; 6181| 797| } 6182| 97| Ct_Temp->len_iso_exchg_atnos = num_at_tg; 6183| 97| } 6184| 657| else 6185| 657| { 6186| 657| Ct_Temp->len_iso_exchg_atnos = 0; 6187| 657| } 6188| 754| } 6189| 0| else 6190| 0| { 6191| 0| goto exit_error_alloc; 6192| 0| } 6193| 754| Ct_BaseIso = Ct_Temp; 6194| 754| Ct_Temp = NULL; 6195| 754| memcpy(nSymmRankBaseIso, nSymmRankBase, num_at_tg * sizeof(nSymmRankBaseIso[0])); 6196| 754| memcpy(nCanonRankBaseIso, nCanonRankBase, num_at_tg * sizeof(nCanonRankBaseIso[0])); 6197| 754| memcpy(nAtomNumberCanonBaseIso, nAtomNumberCanonBase, num_at_tg * sizeof(nAtomNumberCanonBaseIso[0])); 6198| 754| } 6199| | /* in case of non-tautomeric component this is the final result */ 6200| | /* i = CtFullCompare( Ct_BaseIso, Ct_Temp, num_at_tg, 0, 0 );*/ 6201| | 6202| 861| t_group_info->bIgnoreIsotopic = 1; 6203| 861| } 6204| 891| } 6205| 40.8k| } 6206| | 6207| | /**********************************************************************************/ 6208| | /* get "fixed H" canonical numbering, connection table, and equivalence partition */ 6209| | /**********************************************************************************/ 6210| | 6211| 252k| if (bReqTaut && bReqNonTaut) ------------------ | Branch (6211:9): [True: 40.8k, False: 211k] | Branch (6211:21): [True: 36.3k, False: 4.50k] ------------------ 6212| 36.3k| { 6213| 36.3k| maxlenNumHfixed = num_atoms + 1; 6214| 36.3k| nSymmRankFixH = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankFixH[0] ) ); ------------------ | | 1146| 36.3k|#define inchi_calloc calloc ------------------ 6215| 36.3k| nCanonRankFixH = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankFixH[0] ) ); ------------------ | | 1146| 36.3k|#define inchi_calloc calloc ------------------ 6216| 36.3k| nAtomNumberCanonFixH = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonFixH[0] ) ); ------------------ | | 1146| 36.3k|#define inchi_calloc calloc ------------------ 6217| 36.3k| NumHfixed = (NUM_H *) inchi_calloc( maxlenNumHfixed, sizeof( NumHfixed[0] ) ); ------------------ | | 1146| 36.3k|#define inchi_calloc calloc ------------------ 6218| 36.3k| if (!NumHfixed || !nSymmRankFixH || !nCanonRankFixH || !nAtomNumberCanonFixH) ------------------ | Branch (6218:13): [True: 0, False: 36.3k] | Branch (6218:27): [True: 0, False: 36.3k] | Branch (6218:45): [True: 0, False: 36.3k] | Branch (6218:64): [True: 0, False: 36.3k] ------------------ 6219| 0| { 6220| 0| goto exit_error_alloc; 6221| 0| } 6222| 80.4k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6222:21): [True: 44.0k, False: 36.3k] ------------------ 6223| 44.0k| { 6224| | /* fixed and non-tautomeric H different in taut and non-taut structures */ 6225| | 6226| 44.0k| if (at_base[i].endpoint) ------------------ | Branch (6226:17): [True: 2.54k, False: 41.4k] ------------------ 6227| 2.54k| { 6228| 2.54k| NumHfixed[i] = at_other[i].num_H ? at_other[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 37| 818|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 31| 818|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ NumHfixed[i] = at_other[i].num_H ? at_other[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 36| 4.26k|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 31| 1.72k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (6228:32): [True: 818, False: 1.72k] ------------------ 6229| 2.54k| } 6230| 41.4k| else if (at_other[i].num_H != at_base[i].num_H) ------------------ | Branch (6230:22): [True: 539, False: 40.9k] ------------------ 6231| 539| { 6232| 539| NumHfixed[i] = (NUM_H) at_other[i].num_H - (NUM_H) at_base[i].num_H + BASE_H_NUMBER; ------------------ | | 37| 539|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 31| 539|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ 6233| 539| } 6234| 40.9k| else 6235| 40.9k| { 6236| 40.9k| NumHfixed[i] = EMPTY_H_NUMBER; ------------------ | | 36| 40.9k|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 31| 40.9k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ 6237| 40.9k| } 6238| 44.0k| } 6239| | 6240| | /* pointers */ 6241| 36.3k| pCD[iOther].LinearCT = NULL; /* LinearCT; */ 6242| 36.3k| pCD[iOther].NumH = numHNoTautH; 6243| 36.3k| pCD[iOther].NumHfixed = NumHfixed;/* variables - unchanged */ 6244| 36.3k| pCD[iOther].iso_sort_key = NULL; 6245| 36.3k| pCD[iOther].iso_exchg_atnos = NULL; 6246| | 6247| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6248| | pCD[iOther].iso_sort_key_Hfixed = NULL; 6249| |#endif 6250| | 6251| 36.3k| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 6252| 36.3k| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 6253| 36.3k| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 6254| 36.3k| pCD[iOther].maxlenNumHfixed = maxlenNumHfixed; 6255| | /* return values & input/output */ 6256| 36.3k| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 6257| 36.3k| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 6258| 36.3k| pCD[iOther].lenNumH = num_atoms; /* djb-rwth: removing redundant code */ 6259| 36.3k| pCD[iOther].lenNumHfixed = num_atoms; 6260| 36.3k| pCD[iOther].len_iso_sort_key = 0; 6261| 36.3k| pCD[iOther].maxlen_iso_sort_key = 0; 6262| 36.3k| pCD[iOther].len_iso_exchg_atnos = 0; 6263| 36.3k| pCD[iOther].maxlen_iso_exchg_atnos = 0; 6264| | 6265| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6266| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 6267| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 6268| |#endif 6269| | 6270| 36.3k| pCD[iOther].nAuxRank = NULL; 6271| | 6272| 36.3k|#if ( USE_AUX_RANKING == 1 ) 6273| 36.3k| if (!nRankAux) ------------------ | Branch (6273:13): [True: 0, False: 36.3k] ------------------ 6274| 0| { 6275| 0| nRankAux = (AT_RANK *) inchi_calloc( num_max, sizeof( nRankAux[0] ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 6276| 0| } 6277| 36.3k| if (!nAtomNumberAux) ------------------ | Branch (6277:13): [True: 0, False: 36.3k] ------------------ 6278| 0| { 6279| 0| nAtomNumberAux = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberAux[0] ) ); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 6280| 0| } 6281| 36.3k| if (!pAtomInvariantAux) ------------------ | Branch (6281:13): [True: 0, False: 36.3k] ------------------ 6282| 0| { 6283| 0| pAtomInvariantAux = (ATOM_INVARIANT2 *) inchi_malloc( num_max * sizeof( pAtomInvariantAux[0] ) ); ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 6284| 0| } 6285| 36.3k| if (!nRankAux || !nAtomNumberAux || !pAtomInvariantAux) ------------------ | Branch (6285:13): [True: 0, False: 36.3k] | Branch (6285:26): [True: 0, False: 36.3k] | Branch (6285:45): [True: 0, False: 36.3k] ------------------ 6286| 0| { 6287| 0| goto exit_error_alloc; 6288| 0| } 6289| | 6290| | /* refine no-H partition according to non-taut H distribution */ 6291| 36.3k| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6292| 80.4k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6292:21): [True: 44.0k, False: 36.3k] ------------------ 6293| 44.0k| { 6294| 44.0k| pAtomInvariantAux[i].val[0] = nSymmRankBase[i]; 6295| 44.0k| pAtomInvariantAux[i].val[1] = NumHfixed[i]; /* additional differentiation */ 6296| 44.0k| } 6297| | 6298| | /* initial ranks for t-group(s) */ 6299| 36.3k| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 6300| | 6301| | /* make equitable, digraph procedure */ 6302| 36.3k| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6303| 36.3k| nNumCurrRanks, nRankAux, 6304| 36.3k| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 6305| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 6306| 36.3k| pCD[iOther].nAuxRank = nRankAux; 6307| 36.3k|#endif 6308| | 6309| 36.3k| ret = CanonGraph07( ic, pCG, num_atoms, num_atoms, num_max, 0, ------------------ | | 604| 36.3k|#define CanonGraph07 CanonGraph ------------------ 6310| 36.3k| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6311| 36.3k| nSymmRankFixH, nCanonRankFixH, nAtomNumberCanonFixH, 6312| 36.3k| pCD + iOther, pCC, &Ct_NoTautH, &Ct_FixH, LargeMolecules ); 6313| 36.3k| if (ret < 0) ------------------ | Branch (6313:13): [True: 0, False: 36.3k] ------------------ 6314| 0| { 6315| 0| goto exit_error; 6316| 0| } 6317| | 6318| | /*******************************************************************************************/ 6319| | /* get "fixed H" isotopic canonical numbering, connection table, and equivalence partition */ 6320| | /*******************************************************************************************/ 6321| 36.3k| iflag = (s[iBase].num_isotopic_atoms && !s[iBase].bIgnoreIsotopic) || ------------------ | Branch (6321:18): [True: 643, False: 35.7k] | Branch (6321:49): [True: 643, False: 0] ------------------ 6322| 35.7k| (s[iBase].bHasIsotopicTautGroups && !bTautIgnoreIsotopic); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6322:14): [True: 20, False: 35.7k] | Branch (6322:49): [True: 20, False: 0] ------------------ 6323| 36.3k| if (bFixIsoFixedH) /* #if ( FIX_ISO_FIXEDH_BUG == 1 ) */ ------------------ | Branch (6323:13): [True: 36.3k, False: 0] ------------------ 6324| | /* fix bug when iso H was removed as a proton and fixed-H isotopic layer is missing - 2008-09-24 DT*/ 6325| 36.3k| { 6326| 36.3k| iflag = iflag || (s[iOther].num_isotopic_atoms && !s[iOther].bIgnoreIsotopic); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6326:21): [True: 663, False: 35.7k] | Branch (6326:31): [True: 4, False: 35.7k] | Branch (6326:63): [True: 4, False: 0] ------------------ 6327| 36.3k| } 6328| 36.3k| if (iflag) ------------------ | Branch (6328:13): [True: 667, False: 35.7k] ------------------ 6329| 667| { 6330| | 6331| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6332| | maxlen_iso_sort_key_Hfixed = 6333| |#endif 6334| 667| maxlen_iso_sort_key_NoTautH = num_atoms + 1; 6335| 667| nSymmRankFixHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankFixHIso[0] ) ); ------------------ | | 1146| 667|#define inchi_calloc calloc ------------------ 6336| 667| nCanonRankFixHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankFixHIso[0] ) ); ------------------ | | 1146| 667|#define inchi_calloc calloc ------------------ 6337| 667| nAtomNumberCanonFixHIso = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonFixHIso[0] ) ); ------------------ | | 1146| 667|#define inchi_calloc calloc ------------------ 6338| | 6339| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6340| | iso_sort_key_Hfixed = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_key_Hfixed, sizeof( iso_sort_key_Hfixed[0] ) ); 6341| |#endif 6342| | 6343| 667| iso_sort_key_NoTautH = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_key_NoTautH, sizeof( iso_sort_key_NoTautH[0] ) ); ------------------ | | 1146| 667|#define inchi_calloc calloc ------------------ 6344| | 6345| 667| if (!nSymmRankFixHIso || !nCanonRankFixHIso || !nAtomNumberCanonFixHIso || ------------------ | Branch (6345:17): [True: 0, False: 667] | Branch (6345:38): [True: 0, False: 667] | Branch (6345:60): [True: 0, False: 667] ------------------ 6346| | 6347| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6348| | !iso_sort_key_Hfixed || 6349| |#endif 6350| | 6351| 667| !iso_sort_key_NoTautH) ------------------ | Branch (6351:18): [True: 0, False: 667] ------------------ 6352| 0| { 6353| 0| goto exit_error_alloc; 6354| 0| } 6355| | 6356| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6357| | /* fill out isotopic non-tautomeric keys */ 6358| | for (i = 0; i < num_atoms; i++) 6359| | { 6360| | if (at_base[i].endpoint) 6361| | { 6362| | iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, 0, 0, 0 ); 6363| | iso_sort_key2 = make_iso_sort_key( 0, at_base[i].num_iso_H[0], at_base[i].num_iso_H[1], at_base[i].num_iso_H[2] ); 6364| | } 6365| | else 6366| | { 6367| | iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, at_base[i].num_iso_H[0], at_base[i].num_iso_H[1], at_base[i].num_iso_H[2] ); 6368| | iso_sort_key2 = 0; 6369| | } 6370| | if (iso_sort_key) 6371| | { 6372| | iso_sort_key_NoTautH[i] = iso_sort_key; 6373| | num_iso_NoTautH++; 6374| | } 6375| | else 6376| | { 6377| | iso_sort_key_NoTautH[i] = EMPTY_ISO_SORT_KEY; 6378| | } 6379| | if (iso_sort_key2) 6380| | { 6381| | num_iso_Hfixed++; 6382| | iso_sort_key_Hfixed[i] = iso_sort_key2; 6383| | } 6384| | else 6385| | { 6386| | iso_sort_key_Hfixed[i] = EMPTY_ISO_SORT_KEY; 6387| | } 6388| | } 6389| |#else 6390| | /* fill out isotopic non-tautomeric keys */ 6391| 1.99k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6391:25): [True: 1.32k, False: 667] ------------------ 6392| 1.32k| { 6393| | 6394| 1.32k| if (bFixIsoFixedH) /* #if ( FIX_ISO_FIXEDH_BUG == 1 ) */ ------------------ | Branch (6394:21): [True: 1.32k, False: 0] ------------------ 6395| 1.32k| { 6396| | /* fix bug when iso H was removed as a proton and fixed-H isotopic layer is missing - 2008-09-24 DT*/ 6397| 1.32k| if (at_other) ------------------ | Branch (6397:25): [True: 1.32k, False: 0] ------------------ 6398| 1.32k| { 6399| 1.32k| iso_sort_key = make_iso_sort_key( at_other[i].iso_atw_diff, at_other[i].num_iso_H[0], at_other[i].num_iso_H[1], at_other[i].num_iso_H[2] ); 6400| 1.32k| } 6401| 0| else 6402| 0| { 6403| 0| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, at_base[i].num_iso_H[0], at_base[i].num_iso_H[1], at_base[i].num_iso_H[2] ); 6404| 0| } 6405| 1.32k| } 6406| 0| else 6407| 0| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, at_base[i].num_iso_H[0], at_base[i].num_iso_H[1], at_base[i].num_iso_H[2] ); 6408| | 6409| 1.32k| if (iso_sort_key) ------------------ | Branch (6409:21): [True: 675, False: 654] ------------------ 6410| 675| { 6411| 675| iso_sort_key_NoTautH[i] = iso_sort_key; 6412| 675| num_iso_NoTautH++; 6413| 675| } 6414| 654| else 6415| 654| { 6416| 654| iso_sort_key_NoTautH[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 38| 654|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 6417| 654| } 6418| 1.32k| } 6419| 667|#endif 6420| | 6421| | /* pointers */ 6422| 667| pCD[iOther].LinearCT = NULL; /* LinearCT; */ 6423| 667| pCD[iOther].NumH = numHNoTautH; 6424| 667| pCD[iOther].NumHfixed = NumHfixed;/* variables - unchanged */ 6425| 667| pCD[iOther].iso_sort_key = iso_sort_key_NoTautH; 6426| 667| pCD[iOther].iso_exchg_atnos = NULL; 6427| | 6428| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6429| | pCD[iOther].iso_sort_key_Hfixed = iso_sort_key_Hfixed; 6430| |#endif 6431| | 6432| 667| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 6433| 667| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 6434| 667| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 6435| 667| pCD[iOther].maxlenNumHfixed = maxlenNumHfixed; 6436| | /* return values & input/output */ 6437| 667| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 6438| 667| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 6439| 667| pCD[iOther].lenNumH = num_atoms; /* djb-rwth: removing redundant code */ 6440| 667| pCD[iOther].lenNumHfixed = num_atoms; 6441| 667| pCD[iOther].len_iso_sort_key = len_iso_sort_key_NoTautH = num_atoms; 6442| 667| pCD[iOther].maxlen_iso_sort_key = maxlen_iso_sort_key_NoTautH; 6443| 667| pCD[iOther].len_iso_exchg_atnos = 0; 6444| 667| pCD[iOther].maxlen_iso_exchg_atnos = 0; 6445| | 6446| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6447| | pCD[iOther].len_iso_sort_key_Hfixed = len_iso_sort_key_Hfixed = num_atoms; 6448| | pCD[iOther].maxlen_iso_sort_key_Hfixed = maxlen_iso_sort_key_Hfixed; 6449| |#endif 6450| | 6451| 667| pCD[iOther].nAuxRank = NULL; 6452| | 6453| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6454| | if (num_iso_Hfixed || num_iso_NoTautH) 6455| |#else 6456| 667| if (num_iso_NoTautH) ------------------ | Branch (6456:17): [True: 666, False: 1] ------------------ 6457| 666|#endif 6458| | 6459| 666| { 6460| | /* check whether we need NoTautH cononicalization */ 6461| 666| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6462| 1.99k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6462:29): [True: 1.32k, False: 666] ------------------ 6463| 1.32k| { 6464| 1.32k| if (nTempRank[nSymmRankFixH[i] - 1] < i) ------------------ | Branch (6464:25): [True: 661, False: 666] ------------------ 6465| 661| { 6466| 661| nTempRank[nSymmRankFixH[i] - 1] = i; /* greatest class representative */ 6467| 661| } 6468| 1.32k| } 6469| 1.63k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6469:29): [True: 1.00k, False: 629] ------------------ 6470| 1.00k| { 6471| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6472| | if (iso_sort_key_Hfixed[i] != iso_sort_key_Hfixed[nTempRank[nSymmRankFixH[i] - 1]]) 6473| | break; 6474| |#endif 6475| 1.00k| if (iso_sort_key_NoTautH[i] != iso_sort_key_NoTautH[nTempRank[nSymmRankFixH[i] - 1]]) ------------------ | Branch (6475:25): [True: 37, False: 964] ------------------ 6476| 37| break; /* atoms so far found to be equivalent have different isotopic shifts; the canonicalization is needed */ 6477| 1.00k| } 6478| 666| } 6479| 1| else 6480| 1| { 6481| 1| i = num_atoms; /* should not happen */ 6482| 1| } 6483| | 6484| | /* i = 0; *//* debug: force to call the canonicalization */ 6485| | 6486| 667| if (i < num_atoms) ------------------ | Branch (6486:17): [True: 37, False: 630] ------------------ 6487| 37| { 6488| 37| pCD[iOther].nCanonFlags |= CANON_FLAG_ISO_FIXED_H_DIFF; ------------------ | | 210| 37|#define CANON_FLAG_ISO_FIXED_H_DIFF 0x0010 /* iOther: isotopic eq. partition in fixed H non-taut differs from non-isotopic fixed H */ ------------------ 6489| | /* we need canonicalization */ 6490| | /* get aux canonical ranking of the structure with isotopic non-tautomeric H */ 6491| | 6492| 37|#if ( USE_AUX_RANKING == 1 ) 6493| | /* refine fixed-taut-H partition according to the isotopic distribution */ 6494| 37| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6495| 458| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6495:29): [True: 421, False: 37] ------------------ 6496| 421| { 6497| 421| pAtomInvariantAux[i].val[0] = nSymmRankFixH[i]; 6498| | 6499| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6500| | iso_sort_key = 0; 6501| | if (iso_sort_key_NoTautH[i] != EMPTY_ISO_SORT_KEY) 6502| | iso_sort_key |= iso_sort_key_NoTautH[i]; 6503| | if (iso_sort_key_Hfixed[i] != EMPTY_ISO_SORT_KEY) 6504| | iso_sort_key |= iso_sort_key_Hfixed[i]; 6505| | if (!iso_sort_key) 6506| | iso_sort_key = EMPTY_ISO_SORT_KEY; 6507| |#else 6508| 421| iso_sort_key = iso_sort_key_NoTautH[i]; 6509| 421|#endif 6510| | 6511| 421| pAtomInvariantAux[i].iso_sort_key = iso_sort_key; /* additional differentiation */ 6512| 421| } 6513| | 6514| | /* initial ranks for non-taut H isotopic distribution */ 6515| 37| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 6516| | /* make equitable, digraph procedure */ 6517| 37| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 574| 37|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6518| 37| nNumCurrRanks, nRankAux, 6519| 37| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 6520| | 6521| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 6522| 37| pCD[iOther].nAuxRank = nRankAux; 6523| 37|#endif 6524| | 6525| 37| ret = CanonGraph08( ic, pCG, num_atoms, num_atoms, num_max, 1 /* digraph?? was 0 */, ------------------ | | 605| 37|#define CanonGraph08 CanonGraph ------------------ 6526| 37| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 574| 37|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6527| 37| nSymmRankFixHIso, nCanonRankFixHIso, nAtomNumberCanonFixHIso, 6528| 37| pCD + iOther, pCC, &Ct_FixH, &Ct_FixHIso, LargeMolecules ); 6529| 37| if (ret < 0) ------------------ | Branch (6529:21): [True: 0, False: 37] ------------------ 6530| 0| { 6531| 0| goto exit_error; 6532| 0| } 6533| | /* in case of non-tautomeric structure the final results are in: 6534| | 6535| | nSymmRankFixHIso 6536| | nCanonRankFixHIso 6537| | nAtomNumberCanonFixHIso 6538| | Ct_FixHIso 6539| | iso_sort_keyBase ([0..num_atoms] original isotopic atom positions) 6540| | iso_sort_key_Hfixed (original fixed tautomeric H distribution) 6541| | */ 6542| 37| } 6543| 630| else 6544| 630| { 6545| | /* copy the results of the previous (no taut H) canonicalization */ 6546| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 6547| 630| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1146| 630|#define inchi_calloc calloc ------------------ | Branch (6547:21): [True: 630, False: 0] ------------------ 6548| 630| CTableCreate( Ct_Temp, num_atoms, pCD + iOther )) ------------------ | Branch (6548:22): [True: 630, False: 0] ------------------ 6549| 630| { 6550| 630| CtFullCopy( Ct_Temp, Ct_FixH ); 6551| | /* since Ct_FixH does not have Ct_FixH->iso_sort_key and Ct_FixH->iso_sort_key_Hfixed we 6552| | have to fill out Ct_Temp->iso_sort_key and Ct_Temp->iso_sort_key_Hfixed separately */ 6553| 1.53k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6553:33): [True: 908, False: 630] ------------------ 6554| 908| { 6555| 908| Ct_Temp->iso_sort_key[nCanonRankFixH[i] - 1] = iso_sort_key_NoTautH[i]; 6556| | 6557| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6558| | Ct_Temp->iso_sort_key_Hfixed[nCanonRankFixH[i] - 1] = iso_sort_key_Hfixed[i]; 6559| |#endif 6560| 908| } 6561| 630| Ct_Temp->len_iso_sort_key = num_atoms; 6562| | 6563| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6564| | Ct_Temp->len_iso_sort_key_Hfixed = num_atoms; 6565| |#endif 6566| | 6567| | /*Ct_Temp->lenNumH = num_atoms;*/ 6568| 630| } 6569| 0| else 6570| 0| { 6571| 0| goto exit_error_alloc; 6572| 0| } 6573| 630| Ct_FixHIso = Ct_Temp; 6574| 630| Ct_Temp = NULL; 6575| 630| memcpy(nSymmRankFixHIso, nSymmRankFixH, num_atoms * sizeof(nSymmRankFixHIso[0])); 6576| 630| memcpy(nCanonRankFixHIso, nCanonRankFixH, num_atoms * sizeof(nCanonRankFixHIso[0])); 6577| 630| memcpy(nAtomNumberCanonFixHIso, nAtomNumberCanonFixH, num_atoms * sizeof(nAtomNumberCanonFixHIso[0])); 6578| 630| } 6579| | /* in case of non-tautomeric component this is the final result */ 6580| | /* i = CtFullCompare( Ct_NoTautHIso, Ct_Temp, num_atoms, 0, 0 );*/ 6581| 667| } 6582| 36.3k| } /* "fixed H" canonical numbering */ 6583| | 6584| | 6585| | /* consistency check: compare canonical connection tables, H-atoms, isotopic H & taut groups */ 6586| 252k| ret = 0; 6587| 252k| ret |= ( Ct_NoH->lenCt != Ct_NoTautH->lenCt ) || memcmp( Ct_NoH->Ctbl, Ct_NoTautH->Ctbl, Ct_NoH->lenCt * sizeof( Ct_NoH->Ctbl[0] ) ); ------------------ | Branch (6587:12): [True: 0, False: 252k] | Branch (6587:54): [True: 0, False: 252k] ------------------ 6588| 252k| if (bReqTaut) ------------------ | Branch (6588:9): [True: 40.8k, False: 211k] ------------------ 6589| 40.8k| { 6590| 40.8k| if (Ct_FixH) ------------------ | Branch (6590:13): [True: 36.3k, False: 4.50k] ------------------ 6591| 36.3k| { 6592| 36.3k| ret |= ( Ct_NoTautH->lenCt != Ct_FixH->lenCt ) || memcmp( Ct_NoTautH->Ctbl, Ct_FixH->Ctbl, Ct_NoTautH->lenCt * sizeof( Ct_NoTautH->Ctbl[0] ) ); ------------------ | Branch (6592:20): [True: 0, False: 36.3k] | Branch (6592:63): [True: 0, False: 36.3k] ------------------ 6593| 36.3k| ret |= ( Ct_NoTautH->lenNumH != Ct_FixH->lenNumH ) || memcmp( Ct_NoTautH->NumH, Ct_FixH->NumH, Ct_NoTautH->lenNumH * sizeof( Ct_Base->NumH[0] ) ); ------------------ | Branch (6593:20): [True: 0, False: 36.3k] | Branch (6593:67): [True: 0, False: 36.3k] ------------------ 6594| 36.3k| } 6595| 40.8k| ret |= ( Ct_NoTautH->lenCt > Ct_Base->lenCt ) || memcmp( Ct_NoTautH->Ctbl, Ct_Base->Ctbl, Ct_NoTautH->lenCt * sizeof( Ct_NoTautH->Ctbl[0] ) ); ------------------ | Branch (6595:16): [True: 0, False: 40.8k] | Branch (6595:58): [True: 0, False: 40.8k] ------------------ 6596| 40.8k| ret |= ( Ct_NoTautH->lenNumH > Ct_Base->lenNumH ) || memcmp( Ct_NoTautH->NumH, Ct_Base->NumH, Ct_NoTautH->lenNumH * sizeof( Ct_Base->NumH[0] ) ); ------------------ | Branch (6596:16): [True: 0, False: 40.8k] | Branch (6596:62): [True: 0, False: 40.8k] ------------------ 6597| 40.8k| } 6598| | 6599| | /* isotopic canonicalization */ 6600| 252k| if (Ct_NoTautHIso) ------------------ | Branch (6600:9): [True: 594, False: 251k] ------------------ 6601| 594| { 6602| 594| ret |= ( Ct_NoH->lenCt != Ct_NoTautHIso->lenCt ) || memcmp( Ct_NoH->Ctbl, Ct_NoTautHIso->Ctbl, Ct_NoH->lenCt * sizeof( Ct_NoH->Ctbl[0] ) ); ------------------ | Branch (6602:16): [True: 0, False: 594] | Branch (6602:61): [True: 0, False: 594] ------------------ 6603| 594| ret |= ( Ct_NoTautH->lenNumH != Ct_NoTautHIso->lenNumH ) || memcmp( Ct_NoTautH->NumH, Ct_NoTautHIso->NumH, Ct_NoTautH->lenNumH * sizeof( Ct_Base->NumH[0] ) ); ------------------ | Branch (6603:16): [True: 0, False: 594] | Branch (6603:69): [True: 0, False: 594] ------------------ 6604| 594| } 6605| 251k| else if (Ct_BaseIso) ------------------ | Branch (6605:14): [True: 861, False: 250k] ------------------ 6606| 861| { 6607| 861| ret |= ( Ct_BaseIso->lenCt != Ct_Base->lenCt ) || memcmp( Ct_BaseIso->Ctbl, Ct_Base->Ctbl, Ct_BaseIso->lenCt * sizeof( Ct_BaseIso->Ctbl[0] ) ); ------------------ | Branch (6607:16): [True: 0, False: 861] | Branch (6607:59): [True: 0, False: 861] ------------------ 6608| 861| ret |= ( Ct_BaseIso->lenNumH != Ct_Base->lenNumH ) || memcmp( Ct_BaseIso->NumH, Ct_Base->NumH, Ct_BaseIso->lenNumH * sizeof( Ct_BaseIso->NumH[0] ) ); ------------------ | Branch (6608:16): [True: 0, False: 861] | Branch (6608:63): [True: 0, False: 861] ------------------ 6609| 861| if (Ct_FixHIso) ------------------ | Branch (6609:13): [True: 655, False: 206] ------------------ 6610| 655| { 6611| 655| ret |= ( Ct_FixHIso->lenCt > Ct_BaseIso->lenCt ) || memcmp( Ct_FixHIso->Ctbl, Ct_BaseIso->Ctbl, Ct_FixHIso->lenCt * sizeof( Ct_FixHIso->Ctbl[0] ) ); ------------------ | Branch (6611:20): [True: 0, False: 655] | Branch (6611:65): [True: 0, False: 655] ------------------ 6612| 655| ret |= ( Ct_FixHIso->lenNumH > Ct_BaseIso->lenNumH ) || memcmp( Ct_FixHIso->NumH, Ct_BaseIso->NumH, Ct_FixHIso->lenNumH * sizeof( Ct_BaseIso->NumH[0] ) ); ------------------ | Branch (6612:20): [True: 0, False: 655] | Branch (6612:69): [True: 0, False: 655] ------------------ 6613| 655| } 6614| 861| } 6615| | 6616| 252k| if (ret) ------------------ | Branch (6616:9): [True: 0, False: 252k] ------------------ 6617| 0| { 6618| 0| goto exit_error; 6619| 0| } 6620| | 6621| 252k| if (bReqTaut) ------------------ | Branch (6621:9): [True: 40.8k, False: 211k] ------------------ 6622| 40.8k| { 6623| | /* restore save "process isotopic" mark; temporarily set it to NO */ 6624| 40.8k| t_group_info->bIgnoreIsotopic = bTautIgnoreIsotopic; 6625| 40.8k| } 6626| | 6627| | 6628| | /* output the canonicalization results */ 6629| 252k| pBCN->num_max = num_max; 6630| 252k| pBCN->num_at_tg = num_at_tg; 6631| 252k| pBCN->num_atoms = num_atoms; 6632| | 6633| 252k| pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; NeighList[TAUT_NON] = NULL; ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; NeighList[TAUT_NON] = NULL; ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; NeighList[TAUT_NON] = NULL; ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6634| 252k| pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; NeighList[TAUT_YES] = NULL; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; NeighList[TAUT_YES] = NULL; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; NeighList[TAUT_YES] = NULL; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6635| | 6636| 252k| if (bReqTaut) ------------------ | Branch (6636:9): [True: 40.8k, False: 211k] ------------------ 6637| 40.8k| { 6638| | /* tautomeric results */ 6639| | 6640| | /* base tautomeric structure, iBase = TAUT_YES */ 6641| | 6642| 40.8k| pBCN->ftcn[TAUT_YES].num_at_tg = num_at_tg; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6643| 40.8k| pBCN->ftcn[TAUT_YES].num_atoms = num_atoms; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6644| | 6645| 40.8k| pBCN->ftcn[TAUT_YES].LinearCt = Ct_Base->Ctbl; Ct_Base->Ctbl = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6646| 40.8k| pBCN->ftcn[TAUT_YES].nLenLinearCtAtOnly = s[iBase].nLenCTAtOnly; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6647| 40.8k| pBCN->ftcn[TAUT_YES].nMaxLenLinearCt = s[iBase].nLenCT + 1; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6648| 40.8k| pBCN->ftcn[TAUT_YES].nLenLinearCt = s[iBase].nLenCT; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6649| | 6650| 40.8k| pBCN->ftcn[TAUT_YES].PartitionCt.Rank = nCanonRankBase; nCanonRankBase = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6651| 40.8k| pBCN->ftcn[TAUT_YES].PartitionCt.AtNumber = nAtomNumberCanonBase; nAtomNumberCanonBase = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6652| 40.8k| pBCN->ftcn[TAUT_YES].nSymmRankCt = nSymmRankBase; nSymmRankBase = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6653| | 6654| 40.8k| pBCN->ftcn[TAUT_YES].nNumHOrig = numH; numH = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6655| 40.8k| pBCN->ftcn[TAUT_YES].nNumH = Ct_Base->NumH; Ct_Base->NumH = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6656| 40.8k| pBCN->ftcn[TAUT_YES].nLenNumH = inchi_min( maxlenNumH, Ct_Base->maxlenNumH ); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].nLenNumH = inchi_min( maxlenNumH, Ct_Base->maxlenNumH ); ------------------ | | 139| 40.8k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 40.8k, False: 0] | | ------------------ ------------------ 6657| | 6658| | /* fixed H structure: exists only if the structure is tautomeric */ 6659| 40.8k| pBCN->ftcn[TAUT_YES].nNumHOrigFixH = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6660| 40.8k| pBCN->ftcn[TAUT_YES].nNumHFixH = NULL; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6661| 40.8k| pBCN->ftcn[TAUT_YES].nLenNumHFixH = 0; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6662| 40.8k| pBCN->ftcn[TAUT_YES].nCanonFlags |= pCD[iBase].nCanonFlags; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6663| | 6664| 40.8k| CleanNumH( pBCN->ftcn[TAUT_YES].nNumHOrig, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanNumH( pBCN->ftcn[TAUT_YES].nNumHOrig, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6665| 40.8k| CleanNumH( pBCN->ftcn[TAUT_YES].nNumH, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanNumH( pBCN->ftcn[TAUT_YES].nNumH, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6666| 40.8k| CleanCt( pBCN->ftcn[TAUT_YES].LinearCt, pBCN->ftcn[TAUT_YES].nLenLinearCt ); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanCt( pBCN->ftcn[TAUT_YES].LinearCt, pBCN->ftcn[TAUT_YES].nLenLinearCt ); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6667| | 6668| | /* isotopic canonicalization */ 6669| 40.8k| if (Ct_BaseIso) ------------------ | Branch (6669:13): [True: 861, False: 40.0k] ------------------ 6670| 861| { 6671| 861| pBCN->ftcn[TAUT_YES].PartitionCtIso.Rank = nCanonRankBaseIso; nCanonRankBaseIso = NULL; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6672| 861| pBCN->ftcn[TAUT_YES].PartitionCtIso.AtNumber = nAtomNumberCanonBaseIso; nAtomNumberCanonBaseIso = NULL; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6673| 861| pBCN->ftcn[TAUT_YES].nSymmRankCtIso = nSymmRankBaseIso; nSymmRankBaseIso = NULL; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6674| 861| pBCN->ftcn[TAUT_YES].iso_sort_keys = Ct_BaseIso->iso_sort_key; Ct_BaseIso->iso_sort_key = NULL; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6675| 861| pBCN->ftcn[TAUT_YES].iso_sort_keysOrig = iso_sort_keyBase; iso_sort_keyBase = NULL; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6676| 861| pBCN->ftcn[TAUT_YES].len_iso_sort_keys = len_iso_sort_keyBase; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6677| 861| pBCN->ftcn[TAUT_YES].iso_exchg_atnos = Ct_BaseIso->iso_exchg_atnos; Ct_BaseIso->iso_exchg_atnos = NULL; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6678| 861| pBCN->ftcn[TAUT_YES].iso_exchg_atnosOrig = iso_exchg_atnos; iso_exchg_atnos = NULL; ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6679| | 6680| 861| CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keys, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keys, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6681| 861| CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keysOrig, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keysOrig, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 575| 861|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6682| 861| } 6683| 40.8k| } /* tautomeric results */ 6684| | 6685| | 6686| 252k| if (bReqNonTaut) ------------------ | Branch (6686:9): [True: 247k, False: 4.50k] ------------------ 6687| 247k| { 6688| | /* non-tautomeric results */ 6689| | 6690| | /* TAUT_NON if tautomeric + non-tautomeric or special non-taut request 6691| | TAUT_YES if the structure happened to be non-tautomeric while user requested tautomeric processing 6692| | In both cases the correct index is iOther. TAUT_NON replaced with iOther 4-2-2004 */ 6693| | 6694| 247k| if (!bReqTaut) ------------------ | Branch (6694:13): [True: 211k, False: 36.3k] ------------------ 6695| 211k| { 6696| | /* rearrange the results for a non-tautomeric structure */ 6697| 211k| nSymmRankFixH = nSymmRankNoTautH; nSymmRankNoTautH = NULL; 6698| 211k| nCanonRankFixH = nCanonRankNoTautH; nCanonRankNoTautH = NULL; 6699| 211k| nAtomNumberCanonFixH = nAtomNumberCanonNoTautH; nAtomNumberCanonNoTautH = NULL; 6700| 211k| Ct_FixH = Ct_NoTautH; Ct_NoTautH = NULL; 6701| | /* isotopic canonicalization */ 6702| 211k| nSymmRankFixHIso = nSymmRankNoTautHIso; nSymmRankNoTautHIso = NULL; 6703| 211k| nCanonRankFixHIso = nCanonRankNoTautHIso; nCanonRankNoTautHIso = NULL; 6704| 211k| nAtomNumberCanonFixHIso = nAtomNumberCanonNoTautHIso; nAtomNumberCanonNoTautHIso = NULL; 6705| 211k| Ct_FixHIso = Ct_NoTautHIso; Ct_NoTautHIso = NULL; 6706| | 6707| 211k| if (iOther == TAUT_YES && pBCN->ftcn[TAUT_NON].NeighList && !pBCN->ftcn[TAUT_YES].NeighList) ------------------ | | 575| 422k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (iOther == TAUT_YES && pBCN->ftcn[TAUT_NON].NeighList && !pBCN->ftcn[TAUT_YES].NeighList) ------------------ | | 574| 211k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (iOther == TAUT_YES && pBCN->ftcn[TAUT_NON].NeighList && !pBCN->ftcn[TAUT_YES].NeighList) ------------------ | | 575| 211k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (6707:17): [True: 211k, False: 0] | Branch (6707:39): [True: 211k, False: 0] | Branch (6707:73): [True: 211k, False: 0] ------------------ 6708| 211k| { 6709| | /* here only non-taut results go to pBCN->ftcn[TAUT_YES] 6710| | Since non-taut NeighList is always in pBCN->ftcn[TAUT_NON].NeighList, move it to 6711| | pBCN->ftcn[TAUT_YES].NeighList. 2004-04-02. 6712| | */ 6713| 211k| pBCN->ftcn[TAUT_YES].NeighList = pBCN->ftcn[TAUT_NON].NeighList; ------------------ | | 575| 211k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].NeighList = pBCN->ftcn[TAUT_NON].NeighList; ------------------ | | 574| 211k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6714| 211k| pBCN->ftcn[TAUT_NON].NeighList = NULL; ------------------ | | 574| 211k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6715| 211k| } 6716| 211k| } 6717| | 6718| 247k| pBCN->ftcn[iOther].num_at_tg = num_atoms; 6719| 247k| pBCN->ftcn[iOther].num_atoms = num_atoms; 6720| | 6721| 247k| pBCN->ftcn[iOther].LinearCt = Ct_FixH->Ctbl; 6722| 247k| Ct_FixH->Ctbl = NULL; 6723| 247k| pBCN->ftcn[iOther].nLenLinearCtAtOnly = s[iOther].nLenCTAtOnly; 6724| 247k| pBCN->ftcn[iOther].nMaxLenLinearCt = s[iOther].nLenCTAtOnly + 1; 6725| 247k| pBCN->ftcn[iOther].nLenLinearCt = s[iOther].nLenCTAtOnly; 6726| | 6727| 247k| pBCN->ftcn[iOther].PartitionCt.Rank = nCanonRankFixH; 6728| 247k| nCanonRankFixH = NULL; 6729| 247k| pBCN->ftcn[iOther].PartitionCt.AtNumber = nAtomNumberCanonFixH; 6730| 247k| nAtomNumberCanonFixH = NULL; 6731| 247k| pBCN->ftcn[iOther].nSymmRankCt = nSymmRankFixH; 6732| 247k| nSymmRankFixH = NULL; 6733| | 6734| 247k| pBCN->ftcn[iOther].nNumHOrig = numHNoTautH; 6735| 247k| numHNoTautH = NULL; 6736| 247k| pBCN->ftcn[iOther].nNumH = Ct_FixH->NumH; 6737| 247k| Ct_FixH->NumH = NULL; 6738| 247k| pBCN->ftcn[iOther].nLenNumH = inchi_min( maxlenNumHNoTautH, Ct_FixH->maxlenNumH ); ------------------ | | 139| 247k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 247k, False: 0] | | ------------------ ------------------ 6739| | 6740| | /* fixed H structure: exists only if the structure is tautomeric */ 6741| 247k| pBCN->ftcn[iOther].nNumHOrigFixH = NumHfixed; 6742| 247k| NumHfixed = NULL; 6743| 247k| pBCN->ftcn[iOther].nNumHFixH = Ct_FixH->NumHfixed; 6744| 247k| Ct_FixH->NumHfixed = NULL; 6745| 247k| pBCN->ftcn[iOther].nLenNumHFixH = num_atoms; 6746| 247k| pBCN->ftcn[iOther].nCanonFlags |= pCD[iOther].nCanonFlags; 6747| | 6748| | /* original H */ 6749| 247k| CleanNumH( pBCN->ftcn[iOther].nNumHOrig, pBCN->ftcn[iOther].nLenNumH ); 6750| 247k| CleanNumH( pBCN->ftcn[iOther].nNumHOrigFixH, pBCN->ftcn[iOther].nLenNumH ); 6751| | /* canonical H positions */ 6752| 247k| CleanNumH( pBCN->ftcn[iOther].nNumH, pBCN->ftcn[iOther].nLenNumH ); 6753| 247k| CleanNumH( pBCN->ftcn[iOther].nNumHFixH, pBCN->ftcn[iOther].nLenNumH ); 6754| | 6755| | /* connection table */ 6756| 247k| CleanCt( pBCN->ftcn[iOther].LinearCt, pBCN->ftcn[iOther].nLenLinearCt ); 6757| | 6758| | /* isotopic canonicalization */ 6759| 247k| if (Ct_FixHIso) ------------------ | Branch (6759:13): [True: 1.26k, False: 246k] ------------------ 6760| 1.26k| { 6761| 1.26k| pBCN->ftcn[iOther].PartitionCtIso.Rank = nCanonRankFixHIso; nCanonRankFixHIso = NULL; 6762| 1.26k| pBCN->ftcn[iOther].PartitionCtIso.AtNumber = nAtomNumberCanonFixHIso; nAtomNumberCanonFixHIso = NULL; 6763| 1.26k| pBCN->ftcn[iOther].nSymmRankCtIso = nSymmRankFixHIso; nSymmRankFixHIso = NULL; 6764| 1.26k| pBCN->ftcn[iOther].iso_sort_keys = Ct_FixHIso->iso_sort_key; Ct_FixHIso->iso_sort_key = NULL; 6765| 1.26k| pBCN->ftcn[iOther].iso_sort_keysOrig = iso_sort_key_NoTautH; iso_sort_key_NoTautH = NULL; 6766| 1.26k| pBCN->ftcn[iOther].len_iso_sort_keys = len_iso_sort_key_NoTautH; 6767| | 6768| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6769| | MergeCleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keys, Ct_FixHIso->iso_sort_key_Hfixed, pBCN->ftcn[iOther].len_iso_sort_keys ); 6770| | MergeCleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keysOrig, iso_sort_key_Hfixed, pBCN->ftcn[iOther].len_iso_sort_keys ); 6771| |#else 6772| 1.26k| CleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keys, pBCN->ftcn[iOther].len_iso_sort_keys ); 6773| 1.26k| CleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keysOrig, pBCN->ftcn[iOther].len_iso_sort_keys ); 6774| 1.26k|#endif 6775| 1.26k| } 6776| 247k| } /* non-tautomeric results */ 6777| | 6778| 252k| goto exit_function; 6779| | 6780| | 6781| 0|exit_error_alloc: 6782| 0| ret = CT_OUT_OF_RAM; ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6783| 0| goto exit_function; 6784| | 6785| 0|exit_error: 6786| 0| if (!RETURNED_ERROR( ret )) ------------------ | | 44| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 0, False: 0] | | | Branch (44:53): [True: 0, False: 0] | | ------------------ ------------------ 6787| 0| { 6788| 0| ret = CT_CANON_ERR; ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6789| 0| } 6790| 0| goto exit_function; 6791| | 6792| | 6793| 252k|exit_function: 6794| | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); 6797| | 6798| 252k| FreeNeighList( NeighList[TAUT_NON] ); ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6799| 252k| FreeNeighList( NeighList[TAUT_YES] ); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6800| | 6801| 252k| FREE_CONTABLE( Ct_NoH ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 252k, False: 0] | | ------------------ ------------------ 6802| 252k| FREE_CONTABLE( Ct_NoTautH ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 40.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 40.8k, False: 0] | | | | | Branch (1152:50): [Folded, False: 40.8k] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 40.8k, False: 211k] | | ------------------ ------------------ 6803| 252k| FREE_CONTABLE( Ct_Base ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 40.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 40.8k, False: 0] | | | | | Branch (1152:50): [Folded, False: 40.8k] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 40.8k, False: 211k] | | ------------------ ------------------ 6804| 252k| FREE_CONTABLE( Ct_FixH ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 247k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 247k, False: 0] | | | | | Branch (1152:50): [Folded, False: 247k] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 247k, False: 4.50k] | | ------------------ ------------------ 6805| 252k| FREE_CONTABLE( Ct_Temp ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 0, False: 252k] | | ------------------ ------------------ 6806| | /* isotopic canonicalization */ 6807| 252k| FREE_CONTABLE( Ct_NoTautHIso ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 0, False: 252k] | | ------------------ ------------------ 6808| 252k| FREE_CONTABLE( Ct_BaseIso ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 861|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 861, False: 0] | | | | | Branch (1152:50): [Folded, False: 861] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 861, False: 251k] | | ------------------ ------------------ 6809| 252k| FREE_CONTABLE( Ct_FixHIso ) ------------------ | | 6795| 252k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1152| 1.26k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 1.26k, False: 0] | | | | | Branch (1152:50): [Folded, False: 1.26k] | | | | ------------------ | | ------------------ | | | Branch (6795:31): [True: 1.26k, False: 250k] | | ------------------ ------------------ 6810| | 6811| | /* free the first two pointers from pBCN->pRankStack */ 6812| 252k| FREE_ARRAY( nRank ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6813| 252k| FREE_ARRAY( nAtomNumber ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6814| | 6815| 252k| if (pBCN->pRankStack) ------------------ | Branch (6815:13): [True: 252k, False: 0] ------------------ 6816| 252k| { 6817| 252k| pBCN->pRankStack[0] = 6818| 252k| pBCN->pRankStack[1] = NULL; 6819| 252k| } 6820| | 6821| 252k|#if ( USE_AUX_RANKING == 1 ) 6822| 252k| FREE_ARRAY( nRankAux ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6823| 252k| FREE_ARRAY( nAtomNumberAux ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6824| 252k| FREE_ARRAY( pAtomInvariantAux ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6825| 252k|#endif 6826| | 6827| 252k| FREE_ARRAY( pAtomInvariant ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6828| | 6829| 252k| FREE_ARRAY( nCanonRankNoH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6830| 252k| FREE_ARRAY( nAtomNumberCanonNoH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6831| 252k| FREE_ARRAY( nSymmRankNoH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6832| | 6833| 252k| FREE_ARRAY( nSymmRankNoTautH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 40.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 40.8k, False: 0] | | | | | Branch (1152:50): [Folded, False: 40.8k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 40.8k, False: 211k] | | ------------------ ------------------ 6834| 252k| FREE_ARRAY( nCanonRankNoTautH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 40.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 40.8k, False: 0] | | | | | Branch (1152:50): [Folded, False: 40.8k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 40.8k, False: 211k] | | ------------------ ------------------ 6835| 252k| FREE_ARRAY( nAtomNumberCanonNoTautH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 40.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 40.8k, False: 0] | | | | | Branch (1152:50): [Folded, False: 40.8k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 40.8k, False: 211k] | | ------------------ ------------------ 6836| 252k| FREE_ARRAY( numHNoTautH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 4.50k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 4.50k, False: 0] | | | | | Branch (1152:50): [Folded, False: 4.50k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 4.50k, False: 247k] | | ------------------ ------------------ 6837| | 6838| 252k| FREE_ARRAY( nSymmRankBase ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6839| 252k| FREE_ARRAY( nCanonRankBase ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6840| 252k| FREE_ARRAY( nAtomNumberCanonBase ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6841| 252k| FREE_ARRAY( numH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6842| | 6843| 252k| FREE_ARRAY( nSymmRankFixH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6844| 252k| FREE_ARRAY( nCanonRankFixH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6845| 252k| FREE_ARRAY( nAtomNumberCanonFixH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6846| 252k| FREE_ARRAY( NumHfixed ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6847| | 6848| | /* isotopic canonicalization */ 6849| | 6850| 252k| FREE_ARRAY( nSymmRankNoTautHIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6851| 252k| FREE_ARRAY( nCanonRankNoTautHIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6852| 252k| FREE_ARRAY( nAtomNumberCanonNoTautHIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6853| 252k| FREE_ARRAY( iso_sort_key_NoTautH ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6854| | 6855| 252k| FREE_ARRAY( nSymmRankBaseIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6856| 252k| FREE_ARRAY( nCanonRankBaseIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6857| 252k| FREE_ARRAY( nAtomNumberCanonBaseIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6858| 252k| FREE_ARRAY( iso_sort_keyBase ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6859| 252k| FREE_ARRAY( iso_exchg_atnos ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6860| | 6861| 252k| FREE_ARRAY( nSymmRankFixHIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6862| 252k| FREE_ARRAY( nCanonRankFixHIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6863| 252k| FREE_ARRAY( nAtomNumberCanonFixHIso ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 0, False: 252k] | | ------------------ ------------------ 6864| | 6865| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6866| | FREE_ARRAY( iso_sort_key_Hfixed ) 6867| |#endif 6868| | 6869| 252k| FREE_ARRAY( nTempRank ) ------------------ | | 6796| 252k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 252k, False: 0] | | | | | Branch (1152:50): [Folded, False: 252k] | | | | ------------------ | | ------------------ | | | Branch (6796:28): [True: 252k, False: 0] | | ------------------ ------------------ 6870| | 6871| 252k|#undef FREE_CONTABLE 6872| 252k|#undef FREE_ARRAY 6873| | 6874| 252k| return ret; 6875| 252k|} InchiTimeGet: 112| 1.52M|{ 113| 1.52M| TickEnd->clockTime = InchiClock( ); 114| 1.52M|} InchiTimeMsecDiff: 117| 761k|{ 118| 761k| if (FullMaxClock > 0) ------------------ | Branch (118:9): [Folded, False: 761k] ------------------ 119| 0| { 120| 0| clock_t delta; 121| 0| if (!TickEnd || !TickStart) ------------------ | Branch (121:13): [True: 0, False: 0] | Branch (121:25): [True: 0, False: 0] ------------------ 122| 0| return 0; 123| | /* clock_t is unsigned */ 124| 0| if (TickEnd->clockTime > TickStart->clockTime) ------------------ | Branch (124:13): [True: 0, False: 0] ------------------ 125| 0| { 126| 0| if (TickEnd->clockTime > HalfMaxClock && ------------------ | Branch (126:17): [True: 0, False: 0] ------------------ 127| 0| TickEnd->clockTime - TickStart->clockTime > HalfMaxClock) ------------------ | Branch (127:18): [True: 0, False: 0] ------------------ 128| 0| { 129| | /* overflow in TickStart->clockTime, actually TickStart->clockTime was later */ 130| 0| delta = ( FullMaxClock - TickEnd->clockTime ) + TickStart->clockTime; 131| 0| return -INCHI_MSEC( delta ); ------------------ | | 87| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 132| 0| } 133| 0| delta = TickEnd->clockTime - TickStart->clockTime; 134| 0| return INCHI_MSEC( delta ); ------------------ | | 87| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 135| 0| } 136| 0| else if (TickEnd->clockTime < TickStart->clockTime) ------------------ | Branch (136:18): [True: 0, False: 0] ------------------ 137| 0| { 138| 0| if (TickStart->clockTime > HalfMaxClock && ------------------ | Branch (138:17): [True: 0, False: 0] ------------------ 139| 0| TickStart->clockTime - TickEnd->clockTime > HalfMaxClock) ------------------ | Branch (139:18): [True: 0, False: 0] ------------------ 140| 0| { 141| | /* overflow in TickEnd->clockTime, actually TickEnd->clockTime was later */ 142| 0| delta = ( FullMaxClock - TickStart->clockTime ) + TickEnd->clockTime; 143| 0| return INCHI_MSEC( delta ); ------------------ | | 87| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 144| 0| } 145| 0| delta = TickStart->clockTime - TickEnd->clockTime; 146| 0| return -INCHI_MSEC( delta ); ------------------ | | 87| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 147| 0| } 148| 0| return 0; /* TickEnd->clockTime == TickStart->clockTime */ 149| 0| } 150| 761k| else 151| 761k| { 152| | /* may happen under Win32 only where clock_t is SIGNED long */ 153| 761k| clock_t delta; 154| 761k| FillMaxMinClock( ic ); 155| 761k| if (!TickEnd || !TickStart) ------------------ | Branch (155:13): [True: 0, False: 761k] | Branch (155:25): [True: 0, False: 761k] ------------------ 156| 0| return 0; 157| 761k| if ((TickEnd->clockTime >= 0 && TickStart->clockTime >= 0) || ------------------ | Branch (157:14): [True: 761k, False: 0] | Branch (157:41): [True: 761k, False: 0] ------------------ 158| 0| (TickEnd->clockTime <= 0 && TickStart->clockTime <= 0)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (158:15): [True: 0, False: 0] | Branch (158:42): [True: 0, False: 0] ------------------ 159| 761k| { 160| 761k| delta = TickEnd->clockTime - TickStart->clockTime; 161| 761k| } 162| 0| else 163| 0| if (TickEnd->clockTime >= ic->m_HalfMaxPositiveClock && ------------------ | Branch (163:17): [True: 0, False: 0] ------------------ 164| 0| TickStart->clockTime <= ic->m_HalfMinNegativeClock) ------------------ | Branch (164:18): [True: 0, False: 0] ------------------ 165| 0| { 166| |/* end is earlier than start */ 167| 0| delta = ( ic->m_MaxPositiveClock - TickEnd->clockTime ) + ( TickStart->clockTime - ic->m_MinNegativeClock ); 168| 0| delta = -delta; 169| 0| } 170| 0| else 171| 0| if (TickEnd->clockTime <= ic->m_HalfMinNegativeClock && ------------------ | Branch (171:21): [True: 0, False: 0] ------------------ 172| 0| TickStart->clockTime >= ic->m_HalfMaxPositiveClock) ------------------ | Branch (172:22): [True: 0, False: 0] ------------------ 173| 0| { 174| |/* start was earlier than end */ 175| 0| delta = ( ic->m_MaxPositiveClock - TickStart->clockTime ) + ( TickEnd->clockTime - ic->m_MinNegativeClock ); 176| 0| } 177| 0| else 178| 0| { 179| | /* there was no overflow, clock passed zero */ 180| 0| delta = TickEnd->clockTime - TickStart->clockTime; 181| 0| } 182| | return INCHI_MSEC( delta ); ------------------ | | 87| 761k|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 183| 761k| } 184| 761k|} InchiTimeElapsed: 189| 472k|{ 190| 472k| inchiTime TickEnd; 191| 472k| if (!TickStart) ------------------ | Branch (191:9): [True: 0, False: 472k] ------------------ 192| 0| return 0; 193| 472k| InchiTimeGet( &TickEnd ); 194| 472k| return InchiTimeMsecDiff( ic, &TickEnd, TickStart ); 195| 472k|} bInchiTimeIsOver: 223| 1.56M|{ 224| 1.56M| if (FullMaxClock > 0) ------------------ | Branch (224:9): [Folded, False: 1.56M] ------------------ 225| 0| { 226| 0| clock_t clockCurrTime; 227| 0| if (!TickStart) ------------------ | Branch (227:13): [True: 0, False: 0] ------------------ 228| 0| return 0; 229| 0| clockCurrTime = InchiClock( ); 230| | /* clock_t is unsigned */ 231| 0| if (TickStart->clockTime > clockCurrTime) ------------------ | Branch (231:13): [True: 0, False: 0] ------------------ 232| 0| { 233| 0| if (TickStart->clockTime > HalfMaxClock && ------------------ | Branch (233:17): [True: 0, False: 0] ------------------ 234| 0| TickStart->clockTime - clockCurrTime > HalfMaxClock) ------------------ | Branch (234:18): [True: 0, False: 0] ------------------ 235| 0| { 236| | /* overflow in clockCurrTime, actually clockCurrTime was later */ 237| 0| return 1; 238| 0| } 239| 0| return 0; 240| 0| } 241| 0| else if (TickStart->clockTime < clockCurrTime) ------------------ | Branch (241:18): [True: 0, False: 0] ------------------ 242| 0| { 243| 0| if (clockCurrTime > HalfMaxClock && ------------------ | Branch (243:17): [True: 0, False: 0] ------------------ 244| 0| clockCurrTime - TickStart->clockTime > HalfMaxClock) ------------------ | Branch (244:18): [True: 0, False: 0] ------------------ 245| 0| { 246| | /* overflow in TickStart->clockTime, actually TickStart->clockTime was later */ 247| 0| return 0; 248| 0| } 249| 0| return 1; 250| 0| } 251| 0| return 0; /* TickStart->clockTime == clockCurrTime */ 252| 0| } 253| 1.56M| else 254| 1.56M| { 255| | /* may happen under Win32 only where clock_t is SIGNED long */ 256| 1.56M| clock_t clockCurrTime; 257| 1.56M| FillMaxMinClock( ic ); 258| 1.56M| if (!TickStart) ------------------ | Branch (258:13): [True: 1.56M, False: 0] ------------------ 259| 1.56M| return 0; 260| 0| clockCurrTime = InchiClock( ); 261| 0| if ((clockCurrTime >= 0 && TickStart->clockTime >= 0) || ------------------ | Branch (261:14): [True: 0, False: 0] | Branch (261:36): [True: 0, False: 0] ------------------ 262| 0| (clockCurrTime <= 0 && TickStart->clockTime <= 0)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (262:15): [True: 0, False: 0] | Branch (262:37): [True: 0, False: 0] ------------------ 263| 0| { 264| 0| return ( clockCurrTime > TickStart->clockTime ); 265| 0| } 266| 0| else 267| 0| if (clockCurrTime >= ic->m_HalfMaxPositiveClock && ------------------ | Branch (267:17): [True: 0, False: 0] ------------------ 268| 0| TickStart->clockTime <= ic->m_HalfMinNegativeClock) ------------------ | Branch (268:18): [True: 0, False: 0] ------------------ 269| 0| { 270| |/* curr is earlier than start */ 271| 0| return 0; 272| 0| } 273| 0| else 274| 0| if (clockCurrTime <= ic->m_HalfMinNegativeClock && ------------------ | Branch (274:21): [True: 0, False: 0] ------------------ 275| 0| TickStart->clockTime >= ic->m_HalfMaxPositiveClock) ------------------ | Branch (275:22): [True: 0, False: 0] ------------------ 276| 0| { 277| |/* start was earlier than curr */ 278| 0| return 1; 279| 0| } 280| 0| else 281| 0| { 282| | /* there was no overflow, clock passed zero */ 283| 0| return ( clockCurrTime > TickStart->clockTime ); 284| 0| } 285| 0| } 286| 1.56M|} GetCanonLengths: 387| 288k|{ 388| | /* include taut. groups as additional "atoms" to the connection table 07-22-2002 */ 389| | 390| 288k| int i, nNumCT, nNumBonds, nNumTBonds = 0, nNumDblBondsStereo = 0, nNumAsymCarbStereo = 0, nNumIsotopic = 0; 391| 288k| T_GROUP *t_group = ( s->nLenLinearCTTautomer && t_group_info ) ? t_group_info->t_group : NULL; ------------------ | Branch (391:26): [True: 40.8k, False: 247k] | Branch (391:53): [True: 40.8k, False: 0] ------------------ 392| | 393| 1.38M| for (nNumBonds = 0, i = 0; i < num_at; i++) ------------------ | Branch (393:32): [True: 1.09M, False: 288k] ------------------ 394| 1.09M| { 395| 1.09M| nNumBonds += at[i].valence; 396| 1.09M| if (at[i].iso_sort_key) ------------------ | Branch (396:13): [True: 2.41k, False: 1.09M] ------------------ 397| 2.41k| { 398| 2.41k| nNumIsotopic++; /* not including tautomeric endpoints that are isotopic only due to mobile atoms */ 399| 2.41k| } 400| | 401| 1.09M| if (at[i].parity > 0) ------------------ | Branch (401:13): [True: 11.4k, False: 1.08M] ------------------ 402| 11.4k| { 403| | /* ignore hydrogen isotope parities in at[i].parity2 */ 404| 11.4k| int j = 0, nStereoBondsToAtom = 0; /* number of stereo double bonds at this atom */ 405| 11.4k| int k; 406| 15.5k| for (; j < MAX_NUM_STEREO_BONDS && ( k = at[i].stereo_bond_neighbor[j] ); j++) ------------------ | | 873| 31.1k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (406:20): [True: 15.5k, False: 0] | Branch (406:48): [True: 4.07k, False: 11.4k] ------------------ 407| 4.07k| { 408| 4.07k| nStereoBondsToAtom += ( at[k - 1].parity > 0 ); 409| 4.07k| } 410| 11.4k| nNumDblBondsStereo += nStereoBondsToAtom; 411| 11.4k| nNumAsymCarbStereo += !j; 412| 11.4k| } 413| 1.09M| } 414| | 415| 288k| nNumDblBondsStereo /= 2; 416| 288k| nNumBonds /= 2; 417| | 418| 288k| s->nLenBonds = inchi_max( s->nLenBonds, nNumBonds ); ------------------ | | 138| 288k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 288k] | | ------------------ ------------------ 419| 288k| nNumCT = nNumBonds; /* total number of neighbors in the CT */ 420| | 421| 288k|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 422| 288k| nNumCT += num_at; 423| 288k|#endif 424| | 425| 288k| s->nLenCTAtOnly = inchi_max( s->nLenCTAtOnly, nNumCT ); ------------------ | | 138| 288k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 288k] | | ------------------ ------------------ 426| | 427| 288k| if (t_group) ------------------ | Branch (427:9): [True: 40.8k, False: 247k] ------------------ 428| 40.8k| { 429| 44.4k| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (429:21): [True: 3.57k, False: 40.8k] ------------------ 430| 3.57k| { 431| 3.57k| nNumTBonds += t_group[i].nNumEndpoints; 432| 3.57k| } 433| 40.8k| nNumCT += nNumTBonds; 434| | 435| 40.8k|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 436| 40.8k| nNumCT += t_group_info->num_t_groups; 437| 40.8k|#endif 438| 40.8k| } 439| | 440| 288k| nNumCT = inchi_max( 1, nNumCT ); /* keep GetBaseCanonRanking() happy */ ------------------ | | 138| 288k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 288k] | | ------------------ ------------------ 441| 288k| s->nLenCT = inchi_max( s->nLenCT, nNumCT ); ------------------ | | 138| 288k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 288k] | | ------------------ ------------------ 442| 288k| s->nLenIsotopic = inchi_max( s->nLenIsotopic, nNumIsotopic ); ------------------ | | 138| 288k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 288k] | | ------------------ ------------------ 443| 288k| s->nLenLinearCTStereoDble = inchi_max( s->nLenLinearCTStereoDble, nNumDblBondsStereo ); ------------------ | | 138| 288k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 288k] | | ------------------ ------------------ 444| 288k| s->nLenLinearCTStereoCarb = inchi_max( s->nLenLinearCTStereoCarb, nNumAsymCarbStereo ); ------------------ | | 138| 288k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 288k] | | ------------------ ------------------ 445| | 446| 288k| if (t_group_info) ------------------ | Branch (446:9): [True: 252k, False: 36.3k] ------------------ 447| 252k| { 448| 252k| s->nLenIsotopicEndpoints = inchi_max( s->nLenIsotopicEndpoints, t_group_info->nNumIsotopicEndpoints ); ------------------ | | 138| 252k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 252k] | | ------------------ ------------------ 449| 252k| } 450| | 451| 288k| return 0; 452| 288k|} DeAllocateCS: 457| 288k|{ 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) 459| | 460| | /* connection table */ 461| 288k| LOCAL_FREE( pCS->LinearCT ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 462| 288k| LOCAL_FREE( pCS->nCanonOrd ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 463| 288k| LOCAL_FREE( pCS->nSymmRank ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 464| 288k| LOCAL_FREE( pCS->nNum_H ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 465| 288k| LOCAL_FREE( pCS->nNum_H_fixed ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 466| 288k| LOCAL_FREE( pCS->nExchgIsoH ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 467| | /* isotopic */ 468| 288k| LOCAL_FREE( pCS->LinearCTIsotopic ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 2.05k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 2.05k, False: 0] | | | | | Branch (1152:50): [Folded, False: 2.05k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 2.05k, False: 286k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 469| 288k| LOCAL_FREE( pCS->nSymmRankIsotopic ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 2.16k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 2.16k, False: 0] | | | | | Branch (1152:50): [Folded, False: 2.16k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 2.16k, False: 286k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 470| 288k| LOCAL_FREE( pCS->nCanonOrdIsotopic ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 2.16k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 2.16k, False: 0] | | | | | Branch (1152:50): [Folded, False: 2.16k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 2.16k, False: 286k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 471| | /* isotopic tautomeric */ 472| 288k| LOCAL_FREE( pCS->LinearCTIsotopicTautomer ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 0, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 473| 288k| LOCAL_FREE( pCS->nCanonOrdIsotopicTaut ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 124|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 124, False: 0] | | | | | Branch (1152:50): [Folded, False: 124] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 124, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 474| 288k| LOCAL_FREE( pCS->nSymmRankIsotopicTaut ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 124|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 124, False: 0] | | | | | Branch (1152:50): [Folded, False: 124] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 124, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 475| | /* stereo */ 476| 288k| LOCAL_FREE( pCS->LinearCTStereoDble ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 344|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 344, False: 0] | | | | | Branch (1152:50): [Folded, False: 344] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 344, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 477| 288k| LOCAL_FREE( pCS->LinearCTStereoCarb ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 574|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 574, False: 0] | | | | | Branch (1152:50): [Folded, False: 574] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 574, False: 287k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 478| 288k| LOCAL_FREE( pCS->LinearCTStereoDbleInv ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 344|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 344, False: 0] | | | | | Branch (1152:50): [Folded, False: 344] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 344, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 479| 288k| LOCAL_FREE( pCS->LinearCTStereoCarbInv ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 574|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 574, False: 0] | | | | | Branch (1152:50): [Folded, False: 574] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 574, False: 287k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 480| 288k| LOCAL_FREE( pCS->nCanonOrdStereo ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 896|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 896, False: 0] | | | | | Branch (1152:50): [Folded, False: 896] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 896, False: 287k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 481| 288k| LOCAL_FREE( pCS->nCanonOrdStereoInv ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 896|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 896, False: 0] | | | | | Branch (1152:50): [Folded, False: 896] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 896, False: 287k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 482| 288k| LOCAL_FREE( pCS->nCanonOrdStereoTaut ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 35|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 35, False: 0] | | | | | Branch (1152:50): [Folded, False: 35] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 35, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 483| | /* isotopic stereo */ 484| 288k| LOCAL_FREE( pCS->LinearCTIsotopicStereoDble ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 65|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 65, False: 0] | | | | | Branch (1152:50): [Folded, False: 65] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 65, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 485| 288k| LOCAL_FREE( pCS->LinearCTIsotopicStereoCarb ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 209|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 209, False: 0] | | | | | Branch (1152:50): [Folded, False: 209] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 209, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 486| 288k| LOCAL_FREE( pCS->LinearCTIsotopicStereoDbleInv ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 65|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 65, False: 0] | | | | | Branch (1152:50): [Folded, False: 65] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 65, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 487| 288k| LOCAL_FREE( pCS->LinearCTIsotopicStereoCarbInv ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 209|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 209, False: 0] | | | | | Branch (1152:50): [Folded, False: 209] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 209, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 488| 288k| LOCAL_FREE( pCS->bRankUsedForStereo ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 926, False: 0] | | | | | Branch (1152:50): [Folded, False: 926] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 926, False: 287k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 489| 288k| LOCAL_FREE( pCS->bAtomUsedForStereo ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 926, False: 0] | | | | | Branch (1152:50): [Folded, False: 926] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 926, False: 287k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 490| | 491| 288k| LOCAL_FREE( pCS->nCanonOrdIsotopicStereo ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 266|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 266, False: 0] | | | | | Branch (1152:50): [Folded, False: 266] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 266, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 492| 288k| LOCAL_FREE( pCS->nCanonOrdIsotopicStereoInv ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 266|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 266, False: 0] | | | | | Branch (1152:50): [Folded, False: 266] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 266, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 493| 288k| LOCAL_FREE( pCS->nCanonOrdIsotopicStereoTaut ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 45|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 45, False: 0] | | | | | Branch (1152:50): [Folded, False: 45] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 45, False: 288k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 494| | /* tautomeric part of the connection table */ 495| 288k| LOCAL_FREE( pCS->LinearCTTautomer ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 40.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 40.8k, False: 0] | | | | | Branch (1152:50): [Folded, False: 40.8k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 40.8k, False: 247k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 496| 288k| LOCAL_FREE( pCS->nCanonOrdTaut ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 3.46k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 3.46k, False: 0] | | | | | Branch (1152:50): [Folded, False: 3.46k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 3.46k, False: 284k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 497| 288k| LOCAL_FREE( pCS->nSymmRankTaut ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 3.46k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 3.46k, False: 0] | | | | | Branch (1152:50): [Folded, False: 3.46k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 3.46k, False: 284k] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 498| | 499| 288k| LOCAL_FREE( pCS->LinearCT2 ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 500| | 501| | /* for establishing constitutional equivalence */ 502| 288k| LOCAL_FREE( pCS->nPrevAtomNumber ); ------------------ | | 458| 288k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 288k, False: 0] | | | | | Branch (1152:50): [Folded, False: 288k] | | | | ------------------ | | ------------------ | | | Branch (458:30): [True: 288k, False: 0] | | | Branch (458:64): [Folded, False: 288k] | | ------------------ ------------------ 503| | 504| 288k| FreeNeighList( pCS->NeighList ); 505| 288k| pCS->NeighList = NULL; 506| | 507| | /* set zero lengths */ 508| 288k| pCS->nMaxLenLinearCTStereoDble = 0; 509| 288k| pCS->nLenLinearCTStereoDble = 0; 510| 288k| pCS->nMaxLenLinearCTStereoCarb = 0; 511| 288k| pCS->nLenLinearCTStereoCarb = 0; 512| 288k| pCS->nMaxLenLinearCTIsotopicStereoDble = 0; 513| 288k| pCS->nLenLinearCTIsotopicStereoDble = 0; 514| 288k| pCS->nMaxLenLinearCTIsotopicStereoCarb = 0; 515| 288k| pCS->nLenLinearCTIsotopicStereoCarb = 0; 516| 288k| pCS->nMaxLenLinearCTTautomer = 0; 517| 288k| pCS->nLenLinearCTTautomer = 0; 518| 288k| pCS->nMaxLenLinearCTIsotopic = 0; 519| 288k| pCS->nLenLinearCTIsotopic = 0; 520| 288k| pCS->nMaxLenLinearCTIsotopicTautomer = 0; 521| 288k| pCS->nLenLinearCTIsotopicTautomer = 0; 522| | 523| | /* set canon numbering lengths to zero */ 524| 288k| pCS->nLenCanonOrd = 0; 525| 288k| pCS->nLenCanonOrdIsotopic = 0; 526| 288k| pCS->nLenCanonOrdIsotopicTaut = 0; 527| 288k| pCS->nLenCanonOrdStereo = 0; 528| 288k| pCS->nLenCanonOrdStereoTaut = 0; 529| 288k| pCS->nLenCanonOrdIsotopicStereo = 0; 530| 288k| pCS->nLenCanonOrdIsotopicStereoTaut = 0; 531| 288k| pCS->nLenCanonOrdTaut = 0; 532| | 533| 288k| return 0; 534| | 535| 288k|#undef LOCAL_FREE 536| 288k|} AllocateCS: 554| 288k|{ 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) 556| | 557| 288k| int num_err = 0; 558| 288k| int num_t_groups = num_at_tg - num_at; 559| | 560| 288k| pCS->nMode = nMode; 561| | 562| | /* connection table */ 563| 288k| if (( nMode & CMODE_CT ) && nLenCT > 0) ------------------ | | 769| 288k|#define CMODE_CT 0x000001 ------------------ | Branch (563:9): [True: 288k, False: 0] | Branch (563:33): [True: 288k, False: 0] ------------------ 564| 288k| { 565| 288k| num_err += !pCS_CALLOC( LinearCT, AT_NUMB, nLenCT ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 566| 288k| pCS->nMaxLenLinearCT = 567| 288k| pCS->nLenLinearCT = nLenCT; 568| 288k| pCS->nLenLinearCTAtOnly = nLenCTAtOnly; 569| 288k| num_err += !pCS_CALLOC( nCanonOrd, AT_RANK, num_at_tg ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 570| 288k| num_err += !pCS_CALLOC( nSymmRank, AT_RANK, num_at_tg ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 571| 288k| if (pBCN) ------------------ | Branch (571:13): [True: 288k, False: 0] ------------------ 572| 288k| { 573| 288k| num_err += !pCS_CALLOC( nNum_H, S_CHAR, num_at ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 574| 288k| num_err += !pCS_CALLOC( nNum_H_fixed, S_CHAR, num_at ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 575| 288k| num_err += !pCS_CALLOC( nExchgIsoH, S_CHAR, num_at ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 576| 288k| } 577| 288k| } 578| | 579| | /* isotopic */ 580| 288k| if (( nMode & CMODE_ISO ) && nLenIsotopic > 0) ------------------ | | 770| 288k|#define CMODE_ISO 0x000002 ------------------ | Branch (580:9): [True: 2.16k, False: 286k] | Branch (580:34): [True: 2.05k, False: 105] ------------------ 581| 2.05k| { 582| 2.05k| num_err += !pCS_CALLOC( LinearCTIsotopic, AT_ISOTOPIC, nLenIsotopic ); ------------------ | | 555| 2.05k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 2.05k|#define inchi_calloc calloc | | ------------------ ------------------ 583| 2.05k| pCS->nMaxLenLinearCTIsotopic = 584| 2.05k| pCS->nLenLinearCTIsotopic = nLenIsotopic; 585| 2.05k| } 586| | 587| | /* isotopic tautomeric */ 588| 288k| if (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT )) ------------------ | | 770| 288k|#define CMODE_ISO 0x000002 ------------------ if (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT )) ------------------ | | 787| 2.16k|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 769| 2.16k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 774| 2.16k|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ if (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT )) ------------------ | | 787| 2.16k|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 769| 2.16k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 774| 2.16k|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (588:9): [True: 2.16k, False: 286k] | Branch (588:34): [True: 903, False: 1.26k] ------------------ 589| 903| { 590| 903| if (nLenLinearCTIsotopicTautomer > 0) ------------------ | Branch (590:13): [True: 0, False: 903] ------------------ 591| 0| { 592| 0| num_err += !pCS_CALLOC( LinearCTIsotopicTautomer, AT_ISO_TGROUP, nLenLinearCTIsotopicTautomer ); ------------------ | | 555| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 0|#define inchi_calloc calloc | | ------------------ ------------------ 593| 0| pCS->nMaxLenLinearCTIsotopicTautomer = 594| 0| pCS->nLenLinearCTIsotopicTautomer = nLenLinearCTIsotopicTautomer; 595| 0| } 596| 903| if (num_t_groups > 0) ------------------ | Branch (596:13): [True: 124, False: 779] ------------------ 597| 124| { 598| 124| num_err += !pCS_CALLOC( nCanonOrdIsotopicTaut, AT_RANK, num_t_groups ); ------------------ | | 555| 124|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 124|#define inchi_calloc calloc | | ------------------ ------------------ 599| 124| num_err += !pCS_CALLOC( nSymmRankIsotopicTaut, AT_RANK, num_t_groups ); ------------------ | | 555| 124|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 124|#define inchi_calloc calloc | | ------------------ ------------------ 600| 124| } 601| 903| } 602| | /* isotopic atoms & t-groups */ 603| 288k| if (( nMode & CMODE_ISO ) /*&& nLenIsotopic > 0*/ || ------------------ | | 770| 288k|#define CMODE_ISO 0x000002 ------------------ | Branch (603:9): [True: 2.16k, False: 286k] ------------------ 604| 286k| (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT ) && nLenLinearCTIsotopicTautomer > 0 ------------------ | | 770| 286k|#define CMODE_ISO 0x000002 ------------------ (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT ) && nLenLinearCTIsotopicTautomer > 0 ------------------ | | 787| 0|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 769| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 774| 0|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT ) && nLenLinearCTIsotopicTautomer > 0 ------------------ | | 787| 0|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 769| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 774| 0|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (604:10): [True: 0, False: 286k] | Branch (604:35): [True: 0, False: 0] | Branch (604:85): [True: 0, False: 0] ------------------ 605| 286k| )) /* djb-rwth: addressing LLVM warning */ 606| 2.16k| { 607| 2.16k| num_err += !pCS_CALLOC( nSymmRankIsotopic, AT_RANK, num_at_tg ); ------------------ | | 555| 2.16k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 2.16k|#define inchi_calloc calloc | | ------------------ ------------------ 608| 2.16k| num_err += !pCS_CALLOC( nCanonOrdIsotopic, AT_RANK, num_at_tg ); ------------------ | | 555| 2.16k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 2.16k|#define inchi_calloc calloc | | ------------------ ------------------ 609| 2.16k| } 610| | /* stereo */ 611| 288k| if (( nMode & CMODE_STEREO ) && nLenLinearCTStereoDble > 0) ------------------ | | 772| 288k|#define CMODE_STEREO 0x000008 ------------------ | Branch (611:9): [True: 989, False: 287k] | Branch (611:37): [True: 344, False: 645] ------------------ 612| 344| { 613| 344| num_err += !pCS_CALLOC( LinearCTStereoDble, AT_STEREO_DBLE, nLenLinearCTStereoDble ); ------------------ | | 555| 344|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 344|#define inchi_calloc calloc | | ------------------ ------------------ 614| 344| num_err += !pCS_CALLOC( LinearCTStereoDbleInv, AT_STEREO_DBLE, nLenLinearCTStereoDble ); ------------------ | | 555| 344|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 344|#define inchi_calloc calloc | | ------------------ ------------------ 615| 344| pCS->nLenLinearCTStereoDbleInv = 616| 344| pCS->nMaxLenLinearCTStereoDble = 617| 344| pCS->nLenLinearCTStereoDble = nLenLinearCTStereoDble; 618| 344| } 619| 288k| if (( nMode & CMODE_STEREO ) && nLenLinearCTStereoCarb > 0) ------------------ | | 772| 288k|#define CMODE_STEREO 0x000008 ------------------ | Branch (619:9): [True: 989, False: 287k] | Branch (619:37): [True: 574, False: 415] ------------------ 620| 574| { 621| 574| num_err += !pCS_CALLOC( LinearCTStereoCarb, AT_STEREO_CARB, nLenLinearCTStereoCarb ); ------------------ | | 555| 574|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 574|#define inchi_calloc calloc | | ------------------ ------------------ 622| 574| num_err += !pCS_CALLOC( LinearCTStereoCarbInv, AT_STEREO_CARB, nLenLinearCTStereoCarb ); ------------------ | | 555| 574|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 574|#define inchi_calloc calloc | | ------------------ ------------------ 623| 574| pCS->nLenLinearCTStereoCarbInv = 624| 574| pCS->nMaxLenLinearCTStereoCarb = 625| 574| pCS->nLenLinearCTStereoCarb = nLenLinearCTStereoCarb; 626| 574| } 627| 288k| if (( nMode & CMODE_STEREO ) && ( nLenLinearCTStereoDble > 0 || nLenLinearCTStereoCarb > 0 )) ------------------ | | 772| 288k|#define CMODE_STEREO 0x000008 ------------------ | Branch (627:9): [True: 989, False: 287k] | Branch (627:39): [True: 344, False: 645] | Branch (627:69): [True: 552, False: 93] ------------------ 628| 896| { 629| 896| num_err += !pCS_CALLOC( nCanonOrdStereo, AT_RANK, num_at_tg ); ------------------ | | 555| 896|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 896|#define inchi_calloc calloc | | ------------------ ------------------ 630| 896| num_err += !pCS_CALLOC( nCanonOrdStereoInv, AT_RANK, num_at_tg ); ------------------ | | 555| 896|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 896|#define inchi_calloc calloc | | ------------------ ------------------ 631| 896| if (( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0 && num_t_groups > 0) ------------------ | | 774| 896|#define CMODE_TAUT 0x000020 ------------------ | Branch (631:13): [True: 123, False: 773] | Branch (631:39): [True: 123, False: 0] | Branch (631:67): [True: 35, False: 88] ------------------ 632| 35| { 633| 35| num_err += !pCS_CALLOC( nCanonOrdStereoTaut, AT_RANK, num_t_groups ); ------------------ | | 555| 35|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 35|#define inchi_calloc calloc | | ------------------ ------------------ 634| 35| } 635| 896| } 636| | /* isotopic stereo */ 637| 288k| if (( nMode & CMODE_ISO_STEREO ) && nLenLinearCTIsotopicStereoDble > 0) ------------------ | | 773| 288k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (637:9): [True: 266, False: 288k] | Branch (637:41): [True: 65, False: 201] ------------------ 638| 65| { 639| 65| num_err += !pCS_CALLOC( LinearCTIsotopicStereoDble, AT_STEREO_DBLE, nLenLinearCTIsotopicStereoDble ); ------------------ | | 555| 65|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 65|#define inchi_calloc calloc | | ------------------ ------------------ 640| 65| num_err += !pCS_CALLOC( LinearCTIsotopicStereoDbleInv, AT_STEREO_DBLE, nLenLinearCTIsotopicStereoDble ); ------------------ | | 555| 65|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 65|#define inchi_calloc calloc | | ------------------ ------------------ 641| 65| pCS->nLenLinearCTIsotopicStereoDbleInv = 642| 65| pCS->nMaxLenLinearCTIsotopicStereoDble = 643| 65| pCS->nLenLinearCTIsotopicStereoDble = nLenLinearCTIsotopicStereoDble; 644| 65| } 645| 288k| if (( nMode & CMODE_ISO_STEREO ) && nLenLinearCTIsotopicStereoCarb > 0) ------------------ | | 773| 288k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (645:9): [True: 266, False: 288k] | Branch (645:41): [True: 209, False: 57] ------------------ 646| 209| { 647| 209| num_err += !pCS_CALLOC( LinearCTIsotopicStereoCarb, AT_STEREO_CARB, nLenLinearCTIsotopicStereoCarb ); ------------------ | | 555| 209|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 209|#define inchi_calloc calloc | | ------------------ ------------------ 648| 209| num_err += !pCS_CALLOC( LinearCTIsotopicStereoCarbInv, AT_STEREO_CARB, nLenLinearCTIsotopicStereoCarb ); ------------------ | | 555| 209|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 209|#define inchi_calloc calloc | | ------------------ ------------------ 649| 209| pCS->nLenLinearCTIsotopicStereoCarbInv = 650| 209| pCS->nMaxLenLinearCTIsotopicStereoCarb = 651| 209| pCS->nLenLinearCTIsotopicStereoCarb = nLenLinearCTIsotopicStereoCarb; 652| 209| } 653| 288k| if (( nMode & CMODE_ISO_STEREO ) && ( nLenLinearCTIsotopicStereoDble > 0 || nLenLinearCTIsotopicStereoCarb > 0 )) ------------------ | | 773| 288k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (653:9): [True: 266, False: 288k] | Branch (653:43): [True: 65, False: 201] | Branch (653:81): [True: 201, False: 0] ------------------ 654| 266| { 655| 266| num_err += !pCS_CALLOC( nCanonOrdIsotopicStereo, AT_RANK, num_at_tg ); ------------------ | | 555| 266|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 266|#define inchi_calloc calloc | | ------------------ ------------------ 656| 266| num_err += !pCS_CALLOC( nCanonOrdIsotopicStereoInv, AT_RANK, num_at_tg ); ------------------ | | 555| 266|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 266|#define inchi_calloc calloc | | ------------------ ------------------ 657| 266| if (( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0 && num_t_groups > 0) ------------------ | | 774| 266|#define CMODE_TAUT 0x000020 ------------------ | Branch (657:13): [True: 84, False: 182] | Branch (657:39): [True: 84, False: 0] | Branch (657:67): [True: 45, False: 39] ------------------ 658| 45| { 659| 45| num_err += !pCS_CALLOC( nCanonOrdIsotopicStereoTaut, AT_RANK, num_t_groups ); ------------------ | | 555| 45|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 45|#define inchi_calloc calloc | | ------------------ ------------------ 660| 45| } 661| 266| } 662| 288k| if ((( nMode & CMODE_STEREO ) && ( nLenLinearCTStereoDble > 0 || nLenLinearCTStereoCarb > 0 )) || ------------------ | | 772| 288k|#define CMODE_STEREO 0x000008 ------------------ | Branch (662:10): [True: 989, False: 287k] | Branch (662:40): [True: 344, False: 645] | Branch (662:70): [True: 552, False: 93] ------------------ 663| 287k| (( nMode & CMODE_ISO_STEREO ) && ( nLenLinearCTIsotopicStereoDble > 0 || nLenLinearCTIsotopicStereoCarb > 0 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 773| 287k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (663:10): [True: 30, False: 287k] | Branch (663:44): [True: 13, False: 17] | Branch (663:82): [True: 17, False: 0] ------------------ 664| 926| { 665| 926| num_err += !pCS_CALLOC( bRankUsedForStereo, S_CHAR, num_at ); ------------------ | | 555| 926|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 926|#define inchi_calloc calloc | | ------------------ ------------------ 666| 926| num_err += !pCS_CALLOC( bAtomUsedForStereo, S_CHAR, num_at ); ------------------ | | 555| 926|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 926|#define inchi_calloc calloc | | ------------------ ------------------ 667| 926| } 668| | /* tautomeric part of the connection table */ 669| 288k| if (( nMode & CMODE_CT ) && ( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0) ------------------ | | 769| 288k|#define CMODE_CT 0x000001 ------------------ if (( nMode & CMODE_CT ) && ( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0) ------------------ | | 774| 288k|#define CMODE_TAUT 0x000020 ------------------ | Branch (669:9): [True: 288k, False: 0] | Branch (669:33): [True: 40.8k, False: 247k] | Branch (669:59): [True: 40.8k, False: 0] ------------------ 670| 40.8k| { 671| 40.8k| num_err += !pCS_CALLOC( LinearCTTautomer, AT_TAUTOMER, nLenLinearCTTautomer ); ------------------ | | 555| 40.8k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 40.8k|#define inchi_calloc calloc | | ------------------ ------------------ 672| 40.8k| pCS->nMaxLenLinearCTTautomer = 673| 40.8k| pCS->nLenLinearCTTautomer = nLenLinearCTTautomer; 674| 40.8k| if (num_t_groups > 0) ------------------ | Branch (674:13): [True: 3.46k, False: 37.4k] ------------------ 675| 3.46k| { 676| 3.46k| num_err += !pCS_CALLOC( nCanonOrdTaut, AT_RANK, num_t_groups ); ------------------ | | 555| 3.46k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 3.46k|#define inchi_calloc calloc | | ------------------ ------------------ 677| 3.46k| num_err += !pCS_CALLOC( nSymmRankTaut, AT_RANK, num_t_groups ); ------------------ | | 555| 3.46k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 3.46k|#define inchi_calloc calloc | | ------------------ ------------------ 678| 3.46k| } 679| 40.8k| } 680| | 681| 288k| if (nMode & CMODE_CT) ------------------ | | 769| 288k|#define CMODE_CT 0x000001 ------------------ | Branch (681:9): [True: 288k, False: 0] ------------------ 682| 288k| { 683| 288k| num_err += !pCS_CALLOC( LinearCT2, AT_NUMB, nLenCT ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 684| 288k| } 685| | 686| | /* for establishing constitutional equivalence */ 687| 288k| num_err += !pCS_CALLOC( nPrevAtomNumber, AT_RANK, num_at_tg ); ------------------ | | 555| 288k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1146| 288k|#define inchi_calloc calloc | | ------------------ ------------------ 688| | 689| | /* set canon numbering lengths to zero */ 690| 288k| pCS->nLenCanonOrd = 0; 691| 288k| pCS->nLenCanonOrdIsotopic = 0; 692| 288k| pCS->nLenCanonOrdIsotopicTaut = 0; 693| 288k| pCS->nLenCanonOrdStereo = 0; 694| 288k| pCS->nLenCanonOrdStereoTaut = 0; 695| 288k| pCS->nLenCanonOrdIsotopicStereo = 0; 696| 288k| pCS->nLenCanonOrdIsotopicStereoTaut = 0; 697| 288k| pCS->nLenCanonOrdTaut = 0; 698| | 699| | 700| 288k| if (num_err) ------------------ | Branch (700:9): [True: 0, False: 288k] ------------------ 701| 0| { 702| 0| DeAllocateCS( pCS ); 703| 0| return CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 704| 0| } 705| 288k| return 0; 706| | 707| 288k|#undef pCS_CALLOC 708| 288k|} FillIsotopicAtLinearCT: 751| 2.12k|{ 752| | /* at[i].init_rank = initial ranks before canonizing */ 753| | /* nRank[i] = new ordering number for atoms: nRank=1,2,.. */ 754| | /* nAtomNumber[r] = orig. atom number= 0,1,... for r = nRank-1 */ 755| | /* nRank[nAtomNumber[r]] = r; r = 0,1,... */ 756| | /* nAtomNumber[nRank[i]-1] = i; */ 757| | 758| 2.12k| int i, k, rank; 759| 2.12k| int nLinearCTIsotopicLen = 0; 760| | 761| | /* the following parts of the "name" should be compared */ 762| | /* after the connection table comparison is done */ 763| | /* to avoid wrong difference sign. So, these parts */ 764| | /* go to a separate buffers. */ 765| 2.12k| if (LinearCTIsotopic && nMaxLenLinearCTIsotopic > 0) ------------------ | Branch (765:9): [True: 2.05k, False: 61] | Branch (765:29): [True: 2.05k, False: 0] ------------------ 766| 2.05k| { 767| 2.05k| memset( LinearCTIsotopic, 0, nMaxLenLinearCTIsotopic * sizeof( LinearCTIsotopic[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 768| 2.05k| } 769| 61| else 770| 61| { 771| 61| return 0; 772| 61| } 773| | 774| | /* rank = nRank[nAtomNumber[rank-1]] -- proposed atoms canon. numbers */ 775| 13.9k| for (rank = 1; rank <= num_atoms; rank++) ------------------ | Branch (775:20): [True: 11.8k, False: 2.05k] ------------------ 776| 11.8k| { 777| | 778| 11.8k| i = (int) nAtomNumber[rank - 1]; /* current atom */ 779| | 780| | /**************************************************** 781| | add isotopic atom info to LinearCTIsotopic 782| | *****************************************************/ 783| | 784| | /* if the atom itself is not isotopic then add it only if */ 785| | /* the atom is not an endpoint AND has attached T or D or 1H. */ 786| 11.8k| k = ( !at[i].endpoint && !( at[i].cFlags & AT_FLAG_ISO_H_POINT ) && ( at[i].num_iso_H[0] || at[i].num_iso_H[1] || at[i].num_iso_H[2] ) ); ------------------ | | 50| 11.6k|#define AT_FLAG_ISO_H_POINT 0x01 /**< may have isotopic H */ ------------------ | Branch (786:15): [True: 11.6k, False: 236] | Branch (786:34): [True: 11.4k, False: 154] | Branch (786:79): [True: 545, False: 10.9k] | Branch (786:101): [True: 175, False: 10.7k] | Branch (786:123): [True: 183, False: 10.5k] ------------------ 787| 11.8k| if (at[i].iso_atw_diff || k) ------------------ | Branch (787:13): [True: 1.56k, False: 10.2k] | Branch (787:35): [True: 844, False: 9.43k] ------------------ 788| 2.41k| { 789| 2.41k| if (CHECK_OVERFLOW( nLinearCTIsotopicLen, nMaxLenLinearCTIsotopic )) ------------------ | | 43| 2.41k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 2.41k] | | ------------------ ------------------ 790| 0| { 791| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 792| 0| } 793| 2.41k| LinearCTIsotopic[nLinearCTIsotopicLen].at_num = (AT_RANK) rank; 794| 2.41k| LinearCTIsotopic[nLinearCTIsotopicLen].iso_atw_diff = at[i].iso_atw_diff; 795| 2.41k| LinearCTIsotopic[nLinearCTIsotopicLen].num_1H = (NUM_H) ( k ? at[i].num_iso_H[0] : 0 ); ------------------ | Branch (795:71): [True: 903, False: 1.50k] ------------------ 796| 2.41k| LinearCTIsotopic[nLinearCTIsotopicLen].num_D = (NUM_H) ( k ? at[i].num_iso_H[1] : 0 ); ------------------ | Branch (796:70): [True: 903, False: 1.50k] ------------------ 797| 2.41k| LinearCTIsotopic[nLinearCTIsotopicLen].num_T = (NUM_H) ( k ? at[i].num_iso_H[2] : 0 ); ------------------ | Branch (797:70): [True: 903, False: 1.50k] ------------------ 798| 2.41k| nLinearCTIsotopicLen++; 799| 2.41k| } 800| 11.8k| } /* end of cycle over all atoms. */ 801| | 802| 2.05k| if (LinearCTIsotopic) ------------------ | Branch (802:9): [True: 2.05k, False: 0] ------------------ 803| 2.05k| { 804| 2.05k| if (*pnLenLinearCTIsotopic) ------------------ | Branch (804:13): [True: 2.05k, False: 0] ------------------ 805| 2.05k| { 806| 2.05k| if (*pnLenLinearCTIsotopic != nLinearCTIsotopicLen) ------------------ | Branch (806:17): [True: 0, False: 2.05k] ------------------ 807| 0| { 808| 0| return CT_LEN_MISMATCH; /* */ ------------------ | | 20| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 809| 0| } 810| 2.05k| } 811| 0| else 812| 0| { 813| 0| *pnLenLinearCTIsotopic = nLinearCTIsotopicLen; 814| 0| } 815| 2.05k| } 816| | 817| | /* Return value: >0 => OK */ 818| 2.05k| return nLinearCTIsotopicLen; 819| 2.05k|} FillTautLinearCT2: 840| 3.46k|{ 841| | /* nRank[i] = Canonical numbers of atoms,.. */ 842| | /* nAtomNumber[r] = orig. atom number= 0,1,... for r = nRank-1 */ 843| | /* nRank[nAtomNumber[r]] = r; r = 0,1,... */ 844| | /* nAtomNumber[nRank[i]-1] = i; */ 845| | 846| 3.46k| T_GROUP *t_group; 847| | 848| 3.46k| int i, j, len = 0, g, offset, max_len = 0, len_iso = 0; /* djb-rwth: removing redundant variable */ 849| 3.46k| static const int max_num_num = sizeof( t_group->num ) / sizeof( t_group->num[0] ); 850| 3.46k| static const int max_num_iso = sizeof( LinearCTIsotopicTautomer->num ) / sizeof( LinearCTIsotopicTautomer->num[0] ) + T_NUM_NO_ISOTOPIC; ------------------ | | 69| 3.46k|#define T_NUM_NO_ISOTOPIC 2 ------------------ 851| | 852| | /**************************************************************************** 853| | 854| | Tautomeric groups 07-22-2002, modified 12-2003 855| | 856| | ****************************************************************************/ 857| | 858| 3.46k| if (num_at_tg > num_atoms && t_group_info && t_group_info->num_t_groups) ------------------ | Branch (858:9): [True: 3.46k, False: 0] | Branch (858:34): [True: 3.46k, False: 0] | Branch (858:50): [True: 3.46k, False: 0] ------------------ 859| 3.46k| { 860| 3.46k| int num_t_groups = t_group_info->num_t_groups; 861| 3.46k| AT_NUMB *tGroupNumber = t_group_info->tGroupNumber; 862| 3.46k| AT_NUMB *tSymmRank = tGroupNumber + TGSO_SYMM_RANK*num_t_groups; /* equivalence */ ------------------ | | 138| 3.46k|#define TGSO_SYMM_RANK 1 /* tSymmRank: symmetry ranks (no isotopes) = min. ordering number > 0. */ ------------------ 863| 3.46k| AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*(long long)num_t_groups; /* djb-rwth: cast operator added */ ------------------ | | 140| 3.46k|#define TGSO_SYMM_IRANK 3 /* tiSymmRank: isotopic symmetry ranks */ ------------------ 864| 3.46k| AT_NUMB *tiGroupNumber = tGroupNumber + TGSO_SYMM_IORDER*(long long)num_t_groups; /* djb-rwth: cast operator added */ ------------------ | | 139| 3.46k|#define TGSO_SYMM_IORDER 2 /* tiGroupNumber: isotopic symmetry rank sorting order */ ------------------ 865| 3.46k| AT_RANK nOffset = (AT_RANK) num_atoms; 866| | 867| | /* Fill Canonical ranks and Symmetry Ranks */ 868| | /* memcpy( tPrevGroupNumber, tGroupNumber, num_t_groups*sizeof(tPrevGroupNumber[0])); */ 869| 7.03k| for (i = num_atoms, j = 0; i < num_at_tg; i++, j++) ------------------ | Branch (869:36): [True: 3.56k, False: 3.46k] ------------------ 870| 3.56k| { 871| | /* tPrevGroupNumber[j] = */ 872| 3.56k| tGroupNumber[j] = nAtomNumber[i] - nOffset; 873| 3.56k| tSymmRank[j] = nSymmRank[i] - nOffset; 874| 3.56k| if (bIsoTaut) ------------------ | Branch (874:17): [True: 108, False: 3.46k] ------------------ 875| 108| { 876| 108| tiGroupNumber[j] = nAtomNumberIso[i] - nOffset; 877| 108| tiSymmRank[j] = nSymmRankIso[i] - nOffset; 878| 108| } 879| 3.56k| } 880| | 881| | /* Sort enpoints within each tautomeric group according to the canonical ranks */ 882| 3.46k| pCG->m_pn_RankForSort = nRank; 883| 7.03k| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (883:21): [True: 3.56k, False: 3.46k] ------------------ 884| 3.56k| { 885| 3.56k| inchi_qsort( pCG, 886| 3.56k| t_group_info->nEndpointAtomNumber + (int) t_group_info->t_group[i].nFirstEndpointAtNoPos, 887| 3.56k| t_group_info->t_group[i].nNumEndpoints, 888| 3.56k| sizeof( t_group_info->nEndpointAtomNumber[0] ), 889| 3.56k| CompRank ); 890| 3.56k| } 891| | /* fill out LinearCTTautomer */ 892| 3.46k| if (nMaxLenLinearCTTautomer) ------------------ | Branch (892:13): [True: 3.46k, False: 0] ------------------ 893| 3.46k| { 894| 3.46k| max_len = T_GROUP_HDR_LEN * t_group_info->num_t_groups + t_group_info->nNumEndpoints + 1; ------------------ | | 72| 3.46k|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 3.46k|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 895| 3.46k| if (max_len > nMaxLenLinearCTTautomer) ------------------ | Branch (895:17): [True: 0, False: 3.46k] ------------------ 896| 0| { 897| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 898| 0| } 899| 3.46k| } 900| | 901| | /**************************************************************** 902| | * tautomer group format (#: is an offset) 903| | **************************************************************** 904| | * HEADER (T_GROUP_HDR_LEN=3+3iso) 905| | * 0: N = number of endpoints ( t_group->nNumEndpoints ) 906| | * 1: number of mobile groups ( t_group->num[0] ) 907| | * 2: number of neg. charges ( t_group->num[1] ) {note: T_NUM_NO_ISOTOPIC=2} 908| | * ENDPOINT RANKS 909| | * 3..N+2: sorted tautomer group endpoint ranks; the sorting order is in 910| | * t_group_info->nEndpointAtomNumber[t_group->nFirstEndpointAtNoPos+j], j=0..N-1 911| | * 912| | * End mark : N==0 913| | ****************************************************************/ 914| | /* num_num = t_group_info->bIgnoreIsotopic? T_NUM_NO_ISOTOPIC : max_num_num; */ 915| | /* num_num = max_num_num; always include isotopic info; ignore it at the CT comparison step. */ /* djb-rwth: removing redundant code */ 916| 7.03k| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (916:21): [True: 3.56k, False: 3.46k] ------------------ 917| 3.56k| { 918| 3.56k| g = tGroupNumber[i]; /* ith tautomeric group number in canonical order */ 919| 3.56k| t_group = t_group_info->t_group + g; 920| | /******************************************************* 921| | * Tautomer non-isotopic part: LinearCTTautomer 922| | *******************************************************/ 923| | /* check length */ 924| 3.56k| if (CHECK_OVERFLOW( len + T_GROUP_HDR_LEN + t_group->nNumEndpoints, max_len )) ------------------ | | 43| 3.56k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 3.56k] | | ------------------ ------------------ 925| 0| { 926| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 927| 0| } 928| | 929| | /* t_group header: number of endpoints */ 930| 3.56k| LinearCTTautomer[len++] = t_group->nNumEndpoints; 931| | /* t_group header: */ 932| | /* (a) number of mobile groups in the t_group (number of H + number of (-) ) and */ 933| | /* (b) number of mobile negative charges (-) in the t_group */ 934| 10.7k| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 69| 10.7k|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (934:25): [True: 7.13k, False: 3.56k] ------------------ 935| 7.13k| { 936| 7.13k| LinearCTTautomer[len++] = t_group->num[j]; 937| 7.13k| } 938| | /* t_group endpoint ranks link the group to the tautomeric endpoint atoms in the structure */ 939| | /* according to their ranks */ 940| 12.1k| for (j = 0, offset = t_group->nFirstEndpointAtNoPos; j < t_group->nNumEndpoints; j++) ------------------ | Branch (940:66): [True: 8.58k, False: 3.56k] ------------------ 941| 8.58k| { 942| 8.58k| LinearCTTautomer[len++] = nRank[(int) t_group_info->nEndpointAtomNumber[offset + j]]; 943| 8.58k| } 944| 3.56k| } 945| 3.46k| if (nMaxLenLinearCTTautomer) ------------------ | Branch (945:13): [True: 3.46k, False: 0] ------------------ 946| 3.46k| { 947| 3.46k| LinearCTTautomer[len++] = 0; /* or CT_INITVALUE ??? */ 948| 3.46k| if (len != max_len) ------------------ | Branch (948:17): [True: 0, False: 3.46k] ------------------ 949| 0| { 950| 0| len = -len; /* program error */ /* */ 951| 0| } 952| 3.46k| else if (*pnLenLinearCTTautomer && *pnLenLinearCTTautomer != len) ------------------ | Branch (952:22): [True: 3.46k, False: 0] | Branch (952:48): [True: 0, False: 3.46k] ------------------ 953| 0| { 954| 0| return CT_LEN_MISMATCH; ------------------ | | 20| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 955| 0| } 956| 3.46k| else 957| 3.46k| { 958| 3.46k| *pnLenLinearCTTautomer = len; 959| 3.46k| } 960| 3.46k| } 961| 0| else 962| 0| { 963| 0| *pnLenLinearCTTautomer = 0; 964| 0| } 965| | 966| | /****************************************************************** 967| | * Isotopic Tautomeric mobile groups part: LinearCTIsotopicTautomer 968| | ******************************************************************/ 969| 3.46k| if (nMaxLenLinearCTIsotopicTautomer && !t_group_info->nNumIsotopicEndpoints) ------------------ | Branch (969:13): [True: 0, False: 3.46k] | Branch (969:48): [True: 0, False: 0] ------------------ 970| 0| { 971| 0| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (971:25): [True: 0, False: 0] ------------------ 972| 0| { 973| 0| g = tiGroupNumber[i]; /* ith tautomeric group number in canonical order */ 974| 0| t_group = t_group_info->t_group + g; 975| | /* find if mobile hydrogens are isotopic */ 976| 0| if (!t_group->iWeight) ------------------ | Branch (976:21): [True: 0, False: 0] ------------------ 977| 0| { 978| 0| continue; /* no isotopic H */ 979| 0| } 980| 0| if (CHECK_OVERFLOW( len_iso, nMaxLenLinearCTIsotopicTautomer )) ------------------ | | 43| 0|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 0] | | ------------------ ------------------ 981| 0| { 982| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 983| 0| } 984| 0| for (j = T_NUM_NO_ISOTOPIC; j < max_num_num && j < max_num_iso; j++) ------------------ | | 69| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (984:45): [True: 0, False: 0] | Branch (984:64): [True: 0, False: 0] ------------------ 985| 0| { 986| | /* num_T, num_D, num_1H */ 987| 0| LinearCTIsotopicTautomer[len_iso].num[j - T_NUM_NO_ISOTOPIC] = t_group->num[j]; ------------------ | | 69| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ 988| 0| } 989| | /* link to tautomer group LinearCTTautomer[i]: */ 990| 0| LinearCTIsotopicTautomer[len_iso++].tgroup_num = (AT_NUMB) ( i + 1 ); /* t_group isotopic rank */ 991| 0| } 992| 0| } 993| 3.46k| if (nMaxLenLinearCTIsotopicTautomer) ------------------ | Branch (993:13): [True: 0, False: 3.46k] ------------------ 994| 0| { 995| 0| if (*pnLenLinearCTIsotopicTautomer && *pnLenLinearCTIsotopicTautomer != len_iso) ------------------ | Branch (995:17): [True: 0, False: 0] | Branch (995:51): [True: 0, False: 0] ------------------ 996| 0| { 997| 0| return CT_LEN_MISMATCH; ------------------ | | 20| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 998| 0| } 999| 0| *pnLenLinearCTIsotopicTautomer = len_iso; 1000| 0| } 1001| 3.46k| else 1002| 3.46k| { 1003| 3.46k| *pnLenLinearCTIsotopicTautomer = 0; 1004| 3.46k| } 1005| 3.46k| } 1006| | 1007| 3.46k| return len; 1008| 3.46k|} UpdateFullLinearCT: 1023| 290k|{ 1024| | /* at[i].init_rank = initial ranks before canonizing */ 1025| | /* nRank[i] = new ordering number for atoms: nRank=1,2,.. */ 1026| | /* nAtomNumber[r] = orig. atom number= 0,1,... for r = nRank-1 */ 1027| | /* nRank[nAtomNumber[r]] = r; r = 0,1,... */ 1028| | /* nAtomNumber[nRank[i]-1] = i; */ 1029| | 1030| 290k| AT_NUMB nNeighborNumber[MAXVAL]; 1031| 290k| int i, j, k, num_neigh, rank, bCompare; /*, nRetVal; */ 1032| | 1033| 290k| T_GROUP_INFO *t_group_info = NULL; 1034| 290k| T_GROUP *t_group = NULL; 1035| 290k| AT_NUMB *nEndpointAtomNumber = NULL; 1036| | 1037| 290k| int nCTLen = 0, nCTLenAtOnly = 0; 1038| | 1039| | 1040| 290k| AT_NUMB r_neigh; 1041| 290k| AT_NUMB *LinearCT = pCS->LinearCT; 1042| | 1043| | /* the following parts of the "name" should be compared */ 1044| | /* after the connection table comparison is done */ 1045| | /* to avoid wrong difference sign. So, these parts */ 1046| | /* go to a separate buffers. */ 1047| | /* -- currently not used at all at all -- */ 1048| | 1049| 290k|#if CT_ATOMID != CT_ATOMID_DONTINCLUDE 1050| 290k| AT_NUMB r0_at_type; 1051| 290k|#endif 1052| | 1053| 290k| num_neigh = 0; /* Moved from above 2024-09-01 DT; djb-rwth: num_neigh initialisation added */ 1054| | 1055| 290k| bCompare = bFirstTime ? 0 : 1; ------------------ | Branch (1055:16): [True: 0, False: 290k] ------------------ 1056| | 1057| 290k| if (num_at_tg > num_atoms) ------------------ | Branch (1057:9): [True: 3.56k, False: 286k] ------------------ 1058| 3.56k| { 1059| 3.56k| t_group_info = pCS->t_group_info; 1060| 3.56k| t_group = t_group_info->t_group; 1061| 3.56k| } 1062| 286k| else 1063| 286k| { 1064| 286k| t_group_info = NULL; 1065| 286k| t_group = NULL; 1066| 286k| } 1067| | 1068| | /**********************************************************************/ 1069| | /* */ 1070| | /* CYCLE 1: FILL OUT CONNECTION TABLE(S) FOR ALL ATOMS */ 1071| | /* ** NOT INCLUDING ISOTOPIC ATOMS AND 1H, 2H(D), 3H(T) ** */ 1072| | /* */ 1073| | /* rank = nRank[nAtomNumber[rank-1]] -- proposed atoms canon. numbers */ 1074| | /**********************************************************************/ 1075| 1.39M| for (rank = 1; rank <= num_atoms; rank++) ------------------ | Branch (1075:20): [True: 1.10M, False: 290k] ------------------ 1076| 1.10M| { 1077| 1.10M| i = (int) nAtomNumber[rank - 1]; /* current atom */ 1078| | 1079| 1.10M|#if ( CT_ATOMID == CT_ATOMID_IS_CURRANK ) 1080| 1.10M| r0_at_type = (AT_NUMB) rank; /* current Rank */ 1081| |#else 1082| |#if ( CT_ATOMID == CT_ATOMID_IS_INITRANK ) 1083| | r0_at_type = (AT_NUMB) at[i].init_rank; /* chemical + neighborhood ID */ 1084| |#else 1085| |#if ( CT_ATOMID == CT_ATOMID_DONTINCLUDE ) 1086| |#else 1087| |#error Undefined or wrong definition of CT_ATOMID 1088| |#endif 1089| |#endif 1090| |#endif 1091| | 1092| | /* add atom to the CT */ 1093| 1.10M|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 1094| 1.10M| if (CHECK_OVERFLOW( nCTLen, pCS->nMaxLenLinearCT )) ------------------ | | 43| 1.10M|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 1.10M] | | ------------------ ------------------ 1095| 0| { 1096| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1097| 0| } 1098| 2.21M| COMPARE_WITH_CT( LinearCT, nCTLen, r0_at_type, bCompare ); ------------------ | | 715| 1.10M| if ( CONDITION ) { \ | | ------------------ | | | Branch (715:10): [True: 1.10M, False: 0] | | ------------------ | | 716| 1.10M| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (716:14): [True: 0, False: 1.10M] | | ------------------ | | 717| 1.10M| return 1; /* not a minimal CT */ \ | | 718| 1.10M| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 719| 1.10M| } \ | | 720| 1.10M| (CT)[CTLEN] = VALUE; \ | | 721| 1.10M| (CTLEN)++ ------------------ 1099| 2.21M|#endif 1100| | 1101| | /******************************************************* 1102| | add neighbors and (if required) bonds to CT 1103| | ********************************************************/ 1104| | 1105| | /* sort neighbors */ 1106| 2.21M| num_neigh = at[i].valence; 1107| 2.21M| for (k = 0; k < num_neigh; k++) ------------------ | Branch (1107:21): [True: 484k, False: 1.10M] ------------------ 1108| 484k| { 1109| 484k| nNeighborNumber[k] = (AT_NUMB) k; 1110| 484k| } 1111| 2.21M| pCG->m_pNeighborsForSort = at[i].neighbor; 1112| 2.21M| pCG->m_pn_RankForSort = nRank; 1113| 2.21M| insertions_sort( pCG, nNeighborNumber, (size_t) num_neigh, sizeof( nNeighborNumber[0] ), CompNeighborsAT_NUMBER ); 1114| | 1115| 2.21M| for (k = 0; k < num_neigh; k++) ------------------ | Branch (1115:21): [True: 484k, False: 1.10M] ------------------ 1116| 484k| { 1117| | /* rank = (new current atom Rank) */ 1118| 484k| if ((int) ( r_neigh = (AT_NUMB) nRank[(int) at[i].neighbor[(int) nNeighborNumber[k]]] ) ------------------ | Branch (1118:17): [True: 242k, False: 242k] ------------------ 1119| 484k| CT_NEIGH_SMALLER_THAN rank) 1120| 242k| { 1121| 242k| if (CHECK_OVERFLOW( nCTLen, pCS->nMaxLenLinearCT )) ------------------ | | 43| 242k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 242k] | | ------------------ ------------------ 1122| 0| { 1123| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1124| 0| } 1125| 484k| COMPARE_WITH_CT( LinearCT, nCTLen, r_neigh, bCompare ); ------------------ | | 715| 242k| if ( CONDITION ) { \ | | ------------------ | | | Branch (715:10): [True: 242k, False: 0] | | ------------------ | | 716| 242k| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (716:14): [True: 0, False: 242k] | | ------------------ | | 717| 242k| return 1; /* not a minimal CT */ \ | | 718| 242k| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 719| 242k| } \ | | 720| 242k| (CT)[CTLEN] = VALUE; \ | | 721| 242k| (CTLEN)++ ------------------ 1126| 484k| } 1127| 484k| } 1128| | 1129| | /* add CT row delimiter */ 1130| 2.21M| } /* end of cycle over all atoms. */ 1131| | 1132| 290k| nCTLenAtOnly = nCTLen; 1133| | 1134| | /************************************************************** 1135| | 1136| | Tautomeric groups 07-22-2002 1137| | 1138| | ***************************************************************/ 1139| | 1140| 294k| for (rank = num_atoms + 1; rank <= num_at_tg; rank++) ------------------ | Branch (1140:32): [True: 3.67k, False: 290k] ------------------ 1141| 3.67k| { 1142| 3.67k| j = (int) nAtomNumber[rank - 1]; /* current "atom" */ 1143| 3.67k| i = j - num_atoms; /* current t-group */ 1144| | 1145| 3.67k|#if ( CT_ATOMID == CT_ATOMID_IS_CURRANK ) 1146| 3.67k| r0_at_type = (AT_NUMB) rank; /* current Rank */ 1147| |#else 1148| |#if ( CT_ATOMID == CT_ATOMID_IS_INITRANK ) 1149| | r0_at_type = (AT_NUMB) rank; /* current Rank or (AT_NUMB)at[i].init_rank; ==> chemical + neighborhood ID */ 1150| |#else 1151| |#if ( CT_ATOMID == CT_ATOMID_DONTINCLUDE ) 1152| |#else 1153| |#error Undefined or wrong definition of CT_ATOMID 1154| |#endif 1155| |#endif 1156| |#endif 1157| | 1158| | /* add atom to the CT */ 1159| 3.67k|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 1160| 3.67k| if (CHECK_OVERFLOW( nCTLen, pCS->nMaxLenLinearCT )) ------------------ | | 43| 3.67k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 3.67k] | | ------------------ ------------------ 1161| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1162| 7.35k| COMPARE_WITH_CT( LinearCT, nCTLen, r0_at_type, bCompare ); ------------------ | | 715| 3.67k| if ( CONDITION ) { \ | | ------------------ | | | Branch (715:10): [True: 3.67k, False: 0] | | ------------------ | | 716| 3.67k| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (716:14): [True: 0, False: 3.67k] | | ------------------ | | 717| 3.67k| return 1; /* not a minimal CT */ \ | | 718| 3.67k| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 719| 3.67k| } \ | | 720| 3.67k| (CT)[CTLEN] = VALUE; \ | | 721| 3.67k| (CTLEN)++ ------------------ 1163| 7.35k|#endif 1164| | 1165| | /******************************************************* 1166| | add neighbors and (if required) bonds to CT 1167| | ********************************************************/ 1168| | 1169| | /* sort endpoints */ 1170| 7.35k| if (t_group_info) ------------------ | Branch (1170:13): [True: 3.67k, False: 0] ------------------ 1171| 3.67k| nEndpointAtomNumber = t_group_info->nEndpointAtomNumber + (int) t_group[i].nFirstEndpointAtNoPos; /* djb-rwth: fixing a NULL pointer dereference */ 1172| 7.35k| pCG->m_pn_RankForSort = nRank; 1173| 7.35k| if (t_group + i) /* djb-rwth: ignoring GCC warning */ ------------------ | Branch (1173:13): [True: 3.67k, False: 0] ------------------ 1174| 3.67k| num_neigh = (int)t_group[i].nNumEndpoints; 1175| 7.35k| insertions_sort( pCG, nEndpointAtomNumber, (size_t) num_neigh, sizeof( nEndpointAtomNumber[0] ), CompRank ); 1176| | 1177| 12.4k| for (k = 0; k < num_neigh; k++) ------------------ | Branch (1177:21): [True: 8.80k, False: 3.67k] ------------------ 1178| 8.80k| { 1179| | /* rank = (new current atom Rank) */ 1180| 8.80k| if (nEndpointAtomNumber + k) /* djb-rwth: fixing a NULL pointer dereference; ignoring GCC warning */ ------------------ | Branch (1180:17): [True: 8.80k, False: 0] ------------------ 1181| 8.80k| { 1182| 8.80k| if ((int)(r_neigh = (AT_NUMB)nRank[(int)nEndpointAtomNumber[k]]) CT_NEIGH_SMALLER_THAN rank) ------------------ | Branch (1182:21): [True: 8.80k, False: 0] ------------------ 1183| 8.80k| { 1184| 8.80k| if (CHECK_OVERFLOW(nCTLen, pCS->nMaxLenLinearCT)) ------------------ | | 43| 8.80k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 8.80k] | | ------------------ ------------------ 1185| 0| { 1186| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1187| 0| } 1188| 17.6k| COMPARE_WITH_CT(LinearCT, nCTLen, r_neigh, bCompare); ------------------ | | 715| 8.80k| if ( CONDITION ) { \ | | ------------------ | | | Branch (715:10): [True: 8.80k, False: 0] | | ------------------ | | 716| 8.80k| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (716:14): [True: 0, False: 8.80k] | | ------------------ | | 717| 8.80k| return 1; /* not a minimal CT */ \ | | 718| 8.80k| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 719| 8.80k| } \ | | 720| 8.80k| (CT)[CTLEN] = VALUE; \ | | 721| 8.80k| (CTLEN)++ ------------------ 1189| 17.6k| } 1190| 8.80k| } 1191| 8.80k| } 1192| 7.35k| } /* end of cycle over all tautomeric groups. */ 1193| | 1194| | /* compare bonds types */ 1195| | /* compare elements */ 1196| | 1197| 290k| if (LinearCT) ------------------ | Branch (1197:9): [True: 290k, False: 0] ------------------ 1198| 290k| { 1199| | 1200| 290k| if (pCS->nLenLinearCT) ------------------ | Branch (1200:13): [True: 290k, False: 0] ------------------ 1201| 290k| { 1202| 290k| if (pCS->nLenLinearCT != nCTLen) ------------------ | Branch (1202:17): [True: 0, False: 290k] ------------------ 1203| 0| { 1204| 0| return CT_LEN_MISMATCH; /* */ ------------------ | | 20| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1205| 0| } 1206| 290k| } 1207| 0| else 1208| 0| { 1209| 0| pCS->nLenLinearCT = nCTLen; 1210| 0| } 1211| | 1212| 290k| if (pCS->nLenLinearCT) ------------------ | Branch (1212:13): [True: 290k, False: 0] ------------------ 1213| 290k| { 1214| 290k| if (pCS->nLenLinearCTAtOnly != nCTLenAtOnly) ------------------ | Branch (1214:17): [True: 0, False: 290k] ------------------ 1215| 0| { 1216| 0| return CT_LEN_MISMATCH; /* */ ------------------ | | 20| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1217| 0| } 1218| 290k| } 1219| 0| else 1220| 0| { 1221| 0| pCS->nLenLinearCTAtOnly = nCTLenAtOnly; 1222| 0| } 1223| 290k| } 1224| | 1225| | /* Return: 0=> identical CT; -1=> new CT is smaller than the previous one */ 1226| 290k| return ( bCompare - 1 ); 1227| 290k|} FixCanonEquivalenceInfo: 1250| 253k|{ 1251| 253k| int nNumDiffRanks, bChangeSymmRank, bChangeCurrRank = 0; 1252| | /* sort equivalence information */ 1253| | /* 1254| | int i; 1255| | for ( i = 0; i < num_at_tg; i ++ ) 1256| | { 1257| | nAtomNumber[i] = i; 1258| | } 1259| | */ 1260| | 1261| 253k| pCG->m_pn_RankForSort = nSymmRank; /* minimal class representatives: min ranks for equiv. atoms */ 1262| 253k| inchi_qsort( pCG, nAtomNumber, num_at_tg, sizeof( nAtomNumber[0] ), CompRanksOrd ); 1263| | 1264| | /* convert equivalence information nSymmRank[] into ranks array nTempRank[] */ 1265| | /* eq. info contains min. possible ranks for eq. atoms; nCurrRank contains max. possible ranks */ 1266| 253k| nNumDiffRanks = SortedEquInfoToRanks( nSymmRank/*inp*/, nTempRank/*out*/, nAtomNumber, num_at_tg, &bChangeSymmRank ); 1267| | 1268| | /* check whether nCurrRank is same as new initial ranks calculated from nSymmRank[] */ 1269| 253k| bChangeCurrRank = memcmp( nCurrRank, nTempRank, num_at_tg * sizeof( nTempRank[0] ) ); 1270| | 1271| | /*----------------------------------------------------------------------- 1272| | if ( bChangeSymmRank || bChangeCurrRank ) { 1273| | This is the case when the initial equitable partitioning does not produce 1274| | constitutionally equivalent classes of atoms. 1275| | Rebuild nSymmRank[] according to the new nCurrRank[] := nTempRank[] 1276| | For such structures the found canonical numbers of the constitutionally equivalent atoms 1277| | are not contiguous (see nCanonRank and nSymmRank examples below). Here arrays 1278| | nCurrRank, nAtomNumber, and nSymmRank are changed so that later the 1279| | contiguous canonical numbers for equivalent atoms can be obtained 1280| | (see GetCanonRanking under 1281| | "III. Get final canonical numbering (no stereo, no isotopic)". 1282| | 1283| | Example: for CAS=37520-11-9 (ID=21247: Ethane, 1,2-dicyclopropyl-), 1284| | 1285| | the numbers are the "final canon. numbers, nCanonRank" 1286| | 1 1287| | 1288| | HC 7 5 3 1289| | | \ 1290| | | >CH--CH2 CH 1291| | | / \ / | 1292| | HC H2C--CH< | 1293| | \ | 1294| | 2 6 8 CH 1295| | 1296| | 4 1297| | 1298| | the arrays (arranged according to ordering in nAtomNumberTemp) are: 1299| | before SortedEquInfoToRanks after SortedRanksToEquInfo 1300| | orig. atom nos.,nAtomNumberTemp: {4 5 6 7 0 1 2 3} {4 5 6 7 0 1 2 3} 1301| | order numbers for sorted ranks: {0 1 2 3 4 5 6 7} {0 1 2 3 4 5 6 7} 1302| | canonical numbering, nCanonRank: {1 2 5 6 3 4 7 8} {1 2 5 6 3 4 7 8} 1303| | constit. equivalence, nSymmRank: {1 1 1 1 3 3 7 7} {1 1 1 1 5 5 7 7} used later 1304| | initial equivalence, nCurrRank: {6 6 6 6 6 6 8 8} {4 4 4 4 6 6 8 8} used later 1305| | initial numbering, nAtomNumber: {2 3 4 7 0 1 6 7} {0 1 2 3 4 5 6 7} used later 1306| | final, no stereo, no isotopic, after III. GetCanonRanking: 1307| | final canon. numbers, nCanonRank: {1 2 3 4 5 6 7 8} final 1308| | } 1309| | ----------------------------------------------------------------------------------*/ 1310| 253k| if (bChangeCurrRank) ------------------ | Branch (1310:9): [True: 835, False: 252k] ------------------ 1311| 835| { 1312| 835| memcpy(nCurrRank, nTempRank, num_at_tg * sizeof(nCurrRank[0])); 1313| 835| } 1314| 253k| if (bChangeSymmRank) ------------------ | Branch (1314:9): [True: 7, False: 253k] ------------------ 1315| 7| { 1316| 7| SortedRanksToEquInfo( nSymmRank/*out*/, nTempRank/*inp*/, nAtomNumber, num_at_tg ); 1317| 7| } 1318| 253k| if (bChanged) ------------------ | Branch (1318:9): [True: 252k, False: 1.14k] ------------------ 1319| 252k| { 1320| 252k| *bChanged = ( 0 != bChangeSymmRank ) | 2 * ( 0 != bChangeCurrRank ); 1321| 252k| } 1322| | 1323| 253k| return nNumDiffRanks; 1324| 253k|} Canon_INChI3: 1343| 288k|{ 1344| | 1345| |/**************************************************************** 1346| | 1347| |0. Initiation, Prepare initial ranks for GetCanonRanking() 1348| | 1349| |I. Find constitutionally equivalent atoms and possibly canonical numbering 1350| |I.1 Set tautomer=On, stereo=isotopic=Off 1351| |I.2 GetCanonRanking(): Find constitutionally equivalent atoms and possibly canonical numbering 1352| |1.3 Fix canonical equivalence info if needed (if the fix is needed then the numbering is not canonical) 1353| | 1354| |II. Get final non-isotopic canonical numbering. Simultaneously obtain non-minimal isotopic and stereo CTs 1355| | GetCanonRanking() with pCS->bKeepSymmRank = 1 1356| | FillOutStereoParities() (create initial stereo descriptors) 1357| | save non-isotopic canonicalization final results 1358| | hide isotopic and tautomeric results (for historical reasons only) 1359| | 1360| | 1361| |III. Find constitutionally equivalent isotopic atoms (for isotopic stereo canonicalization) 1362| |III.1 Allocate more memory 1363| |III.2 fill allocated memory with the initial data 1364| |III.3 duplicate, save old and add isotopic info to the new pCS->t_group_info 1365| |III.4 Prepare initial isotopic ranks for GetCanonRanking() 1366| |III.5 GetCanonRanking() to Find constitutionally equivalent ISOTOPIC atoms and tautomer groups 1367| |III.6 Fix canonical isotopic equivalence information and derive ranks out of it 1368| | 1369| |IV. Prepare a second Rank/AtomNumber Stack for mapping. 1370| | 1371| |V. Optimize isotopic part (optimized) 1372| | map_isotopic_atoms2() 1373| | save isotopic canonical numbering 1374| | 1375| |VI. Optimize stereo descriptors (optimized) 1376| | map_stereo_bonds4() 1377| | 1378| | 1379| |VII. Optimize isotopic stereo descriptors (optimized) 1380| | SwitchAtomStereoAndIsotopicStereo() 1381| | SetCtToIsotopicStereo() 1382| | FillOutStereoParities() 1383| | SetUseAtomForStereo() 1384| | map_stereo_bonds4() 1385| | 1386| | SwitchAtomStereoAndIsotopicStereo() 1387| | SetCtToNonIsotopicStereo() 1388| | 1389| | 1390| | 1391| | 1392| |*****************************************************************/ 1393| | 1394| 288k| int nRet = 0, i, n; 1395| | 1396| | 1397| | /******************************************************** 1398| | input non-stereo canonical info 1399| | ********************************************************/ 1400| 288k| BCN *pBCN = pCS->pBCN; 1401| 288k| FTCN *ftcn = pBCN->ftcn + bTautFtcn; 1402| | 1403| | /******************************************************** 1404| | set mode flags 1405| | ********************************************************/ 1406| | 1407| | /* tautomeric structure */ 1408| 288k| int bTaut = ( num_at_tg > num_atoms ) && pCS->t_group_info && pCS->t_group_info->num_t_groups && pCS->t_group_info->t_group; ------------------ | Branch (1408:17): [True: 3.46k, False: 284k] | Branch (1408:46): [True: 3.46k, False: 0] | Branch (1408:67): [True: 3.46k, False: 0] | Branch (1408:102): [True: 3.46k, False: 0] ------------------ 1409| | 1410| | /* special case: induced by exchangable isotopic H inequivalence of atoms in formally non-tautomeric structure */ 1411| 288k| int bIsoXchgH = pCS->t_group_info && pCS->t_group_info->nNumIsotopicEndpoints > 1 && ------------------ | Branch (1411:21): [True: 252k, False: 36.3k] | Branch (1411:42): [True: 157, False: 251k] ------------------ 1412| 157| pCS->t_group_info->nIsotopicEndpointAtomNumber && pCS->t_group_info->nIsotopicEndpointAtomNumber[0] && ------------------ | Branch (1412:9): [True: 157, False: 0] | Branch (1412:59): [True: 157, False: 0] ------------------ 1413| 157| ( pCS->t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) ------------------ | | 981| 157|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ ( pCS->t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) ------------------ | | 982| 157|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (1413:9): [True: 157, False: 0] ------------------ 1414| 288k| /* && (ftcn->nCanonFlags & CANON_FLAG_ISO_TAUT_DIFF)*/; 1415| 288k| int bHasIsotopicCanonData = ( ftcn->PartitionCtIso.AtNumber && ftcn->PartitionCtIso.Rank && ftcn->nSymmRankCtIso ); ------------------ | Branch (1415:35): [True: 2.12k, False: 286k] | Branch (1415:68): [True: 2.12k, False: 0] | Branch (1415:97): [True: 2.12k, False: 0] ------------------ 1416| | 1417| | /* bHasIsotopicCanonData==0 means 1418| | * (1) No isotopic atoms in the component OR 1419| | * (2) the component has only exchangable isotopic H that do not change canonical numbering and equivalence. 1420| | */ 1421| 288k| T_GROUP_INFO *t_group_info1 = bTaut ? pCS->t_group_info : NULL; ------------------ | Branch (1421:35): [True: 3.46k, False: 284k] ------------------ 1422| | 1423| | /*int bIsoXchgH = t_group_info1 && t_group_info1->nNumIsotopicEndpoints && t_group_info1->nIsotopicEndpointAtomNumber;*/ 1424| | /* isotopic canonicalization */ 1425| 288k| int bCanonIsotopic = bHasIsotopicCanonData && ( nMode & CMODE_ISO ) && ( pCS->LinearCTIsotopic || pCS->LinearCTIsotopicTautomer || bIsoXchgH ); ------------------ | | 770| 2.12k|#define CMODE_ISO 0x000002 ------------------ | Branch (1425:26): [True: 2.12k, False: 286k] | Branch (1425:51): [True: 2.12k, False: 0] | Branch (1425:78): [True: 2.05k, False: 62] | Branch (1425:103): [True: 0, False: 62] | Branch (1425:136): [True: 61, False: 1] ------------------ 1426| | 1427| | /* stereo canonicalization */ 1428| 288k| int bCanonStereo = ( nMode & CMODE_STEREO ) && ( pCS->LinearCTStereoDble || pCS->LinearCTStereoCarb ); ------------------ | | 772| 288k|#define CMODE_STEREO 0x000008 ------------------ | Branch (1428:24): [True: 989, False: 287k] | Branch (1428:54): [True: 344, False: 645] | Branch (1428:81): [True: 552, False: 93] ------------------ 1429| | 1430| | /* stereo isotopic canonicalization */ 1431| 288k| int bCanonIsoStereo = bHasIsotopicCanonData && ( nMode & CMODE_ISO_STEREO ) && ( pCS->LinearCTIsotopicStereoDble || pCS->LinearCTIsotopicStereoCarb ) && bCanonIsotopic; ------------------ | | 773| 2.12k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (1431:27): [True: 2.12k, False: 286k] | Branch (1431:52): [True: 251, False: 1.87k] | Branch (1431:86): [True: 65, False: 186] | Branch (1431:121): [True: 186, False: 0] | Branch (1431:158): [True: 251, False: 0] ------------------ 1432| 288k| int bIsoTaut = ( bTaut && bCanonIsotopic ); ------------------ | Branch (1432:22): [True: 3.46k, False: 284k] | Branch (1432:31): [True: 94, False: 3.37k] ------------------ 1433| | 1434| 288k| int bIgnoreIsotopicInputGroups; 1435| 288k| int bIgnoreIsotopicInputAtoms; 1436| | 1437| 288k| AT_RANK **pRankStack1 = pBCN->pRankStack; 1438| 288k| int nRankStackLen = pBCN->nMaxLenRankStack; 1439| 288k| int num_max = pBCN->num_max; /* allocation lengths in *pRankStack1[] */ 1440| 288k| NEIGH_LIST *NeighList = ftcn->NeighList; 1441| | 1442| 288k| int nNumCurrRanks = 0; 1443| 288k| AT_RANK *nTempRank = NULL; 1444| | 1445| 288k| AT_RANK *nSymmRank = NULL; 1446| | 1447| 288k| AT_RANK *nAtomNumber = NULL; 1448| 288k| AT_RANK *nRank = NULL; 1449| | 1450| 288k| AT_RANK **pRankStack2 = NULL; 1451| 288k| AT_RANK *nCanonRankStereo = NULL; 1452| 288k| AT_RANK *nCanonRankStereoInv = NULL; 1453| 288k| AT_RANK *nSymmStereo = NULL; 1454| | 1455| 288k| AT_RANK *nCanonRankIsotopicStereo = NULL; 1456| 288k| AT_RANK *nCanonRankIsotopicStereoInv = NULL; 1457| | 1458| 288k| CUR_TREE *cur_tree = NULL; 1459| 288k| CUR_TREE CurrentTree; 1460| | 1461| | 1462| | /*AT_ISO_TGROUP *LinearCTIsotopicTautomer = NULL; */ 1463| | 1464| | 1465| 288k| CANON_STAT CS2; 1466| 288k| CANON_STAT* pCS2 = &CS2; 1467| | 1468| 288k| inchiTime ulStartTime, ulEndTime; 1469| | /*=========== Mode Bits (low 8 bits, bit 0 is Least Significant Bit) =========== 1470| | 1471| | Mode Bits Description 1472| | '0' c 0 Only one connection table canonicalization 1473| | '1' C 1 Recalculate CT using fixed nSymmRank 1474| | '2' i 1|2 Isotopic canonicalization (internal) 1475| | '3' I 1|2|4 Isotopic canonicalization (output) 1476| | '4' s 1|8 Stereo canonicalization 1477| | '5' S 1|2|4|16 Stereo isotopic canonicalization 1478| | '6' A 1|2|4|8|16 Output All 1479| | 1480| | --- high 8 bits ---- 1481| | --- obsolete, only historical interest. ------ 1482| | 1-2 : 0 => at[i].init_rank from Morgan+NeighList 1483| | 1 => at[i].init_rank from Atom Invariants 1484| | 2 => at[i].init_rank from nSymmRank[] 1485| | (at[i].init_rank is included in LinearCT 1486| | depending on CT_ATOMID definition) 1487| | 3 : 1 => Get Stereo canonical info 1488| | 4 : 1 => Get Isotopic canonical info 1489| | 5 : 1 => Get Charge/Radical canonical info 1490| | ==================================================================*/ 1491| | /*int nOutputMode = 0;*/ /* obsolete */ 1492| | 1493| | 1494| 288k| int bSwitchedAtomToIsotopic = 0; 1495| | 1496| | 1497| | /* vABParityUnknown holds actual value of an internal constant signifying */ 1498| | /* unknown parity: either the same as for undefined parity (default==standard) */ 1499| | /* or a specific one (non-std; requested by SLUUD switch). */ 1500| 288k| int vABParityUnknown = AB_PARITY_UNDF; ------------------ | | 222| 288k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 1501| 288k| if (0 != ( nMode & REQ_MODE_DIFF_UU_STEREO )) ------------------ | | 40| 288k|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (1501:9): [True: 0, False: 288k] ------------------ 1502| 0| { 1503| | /* Make labels for unknown and undefined stereo different */ 1504| 0| vABParityUnknown = AB_PARITY_UNKN; ------------------ | | 221| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ 1505| 0| } 1506| | 1507| 288k| InchiTimeGet( &ulStartTime ); 1508| | 1509| 288k| *pCS2 = *pCS; /* save input information and pointers to allocated memory */ 1510| | 1511| | /* Set "ignore isotopic differences in tautomer groups" true */ 1512| 288k| if (bTaut) ------------------ | Branch (1512:9): [True: 3.46k, False: 284k] ------------------ 1513| 3.46k| { 1514| | /* save request for isotopic tautomeric groups */ 1515| 3.46k| bIgnoreIsotopicInputGroups = pCS->t_group_info->bIgnoreIsotopic; 1516| 3.46k| pCS->t_group_info->bIgnoreIsotopic = 1; 1517| 3.46k| } 1518| 284k| else 1519| 284k| { 1520| 284k| bIgnoreIsotopicInputGroups = 1; 1521| 284k| } 1522| | /* Save request for isotopic name */ 1523| 288k| bIgnoreIsotopicInputAtoms = pCS->bIgnoreIsotopic; 1524| | /* set "ignore isotopic differences in atoms" true */ 1525| 288k| pCS->bIgnoreIsotopic = 1; 1526| | 1527| | 1528| | /* Save non-isotopic and isotopic canonicalization results */ 1529| 288k| pCS->nCanonFlags = ftcn->nCanonFlags; 1530| | /* 1. non-isotopic */ 1531| | 1532| | /* linear CT, H */ 1533| 288k| memcpy(pCS->LinearCT, ftcn->LinearCt, ftcn->nLenLinearCt * sizeof(pCS->LinearCT[0])); 1534| 288k| if (pCS->nNum_H && ftcn->nNumH) ------------------ | Branch (1534:9): [True: 288k, False: 0] | Branch (1534:24): [True: 288k, False: 0] ------------------ 1535| 288k| { 1536| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1536:21): [True: 1.09M, False: 288k] ------------------ 1537| 1.09M| { 1538| 1.09M| pCS->nNum_H[i] = /*(S_CHAR)*/( CHAR_MASK & ftcn->nNumH[i] ); ------------------ | | 19| 1.09M|#define CHAR_MASK 0xFF ------------------ 1539| 1.09M| } 1540| 288k| } 1541| 288k| if (pCS->nNum_H_fixed && ftcn->nNumHFixH) ------------------ | Branch (1541:9): [True: 288k, False: 0] | Branch (1541:30): [True: 36.3k, False: 252k] ------------------ 1542| 36.3k| { 1543| 80.2k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1543:21): [True: 43.9k, False: 36.3k] ------------------ 1544| 43.9k| { 1545| 43.9k| pCS->nNum_H_fixed[i] = /*(S_CHAR)*/( CHAR_MASK & ftcn->nNumHFixH[i] ); ------------------ | | 19| 43.9k|#define CHAR_MASK 0xFF ------------------ 1546| 43.9k| } 1547| 36.3k| } 1548| 288k| pCS->nLenLinearCT = ftcn->nLenLinearCt; 1549| 288k| pCS->nLenLinearCTAtOnly = ftcn->nLenLinearCtAtOnly; 1550| | 1551| | /* save non-isotopic atoms equivalence and numbering */ 1552| 288k| if (pCS->nSymmRank) ------------------ | Branch (1552:9): [True: 288k, False: 0] ------------------ 1553| 288k| { 1554| 288k| memcpy(pCS->nSymmRank, ftcn->nSymmRankCt, num_at_tg * sizeof(pCS->nSymmRank[0])); 1555| 288k| } 1556| 288k| if (pCS->nCanonOrd) ------------------ | Branch (1556:9): [True: 288k, False: 0] ------------------ 1557| 288k| { 1558| 288k| memcpy(pCS->nCanonOrd, ftcn->PartitionCt.AtNumber, num_at_tg * sizeof(pCS->nCanonOrd[0])); 1559| 288k| pCS->nLenCanonOrd = num_atoms; 1560| 288k| } 1561| 288k| if (ftcn->iso_exchg_atnos && pCS->nExchgIsoH) ------------------ | Branch (1561:9): [True: 157, False: 288k] | Branch (1561:34): [True: 157, False: 0] ------------------ 1562| 157| { 1563| 3.60k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1563:21): [True: 3.45k, False: 157] ------------------ 1564| 3.45k| { 1565| 3.45k| pCS->nExchgIsoH[i] = !ftcn->iso_exchg_atnos[i]; /* (pCS->nExchgIsoH[i]==1) => tautomeric or hetero atoms that may exchange isotopic H */ 1566| 3.45k| } 1567| 157| } 1568| | /* 2. isotopic */ 1569| | 1570| 288k| if (bCanonIsotopic) ------------------ | Branch (1570:9): [True: 2.12k, False: 286k] ------------------ 1571| 2.12k| { 1572| | /* linear CT, num_H are same as non-isotopic */ 1573| | /* save atoms equivalence and numbering */ 1574| 2.12k| if (pCS->nSymmRankIsotopic) ------------------ | Branch (1574:13): [True: 2.12k, False: 0] ------------------ 1575| 2.12k| { 1576| 2.12k| memcpy(pCS->nSymmRankIsotopic, ftcn->nSymmRankCtIso, num_at_tg * sizeof(pCS->nSymmRankIsotopic[0])); 1577| 2.12k| } 1578| 2.12k| if (pCS->nCanonOrdIsotopic) ------------------ | Branch (1578:13): [True: 2.12k, False: 0] ------------------ 1579| 2.12k| { 1580| 2.12k| memcpy(pCS->nCanonOrdIsotopic, ftcn->PartitionCtIso.AtNumber, num_at_tg * sizeof(pCS->nCanonOrdIsotopic[0])); 1581| 2.12k| pCS->nLenCanonOrdIsotopic = num_at_tg; 1582| 2.12k| } 1583| | 1584| 2.12k| nRet = FillIsotopicAtLinearCT( num_atoms, at, 1585| 2.12k| ftcn->PartitionCtIso.AtNumber, 1586| 2.12k| pCS->LinearCTIsotopic, 1587| 2.12k| pCS->nMaxLenLinearCTIsotopic, 1588| 2.12k| &pCS->nLenLinearCTIsotopic ); 1589| | 1590| 2.12k| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 2.12k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.12k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.12k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.12k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.12k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.12k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.12k, False: 0] | | | Branch (44:53): [True: 0, False: 2.12k] | | ------------------ ------------------ 1591| 0| { 1592| 0| goto exit_function; 1593| 0| } 1594| 2.12k| if (nRet < 0) ------------------ | Branch (1594:13): [True: 0, False: 2.12k] ------------------ 1595| 0| { 1596| 0| nRet = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1597| 0| goto exit_function; 1598| 0| } 1599| 2.12k| } 1600| 286k| else 1601| 286k| { 1602| 286k| pCS->nMaxLenLinearCTIsotopic = 0; 1603| 286k| pCS->nMaxLenLinearCTIsotopicTautomer = 0; 1604| 286k| } 1605| | 1606| | /* fill out tautomeric groups, isotopic and non-isotopic tautomeric CT and t_group_info1->tGroupNumber */ 1607| 288k| if (bTaut) ------------------ | Branch (1607:9): [True: 3.46k, False: 284k] ------------------ 1608| 3.46k| { 1609| 3.46k| bIsoTaut = bIsoTaut && ftcn->PartitionCtIso.Rank && ------------------ | Branch (1609:20): [True: 94, False: 3.37k] | Branch (1609:32): [True: 94, False: 0] ------------------ 1610| 94| ftcn->PartitionCtIso.AtNumber && ftcn->nSymmRankCtIso; ------------------ | Branch (1610:13): [True: 94, False: 0] | Branch (1610:46): [True: 94, False: 0] ------------------ 1611| | 1612| 3.46k| nRet = FillTautLinearCT2( pCG, num_atoms, num_at_tg, bIsoTaut, 1613| 3.46k| ftcn->PartitionCt.Rank, ftcn->PartitionCt.AtNumber, ftcn->nSymmRankCt, 1614| 3.46k| ftcn->PartitionCtIso.Rank, ftcn->PartitionCtIso.AtNumber, ftcn->nSymmRankCtIso, 1615| 3.46k| pCS->LinearCTTautomer, pCS->nMaxLenLinearCTTautomer, &pCS->nLenLinearCTTautomer, 1616| 3.46k| pCS->LinearCTIsotopicTautomer, pCS->nMaxLenLinearCTIsotopicTautomer, &pCS->nLenLinearCTIsotopicTautomer, 1617| 3.46k| t_group_info1 ); 1618| | 1619| 3.46k| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 3.46k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 3.46k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 3.46k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 3.46k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 3.46k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 3.46k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 3.46k, False: 0] | | | Branch (44:53): [True: 0, False: 3.46k] | | ------------------ ------------------ 1620| 0| { 1621| 0| goto exit_function; 1622| 0| } 1623| 3.46k| if (nRet <= 0) ------------------ | Branch (1623:13): [True: 0, False: 3.46k] ------------------ 1624| 0| { 1625| 0| nRet = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1626| 0| goto exit_function; 1627| 0| } 1628| 3.46k| else 1629| 3.46k| { 1630| | /* tautomeric groups: save non-isotopic symmetry & t_group order */ 1631| 3.46k| int num_t_groups = t_group_info1->num_t_groups; 1632| 3.46k| AT_NUMB *tGroupNumber = t_group_info1->tGroupNumber; 1633| 3.46k| AT_NUMB *tSymmRank = tGroupNumber + TGSO_SYMM_RANK*num_t_groups; ------------------ | | 138| 3.46k|#define TGSO_SYMM_RANK 1 /* tSymmRank: symmetry ranks (no isotopes) = min. ordering number > 0. */ ------------------ 1634| 3.46k| if (pCS->nSymmRankTaut) ------------------ | Branch (1634:17): [True: 3.46k, False: 0] ------------------ 1635| 3.46k| { 1636| 3.46k| memcpy(pCS->nSymmRankTaut, tSymmRank, num_t_groups * sizeof(pCS->nSymmRank[0])); /* fixed 5-23-02 */ 1637| 3.46k| } 1638| 3.46k| if (pCS->nCanonOrdTaut) ------------------ | Branch (1638:17): [True: 3.46k, False: 0] ------------------ 1639| 3.46k| { 1640| 3.46k| memcpy(pCS->nCanonOrdTaut, tGroupNumber, num_t_groups * sizeof(pCS->nCanonOrdTaut[0])); 1641| 3.46k| pCS->nLenCanonOrdTaut = num_t_groups; 1642| 3.46k| } 1643| 3.46k| if (bCanonIsotopic /*&& pCS->nLenLinearCTIsotopicTautomer*/) ------------------ | Branch (1643:17): [True: 94, False: 3.37k] ------------------ 1644| 94| { 1645| | /* tautomeric groups: save isotopic symmetry & t_group order */ 1646| | /*AT_NUMB ntRankOffset = (AT_RANK)num_atoms;*/ 1647| 94| AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*(long long)num_t_groups; /* djb-rwth: cast operator added */ ------------------ | | 140| 94|#define TGSO_SYMM_IRANK 3 /* tiSymmRank: isotopic symmetry ranks */ ------------------ 1648| 94| AT_NUMB *tiGroupNumber = tGroupNumber + TGSO_SYMM_IORDER*(long long)num_t_groups; /* djb-rwth: cast operator added */ ------------------ | | 139| 94|#define TGSO_SYMM_IORDER 2 /* tiGroupNumber: isotopic symmetry rank sorting order */ ------------------ 1649| 94| if (pCS->nSymmRankIsotopicTaut) ------------------ | Branch (1649:21): [True: 94, False: 0] ------------------ 1650| 94| { 1651| 94| memcpy(pCS->nSymmRankIsotopicTaut, tiSymmRank, num_t_groups * sizeof(pCS->nSymmRankIsotopicTaut[0])); 1652| 94| } 1653| 94| memcpy(pCS->nCanonOrdIsotopicTaut, tiGroupNumber, num_t_groups * sizeof(pCS->nCanonOrdIsotopicTaut[0])); 1654| 94| pCS->nLenCanonOrdIsotopicTaut = num_t_groups; 1655| 94| } 1656| 3.46k| } 1657| 3.46k| } 1658| | /* save connection table if requested */ 1659| 288k| if (pCS->LinearCT2) ------------------ | Branch (1659:9): [True: 288k, False: 0] ------------------ 1660| 288k| { 1661| 288k| memcpy(pCS->LinearCT2, pCS->LinearCT, sizeof(pCS->LinearCT2[0])* pCS->nLenLinearCT); 1662| 288k| pCS->nLenLinearCT2 = pCS->nLenLinearCT; 1663| 288k| pCS->nLenLinearCTAtOnly2 = pCS->nLenLinearCTAtOnly; 1664| 288k| } 1665| | 1666| 288k| if (num_atoms <= 1) ------------------ | Branch (1666:9): [True: 184k, False: 103k] ------------------ 1667| 184k| { 1668| 184k| bCanonStereo = 0; /* a sinle atom + possibly terminal hydrogen atoms */ 1669| 184k| if (num_atoms < 1 || !at[0].parity2) ------------------ | Branch (1669:13): [True: 0, False: 184k] | Branch (1669:30): [True: 184k, False: 0] ------------------ 1670| 184k| { 1671| 184k| bCanonIsoStereo = 0; /* structure; for example Cl- or CH4 */ 1672| 184k| } 1673| 184k| } 1674| | 1675| 288k| if (!bCanonStereo && !( bCanonIsotopic && bCanonIsoStereo )) ------------------ | Branch (1675:9): [True: 287k, False: 896] | Branch (1675:29): [True: 1.89k, False: 285k] | Branch (1675:47): [True: 30, False: 1.86k] ------------------ 1676| 287k| { 1677| 287k| goto exit_function; /* skip stereo canonicalization */ 1678| 287k| } 1679| | 1680| | 1681| | 1682| | /********************************************************** 1683| | Mode 1684| | ***********************************************************/ 1685| 926| nMode = nMode & CANON_MODE_MASK; ------------------ | | 792| 926|#define CANON_MODE_MASK 0x00FF /* used to determine canonicalization mode */ ------------------ 1686| | 1687| | /* memory allocation */ 1688| | 1689| 926| nAtomNumber = (AT_RANK *) qmalloc( num_max * sizeof( *nAtomNumber ) ); ------------------ | | 1164| 926|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 926|#define inchi_malloc malloc | | ------------------ ------------------ 1690| 926| nRank = (AT_RANK *) qmalloc( num_max * sizeof( *nRank ) ); ------------------ | | 1164| 926|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 926|#define inchi_malloc malloc | | ------------------ ------------------ 1691| 926| nTempRank = (AT_RANK *) qmalloc( num_max * sizeof( *nTempRank ) ); ------------------ | | 1164| 926|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 926|#define inchi_malloc malloc | | ------------------ ------------------ 1692| 926| nSymmRank = (AT_RANK *) qmalloc( num_max * sizeof( *nSymmRank ) ); ------------------ | | 1164| 926|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 926|#define inchi_malloc malloc | | ------------------ ------------------ 1693| | 1694| | /*********************************************** 1695| | 0.1 Initialization 1696| | ************************************************/ 1697| | 1698| | 1699| 926| if (!NeighList || !nAtomNumber || !nTempRank || ------------------ | Branch (1699:9): [True: 0, False: 926] | Branch (1699:23): [True: 0, False: 926] | Branch (1699:39): [True: 0, False: 926] ------------------ 1700| 926| !nRank || !pCS->LinearCT) ------------------ | Branch (1700:10): [True: 0, False: 926] | Branch (1700:20): [True: 0, False: 926] ------------------ 1701| 0| { 1702| 0| nRet = CT_OUT_OF_RAM; /* program error */ /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1703| 0| goto exit_function; 1704| 0| } 1705| | 1706| 926| pCS->NeighList = NeighList; 1707| | 1708| 926| *pCS2 = *pCS; /* save input information and pointers to allocated memory */ 1709| | 1710| 926| if (!( nMode & CMODE_NOEQ_STEREO ) && ( bCanonStereo || bCanonIsoStereo )) ------------------ | | 775| 926|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1710:9): [True: 926, False: 0] | Branch (1710:45): [True: 896, False: 30] | Branch (1710:61): [True: 30, False: 0] ------------------ 1711| 926| { 1712| | /* will be used to discover vertex equivalences in stereo canonicalization */ 1713| 926| memset( &CurrentTree, 0, sizeof( CurrentTree ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1714| 926| cur_tree = &CurrentTree; 1715| 926| } 1716| | 1717| | 1718| 926| pCS->bCmpStereo = 0; 1719| 926| pCS->bCmpIsotopicStereo = 0; 1720| | 1721| | 1722| 926| if (bCanonStereo || bCanonIsoStereo) ------------------ | Branch (1722:9): [True: 896, False: 30] | Branch (1722:25): [True: 30, False: 0] ------------------ 1723| 926| { 1724| 926| int ii, nn; 1725| | 1726| | /* stereo or isotopic canonicalization: we need a second set of ranks for mapping */ 1727| | /* (isotopic atoms or stereo can only increase nNumCurrRanks) */ 1728| 926| pRankStack2 = (AT_RANK **) inchi_calloc( nRankStackLen, sizeof( AT_RANK * ) ); ------------------ | | 1146| 926|#define inchi_calloc calloc ------------------ 1729| 926| if (pRankStack2) ------------------ | Branch (1729:13): [True: 926, False: 0] ------------------ 1730| 926| { 1731| | /* prepare for ranks reuse */ 1732| 4.88k| for (nn = 2; nn < nRankStackLen && pRankStack1[nn]; nn++) ------------------ | Branch (1732:26): [True: 4.88k, False: 0] | Branch (1732:48): [True: 3.95k, False: 926] ------------------ 1733| 3.95k| { 1734| 3.95k| pRankStack1[nn][0] = 0; /* means ranks have to be calculated */ 1735| 3.95k| } 1736| | /* reuse memory to reduce number of allocations: */ 1737| | /* move last half of pointers from pRankStack1 to pRankStack2 */ 1738| | /* The first 2 elements will be assigned separately */ 1739| 926| if (( nn = ( nn - 2 ) / 2 ) > 0) ------------------ | Branch (1739:17): [True: 746, False: 180] ------------------ 1740| 746| { 1741| 2.73k| for (ii = 2 + nn; ii < nRankStackLen && pRankStack1[ii]; ii++) ------------------ | Branch (1741:35): [True: 2.73k, False: 0] | Branch (1741:57): [True: 1.98k, False: 746] ------------------ 1742| 1.98k| { 1743| 1.98k| pRankStack2[ii - nn] = pRankStack1[ii]; 1744| 1.98k| pRankStack1[ii] = NULL; 1745| 1.98k| } 1746| 746| } 1747| 926| } 1748| 0| else 1749| 0| { 1750| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1751| 0| goto exit_function; /* program error */ 1752| 0| } 1753| 926| } 1754| | 1755| 926| if (bCanonStereo) ------------------ | Branch (1755:9): [True: 896, False: 30] ------------------ 1756| 896| { 1757| | 1758| | /* *pCS2 = *pCS; */ /* save input information and pointers to allocated memory */ 1759| | 1760| | /* initial ranking for non-isotopic mapping */ 1761| 896| memcpy(nAtomNumber, ftcn->PartitionCt.AtNumber, num_at_tg * sizeof(nAtomNumber[0])); 1762| 896| memcpy(nRank, ftcn->PartitionCt.Rank, num_at_tg * sizeof(nRank[0])); 1763| 896| memcpy(nSymmRank, ftcn->nSymmRankCt, num_at_tg * sizeof(nSymmRank[0])); 1764| | 1765| | /* nSymmRank changes if canonical numbers of constitutionally equivalent atoms are not contiguous */ 1766| 896| nNumCurrRanks = FixCanonEquivalenceInfo( pCG, num_at_tg, 1767| 896| nSymmRank /* in&out*/, 1768| 896| nRank, nTempRank /* out */, 1769| 896| nAtomNumber /* in&out */, 1770| 896| NULL ); 1771| | /* atom numbers in canonical order */ 1772| 896| memcpy(pCS->nPrevAtomNumber, ftcn->PartitionCt.AtNumber, num_at_tg * sizeof(nAtomNumber[0])); 1773| | 1774| | /* fill stereo part of the connection table with initial (not optimized) parities */ 1775| | /* input 1776| | pCS->LinearCTStereoDble 1777| | pCS->LinearCTStereoCarb 1778| | pCS->nMaxLenLinearCTStereoCarb 1779| | pCS->nMaxLenLinearCTStereoDble 1780| | */ 1781| | 1782| 896| nRet = FillOutStereoParities( at, num_atoms, ftcn->PartitionCt.Rank, ftcn->PartitionCt.AtNumber, 1783| 896| nRank, nAtomNumber, pCS, pCG, 0 /* bIsotopic */ ); 1784| | 1785| | /* output 1786| | pCS->LinearCTStereoDble 1787| | pCS->LinearCTStereoCarb 1788| | pCS2->nLenLinearCTStereoCarb 1789| | pCS2->nLenLinearCTStereoDble 1790| | */ 1791| | 1792| 896| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 896|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 896|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 896|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 896|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 896|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 896|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 896, False: 0] | | | Branch (44:53): [True: 0, False: 896] | | ------------------ ------------------ 1793| 0| { 1794| 0| goto exit_function; 1795| 0| } 1796| 896| if (nRet < 0) ------------------ | Branch (1796:13): [True: 0, False: 896] ------------------ 1797| 0| { 1798| 0| nRet = CT_STEREOCOUNT_ERR; ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1799| 0| goto exit_function; 1800| 0| } 1801| | 1802| | /*************************************************************** 1803| | * 1804| | * VI. Optimize non-isotopic stereo descriptors (optimized) 1805| | * 1806| | ***************************************************************/ 1807| | 1808| | /* allocate memory for stereo canonicalization */ 1809| | 1810| 896| if (!nCanonRankStereo) ------------------ | Branch (1810:13): [True: 896, False: 0] ------------------ 1811| 896| { 1812| 896| nCanonRankStereo = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankStereo ) ); ------------------ | | 1164| 896|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 896|#define inchi_malloc malloc | | ------------------ ------------------ 1813| 896| } 1814| 896| if (!nSymmStereo && !( nMode & CMODE_NOEQ_STEREO )) ------------------ | | 775| 896|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1814:13): [True: 896, False: 0] | Branch (1814:29): [True: 896, False: 0] ------------------ 1815| 896| { 1816| 896| nSymmStereo = (AT_RANK *) qmalloc( ( (long long)num_max + 1 ) * sizeof( *nSymmStereo ) ); /* djb-rwth: cast operator added */ ------------------ | | 1164| 896|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 896|#define inchi_malloc malloc | | ------------------ ------------------ 1817| 896| } 1818| | 1819| 896| if (!( nMode & CMODE_NOEQ_STEREO ) && 0 > CurTreeAlloc( cur_tree, num_at_tg )) ------------------ | | 775| 896|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1819:13): [True: 896, False: 0] | Branch (1819:47): [True: 0, False: 896] ------------------ 1820| 0| { 1821| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1822| 0| goto exit_function; 1823| 0| } 1824| | /* check allocations and assign first 2 elements of pRankStack2 */ 1825| 896| if (pRankStack1 && pRankStack2 && ------------------ | Branch (1825:13): [True: 896, False: 0] | Branch (1825:28): [True: 896, False: 0] ------------------ 1826| 896| nCanonRankStereo && ------------------ | Branch (1826:14): [True: 896, False: 0] ------------------ 1827| | /* nCurrRankStereo && nAtomNumberCurrStereo &&*/ 1828| 896| ( nSymmStereo || ( nMode & CMODE_NOEQ_STEREO ) )) ------------------ | | 775| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1828:16): [True: 896, False: 0] | Branch (1828:31): [True: 0, False: 0] ------------------ 1829| 896| { 1830| 896| pRankStack1[0] = pRankStack2[0] = nRank; 1831| 896| pRankStack1[1] = pRankStack2[1] = nAtomNumber; 1832| 896| } 1833| 0| else 1834| 0| { 1835| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1836| 0| goto exit_function; 1837| 0| } 1838| | 1839| | /**************************************************************** 1840| | * 1841| | * VI-A. Optimize non-isotopic non-inverted stereo descriptors 1842| | * 1843| | ****************************************************************/ 1844| | 1845| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 1846| 2.83k| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (1846:21): [True: 2.83k, False: 0] | Branch (1846:42): [True: 1.93k, False: 896] ------------------ 1847| 1.93k| { 1848| 1.93k| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 1849| 1.93k| } 1850| | /* set the 1st ranks to zero: prepare for ranks reuse */ 1851| 2.85k| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (1851:21): [True: 2.85k, False: 0] | Branch (1851:42): [True: 1.95k, False: 896] ------------------ 1852| 1.95k| { 1853| 1.95k| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 1854| 1.95k| } 1855| | 1856| | /* for debugging or statistics */ 1857| 896| pCS->lNumBreakTies = 1858| 896| pCS->lNumNeighListIter = 1859| 896| pCS->lNumTotCT = 1860| 896| pCS->lNumDecreasedCT = 1861| 896| pCS->lNumRejectedCT = 1862| 896| pCS->lNumEqualCT = 0; 1863| 896| pCS->bKeepSymmRank = 0; 1864| 896| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 1865| | 1866| | /****************************************************************************** 1867| | nCanonRank contains input canonical numbering 1868| | nCanonRankStereo will be filled with a transposition of canonical numbering 1869| | which (1) keeps connection table unchanged and 1870| | (2) provides minimal stereo descriptors in 1871| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 1872| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 1873| | */ 1874| | 1875| 896| nRet = map_stereo_bonds4( ic, pCG, at, num_atoms, num_at_tg, num_max, 0, 1876| 896| ftcn->PartitionCt.Rank, ftcn->PartitionCt.AtNumber, 1877| 896| nCanonRankStereo, nSymmRank, 1878| 896| pRankStack1, pRankStack2, 1879| 896| nTempRank, nNumCurrRanks,nSymmStereo, 1880| 896| NeighList, pCS, cur_tree, 0 /* nNumMappedBonds */, 1881| 896| vABParityUnknown ); 1882| | 1883| 896| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 896|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 896|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 896|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 896|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 896|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 896|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 896, False: 0] | | | Branch (44:53): [True: 0, False: 896] | | ------------------ ------------------ 1884| 0| { 1885| 0| if (nRet == CT_TIMEOUT_ERR) ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1885:17): [True: 0, False: 0] ------------------ 1886| 0| { 1887| 0| goto exit_function; 1888| 0| } 1889| 0| else 1890| 0| { 1891| 0| goto exit_function; /* program error */ 1892| 0| } 1893| 0| } 1894| 896| else 1895| 896| { 1896| 896| int bFailed = 0; 1897| 896| if (!nRet) ------------------ | Branch (1897:17): [True: 0, False: 896] ------------------ 1898| 0| { 1899| | /* djb-rwth: removing redundant code */ 1900| 0| pCS2->nLenLinearCTStereoCarb = 1901| 0| pCS->nLenLinearCTStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 1902| 0| pCS2->nLenLinearCTStereoDble = 1903| 0| pCS->nLenLinearCTStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 1904| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1905| 0| goto exit_function; /* program error */ 1906| 0| } 1907| 896| else 1908| 896| { 1909| | /* save non-isotopic lengths */ 1910| 896| pCS2->nLenLinearCTStereoDble = pCS->nLenLinearCTStereoDble; 1911| 896| pCS2->nLenLinearCTStereoCarb = pCS->nLenLinearCTStereoCarb; 1912| | /* djb-rwth: removing redundant code */ 1913| 896| } 1914| | 1915| | /* save stereo canonical numbering */ 1916| 896| if (pCS->nCanonOrdStereo) ------------------ | Branch (1916:17): [True: 896, False: 0] ------------------ 1917| 896| { 1918| 6.29k| for (i = 0; i < num_at_tg; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (1918:29): [True: 5.39k, False: 896] ------------------ 1919| 5.39k| { 1920| 5.39k| if (nCanonRankStereo[i] && (int) nCanonRankStereo[i] <= num_at_tg) ------------------ | Branch (1920:25): [True: 5.39k, False: 0] | Branch (1920:48): [True: 5.39k, False: 0] ------------------ 1921| 5.39k| { 1922| 5.39k| pCS->nCanonOrdStereo[(int) nCanonRankStereo[i] - 1] = (AT_NUMB) i; 1923| 5.39k| } 1924| 0| else 1925| 0| { 1926| 0| bFailed++; 1927| 0| } 1928| 5.39k| } 1929| 896| pCS->nLenCanonOrdStereo = ( bFailed ) ? -num_atoms : num_atoms; ------------------ | Branch (1929:43): [True: 0, False: 896] ------------------ 1930| 896| } 1931| | 1932| | /* save stereo tautomer groups numbering */ 1933| 896| if (bTaut && pCS->nCanonOrdStereoTaut) ------------------ | Branch (1933:17): [True: 35, False: 861] | Branch (1933:26): [True: 35, False: 0] ------------------ 1934| 35| { 1935| 35| if (0 < ( nRet = SortTautomerGroupsAndEndpoints( pCG, t_group_info1, num_atoms, num_at_tg, nCanonRankStereo ) )) ------------------ | Branch (1935:21): [True: 35, False: 0] ------------------ 1936| 35| { 1937| | /*non-isotopic contains symmetry ranks */ 1938| 35| int num_t_groups = t_group_info1->num_t_groups; 1939| 35| AT_NUMB *tGroupNumber = t_group_info1->tGroupNumber; 1940| | /*AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*num_t_groups; */ 1941| 35| memcpy(pCS->nCanonOrdStereoTaut, tGroupNumber, num_t_groups * sizeof(pCS->nCanonOrdStereoTaut[0])); 1942| 35| pCS->nLenCanonOrdStereoTaut = ( bFailed ) ? -num_t_groups ------------------ | Branch (1942:51): [True: 0, False: 35] ------------------ 1943| 35| : num_t_groups; 1944| 35| } 1945| 0| else 1946| 0| { 1947| 0| if (RETURNED_ERROR(nRet)) ------------------ | | 44| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 0, False: 0] | | | Branch (44:53): [True: 0, False: 0] | | ------------------ ------------------ 1948| 0| { 1949| 0| goto exit_function; 1950| 0| } 1951| 0| } 1952| | /* djb-rwth: removing redundant code */ 1953| | /*SortTautomerGroupsAndEndpoints( t_group_info1, nCanonRank ); */ /* ??? return to non-isotopic canonical numbering */ 1954| 35| } 1955| 896| } 1956| | 1957| | 1958| | /**************************************************** 1959| | * 1960| | * VI-B. Optimize INVERTED stereo descriptors 1961| | * 1962| | ****************************************************/ 1963| 896| if (!nCanonRankStereoInv) ------------------ | Branch (1963:13): [True: 896, False: 0] ------------------ 1964| 896| { 1965| 896| nCanonRankStereoInv = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankStereoInv ) ); ------------------ | | 1164| 896|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 896|#define inchi_malloc malloc | | ------------------ ------------------ 1966| 896| } 1967| 896| if (!nCanonRankStereoInv) ------------------ | Branch (1967:13): [True: 0, False: 896] ------------------ 1968| 0| { 1969| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1970| 0| goto exit_function; 1971| 0| } 1972| | 1973| | /* copy previous non-isotopic stereo canonicalization results to Inv initial data */ 1974| | /* assign pointers */ 1975| 896| pCS->LinearCTStereoDble = pCS2->LinearCTStereoDbleInv; 1976| 896| pCS->LinearCTStereoCarb = pCS2->LinearCTStereoCarbInv; 1977| | 1978| | /* copy the lengths */ 1979| 896| pCS2->nLenLinearCTStereoDbleInv = 1980| 896| pCS->nLenLinearCTStereoDbleInv = 1981| 896| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble; 1982| | 1983| 896| pCS2->nLenLinearCTStereoCarbInv = 1984| 896| pCS->nLenLinearCTStereoCarbInv = 1985| 896| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb; 1986| | 1987| 896| if (pCS->nLenLinearCTStereoDble > 0 || pCS->nLenLinearCTStereoCarb > 0) ------------------ | Branch (1987:13): [True: 311, False: 585] | Branch (1987:48): [True: 487, False: 98] ------------------ 1988| 798| { 1989| | /* copy previous results, the canonical stereo CT */ 1990| 798| memcpy(pCS->LinearCTStereoDble, pCS2->LinearCTStereoDble, pCS->nLenLinearCTStereoDble * sizeof(pCS->LinearCTStereoDble[0])); 1991| 798| memcpy(pCS->LinearCTStereoCarb, pCS2->LinearCTStereoCarb, pCS->nLenLinearCTStereoCarb * sizeof(pCS->LinearCTStereoCarb[0])); 1992| 798| } 1993| 896| memcpy(nCanonRankStereoInv, nCanonRankStereo, num_max * sizeof(nCanonRankStereoInv[0])); 1994| 896| if (pCS->nCanonOrdStereoInv && pCS->nCanonOrdStereo) ------------------ | Branch (1994:13): [True: 896, False: 0] | Branch (1994:40): [True: 896, False: 0] ------------------ 1995| 896| { 1996| | /* in case there is nothing to invert */ 1997| 896| memcpy(pCS->nCanonOrdStereoInv, pCS->nCanonOrdStereo, num_at_tg * sizeof(pCS->nCanonOrdStereoInv[0])); 1998| 896| } 1999| | 2000| | /****************************** 2001| | * 2002| | * Invert stereo 2003| | * 2004| | ******************************/ 2005| | 2006| | /********************************************************************************* 2007| | * Create initial approximation for the minimization of the stereo descriptors: 2008| | * invert stereogenic atom parities, one parity in each allene, all parities in 2009| | * pCS->LinearCTStereoCarb and allene parities in pCS->nLenLinearCTStereoDble 2010| | */ 2011| 896| nRet = InvertStereo( at, num_at_tg, nCanonRankStereo, nTempRank, pCS, 1 /* bInvertLinearCTStereo */ ); 2012| 896| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 896|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 896|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 896|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 896|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 896|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 896|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 896, False: 0] | | | Branch (44:53): [True: 0, False: 896] | | ------------------ ------------------ 2013| 0| { 2014| 0| goto exit_function; 2015| 0| } 2016| 896| else if (nRet > 0) ------------------ | Branch (2016:18): [True: 324, False: 572] ------------------ 2017| 324| { 2018| | /* InvertStereo() has done some changes */ 2019| | /* djb-rwth: removing redundant code */ 2020| | /* FillOutStereoParities() has already been called to fill out these 2 LinearCTs */ 2021| | 2022| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 2023| 1.92k| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (2023:25): [True: 1.92k, False: 0] | Branch (2023:46): [True: 1.59k, False: 324] ------------------ 2024| 1.59k| { 2025| 1.59k| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 2026| 1.59k| } 2027| | /* set the 1st ranks to zero: prepare for ranks reuse */ 2028| 1.92k| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2028:25): [True: 1.92k, False: 0] | Branch (2028:46): [True: 1.59k, False: 324] ------------------ 2029| 1.59k| { 2030| 1.59k| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 2031| 1.59k| } 2032| | 2033| | /* for debugging or statistics */ 2034| 324| pCS->lNumBreakTies = 2035| 324| pCS->lNumNeighListIter = 2036| 324| pCS->lNumTotCT = 2037| 324| pCS->lNumDecreasedCT = 2038| 324| pCS->lNumRejectedCT = 2039| 324| pCS->lNumEqualCT = 0; 2040| 324| pCS->bKeepSymmRank = 0; 2041| 324| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 2042| | 2043| 324|#ifdef FIX_STEREOCOUNT_ERR 2044| 324| CurTreeSetPos( cur_tree, 0 ); 2045| 324|#endif 2046| | 2047| | /****************************************************************************** 2048| | ftcn->PartitionCt.Rank contains input canonical numbering 2049| | nCanonRankStereoInv will be filled with a transposition of canonical numbering 2050| | which (1) keeps connection table unchanged and 2051| | (2) provides minimal stereo descriptors in 2052| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 2053| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 2054| | ******************************************************************************/ 2055| | 2056| 324| nRet = map_stereo_bonds4( ic,pCG, at, num_atoms, num_at_tg, num_max, 0, 2057| 324| ftcn->PartitionCt.Rank, 2058| 324| ftcn->PartitionCt.AtNumber, 2059| 324| nCanonRankStereoInv, 2060| 324| nSymmRank, pRankStack1, pRankStack2, 2061| 324| nTempRank, nNumCurrRanks, nSymmStereo, 2062| 324| NeighList, pCS, cur_tree, 0, 2063| 324| vABParityUnknown ); 2064| | 2065| 324| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 324|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 324|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 324|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 324|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 324|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 324|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 324, False: 0] | | | Branch (44:53): [True: 0, False: 324] | | ------------------ ------------------ 2066| 0| { 2067| 0| if (nRet == CT_TIMEOUT_ERR) ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (2067:21): [True: 0, False: 0] ------------------ 2068| 0| { 2069| 0| goto exit_function; 2070| 0| } 2071| 0| else 2072| 0| { 2073| 0| goto exit_function; /* program error */ 2074| 0| } 2075| 0| } 2076| 324| else 2077| 324| { 2078| 324| int bFailed = 0; 2079| 324| if (!nRet) ------------------ | Branch (2079:21): [True: 0, False: 324] ------------------ 2080| 0| { 2081| | /* djb-rwth: removing redundant code */ 2082| 0| pCS2->nLenLinearCTStereoCarb = 2083| 0| pCS->nLenLinearCTStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 2084| 0| pCS2->nLenLinearCTStereoDble = 2085| 0| pCS->nLenLinearCTStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 2086| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2087| 0| goto exit_function; /* program error */ 2088| 0| } 2089| | 2090| | /* save non-isotopic pointers & lengths for INVERTED stereo */ 2091| 324| pCS->nLenLinearCTStereoDbleInv = 2092| 324| pCS2->nLenLinearCTStereoDbleInv = pCS->nLenLinearCTStereoDble; 2093| 324| pCS->nLenLinearCTStereoCarbInv = 2094| 324| pCS2->nLenLinearCTStereoCarbInv = pCS->nLenLinearCTStereoCarb; 2095| | 2096| | /* restore pointers and lengths to non-inverted stereo */ 2097| | /* -- this is needed for InvertStereo() back, see below */ 2098| 324| pCS->LinearCTStereoDble = pCS2->LinearCTStereoDble; 2099| 324| pCS->LinearCTStereoCarb = pCS2->LinearCTStereoCarb; 2100| 324| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble; 2101| 324| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb; 2102| | /* consistency check */ 2103| 324| if (pCS->nLenLinearCTStereoDbleInv != pCS->nLenLinearCTStereoDble || ------------------ | Branch (2103:21): [True: 0, False: 324] ------------------ 2104| 324| pCS->nLenLinearCTStereoCarbInv != pCS->nLenLinearCTStereoCarb) ------------------ | Branch (2104:22): [True: 0, False: 324] ------------------ 2105| 0| { 2106| 0| nRet = CT_CALC_STEREO_ERR; ------------------ | | 34| 0|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2107| 0| goto exit_function; /* program error */ 2108| 0| } 2109| | 2110| | /****************************** 2111| | * 2112| | * Invert stereo back 2113| | * 2114| | ****************************** 2115| | * (make sure that pointers 2116| | * pCS->LinearCTStereoCarb, 2117| | * pCS->LinearCTStereoDble 2118| | * and corresponding lengths 2119| | * have been restored) 2120| | ******************************/ 2121| | /********************************************************************************* 2122| | * invert only stereogenic atom parities and one parity in each allene, DO NOT 2123| | * change parities in pCS->LinearCTStereoCarb and pCS->nLenLinearCTStereoDble 2124| | */ 2125| 324| nRet = InvertStereo( at, 2126| 324| num_at_tg, 2127| 324| nCanonRankStereo, 2128| 324| nTempRank, 2129| 324| pCS, 2130| 324| 0 ); 2131| | 2132| 324| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 324|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 324|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 324|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 324|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 324|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 324|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 324, False: 0] | | | Branch (44:53): [True: 1, False: 323] | | ------------------ ------------------ 2133| 1| { 2134| 1| goto exit_function; 2135| 1| } 2136| 323| nRet = 0; 2137| | 2138| | 2139| | /* save stereo canonical numbering */ 2140| 323| if (pCS->nCanonOrdStereoInv) ------------------ | Branch (2140:21): [True: 323, False: 0] ------------------ 2141| 323| { 2142| 2.24k| for (i = 0; i < num_at_tg; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (2142:33): [True: 1.92k, False: 323] ------------------ 2143| 1.92k| { 2144| 1.92k| if (nCanonRankStereoInv[i] && (int) nCanonRankStereoInv[i] <= num_at_tg) ------------------ | Branch (2144:29): [True: 1.92k, False: 0] | Branch (2144:55): [True: 1.92k, False: 0] ------------------ 2145| 1.92k| { 2146| 1.92k| pCS->nCanonOrdStereoInv[(int) nCanonRankStereoInv[i] - 1] = (AT_NUMB) i; 2147| 1.92k| } 2148| 0| else 2149| 0| { 2150| 0| bFailed++; 2151| 0| } 2152| 1.92k| } 2153| 323| pCS->nLenCanonOrdStereo = ( bFailed ) ? -num_atoms : num_atoms; ------------------ | Branch (2153:47): [True: 0, False: 323] ------------------ 2154| 323| } 2155| | 2156| | /* compare inverted and non-inverted stereo */ 2157| 323| pCS->bCmpStereo = 2 + CompareLinCtStereo( 2158| 323| pCS->LinearCTStereoDbleInv, pCS->nLenLinearCTStereoDbleInv, 2159| 323| pCS->LinearCTStereoCarbInv, pCS->nLenLinearCTStereoCarbInv, 2160| 323| pCS->LinearCTStereoDble, pCS->nLenLinearCTStereoDble, 2161| 323| pCS->LinearCTStereoCarb, pCS->nLenLinearCTStereoCarb 2162| 323| ); 2163| 323| } 2164| 324| } 2165| 572| else if (0 == nRet) ------------------ | Branch (2165:18): [True: 572, False: 0] ------------------ 2166| 572| { 2167| | /* nothing has been done, restore pointers and lengths for stereo */ 2168| 572| pCS->LinearCTStereoDble = pCS2->LinearCTStereoDble; 2169| 572| pCS->LinearCTStereoCarb = pCS2->LinearCTStereoCarb; 2170| 572| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble; 2171| 572| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb; 2172| 572| } 2173| 896| } 2174| | 2175| | /* restore "ignore isotopic differences in tautomer groups" */ 2176| 925| if (bTaut) ------------------ | Branch (2176:9): [True: 47, False: 878] ------------------ 2177| 47| { 2178| | /* save request for isotopic tautomeric groups */ 2179| 47| pCS->t_group_info->bIgnoreIsotopic = bIgnoreIsotopicInputGroups; 2180| 47| } 2181| | 2182| | /* restore request for isotopic name */ 2183| 925| pCS->bIgnoreIsotopic = bIgnoreIsotopicInputAtoms; 2184| | 2185| 925| if (bCanonIsoStereo && bCanonIsotopic) ------------------ | Branch (2185:9): [True: 251, False: 674] | Branch (2185:28): [True: 251, False: 0] ------------------ 2186| 251| { 2187| | 2188| | /**************************************************************** 2189| | * 2190| | * VII. Optimize isotopic stereo descriptors (optimized) 2191| | * 2192| | ****************************************************************/ 2193| | /* 2194| | pCS->LinearCTIsotopic = NULL; 2195| | */ 2196| | 2197| | /* Initial ranking for isotopic mapping */ 2198| 251| memcpy(nAtomNumber, ftcn->PartitionCtIso.AtNumber, num_at_tg * sizeof(nAtomNumber[0])); 2199| 251| memcpy(nRank, ftcn->PartitionCtIso.Rank, num_at_tg * sizeof(nRank[0])); 2200| 251| memcpy(nSymmRank, ftcn->nSymmRankCtIso, num_at_tg * sizeof(nSymmRank[0])); 2201| | /* nSymmRank will change if canonical numbers of of constitutionally equivalent atoms are not contiguous */ 2202| 251| nNumCurrRanks = FixCanonEquivalenceInfo( pCG, num_at_tg, nSymmRank /* in&out*/, 2203| 251| nRank, nTempRank /* out */, nAtomNumber /* in&out */, NULL ); 2204| 251| memcpy(pCS->nPrevAtomNumber, ftcn->PartitionCtIso.AtNumber, num_at_tg * sizeof(nAtomNumber[0])); 2205| | /* Allocate memory for optimized stereo canonicalization */ 2206| | /* for stereo canonical numbering to be found. */ 2207| 251| if (!nCanonRankIsotopicStereo) ------------------ | Branch (2207:13): [True: 251, False: 0] ------------------ 2208| 251| { 2209| 251| nCanonRankIsotopicStereo = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankIsotopicStereo ) ); ------------------ | | 1164| 251|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 251|#define inchi_malloc malloc | | ------------------ ------------------ 2210| 251| } 2211| 251| if (!nSymmStereo && !( nMode & CMODE_NOEQ_STEREO )) ------------------ | | 775| 30|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (2211:13): [True: 30, False: 221] | Branch (2211:29): [True: 30, False: 0] ------------------ 2212| 30| { 2213| 30| nSymmStereo = (AT_RANK *) qmalloc( ( (long long)num_max + 1 ) * sizeof( *nSymmStereo ) ); /* djb-rwth: cast operator added */ ------------------ | | 1164| 30|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 30|#define inchi_malloc malloc | | ------------------ ------------------ 2214| 30| } 2215| 251| if (!( nMode & CMODE_NOEQ_STEREO ) && CurTreeAlloc( cur_tree, num_at_tg )) ------------------ | | 775| 251|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (2215:13): [True: 251, False: 0] | Branch (2215:47): [True: 0, False: 251] ------------------ 2216| 0| { 2217| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2218| 0| goto exit_function; 2219| 0| } 2220| | 2221| | /* Check allocations and assign first 2 elements of pRankStack2 */ 2222| 251| if (pRankStack1 && pRankStack2 && ------------------ | Branch (2222:13): [True: 251, False: 0] | Branch (2222:28): [True: 251, False: 0] ------------------ 2223| 251| nCanonRankIsotopicStereo && ------------------ | Branch (2223:14): [True: 251, False: 0] ------------------ 2224| 251| ( nSymmStereo || ( nMode & CMODE_NOEQ_STEREO ) )) ------------------ | | 775| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (2224:16): [True: 251, False: 0] | Branch (2224:31): [True: 0, False: 0] ------------------ 2225| 251| { 2226| | 2227| 251| pRankStack1[0] = pRankStack2[0] = nRank; /* pRankStack1[0,1] shall be unchanged */ 2228| 251| pRankStack1[1] = pRankStack2[1] = nAtomNumber; 2229| 251| } 2230| 0| else 2231| 0| { 2232| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2233| 0| goto exit_function; 2234| 0| } 2235| | 2236| | /****************************************************************** 2237| | Important: fill out a list of stereo atoms and bonds including 2238| | those which are stereo due to isotopic atoms only and create 2239| | LinearCT stereo descriptors for the canonical numbering 2240| | ******************************************************************/ 2241| | 2242| | 2243| | /* at[] has certain members for non-isotopic and isotopic stereo; switch them */ 2244| 251| SwitchAtomStereoAndIsotopicStereo( at, num_atoms, &bSwitchedAtomToIsotopic ); 2245| | 2246| | /* Prepare stereo connection tables' pointers */ 2247| 251| SetCtToIsotopicStereo( pCS, pCS2 ); 2248| | 2249| 251| nRet = FillOutStereoParities( at, num_atoms, 2250| 251| ftcn->PartitionCtIso.Rank, 2251| 251| ftcn->PartitionCtIso.AtNumber, 2252| 251| nRank, nAtomNumber, 2253| 251| pCS, pCG, 1 /* bIsotopic */ ); 2254| | 2255| | 2256| 251| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 251|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 251|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 251|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 251|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 251|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 251|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 251, False: 0] | | | Branch (44:53): [True: 0, False: 251] | | ------------------ ------------------ 2257| 0| { 2258| 0| goto exit_function; /* program error */ 2259| 0| } 2260| 251| else 2261| 251| { 2262| 251| if (!nRet) ------------------ | Branch (2262:17): [True: 21, False: 230] ------------------ 2263| 21| { 2264| | /* no isotopic stereo */ 2265| 21| pCS2->nLenLinearCTIsotopicStereoDble = pCS->nLenLinearCTIsotopicStereoDble = 0; 2266| 21| pCS2->nLenLinearCTIsotopicStereoCarb = pCS->nLenLinearCTIsotopicStereoCarb = 0; 2267| 21| pCS->nLenCanonOrdIsotopicStereo = 0; 2268| 21| pCS->nLenCanonOrdIsotopicStereoTaut = 0; 2269| 21| pCS2->nLenLinearCTIsotopicStereoDbleInv = pCS->nLenLinearCTIsotopicStereoDbleInv = 0; 2270| 21| pCS2->nLenLinearCTIsotopicStereoCarbInv = pCS->nLenLinearCTIsotopicStereoCarbInv = 0; 2271| 21| goto bypass_isotopic_stereo; 2272| 21| } 2273| 251| } 2274| | 2275| | /* djb-rwth: removing redundant code */ 2276| | 2277| | 2278| | /************************************************************* 2279| | * 2280| | * VII-A. Optimize non-inverted isotopic stereo descriptors 2281| | * 2282| | *************************************************************/ 2283| | 2284| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 2285| 1.08k| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (2285:21): [True: 1.08k, False: 0] | Branch (2285:42): [True: 854, False: 230] ------------------ 2286| 854| { 2287| 854| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 2288| 854| } 2289| | /* set the 1st ranks to zero: prepare for ranks reuse */ 2290| 1.08k| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2290:21): [True: 1.08k, False: 0] | Branch (2290:42): [True: 854, False: 230] ------------------ 2291| 854| { 2292| 854| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 2293| 854| } 2294| | 2295| | /* for debugging or statistics */ 2296| 230| pCS->lNumBreakTies = 2297| 230| pCS->lNumNeighListIter = 2298| 230| pCS->lNumTotCT = 2299| 230| pCS->lNumDecreasedCT = 2300| 230| pCS->lNumRejectedCT = 2301| 230| pCS->lNumEqualCT = 0; 2302| 230| pCS->bKeepSymmRank = 0; 2303| 230| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 2304| | 2305| | /************************************************************************************** 2306| | nCanonRankIsotopic contains input canonical numbering 2307| | nCanonRankIsotopicStereo will be filled with a transposition of canonical numbering 2308| | that (1) keeps connection table unchanged and 2309| | (2) provides minimal stereo descriptors in 2310| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 2311| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 2312| | ***************************************************************************************/ 2313| | 2314| 230| nRet = map_stereo_bonds4( ic, pCG,at, num_atoms, num_at_tg, num_max, 0, 2315| 230| ftcn->PartitionCtIso.Rank, 2316| 230| ftcn->PartitionCtIso.AtNumber, 2317| 230| nCanonRankIsotopicStereo, 2318| 230| nSymmRank, pRankStack1, pRankStack2, 2319| 230| nTempRank, nNumCurrRanks, nSymmStereo, 2320| 230| NeighList, pCS, cur_tree, 2321| 230| 0, vABParityUnknown ); 2322| | 2323| 230| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 230|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 230|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 230|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 230|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 230|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 230|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 230, False: 0] | | | Branch (44:53): [True: 0, False: 230] | | ------------------ ------------------ 2324| 0| { 2325| 0| goto exit_function; 2326| 0| } 2327| 230| else 2328| 230| { 2329| 230| int bFailed = 0; 2330| | 2331| 230| if (!nRet) ------------------ | Branch (2331:17): [True: 0, False: 230] ------------------ 2332| 0| { 2333| | /* djb-rwth: removing redundant code */ 2334| 0| pCS2->nLenLinearCTIsotopicStereoDble = 2335| 0| pCS->nLenLinearCTIsotopicStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 2336| 0| pCS2->nLenLinearCTIsotopicStereoCarb = 2337| 0| pCS->nLenLinearCTIsotopicStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 2338| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2339| 0| goto exit_function; /* program error */ 2340| 0| } 2341| 230| else 2342| 230| { 2343| | /* save isotopic lengths */ 2344| 230| pCS->nLenLinearCTIsotopicStereoDble = 2345| 230| pCS2->nLenLinearCTIsotopicStereoDble = pCS->nLenLinearCTStereoDble; 2346| 230| pCS->nLenLinearCTIsotopicStereoCarb = 2347| 230| pCS2->nLenLinearCTIsotopicStereoCarb = pCS->nLenLinearCTStereoCarb; 2348| | 2349| | /* save stereo canonical numbering */ 2350| 230| if (pCS->nCanonOrdIsotopicStereo) ------------------ | Branch (2350:21): [True: 230, False: 0] ------------------ 2351| 230| { 2352| 1.69k| for (i = 0; i < num_at_tg; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (2352:33): [True: 1.46k, False: 230] ------------------ 2353| 1.46k| { 2354| 1.46k| if (nCanonRankIsotopicStereo[i] && (int) nCanonRankIsotopicStereo[i] <= num_at_tg) ------------------ | Branch (2354:29): [True: 1.46k, False: 0] | Branch (2354:60): [True: 1.46k, False: 0] ------------------ 2355| 1.46k| { 2356| 1.46k| pCS->nCanonOrdIsotopicStereo[(int) nCanonRankIsotopicStereo[i] - 1] = (AT_NUMB) i; 2357| 1.46k| } 2358| 0| else 2359| 0| { 2360| 0| bFailed++; 2361| 0| } 2362| 1.46k| } 2363| 230| pCS->nLenCanonOrdIsotopicStereo = bFailed ? -num_atoms : num_atoms; ------------------ | Branch (2363:55): [True: 0, False: 230] ------------------ 2364| 230| } 2365| | 2366| | /* save stereo tautomer groups numbering */ 2367| 230| if (pCS->nCanonOrdIsotopicStereoTaut) ------------------ | Branch (2367:21): [True: 18, False: 212] ------------------ 2368| 18| { 2369| 18| if (0 < ( nRet = SortTautomerGroupsAndEndpoints( pCG, t_group_info1, num_atoms, num_at_tg, nCanonRankIsotopicStereo ) )) ------------------ | Branch (2369:25): [True: 18, False: 0] ------------------ 2370| 18| { 2371| | /*non-isotopic contains symmetry ranks */ 2372| 18| int num_t_groups = t_group_info1->num_t_groups; 2373| 18| AT_NUMB *tGroupNumber = t_group_info1->tGroupNumber; 2374| | /*AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*num_t_groups; */ 2375| 18| memcpy(pCS->nCanonOrdIsotopicStereoTaut, tGroupNumber, num_t_groups * sizeof(pCS->nCanonOrdIsotopicStereoTaut[0])); 2376| 18| pCS->nLenCanonOrdIsotopicStereoTaut = bFailed ? -num_t_groups : num_t_groups; ------------------ | Branch (2376:63): [True: 0, False: 18] ------------------ 2377| | 2378| | /*SortTautomerGroupsAndEndpoints( t_group_info1, nCanonRank ); */ /* ??? return to non-isotopic canonical numbering */ 2379| 18| } 2380| 0| else 2381| 0| { 2382| 0| if (RETURNED_ERROR(nRet)) ------------------ | | 44| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 0, False: 0] | | | Branch (44:53): [True: 0, False: 0] | | ------------------ ------------------ 2383| 0| { 2384| 0| goto exit_function; 2385| 0| } 2386| 0| } 2387| | /* djb-rwth: removing redundant code */ 2388| 18| } 2389| 230| } 2390| 230| } 2391| | 2392| | /********************************************************** 2393| | * 2394| | * VII-B. Optimize INVERTED isotopic stereo descriptors 2395| | * 2396| | **********************************************************/ 2397| 230| if (!nCanonRankIsotopicStereoInv) ------------------ | Branch (2397:13): [True: 230, False: 0] ------------------ 2398| 230| nCanonRankIsotopicStereoInv = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankIsotopicStereoInv ) ); ------------------ | | 1164| 230|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1143| 230|#define inchi_malloc malloc | | ------------------ ------------------ 2399| 230| if (!nCanonRankIsotopicStereoInv) ------------------ | Branch (2399:13): [True: 0, False: 230] ------------------ 2400| 0| { 2401| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2402| 0| goto exit_function; 2403| 0| } 2404| | 2405| | /* copy previous isotopic stereo canonicalization results to Inv initial data */ 2406| | /* assign pointers */ 2407| 230| pCS->LinearCTStereoDble = pCS2->LinearCTIsotopicStereoDbleInv; /* enable stereo */ 2408| 230| pCS->LinearCTStereoCarb = pCS2->LinearCTIsotopicStereoCarbInv; 2409| | 2410| | /* copy the lengths */ 2411| 230| pCS2->nLenLinearCTIsotopicStereoDbleInv = 2412| 230| pCS->nLenLinearCTStereoDbleInv = 2413| 230| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 2414| | 2415| 230| pCS2->nLenLinearCTIsotopicStereoCarbInv = 2416| 230| pCS->nLenLinearCTStereoCarbInv = 2417| 230| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 2418| | 2419| 230| if (pCS->nLenLinearCTStereoDble > 0 || pCS->nLenLinearCTStereoCarb > 0) ------------------ | Branch (2419:13): [True: 55, False: 175] | Branch (2419:48): [True: 164, False: 11] ------------------ 2420| 219| { 2421| | /* copy previous results, the canonical stereo CT */ 2422| 219| memcpy(pCS->LinearCTStereoDble, pCS2->LinearCTIsotopicStereoDble, pCS->nLenLinearCTStereoDble * sizeof(pCS->LinearCTStereoDble[0])); 2423| 219| memcpy(pCS->LinearCTStereoCarb, pCS2->LinearCTIsotopicStereoCarb, pCS->nLenLinearCTStereoCarb * sizeof(pCS->LinearCTStereoCarb[0])); 2424| 219| } 2425| 230| memcpy(nCanonRankIsotopicStereoInv, nCanonRankIsotopicStereo, num_max * sizeof(nCanonRankIsotopicStereoInv[0])); 2426| 230| if (pCS->nCanonOrdIsotopicStereoInv && pCS->nCanonOrdIsotopicStereo) ------------------ | Branch (2426:13): [True: 230, False: 0] | Branch (2426:48): [True: 230, False: 0] ------------------ 2427| 230| { 2428| | /* in case there is nothing to invert */ 2429| 230| memcpy(pCS->nCanonOrdIsotopicStereoInv, pCS->nCanonOrdIsotopicStereo, num_at_tg * sizeof(pCS->nCanonOrdIsotopicStereoInv[0])); 2430| 230| } 2431| | 2432| | /****************************** 2433| | * 2434| | * Invert isotopic stereo 2435| | * 2436| | ******************************/ 2437| | 2438| | /********************************************************************************* 2439| | * Create initial approximation for the minimization of the stereo descriptors: 2440| | * invert stereogenic atom parities, one parity in each allene, all parities in 2441| | * pCS->LinearCTStereoCarb and allene parities in pCS->nLenLinearCTStereoDble 2442| | */ 2443| | 2444| 230| nRet = InvertStereo( at, 2445| 230| num_at_tg, 2446| 230| nCanonRankIsotopicStereo, 2447| 230| nTempRank, 2448| 230| pCS, 2449| 230| 1 ); 2450| | 2451| 230| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 230|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 230|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 230|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 230|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 230|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 230|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 230, False: 0] | | | Branch (44:53): [True: 0, False: 230] | | ------------------ ------------------ 2452| 0| { 2453| 0| goto exit_function; 2454| 0| } 2455| 230| else if (nRet > 0) ------------------ | Branch (2455:18): [True: 113, False: 117] ------------------ 2456| 113| { 2457| | /* InvertStereo() has done some changes */ 2458| | /* djb-rwth: removing redundant code */ 2459| | /* FillOutStereoParities() has already been called to fill out these 2 LinearCTs */ 2460| | 2461| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 2462| 539| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (2462:25): [True: 539, False: 0] | Branch (2462:46): [True: 426, False: 113] ------------------ 2463| 426| { 2464| 426| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 2465| 426| } 2466| | /* set the 1st ranks to zero: prepare for ranks reuse */ 2467| 539| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2467:25): [True: 539, False: 0] | Branch (2467:46): [True: 426, False: 113] ------------------ 2468| 426| { 2469| 426| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 2470| 426| } 2471| | /* for debugging or statistics */ 2472| 113| pCS->lNumBreakTies = 2473| 113| pCS->lNumNeighListIter = 2474| 113| pCS->lNumTotCT = 2475| 113| pCS->lNumDecreasedCT = 2476| 113| pCS->lNumRejectedCT = 2477| 113| pCS->lNumEqualCT = 0; 2478| 113| pCS->bKeepSymmRank = 0; 2479| 113| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 2480| | 2481| | /************************************************************************************** 2482| | nCanonRankIsotopic contains input canonical numbering 2483| | nCanonRankIsotopicStereo will be filled with a transposition of canonical numbering 2484| | that (1) keeps connection table unchanged and 2485| | (2) provides minimal stereo descriptors in 2486| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 2487| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 2488| | */ 2489| 113| nRet = map_stereo_bonds4( ic, pCG, 2490| 113| at, 2491| 113| num_atoms, 2492| 113| num_at_tg, 2493| 113| num_max, 2494| 113| 0, 2495| 113| ftcn->PartitionCtIso.Rank, 2496| 113| ftcn->PartitionCtIso.AtNumber, 2497| 113| nCanonRankIsotopicStereoInv, 2498| 113| nSymmRank, 2499| 113| pRankStack1, 2500| 113| pRankStack2, 2501| 113| nTempRank, 2502| 113| nNumCurrRanks, 2503| 113| nSymmStereo, 2504| 113| NeighList, 2505| 113| pCS, 2506| 113| cur_tree, 2507| 113| 0, 2508| 113| vABParityUnknown ); 2509| | 2510| 113| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 113|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 113|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 113|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 113|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 113|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 113|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 113, False: 0] | | | Branch (44:53): [True: 0, False: 113] | | ------------------ ------------------ 2511| 0| { 2512| 0| if (nRet == CT_TIMEOUT_ERR) ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (2512:21): [True: 0, False: 0] ------------------ 2513| 0| goto exit_function; 2514| 0| else 2515| 0| goto exit_function; /* program error */ 2516| 0| } 2517| 113| else 2518| 113| { 2519| 113| int bFailed = 0; 2520| | 2521| 113| if (!nRet) ------------------ | Branch (2521:21): [True: 0, False: 113] ------------------ 2522| 0| { 2523| | /* djb-rwth: removing redundant code */ 2524| 0| pCS2->nLenLinearCTIsotopicStereoDble = 2525| 0| pCS->nLenLinearCTIsotopicStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 2526| 0| pCS2->nLenLinearCTIsotopicStereoCarb = 2527| 0| pCS->nLenLinearCTIsotopicStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 2528| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2529| 0| goto exit_function; /* program error */ 2530| 0| } 2531| | 2532| | /* save isotopic pointers & lengths for INVERTED stereo */ 2533| | 2534| | /* save isotopic lengths */ 2535| 113| pCS->nLenLinearCTIsotopicStereoDbleInv = 2536| 113| pCS2->nLenLinearCTIsotopicStereoDbleInv = pCS->nLenLinearCTStereoDble; 2537| 113| pCS->nLenLinearCTIsotopicStereoCarbInv = 2538| 113| pCS2->nLenLinearCTIsotopicStereoCarbInv = pCS->nLenLinearCTStereoCarb; 2539| | 2540| | /* restore pointers and lengths to non-inverted isotopic stereo */ 2541| | /* -- this is needed for InvertStereo() back, see below */ 2542| 113| pCS->LinearCTStereoDble = pCS2->LinearCTIsotopicStereoDble; 2543| 113| pCS->LinearCTStereoCarb = pCS2->LinearCTIsotopicStereoCarb; 2544| 113| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 2545| 113| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 2546| | 2547| | /* consistency check */ 2548| 113| if (pCS->nLenLinearCTIsotopicStereoDbleInv != pCS->nLenLinearCTIsotopicStereoDble || ------------------ | Branch (2548:21): [True: 0, False: 113] ------------------ 2549| 113| pCS->nLenLinearCTIsotopicStereoCarbInv != pCS->nLenLinearCTIsotopicStereoCarb) ------------------ | Branch (2549:22): [True: 0, False: 113] ------------------ 2550| 0| { 2551| 0| nRet = CT_CALC_STEREO_ERR; ------------------ | | 34| 0|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2552| 0| goto exit_function; /* program error */ 2553| 0| } 2554| | 2555| | /****************************** 2556| | * 2557| | * Invert stereo back 2558| | * 2559| | ****************************** 2560| | * (make sure that pointers 2561| | * pCS->LinearCTStereoCarb, 2562| | * pCS->LinearCTStereoDble 2563| | * and corresponding lengths 2564| | * have been restored) 2565| | ******************************/ 2566| | 2567| 113| nRet = InvertStereo( at, num_at_tg, nCanonRankIsotopicStereo, 2568| 113| nTempRank, pCS, 0 ); 2569| | 2570| 113| if (RETURNED_ERROR( nRet )) ------------------ | | 44| 113|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 113|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 113|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 113|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 113|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 113|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 113, False: 0] | | | Branch (44:53): [True: 0, False: 113] | | ------------------ ------------------ 2571| 0| { 2572| 0| goto exit_function; 2573| 0| } 2574| 113| nRet = 0; 2575| | 2576| | /* save stereo canonical numbering */ 2577| 113| if (pCS->nCanonOrdIsotopicStereoInv) ------------------ | Branch (2577:21): [True: 113, False: 0] ------------------ 2578| 113| { 2579| 875| for (i = 0; i < num_at_tg; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (2579:33): [True: 762, False: 113] ------------------ 2580| 762| { 2581| 762| if (nCanonRankIsotopicStereoInv[i] && (int) nCanonRankIsotopicStereoInv[i] <= num_at_tg) ------------------ | Branch (2581:29): [True: 762, False: 0] | Branch (2581:63): [True: 762, False: 0] ------------------ 2582| 762| { 2583| 762| pCS->nCanonOrdIsotopicStereoInv[(int) nCanonRankIsotopicStereoInv[i] - 1] = (AT_NUMB) i; 2584| 762| } 2585| 0| else 2586| 0| { 2587| 0| bFailed++; 2588| 0| } 2589| 762| } 2590| 113| pCS->nLenCanonOrdIsotopicStereo = bFailed ? -num_atoms : num_atoms; ------------------ | Branch (2590:55): [True: 0, False: 113] ------------------ 2591| 113| } 2592| | 2593| | /* compare inverted and non-inverted isotopic stereo */ 2594| 113| pCS->bCmpIsotopicStereo = 2 + CompareLinCtStereo( 2595| 113| pCS->LinearCTIsotopicStereoDbleInv, pCS->nLenLinearCTIsotopicStereoDbleInv, 2596| 113| pCS->LinearCTIsotopicStereoCarbInv, pCS->nLenLinearCTIsotopicStereoCarbInv, 2597| 113| pCS->LinearCTIsotopicStereoDble, pCS->nLenLinearCTIsotopicStereoDble, 2598| 113| pCS->LinearCTIsotopicStereoCarb, pCS->nLenLinearCTIsotopicStereoCarb 2599| 113| ); 2600| 113| } 2601| 113| } 2602| 117| else if (0 == nRet) ------------------ | Branch (2602:18): [True: 117, False: 0] ------------------ 2603| 117| { 2604| | /* nothing has been done, restore pointers and lengths for stereo */ 2605| 117| pCS->LinearCTStereoDble = pCS2->LinearCTIsotopicStereoDble; 2606| 117| pCS->LinearCTStereoCarb = pCS2->LinearCTIsotopicStereoCarb; 2607| 117| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 2608| 117| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 2609| 117| } 2610| | 2611| | 2612| 251| bypass_isotopic_stereo:; /* ??? */ 2613| | 2614| 251| pCS->LinearCTIsotopic = pCS2->LinearCTIsotopic; 2615| 251| } 2616| | 2617| | 2618| | 2619| 288k|exit_function: 2620| | 2621| 288k| if (bSwitchedAtomToIsotopic) ------------------ | Branch (2621:9): [True: 251, False: 288k] ------------------ 2622| 251| { 2623| 251| SwitchAtomStereoAndIsotopicStereo( at, num_atoms, &bSwitchedAtomToIsotopic ); 2624| 251| SetCtToNonIsotopicStereo( pCS, pCS2 ); /* ??? */ 2625| 251| } 2626| | 2627| | /* restore non-isotopic connection table */ 2628| 288k| if (pCS->LinearCT2) ------------------ | Branch (2628:9): [True: 288k, False: 0] ------------------ 2629| 288k| { 2630| 288k| inchi_swap( (char*) &pCS->LinearCT, (char*) &pCS->LinearCT2, sizeof( pCS->LinearCT ) ); 2631| 288k| inchi_swap( (char*) &pCS->nLenLinearCT, (char*) &pCS->nLenLinearCT2, sizeof( pCS->nLenLinearCT ) ); 2632| 288k| inchi_swap( (char*) &pCS->nLenLinearCTAtOnly, (char*) &pCS->nLenLinearCTAtOnly2, sizeof( pCS->nLenLinearCTAtOnly ) ); 2633| 288k| } 2634| | 2635| | /* free memory */ 2636| 288k| i = 2; 2637| 288k| if (pRankStack1) ------------------ | Branch (2637:9): [True: 288k, False: 0] ------------------ 2638| 288k| { 2639| 288k| pRankStack1[0] = 2640| 288k| pRankStack1[1] = NULL; /* deallocated separately */ 2641| 1.16M| for (; i < nRankStackLen && pRankStack1[i]; i++) ------------------ | Branch (2641:16): [True: 1.16M, False: 0] | Branch (2641:37): [True: 873k, False: 288k] ------------------ 2642| 873k| { 2643| 873k| ; 2644| 873k| } 2645| 288k| } 2646| 288k| if (pRankStack1 && pRankStack2) ------------------ | Branch (2646:9): [True: 288k, False: 0] | Branch (2646:24): [True: 926, False: 287k] ------------------ 2647| 926| { 2648| 4.55k| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2648:21): [True: 4.55k, False: 0] | Branch (2648:42): [True: 3.62k, False: 926] ------------------ 2649| 3.62k| { 2650| 3.62k| if (i < nRankStackLen - 1) ------------------ | Branch (2650:17): [True: 2.75k, False: 873] ------------------ 2651| 2.75k| { 2652| 2.75k| pRankStack1[i++] = pRankStack2[n]; 2653| 2.75k| } 2654| 873| else 2655| 873| { 2656| 873| inchi_free( pRankStack2[n] ); ------------------ | | 1152| 873|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 873, False: 0] | | | Branch (1152:50): [Folded, False: 873] | | ------------------ ------------------ 2657| 873| } 2658| 3.62k| } 2659| 926| } 2660| | 2661| 288k| inchi_free(pRankStack2); /* djb-rwth: fixing coverity ID #499631 */ ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 926, False: 287k] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 2662| | 2663| 288k| pCS->NeighList = NULL; /* keep the pointer in pBCN->ftcn[bTaut].NeighList for further deallocation */ 2664| 288k| qfree( nAtomNumber ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 926, False: 0] | | | | | Branch (1152:50): [Folded, False: 926] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 926, False: 287k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2665| 288k| qfree( nTempRank ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 926, False: 0] | | | | | Branch (1152:50): [Folded, False: 926] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 926, False: 287k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2666| 288k| qfree( nRank ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 926, False: 0] | | | | | Branch (1152:50): [Folded, False: 926] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 926, False: 287k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2667| 288k| qfree( nSymmRank ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 926, False: 0] | | | | | Branch (1152:50): [Folded, False: 926] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 926, False: 287k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2668| | 2669| 288k| qfree( nSymmStereo ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 926, False: 0] | | | | | Branch (1152:50): [Folded, False: 926] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 926, False: 287k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2670| 288k| CurTreeFree( cur_tree ); 2671| | /* memory leak fix */ 2672| | /* 2673| | qfree ( nCurrRankIsotopicStereo ); 2674| | qfree ( nAtomNumberCurrIsotopicStereo); 2675| | */ 2676| 288k| qfree( nCanonRankIsotopicStereo ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 251|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 251, False: 0] | | | | | Branch (1152:50): [Folded, False: 251] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 251, False: 288k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2677| 288k| qfree( nCanonRankIsotopicStereoInv ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 230|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 230, False: 0] | | | | | Branch (1152:50): [Folded, False: 230] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 230, False: 288k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2678| | 2679| 288k| qfree( nCanonRankStereo ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 896|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 896, False: 0] | | | | | Branch (1152:50): [Folded, False: 896] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 896, False: 287k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2680| 288k| qfree( nCanonRankStereoInv ); ------------------ | | 1165| 288k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 896|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 896, False: 0] | | | | | Branch (1152:50): [Folded, False: 896] | | | | ------------------ | | ------------------ | | | Branch (1165:26): [True: 896, False: 287k] | | | Branch (1165:60): [Folded, False: 288k] | | ------------------ ------------------ 2681| | 2682| 288k| InchiTimeGet( &ulEndTime ); 2683| | 2684| 288k| pCS->lTotalTime = InchiTimeMsecDiff( ic, &ulEndTime, &ulStartTime ); 2685| | 2686| 288k| return ( nRet >= -1 ) ? num_atoms : nRet; ------------------ | Branch (2686:12): [True: 288k, False: 1] ------------------ 2687| | /* cannot easily get number of ranks for now */ 2688| 925|} Canon_INChI: 2700| 288k|{ 2701| 288k| if (pCS->pBCN && !pCS->NeighList) ------------------ | Branch (2701:9): [True: 288k, False: 0] | Branch (2701:22): [True: 288k, False: 0] ------------------ 2702| 288k| { 2703| 288k| return Canon_INChI3( ic, num_atoms, num_at_tg, at, pCS, pCG, nMode, bTautFtcn ); 2704| 288k| } 2705| | 2706| 0| return CT_CANON_ERR; ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2707| 288k|} ichicano.c:InchiClock: 77| 1.52M|{ 78| 1.52M| clock_t c = clock( ); 79| 1.52M| if (c != (clock_t) -1) ------------------ | Branch (79:9): [True: 1.52M, False: 0] ------------------ 80| 1.52M| { 81| 1.52M| return c; 82| 1.52M| } 83| 0| return 0; 84| 1.52M|} ichicano.c:FillMaxMinClock: 94| 2.32M|{ 95| 2.32M| if (!ic->m_MaxPositiveClock) ------------------ | Branch (95:9): [True: 12.5k, False: 2.31M] ------------------ 96| 12.5k| { 97| 12.5k| clock_t valPos = 0, val1 = 1; 98| 791k| while (0 < ( ( val1 <<= 1 ), ( val1 |= 1 ) )) /* djb-rwth: ignoring GH issue #59.3 -- LLONG_MIN/LLONG_MAX not found in on Linux */ ------------------ | Branch (98:16): [True: 778k, False: 12.5k] ------------------ 99| 778k| { 100| 778k| valPos = val1; 101| 778k| } 102| 12.5k| ic->m_MaxPositiveClock = valPos; 103| 12.5k| ic->m_MinNegativeClock = -valPos; 104| 12.5k| ic->m_HalfMaxPositiveClock = ic->m_MaxPositiveClock / 2; 105| 12.5k| ic->m_HalfMinNegativeClock = ic->m_MinNegativeClock / 2; 106| 12.5k| } 107| 2.32M|} find_atoms_with_parity: 124| 7.45k|{ 125| 7.45k| int i, next_atom; 126| | 127| 7.45k| if (visited[cur_atom]) ------------------ | Branch (127:9): [True: 842, False: 6.61k] ------------------ 128| 842| { 129| 842| return 0; 130| 842| } 131| 6.61k| if (at[cur_atom].parity) ------------------ | Branch (131:9): [True: 4.76k, False: 1.85k] ------------------ 132| 4.76k| { 133| 4.76k| return 1; 134| 4.76k| } 135| | 136| 1.85k| visited[cur_atom] = 1; 137| | 138| 4.50k| for (i = 0; i < at[cur_atom].valence; i++) ------------------ | Branch (138:17): [True: 3.60k, False: 894] ------------------ 139| 3.60k| { 140| 3.60k| next_atom = at[cur_atom].neighbor[i]; 141| | 142| 3.60k| if (next_atom != from_atom && ------------------ | Branch (142:13): [True: 2.33k, False: 1.27k] ------------------ 143| 2.33k| find_atoms_with_parity( at, visited, cur_atom, next_atom )) ------------------ | Branch (143:14): [True: 957, False: 1.37k] ------------------ 144| 957| { 145| 957| return 1; 146| 957| } 147| 3.60k| } 148| | 149| 894| return 0; 150| 1.85k|} RemoveHalfStereoBond: 176| 72|{ 177| 72| int k2; 178| 72| if (k1 < MAX_NUM_STEREO_BOND_NEIGH && at[jn].stereo_bond_neighbor[k1]) ------------------ | | 874| 144|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (178:9): [True: 72, False: 0] | Branch (178:43): [True: 72, False: 0] ------------------ 179| 72| { 180| 216| for (k2 = k1; k2 < MAX_NUM_STEREO_BOND_NEIGH - 1; k2++) /* djb-rwth: loop condition corrected (buffer error) */ ------------------ | | 874| 216|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (180:23): [True: 144, False: 72] ------------------ 181| 144| { 182| 144| at[jn].stereo_bond_neighbor[k2] = at[jn].stereo_bond_neighbor[k2 + 1]; 183| 144| at[jn].stereo_bond_ord[k2] = at[jn].stereo_bond_ord[k2 + 1]; 184| 144| at[jn].stereo_bond_z_prod[k2] = at[jn].stereo_bond_z_prod[k2 + 1]; 185| 144| at[jn].stereo_bond_parity[k2] = at[jn].stereo_bond_parity[k2 + 1]; 186| 144| } 187| 72| at[jn].stereo_bond_neighbor[k2] = 0; 188| 72| at[jn].stereo_bond_ord[k2] = 0; 189| 72| at[jn].stereo_bond_z_prod[k2] = 0; 190| 72| at[jn].stereo_bond_parity[k2] = 0; 191| | 192| 72| if (!at[jn].stereo_bond_neighbor[0]) ------------------ | Branch (192:13): [True: 72, False: 0] ------------------ 193| 72| { /* curled braces added 6-6-2002 */ 194| 72| at[jn].parity = 0; 195| 72| at[jn].stereo_atom_parity = 0; 196| 72| at[jn].final_parity = 0; 197| | /* at[jn].bHasStereoOrEquToStereo = 0; */ 198| 72| } 199| 72| return 1; /* success */ 200| 72| } 201| | 202| 0| return 0; /* failed */ 203| 72|} RemoveOneStereoBond: 240| 34|{ 241| 34| int k1, ret = 0, kn, jn = (int) at[jc].stereo_bond_neighbor[k] - 1; 242| | 243| | /* opposite end */ 244| 34| for (k1 = ret = 0; 245| 34| k1 < MAX_NUM_STEREO_BOND_NEIGH && ( kn = at[jn].stereo_bond_neighbor[k1] ); ------------------ | | 874| 68|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (245:13): [True: 34, False: 0] | Branch (245:47): [True: 34, False: 0] ------------------ 246| 34| k1++) /* djb-rwth: removing redundant code */ 247| 34| { 248| 34| if (kn - 1 == jc) ------------------ | Branch (248:13): [True: 34, False: 0] ------------------ 249| 34| { 250| 34| ret = RemoveHalfStereoBond( at, jn, k1 ); 251| 34| break; 252| 34| } 253| 34| } 254| | 255| 34| if (ret) ------------------ | Branch (255:9): [True: 34, False: 0] ------------------ 256| 34| { 257| 34| ret = RemoveHalfStereoBond( at, jc, k ); 258| 34| } 259| | 260| 34| return ret; 261| 34|} RemoveOneStereoCenter: 267| 89|{ 268| 89| if (at[jc].parity) ------------------ | Branch (268:9): [True: 89, False: 0] ------------------ 269| 89| { 270| 89| at[jc].parity = 0; /* remove parity */ 271| 89| at[jc].stereo_atom_parity = 0; 272| 89| at[jc].final_parity = 0; 273| | /* at[jc].bHasStereoOrEquToStereo = 0; */ 274| 89| return 1; 275| 89| } 276| | 277| 0| return 0; /* failed: not a stereo center */ 278| 89|} UnmarkNonStereo: 293| 1.14k|{ 294| 1.14k| int i, i1, i2, j, k, k1, k2, kn /* neigh*/, val, ic/* center*/, jc, num_implicit_H; 295| 1.14k| int num_neighbors_with_parity, num_no_parity_atoms, num_removed_parities = -1, num_removed_parities0; 296| 1.14k| AT_RANK nNeighborNumber[MAX_NUM_STEREO_ATOM_NEIGH]; 297| 1.14k| AT_RANK nPrevAtomRank, nPrevNeighRank; 298| 1.14k|#ifdef FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG 299| 1.14k| int num_in_same_ring_system = 1, nRingSystem, num_with_eq_neigh_in_same_ring_system = 0; /* djb-rwth: although unlikely to ever occur, uninitialised num_in_same_ring_system variable can lead to garbage value, including 0 which leads to various errors and inconsistency with 1.06 outputs -- function rewriting and discussion required */ 300| 1.14k|#endif 301| | 302| | 303| 1.14k| S_CHAR *visited = (S_CHAR *) inchi_malloc( num_atoms * sizeof( visited[0] ) ); ------------------ | | 1143| 1.14k|#define inchi_malloc malloc ------------------ 304| | 305| 1.14k| if (!visited) ------------------ | Branch (305:9): [True: 0, False: 1.14k] ------------------ 306| 0| { 307| 0| goto exit_function; 308| 0| } 309| | 310| 1.14k| num_removed_parities = 0; 311| 1.14k| num_no_parity_atoms = 0; 312| | 313| 1.14k| do 314| 1.16k| { 315| 1.16k| num_removed_parities0 = num_removed_parities; 316| | 317| 9.40k| for (i = i1 = 0, nPrevAtomRank = 0; i <= num_atoms; i++) ------------------ | Branch (317:45): [True: 8.24k, False: 1.16k] ------------------ 318| 8.24k| { 319| | /* bounds violation check (i!=num_atoms) added 6-21-2002 */ 320| 8.24k| if (i == num_atoms || nPrevAtomRank != nRank[j = nAtomNumber[i]] ------------------ | Branch (320:17): [True: 1.16k, False: 7.07k] | Branch (320:35): [True: 5.00k, False: 2.06k] ------------------ 321| 8.24k| /* at[j].parity && 1 < at[j].valence && at[j].valence < MAX_NUM_STEREO_ATOM_NEIGH*/) 322| 6.17k| { 323| | /* end of constitutionally equivalent atoms sequence */ 324| | /* nPrevRank = nRank[j]; */ 325| 6.17k| i2 = i; 326| 6.17k| if (i2 - i1 > num_no_parity_atoms /*&& at[jc = nAtomNumber[i1]].parity*/) ------------------ | Branch (326:21): [True: 2.17k, False: 4.00k] ------------------ 327| 2.17k| { 328| | /* at[nAtomNumber[i1]]..at[nAtomNumber[i2-1]] are constitutionally equivalent and some of them have parity */ 329| 2.17k| jc = nAtomNumber[i1]; 330| 2.17k| num_no_parity_atoms = 0; 331| 2.17k| val = at[jc].valence; /* all equivalent atoms have equal valences, etc. (except parities) */ 332| 2.17k| num_implicit_H = at[jc].endpoint ? 0 : at[jc].num_H; ------------------ | Branch (332:38): [True: 3, False: 2.17k] ------------------ 333| | /* Only atoms with valence <= MAX_NUM_STEREO_ATOM_NEIGH may have parity. However, check: */ 334| 2.17k| if (val + num_implicit_H > MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 2.17k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (334:25): [True: 0, False: 2.17k] ------------------ 335| 0| { 336| 0| continue; /* program error ??? */ /* */ 337| 0| } 338| 8.69k| for (k = 0; k < val; k++) ------------------ | Branch (338:33): [True: 6.52k, False: 2.17k] ------------------ 339| 6.52k| { 340| 6.52k| nNeighborNumber[k] = k; /* initialize an array of indexes for sorting */ 341| 6.52k| } 342| | /* check parities */ 343| 5.98k| for (ic = i1; ic < i2; ic++) ------------------ | Branch (343:35): [True: 3.80k, False: 2.17k] ------------------ 344| 3.80k| { 345| 3.80k| jc = nAtomNumber[ic]; 346| | /* sort neighbors according to their canon. equivalence ranks */ 347| 3.80k| pCG->m_pNeighborsForSort = at[jc].neighbor; 348| 3.80k| pCG->m_pn_RankForSort = nRank; 349| 3.80k| insertions_sort( pCG, nNeighborNumber, val, sizeof( nNeighborNumber[0] ), CompNeighborsAT_NUMBER ); 350| 3.80k| num_neighbors_with_parity = -1; /* non-zero */ 351| 12.5k| for (k = k1 = 0, nPrevNeighRank = 0; k <= val; k++) ------------------ | Branch (351:62): [True: 12.5k, False: 0] ------------------ 352| 12.5k| { 353| 12.5k| if (k == val || nPrevNeighRank != nRank[at[jc].neighbor[nNeighborNumber[k]]]) ------------------ | Branch (353:33): [True: 1.50k, False: 11.0k] | Branch (353:45): [True: 8.19k, False: 2.87k] ------------------ 354| 9.69k| { 355| 9.69k| k2 = k; 356| 9.69k| if (k2 - k1 > 1) ------------------ | Branch (356:37): [True: 2.25k, False: 7.44k] ------------------ 357| 2.25k| { 358| | /* found 2 or more constitutionally equivalent neighbors */ 359| | /* Check if they have only non-stereogenic neighbors */ 360| 2.25k|#ifdef FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG 361| 2.25k| num_in_same_ring_system = nRingSystem = 0; 362| 7.37k| for (kn = k1; kn < k2; kn++) /* djb-rwth: removing redundant code */ ------------------ | Branch (362:51): [True: 5.12k, False: 2.25k] ------------------ 363| 5.12k| { 364| 5.12k| int nCurNeighRingSystem = at[(int) at[jc].neighbor[nNeighborNumber[kn]]].nRingSystem; 365| 5.12k| if (!nRingSystem) ------------------ | Branch (365:45): [True: 2.25k, False: 2.87k] ------------------ 366| 2.25k| { 367| 2.25k| nRingSystem = nCurNeighRingSystem; 368| 2.25k| } 369| 2.87k| else 370| 2.87k| { 371| 2.87k| num_in_same_ring_system += ( nRingSystem == nCurNeighRingSystem ); 372| 2.87k| } 373| 5.12k| } 374| 2.25k|#endif 375| | 376| 7.37k| for (kn = k1, num_neighbors_with_parity = 0; kn < k2; kn++) ------------------ | Branch (376:82): [True: 5.12k, False: 2.25k] ------------------ 377| 5.12k| { 378| 5.12k| memset( visited, 0, num_atoms * sizeof( visited[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 379| 5.12k| visited[jc] = 1; /* starting point; the only atom with parity */ 380| 5.12k| num_neighbors_with_parity += 381| 5.12k| find_atoms_with_parity( at, visited, jc, (int) at[jc].neighbor[nNeighborNumber[kn]] ); 382| 5.12k| } 383| 2.25k| } 384| | /* if ( !num_neighbors_with_parity ) */ 385| 9.69k|#ifdef FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG 386| 9.69k| if (!num_neighbors_with_parity && !num_in_same_ring_system) ------------------ | Branch (386:37): [True: 170, False: 9.52k] | Branch (386:67): [True: 48, False: 122] ------------------ 387| |#else 388| | if (!num_neighbors_with_parity) 389| |#endif 390| 48| { 391| 48| break; /* at[jc] cannot have defined parity */ 392| 48| } 393| 9.64k| if (k + 1 < val) ------------------ | Branch (393:37): [True: 5.88k, False: 3.75k] ------------------ 394| 5.88k| { 395| 5.88k| k1 = k; /* at least 2 more neighbors left */ 396| 5.88k| nPrevNeighRank = nRank[at[jc].neighbor[nNeighborNumber[k]]]; 397| 5.88k| } 398| 3.75k| else 399| 3.75k| { 400| 3.75k| break; 401| 3.75k| } 402| 9.64k| } 403| 12.5k| } 404| 3.80k| if (num_implicit_H > 1) ------------------ | Branch (404:29): [True: 14, False: 3.79k] ------------------ 405| 14| { 406| 14| if ((bIsotopic && ( at[jc].num_iso_H[0] > 1 || ------------------ | Branch (406:34): [True: 10, False: 4] | Branch (406:49): [True: 0, False: 10] ------------------ 407| 10| at[jc].num_iso_H[1] > 1 || ------------------ | Branch (407:33): [True: 0, False: 10] ------------------ 408| 10| at[jc].num_iso_H[2] > 1 )) || ------------------ | Branch (408:33): [True: 0, False: 10] ------------------ 409| 14| num_implicit_H > NUM_H_ISOTOPES || ------------------ | | 25| 28|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (409:35): [True: 0, False: 14] ------------------ 410| 14| !bIsotopic) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (410:35): [True: 4, False: 10] ------------------ 411| 4| { 412| 4| num_neighbors_with_parity = 0; 413| 4| } 414| 14| } 415| | /* increment if: */ 416| | /* (a) constitutionally equivalent neighbors do exist, and */ 417| | /* (b) all constitutionally equivalent neighbors do not have parity, and */ 418| | /* (c) all constitutionally equivalent neighbors are not connected to atoms with parity */ 419| 3.80k| num_no_parity_atoms += !num_neighbors_with_parity; 420| 3.80k|#ifdef FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG 421| 3.80k| num_with_eq_neigh_in_same_ring_system += ( num_in_same_ring_system != 0 ); /* djb-rwth: initialisation of num_in_same_ring_system is required to avoid garbage value */ 422| 3.80k|#endif 423| 3.80k| } 424| 2.17k|#ifdef FIX_OLEAN_SPIRO_CHIRALITY_DETECTION_BUG 425| 2.17k| if (num_no_parity_atoms == i2 - i1 && num_with_eq_neigh_in_same_ring_system != i2 - i1) ------------------ | Branch (425:25): [True: 136, False: 2.03k] | Branch (425:59): [True: 18, False: 118] ------------------ 426| |#else 427| | if (num_no_parity_atoms == i2 - i1) 428| |#endif 429| | 430| 18| { 431| | /* all atoms at[nAtomNumber[i1]]..at[nAtomNumber[i2-1]] cannot be */ 432| | /* stereo centers or belong to stereo bonds */ 433| 36| for (ic = i1; ic < i2; ic++) ------------------ | Branch (433:39): [True: 18, False: 18] ------------------ 434| 18| { 435| 18| int jn; 436| 18| jc = nAtomNumber[ic]; 437| 18| at[jc].parity = 0; /* remove parity */ 438| 18| at[jc].stereo_atom_parity = 0; 439| 18| at[jc].final_parity = 0; 440| 18| at[jc].bHasStereoOrEquToStereo = 0; 441| | /* remove stereo bonds */ 442| 22| for (k = 0; k < MAX_NUM_STEREO_BOND_NEIGH && ( jn = at[jc].stereo_bond_neighbor[k] ); k++) ------------------ | | 874| 44|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (442:41): [True: 22, False: 0] | Branch (442:74): [True: 4, False: 18] ------------------ 443| 4| { 444| 4| jn--; /* stereo bond neighbor */ 445| | /* opposite end */ 446| 4| for (k1 = 0; k1 < MAX_NUM_STEREO_BOND_NEIGH && ( kn = at[jn].stereo_bond_neighbor[k1] ); k1++) ------------------ | | 874| 8|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (446:46): [True: 4, False: 0] | Branch (446:80): [True: 4, False: 0] ------------------ 447| 4| { 448| 4| if (kn - 1 == jc) ------------------ | Branch (448:41): [True: 4, False: 0] ------------------ 449| 4| { 450| 4| RemoveHalfStereoBond( at, jn, k1 ); 451| 4| break; 452| 4| } 453| 4| } 454| | /* at at[jc] stereo bond end; since references to all at[jc] */ 455| | /* stereo bond neighbors are to be removed, do not shift them */ 456| 4| at[jc].stereo_bond_neighbor[k] = 0; 457| 4| at[jc].stereo_bond_ord[k] = 0; 458| 4| at[jc].stereo_bond_z_prod[k] = 0; 459| 4| at[jc].stereo_bond_parity[k] = 0; 460| 4| } 461| 18| } 462| 18| num_removed_parities += num_no_parity_atoms; 463| 18| } 464| 2.17k| } 465| 6.17k| if (i < num_atoms) ------------------ | Branch (465:21): [True: 5.00k, False: 1.16k] ------------------ 466| 5.00k| { 467| 5.00k| nPrevAtomRank = nRank[j]; 468| 5.00k| i1 = i; 469| 5.00k| } 470| 6.17k| num_no_parity_atoms = 0; 471| 6.17k| } 472| 8.24k| num_no_parity_atoms += ( i < num_atoms && !at[j].parity ); ------------------ | Branch (472:38): [True: 7.07k, False: 1.16k] | Branch (472:55): [True: 3.47k, False: 3.59k] ------------------ 473| 8.24k| } 474| 1.16k| } 475| 1.16k| while (num_removed_parities != num_removed_parities0); ------------------ | Branch (475:12): [True: 18, False: 1.14k] ------------------ 476| | 477| 1.14k|exit_function: 478| 1.14k| if (visited) ------------------ | Branch (478:9): [True: 1.14k, False: 0] ------------------ 479| 1.14k| { 480| 1.14k| inchi_free( visited ); ------------------ | | 1152| 1.14k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.14k, False: 0] | | | Branch (1152:50): [Folded, False: 1.14k] | | ------------------ ------------------ 481| 1.14k| } 482| | 483| 1.14k| return num_removed_parities; 484| 1.14k|} FillSingleStereoDescriptors: 502| 13.8k|{ 503| | 504| 13.8k| if (!LinearCTStereoDble && !LinearCTStereoCarb) ------------------ | Branch (504:9): [True: 8.49k, False: 5.39k] | Branch (504:32): [True: 0, False: 8.49k] ------------------ 505| 0| { 506| 0| return 0; /* return immediately if no stereo have been requested */ 507| 0| } 508| | 509| | /*************************************************** 510| | add stereo centers and stereo bonds to the CT 511| | ***************************************************/ 512| 13.8k| if (at[i].parity || at[i].stereo_bond_neighbor[0]) ------------------ | Branch (512:9): [True: 7.12k, False: 6.75k] | Branch (512:25): [True: 0, False: 6.75k] ------------------ 513| 7.12k| { 514| 7.12k| AT_RANK r_neigh, rank = nRank[i]; 515| 7.12k| AT_NUMB nNeighborNumber2[MAXVAL]; 516| 7.12k| unsigned parity; 517| 7.12k| int k; 518| 7.12k| int num_allene = 0; 519| | 520| 7.12k| if (ATOM_PARITY_WELL_DEF( at[i].parity ) && num_trans < 0) ------------------ | | 259| 14.2k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 7.12k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 7.12k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 7.12k, False: 0] | | | Branch (259:75): [True: 2.40k, False: 4.72k] | | ------------------ ------------------ | Branch (520:53): [True: 2.40k, False: 0] ------------------ 521| 2.40k| { 522| | /* number of neighbors transpositions to the sorted order is unknown. Find it. */ 523| | /* If parity is not well-defined then doing this is a waste of time */ 524| 2.40k| int num_neigh = at[i].valence; 525| 9.56k| for (k = 0; k < num_neigh; k++) ------------------ | Branch (525:25): [True: 7.15k, False: 2.40k] ------------------ 526| 7.15k| { 527| 7.15k| nNeighborNumber2[k] = k; 528| 7.15k| } 529| | 530| 2.40k| pCG->m_pNeighborsForSort = at[i].neighbor; 531| 2.40k| pCG->m_pn_RankForSort = nRank; 532| 2.40k| num_trans = insertions_sort( pCG, nNeighborNumber2, num_neigh, sizeof( nNeighborNumber2[0] ), CompNeighborsAT_NUMBER ); 533| | 534| |#ifndef CT_NEIGH_INCREASE 535| | num_trans += ( ( num_neigh*( num_neigh - 1 ) ) / 2 ) % 2; /* get correct parity for ascending order */ 536| |#endif 537| 2.40k| } 538| | 539| | /* stereo bonds */ 540| 7.12k| if (LinearCTStereoDble && at[i].stereo_bond_neighbor[0]) ------------------ | Branch (540:13): [True: 3.54k, False: 3.58k] | Branch (540:35): [True: 3.48k, False: 60] ------------------ 541| 3.48k| { 542| | 543| | /* HalfStereoBondParity( sp_ATOM *at, int at_no1, int i_sb_neigh, AT_RANK *nRank ) */ 544| 3.48k| AT_NUMB nStereoNeighNumber[MAX_NUM_STEREO_BONDS], nStereoNeigh[MAX_NUM_STEREO_BONDS], n; 545| 3.48k| int num_stereo, stereo_neigh, stereo_neigh_ord, stereo_bond_parity; 546| 3.48k| for (num_stereo = 0; 547| 8.84k| num_stereo < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 17.6k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (547:23): [True: 8.84k, False: 0] ------------------ 548| 8.84k| ( n = at[i].stereo_bond_neighbor[num_stereo] ); num_stereo++) ------------------ | Branch (548:23): [True: 5.35k, False: 3.48k] ------------------ 549| 5.35k| { 550| 5.35k| nStereoNeighNumber[num_stereo] = num_stereo; 551| 5.35k| nStereoNeigh[num_stereo] = n - 1; 552| 5.35k| num_allene += IS_ALLENE_CHAIN( at[i].stereo_bond_parity[num_stereo] ); ------------------ | | 215| 5.35k|#define IS_ALLENE_CHAIN(X) ((GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND)%2) | | ------------------ | | | | 213| 5.35k|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 5.35k|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define IS_ALLENE_CHAIN(X) ((GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND)%2) | | ------------------ | | | | 209| 5.35k|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 553| 5.35k| } 554| 3.48k| if ((bAllene > 0 && !num_allene) || (bAllene == 0 && num_allene)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (554:18): [True: 1.74k, False: 1.74k] | Branch (554:33): [True: 1.72k, False: 20] | Branch (554:50): [True: 1.74k, False: 20] | Branch (554:66): [True: 20, False: 1.72k] ------------------ 555| 1.74k| { 556| 1.74k| return 0; 557| 1.74k| } 558| | 559| | /* sort stereo bonds according to the ranks of the neighbors */ 560| 1.74k| pCG->m_pNeighborsForSort = nStereoNeigh; 561| 1.74k| pCG->m_pn_RankForSort = nRank; 562| 1.74k| insertions_sort( pCG, nStereoNeighNumber, num_stereo, sizeof( nStereoNeighNumber[0] ), CompNeighborsAT_NUMBER ); 563| | 564| | /* process stereo bonds one by one */ 565| 4.42k| for (k = 0; k < num_stereo; k++) ------------------ | Branch (565:25): [True: 2.67k, False: 1.74k] ------------------ 566| 2.67k| { 567| 2.67k| stereo_neigh = nStereoNeigh[stereo_neigh_ord = (int) nStereoNeighNumber[k]]; 568| | 569| 2.67k| if (( r_neigh = (AT_NUMB) nRank[stereo_neigh] ) CT_NEIGH_SMALLER_THAN rank) ------------------ | Branch (569:21): [True: 1.33k, False: 1.33k] ------------------ 570| 1.33k| { 571| | /* accept only neighbors that have smaller ranks */ 572| 1.33k| stereo_bond_parity = PARITY_VAL( at[i].stereo_bond_parity[stereo_neigh_ord] ); ------------------ | | 262| 1.33k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 1.33k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 573| 1.33k| if (stereo_bond_parity == AB_PARITY_NONE) ------------------ | | 218| 1.33k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (573:25): [True: 0, False: 1.33k] ------------------ 574| 0| { 575| 0| continue; 576| 0| } 577| | 578| | /* stereo_neigh = at[i].stereo_bond_neighbor[nStereoNeighNumber[k]]-1; */ 579| 1.33k| if (ATOM_PARITY_KNOWN( stereo_bond_parity )) ------------------ | | 258| 1.33k|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 1.33k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 1.33k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (258:38): [True: 1.33k, False: 0] | | | Branch (258:68): [True: 1.07k, False: 269] | | ------------------ ------------------ 580| 1.07k| { 581| 1.07k| parity = stereo_bond_parity; 582| 1.07k| } 583| 269| else if (ATOM_PARITY_WELL_DEF( at[i].parity ) && ------------------ | | 259| 538|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 269|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 269|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 269, False: 0] | | | Branch (259:75): [True: 269, False: 0] | | ------------------ ------------------ 584| 269| ATOM_PARITY_WELL_DEF( at[stereo_neigh].parity ) && ------------------ | | 259| 538|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 269|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 269|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 269, False: 0] | | | Branch (259:75): [True: 269, False: 0] | | ------------------ ------------------ 585| 269| MIN_DOT_PROD <= abs( at[i].stereo_bond_z_prod[stereo_neigh_ord] )) ------------------ | | 253| 269|#define MIN_DOT_PROD 50 /* min value of at->stereo_bond_z_prod[i] to define parity */ ------------------ | Branch (585:31): [True: 269, False: 0] ------------------ 586| 269| { 587| | /* bond parity can be calculated */ 588| 269| int half_parity1, half_parity2, j, nn, stereo_neigh_ord2; 589| 269| stereo_neigh_ord2 = -1; 590| 368| for (j = 0; j < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 736|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (590:37): [True: 368, False: 0] ------------------ 591| 368| ( nn = (int) at[stereo_neigh].stereo_bond_neighbor[j] ); ------------------ | Branch (591:29): [True: 368, False: 0] ------------------ 592| 269| j++) 593| 368| { 594| 368| if (i + 1 == nn) ------------------ | Branch (594:33): [True: 269, False: 99] ------------------ 595| 269| { 596| | /* found the opposite end of the stereo bond */ 597| 269| stereo_neigh_ord2 = j; 598| 269| break; 599| 269| } 600| 368| } 601| 269| if (stereo_neigh_ord2 >= 0) ------------------ | Branch (601:29): [True: 269, False: 0] ------------------ 602| 269| { 603| 269| half_parity1 = HalfStereoBondParity( at, i, stereo_neigh_ord, nRank ); 604| 269| half_parity2 = HalfStereoBondParity( at, stereo_neigh, stereo_neigh_ord2, nRank ); 605| 269| if (ATOM_PARITY_WELL_DEF( half_parity1 ) && ------------------ | | 259| 538|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 269|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 269|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 269, False: 0] | | | Branch (259:75): [True: 269, False: 0] | | ------------------ ------------------ 606| 269| ATOM_PARITY_WELL_DEF( half_parity2 )) ------------------ | | 259| 269|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 269|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 269|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 269, False: 0] | | | Branch (259:75): [True: 269, False: 0] | | ------------------ ------------------ 607| 269| { 608| 269| parity = 2 - ( half_parity1 + half_parity2 609| 269| + ( at[i].stereo_bond_z_prod[stereo_neigh_ord] < 0 ) ) % 2; 610| 269| } 611| 0| else 612| 0| { 613| 0| return CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 614| 0| } 615| 269| } 616| 0| else 617| 0| { 618| 0| return CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 619| 0| } 620| 269| } 621| 0| else 622| 0| { 623| | /* parity cannot be calculated: not enough info or 'unknown' */ 624| 0| if (AB_PARITY_NONE == ( parity = inchi_max( at[i].parity, at[stereo_neigh].parity ) )) ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (AB_PARITY_NONE == ( parity = inchi_max( at[i].parity, at[stereo_neigh].parity ) )) ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (624:29): [True: 0, False: 0] ------------------ 625| 0| { 626| 0| continue; 627| 0| } 628| 0| if (ATOM_PARITY_WELL_DEF( parity )) ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 629| 0| { 630| 0| parity = AB_PARITY_UNDF; /* should not happen */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 631| 0| } 632| 0| } 633| 1.33k| if (CHECK_OVERFLOW( *nStereoDbleLen, nMaxStereoDbleLen )) ------------------ | | 43| 1.33k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 1.33k] | | ------------------ ------------------ 634| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 635| | /* first stereo bond atom */ 636| 1.33k| LinearCTStereoDble[*nStereoDbleLen].at_num1 = rank; 637| | /* second stereo bond atom (opposite end) */ 638| 1.33k| LinearCTStereoDble[*nStereoDbleLen].at_num2 = r_neigh; 639| | /* bond parity */ 640| 1.33k| LinearCTStereoDble[*nStereoDbleLen].parity = parity; 641| 1.33k| ( *nStereoDbleLen )++; 642| 1.33k| } 643| 2.67k| } 644| 1.74k| } 645| | 646| | /* stereo carbon */ 647| 5.38k| if (bAllene > 0) ------------------ | Branch (647:13): [True: 1.84k, False: 3.54k] ------------------ 648| 1.84k| { 649| 1.84k| return 0; 650| 1.84k| } 651| | 652| 3.54k| if (LinearCTStereoCarb && !at[i].stereo_bond_neighbor[0]) ------------------ | Branch (652:13): [True: 1.93k, False: 1.61k] | Branch (652:35): [True: 1.82k, False: 110] ------------------ 653| 1.82k| { 654| 1.82k| if (CHECK_OVERFLOW( *nStereoCarbLen, nMaxStereoCarbLen )) ------------------ | | 43| 1.82k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (43:37): [True: 0, False: 1.82k] | | ------------------ ------------------ 655| 0| return CT_OVERFLOW; /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 656| | /* stereo atom rank */ 657| 1.82k| LinearCTStereoCarb[*nStereoCarbLen].at_num = rank; 658| | /* stereo atom parity */ 659| 1.82k| parity = ATOM_PARITY_WELL_DEF( at[i].parity ) ? ( 2 - ( at[i].parity + num_trans ) % 2 ) : at[i].parity; ------------------ | | 259| 1.82k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.82k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.82k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 1.82k, False: 0] | | | Branch (259:75): [True: 678, False: 1.14k] | | ------------------ ------------------ 660| 1.82k| LinearCTStereoCarb[*nStereoCarbLen].parity = parity; 661| 1.82k| ( *nStereoCarbLen )++; 662| 1.82k| } 663| 3.54k| } 664| | 665| 10.3k| return 0; 666| 13.8k|} SwitchAtomStereoAndIsotopicStereo: 673| 502|{ 674| 502| int i; 675| | /* switch atom stereo data */ 676| 3.68k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (676:17): [True: 3.18k, False: 502] ------------------ 677| 3.18k| { 678| 3.18k| inchi_swap( (char*) &at[i].parity, (char*) &at[i].parity2, sizeof( at[i].parity ) ); 679| 3.18k| inchi_swap( (char*) &at[i].final_parity, (char*) &at[i].final_parity2, sizeof( at[i].final_parity ) ); 680| 3.18k| inchi_swap( (char*) &at[i].stereo_atom_parity, (char*) &at[i].stereo_atom_parity2, sizeof( at[i].stereo_atom_parity ) ); 681| 3.18k| inchi_swap( (char*) &at[i].bHasStereoOrEquToStereo, (char*) &at[i].bHasStereoOrEquToStereo2, sizeof( at[i].bHasStereoOrEquToStereo ) ); 682| | 683| 3.18k| inchi_swap( (char*) at[i].stereo_bond_neighbor, (char*) at[i].stereo_bond_neighbor2, sizeof( at[i].stereo_bond_neighbor ) ); 684| 3.18k| inchi_swap( (char*) at[i].stereo_bond_ord, (char*) at[i].stereo_bond_ord2, sizeof( at[i].stereo_bond_ord ) ); 685| 3.18k| inchi_swap( (char*) at[i].stereo_bond_z_prod, (char*) at[i].stereo_bond_z_prod2, sizeof( at[i].stereo_bond_z_prod ) ); 686| 3.18k| inchi_swap( (char*) at[i].stereo_bond_parity, (char*) at[i].stereo_bond_parity2, sizeof( at[i].stereo_bond_parity ) ); 687| 3.18k| } 688| | 689| 502| *bSwitched = !*bSwitched; 690| 502|} SetCtToIsotopicStereo: 696| 251|{ 697| 251| pCS->LinearCTStereoDble = pCS2->LinearCTIsotopicStereoDble; /* enable stereo */ 698| 251| pCS->LinearCTStereoCarb = pCS2->LinearCTIsotopicStereoCarb; 699| | 700| 251| pCS->LinearCTStereoDbleInv = pCS2->LinearCTIsotopicStereoDbleInv; /* enable inv. stereo */ 701| 251| pCS->LinearCTStereoCarbInv = pCS2->LinearCTIsotopicStereoCarbInv; 702| 251| pCS->nMaxLenLinearCTStereoDble = pCS2->nMaxLenLinearCTIsotopicStereoDble; 703| 251| pCS->nMaxLenLinearCTStereoCarb = pCS2->nMaxLenLinearCTIsotopicStereoCarb; 704| | 705| 251| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 706| 251| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 707| 251|} SetCtToNonIsotopicStereo: 713| 251|{ 714| 251| pCS->LinearCTStereoDble = pCS2->LinearCTStereoDble; /* enable stereo */ 715| 251| pCS->LinearCTStereoCarb = pCS2->LinearCTStereoCarb; 716| | 717| 251| pCS->LinearCTStereoDbleInv = pCS2->LinearCTStereoDbleInv; /* enable inv. stereo */ 718| 251| pCS->LinearCTStereoCarbInv = pCS2->LinearCTStereoCarbInv; 719| 251| pCS->nMaxLenLinearCTStereoDble = pCS2->nMaxLenLinearCTStereoDble; 720| 251| pCS->nMaxLenLinearCTStereoCarb = pCS2->nMaxLenLinearCTStereoCarb; 721| | 722| 251| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble; 723| 251| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb; 724| | 725| 251| pCS->nLenLinearCTIsotopicStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 726| 251| pCS->nLenLinearCTIsotopicStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 727| 251|} FillAllStereoDescriptors: 737| 1.14k|{ 738| 1.14k| int ret = 0, i; 739| | /* initialize zero lengths */ 740| 1.14k| pCS->nLenLinearCTStereoCarb = 0; 741| 1.14k| pCS->nLenLinearCTStereoDble = 0; 742| | 743| | /* fill atom by atom */ 744| 8.08k| for (i = 0; !ret && i < num_atoms; i++) ------------------ | Branch (744:17): [True: 8.08k, False: 0] | Branch (744:25): [True: 6.94k, False: 1.14k] ------------------ 745| 6.94k| { 746| 6.94k| ret = FillSingleStereoDescriptors( pCG, at, (int) nAtomNumberCanon[i], -1, nCanonRank 747| 6.94k| , pCS->LinearCTStereoCarb, &pCS->nLenLinearCTStereoCarb, pCS->nMaxLenLinearCTStereoCarb 748| 6.94k| , pCS->LinearCTStereoDble, &pCS->nLenLinearCTStereoDble, pCS->nMaxLenLinearCTStereoDble 749| 6.94k| , 0 /* bAllene */ ); 750| 6.94k| } 751| 8.08k| for (i = 0; !ret && i < num_atoms; i++) ------------------ | Branch (751:17): [True: 8.08k, False: 0] | Branch (751:25): [True: 6.94k, False: 1.14k] ------------------ 752| 6.94k| { 753| 6.94k| ret = FillSingleStereoDescriptors( pCG, at, (int) nAtomNumberCanon[i], -1, nCanonRank 754| 6.94k| , pCS->LinearCTStereoCarb, &pCS->nLenLinearCTStereoCarb, pCS->nMaxLenLinearCTStereoCarb 755| 6.94k| , pCS->LinearCTStereoDble, &pCS->nLenLinearCTStereoDble, pCS->nMaxLenLinearCTStereoDble 756| 6.94k| , 1 /* bAllene */ ); 757| 6.94k| } 758| | 759| 1.14k| return ret; 760| 1.14k|} SetKnownStereoBondParities: 772| 1.14k|{ 773| 1.14k| int i, j, n, m, j1, k, num_neigh1, num_neigh2, iMax1, parity; 774| 1.14k| int trans_i1, trans_i2, trans_k1, trans_k2, prev_trans, trans_k, num_set; 775| 1.14k| int i1, i2, k1, k2, n1, n2, m1, m2, /*stereo_bond_parity,*/ cumulene_len; 776| | 777| 1.14k| AT_RANK nAtomRank1, nAtomRank2, nAtom1NeighRank; 778| 1.14k| AT_RANK nNeighRank1[MAX_NUM_STEREO_BONDS], 779| 1.14k| nNeighRank2[MAX_NUM_STEREO_BONDS]; 780| 1.14k| AT_RANK nNeighCanonRank1[MAX_NUM_STEREO_BONDS], 781| 1.14k| nNeighCanonRank2[MAX_NUM_STEREO_BONDS]; 782| | 783| 8.08k| for (i1 = 0, num_set = 0; i1 < num_atoms; i1++) ------------------ | Branch (783:31): [True: 6.94k, False: 1.14k] ------------------ 784| 6.94k| { 785| 6.94k| if (!at[i1].parity || !at[i1].stereo_bond_neighbor[0]) ------------------ | Branch (785:13): [True: 3.37k, False: 3.56k] | Branch (785:31): [True: 1.82k, False: 1.74k] ------------------ 786| 5.19k| { 787| 5.19k| continue; 788| 5.19k| } 789| | 790| 1.74k| if (!PARITY_WELL_DEF( at[i1].parity )) ------------------ | | 266| 1.74k|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.74k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 3.48k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.74k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 1.74k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.74k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.74k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 1.74k, False: 0] | | | Branch (266:85): [True: 526, False: 1.21k] | | ------------------ ------------------ 791| 1.21k| { 792| 1.21k| continue; 793| 1.21k| } 794| | 795| 526| nAtomRank1 = nRank[i1]; 796| 526| iMax1 = (int) nAtomRank1 - 1; 797| 526| num_neigh1 = at[i1].valence; 798| | 799| 1.33k| for (n1 = 0; n1 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 2.66k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (799:25): [True: 1.33k, False: 0] ------------------ 800| 1.33k| ( i2 = (int) at[i1].stereo_bond_neighbor[n1] ); ------------------ | Branch (800:13): [True: 808, False: 526] ------------------ 801| 808| n1++) 802| 808| { 803| 808| i2--; 804| | 805| | /* found a stereo bond at[i1]-at[i2] adjacent to at[i1] */ 806| 808| for (n2 = 0, m = 0; 807| 1.02k| n2 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 2.04k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (807:21): [True: 1.02k, False: 0] ------------------ 808| 1.02k| ( m = (int) at[i2].stereo_bond_neighbor[n2] ) && m - 1 != i1; ------------------ | Branch (808:21): [True: 1.02k, False: 0] | Branch (808:70): [True: 213, False: 808] ------------------ 809| 808| n2++) 810| 213| ; /* locate stereo bond (#n2) at the opposite atom at[i2] */ 811| | 812| 808| if (m - 1 != i1 || at[i1].stereo_bond_parity[n1] != at[i2].stereo_bond_parity[n2]) ------------------ | Branch (812:17): [True: 0, False: 808] | Branch (812:32): [True: 0, False: 808] ------------------ 813| 0| { 814| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 815| 0| } 816| 808| if (i1 < i2) ------------------ | Branch (816:17): [True: 436, False: 372] ------------------ 817| 436| { 818| 436| continue; /* do not process same bond 2 times */ 819| 436| } 820| 372| if (PARITY_KNOWN( at[i1].stereo_bond_parity[n1] ) || ------------------ | | 265| 744|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 372|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 744|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 372|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 372|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 372|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 372|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 372, False: 0] | | | Branch (265:78): [True: 103, False: 269] | | ------------------ ------------------ 821| 269| !PARITY_VAL( at[i1].stereo_bond_parity[n1] )) ------------------ | | 262| 269|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 269|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ | Branch (821:17): [True: 0, False: 269] ------------------ 822| 103| { 823| 103| continue; 824| 103| } 825| 269| if (!PARITY_WELL_DEF( at[i1].parity ) || ------------------ | | 266| 538|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 269|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 538|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 269|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 269|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 269|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 269|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 269, False: 0] | | | Branch (266:85): [True: 269, False: 0] | | ------------------ ------------------ 826| 269| !PARITY_WELL_DEF( at[i2].parity )) ------------------ | | 266| 269|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 269|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 538|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 269|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 269|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 269|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 269|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 269, False: 0] | | | Branch (266:85): [True: 269, False: 0] | | ------------------ ------------------ 827| 0| { 828| 0| continue; 829| 0| } 830| 269| if (PARITY_VAL( at[i1].stereo_bond_parity[n1] ) != AB_PARITY_CALC) ------------------ | | 262| 269|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 269|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ if (PARITY_VAL( at[i1].stereo_bond_parity[n1] ) != AB_PARITY_CALC) ------------------ | | 224| 269|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ | Branch (830:17): [True: 0, False: 269] ------------------ 831| 0| { 832| 0| continue; /* ?? program error ?? should not happen */ /* */ 833| 0| } 834| | 835| | /*stereo_bond_parity = PARITY_VAL(at[i1].stereo_bond_parity[n1]);*/ 836| 269| cumulene_len = BOND_CHAIN_LEN( at[i1].stereo_bond_parity[n1] ); ------------------ | | 214| 269|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 269|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 269|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 269|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 837| 269| nAtomRank2 = nRank[i2]; 838| 269| nAtom1NeighRank = nRank[(int) at[i1].neighbor[(int) at[i1].stereo_bond_ord[n1]]]; 839| 269| num_neigh2 = at[i2].valence; 840| | 841| | /* store ranks of at[i1] stereo bond neighbors except one connected by a stereo bond */ 842| 269| k = (int) at[i1].stereo_bond_ord[n1]; 843| 269| trans_i1 = 0; 844| 816| for (i = j = 0; i < num_neigh1; i++) ------------------ | Branch (844:29): [True: 547, False: 269] ------------------ 845| 547| { 846| 547| if (i != k) ------------------ | Branch (846:21): [True: 278, False: 269] ------------------ 847| 278| { 848| 278| nNeighRank1[j] = nRank[(int) at[i1].neighbor[i]]; 849| 278| j++; 850| 278| } 851| 547| } 852| 269| if (j == 2) ------------------ | Branch (852:17): [True: 23, False: 246] ------------------ 853| 23| { 854| 23| if (nNeighRank1[0] == nNeighRank1[1]) ------------------ | Branch (854:21): [True: 13, False: 10] ------------------ 855| 13| { 856| | /* neighbors are constitutionally identical, can't find bond parity */ 857| 13| continue; 858| 13| } 859| 10| trans_i1 = insertions_sort( pCG, nNeighRank1, j, sizeof( nNeighRank1[0] ), comp_AT_RANK ); 860| 10| } 861| | 862| | /* store ranks of at[i2] stereo bond neighbors except one connected by a stereo bond */ 863| 256| k = (int) at[i2].stereo_bond_ord[n2]; 864| 256| trans_i2 = 0; 865| 781| for (i = j = 0; i < num_neigh2; i++) ------------------ | Branch (865:29): [True: 525, False: 256] ------------------ 866| 525| { 867| 525| if (i != k) ------------------ | Branch (867:21): [True: 269, False: 256] ------------------ 868| 269| { 869| 269| nNeighRank2[j] = nRank[(int) at[i2].neighbor[i]]; 870| 269| j++; 871| 269| } 872| 525| } 873| | 874| 256| if (j == 2) ------------------ | Branch (874:17): [True: 26, False: 230] ------------------ 875| 26| { 876| 26| if (nNeighRank2[0] == nNeighRank2[1]) ------------------ | Branch (876:21): [True: 1, False: 25] ------------------ 877| 1| { 878| | /* neighbors are constitutionally identical, can't find bond parity */ 879| 1| continue; 880| 1| } 881| 25| trans_i2 = insertions_sort( pCG, nNeighRank2, j, sizeof( nNeighRank2[0] ), comp_AT_RANK ); 882| 25| } 883| | 884| 255| prev_trans = -1; 885| 255| trans_k1 = -2; /* djb-rwth: ignoring LLVM warning: value used */ 886| 255| trans_k = -4; /* 2004-04-28 */ 887| | 888| | /* find all pairs of atoms that can be mapped on at[i1], at[i2] pair */ 889| 255| for (j1 = 0; 890| 1.41k| j1 <= iMax1 && nAtomRank1 == nRank[k1 = (int) nAtomNumber[iMax1 - j1]]; ------------------ | Branch (890:21): [True: 1.27k, False: 145] | Branch (890:36): [True: 1.16k, False: 110] ------------------ 891| 1.16k| j1++) 892| 1.16k| { 893| | /* at[k1] is constitutionally equivalent to at[i1] */ 894| | /* find all at[k1] neighbors that have rank nAtomRank2; */ 895| | /* then find at[k2] constitutionally equivalent at at[i2] */ 896| 1.16k| if (at[k1].valence != num_neigh1) ------------------ | Branch (896:21): [True: 0, False: 1.16k] ------------------ 897| 0| { 898| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 899| 0| } 900| 3.47k| for (m1 = 0; m1 < num_neigh1; m1++) ------------------ | Branch (900:30): [True: 2.31k, False: 1.16k] ------------------ 901| 2.31k| { 902| 2.31k| int prev, next, len; 903| 2.31k| if (nAtom1NeighRank != nRank[k2 = (int) at[k1].neighbor[m1]]) ------------------ | Branch (903:25): [True: 180, False: 2.13k] ------------------ 904| 180| { 905| 180| continue; 906| 180| } 907| 2.13k| m2 = -1; /* undefined yet */ 908| 2.13k| prev = k1; 909| | /* djb-rwth: removing redundant code */ 910| 2.13k| if (cumulene_len) ------------------ | Branch (910:25): [True: 3, False: 2.13k] ------------------ 911| 3| { 912| 6| for (len = 0, next = (int) at[k1].neighbor[m1]; len < cumulene_len; len++) ------------------ | Branch (912:73): [True: 3, False: 3] ------------------ 913| 3| { 914| 3| if (at[next].valence == 2 && !at[next].num_H) ------------------ | Branch (914:33): [True: 3, False: 0] | Branch (914:58): [True: 3, False: 0] ------------------ 915| 3| { 916| 3| j = ( (int) at[next].neighbor[0] == prev ); 917| 3| prev = next; 918| 3| next = at[next].neighbor[j]; 919| 3| } 920| 0| else 921| 0| { 922| 0| break; /* cannot continue */ 923| 0| } 924| 3| } 925| 3| if (len != cumulene_len || nAtomRank2 != nRank[next]) ------------------ | Branch (925:29): [True: 0, False: 3] | Branch (925:52): [True: 0, False: 3] ------------------ 926| 0| { 927| 0| continue; /* not found */ 928| 0| } 929| 3| k2 = next; 930| 3| } 931| 2.13k| if (at[k2].valence != num_neigh2) ------------------ | Branch (931:25): [True: 0, False: 2.13k] ------------------ 932| 0| { 933| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 934| 0| } 935| | 936| | /* store canon. ranks of at[k1] neighbors */ /* use i,j,k,m,n */ 937| 6.39k| for (n = j = 0; n < num_neigh1; n++) ------------------ | Branch (937:37): [True: 4.26k, False: 2.13k] ------------------ 938| 4.26k| { 939| 4.26k| if (n != m1) ------------------ | Branch (939:29): [True: 2.12k, False: 2.13k] ------------------ 940| 2.12k| { 941| 2.12k| i = (int) at[k1].neighbor[n]; 942| 2.13k| for (m = 0; m < num_neigh1 - 1; m++) ------------------ | Branch (942:41): [True: 2.13k, False: 0] ------------------ 943| 2.13k| { 944| 2.13k| if (nRank[i] == nNeighRank1[m]) ------------------ | Branch (944:37): [True: 2.12k, False: 11] ------------------ 945| 2.12k| { 946| 2.12k| nNeighCanonRank1[m] = nCanonRank[i]; 947| 2.12k| j++; 948| 2.12k| break; 949| 2.12k| } 950| 2.13k| } 951| 2.12k| } 952| 4.26k| } 953| 2.13k| if (j != num_neigh1 - 1) ------------------ | Branch (953:25): [True: 0, False: 2.13k] ------------------ 954| 0| { 955| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 956| 0| } 957| 2.13k| if (j == 2) ------------------ | Branch (957:25): [True: 11, False: 2.12k] ------------------ 958| 11| { 959| 11| trans_k1 = insertions_sort( pCG, nNeighCanonRank1, j, sizeof( nNeighCanonRank1[0] ), comp_AT_RANK ); 960| 11| } 961| 2.12k| else 962| 2.12k| { 963| 2.12k| trans_k1 = 0; 964| 2.12k| } 965| | 966| | /* store canon. ranks of at[k2] neighbors */ /* use i,j,k,m,n */ 967| 6.41k| for (n = j = 0; n < num_neigh2; n++) ------------------ | Branch (967:37): [True: 4.27k, False: 2.13k] ------------------ 968| 4.27k| { 969| 4.27k| i = (int) at[k2].neighbor[n]; 970| 4.27k| if (i == prev) ------------------ | Branch (970:29): [True: 2.13k, False: 2.14k] ------------------ 971| 2.13k| { 972| | /* neighbor belongs to the stereobond */ 973| 2.13k| m2 = n; 974| 2.13k| } 975| 2.14k| else 976| 2.14k| { 977| 2.16k| for (m = 0; m < num_neigh2 - 1; m++) ------------------ | Branch (977:41): [True: 2.16k, False: 0] ------------------ 978| 2.16k| { 979| 2.16k| if (nRank[i] == nNeighRank2[m]) ------------------ | Branch (979:37): [True: 2.14k, False: 26] ------------------ 980| 2.14k| { 981| 2.14k| nNeighCanonRank2[m] = nCanonRank[i]; 982| 2.14k| j++; 983| 2.14k| break; 984| 2.14k| } 985| 2.16k| } 986| 2.14k| } 987| 4.27k| } 988| 2.13k| if (j != num_neigh2 - 1 || m2 < 0) ------------------ | Branch (988:25): [True: 0, False: 2.13k] | Branch (988:48): [True: 0, False: 2.13k] ------------------ 989| 0| { 990| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 991| 0| } 992| 2.13k| if (j == 2) ------------------ | Branch (992:25): [True: 26, False: 2.10k] ------------------ 993| 26| { 994| 26| trans_k2 = insertions_sort( pCG, nNeighCanonRank2, j, sizeof( nNeighCanonRank2[0] ), comp_AT_RANK ); 995| 26| } 996| 2.10k| else 997| 2.10k| { 998| 2.10k| trans_k2 = 0; 999| 2.10k| } 1000| 2.13k| trans_k = ( trans_k1 + trans_k2 ) % 2; 1001| 2.13k| if (prev_trans < 0) ------------------ | Branch (1001:25): [True: 255, False: 1.87k] ------------------ 1002| 255| { 1003| 255| prev_trans = trans_k; 1004| 255| } 1005| 1.87k| else if (prev_trans != trans_k) ------------------ | Branch (1005:30): [True: 0, False: 1.87k] ------------------ 1006| 0| { 1007| | /* was != trans_k1, changed 9-23-2003 */ 1008| 0| break; /* different number of transpositions */ 1009| 0| } 1010| 2.13k| } /* end of the second atom mapping cycle */ 1011| 1.16k| if (prev_trans >= 0 && prev_trans != trans_k) ------------------ | Branch (1011:21): [True: 1.16k, False: 0] | Branch (1011:40): [True: 0, False: 1.16k] ------------------ 1012| 0| { /* was != trans_k1, changed 9-23-2003 */ 1013| 0| break; 1014| 0| } 1015| 1.16k| } /* end of the first atom mapping cycle */ 1016| | 1017| 255| if (prev_trans == trans_k) ------------------ | Branch (1017:17): [True: 255, False: 0] ------------------ 1018| 255| { 1019| | /* was == trans_k1, changed 9-23-2003 */ 1020| 255| int z_prod; 1021| | 1022| | /* all mappings of canonical numbers on the */ 1023| | /* stereo bond at[i1]-at[i2] produce equivalent numberings. */ 1024| | /* Therefore the stereo bond parity is known at this time. */ 1025| | /* parity_1 = at[i1].parity + (trans_i1 + trans_k1 + num_neigh1 - 1) + (int)at[i1].stereo_bond_ord[n1] */ 1026| | /* expression in parentheses is equivalent to rank[first neigh] > rank[second neigh] */ 1027| | /* same for parity_2. */ 1028| | /* parity_2 = at[i2].parity + (trans_i2 + trans_k2 + num_neigh2 - 1) + (int)at[i2].stereo_bond_ord[n2] */ 1029| | /* Sum of the two parities (without stereo_bond_z_prod) is: */ 1030| | 1031| 255| parity = ( at[i1].parity + at[i2].parity + prev_trans + trans_i1 + trans_i2 1032| 255| + num_neigh1 + num_neigh2 1033| 255| + (int) at[i1].stereo_bond_ord[n1] + (int) at[i2].stereo_bond_ord[n2] ) % 2; 1034| | 1035| 255| z_prod = at[i1].stereo_bond_z_prod[n1]; 1036| 255| if (MIN_DOT_PROD > abs( z_prod )) ------------------ | | 253| 255|#define MIN_DOT_PROD 50 /* min value of at->stereo_bond_z_prod[i] to define parity */ ------------------ | Branch (1036:21): [True: 0, False: 255] ------------------ 1037| 0| { 1038| 0| parity = AB_PARITY_UNDF; /* undefined because of geometry */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 1039| 0| } 1040| 255| else 1041| 255| { 1042| 255| parity = ( z_prod > 0 ) ? 2 - parity : 1 + parity; ------------------ | Branch (1042:30): [True: 255, False: 0] ------------------ 1043| 255| } 1044| 255| at[i1].stereo_bond_parity[n1] = ALL_BUT_PARITY( at[i1].stereo_bond_parity[n1] ) | parity; ------------------ | | 270| 255|#define ALL_BUT_PARITY(X) ((X)&~BITS_PARITY) | | ------------------ | | | | 204| 255|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 1045| 255| at[i2].stereo_bond_parity[n2] = ALL_BUT_PARITY( at[i2].stereo_bond_parity[n2] ) | parity; ------------------ | | 270| 255|#define ALL_BUT_PARITY(X) ((X)&~BITS_PARITY) | | ------------------ | | | | 204| 255|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 1046| 255| num_set++; 1047| 255| } 1048| 255| } 1049| 526| } 1050| | 1051| 1.14k| return num_set; 1052| 1.14k|} MarkKnownEqualStereoBondParities: 1062| 1.14k|{ 1063| 1.14k| int j, n, m, j1, num_neigh1, num_neigh2, iMax1; 1064| 1.14k| int num_set, /*num_sb1, num_sb2,*/ bDifferentParities; 1065| 1.14k| int i1, i2, k1, k2, n1, n2, m1, m2, s1, s2, stereo_bond_parity, stereo_bond_parity2, cumulene_len; 1066| 1.14k| AT_RANK nAtomRank1, nAtomRank2, nAtom1NeighRank, nAtom2NeighRank; 1067| | 1068| | /* djb-rwth: removing redundant code */ 1069| | 1070| 8.08k| for (i1 = 0, num_set = 0; i1 < num_atoms; i1++) ------------------ | Branch (1070:31): [True: 6.94k, False: 1.14k] ------------------ 1071| 6.94k| { 1072| 6.94k| if (!at[i1].parity || !at[i1].stereo_bond_neighbor[0]) ------------------ | Branch (1072:13): [True: 3.37k, False: 3.56k] | Branch (1072:31): [True: 1.82k, False: 1.74k] ------------------ 1073| 5.19k| { 1074| 5.19k| continue; 1075| 5.19k| } 1076| | 1077| 1.74k| nAtomRank1 = nRank[i1]; 1078| 1.74k| iMax1 = (int) nAtomRank1 - 1; 1079| 1.74k| num_neigh1 = at[i1].valence; 1080| | 1081| | /* count stereogenic bonds adjacent to at[i1] */ 1082| 1.74k| for (n1 = 0; 1083| 4.42k| n1 < MAX_NUM_STEREO_BONDS && at[i1].stereo_bond_neighbor[n1]; ------------------ | | 873| 8.84k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1083:17): [True: 4.42k, False: 0] | Branch (1083:46): [True: 2.67k, False: 1.74k] ------------------ 1084| 2.67k| n1++); 1085| | 1086| | 1087| | /*num_sb1 = n1;*/ 1088| | /* search for bonds possibly constitutionally equivalent to each of the adjacent bonds */ 1089| | /* and find if all of them have same already known parity */ 1090| | 1091| 1.74k| for (n1 = 0; 1092| 4.42k| n1 < MAX_NUM_STEREO_BONDS && ( i2 = (int) at[i1].stereo_bond_neighbor[n1] ); ------------------ | | 873| 8.84k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1092:17): [True: 4.42k, False: 0] | Branch (1092:46): [True: 2.67k, False: 1.74k] ------------------ 1093| 2.67k| n1++) /* djb-rwth: removing redundant code */ 1094| 2.67k| { 1095| 2.67k| i2--; 1096| | 1097| 2.67k| nAtomRank2 = nRank[i2]; 1098| 2.67k| if (nAtomRank2 < nAtomRank1 || (nAtomRank2 == nAtomRank1 && i1 < i2)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1098:17): [True: 624, False: 2.05k] | Branch (1098:45): [True: 1.43k, False: 624] | Branch (1098:73): [True: 715, False: 715] ------------------ 1099| 1.33k| { 1100| | /* An attempt to reduce unnecessary repetitions. */ 1101| | /* We still have repetitions because we do not accumulate a list of */ 1102| | /* processed (nAtomRank2, nAtomRank1) pairs. */ 1103| 1.33k| continue; 1104| 1.33k| } 1105| | 1106| 1.33k| bDifferentParities = -1; /* parities have not been compared yet */ 1107| | 1108| | /* found a stereo bond at[i1]-at[i2] (adjacent to at[i1]) */ 1109| | /* 1110| | if ( !PARITY_KNOWN(at[i1].stereo_bond_parity[n1]) || (at[i1].stereo_bond_parity[n1] & KNOWN_PARITIES_EQL) ) 1111| | { 1112| | continue; 1113| | } 1114| | */ 1115| 1.33k| if (at[i1].stereo_bond_parity[n1] & KNOWN_PARITIES_EQL) ------------------ | | 206| 1.33k|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ | Branch (1115:17): [True: 149, False: 1.19k] ------------------ 1116| 149| { 1117| 149| continue; 1118| 149| } 1119| | 1120| | 1121| | /* stereo bond has known or unknown parity; we have not checked it yet */ 1122| | 1123| 1.19k| for (n2 = 0; 1124| 3.19k| n2 < MAX_NUM_STEREO_BONDS && at[i2].stereo_bond_neighbor[n2]; ------------------ | | 873| 6.38k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1124:18): [True: 3.19k, False: 0] | Branch (1124:47): [True: 2.00k, False: 1.19k] ------------------ 1125| 2.00k| n2++) 1126| 2.00k| { 1127| 2.00k| ; 1128| 2.00k| } 1129| | 1130| | /*num_sb2 = n2;*/ 1131| 1.19k| for (n2 = 0, m = 0; 1132| 1.75k| n2 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 3.51k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1132:18): [True: 1.75k, False: 0] ------------------ 1133| 1.75k| ( m = (int) at[i2].stereo_bond_neighbor[n2] ) && ------------------ | Branch (1133:18): [True: 1.75k, False: 0] ------------------ 1134| 1.75k| m - 1 != i1; ------------------ | Branch (1134:21): [True: 565, False: 1.19k] ------------------ 1135| 1.19k| n2++) 1136| 565| { 1137| 565| ; 1138| 565| } 1139| | 1140| 1.19k| if (m - 1 != i1 || at[i1].stereo_bond_parity[n1] != at[i2].stereo_bond_parity[n2]) ------------------ | Branch (1140:17): [True: 0, False: 1.19k] | Branch (1140:32): [True: 0, False: 1.19k] ------------------ 1141| 0| { 1142| 0| return CT_STEREOCOUNT_ERR; /* program error: stereo bonds data in two directions are different */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1143| 0| } 1144| | 1145| 1.19k| stereo_bond_parity = PARITY_VAL( at[i1].stereo_bond_parity[n1] ); ------------------ | | 262| 1.19k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 1.19k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 1146| 1.19k| cumulene_len = BOND_CHAIN_LEN( at[i1].stereo_bond_parity[n1] ); ------------------ | | 214| 1.19k|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 1.19k|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 1.19k|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 1.19k|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 1147| 1.19k| nAtom1NeighRank = nRank[(int) at[i1].neighbor[(int) at[i1].stereo_bond_ord[n1]]]; 1148| 1.19k| nAtom2NeighRank = nRank[(int) at[i2].neighbor[(int) at[i2].stereo_bond_ord[n2]]]; 1149| 1.19k| num_neigh2 = at[i2].valence; 1150| | 1151| | /* find all pairs of atoms that possibly can be mapped on at[i1], at[i2] pair */ 1152| | /* (we may also find pairs that cannot be mapped, but we cannot miss any pair */ 1153| | /* that can be mapped) */ 1154| | 1155| 7.15k| for (j1 = 0; j1 <= iMax1 && nAtomRank1 == nRank[k1 = (int) nAtomNumber[iMax1 - j1]]; j1++) ------------------ | Branch (1155:26): [True: 6.23k, False: 917] | Branch (1155:41): [True: 5.96k, False: 273] ------------------ 1156| 5.96k| { 1157| | /* at[k1] is constitutionally equivalent to at[i1] */ 1158| | /* find all at[k1] stereo bond neighbors at[k2] that have rank nAtomRank2; */ 1159| | /* then find at[k2] constitutionally equivalent at at[i2] */ 1160| | 1161| 5.96k| if (at[k1].valence != num_neigh1) ------------------ | Branch (1161:21): [True: 0, False: 5.96k] ------------------ 1162| 0| { 1163| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1164| 0| } 1165| | 1166| 5.96k| if (!at[k1].bHasStereoOrEquToStereo) ------------------ | Branch (1166:21): [True: 629, False: 5.33k] ------------------ 1167| 629| { 1168| 629| at[k1].bHasStereoOrEquToStereo = 1; 1169| 629| } 1170| | 1171| | /* -- do not check number of stereo bonds, check bonds themselves -- 1172| | for ( s1 = 0; s1 < MAX_NUM_STEREO_BONDS && at[k1].stereo_bond_neighbor[s1]; s1++ ) 1173| | { 1174| | ; 1175| | } 1176| | if ( num_sb1 != s1 ) 1177| | { 1178| | bDifferentParities = 1; 1179| | } 1180| | */ 1181| | 1182| 17.9k| for (m1 = 0; m1 < num_neigh1; m1++) ------------------ | Branch (1182:30): [True: 11.9k, False: 5.96k] ------------------ 1183| 11.9k| { 1184| | /* Looking for at[k1] neighbor with nRank=nAtom1NeighRank. */ 1185| | /* This neighbor may be on the bond constit. equivalent to at[i1]-at[i2] stereo bond */ 1186| | /* (or may be constit. equivalent an adjacent to at[i1] atom in a stereogenic cumulene chain) */ 1187| 11.9k| int prev, next, len; 1188| 11.9k| if (nAtom1NeighRank != nRank[k2 = (int) at[k1].neighbor[m1]]) ------------------ | Branch (1188:25): [True: 742, False: 11.2k] ------------------ 1189| 742| continue; 1190| | 1191| | /* found at[k1] neighbor with nRank=nAtom1NeighRank */ 1192| | 1193| 11.2k| m2 = -1; /* undefined yet */ 1194| 11.2k| prev = k1; 1195| | /* djb-rwth: removing redundant code */ 1196| | 1197| | /* if cumulene then bypass the cumulene chain */ 1198| | 1199| 11.2k| if (cumulene_len) ------------------ | Branch (1199:25): [True: 15, False: 11.2k] ------------------ 1200| 15| { 1201| | 1202| 30| for (len = 0, next = (int) at[k1].neighbor[m1]; len < cumulene_len; len++) ------------------ | Branch (1202:73): [True: 15, False: 15] ------------------ 1203| 15| { 1204| 15| if (at[next].valence == 2 && !at[next].num_H) ------------------ | Branch (1204:33): [True: 15, False: 0] | Branch (1204:58): [True: 15, False: 0] ------------------ 1205| 15| { 1206| 15| j = ( (int) at[next].neighbor[0] == prev ); 1207| 15| prev = next; 1208| 15| next = at[next].neighbor[j]; 1209| 15| } 1210| 0| else 1211| 0| { 1212| 0| break; /* cannot continue: end of cumulene chain */ 1213| 0| } 1214| 15| } 1215| | 1216| 15| if (len != cumulene_len || nAtomRank2 != nRank[next]) ------------------ | Branch (1216:29): [True: 0, False: 15] | Branch (1216:52): [True: 0, False: 15] ------------------ 1217| 0| { 1218| 0| continue; /* cumulene chain not found at this neighbor */ 1219| 0| } 1220| | 1221| 15| if (nAtom2NeighRank != nRank[prev]) ------------------ | Branch (1221:29): [True: 0, False: 15] ------------------ 1222| 0| { 1223| | /* continue; */ /* ??? program error ??? If not, must be a very rare event */ 1224| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1225| 0| } 1226| | 1227| 15| k2 = next; 1228| 15| } 1229| | 1230| | /* a connected pair of constit. equivalent atoms found */ 1231| | 1232| 11.2k| if (at[k2].valence != num_neigh2) ------------------ | Branch (1232:25): [True: 0, False: 11.2k] ------------------ 1233| 0| { 1234| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1235| 0| } 1236| | 1237| 16.6k| for (n = 0; n < num_neigh2; n++) ------------------ | Branch (1237:33): [True: 16.6k, False: 0] ------------------ 1238| 16.6k| { 1239| 16.6k| if (prev == (int) at[k2].neighbor[n]) ------------------ | Branch (1239:29): [True: 11.2k, False: 5.40k] ------------------ 1240| 11.2k| { 1241| 11.2k| m2 = n; /* found bond from the opposite end of a possibly stereogenic bond */ 1242| 11.2k| break; 1243| 11.2k| } 1244| 16.6k| } 1245| | 1246| 11.2k| if (m2 < 0) ------------------ | Branch (1246:25): [True: 0, False: 11.2k] ------------------ 1247| 0| { 1248| 0| return CT_STEREOCOUNT_ERR; /* program error: opposite direction bond not found */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1249| 0| } 1250| | 1251| 11.2k| if (!at[k2].bHasStereoOrEquToStereo) ------------------ | Branch (1251:25): [True: 1.18k, False: 10.0k] ------------------ 1252| 1.18k| { 1253| 1.18k| at[k2].bHasStereoOrEquToStereo = 1; 1254| 1.18k| } 1255| | 1256| | 1257| | /* check if atoms at[k1] and at[k2] are connected by a stereo bond */ 1258| 11.2k| for (s1 = 0, m = 0; 1259| 16.5k| s1 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 33.0k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1259:26): [True: 16.5k, False: 0] ------------------ 1260| 16.5k| ( m = (int) at[k1].stereo_bond_neighbor[s1] ) && ------------------ | Branch (1260:26): [True: 15.8k, False: 701] ------------------ 1261| 15.8k| m - 1 != k2; ------------------ | Branch (1261:37): [True: 5.28k, False: 10.5k] ------------------ 1262| 11.2k| s1++) 1263| 5.28k| { 1264| 5.28k| ; 1265| 5.28k| } 1266| 11.2k| if (m - 1 != k2) ------------------ | Branch (1266:25): [True: 701, False: 10.5k] ------------------ 1267| 701| { 1268| 701| bDifferentParities = 1; /* cannot find the stereo bond */ 1269| 701| at[k1].bHasStereoOrEquToStereo = 1270| 701| at[k2].bHasStereoOrEquToStereo = 2; 1271| 701| continue; 1272| 701| } 1273| | 1274| | /* -- do not check number of stereo bonds, check bonds themselves -- 1275| | for ( s2 = 0; s2 < MAX_NUM_STEREO_BONDS && at[k2].stereo_bond_neighbor[s2]; s2++ ) 1276| | { 1277| | ; 1278| | } 1279| | if ( num_sb2 != s2 ) 1280| | { 1281| | bDifferentParities = 1; 1282| | continue; 1283| | } 1284| | */ 1285| | 1286| 10.5k| for (s2 = 0, m = 0; 1287| 15.3k| s2 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 30.7k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1287:26): [True: 15.3k, False: 0] ------------------ 1288| 15.3k| ( m = (int) at[k2].stereo_bond_neighbor[s2] ) && ------------------ | Branch (1288:26): [True: 15.3k, False: 0] ------------------ 1289| 15.3k| m - 1 != k1; ------------------ | Branch (1289:37): [True: 4.83k, False: 10.5k] ------------------ 1290| 10.5k| s2++) 1291| 4.83k| { 1292| 4.83k| ; 1293| 4.83k| } 1294| | 1295| 10.5k| if (m - 1 != k1) ------------------ | Branch (1295:25): [True: 0, False: 10.5k] ------------------ 1296| 0| { 1297| | /* 1298| | bDifferentParities = 1; // cannot find the stereo bond 1299| | continue; 1300| | */ 1301| 0| return CT_STEREOCOUNT_ERR; /* program error: opposite direction bond not found */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1302| 0| } 1303| | 1304| 10.5k| if (at[k1].stereo_bond_parity[s1] != at[k2].stereo_bond_parity[s2]) ------------------ | Branch (1304:25): [True: 0, False: 10.5k] ------------------ 1305| 0| { 1306| 0| bDifferentParities = 1; 1307| 0| continue; 1308| 0| } 1309| 10.5k| stereo_bond_parity2 = PARITY_VAL( at[k1].stereo_bond_parity[s1] ); ------------------ | | 262| 10.5k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 10.5k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 1310| 10.5k| if (stereo_bond_parity2 != stereo_bond_parity) ------------------ | Branch (1310:25): [True: 2.92k, False: 7.61k] ------------------ 1311| 2.92k| { 1312| 2.92k| bDifferentParities = 1; 1313| 2.92k| continue; 1314| 2.92k| } 1315| 7.61k| if (stereo_bond_parity2 == stereo_bond_parity && bDifferentParities < 0) ------------------ | Branch (1315:25): [True: 7.61k, False: 0] | Branch (1315:70): [True: 917, False: 6.69k] ------------------ 1316| 917| { 1317| 917| bDifferentParities = 0; 1318| 917| } 1319| 7.61k| } 1320| 5.96k| } 1321| | 1322| | /* mark equal parities */ 1323| 1.19k| if (0 == bDifferentParities && PARITY_KNOWN( stereo_bond_parity )) ------------------ | | 265| 442|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 442|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 884|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 442|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 442|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 442|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 442|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 442, False: 0] | | | Branch (265:78): [True: 428, False: 14] | | ------------------ ------------------ | Branch (1323:17): [True: 442, False: 748] ------------------ 1324| 428| { 1325| 428| for (j1 = 0; 1326| 1.01k| j1 <= iMax1 && nAtomRank1 == nRank[k1 = (int) nAtomNumber[iMax1 - j1]]; ------------------ | Branch (1326:25): [True: 791, False: 219] | Branch (1326:40): [True: 582, False: 209] ------------------ 1327| 582| j1++) 1328| 582| { 1329| | /* at[k1] is constitutionally equivalent to at[i1] */ 1330| 1.44k| for (s1 = 0; s1 < MAX_NUM_STEREO_BONDS && ( k2 = (int) at[k1].stereo_bond_neighbor[s1] ); s1++) /* djb-rwth: removing redundant code */ ------------------ | | 873| 2.89k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1330:34): [True: 1.44k, False: 0] | Branch (1330:63): [True: 863, False: 582] ------------------ 1331| 863| { 1332| 863| k2--; 1333| 863| if (nRank[k2] == nAtomRank2) ------------------ | Branch (1333:29): [True: 640, False: 223] ------------------ 1334| 640| { 1335| 640| int b1, b2; 1336| 640| for (s2 = 0, m = 0; 1337| 778| s2 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 1.55k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1337:34): [True: 778, False: 0] ------------------ 1338| 778| ( m = (int) at[k2].stereo_bond_neighbor[s2] ) && ------------------ | Branch (1338:37): [True: 778, False: 0] ------------------ 1339| 778| m - 1 != k1; ------------------ | Branch (1339:37): [True: 138, False: 640] ------------------ 1340| 640| s2++) 1341| 138| { 1342| 138| ; 1343| 138| } 1344| | 1345| 640| if (m - 1 != k1) ------------------ | Branch (1345:33): [True: 0, False: 640] ------------------ 1346| 0| { 1347| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1348| 0| } 1349| | /* mark the stereo bonds */ 1350| 640| b1 = !( at[k1].stereo_bond_parity[s1] & KNOWN_PARITIES_EQL ); ------------------ | | 206| 640|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ 1351| 640| b2 = !( at[k2].stereo_bond_parity[s2] & KNOWN_PARITIES_EQL ); ------------------ | | 206| 640|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ 1352| 640| if (2 == b1 + b2) ------------------ | Branch (1352:33): [True: 577, False: 63] ------------------ 1353| 577| { 1354| 577| at[k1].stereo_bond_parity[s1] |= KNOWN_PARITIES_EQL; ------------------ | | 206| 577|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ 1355| 577| at[k2].stereo_bond_parity[s2] |= KNOWN_PARITIES_EQL; ------------------ | | 206| 577|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ 1356| 577| num_set++; 1357| 577| } 1358| 63| else if (b1 || b2) ------------------ | Branch (1358:38): [True: 0, False: 63] | Branch (1358:44): [True: 0, False: 63] ------------------ 1359| 0| { 1360| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1361| 0| } 1362| 640| } 1363| 863| } 1364| 582| } 1365| 428| } 1366| 1.19k| } 1367| 1.74k| } 1368| | 1369| 1.14k| return num_set; 1370| 1.14k|} PathsHaveIdenticalKnownParities: 1505| 34|{ 1506| 34| int k; 1507| 34| AT_RANK n1, n2; 1508| | 1509| 34| nLength++; /* number of successfully traversed pairs of atoms */ 1510| 34| nVisited1[cur1] = nLength; 1511| 34| nVisited2[cur2] = nLength; 1512| | 1513| | /* the atoms must be either both stereogenic and have well-defined parities or non-stereogenic at all. */ 1514| 34| if (at[cur1].stereo_atom_parity != at[cur2].stereo_atom_parity || ------------------ | Branch (1514:9): [True: 0, False: 34] ------------------ 1515| 34| (at[cur1].stereo_atom_parity && !PARITY_WELL_DEF( at[cur1].stereo_atom_parity )) ) /* djb-rwth: addressing LLVM warning */ ------------------ | | 266| 0|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 0, False: 0] | | | Branch (266:85): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1515:11): [True: 0, False: 34] ------------------ 1516| 0| { 1517| 0| return 0; /* Reject: Different or unknown in advance parities */ 1518| 0| } 1519| | 1520| 34| if (at[cur1].valence != at[cur2].valence) ------------------ | Branch (1520:9): [True: 0, False: 34] ------------------ 1521| 0| { 1522| 0| return 0; /* program error */ /* */ 1523| 0| } 1524| | 1525| 34| if (at[cur1].valence == 1) ------------------ | Branch (1525:9): [True: 34, False: 0] ------------------ 1526| 34| { 1527| 34| return nLength; /* so far success */ 1528| 34| } 1529| | 1530| | 1531| 0| for (k = 1, n1 = MAX_ATOMS + 1, n2 = MAX_ATOMS + 1; k < at[cur1].valence; k++) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ for (k = 1, n1 = MAX_ATOMS + 1, n2 = MAX_ATOMS + 1; k < at[cur1].valence; k++) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ | Branch (1531:57): [True: 0, False: 0] ------------------ 1532| 0| { 1533| | /* start from 1: since we do not go back, we have only (at[cur1].valence-1) bonds to try */ 1534| | 1535| 0| if (!GetAndCheckNextNeighbors( at, cur1, prev1, cur2, prev2, ------------------ | Branch (1535:13): [True: 0, False: 0] ------------------ 1536| 0| &n1, &n2, nVisited1, nVisited2, 1537| 0| nRank, nCanonRank )) 1538| 0| { 1539| 0| return 0; /* different neighbors */ 1540| 0| } 1541| | 1542| | /* In a DFS we do not traverse already visited atoms */ 1543| 0| if (!nVisited1[n1]) ------------------ | Branch (1543:13): [True: 0, False: 0] ------------------ 1544| 0| { 1545| | /* recursion */ 1546| 0| if (!( nLength = PathsHaveIdenticalKnownParities( at, cur1, n1, cur2, n2, nVisited1, nVisited2, nRank, nCanonRank, nLength ) )) ------------------ | Branch (1546:17): [True: 0, False: 0] ------------------ 1547| 0| { 1548| 0| return 0; 1549| 0| } 1550| 0| } 1551| 0| } 1552| | 1553| | /* To be on a safe side, recheck after all nVisited[] have been set */ 1554| 0| for (k = 1, n1 = MAX_ATOMS + 1, n2 = MAX_ATOMS + 1; k < at[cur1].valence; k++) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ for (k = 1, n1 = MAX_ATOMS + 1, n2 = MAX_ATOMS + 1; k < at[cur1].valence; k++) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ | Branch (1554:57): [True: 0, False: 0] ------------------ 1555| 0| { 1556| | /* start from 1: since we do not go back, we have only (at[cur1].valence-1) bonds to try */ 1557| 0| if (!GetAndCheckNextNeighbors( at, cur1, prev1, cur2, prev2, ------------------ | Branch (1557:13): [True: 0, False: 0] ------------------ 1558| 0| &n1, &n2, nVisited1, nVisited2, 1559| 0| nRank, nCanonRank )) 1560| 0| { 1561| 0| return 0; /* different neighbors */ 1562| 0| } 1563| 0| } 1564| | 1565| 0| return nLength; 1566| 0|} RemoveKnownNonStereoBondParities: 1578| 1.18k|{ 1579| 1.18k| int j, n, m, ret; 1580| | 1581| 1.18k| int i1, n1, s2; 1582| 1.18k| AT_RANK nAtomRank1, nAtomRank2, neigh[3], opposite_atom, *nVisited = NULL; 1583| 1.18k| ret = 0; 1584| 8.39k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (1584:18): [True: 7.21k, False: 1.18k] ------------------ 1585| 7.21k| { 1586| 7.21k| if (at[i1].valence != 3 || !at[i1].stereo_bond_neighbor[0]) ------------------ | Branch (1586:13): [True: 6.05k, False: 1.15k] | Branch (1586:36): [True: 1.01k, False: 139] ------------------ 1587| 7.07k| { 1588| 7.07k| continue; 1589| 7.07k| } 1590| 281| for (n1 = 0; n1 < MAX_NUM_STEREO_BONDS && ( s2 = at[i1].stereo_bond_neighbor[n1] ); n1++) ------------------ | | 873| 562|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1590:22): [True: 281, False: 0] | Branch (1590:51): [True: 142, False: 139] ------------------ 1591| 142| { 1592| 142| if (!PARITY_CALCULATE( at[i1].stereo_bond_parity[n1] ) && PARITY_WELL_DEF( at[i1].stereo_bond_parity[n1] )) ------------------ | | 267| 284|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 142|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 142|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 142|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ ------------------ if (!PARITY_CALCULATE( at[i1].stereo_bond_parity[n1] ) && PARITY_WELL_DEF( at[i1].stereo_bond_parity[n1] )) ------------------ | | 266| 115|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 115|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 230|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 115|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 115|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 115|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 115|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 115, False: 0] | | | Branch (266:85): [True: 35, False: 80] | | ------------------ ------------------ | Branch (1592:17): [True: 115, False: 27] ------------------ 1593| 35| { 1594| 35| continue; 1595| 35| } 1596| 107| opposite_atom = (AT_RANK) ( s2 - 1 ); 1597| | /* s2 = at[i1].neighbor[m=(int)at[i1].stereo_bond_ord[n1]]; */ 1598| 107| m = (int) at[i1].stereo_bond_ord[n1]; 1599| 428| for (j = 0, n = 0; j < at[i1].valence; j++) ------------------ | Branch (1599:32): [True: 321, False: 107] ------------------ 1600| 321| { 1601| | /* if ( at[i1].neighbor[j] != s2 ) */ 1602| 321| if (j != m) ------------------ | Branch (1602:21): [True: 214, False: 107] ------------------ 1603| 214| { 1604| 214| neigh[n++] = at[i1].neighbor[j]; 1605| 214| } 1606| 321| } 1607| 107| if (n > 2) ------------------ | Branch (1607:17): [True: 0, False: 107] ------------------ 1608| 0| { 1609| 0| ret = CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1610| 0| goto exit_function; 1611| 0| } 1612| 107| if (n != 2 || nRank[(int) neigh[0]] != nRank[(int) neigh[1]]) ------------------ | Branch (1612:17): [True: 0, False: 107] | Branch (1612:27): [True: 69, False: 38] ------------------ 1613| 69| { 1614| 69| continue; /* may happen if another half-bond has not a defined parity */ 1615| 69| } 1616| 38| if (at[i1].nRingSystem == at[(int) neigh[0]].nRingSystem) ------------------ | Branch (1616:17): [True: 18, False: 20] ------------------ 1617| 18| { 1618| 18| continue; /* no more ring system membership check is necessary because */ 1619| 18| } /* the two neighbors are to be constitutionally equivalent atoms */ 1620| 20| if (!nVisited && !( nVisited = (AT_RANK*) inchi_malloc( sizeof( nVisited[0] )*num_atoms ) )) ------------------ | | 1143| 20|#define inchi_malloc malloc ------------------ | Branch (1620:17): [True: 20, False: 0] | Branch (1620:30): [True: 0, False: 20] ------------------ 1621| 0| { 1622| 0| ret = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1623| 0| goto exit_function; 1624| 0| } 1625| 20| memset( nVisited, 0, sizeof( nVisited[0] )*num_atoms ); /* djb-rwth: memset_s C11/Annex K variant? */ 1626| 20| nVisited[i1] = 1; 1627| 20| if (PathsHaveIdenticalKnownParities( at, (AT_RANK) i1, neigh[0], (AT_RANK) i1, neigh[1], nVisited, nVisited, nRank, nCanonRank, 1 )) ------------------ | Branch (1627:17): [True: 20, False: 0] ------------------ 1628| 20| { 1629| 20| if (!RemoveOneStereoBond( at, i1, /* atom number*/ n1 /* stereo bond number*/ )) ------------------ | Branch (1629:21): [True: 0, False: 20] ------------------ 1630| 0| { 1631| 0| ret = CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1632| 0| goto exit_function; 1633| 0| } 1634| 20| n1--; /* cycle counter may temporarily become negative */ 1635| | /* Remove from pCS */ 1636| 20| nAtomRank1 = inchi_max( nCanonRank[i1], nCanonRank[opposite_atom] ); ------------------ | | 138| 20|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 20, False: 0] | | ------------------ ------------------ 1637| 20| nAtomRank2 = inchi_min( nCanonRank[i1], nCanonRank[opposite_atom] ); ------------------ | | 139| 20|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 20] | | ------------------ ------------------ 1638| 20| for (n = 0, m = pCS->nLenLinearCTStereoDble - 1; n <= m; n++) ------------------ | Branch (1638:66): [True: 20, False: 0] ------------------ 1639| 20| { 1640| 20| if (pCS->LinearCTStereoDble[n].at_num1 == nAtomRank1 && ------------------ | Branch (1640:25): [True: 20, False: 0] ------------------ 1641| 20| pCS->LinearCTStereoDble[n].at_num2 == nAtomRank2) ------------------ | Branch (1641:26): [True: 20, False: 0] ------------------ 1642| 20| { 1643| 20| if (n < m) ------------------ | Branch (1643:29): [True: 0, False: 20] ------------------ 1644| 0| { /* remove pCS->LinearCTStereoDble[n] */ 1645| 0| memmove( pCS->LinearCTStereoDble + n, pCS->LinearCTStereoDble + n + 1, ( (long long)m - (long long)n ) * sizeof( pCS->LinearCTStereoDble[0] ) ); /* djb-rwth: cast operators added */ 1646| 0| } 1647| 20| pCS->nLenLinearCTStereoDble--; 1648| |#if ( bRELEASE_VERSION == 0 ) 1649| | pCS->bExtract |= EXTR_KNOWN_USED_TO_REMOVE_PARITY; 1650| |#endif 1651| 20| m = -1; /* set flag "found" */ 1652| 20| break; 1653| 20| } 1654| 20| } 1655| 20| if (m >= 0) ------------------ | Branch (1655:21): [True: 0, False: 20] ------------------ 1656| 0| { 1657| 0| ret = CT_STEREOCOUNT_ERR; /* bond not found */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1658| 0| goto exit_function; 1659| 0| } 1660| 20| ret++; /* number of removed known in advance non-stereo bonds */ 1661| 20| } 1662| 20| } 1663| 139| } 1664| | 1665| 1.18k|exit_function: 1666| 1.18k| if (nVisited) ------------------ | Branch (1666:9): [True: 20, False: 1.16k] ------------------ 1667| 20| { 1668| 20| inchi_free( nVisited ); ------------------ | | 1152| 20|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 20, False: 0] | | | Branch (1152:50): [Folded, False: 20] | | ------------------ ------------------ 1669| 20| } 1670| | 1671| 1.18k| return ret; 1672| 1.18k|} SetKnownStereoCenterParities: 1685| 1.14k|{ 1686| 1.14k| int i, j, n, m, j1, k, num_neigh, iMax, trans_i, trans_k, prev_trans, num_set; 1687| 1.14k| AT_RANK nAtomRank; 1688| 1.14k| AT_RANK nNeighRank[MAX_NUM_STEREO_ATOM_NEIGH]; 1689| 1.14k| AT_RANK nNeighCanonRank[MAX_NUM_STEREO_ATOM_NEIGH]; 1690| | 1691| 8.08k| for (i = 0, num_set = 0; i < num_atoms; i++) ------------------ | Branch (1691:30): [True: 6.94k, False: 1.14k] ------------------ 1692| 6.94k| { 1693| 6.94k| if (!at[i].parity || at[i].stereo_bond_neighbor[0]) ------------------ | Branch (1693:13): [True: 3.37k, False: 3.56k] | Branch (1693:30): [True: 1.74k, False: 1.82k] ------------------ 1694| 5.12k| { 1695| 5.12k| continue; 1696| 5.12k| } 1697| 1.82k| if (at[i].stereo_atom_parity != AB_PARITY_CALC || ------------------ | | 224| 3.64k|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ | Branch (1697:13): [True: 1.14k, False: 678] ------------------ 1698| 678| !PARITY_WELL_DEF( at[i].parity )) ------------------ | | 266| 678|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 678|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 1.35k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 678|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 678|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 678|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 678|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 678, False: 0] | | | Branch (266:85): [True: 678, False: 0] | | ------------------ ------------------ 1699| 1.14k| { 1700| 1.14k| continue; 1701| 1.14k| } 1702| 678| num_neigh = at[i].valence; 1703| 3.17k| for (j = 0; j < num_neigh; j++) ------------------ | Branch (1703:21): [True: 2.49k, False: 678] ------------------ 1704| 2.49k| { 1705| 2.49k| nNeighRank[j] = nRank[(int) at[i].neighbor[j]]; 1706| 2.49k| } 1707| 678| nAtomRank = nRank[i]; 1708| 678| if (num_neigh == 1) ------------------ | Branch (1708:13): [True: 0, False: 678] ------------------ 1709| 0| { 1710| | /* other neighbors must be implicit H */ 1711| 0| at[i].stereo_atom_parity = at[i].parity; 1712| 0| trans_i = 0; 1713| 0| } 1714| 678| else 1715| 678| { 1716| | /* sort constitutional equivalence ranks of the neighbors */ 1717| 678| trans_i = insertions_sort( pCG, nNeighRank, num_neigh, sizeof( nNeighRank[0] ), comp_AT_RANK ); 1718| 1.38k| for (j = 1; j < num_neigh; j++) ------------------ | Branch (1718:25): [True: 1.18k, False: 206] ------------------ 1719| 1.18k| { 1720| 1.18k| if (nNeighRank[j - 1] == nNeighRank[j]) ------------------ | Branch (1720:21): [True: 472, False: 709] ------------------ 1721| 472| { 1722| 472| break; /* at[i] has consitutionally identical neighbors */ 1723| 472| } 1724| 1.18k| } 1725| 678| if (j < num_neigh) ------------------ | Branch (1725:17): [True: 472, False: 206] ------------------ 1726| 472| { 1727| | /* at least 2 neighbors are const. identical; parity cannot be calculated at this time */ 1728| 472| continue; /* try next stereo atom */ 1729| 472| } 1730| 678| } 1731| 206| prev_trans = -1; 1732| 206| trans_k = 0; 1733| | /* find neighbors of constitutionally equivalent stereo centers */ 1734| | /* and at[i] parities in case those centers are mapped on at[i] */ 1735| 206| for (iMax = (int) nAtomRank - 1, j1 = 0; 1736| 471| j1 <= iMax && nAtomRank == nRank[k = (int) nAtomNumber[iMax - j1]]; ------------------ | Branch (1736:17): [True: 446, False: 25] | Branch (1736:31): [True: 265, False: 181] ------------------ 1737| 265| j1++) 1738| 265| { 1739| | /* at[k] is constitutionally equivalent to at[i] */ 1740| 265| if ((int) at[k].valence != num_neigh) ------------------ | Branch (1740:17): [True: 0, False: 265] ------------------ 1741| 0| { 1742| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1743| 0| } 1744| | /* -- commented out to accept non-stereogenic atoms since -- 1745| | -- they may participate in mapping stereocenters 12-16-2003 -- 1746| | if ( !PARITY_VAL(at[k].parity) ) { 1747| | continue; // not a stereogenic atom 1748| | } 1749| | */ 1750| 1.19k| for (j = 0, m = 0; m < num_neigh; m++) ------------------ | Branch (1750:32): [True: 931, False: 265] ------------------ 1751| 931| { 1752| 2.13k| for (n = 0; n < num_neigh; n++) ------------------ | Branch (1752:29): [True: 2.13k, False: 0] ------------------ 1753| 2.13k| { 1754| 2.13k| if (nRank[(int) at[k].neighbor[n]] == nNeighRank[m]) ------------------ | Branch (1754:25): [True: 931, False: 1.20k] ------------------ 1755| 931| { 1756| | /* save canonical numbers (ranks) of the neighbors in 1757| | * order of increasing constit. equivalence ranks */ 1758| 931| nNeighCanonRank[m] = nCanonRank[(int) at[k].neighbor[n]]; 1759| 931| j++; 1760| 931| break; 1761| 931| } 1762| 2.13k| } 1763| 931| } 1764| 265| if (j != num_neigh) ------------------ | Branch (1764:17): [True: 0, False: 265] ------------------ 1765| 0| { 1766| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1767| 0| } 1768| 265| trans_k = insertions_sort( pCG, nNeighCanonRank, num_neigh, sizeof( nNeighCanonRank[0] ), comp_AT_RANK ); 1769| 265| trans_k %= 2; 1770| 265| if (prev_trans < 0) ------------------ | Branch (1770:17): [True: 206, False: 59] ------------------ 1771| 206| { 1772| 206| prev_trans = trans_k; 1773| 206| } 1774| 59| else if (trans_k != prev_trans) ------------------ | Branch (1774:22): [True: 0, False: 59] ------------------ 1775| 0| { 1776| | /* different mappings may produce different parities. Cannot find the parity at this time */ 1777| | /* this may happen when a set of constit. equivalent atoms has non-contiguous canonical numbers */ 1778| 0| break; 1779| 0| } 1780| 265| } 1781| 206| if (trans_k == prev_trans) ------------------ | Branch (1781:13): [True: 206, False: 0] ------------------ 1782| 206| { 1783| 206| at[i].stereo_atom_parity = 2 - ( at[i].parity + trans_i + prev_trans ) % 2; 1784| 206| num_set++; 1785| 206| } 1786| 206| } 1787| | 1788| 1.14k| return num_set; 1789| 1.14k|} RemoveKnownNonStereoCenterParities: 1804| 1.18k|{ 1805| 1.18k| int i, j, n, m, k, num_neigh, ret = 0; 1806| | /*AT_RANK nAtomRank;*/ 1807| 1.18k| AT_RANK nNeighRank[MAX_NUM_STEREO_ATOM_NEIGH], nNeighOrd[MAX_NUM_STEREO_ATOM_NEIGH]; 1808| 1.18k| AT_RANK *nVisited = NULL; 1809| | 1810| 8.39k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1810:17): [True: 7.21k, False: 1.18k] ------------------ 1811| 7.21k| { 1812| 7.21k| if (!at[i].parity || at[i].stereo_bond_neighbor[0]) ------------------ | Branch (1812:13): [True: 3.61k, False: 3.59k] | Branch (1812:30): [True: 1.74k, False: 1.84k] ------------------ 1813| 5.36k| { 1814| 5.36k| continue; 1815| 5.36k| } 1816| 1.84k| if (!PARITY_CALCULATE( at[i].stereo_atom_parity ) && PARITY_WELL_DEF( at[i].stereo_atom_parity )) ------------------ | | 267| 3.69k|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 1.84k|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 1.84k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.84k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ ------------------ if (!PARITY_CALCULATE( at[i].stereo_atom_parity ) && PARITY_WELL_DEF( at[i].stereo_atom_parity )) ------------------ | | 266| 1.37k|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.37k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 2.75k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.37k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 1.37k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.37k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.37k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 1.37k, False: 0] | | | Branch (266:85): [True: 230, False: 1.14k] | | ------------------ ------------------ | Branch (1816:13): [True: 1.37k, False: 472] ------------------ 1817| 230| { 1818| 230| continue; 1819| 230| } 1820| 1.61k| num_neigh = at[i].valence; 1821| 7.63k| for (j = 0; j < num_neigh; j++) ------------------ | Branch (1821:21): [True: 6.02k, False: 1.61k] ------------------ 1822| 6.02k| { 1823| 6.02k| nNeighRank[j] = nRank[(int) at[i].neighbor[j]]; 1824| 6.02k| nNeighOrd[j] = j; 1825| 6.02k| } 1826| | /*nAtomRank = nRank[i];*/ 1827| 1.61k| if (num_neigh == 1) ------------------ | Branch (1827:13): [True: 0, False: 1.61k] ------------------ 1828| 0| { 1829| 0| continue; 1830| 0| } 1831| 1.61k| pCG->m_pn_RankForSort = nNeighRank; 1832| 1.61k| insertions_sort( pCG, nNeighOrd, num_neigh, sizeof( nNeighRank[0] ), CompRanksOrd ); 1833| 6.01k| for (j = k = 1; k && j < num_neigh; j++) ------------------ | Branch (1833:25): [True: 5.99k, False: 14] | Branch (1833:30): [True: 4.39k, False: 1.60k] ------------------ 1834| 4.39k| { 1835| 4.39k| if (at[i].nRingSystem != at[(int) at[i].neighbor[(int) nNeighOrd[j]]].nRingSystem && ------------------ | Branch (1835:17): [True: 307, False: 4.08k] ------------------ 1836| | /* no more ring system membership check is necessary because */ 1837| | /* the two neighbors are to be constitutionally equivalent atoms: */ 1838| 307| nNeighRank[nNeighOrd[j - 1]] == nNeighRank[nNeighOrd[j]]) ------------------ | Branch (1838:17): [True: 14, False: 293] ------------------ 1839| 14| { 1840| 14| k = j; 1841| 14| do 1842| 14| { 1843| 14| if (!nVisited && !( nVisited = (AT_RANK*) inchi_malloc( sizeof( nVisited[0] )*num_atoms ) )) ------------------ | | 1143| 14|#define inchi_malloc malloc ------------------ | Branch (1843:25): [True: 14, False: 0] | Branch (1843:38): [True: 0, False: 14] ------------------ 1844| 0| { 1845| 0| ret = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1846| 0| goto exit_function; 1847| 0| } 1848| 14| memset( nVisited, 0, sizeof( nVisited[0] )*num_atoms ); /* djb-rwth: memset_s C11/Annex K variant? */ 1849| 14| nVisited[i] = 1; 1850| 14| if (PathsHaveIdenticalKnownParities( at, (AT_RANK) i, at[i].neighbor[(int) nNeighOrd[j - 1]], ------------------ | Branch (1850:25): [True: 14, False: 0] ------------------ 1851| 14| (AT_RANK) i, at[i].neighbor[(int) nNeighOrd[k]], 1852| 14| nVisited, nVisited, nRank, nCanonRank, 1 )) 1853| 14| { 1854| 14| at[i].parity = 0; /* remove parity */ 1855| 14| at[i].stereo_atom_parity = 0; 1856| 14| at[i].final_parity = 0; 1857| | /* at[i].bHasStereoOrEquToStereo = 0; */ 1858| 28| for (n = 0, m = pCS->nLenLinearCTStereoCarb - 1; n <= m; n++) ------------------ | Branch (1858:74): [True: 28, False: 0] ------------------ 1859| 28| { 1860| 28| if (pCS->LinearCTStereoCarb[n].at_num == nCanonRank[i]) ------------------ | Branch (1860:33): [True: 14, False: 14] ------------------ 1861| 14| { 1862| 14| if (n < m) ------------------ | Branch (1862:37): [True: 3, False: 11] ------------------ 1863| 3| { /* remove pCS->LinearCTStereoCarb[n] */ 1864| 3| memmove( pCS->LinearCTStereoCarb + n, pCS->LinearCTStereoCarb + n + 1, ( (long long)m - (long long)n ) * sizeof( pCS->LinearCTStereoCarb[0] ) ); /* djb-rwth: cast operators added */ 1865| 3| } 1866| 14| pCS->nLenLinearCTStereoCarb--; 1867| 14| k = 0; 1868| | 1869| |#if ( bRELEASE_VERSION == 0 ) 1870| | pCS->bExtract |= EXTR_KNOWN_USED_TO_REMOVE_PARITY; 1871| |#endif 1872| | 1873| 14| break; 1874| 14| } 1875| 28| } 1876| 14| if (k) ------------------ | Branch (1876:29): [True: 0, False: 14] ------------------ 1877| 0| { 1878| 0| ret = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1879| 0| goto exit_function; 1880| 0| } 1881| 14| ret++; 1882| 14| break; 1883| 14| } 1884| 14| } 1885| 14| while (++k < num_neigh && nNeighRank[nNeighOrd[j - 1]] == nNeighRank[nNeighOrd[k]]); ------------------ | Branch (1885:24): [True: 0, False: 0] | Branch (1885:43): [True: 0, False: 0] ------------------ 1886| 14| } 1887| 4.39k| } 1888| 1.61k| } 1889| | 1890| 1.18k|exit_function: 1891| 1.18k| if (nVisited) ------------------ | Branch (1891:9): [True: 14, False: 1.16k] ------------------ 1892| 14| { 1893| 14| inchi_free( nVisited ); ------------------ | | 1152| 14|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 14, False: 0] | | | Branch (1152:50): [Folded, False: 14] | | ------------------ ------------------ 1894| 14| } 1895| | 1896| 1.18k| return ret; 1897| 1.18k|} MarkKnownEqualStereoCenterParities: 1911| 1.14k|{ 1912| 1.14k| int i, j1, k, num_centers, iMax, bDifferentParities; 1913| 1.14k| AT_RANK nAtomRank; 1914| 1.14k| int parity, parity_k; 1915| | 1916| 1.14k| num_centers = 0; 1917| 8.08k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1917:17): [True: 6.94k, False: 1.14k] ------------------ 1918| 6.94k| { 1919| 6.94k| if (!at[i].parity || at[i].stereo_bond_neighbor[0]) ------------------ | Branch (1919:13): [True: 3.37k, False: 3.56k] | Branch (1919:30): [True: 1.74k, False: 1.82k] ------------------ 1920| 5.12k| { 1921| 5.12k| continue; 1922| 5.12k| } 1923| 1.82k| if (at[i].bHasStereoOrEquToStereo) ------------------ | Branch (1923:13): [True: 584, False: 1.23k] ------------------ 1924| 584| { 1925| 584| continue; /* already marked */ 1926| 584| } 1927| 1.23k| if ( /*!PARITY_KNOWN(at[i].stereo_atom_parity) ||*/ ( at[i].stereo_atom_parity & KNOWN_PARITIES_EQL )) ------------------ | | 206| 1.23k|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ | Branch (1927:61): [True: 0, False: 1.23k] ------------------ 1928| 0| { 1929| 0| continue; 1930| 0| } 1931| 1.23k| parity = PARITY_VAL( at[i].stereo_atom_parity ); ------------------ | | 262| 1.23k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 1.23k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 1932| 1.23k| if (parity == AB_PARITY_NONE) ------------------ | | 218| 1.23k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (1932:13): [True: 0, False: 1.23k] ------------------ 1933| 0| { 1934| 0| continue; 1935| 0| } 1936| 1.23k| nAtomRank = nRank[i]; 1937| 1.23k| bDifferentParities = -1; 1938| | /* find constitutionally equivalent stereo centers and compare their known at this time parities */ 1939| 3.19k| for (iMax = (int) nAtomRank - 1, j1 = 0; j1 <= iMax && nAtomRank == nRank[k = (int) nAtomNumber[iMax - j1]]; j1++) ------------------ | Branch (1939:50): [True: 2.93k, False: 257] | Branch (1939:64): [True: 1.95k, False: 979] ------------------ 1940| 1.95k| { 1941| | /* at[k] is constitutionally equivalent to at[i] */ 1942| 1.95k| parity_k = PARITY_VAL( at[k].stereo_atom_parity ); ------------------ | | 262| 1.95k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 1.95k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 1943| 1.95k| if (parity_k != parity) ------------------ | Branch (1943:17): [True: 405, False: 1.54k] ------------------ 1944| 405| { 1945| 405| bDifferentParities = 1; 1946| 405| } 1947| 1.54k| else if (parity_k == parity && bDifferentParities < 0) ------------------ | Branch (1947:22): [True: 1.54k, False: 0] | Branch (1947:44): [True: 1.02k, False: 526] ------------------ 1948| 1.02k| { 1949| 1.02k| bDifferentParities = 0; 1950| 1.02k| } 1951| 1.95k| if (!parity_k) ------------------ | Branch (1951:17): [True: 134, False: 1.82k] ------------------ 1952| 134| { 1953| 134| at[k].bHasStereoOrEquToStereo = 2; 1954| 134| } 1955| 1.82k| else if (!at[k].bHasStereoOrEquToStereo) ------------------ | Branch (1955:22): [True: 1.82k, False: 0] ------------------ 1956| 1.82k| { 1957| 1.82k| at[k].bHasStereoOrEquToStereo = 1; 1958| 1.82k| } 1959| 1.95k| } 1960| 1.23k| if (0 == bDifferentParities && PARITY_KNOWN( parity )) ------------------ | | 265| 950|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 950|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 1.90k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 950|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 950|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 950|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 950|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 950, False: 0] | | | Branch (265:78): [True: 731, False: 219] | | ------------------ ------------------ | Branch (1960:13): [True: 950, False: 286] ------------------ 1961| 731| { 1962| 1.64k| for (iMax = (int) nAtomRank - 1, j1 = 0; j1 <= iMax && nAtomRank == nRank[k = (int) nAtomNumber[iMax - j1]]; j1++) ------------------ | Branch (1962:54): [True: 1.55k, False: 86] | Branch (1962:68): [True: 911, False: 645] ------------------ 1963| 911| { 1964| | /* at[k] is constitutionally equivalent to at[i] */ 1965| 911| at[k].stereo_atom_parity |= KNOWN_PARITIES_EQL; ------------------ | | 206| 911|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ 1966| 911| num_centers++; 1967| 911| } 1968| 731| } 1969| 1.23k| } 1970| | 1971| 1.14k| return num_centers; 1972| 1.14k|} InvertStereo: 1987| 1.56k|{ 1988| 1.56k| int i, j, j1, j2, num_changes, parity, cumulene_len; 1989| | 1990| 1.56k| num_changes = 0; 1991| 11.1k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (1991:17): [True: 9.55k, False: 1.56k] ------------------ 1992| 9.55k| { 1993| 9.55k| nAtomNumberCanon[(int) nCanonRank[i] - 1] = i; 1994| 9.55k| } 1995| 4.52k| for (i = 0; i < pCS->nLenLinearCTStereoCarb; i++) ------------------ | Branch (1995:17): [True: 2.96k, False: 1.56k] ------------------ 1996| 2.96k| { 1997| 2.96k| parity = pCS->LinearCTStereoCarb[i].parity; 1998| 2.96k| if (ATOM_PARITY_WELL_DEF( parity )) ------------------ | | 259| 2.96k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 2.96k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 2.96k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 2.96k, False: 0] | | | Branch (259:75): [True: 1.14k, False: 1.82k] | | ------------------ ------------------ 1999| 1.14k| { 2000| 1.14k| j = nAtomNumberCanon[(int) pCS->LinearCTStereoCarb[i].at_num - 1]; 2001| 1.14k| if (PARITY_WELL_DEF( at[j].parity )) ------------------ | | 266| 1.14k|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.14k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 2.28k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.14k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 1.14k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.14k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.14k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 1.14k, False: 0] | | | Branch (266:85): [True: 1.14k, False: 1] | | ------------------ ------------------ 2002| 1.14k| { 2003| 1.14k| at[j].parity ^= AB_INV_PARITY_BITS; ------------------ | | 227| 1.14k|#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 219| 1.14k|#define AB_PARITY_ODD 1 /* 1 => odd parity */ | | ------------------ | | #define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 220| 1.14k|#define AB_PARITY_EVEN 2 /* 2 => even parity */ | | ------------------ ------------------ 2004| 1.14k| } 2005| 1| else 2006| 1| { 2007| 1| goto exit_error; /* inconsistency */ 2008| 1| } 2009| 1.14k| if (bInvertLinearCTStereo) ------------------ | Branch (2009:17): [True: 572, False: 570] ------------------ 2010| 572| { 2011| 572|#ifdef FIX_STEREOCOUNT_ERR 2012| 572| pCS->LinearCTStereoCarb[i].parity = AB_PARITY_EVEN; /* deliberately worse */ ------------------ | | 220| 572|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ 2013| |#else 2014| | pCS->LinearCTStereoCarb[i].parity ^= AB_INV_PARITY_BITS; 2015| |#endif 2016| 572| } 2017| 1.14k| num_changes++; 2018| 1.14k| if (PARITY_WELL_DEF( at[j].stereo_atom_parity )) ------------------ | | 266| 1.14k|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.14k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 2.28k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.14k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 1.14k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.14k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.14k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 1.14k, False: 0] | | | Branch (266:85): [True: 412, False: 730] | | ------------------ ------------------ 2019| 412| { 2020| 412| at[j].stereo_atom_parity ^= AB_INV_PARITY_BITS; ------------------ | | 227| 412|#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 219| 412|#define AB_PARITY_ODD 1 /* 1 => odd parity */ | | ------------------ | | #define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 220| 412|#define AB_PARITY_EVEN 2 /* 2 => even parity */ | | ------------------ ------------------ 2021| 412| } 2022| 1.14k| if (PARITY_WELL_DEF( at[j].final_parity )) ------------------ | | 266| 1.14k|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.14k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 2.28k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.14k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 0, False: 1.14k] | | | Branch (266:85): [True: 0, False: 0] | | ------------------ ------------------ 2023| 0| { 2024| 0| at[j].final_parity ^= AB_INV_PARITY_BITS; ------------------ | | 227| 0|#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 219| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ | | ------------------ | | #define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 220| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ | | ------------------ ------------------ 2025| 0| } 2026| 1.14k| } 2027| 2.96k| } 2028| 2.87k| for (i = 0; i < pCS->nLenLinearCTStereoDble; i++) ------------------ | Branch (2028:17): [True: 1.31k, False: 1.56k] ------------------ 2029| 1.31k| { 2030| 1.31k| parity = pCS->LinearCTStereoDble[i].parity; 2031| 1.31k| if (ATOM_PARITY_WELL_DEF( parity )) ------------------ | | 259| 1.31k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.31k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.31k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 1.31k, False: 0] | | | Branch (259:75): [True: 257, False: 1.05k] | | ------------------ ------------------ 2032| 257| { 2033| 257| j1 = nAtomNumberCanon[(int) pCS->LinearCTStereoDble[i].at_num1 - 1]; 2034| 257| cumulene_len = BOND_CHAIN_LEN( at[j1].stereo_bond_parity[0] ); ------------------ | | 214| 257|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 257|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 257|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 257|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 2035| 257| if (cumulene_len % 2) ------------------ | Branch (2035:17): [True: 4, False: 253] ------------------ 2036| 4| { 2037| | /* invert only in case of allene */ 2038| 4| j2 = nAtomNumberCanon[(int) pCS->LinearCTStereoDble[i].at_num2 - 1]; 2039| | /* checks for debug only */ 2040| 4| if (1 < MAX_NUM_STEREO_BONDS) ------------------ | | 873| 4|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2040:21): [True: 4, Folded] ------------------ 2041| 4| { 2042| 4| if (at[j1].stereo_bond_neighbor[1] || ------------------ | Branch (2042:25): [True: 0, False: 4] ------------------ 2043| 4| at[j2].stereo_bond_neighbor[1]) ------------------ | Branch (2043:26): [True: 0, False: 4] ------------------ 2044| 0| { 2045| 0| goto exit_error; /* inconsitency: atom has more than one cumulene bond */ 2046| 0| } 2047| 4| } 2048| 4| if (cumulene_len != BOND_CHAIN_LEN( at[j2].stereo_bond_parity[0] ) || ------------------ | | 214| 8|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 4|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 4|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 4|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ | Branch (2048:21): [True: 0, False: 4] ------------------ 2049| 4| j1 + 1 != at[j2].stereo_bond_neighbor[0] || ------------------ | Branch (2049:22): [True: 0, False: 4] ------------------ 2050| 4| j2 + 1 != at[j1].stereo_bond_neighbor[0]) ------------------ | Branch (2050:22): [True: 0, False: 4] ------------------ 2051| 0| { 2052| 0| goto exit_error; /* inconsitency: atoms should refer to each other */ 2053| 0| } 2054| | /* invert parities */ 2055| 4| if (PARITY_WELL_DEF( at[j1].parity ) && PARITY_WELL_DEF( at[j2].parity )) ------------------ | | 266| 8|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 4|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 8|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 4|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 4|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 4, False: 0] | | | Branch (266:85): [True: 4, False: 0] | | ------------------ ------------------ if (PARITY_WELL_DEF( at[j1].parity ) && PARITY_WELL_DEF( at[j2].parity )) ------------------ | | 266| 4|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 4|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 8|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 4|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 4|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 4, False: 0] | | | Branch (266:85): [True: 4, False: 0] | | ------------------ ------------------ 2056| 4| { 2057| 4| j = inchi_min( j1, j2 ); ------------------ | | 139| 4|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 2, False: 2] | | ------------------ ------------------ 2058| 4| at[j].parity ^= AB_INV_PARITY_BITS; /* for reversability always invert only atom with the smaller number */ ------------------ | | 227| 4|#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 219| 4|#define AB_PARITY_ODD 1 /* 1 => odd parity */ | | ------------------ | | #define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 220| 4|#define AB_PARITY_EVEN 2 /* 2 => even parity */ | | ------------------ ------------------ 2059| 4| } 2060| 0| else 2061| 0| { 2062| 0| goto exit_error; /* inconsistency */ 2063| 0| } 2064| 4| if (bInvertLinearCTStereo) ------------------ | Branch (2064:21): [True: 2, False: 2] ------------------ 2065| 2| { 2066| 2| pCS->LinearCTStereoDble[i].parity ^= AB_INV_PARITY_BITS; ------------------ | | 227| 2|#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 219| 2|#define AB_PARITY_ODD 1 /* 1 => odd parity */ | | ------------------ | | #define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 220| 2|#define AB_PARITY_EVEN 2 /* 2 => even parity */ | | ------------------ ------------------ 2067| 2| } 2068| 4| num_changes++; 2069| 4| if (PARITY_WELL_DEF( at[j1].stereo_bond_parity[0] )) ------------------ | | 266| 4|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 4|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 8|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 4|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 4|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 4, False: 0] | | | Branch (266:85): [True: 4, False: 0] | | ------------------ ------------------ 2070| 4| { 2071| 4| at[j1].stereo_bond_parity[0] ^= AB_INV_PARITY_BITS; ------------------ | | 227| 4|#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 219| 4|#define AB_PARITY_ODD 1 /* 1 => odd parity */ | | ------------------ | | #define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 220| 4|#define AB_PARITY_EVEN 2 /* 2 => even parity */ | | ------------------ ------------------ 2072| 4| } 2073| 4| if (PARITY_WELL_DEF( at[j2].stereo_bond_parity[0] )) ------------------ | | 266| 4|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 4|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 8|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 4|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 4|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 4|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 4, False: 0] | | | Branch (266:85): [True: 4, False: 0] | | ------------------ ------------------ 2074| 4| { 2075| 4| at[j2].stereo_bond_parity[0] ^= AB_INV_PARITY_BITS; ------------------ | | 227| 4|#define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 219| 4|#define AB_PARITY_ODD 1 /* 1 => odd parity */ | | ------------------ | | #define AB_INV_PARITY_BITS (AB_PARITY_ODD ^ AB_PARITY_EVEN) | | ------------------ | | | | 220| 4|#define AB_PARITY_EVEN 2 /* 2 => even parity */ | | ------------------ ------------------ 2076| 4| } 2077| 4| } 2078| 257| } 2079| 1.31k| } 2080| | 2081| 1.56k| return num_changes; 2082| | 2083| 1|exit_error: 2084| 1| return CT_STEREOCOUNT_ERR; ------------------ | | 29| 1|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 1|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2085| 1.56k|} FillOutStereoParities: 2101| 1.14k|{ 2102| 1.14k| int ret; 2103| | /* unmark atoms with 2 or more constitutionally equivalent neighbors */ 2104| | /* such that there is no path through them to an atom with parity */ 2105| 1.14k| ret = UnmarkNonStereo( pCG, at, num_atoms, nRank, nAtomNumber, bIsotopic ); 2106| 1.14k| if (ret < 0) ------------------ | Branch (2106:9): [True: 0, False: 1.14k] ------------------ 2107| 0| return ret; /* program error? */ /* */ 2108| 1.14k| ret = FillAllStereoDescriptors( pCG, at, num_atoms, nCanonRank, nAtomNumberCanon, pCS ); /* ret<0: error */ 2109| 1.14k| if (!ret) ------------------ | Branch (2109:9): [True: 1.14k, False: 0] ------------------ 2110| 1.14k| { 2111| 1.14k| ret = pCS->nLenLinearCTStereoCarb + pCS->nLenLinearCTStereoDble; 2112| 1.14k| } 2113| 1.14k| if (ret < 0) ------------------ | Branch (2113:9): [True: 0, False: 1.14k] ------------------ 2114| 0| { 2115| 0| return ret; /* program error? */ /* */ 2116| 0| } 2117| | 2118| 1.14k| if (ret >= 0) ------------------ | Branch (2118:9): [True: 1.14k, False: 0] ------------------ 2119| 1.14k| { 2120| 1.14k| int ret2; 2121| 1.14k| ret2 = SetKnownStereoCenterParities( pCG, at, num_atoms, nCanonRank, nRank, nAtomNumber ); 2122| 1.14k| if (ret2 >= 0) ------------------ | Branch (2122:13): [True: 1.14k, False: 0] ------------------ 2123| 1.14k| { 2124| 1.14k| ret2 = MarkKnownEqualStereoCenterParities( at, num_atoms, nRank, nAtomNumber ); 2125| 1.14k| } 2126| 1.14k| if (ret2 >= 0) ------------------ | Branch (2126:13): [True: 1.14k, False: 0] ------------------ 2127| 1.14k| { 2128| 1.14k| ret2 = SetKnownStereoBondParities( pCG, at, num_atoms, nCanonRank, nRank, nAtomNumber ); 2129| 1.14k| if (ret2 >= 0) ------------------ | Branch (2129:17): [True: 1.14k, False: 0] ------------------ 2130| 1.14k| { 2131| 1.14k| ret2 = MarkKnownEqualStereoBondParities( at, num_atoms, nRank, nAtomNumber ); 2132| 1.14k| } 2133| 1.14k| } 2134| 1.14k|#if ( REMOVE_KNOWN_NONSTEREO == 1 ) /* { */ 2135| 1.14k| if (ret2 >= 0) ------------------ | Branch (2135:13): [True: 1.14k, False: 0] ------------------ 2136| 1.14k| { 2137| 1.14k| int ret3; 2138| 1.14k| do 2139| 1.18k| { 2140| 1.18k| ret2 = RemoveKnownNonStereoCenterParities( pCG, at, num_atoms, nCanonRank, nRank, pCS ); 2141| 1.18k| if (ret2 >= 0) ------------------ | Branch (2141:21): [True: 1.18k, False: 0] ------------------ 2142| 1.18k| { 2143| 1.18k| ret3 = RemoveKnownNonStereoBondParities( at, num_atoms, nCanonRank, nRank, pCS ); 2144| 1.18k| ret2 = ret3 >= 0 ? ret2 + ret3 : ret3; ------------------ | Branch (2144:28): [True: 1.18k, False: 0] ------------------ 2145| 1.18k| } 2146| 1.18k| } 2147| 1.18k| while (ret2 > 0); ------------------ | Branch (2147:20): [True: 34, False: 1.14k] ------------------ 2148| 1.14k| } 2149| 1.14k| if (RETURNED_ERROR( ret2 )) ------------------ | | 44| 1.14k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 1.14k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 1.14k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 1.14k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 1.14k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 1.14k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 1.14k, False: 0] | | | Branch (44:53): [True: 0, False: 1.14k] | | ------------------ ------------------ 2150| 0| { 2151| 0| ret = ret2; 2152| 0| } 2153| 1.14k|#endif /* } REMOVE_KNOWN_NONSTEREO */ 2154| 1.14k| } 2155| | 2156| 1.14k| return ret; /* non-zero means error */ 2157| 1.14k|} GetStereoNeighborPos: 2165| 34|{ 2166| 34| int k1; 2167| 34| AT_RANK sNeigh = (AT_RANK) ( iAt2 + 1 ); 2168| 34| AT_RANK s; 2169| 47| for (k1 = 0; k1 < MAX_NUM_STEREO_BONDS && ( s = at[iAt1].stereo_bond_neighbor[k1] ); k1++) ------------------ | | 873| 94|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2169:18): [True: 47, False: 0] | Branch (2169:47): [True: 47, False: 0] ------------------ 2170| 47| { 2171| 47| if (s == sNeigh) ------------------ | Branch (2171:13): [True: 34, False: 13] ------------------ 2172| 34| { 2173| 34| return k1; 2174| 34| } 2175| 47| } 2176| | 2177| 0| return -1; /* neighbor not found */ 2178| 34|} GetStereoBondParity: 2188| 68|{ 2189| 68| int k1, k2, s, parity; 2190| | 2191| 68| if (at[i].stereo_bond_neighbor[0]) ------------------ | Branch (2191:9): [True: 68, False: 0] ------------------ 2192| 68| { 2193| 94| for (k1 = 0; k1 < MAX_NUM_STEREO_BONDS && ( s = (int) at[i].stereo_bond_neighbor[k1] ); k1++) ------------------ | | 873| 188|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2193:22): [True: 94, False: 0] | Branch (2193:51): [True: 94, False: 0] ------------------ 2194| 94| { 2195| 94| if (--s == n) ------------------ | Branch (2195:17): [True: 68, False: 26] ------------------ 2196| 68| { 2197| 68| goto neigh1_found; 2198| 68| } 2199| 94| } 2200| 0| return -1; /* error: not a stereo neighbor */ 2201| 68| neigh1_found: 2202| 68| if (PARITY_KNOWN( at[i].stereo_bond_parity[k1] )) ------------------ | | 265| 68|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 68|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 136|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 68|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 68|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 68|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 68|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 68, False: 0] | | | Branch (265:78): [True: 68, False: 0] | | ------------------ ------------------ 2203| 68| { 2204| 68| return PARITY_VAL( at[i].stereo_bond_parity[k1] ); ------------------ | | 262| 68|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 68|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 2205| 68| } 2206| 0| for (k2 = 0; k2 < MAX_NUM_STEREO_BONDS && ( s = (int) at[n].stereo_bond_neighbor[k2] ); k2++) ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2206:22): [True: 0, False: 0] | Branch (2206:51): [True: 0, False: 0] ------------------ 2207| 0| { 2208| 0| if (--s == i) ------------------ | Branch (2208:17): [True: 0, False: 0] ------------------ 2209| 0| { 2210| 0| goto neigh2_found; 2211| 0| } 2212| 0| } 2213| 0| return -1; /* error: not a stereo neighbor */ 2214| 0| neigh2_found:; 2215| 0| } 2216| 0| else 2217| 0| { 2218| 0| return -1; /* error: not a stereo bond */ 2219| 0| } 2220| | 2221| 0| if (ATOM_PARITY_WELL_DEF( at[i].parity ) && ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2222| 0| ATOM_PARITY_WELL_DEF( at[n].parity ) && ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2223| 0| MIN_DOT_PROD <= abs( at[i].stereo_bond_z_prod[k1] )) ------------------ | | 253| 0|#define MIN_DOT_PROD 50 /* min value of at->stereo_bond_z_prod[i] to define parity */ ------------------ | Branch (2223:10): [True: 0, False: 0] ------------------ 2224| 0| { 2225| | /* bond parity can be calculated */ 2226| 0| int half_parity1, half_parity2; 2227| | /* check whether all neighbors are defined */ 2228| | 2229| | 2230| 0| half_parity1 = HalfStereoBondParity( at, i, k1, nRank ); 2231| 0| half_parity2 = HalfStereoBondParity( at, n, k2, nRank ); 2232| 0| if (!half_parity1 || !half_parity2) ------------------ | Branch (2232:13): [True: 0, False: 0] | Branch (2232:30): [True: 0, False: 0] ------------------ 2233| 0| return 0; /* ranks undefined or not a stereo bond */ 2234| 0| if (ATOM_PARITY_WELL_DEF( half_parity1 ) && ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2235| 0| ATOM_PARITY_WELL_DEF( half_parity2 )) ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2236| 0| { 2237| 0| parity = 2 - ( half_parity1 + half_parity2 2238| 0| + ( at[i].stereo_bond_z_prod[k1] < 0 ) ) % 2; 2239| 0| } 2240| 0| else 2241| 0| { 2242| 0| return CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2243| 0| } 2244| 0| } 2245| 0| else 2246| 0| { 2247| | /* parity cannot be calculated: not enough info or 'unknown' */ 2248| 0| if (AB_PARITY_NONE != ( parity = inchi_max( at[i].parity, at[n].parity ) )) ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (AB_PARITY_NONE != ( parity = inchi_max( at[i].parity, at[n].parity ) )) ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2248:13): [True: 0, False: 0] ------------------ 2249| 0| { 2250| 0| parity = AB_PARITY_UNDF; /* should not happen */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2251| 0| } 2252| 0| } 2253| | 2254| 0| return parity; 2255| 0|} GetPermutationParity: 2265| 16.8k|{ 2266| 16.8k| AT_RANK nNeighRank[MAX_NUM_STEREO_ATOM_NEIGH]; 2267| 16.8k| int j, k, parity; 2268| 16.8k| if (at->valence > MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 16.8k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2268:9): [True: 0, False: 16.8k] ------------------ 2269| 0| { 2270| 0| parity = -1; /* error */ 2271| 0| } 2272| 16.8k| else 2273| 16.8k| { 2274| 82.8k| for (j = k = 0; j < at->valence; j++) ------------------ | Branch (2274:25): [True: 66.0k, False: 16.8k] ------------------ 2275| 66.0k| { 2276| 66.0k| if (at->neighbor[j] != nAvoidNeighbor) ------------------ | Branch (2276:17): [True: 66.0k, False: 0] ------------------ 2277| 66.0k| { 2278| 66.0k| nNeighRank[k++] = nCanonRank[(int) at->neighbor[j]]; 2279| 66.0k| } 2280| 66.0k| } 2281| 16.8k| if (k) ------------------ | Branch (2281:13): [True: 16.8k, False: 0] ------------------ 2282| 16.8k| { 2283| 16.8k| parity = insertions_sort( pCG, nNeighRank, k, sizeof( nNeighRank[0] ), comp_AT_RANK ); 2284| 16.8k| if (nNeighRank[0]) ------------------ | Branch (2284:17): [True: 16.8k, False: 0] ------------------ 2285| 16.8k| { 2286| 16.8k| parity = 2 - parity % 2; 2287| 16.8k| } 2288| 0| else 2289| 0| { 2290| 0| parity = 0; /* not all ranks are known */ 2291| 0| } 2292| 16.8k| } 2293| 0| else 2294| 0| { 2295| | /* special case: HX= with implicit H */ 2296| 0| parity = 2; 2297| 0| } 2298| 16.8k| } 2299| | 2300| 16.8k| return parity; 2301| 16.8k|} GetStereoCenterParity: 2309| 10.0k|{ 2310| 10.0k| AT_NUMB nNeighborNumber2[MAXVAL]; 2311| 10.0k| int parity; 2312| 10.0k| int k, num_trans; 2313| | 2314| 10.0k| if (!at[i].parity) ------------------ | Branch (2314:9): [True: 0, False: 10.0k] ------------------ 2315| 0| { 2316| 0| return 0; /* not a stereo center */ 2317| 0| } 2318| 10.0k| if (at[i].stereo_bond_neighbor[0]) ------------------ | Branch (2318:9): [True: 0, False: 10.0k] ------------------ 2319| 0| { 2320| 0| return -1; /* a stereo bond atom, not a stereo center */ 2321| 0| } 2322| | 2323| 10.0k| if (ATOM_PARITY_WELL_DEF( at[i].parity )) ------------------ | | 259| 10.0k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 10.0k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 10.0k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 10.0k, False: 0] | | | Branch (259:75): [True: 3.99k, False: 6.09k] | | ------------------ ------------------ 2324| 3.99k| { 2325| | /* number of neighbors transpositions to the sorted order is unknown. Find it. */ 2326| | /* If parity is not well-defined then doing this is a waste of time */ 2327| 3.99k| int num_neigh = at[i].valence; 2328| 19.5k| for (k = 0; k < num_neigh; k++) ------------------ | Branch (2328:21): [True: 15.5k, False: 3.99k] ------------------ 2329| 15.5k| { 2330| 15.5k| if (!nRank[(int) at[i].neighbor[k]]) ------------------ | Branch (2330:17): [True: 0, False: 15.5k] ------------------ 2331| 0| return 0; /* stereo at[i] does not belong to the traversed part of the structure */ 2332| 15.5k| nNeighborNumber2[k] = k; 2333| 15.5k| } 2334| 3.99k| pCG->m_pNeighborsForSort = at[i].neighbor; 2335| 3.99k| pCG->m_pn_RankForSort = nRank; 2336| 3.99k| num_trans = insertions_sort( pCG, nNeighborNumber2, num_neigh, sizeof( nNeighborNumber2[0] ), CompNeighborsAT_NUMBER ); 2337| |#ifndef CT_NEIGH_INCREASE 2338| | num_trans += ( ( num_neigh*( num_neigh - 1 ) ) / 2 ) % 2; /* get correct parity for ascending order */ 2339| |#endif 2340| 3.99k| parity = 2 - ( at[i].parity + num_trans ) % 2; 2341| 3.99k| } 2342| 6.09k| else 2343| 6.09k| { 2344| 6.09k| parity = at[i].parity; 2345| 6.09k| } 2346| | 2347| 10.0k| return parity; 2348| 10.0k|} ErrMsg: 20| 4|{ 21| 4| const char *p; 22| 4| static char szErrMsg[64]; 23| 4| switch (nErrorCode) 24| 4| { 25| 0| case 0: p = ""; break; ------------------ | Branch (25:9): [True: 0, False: 4] ------------------ 26| 0| case CT_OVERFLOW: p = "ARRAY OVERFLOW"; break; ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (26:9): [True: 0, False: 4] ------------------ 27| 0| case CT_LEN_MISMATCH: p = "LENGTH_MISMATCH"; break; ------------------ | | 20| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (27:9): [True: 0, False: 4] ------------------ 28| 2| case CT_OUT_OF_RAM: p = "Out of RAM"; break; ------------------ | | 21| 2|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 2|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (28:9): [True: 2, False: 2] ------------------ 29| 0| case CT_RANKING_ERR: p = "RANKING_ERR"; break; ------------------ | | 22| 0|#define CT_RANKING_ERR (CT_ERR_FIRST- 3) /*(-30003) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (29:9): [True: 0, False: 4] ------------------ 30| 0| case CT_ISOCOUNT_ERR: p = "ISOCOUNT_ERR"; break; ------------------ | | 23| 0|#define CT_ISOCOUNT_ERR (CT_ERR_FIRST- 4) /*(-30004) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (30:9): [True: 0, False: 4] ------------------ 31| 0| case CT_TAUCOUNT_ERR: p = "TAUCOUNT_ERR"; break; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (31:9): [True: 0, False: 4] ------------------ 32| 0| case CT_ISOTAUCOUNT_ERR: p = "ISOTAUCOUNT_ERR"; break; ------------------ | | 25| 0|#define CT_ISOTAUCOUNT_ERR (CT_ERR_FIRST- 6) /*(-30006) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (32:9): [True: 0, False: 4] ------------------ 33| 0| case CT_MAPCOUNT_ERR: p = "MAPCOUNT_ERR"; break; ------------------ | | 26| 0|#define CT_MAPCOUNT_ERR (CT_ERR_FIRST- 7) /*(-30007) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (33:9): [True: 0, False: 4] ------------------ 34| 0| case CT_TIMEOUT_ERR: p = "Time limit exceeded"; break; ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (34:9): [True: 0, False: 4] ------------------ 35| 0| case CT_ISO_H_ERR: p = "ISO_H_ERR"; break; ------------------ | | 28| 0|#define CT_ISO_H_ERR (CT_ERR_FIRST- 9) /*(-30009) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (35:9): [True: 0, False: 4] ------------------ 36| 0| case CT_STEREOCOUNT_ERR: p = "STEREOCOUNT_ERR"; break; ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (36:9): [True: 0, False: 4] ------------------ 37| 0| case CT_ATOMCOUNT_ERR: p = "ATOMCOUNT_ERR"; break; ------------------ | | 30| 0|#define CT_ATOMCOUNT_ERR (CT_ERR_FIRST-11) /*(-30011) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (37:9): [True: 0, False: 4] ------------------ 38| 0| case CT_STEREOBOND_ERROR: p = "STEREOBOND_ERR"; break; ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (38:9): [True: 0, False: 4] ------------------ 39| 0| case CT_USER_QUIT_ERR: p = "User requested termination"; break; ------------------ | | 32| 0|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (39:9): [True: 0, False: 4] ------------------ 40| 0| case CT_REMOVE_STEREO_ERR: p = "REMOVE_STEREO_ERR"; break; ------------------ | | 33| 0|#define CT_REMOVE_STEREO_ERR (CT_ERR_FIRST-14) /*(-30014) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (40:9): [True: 0, False: 4] ------------------ 41| 1| case CT_CALC_STEREO_ERR: p = "CALC_STEREO_ERR"; break; ------------------ | | 34| 1|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 18| 1|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (41:9): [True: 1, False: 3] ------------------ 42| 0| case CT_STEREO_CANON_ERR: p = "STEREO_CANON_ERR"; break; ------------------ | | 36| 0|#define CT_STEREO_CANON_ERR (CT_ERR_FIRST-17) /*(-30017) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (42:9): [True: 0, False: 4] ------------------ 43| 0| case CT_CANON_ERR: p = "CANON_ERR"; break; ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (43:9): [True: 0, False: 4] ------------------ 44| 0| case CT_WRONG_FORMULA: p = "Wrong or missing chemical formula"; break; ------------------ | | 37| 0|#define CT_WRONG_FORMULA (CT_ERR_FIRST-18) /*(-30017) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (44:9): [True: 0, False: 4] ------------------ 45| | /*case CT_CANON_ERR2: p = "CT_CANON_ERR2"; break;*/ 46| 0| case CT_UNKNOWN_ERR: p = "UNKNOWN_ERR"; break; ------------------ | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (46:9): [True: 0, False: 4] ------------------ 47| 0| case BNS_RADICAL_ERR: p = "Cannot process free radical center"; break; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (47:9): [True: 0, False: 4] ------------------ 48| 0| case BNS_ALTBOND_ERR: p = "Cannot process aromatic bonds"; break; ------------------ | | 61| 0|#define BNS_ALTBOND_ERR (BNS_ERR + 13) /*(-9986)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (48:9): [True: 0, False: 4] ------------------ 49| | /* v. 1.05 */ 50| 0| case BNS_TIMEOUT: p = "Structure normalization timeout"; break; ------------------ | | 63| 0|#define BNS_TIMEOUT (BNS_ERR + 14) /*(-9985)*/ /* v. 1.05 */ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (50:9): [True: 0, False: 4] ------------------ 51| | 52| 1| default: ------------------ | Branch (52:9): [True: 1, False: 3] ------------------ 53| 1| if (nErrorCode > CT_UNKNOWN_ERR) ------------------ | | 38| 1|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | ------------------ | | | | 18| 1|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (53:17): [True: 1, False: 0] ------------------ 54| 1| { 55| 1| sprintf(szErrMsg, "No description(%d)", nErrorCode); 56| 1| p = szErrMsg; 57| 1| } 58| 0| else 59| 0| { 60| 0| sprintf(szErrMsg, "UNKNOWN_ERR(%d)", CT_UNKNOWN_ERR - nErrorCode); ------------------ | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 61| 0| p = szErrMsg; 62| 0| } 63| 1| break; 64| 4| } 65| | 66| 4| return p; 67| 4|} AddErrorMessage: 72| 67.3k|{ 73| 67.3k| int len_all, len; 74| | 75| 67.3k| if (!all_messages) ------------------ | Branch (75:9): [True: 0, False: 67.3k] ------------------ 76| 0| { 77| 0| return 0; 78| 0| } 79| 67.3k| if (!new_message) ------------------ | Branch (79:9): [True: 0, False: 67.3k] ------------------ 80| 0| { 81| 0| return 0; 82| 0| } 83| 67.3k| if (!new_message[0]) ------------------ | Branch (83:9): [True: 0, False: 67.3k] ------------------ 84| 0| { 85| 0| return 0; 86| 0| } 87| 67.3k| if (already_have_this_message( all_messages, new_message )) ------------------ | Branch (87:9): [True: 40.8k, False: 26.5k] ------------------ 88| 40.8k| { 89| 40.8k| return 1; 90| 40.8k| } 91| | 92| 26.5k| len_all = (int) strlen( all_messages ); 93| 26.5k| len = (int) strlen( new_message ); 94| | 95| 26.5k| if (len_all + len + 2 * ( len_all > 0 ) < STR_ERR_LEN) ------------------ | | 126| 26.5k|#define STR_ERR_LEN 256 ------------------ | Branch (95:9): [True: 26.5k, False: 0] ------------------ 96| 26.5k| { 97| | /* enough room... add message and return */ 98| 26.5k| if (len_all > 0) ------------------ | Branch (98:13): [True: 13.4k, False: 13.0k] ------------------ 99| 13.4k| { 100| 13.4k| if (all_messages[len_all - 1] != ':') ------------------ | Branch (100:17): [True: 4.91k, False: 8.55k] ------------------ 101| 4.91k| { 102| 4.91k| strcat(all_messages, ";"); 103| 4.91k| } 104| 13.4k| strcat(all_messages, " "); 105| 13.4k| } 106| 26.5k| strcat(all_messages, new_message); 107| 26.5k| return 1; 108| 26.5k| } 109| | 110| | /* not enough room... add no-room marker if not yet added */ 111| 0| if (strstr( all_messages, "..." )) ------------------ | Branch (111:9): [True: 0, False: 0] ------------------ 112| 0| { 113| 0| return 0; 114| 0| } 115| 0| if (len_all + 3 < STR_ERR_LEN) ------------------ | | 126| 0|#define STR_ERR_LEN 256 ------------------ | Branch (115:9): [True: 0, False: 0] ------------------ 116| 0| { 117| 0| strcat(all_messages, "..."); 118| 0| } 119| | 120| 0| return 0; 121| 0|} ichierr.c:already_have_this_message: 126| 67.3k|{ 127| 67.3k| int have = 0; 128| | 129| 67.3k| char *p = strstr( prev_messages, new_message ); 130| | 131| 67.3k| if (p) ------------------ | Branch (131:9): [True: 40.8k, False: 26.5k] ------------------ 132| 40.8k| { 133| 40.8k| have = ( p == prev_messages || (*( p - 1 ) == ' ' && ( *( p - 2 ) == ';' || *( p - 2 ) == ':' )) ); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (133:18): [True: 39.5k, False: 1.33k] | Branch (133:41): [True: 1.33k, False: 0] | Branch (133:64): [True: 522, False: 810] | Branch (133:85): [True: 810, False: 0] ------------------ 134| 40.8k| if (have) ------------------ | Branch (134:13): [True: 40.8k, False: 0] ------------------ 135| 40.8k| { 136| 40.8k| int len_prev = (int) strlen( prev_messages ); 137| 40.8k| int len = (int) strlen( new_message ); 138| 40.8k| have = ( p + len == prev_messages + len_prev || (p[len] == ';' && p[len + 1] == ' ') || (p[len - 1] == ':' && p[len] == ' ') ); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (138:22): [True: 35.9k, False: 4.84k] | Branch (138:62): [True: 74, False: 4.77k] | Branch (138:79): [True: 74, False: 0] | Branch (138:102): [True: 4.77k, False: 0] | Branch (138:123): [True: 4.77k, False: 0] ------------------ 139| 40.8k| } 140| 40.8k| } 141| | 142| 67.3k| return have; 143| 67.3k|} make_iso_sort_key: 13| 1.10M|{ 14| 1.10M| AT_ISO_SORT_KEY iso_sort_key = 0, mult = 1; 15| | 16| 1.10M| iso_sort_key += mult * num_1H; 17| 1.10M| mult *= AT_ISO_SORT_KEY_MULT; ------------------ | | 30| 1.10M|#define AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */ ------------------ 18| 1.10M| iso_sort_key += mult * num_2H; 19| 1.10M| mult *= AT_ISO_SORT_KEY_MULT; ------------------ | | 30| 1.10M|#define AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */ ------------------ 20| 1.10M| iso_sort_key += mult * num_3H; 21| 1.10M| mult *= AT_ISO_SORT_KEY_MULT; ------------------ | | 30| 1.10M|#define AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */ ------------------ 22| 1.10M| iso_sort_key += mult * iso_atw_diff; 23| | 24| 1.10M| return iso_sort_key; 25| 1.10M|} set_atom_iso_sort_keys: 36| 288k|{ 37| 288k| int i, num_isotopic = 0, bMergedTgroup; 38| 288k| AT_ISO_SORT_KEY iso_sort_key; 39| 288k| T_GROUP *t_group = 40| 288k| ( t_group_info && ------------------ | Branch (40:11): [True: 252k, False: 36.3k] ------------------ 41| 252k| t_group_info->t_group && ------------------ | Branch (41:10): [True: 252k, False: 0] ------------------ 42| 288k| t_group_info->num_t_groups > 0 ) ? t_group_info->t_group : NULL; ------------------ | Branch (42:10): [True: 5.45k, False: 246k] ------------------ 43| | 44| 288k| if (bHasIsotopicInTautomerGroups) ------------------ | Branch (44:9): [True: 252k, False: 36.3k] ------------------ 45| 252k| { 46| 252k| *bHasIsotopicInTautomerGroups = 0; 47| 252k| } 48| 1.38M| for (i = 0; i < num_at; i++) ------------------ | Branch (48:17): [True: 1.09M, False: 288k] ------------------ 49| 1.09M| { 50| 1.09M| bMergedTgroup = ( t_group_info && t_group_info->nIsotopicEndpointAtomNumber && ( at[i].cFlags & AT_FLAG_ISO_H_POINT ) ); ------------------ | | 50| 5.34k|#define AT_FLAG_ISO_H_POINT 0x01 /**< may have isotopic H */ ------------------ | Branch (50:27): [True: 1.04M, False: 44.0k] | Branch (50:43): [True: 5.34k, False: 1.04M] | Branch (50:88): [True: 539, False: 4.80k] ------------------ 51| 1.09M| if (( !at[i].endpoint || !t_group ) && !bMergedTgroup) ------------------ | Branch (51:15): [True: 1.08M, False: 13.2k] | Branch (51:34): [True: 0, False: 13.2k] | Branch (51:48): [True: 1.08M, False: 242] ------------------ 52| 1.08M| { 53| 1.08M| iso_sort_key = make_iso_sort_key( at[i].iso_atw_diff, at[i].num_iso_H[0], at[i].num_iso_H[1], at[i].num_iso_H[2] ); 54| 1.08M| } 55| 13.5k| else 56| 13.5k| { 57| | /* H isotopes go to the tautomer part of the CT (name) */ 58| | /* if (at[i].endpoint && t_group) ... */ 59| 13.5k| iso_sort_key = make_iso_sort_key( at[i].iso_atw_diff, 0, 0, 0 ); 60| 13.5k| if (bHasIsotopicInTautomerGroups) ------------------ | Branch (60:17): [True: 13.5k, False: 0] ------------------ 61| 13.5k| { 62| 13.5k| *bHasIsotopicInTautomerGroups += ( at[i].num_iso_H[0] || at[i].num_iso_H[1] || at[i].num_iso_H[2] || bMergedTgroup ); ------------------ | Branch (62:52): [True: 62, False: 13.4k] | Branch (62:74): [True: 12, False: 13.4k] | Branch (62:96): [True: 28, False: 13.4k] | Branch (62:118): [True: 438, False: 12.9k] ------------------ 63| 13.5k| } 64| 13.5k| } 65| 1.09M| at[i].iso_sort_key = iso_sort_key; 66| 1.09M| num_isotopic += ( iso_sort_key != 0 ); 67| 1.09M| } 68| | 69| 288k| return num_isotopic; 70| 288k|} MakeHillFormulaString: 89| 5.62k|{ 90| 5.62k| int nUsedLength0 = strbuf->nUsedLength; 91| 5.62k| if (szHillFormula && !*bOverflow) ------------------ | Branch (91:9): [True: 5.62k, False: 0] | Branch (91:26): [True: 5.62k, False: 0] ------------------ 92| 5.62k| { 93| 5.62k| if (-1 == inchi_strbuf_printf( strbuf, "%s", szHillFormula )) ------------------ | Branch (93:13): [True: 0, False: 5.62k] ------------------ 94| 0| { 95| 0| *bOverflow |= 1; 96| 0| return nUsedLength0 + 1; 97| 0| } 98| 5.62k| } 99| 5.62k| return ( strbuf->nUsedLength - nUsedLength0 ); 100| 5.62k|} GetHillFormulaIndexLength: 110| 1.14M|{ 111| 1.14M| char szCount[16]; 112| 1.14M| if (count > 1) ------------------ | Branch (112:9): [True: 374k, False: 774k] ------------------ 113| 374k| { 114| 374k| return sprintf(szCount, "%d", count); 115| 374k| } 116| | 117| 774k| return 0; 118| 1.14M|} GetHillFormulaCounts: 133| 385k|{ 134| 385k| char szElement[4]; 135| 385k| U_CHAR nPrevAtom = (U_CHAR) -2; 136| 385k| int bCarbon, bHydrogen, nElemLen, nFormLen, nNumNonHAtoms; 137| 385k| int mult, i, num_H, num_C; 138| | 139| 385k| num_H = 0; 140| 385k| num_C = 0; 141| 385k| bCarbon = 0; 142| 385k| bHydrogen = 0; 143| 385k| nElemLen = 0; 144| 385k| nFormLen = 0; 145| 385k| mult = 0; 146| 385k| nNumNonHAtoms = num_atoms; 147| | 148| 2.97M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (148:17): [True: 2.59M, False: 385k] ------------------ 149| 2.59M| { 150| 2.59M| if (nPrevAtom != nAtom[i]) ------------------ | Branch (150:13): [True: 1.17M, False: 1.42M] ------------------ 151| 1.17M| { 152| 1.17M| if (mult) ------------------ | Branch (152:17): [True: 785k, False: 385k] ------------------ 153| 785k| { 154| 785k| if (bHydrogen) ------------------ | Branch (154:21): [True: 5.78k, False: 780k] ------------------ 155| 5.78k| { 156| 5.78k| num_H += mult; 157| 5.78k| } 158| 780k| else if (bCarbon) ------------------ | Branch (158:26): [True: 133k, False: 646k] ------------------ 159| 133k| { 160| 133k| num_C += mult; 161| 133k| } 162| 646k| else 163| 646k| { 164| 646k| nFormLen += nElemLen; 165| 646k| nFormLen += GetHillFormulaIndexLength( mult ); 166| 646k| } 167| 785k| } 168| | /*if (-1 == get_element_chemical_symbol( (int) nAtom[i], szElement ))*/ 169| 1.17M| if (-1 == get_element_or_pseudoelement_symbol( (int) nAtom[i], szElement )) ------------------ | Branch (169:17): [True: 0, False: 1.17M] ------------------ 170| 0| { 171| 0| return -1; 172| 0| } 173| 1.17M| mult = 1; 174| 1.17M| nElemLen = (int) strlen( szElement ); 175| 1.17M| nPrevAtom = nAtom[i]; 176| 1.17M| bCarbon = !strcmp( szElement, "C" ); 177| 1.17M| bHydrogen = !strcmp( szElement, "H" ); 178| 1.17M| if (bHydrogen) ------------------ | Branch (178:17): [True: 145k, False: 1.02M] ------------------ 179| 145k| { 180| 145k| nNumNonHAtoms = i; 181| 145k| } 182| 1.17M| } 183| 1.42M| else 184| 1.42M| { 185| 1.42M| mult++; 186| 1.42M| } 187| | 188| 2.59M| num_H += nNum_H[i]; 189| 2.59M| } 190| | 191| | /* NumGroups; ((NumAt+1, NumH, At1..AtNumAt),...) */ 192| | 193| 385k| if (nTautomer && lenTautomer > 0) ------------------ | Branch (193:9): [True: 289k, False: 96.3k] | Branch (193:22): [True: 42.1k, False: 247k] ------------------ 194| 42.1k| { 195| 42.1k| int num_groups = nTautomer[0]; 196| | 197| 47.9k| for (i = 1; i < lenTautomer && num_groups > 0; i += nTautomer[i] + 1, num_groups--) ------------------ | Branch (197:21): [True: 5.85k, False: 42.1k] | Branch (197:40): [True: 5.85k, False: 0] ------------------ 198| 5.85k| { 199| 5.85k| num_H += nTautomer[i + 1]; 200| 5.85k| } 201| 42.1k| } 202| | 203| 385k| if (mult) ------------------ | Branch (203:9): [True: 385k, False: 0] ------------------ 204| 385k| { 205| 385k| if (bHydrogen) ------------------ | Branch (205:13): [True: 140k, False: 245k] ------------------ 206| 140k| { 207| 140k| num_H += mult; 208| 140k| } 209| 245k| else if (bCarbon) ------------------ | Branch (209:18): [True: 8.31k, False: 237k] ------------------ 210| 8.31k| { 211| 8.31k| num_C += mult; 212| 8.31k| } 213| 237k| else 214| 237k| { 215| 237k| nFormLen += nElemLen; 216| 237k| nFormLen += GetHillFormulaIndexLength( mult ); 217| 237k| } 218| 385k| } 219| | 220| 385k| if (num_C) ------------------ | Branch (220:9): [True: 112k, False: 273k] ------------------ 221| 112k| { 222| 112k| nFormLen += (int) strlen( "C" ); 223| 112k| nFormLen += GetHillFormulaIndexLength( num_C ); 224| 112k| } 225| | 226| 385k| if (num_H) ------------------ | Branch (226:9): [True: 151k, False: 234k] ------------------ 227| 151k| { 228| 151k| nFormLen += (int) strlen( "H" ); 229| 151k| nFormLen += GetHillFormulaIndexLength( num_H ); 230| 151k| } 231| | 232| 385k| *pnum_C = num_C; 233| 385k| *pnum_H = num_H; 234| 385k| *pnLen = nFormLen; 235| 385k| *pnNumNonHAtoms = nNumNonHAtoms; 236| | 237| 385k| return 0; 238| 385k|} AddElementAndCount: 245| 1.02M|{ 246| 1.02M| char szMult[16]; 247| 1.02M| int len1, len2; 248| 1.02M| if (mult > 0 && !*bOverflow && 0 < ( len1 = strlen( szElement ) )) ------------------ | Branch (248:9): [True: 1.02M, False: 14] | Branch (248:21): [True: 1.02M, False: 0] | Branch (248:36): [True: 1.02M, False: 0] ------------------ 249| 1.02M| { 250| 1.02M| if (mult > 1) ------------------ | Branch (250:13): [True: 313k, False: 716k] ------------------ 251| 313k| { 252| 313k| len2 = sprintf(szMult, "%d", mult); 253| 313k| } 254| 716k| else 255| 716k| { 256| 716k| len2 = 0; 257| 716k| szMult[0] = '\0'; 258| 716k| } 259| 1.02M| if (len1 + len2 < nLenLinearCT) ------------------ | Branch (259:13): [True: 1.02M, False: 0] ------------------ 260| 1.02M| { 261| 1.02M| memcpy(szLinearCT, szElement, len1); 262| 1.02M| memcpy(szLinearCT + len1, szMult, (long long)len2 + 1); /* adding zero termination */ /* djb-rwth: added cast operator */ 263| 1.02M| return len1 + len2; 264| 1.02M| } 265| 0| else 266| 0| { 267| 0| ( *bOverflow )++; 268| 0| } 269| 1.02M| } 270| | 271| 14| return 0; 272| 1.02M|} MakeHillFormula: 288| 385k|{ 289| 385k| char szElement[4]; 290| 385k| int mult, compare2H; 291| 385k| int i, nLen, bOvfl; 292| 385k| U_CHAR nPrevAtom; 293| | 294| 385k| nLen = 0; 295| 385k| mult = 0; 296| 385k| bOvfl = 0; 297| 385k| nPrevAtom = (U_CHAR) -2; /* non-existent number */ 298| 385k| memset(szElement, '\0', sizeof(szElement)); /* djb-rwth: fixing coverity ID #499542 */ 299| | 300| 385k| if (num_C) ------------------ | Branch (300:9): [True: 112k, False: 273k] ------------------ 301| 112k| { 302| 112k| nLen += AddElementAndCount( "C", num_C, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 303| 112k| if (num_H) ------------------ | Branch (303:13): [True: 25.6k, False: 86.9k] ------------------ 304| 25.6k| { 305| 25.6k| nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 306| 25.6k| num_H = 0; 307| 25.6k| } 308| 112k| } 309| | 310| 2.01M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (310:17): [True: 1.65M, False: 352k] ------------------ 311| 1.65M| { 312| | 313| 1.65M| if (nPrevAtom != nAtom[i]) ------------------ | Branch (313:13): [True: 799k, False: 858k] ------------------ 314| 799k| { 315| 799k| if (mult) ------------------ | Branch (315:17): [True: 514k, False: 284k] ------------------ 316| 514k| { 317| 514k| nLen += AddElementAndCount( szElement, mult, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 318| 514k| } 319| 799k| mult = 1; 320| | /*if (-1 == get_element_chemical_symbol( (int) nAtom[i], szElement ))*/ 321| 799k| if (-1 == get_element_or_pseudoelement_symbol( (int) nAtom[i], szElement )) ------------------ | Branch (321:17): [True: 0, False: 799k] ------------------ 322| 0| { 323| 0| return -1; /* wrong element */ 324| 0| } 325| | 326| 799k| nPrevAtom = nAtom[i]; 327| 799k| if (!strcmp( "C", szElement )) ------------------ | Branch (327:17): [True: 31.1k, False: 768k] ------------------ 328| 31.1k| { 329| 31.1k| return -1; 330| 31.1k| } 331| 768k| compare2H = strcmp( "H", szElement ); 332| 768k| if (!compare2H) ------------------ | Branch (332:17): [True: 2.28k, False: 765k] ------------------ 333| 2.28k| { 334| 2.28k| return -1; 335| 2.28k| } 336| 765k| if (compare2H < 0 && num_H) ------------------ | Branch (336:17): [True: 675k, False: 90.2k] | Branch (336:34): [True: 32.1k, False: 643k] ------------------ 337| 32.1k| { 338| | /* H-atom should be located in front of szElement */ 339| 32.1k| nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 340| 32.1k| num_H = 0; 341| 32.1k| } 342| 765k| } 343| 858k| else 344| 858k| { 345| 858k| mult++; 346| 858k| } 347| 1.65M| } 348| 352k| if (mult) ------------------ | Branch (348:9): [True: 251k, False: 101k] ------------------ 349| 251k| { 350| | /* the last element if any */ 351| 251k| nLen += AddElementAndCount( szElement, mult, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 352| 251k| } 353| 352k| if (num_H) ------------------ | Branch (353:9): [True: 93.2k, False: 259k] ------------------ 354| 93.2k| { 355| | /* if H has not been output... */ 356| 93.2k| nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 357| 93.2k| } 358| 352k| *bOverflow |= ( 0 != bOvfl ); 359| | 360| 352k| return bOvfl ? nLen_szLinearCT + 1 : nLen; ------------------ | Branch (360:12): [True: 0, False: 352k] ------------------ 361| 385k|} AllocateAndFillHillFormula: 368| 385k|{ 369| 385k| int num_C, num_H, nLen, nNumNonHAtoms, ret, bOverflow; 370| 385k| char *pHillFormula = NULL; 371| | 372| 385k| bOverflow = 0; 373| | 374| 385k| if (!GetHillFormulaCounts( pINChI->nAtom, ------------------ | Branch (374:9): [True: 385k, False: 0] ------------------ 375| 385k| pINChI->nNum_H, 376| 385k| pINChI->nNumberOfAtoms, 377| 385k| pINChI->nTautomer, 378| 385k| pINChI->lenTautomer, 379| 385k| &num_C, &num_H, 380| 385k| &nLen, 381| 385k| &nNumNonHAtoms )) 382| 385k| { 383| | 384| 385k|#if ( FIX_GAF_2019_2==1 ) 385| 385k| pHillFormula = (char*)inchi_calloc((long long )nLen + 1, sizeof(char)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 385k|#define inchi_calloc calloc ------------------ 386| |#else 387| | pHillFormula = (char*)inchi_malloc(nLen + 1); 388| |#endif 389| | 390| 385k| if (pHillFormula) ------------------ | Branch (390:13): [True: 385k, False: 0] ------------------ 391| 385k| { 392| | 393| 385k| ret = MakeHillFormula( pINChI->nAtom + num_C, 394| 385k| nNumNonHAtoms - num_C, 395| 385k| pHillFormula, 396| 385k| nLen + 1, 397| 385k| num_C, num_H, 398| 385k| &bOverflow ); 399| | 400| 385k| if (ret != nLen || bOverflow) ------------------ | Branch (400:17): [True: 35.3k, False: 350k] | Branch (400:32): [True: 0, False: 350k] ------------------ 401| 35.3k| { 402| 35.3k| inchi_free( pHillFormula ); ------------------ | | 1152| 35.3k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 35.3k, False: 0] | | | Branch (1152:50): [Folded, False: 35.3k] | | ------------------ ------------------ 403| 35.3k| pHillFormula = NULL; 404| 35.3k| } 405| 385k| } 406| 385k| } 407| | 408| 385k| return pHillFormula; 409| 385k|} Copy2StereoBondOrAllene: 424| 2.61k|{ 425| 2.61k| int cumulene_len, 426| 2.61k| j, 427| 2.61k| next_j = 0 /* ordering number of the central allene atom */, 428| 2.61k| next_neigh; 429| 2.61k| AT_RANK 430| 2.61k| at_num; 431| 2.61k| int parity; 432| | 433| 2.61k| if (pCanonOrd && pCanonRank) ------------------ | Branch (433:9): [True: 2.61k, False: 0] | Branch (433:22): [True: 2.61k, False: 0] ------------------ 434| 2.61k| { 435| 2.61k| j = pCanonOrd[(int) LinearCTStereoDble->at_num1 - 1]; 436| | 437| | /* if allene then find the central atom, at[next_j] */ 438| | 439| 2.61k| if (bIsotopic) ------------------ | Branch (439:13): [True: 336, False: 2.27k] ------------------ 440| 336| { 441| 336| cumulene_len = BOND_CHAIN_LEN( at[j].stereo_bond_parity2[0] ); ------------------ | | 214| 336|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 336|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 336|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 336|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 442| | 443| 336| if (cumulene_len % 2 && ( 1 >= MAX_NUM_STEREO_BONDS || !at[j].stereo_bond_neighbor2[1] )) ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (443:17): [True: 0, False: 336] | Branch (443:39): [Folded, False: 0] | Branch (443:68): [True: 0, False: 0] ------------------ 444| 0| { 445| 0| next_j = at[j].neighbor[(int) at[j].stereo_bond_ord2[0]]; 446| | 447| 0| for (cumulene_len = ( cumulene_len - 1 ) / 2; cumulene_len && 2 == at[next_j].valence; cumulene_len--) ------------------ | Branch (447:63): [True: 0, False: 0] | Branch (447:79): [True: 0, False: 0] ------------------ 448| 0| { 449| 0| next_neigh = ( j == at[next_j].neighbor[0] ); 450| 0| j = next_j; 451| 0| next_j = at[next_j].neighbor[next_neigh]; 452| 0| } 453| | /* next_j is the central atom */ 454| 0| } 455| 336| else 456| 336| { 457| 336| cumulene_len = -1; /* not an allene */ 458| 336| } 459| 336| } 460| 2.27k| else 461| 2.27k| { 462| 2.27k| cumulene_len = BOND_CHAIN_LEN( at[j].stereo_bond_parity[0] ); ------------------ | | 214| 2.27k|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 2.27k|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 2.27k|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 2.27k|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 463| | 464| 2.27k| if (cumulene_len % 2 && ( 1 >= MAX_NUM_STEREO_BONDS || !at[j].stereo_bond_neighbor[1] )) ------------------ | | 873| 12|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (464:17): [True: 6, False: 2.26k] | Branch (464:39): [Folded, False: 6] | Branch (464:68): [True: 6, False: 0] ------------------ 465| 6| { 466| 6| next_j = at[j].neighbor[(int) at[j].stereo_bond_ord[0]]; 467| | 468| 6| for (cumulene_len = ( cumulene_len - 1 ) / 2; cumulene_len && 2 == at[next_j].valence; cumulene_len--) ------------------ | Branch (468:63): [True: 0, False: 6] | Branch (468:79): [True: 0, False: 0] ------------------ 469| 0| { 470| 0| next_neigh = ( j == at[next_j].neighbor[0] ); 471| 0| j = next_j; 472| 0| next_j = at[next_j].neighbor[next_neigh]; 473| 0| } 474| 6| } 475| 2.26k| else 476| 2.26k| { 477| 2.26k| cumulene_len = -1; /* not an allene */ 478| 2.26k| } 479| 2.27k| } 480| | 481| 2.61k| if (!cumulene_len) ------------------ | Branch (481:13): [True: 6, False: 2.60k] ------------------ 482| 6| { 483| | /* allene has been found; insert new stereocenter and parity */ 484| | 485| 6| AT_NUMB *nNumber; 486| 6| S_CHAR *t_parity; 487| | 488| 6| nNumber = nNumberOfStereoBonds ? Stereo->nNumber : Stereo->nNumberInv; ------------------ | Branch (488:23): [True: 3, False: 3] ------------------ 489| 6| t_parity = nNumberOfStereoBonds ? Stereo->t_parity : Stereo->t_parityInv; ------------------ | Branch (489:24): [True: 3, False: 3] ------------------ 490| | 491| 6| at_num = pCanonRank[next_j]; 492| 6| parity = LinearCTStereoDble->parity; 493| | 494| | /* free room for the new stereocenter */ 495| 6| for (j = 0; j < *nNumberOfStereoCenters && Stereo->nNumber[j] < at_num; j++) ------------------ | Branch (495:25): [True: 0, False: 6] | Branch (495:56): [True: 0, False: 0] ------------------ 496| 0| { 497| 0| ; 498| 0| } 499| | 500| 6| if (j < *nNumberOfStereoCenters) ------------------ | Branch (500:17): [True: 0, False: 6] ------------------ 501| 0| { 502| 0| memmove(nNumber + j + 1, nNumber + j, (*nNumberOfStereoCenters - (long long)j) * sizeof(nNumber[0])); /* djb-rwth: cast operator added */ 503| 0| memmove(t_parity + j + 1, t_parity + j, (*nNumberOfStereoCenters - (long long)j) * sizeof(t_parity[0])); /* djb-rwth: cast operator added */ 504| 0| } 505| | 506| | /* fill the new stereo center info */ 507| | 508| 6| nNumber[j] = at_num; 509| 6| t_parity[j] = parity; 510| 6| ( *nNumberOfStereoCenters )++; 511| 6| return 1; 512| 6| } 513| 2.61k| } 514| | 515| | /* Save the stereo bond info */ 516| | 517| 2.60k| if (nNumberOfStereoBonds) ------------------ | Branch (517:9): [True: 1.30k, False: 1.30k] ------------------ 518| 1.30k| { 519| 1.30k| j = *nNumberOfStereoBonds; 520| 1.30k| Stereo->b_parity[j] = LinearCTStereoDble->parity; 521| 1.30k| Stereo->nBondAtom1[j] = LinearCTStereoDble->at_num1; 522| 1.30k| Stereo->nBondAtom2[j] = LinearCTStereoDble->at_num2; 523| 1.30k| ( *nNumberOfStereoBonds )++; 524| 1.30k| } 525| | 526| 2.60k| return 0; 527| 2.61k|} CopyLinearCTStereoToINChIStereo: 542| 1.01k|{ 543| 1.01k| int n, i, nErrorCode = 0, len; 544| 1.01k| int bAllene; 545| 1.01k| int diff; 546| 1.01k| int lenInv, bAlleneInv; 547| | 548| | /* Stereo centers */ 549| | 550| | /* djb-rwth: fixing oss-fuzz issue #68271 */ 551| 1.01k| if (Stereo) ------------------ | Branch (551:9): [True: 1.01k, False: 3] ------------------ 552| 1.01k| { 553| 1.01k| n = Stereo->nNumberOfStereoCenters = nLenLinearCTStereoCarb; 554| | 555| 2.71k| for (i = 0; i < n; i++) ------------------ | Branch (555:21): [True: 1.70k, False: 1.01k] ------------------ 556| 1.70k| { 557| 1.70k| if (LinearCTStereoCarb) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (557:17): [True: 1.70k, False: 0] ------------------ 558| 1.70k| { 559| 1.70k| Stereo->nNumber[i] = LinearCTStereoCarb[i].at_num; 560| 1.70k| Stereo->t_parity[i] = LinearCTStereoCarb[i].parity; 561| 1.70k| } 562| 1.70k| if (LinearCTStereoCarbInv) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (562:17): [True: 1.70k, False: 0] ------------------ 563| 1.70k| { 564| 1.70k| Stereo->nNumberInv[i] = LinearCTStereoCarbInv[i].at_num; 565| 1.70k| Stereo->t_parityInv[i] = LinearCTStereoCarbInv[i].parity; 566| 1.70k| } 567| 1.70k| } 568| | 569| | /* Stereo bonds */ 570| | 571| 1.01k| n = nLenLinearCTStereoDble; 572| 1.01k| lenInv = Stereo->nNumberOfStereoCenters; 573| | 574| 2.31k| for (i = len = 0; i < n; i++) ------------------ | Branch (574:27): [True: 1.30k, False: 1.01k] ------------------ 575| 1.30k| { 576| 1.30k| bAllene = 577| 1.30k| Copy2StereoBondOrAllene(Stereo, 578| 1.30k| &Stereo->nNumberOfStereoCenters, 579| 1.30k| &len, 580| 1.30k| LinearCTStereoDble + i, 581| 1.30k| pCanonOrd, pCanonRank, 582| 1.30k| at, 583| 1.30k| bIsotopic); 584| | 585| 1.30k| bAlleneInv = 586| 1.30k| Copy2StereoBondOrAllene(Stereo, 587| 1.30k| &lenInv, 588| 1.30k| NULL, 589| 1.30k| LinearCTStereoDbleInv + i, 590| 1.30k| pCanonOrdInv, pCanonRankInv, 591| 1.30k| at, 592| 1.30k| bIsotopic); 593| | 594| | /* make sure double bond stereo is identical in original and inverted geometry */ 595| | /* Note: all allenes are AFTER double bonds in LinearCTStereoDble... */ 596| 1.30k| if (bAllene != bAlleneInv || (!bAllene && ------------------ | Branch (596:17): [True: 0, False: 1.30k] | Branch (596:43): [True: 1.30k, False: 3] ------------------ 597| 1.30k| CompareLinCtStereoDble(LinearCTStereoDble + i, 1, ------------------ | Branch (597:17): [True: 0, False: 1.30k] ------------------ 598| 1.30k| LinearCTStereoDbleInv + i, 1))) /* djb-rwth: addressing LLVM warning */ 599| 0| { 600| | /* double bond stereo Inv is NOT identical to Abs */ 601| 0| nErrorCode = -4; 602| 0| goto exit_function; 603| 0| } 604| 1.30k| } 605| | 606| 1.01k| Stereo->nNumberOfStereoBonds = len; 607| | 608| 1.01k| if (lenInv != Stereo->nNumberOfStereoCenters) ------------------ | Branch (608:13): [True: 0, False: 1.01k] ------------------ 609| 0| { 610| 0| nErrorCode = -5; /* different number of stereo centers in Abs and Inv */ 611| 0| goto exit_function; 612| 0| } 613| | 614| | 615| | /* compare inverted stereocenters to absolute */ 616| | 617| 1.01k| n = Stereo->nNumberOfStereoCenters; 618| | /* djb-rwth: removing redundant code */ 619| | 620| 2.37k| for (i = 0, diff = 0; i < n; i++) ------------------ | Branch (620:31): [True: 1.60k, False: 768] ------------------ 621| 1.60k| { 622| 1.60k| if (Stereo->nNumberInv[i] != Stereo->nNumber[i]) ------------------ | Branch (622:17): [True: 27, False: 1.57k] ------------------ 623| 27| { 624| 27| diff = (Stereo->nNumberInv[i] > Stereo->nNumber[i]) ? 2 : -2; ------------------ | Branch (624:24): [True: 8, False: 19] ------------------ 625| 27| break; /* Abs != Inv */ 626| 27| } 627| 1.57k| if (Stereo->t_parityInv[i] != Stereo->t_parity[i]) ------------------ | Branch (627:17): [True: 218, False: 1.35k] ------------------ 628| 218| { 629| 218| diff = (Stereo->t_parityInv[i] > Stereo->t_parity[i]) ? 1 : -1; ------------------ | Branch (629:24): [True: 93, False: 125] ------------------ 630| 218| break; /* Abs != Inv */ 631| 218| } 632| 1.57k| } 633| | 634| 1.01k| Stereo->nCompInv2Abs = 635| 1.01k| (diff > 0) ? 1 : (diff < 0) ? -1 : 0; ------------------ | Branch (635:13): [True: 101, False: 912] | Branch (635:30): [True: 144, False: 768] ------------------ 636| | 637| 1.01k| if (diff == -1 || diff == 1) ------------------ | Branch (637:13): [True: 125, False: 888] | Branch (637:27): [True: 93, False: 795] ------------------ 638| 218| { 639| | /* The first found difference was in parities */ 640| 391| for (i = 0, diff = 0; i < n; i++) ------------------ | Branch (640:35): [True: 280, False: 111] ------------------ 641| 280| { 642| 280| if (Stereo->nNumberInv[i] != Stereo->nNumber[i]) ------------------ | Branch (642:21): [True: 0, False: 280] ------------------ 643| 0| { 644| 0| diff = 2; /* difference in stereo center numbering */ 645| 0| break; 646| 0| } 647| | 648| | /* Parities can be only 1, 2, 3, 4. Therefore only mutually inverted pairs 649| | * (t_parityInv, t_parity) = (1,2) or (2,1) statisfy conditions 650| | * (t_parityInv != t_parity) && (t_parityInv + t_parity == 3) 651| | */ 652| | 653| 280| if (Stereo->t_parityInv[i] == Stereo->t_parity[i] || ------------------ | Branch (653:21): [True: 107, False: 173] ------------------ 654| 173| Stereo->t_parityInv[i] + Stereo->t_parity[i] != 3) ------------------ | Branch (654:21): [True: 0, False: 173] ------------------ 655| 107| { 656| 107| diff = 1; /* parities are same or different and cannot be obtained by simple inversion */ 657| 107| break; 658| 107| } 659| 280| } 660| 218| Stereo->bTrivialInv = !diff; 661| 218| } 662| 795| else 663| 795| { 664| 795| Stereo->bTrivialInv = 0; 665| 795| } 666| 1.01k| } 667| 3| else 668| 3| { 669| 3| nErrorCode = 1; 670| 3| } 671| | 672| 1.01k|exit_function: 673| 1.01k| return nErrorCode; 674| 1.01k|} MarkAmbiguousStereo: 686| 290k|{ 687| 290k| int n, i, j1, j2, num, mark_atom, mark_bond; 688| | 689| 290k| if (!pCanonOrd) ------------------ | Branch (689:9): [True: 0, False: 290k] ------------------ 690| 0| { 691| 0| return -1; 692| 0| } 693| | 694| 290k| num = 0; 695| | 696| 290k| n = nLenLinearCTStereoCarb; 697| | 698| 290k| mark_atom = bIsotopic ? AMBIGUOUS_STEREO_ATOM_ISO : AMBIGUOUS_STEREO_ATOM; ------------------ | | 248| 2.10k|#define AMBIGUOUS_STEREO_ATOM_ISO 8 ------------------ mark_atom = bIsotopic ? AMBIGUOUS_STEREO_ATOM_ISO : AMBIGUOUS_STEREO_ATOM; ------------------ | | 246| 578k|#define AMBIGUOUS_STEREO_ATOM 2 ------------------ | Branch (698:17): [True: 2.10k, False: 288k] ------------------ 699| | 700| 292k| for (i = 0; i < n; i++) ------------------ | Branch (700:17): [True: 1.70k, False: 290k] ------------------ 701| 1.70k| { 702| | /* Mark ambiguous stereo centers (for displaying and "Ambiguous stereo" message) */ 703| 1.70k| if (ATOM_PARITY_NOT_UNKN( LinearCTStereoCarb[i].parity ) && ------------------ | | 260| 3.40k|#define ATOM_PARITY_NOT_UNKN(X) (ATOM_PARITY_KNOWN(X) && (X) != AB_PARITY_UNKN) | | ------------------ | | | | 258| 3.40k|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | | | ------------------ | | | | | | 231| 1.70k|#define AB_MIN_KNOWN_PARITY 1 | | | | ------------------ | | | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | | | ------------------ | | | | | | 230| 1.70k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | | | ------------------ | | | | | Branch (258:38): [True: 1.70k, False: 0] | | | | | Branch (258:68): [True: 1.70k, False: 0] | | | | ------------------ | | ------------------ | | #define ATOM_PARITY_NOT_UNKN(X) (ATOM_PARITY_KNOWN(X) && (X) != AB_PARITY_UNKN) | | ------------------ | | | | 221| 1.70k|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ | | ------------------ | | | Branch (260:62): [True: 1.66k, False: 44] | | ------------------ ------------------ 704| 1.66k| at[j1 = pCanonOrd[(int) LinearCTStereoCarb[i].at_num - 1]].bAmbiguousStereo) ------------------ | Branch (704:14): [True: 0, False: 1.66k] ------------------ 705| 0| { 706| 0| at[j1].bAmbiguousStereo |= mark_atom; 707| 0| norm_at[j1].bAmbiguousStereo |= mark_atom; 708| 0| num++; 709| 0| } 710| 1.70k| } 711| | 712| 290k| n = nLenLinearCTStereoDble; 713| | 714| 290k| mark_bond = bIsotopic ? AMBIGUOUS_STEREO_BOND_ISO : AMBIGUOUS_STEREO_BOND; ------------------ | | 249| 2.10k|#define AMBIGUOUS_STEREO_BOND_ISO 16 ------------------ mark_bond = bIsotopic ? AMBIGUOUS_STEREO_BOND_ISO : AMBIGUOUS_STEREO_BOND; ------------------ | | 247| 578k|#define AMBIGUOUS_STEREO_BOND 4 ------------------ | Branch (714:17): [True: 2.10k, False: 288k] ------------------ 715| | 716| 291k| for (i = 0; i < n; i++) ------------------ | Branch (716:17): [True: 1.30k, False: 290k] ------------------ 717| 1.30k| { 718| | /* Mark ambiguous stereo bonds or allenes (for displaying and "Ambiguous stereo" message) */ 719| | 720| 1.30k| if (ATOM_PARITY_WELL_DEF( LinearCTStereoDble[i].parity )) ------------------ | | 259| 1.30k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.30k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.30k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 1.30k, False: 0] | | | Branch (259:75): [True: 255, False: 1.05k] | | ------------------ ------------------ 721| 255| { 722| 255| j1 = pCanonOrd[(int) LinearCTStereoDble[i].at_num1 - 1]; 723| 255| j2 = pCanonOrd[(int) LinearCTStereoDble[i].at_num2 - 1]; 724| | 725| 255| if (at[j1].bAmbiguousStereo || at[j2].bAmbiguousStereo) ------------------ | Branch (725:17): [True: 0, False: 255] | Branch (725:44): [True: 0, False: 255] ------------------ 726| 0| { 727| | /* If it is an allene then mark the central atom only 728| | because the bonds should not be marked to avoid misleading 729| | message "Ambiguous stereo: bond(s)": Allene makes a stereocenter 730| | */ 731| | 732| 0| int j1_parity = bIsotopic ? at[j1].stereo_bond_parity2[0] : at[j1].stereo_bond_parity[0]; ------------------ | Branch (732:33): [True: 0, False: 0] ------------------ 733| | 734| 0| int cumulene_len = BOND_CHAIN_LEN( j1_parity ); /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ ------------------ | | 214| 0|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 0|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 0|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 0|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 735| | 736| 0| if (cumulene_len % 2 && ( 1 >= MAX_NUM_STEREO_BONDS || ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (736:21): [True: 0, False: 0] | Branch (736:43): [Folded, False: 0] ------------------ 737| 0| !( bIsotopic ? at[j1].stereo_bond_neighbor2[1] : at[j1].stereo_bond_neighbor[1] ) ) ------------------ | Branch (737:21): [True: 0, False: 0] | Branch (737:24): [True: 0, False: 0] ------------------ 738| 0| ) 739| 0| { 740| | /* found an allene; locate its central atom */ 741| | 742| 0| int next_j, next_neigh; 743| 0| int j = j1; 744| | 745| 0| next_j = at[j].neighbor[bIsotopic ? at[j].stereo_bond_ord2[0] : at[j].stereo_bond_ord[0]]; ------------------ | Branch (745:45): [True: 0, False: 0] ------------------ 746| | 747| 0| for (cumulene_len = ( cumulene_len - 1 ) / 2; 748| 0| cumulene_len && 2 == at[next_j].valence; ------------------ | Branch (748:26): [True: 0, False: 0] | Branch (748:42): [True: 0, False: 0] ------------------ 749| 0| cumulene_len--) 750| 0| { 751| 0| next_neigh = ( j == at[next_j].neighbor[0] ); 752| 0| j = next_j; 753| 0| next_j = at[next_j].neighbor[next_neigh]; 754| 0| } 755| | /* next_j is the central atom */ 756| 0| if (2 == at[next_j].valence) ------------------ | Branch (756:25): [True: 0, False: 0] ------------------ 757| 0| { 758| 0| at[next_j].bAmbiguousStereo |= mark_atom; 759| 0| norm_at[next_j].bAmbiguousStereo |= mark_atom; 760| 0| num++; 761| 0| continue; /* do not mark the cumulene "bond" endpoints */ 762| 0| } 763| 0| } 764| | 765| | /* Not an allene, mark double bond or cumulene end atoms */ 766| 0| if (at[j1].bAmbiguousStereo) ------------------ | Branch (766:21): [True: 0, False: 0] ------------------ 767| 0| { 768| 0| at[j1].bAmbiguousStereo |= mark_bond; /* ??? */ 769| 0| norm_at[j1].bAmbiguousStereo |= mark_bond; 770| 0| num++; 771| 0| } 772| | 773| 0| if (at[j2].bAmbiguousStereo) ------------------ | Branch (773:21): [True: 0, False: 0] ------------------ 774| 0| { 775| 0| at[j2].bAmbiguousStereo |= mark_bond; /* ??? */ 776| 0| norm_at[j2].bAmbiguousStereo |= mark_bond; 777| 0| num++; 778| 0| } 779| 0| } 780| 255| } 781| 1.30k| } 782| | 783| 290k| return num; 784| 290k|} UnmarkAllUndefinedUnknownStereo: 790| 290k|{ 791| 290k| INCHI_MODE nRet = 0; 792| 290k| int i, n; 793| | 794| 290k| if (!Stereo || (Stereo && !Stereo->nNumberOfStereoCenters && !Stereo->nNumberOfStereoBonds)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (794:9): [True: 0, False: 290k] | Branch (794:21): [True: 290k, False: 0] | Branch (794:31): [True: 289k, False: 665] | Branch (794:66): [True: 289k, False: 348] ------------------ 795| 289k| { 796| 289k| return nRet; 797| 289k| } 798| | 799| | /* Stereocenters */ 800| 1.01k| if (!Stereo->nCompInv2Abs && ------------------ | Branch (800:9): [True: 768, False: 245] ------------------ 801| 768| ( n = Stereo->nNumberOfStereoCenters ) > 0 && ( nUserMode & REQ_MODE_SC_IGN_ALL_UU )) ------------------ | | 30| 420|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (801:9): [True: 420, False: 348] | Branch (801:55): [True: 349, False: 71] ------------------ 802| 349| { 803| | 804| 837| for (i = 0; i < n && !ATOM_PARITY_WELL_DEF( Stereo->t_parity[i] ); i++) ------------------ | | 259| 676|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 676|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 676|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 676, False: 0] | | | Branch (259:75): [True: 188, False: 488] | | ------------------ ------------------ | Branch (804:21): [True: 676, False: 161] ------------------ 805| 488| { 806| 488| ; 807| 488| } 808| | 809| 349| if (i == n) ------------------ | Branch (809:13): [True: 161, False: 188] ------------------ 810| 161| { 811| 161| Stereo->nNumberOfStereoCenters = 0; 812| | 813| 519| for (i = 0; i < n; i++) ------------------ | Branch (813:25): [True: 358, False: 161] ------------------ 814| 358| { 815| 358| Stereo->t_parity[i] = 0; 816| 358| Stereo->nNumber[i] = 0; 817| 358| Stereo->t_parityInv[i] = 0; 818| 358| Stereo->nNumberInv[i] = 0; 819| 358| } 820| | 821| 161| nRet |= REQ_MODE_SC_IGN_ALL_UU; ------------------ | | 30| 161|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 822| 161| } 823| 349| } 824| | 825| | /* Stereobonds */ 826| | 827| 1.01k| if (( n = Stereo->nNumberOfStereoBonds ) > 0 && ( nUserMode & REQ_MODE_SB_IGN_ALL_UU )) ------------------ | | 32| 363|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (827:9): [True: 363, False: 650] | Branch (827:53): [True: 265, False: 98] ------------------ 828| 265| { 829| 459| for (i = 0; i < n && !ATOM_PARITY_WELL_DEF( Stereo->b_parity[i] ); i++) ------------------ | | 259| 383|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 383|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 383|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 383, False: 0] | | | Branch (259:75): [True: 189, False: 194] | | ------------------ ------------------ | Branch (829:21): [True: 383, False: 76] ------------------ 830| 194| { 831| 194| ; 832| 194| } 833| | 834| 265| if (i == n) ------------------ | Branch (834:13): [True: 76, False: 189] ------------------ 835| 76| { 836| 76| Stereo->nNumberOfStereoBonds = 0; 837| 231| for (i = 0; i < n; i++) ------------------ | Branch (837:25): [True: 155, False: 76] ------------------ 838| 155| { 839| 155| Stereo->b_parity[i] = 0; 840| 155| Stereo->nBondAtom1[i] = 0; 841| 155| Stereo->nBondAtom2[i] = 0; 842| 155| } 843| 76| nRet |= REQ_MODE_SB_IGN_ALL_UU; ------------------ | | 32| 76|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 844| 76| } 845| 265| } 846| | 847| 1.01k| return nRet; 848| 290k|} FillOutINChI: 1050| 288k|{ 1051| 288k| int i, j, m, n, g, len, ii, ret = 0; 1052| | 1053| 288k| AT_NUMB *pSymmRank, *pOrigNosInCanonOrd, *pConstitEquNumb, *pCanonOrd = NULL, *pCanonOrdInv = NULL, *pCanonOrdTaut; 1054| 288k| T_GROUP_INFO *t_group_info = pCS->t_group_info; 1055| 288k| T_GROUP *t_group; 1056| | 1057| 288k| int nErrorCode = 0; 1058| 288k| AT_NUMB *pCanonRank, *pCanonRankInv; /* canonical ranks of the atoms or tautomeric groups */ 1059| 288k| AT_NUMB *pCanonRankAtoms = NULL, *pSortOrd = NULL; 1060| 288k| AT_RANK nMinOrd; 1061| | 1062| 288k| INChI_Stereo *Stereo; 1063| 288k| int bUseNumberingInv = 0, bUseIsotopicNumberingInv = 0; 1064| | 1065| 288k| INCHI_MODE nStereoUnmarkMode; 1066| | 1067| | /*AT_NUMB *pCanonOrdNonIso = NULL, *pCanonOrdIso = NULL;*/ 1068| | /*AT_NUMB *nOrigAtNosInCanonOrdNonIso = NULL, *nOrigAtNosInCanonOrdIso = NULL;*/ 1069| | 1070| | 1071| | /* Check for warnings */ 1072| 288k| if (pCS->nLenLinearCTStereoCarb < 0 || pCS->nLenLinearCTStereoDble < 0 || ------------------ | Branch (1072:9): [True: 0, False: 288k] | Branch (1072:44): [True: 0, False: 288k] ------------------ 1073| 288k| pCS->nLenCanonOrdStereo < 0 || pCS->nLenCanonOrdStereoTaut < 0) ------------------ | Branch (1073:10): [True: 0, False: 288k] | Branch (1073:41): [True: 0, False: 288k] ------------------ 1074| 0| { 1075| 0| nErrorCode |= WARN_FAILED_STEREO; ------------------ | | 48| 0|#define WARN_FAILED_STEREO 0x0001 ------------------ 1076| 0| } 1077| 288k| if (pCS->nLenLinearCTIsotopic < 0 || pCS->nLenLinearCTIsotopicTautomer < 0 || ------------------ | Branch (1077:9): [True: 0, False: 288k] | Branch (1077:42): [True: 0, False: 288k] ------------------ 1078| 288k| pCS->nLenCanonOrdIsotopic < 0 || pCS->nLenCanonOrdIsotopicTaut < 0) ------------------ | Branch (1078:10): [True: 0, False: 288k] | Branch (1078:43): [True: 0, False: 288k] ------------------ 1079| 0| { 1080| 0| nErrorCode |= WARN_FAILED_ISOTOPIC; ------------------ | | 49| 0|#define WARN_FAILED_ISOTOPIC 0x0002 ------------------ 1081| 0| } 1082| 288k| if (pCS->nLenLinearCTIsotopicStereoCarb < 0 || pCS->nLenLinearCTIsotopicStereoDble < 0 || ------------------ | Branch (1082:9): [True: 0, False: 288k] | Branch (1082:52): [True: 0, False: 288k] ------------------ 1083| 288k| pCS->nLenCanonOrdIsotopicStereo < 0 || pCS->nLenCanonOrdIsotopicStereoTaut < 0) ------------------ | Branch (1083:10): [True: 0, False: 288k] | Branch (1083:49): [True: 0, False: 288k] ------------------ 1084| 0| { 1085| 0| nErrorCode |= WARN_FAILED_ISOTOPIC_STEREO; ------------------ | | 50| 0|#define WARN_FAILED_ISOTOPIC_STEREO 0x0004 ------------------ 1086| 0| } 1087| | 1088| 288k| pCanonRankAtoms = (AT_NUMB *) inchi_calloc( (long long)num_at_tg + 1, sizeof( pCanonRankAtoms[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ 1089| | 1090| 288k| pSortOrd = (AT_NUMB *) inchi_calloc( (long long)num_at_tg + 1, sizeof( pSortOrd[0] ) ); /* must have more than num_atoms */ /* djb-rwth: cast operator added */ ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ 1091| | 1092| 288k| if (!pCanonRankAtoms || !pSortOrd) ------------------ | Branch (1092:9): [True: 0, False: 288k] | Branch (1092:29): [True: 0, False: 288k] ------------------ 1093| 0| { 1094| 0| nErrorCode = 0; 1095| 0| ret = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1096| 0| pINChI->nErrorCode = pINChI_Aux->nErrorCode = CT_OUT_OF_RAM; ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1097| 0| goto exit_function; 1098| 0| } 1099| | 1100| | /* Total charge */ 1101| | /* djb-rwth: fixing oss-fuzz issue #69656 */ 1102| 1.38M| for (i = 0, n = 0; i < num_atoms + num_removed_H; i++) ------------------ | Branch (1102:24): [True: 1.10M, False: 288k] ------------------ 1103| 1.10M| { 1104| 1.10M| n += at[i].charge; 1105| 1.10M| } 1106| 288k| pINChI->nTotalCharge = n; 1107| | 1108| | /* Number of atoms */ 1109| 288k| pINChI->nNumberOfAtoms = num_atoms; 1110| 288k| pINChI_Aux->nNumberOfAtoms = num_atoms; 1111| | 1112| | /* Removed protons and detachable isotopic H */ 1113| 288k| if (bTautomeric && t_group_info) ------------------ | Branch (1113:9): [True: 252k, False: 36.3k] | Branch (1113:24): [True: 252k, False: 0] ------------------ 1114| 252k| { 1115| 252k| pINChI_Aux->nNumRemovedProtons = t_group_info->tni.nNumRemovedProtons; 1116| | 1117| 1.00M| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 25| 1.00M|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1117:21): [True: 756k, False: 252k] ------------------ 1118| 756k| { 1119| 756k| pINChI_Aux->nNumRemovedIsotopicH[i] = t_group_info->num_iso_H[i] 1120| 756k| + t_group_info->tni.nNumRemovedProtonsIsotopic[i]; 1121| 756k| } 1122| | 1123| 252k| if (pINChI_Aux->bNormalizationFlags & FLAG_FORCE_SALT_TAUT) ------------------ | | 172| 252k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 252k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 173| 252k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 252k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 174| 252k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 151| 252k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (1123:13): [True: 172, False: 251k] ------------------ 1124| 172| { 1125| 172| pINChI->nFlags |= INCHI_FLAG_HARD_ADD_REM_PROTON; ------------------ | | 127| 172|#define INCHI_FLAG_HARD_ADD_REM_PROTON 0x0080 /* in normalization a proton has been added or removed along alt path */ ------------------ 1126| 172| } 1127| 252k| if (pINChI_Aux->bNormalizationFlags & ( FLAG_NORM_CONSIDER_TAUT &~FLAG_PROTON_CHARGE_CANCEL )) ------------------ | | 156| 252k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 146| 252k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 157| 252k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 252k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 158| 252k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 148| 252k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 159| 252k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 149| 252k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 160| 252k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 252k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 161| 252k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 151| 252k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 162| 252k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 153| 252k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 163| 252k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 152| 252k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ if (pINChI_Aux->bNormalizationFlags & ( FLAG_NORM_CONSIDER_TAUT &~FLAG_PROTON_CHARGE_CANCEL )) ------------------ | | 152| 252k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 ------------------ | Branch (1127:13): [True: 39.6k, False: 212k] ------------------ 1128| 39.6k| { 1129| 39.6k| if (!bNoWarnings) ------------------ | Branch (1129:17): [True: 39.6k, False: 0] ------------------ 1130| 39.6k| { 1131| 39.6k| WarningMessage( pStrErrStruct, "Proton(s) added/removed" ); ------------------ | | 132| 39.6k|#define WarningMessage AddErrorMessage ------------------ 1132| 39.6k| } 1133| 39.6k| } 1134| 252k| if (pINChI_Aux->bNormalizationFlags & FLAG_PROTON_CHARGE_CANCEL) ------------------ | | 152| 252k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 ------------------ | Branch (1134:13): [True: 19, False: 252k] ------------------ 1135| 19| { 1136| 19| if (!bNoWarnings) ------------------ | Branch (1136:17): [True: 19, False: 0] ------------------ 1137| 19| { 1138| 19| WarningMessage( pStrErrStruct, "Charges neutralized" ); ------------------ | | 132| 19|#define WarningMessage AddErrorMessage ------------------ 1139| 19| } 1140| 19| } 1141| 252k| } 1142| | 1143| | /* Abs or rel stereo may establish one of two canonical numberings */ 1144| 288k| if (( pCS->nLenLinearCTStereoCarb > 0 || pCS->nLenLinearCTStereoDble > 0 ) && ------------------ | Branch (1144:11): [True: 498, False: 287k] | Branch (1144:46): [True: 299, False: 287k] ------------------ 1145| 797| pCS->nLenCanonOrdStereo > 0 && ------------------ | Branch (1145:11): [True: 797, False: 0] ------------------ 1146| 797| ( (pCS->LinearCTStereoCarb && pCS->LinearCTStereoCarbInv) || ------------------ | Branch (1146:14): [True: 501, False: 296] | Branch (1146:41): [True: 501, False: 0] ------------------ 1147| 296| (pCS->LinearCTStereoDble && pCS->LinearCTStereoDbleInv) ) && ------------------ | Branch (1147:16): [True: 296, False: 0] | Branch (1147:43): [True: 296, False: 0] ------------------ 1148| 797| pCS->nCanonOrdStereo && pCS->nCanonOrdStereoInv ------------------ | Branch (1148:11): [True: 797, False: 0] | Branch (1148:35): [True: 797, False: 0] ------------------ 1149| 288k| ) /* djb-rwth: addressing LLVM warning */ 1150| 797| { 1151| 797| pCanonRank = pCanonRankAtoms; 1152| 797| pCanonOrd = pCS->nCanonOrdStereo; 1153| 797| pCanonRankInv = pSortOrd; 1154| 797| pCanonOrdInv = pCS->nCanonOrdStereoInv; 1155| 797| Stereo = pINChI->Stereo; 1156| | 1157| 5.66k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (1157:21): [True: 4.86k, False: 797] ------------------ 1158| 4.86k| { 1159| 4.86k| pCanonRankInv[pCanonOrdInv[i]] = 1160| 4.86k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1161| 4.86k| } 1162| | 1163| | /********************************************************************/ 1164| | /* Copy stereo bonds and stereo centers; compare Inv and Abs stereo */ 1165| | /********************************************************************/ 1166| | 1167| 797| nErrorCode = CopyLinearCTStereoToINChIStereo( Stereo, 1168| 797| pCS->LinearCTStereoCarb, 1169| 797| pCS->nLenLinearCTStereoCarb, 1170| 797| pCS->LinearCTStereoDble, 1171| 797| pCS->nLenLinearCTStereoDble, 1172| 797| pCanonOrd, pCanonRank, 1173| 797| at, 0 /* non-isotopic */, 1174| 797| pCS->LinearCTStereoCarbInv, 1175| 797| pCS->LinearCTStereoDbleInv, 1176| 797| pCanonOrdInv, pCanonRankInv ); 1177| | 1178| | /* djb-rwth: fixing oss-fuzz issue #68271 */ 1179| 797| if (nErrorCode == 1) ------------------ | Branch (1179:13): [True: 0, False: 797] ------------------ 1180| 0| { 1181| 0| nErrorCode = 0; 1182| 0| ret = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1183| 0| pINChI->nErrorCode = pINChI_Aux->nErrorCode = CT_OUT_OF_RAM; ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1184| 0| goto exit_function; 1185| 0| } 1186| | 1187| 797| if (Stereo->t_parityInv && Stereo->nNumberInv) ------------------ | Branch (1187:13): [True: 797, False: 0] | Branch (1187:36): [True: 797, False: 0] ------------------ 1188| 797| { 1189| 797| if (nUserMode & REQ_MODE_RELATIVE_STEREO) ------------------ | | 26| 797|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (1189:17): [True: 34, False: 763] ------------------ 1190| 34| { 1191| 34| pINChI->nFlags |= INCHI_FLAG_REL_STEREO; ------------------ | | 121| 34|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ 1192| 34| } 1193| 797| if (nUserMode & REQ_MODE_RACEMIC_STEREO) ------------------ | | 28| 797|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (1193:17): [True: 27, False: 770] ------------------ 1194| 27| { 1195| 27| pINChI->nFlags |= INCHI_FLAG_RAC_STEREO; ------------------ | | 122| 27|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 1196| 27| } 1197| 797| if (Stereo->nCompInv2Abs) ------------------ | Branch (1197:17): [True: 180, False: 617] ------------------ 1198| 180| { 1199| 180| if (Stereo->nCompInv2Abs == -1) ------------------ | Branch (1199:21): [True: 94, False: 86] ------------------ 1200| 94| { 1201| | /* switch pointers in Stereo so that the stereo becomes the smallest (relative) */ 1202| | /* flag Stereo->nCompInv2Abs == -1 will keep track of this exchange */ 1203| 94| AT_NUMB *nNumberInv = Stereo->nNumberInv; 1204| 94| S_CHAR *t_parityInv = Stereo->t_parityInv; 1205| 94| Stereo->nNumberInv = Stereo->nNumber; 1206| 94| Stereo->t_parityInv = Stereo->t_parity; 1207| 94| Stereo->nNumber = nNumberInv; 1208| 94| Stereo->t_parity = t_parityInv; 1209| | /* switch pointers to set rel. stereo to pINChI_Aux->nOrigAtNosInCanonOrd 1210| | and inv. stereo to pINChI_Aux->nOrigAtNosInCanonOrdInv */ 1211| 94| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1212| 94| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1213| 94| bUseNumberingInv = 1; /* use inverted stereo numbering instead of normal */ 1214| 94| } 1215| 180| } 1216| 797| } 1217| | 1218| 797| LOG_NO_ARGS("************************** Canonical Ordering with Stereo (L1183:ichimak2.c) ***************************\n"); 1219| 5.61k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1219:21): [True: 4.82k, False: 797] ------------------ 1220| 4.82k| { 1221| 4.82k| pINChI_Aux->nOrigAtNosInCanonOrdInv[i] = at[pCanonOrdInv[i]].orig_at_number; 1222| 4.82k| pINChI_Aux->nOrigAtNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1223| 4.82k| LOG_MULT_ARGS("Atom Nr: %d, Canonical Numbering Normal: %d, Element Name: %s\n", i + 1, at[pCanonOrd[i]].orig_at_number, at[i].elname); 1224| 4.82k| } 1225| | 1226| 797| LOG_NO_ARGS("\n******************************************************************************************************\n"); 1227| | 1228| 797| if (bUseNumberingInv) ------------------ | Branch (1228:13): [True: 94, False: 703] ------------------ 1229| 94| { 1230| | /* switch ptrs back to avoid confusion */ 1231| 94| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1232| 94| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1233| | /* save inverted stereo ranks & order because it represents the smallest (relative) */ 1234| 94| memcpy(pCanonRank, pCanonRankInv, num_at_tg * sizeof(pCanonRank[0])); 1235| | /* change pCS->nCanonOrdStereo[] to inverted: */ 1236| 94| memcpy(pCanonOrd, pCanonOrdInv, num_at_tg * sizeof(pCanonOrd[0])); 1237| 94| } 1238| | 1239| 797| pCanonRankInv = NULL; 1240| 797| pCanonOrdInv = NULL; 1241| 797| pOrigNosInCanonOrd = NULL; 1242| 797| } 1243| 287k| else 1244| 287k| { 1245| | /*------------------------------ no stereo */ 1246| 287k| pCanonOrd = pCS->nLenCanonOrdStereo > 0 ? pCS->nCanonOrdStereo ------------------ | Branch (1246:21): [True: 98, False: 287k] ------------------ 1247| 287k| : pCS->nLenCanonOrd > 0 ? pCS->nCanonOrd ------------------ | Branch (1247:51): [True: 287k, False: 0] ------------------ 1248| 287k| : NULL; 1249| 287k| pCanonRank = pCanonRankAtoms; 1250| 287k| pOrigNosInCanonOrd = pINChI_Aux->nOrigAtNosInCanonOrd; 1251| | 1252| 287k| if (pCanonOrd && pCanonRank) ------------------ | Branch (1252:13): [True: 287k, False: 0] | Branch (1252:26): [True: 287k, False: 0] ------------------ 1253| 287k| { 1254| 1.37M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1254:25): [True: 1.08M, False: 287k] ------------------ 1255| 1.08M| { 1256| 1.08M| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1257| 1.08M| pOrigNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1258| 1.08M| } 1259| 291k| for (; i < num_at_tg; i++) ------------------ | Branch (1259:20): [True: 3.52k, False: 287k] ------------------ 1260| 3.52k| { 1261| 3.52k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1262| 3.52k| } 1263| 287k| } 1264| 287k| } 1265| | /*pCanonOrdNonIso = pCanonOrd;*/ /* save for aux info */ 1266| | 1267| | 1268| 288k| if (pINChI_Aux->OrigInfo) ------------------ | Branch (1268:9): [True: 288k, False: 0] ------------------ 1269| 288k| { 1270| | /* charges, radicals, valences */ 1271| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1271:21): [True: 1.09M, False: 288k] ------------------ 1272| 1.09M| { 1273| 1.09M| if (pCanonOrd) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (1273:17): [True: 1.09M, False: 0] ------------------ 1274| 1.09M| { 1275| 1.09M| ii = pCanonOrd[i]; 1276| 1.09M| if (norm_at[ii].valence || norm_at[ii].num_H) ------------------ | Branch (1276:21): [True: 261k, False: 831k] | Branch (1276:44): [True: 1.84k, False: 829k] ------------------ 1277| 263k| { 1278| 263k| pINChI_Aux->OrigInfo[i].cCharge = norm_at[ii].charge; 1279| | 1280| 263k| pINChI_Aux->OrigInfo[i].cRadical = (norm_at[ii].radical == RADICAL_SINGLET) ? 0 : ------------------ | | 75| 263k|#define RADICAL_SINGLET 1 ------------------ | Branch (1280:56): [True: 0, False: 263k] ------------------ 1281| 263k| (norm_at[ii].radical == RADICAL_DOUBLET) ? 1 : ------------------ | | 76| 263k|#define RADICAL_DOUBLET 2 ------------------ | Branch (1281:25): [True: 17.6k, False: 245k] ------------------ 1282| 263k| (norm_at[ii].radical == RADICAL_TRIPLET) ? 2 : ------------------ | | 77| 245k|#define RADICAL_TRIPLET 3 ------------------ | Branch (1282:25): [True: 5.78k, False: 240k] ------------------ 1283| 245k| norm_at[ii].radical ? 3 : 0; ------------------ | Branch (1283:25): [True: 668, False: 239k] ------------------ 1284| | 1285| 263k| pINChI_Aux->OrigInfo[i].cUnusualValence = 1286| 263k| get_unusual_el_valence(norm_at[ii].el_number, norm_at[ii].charge, norm_at[ii].radical, 1287| 263k| norm_at[ii].chem_bonds_valence, norm_at[ii].num_H, norm_at[ii].valence); 1288| 263k| } 1289| 829k| else 1290| 829k| { 1291| | /* charge of a single atom component is in the INChI; valence = 0 is standard */ 1292| 829k| pINChI_Aux->OrigInfo[i].cRadical = (norm_at[ii].radical == RADICAL_SINGLET) ? 0 : ------------------ | | 75| 829k|#define RADICAL_SINGLET 1 ------------------ | Branch (1292:56): [True: 0, False: 829k] ------------------ 1293| 829k| (norm_at[ii].radical == RADICAL_DOUBLET) ? 1 : ------------------ | | 76| 829k|#define RADICAL_DOUBLET 2 ------------------ | Branch (1293:25): [True: 0, False: 829k] ------------------ 1294| 829k| (norm_at[ii].radical == RADICAL_TRIPLET) ? 2 : ------------------ | | 77| 829k|#define RADICAL_TRIPLET 3 ------------------ | Branch (1294:25): [True: 0, False: 829k] ------------------ 1295| 829k| norm_at[ii].radical ? 3 : 0; ------------------ | Branch (1295:25): [True: 0, False: 829k] ------------------ 1296| 829k| } 1297| 1.09M| } 1298| 1.09M| } 1299| 288k| } 1300| | 1301| | /* Non-isotopic canonical numbers and equivalence of atoms (Aux) */ 1302| 288k| pConstitEquNumb = pINChI_Aux->nConstitEquNumbers; /* contitutional equivalence */ 1303| 288k| pSymmRank = pCS->nSymmRank; 1304| | 1305| 288k| if (pCanonOrd && pCanonRank && pSymmRank && pConstitEquNumb) ------------------ | Branch (1305:9): [True: 288k, False: 0] | Branch (1305:22): [True: 288k, False: 0] | Branch (1305:36): [True: 288k, False: 0] | Branch (1305:49): [True: 288k, False: 0] ------------------ 1306| 288k| { 1307| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1307:21): [True: 1.09M, False: 288k] ------------------ 1308| 1.09M| { 1309| 1.09M| pConstitEquNumb[i] = pSymmRank[pCanonOrd[i]]; /* constit. equ. ranks in order of canonical numbers */ 1310| 1.09M| pSortOrd[i] = i; 1311| 1.09M| } 1312| 292k| for (; i < num_at_tg; i++) ------------------ | Branch (1312:16): [True: 3.56k, False: 288k] ------------------ 1313| 3.56k| { 1314| 3.56k| pSortOrd[i] = MAX_ATOMS; /* for debugging only */ ------------------ | | 15| 3.56k|#define MAX_ATOMS 32766 ------------------ 1315| 3.56k| } 1316| | 1317| 288k| pCG->m_pn_RankForSort = pConstitEquNumb; 1318| 288k| inchi_qsort( pCG, pSortOrd, num_atoms, sizeof( pSortOrd[0] ), CompRanksOrd ); 1319| | 1320| 1.38M| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= num_atoms; j++) ------------------ | Branch (1320:51): [True: 1.09M, False: 288k] ------------------ 1321| 1.09M| { 1322| 1.09M| if (j == num_atoms || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1322:17): [True: 288k, False: 805k] | Branch (1322:35): [True: 437k, False: 367k] ------------------ 1323| 726k| { 1324| 726k| nMinOrd++; 1325| 726k| if (j - i > 1) ------------------ | Branch (1325:21): [True: 171k, False: 554k] ------------------ 1326| 171k| { 1327| | /* found a sequence of equivalent atoms: i..j-1 */ 1328| 710k| while (i < j) ------------------ | Branch (1328:28): [True: 538k, False: 171k] ------------------ 1329| 538k| { 1330| 538k| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; /* = min. canon. rank in the group of equ. atoms */ 1331| 538k| } 1332| | /* at this point j == i */ 1333| 171k| } 1334| 554k| else 1335| 554k| { 1336| 554k| pConstitEquNumb[pSortOrd[i++]] = 0; /* means the atom is not equivalent to any other */ 1337| 554k| } 1338| 726k| nMinOrd = pSortOrd[j]; /* at the end j = num_atoms */ 1339| 726k| } 1340| 1.09M| } 1341| 288k| } 1342| | 1343| 0| else 1344| 0| { 1345| 0| nErrorCode |= ERR_NO_CANON_RESULTS; ------------------ | | 51| 0|#define ERR_NO_CANON_RESULTS 0x0008 ------------------ 1346| 0| ret = -1; /* program error; no breakpoint here */ 1347| 0| goto exit_function; 1348| 0| } 1349| | 1350| | 1351| | /* Atomic numbers from the Periodic Table */ 1352| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1352:17): [True: 1.09M, False: 288k] ------------------ 1353| 1.09M| { 1354| 1.09M| pINChI->nAtom[i] = (int) at[pCanonOrd[i]].el_number; 1355| 1.09M| } 1356| | 1357| | 1358| | /* Connection table: atoms only (before 7-29-2003 pCS->LinearCT2 contained non-isotopic CT) */ 1359| 288k| if (pCS->nLenLinearCTAtOnly <= 0 || !pCS->LinearCT || !pINChI->nConnTable) ------------------ | Branch (1359:9): [True: 0, False: 288k] | Branch (1359:41): [True: 0, False: 288k] | Branch (1359:59): [True: 0, False: 288k] ------------------ 1360| 0| { 1361| 0| nErrorCode |= ERR_NO_CANON_RESULTS; ------------------ | | 51| 0|#define ERR_NO_CANON_RESULTS 0x0008 ------------------ 1362| 0| ret = -2; 1363| 0| goto exit_function; 1364| 0| } 1365| | 1366| 288k| memcpy(pINChI->nConnTable, pCS->LinearCT, sizeof(pINChI->nConnTable[0]) * pCS->nLenLinearCTAtOnly); 1367| | 1368| 288k| pINChI->lenConnTable = pCS->nLenLinearCTAtOnly; 1369| | 1370| | /* Tautomeric group(s) canonical representation */ 1371| 288k| len = 0; 1372| 288k| if (bTautomeric && 0 < ( n = SortTautomerGroupsAndEndpoints( ------------------ | Branch (1372:9): [True: 252k, False: 36.3k] | Branch (1372:24): [True: 3.46k, False: 248k] ------------------ 1373| 252k| pCG, t_group_info, 1374| 252k| num_atoms, num_at_tg, pCanonRank ) )) 1375| 3.46k| { 1376| | /* SortTautomerGroupsAndEndpoints() produces canonically ordered t-groups */ 1377| 3.46k| pINChI->nFlags |= 1378| 3.46k| ( t_group_info->bTautFlagsDone & TG_FLAG_ALL_SALT_DONE ) ? INCHI_FLAG_ACID_TAUT ------------------ | | 971| 3.46k|#define TG_FLAG_ALL_SALT_DONE (TG_FLAG_TEST_TAUT__SALTS_DONE | \ | | ------------------ | | | | 965| 3.46k|#define TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */ | | ------------------ | | 972| 3.46k| TG_FLAG_TEST_TAUT2_SALTS_DONE | \ | | ------------------ | | | | 967| 3.46k|#define TG_FLAG_TEST_TAUT2_SALTS_DONE 0x00000020 /* merged t-groups */ | | ------------------ | | 973| 3.46k| TG_FLAG_MERGE_TAUT_SALTS_DONE ) | | ------------------ | | | | 969| 3.46k|#define TG_FLAG_MERGE_TAUT_SALTS_DONE 0x00000080 /* added non-taut O to taut groups */ | | ------------------ ------------------ ( t_group_info->bTautFlagsDone & TG_FLAG_ALL_SALT_DONE ) ? INCHI_FLAG_ACID_TAUT ------------------ | | 120| 322|#define INCHI_FLAG_ACID_TAUT 0x0001 /* tautomerism of dissociated acid invoked */ ------------------ | Branch (1378:13): [True: 322, False: 3.14k] ------------------ 1379| 3.46k| : 0; 1380| | 1381| | /* number of tautomeric groups */ 1382| 3.46k| pINChI->nTautomer[len++] = (AT_NUMB) n; 1383| | 1384| | /* store each tautomeric group, one by one */ 1385| 7.03k| for (i = 0; i < n; i++) ------------------ | Branch (1385:21): [True: 3.56k, False: 3.46k] ------------------ 1386| 3.56k| { 1387| 3.56k| g = (int) t_group_info->tGroupNumber[i]; /* original group numbers in sorted order */ 1388| 3.56k| t_group = t_group_info->t_group + g; /* pointer to the tautomeric group */ 1389| | 1390| | /* NumAt+INCHI_T_NUM_MOVABLE (group length excluding this number) */ 1391| | 1392| 3.56k| pINChI->nTautomer[len++] = t_group->nNumEndpoints + INCHI_T_NUM_MOVABLE; ------------------ | | 749| 3.56k|#define INCHI_T_NUM_MOVABLE 2 ------------------ 1393| | 1394| | /* Num(H), Num(-) */ 1395| | 1396| 10.7k| for (j = 0; j < INCHI_T_NUM_MOVABLE; j++) /* djb-rwth: redundant condition; && j < T_NUM_NO_ISOTOPIC part should be checked; can INCHI_T_NUM_MOVABLE and T_NUM_NO_ISOTOPIC change values from 2? */ ------------------ | | 749| 10.7k|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (1396:25): [True: 7.13k, False: 3.56k] ------------------ 1397| 7.13k| { 1398| 7.13k| pINChI->nTautomer[len++] = t_group->num[j]; 1399| 7.13k| } 1400| | 1401| | 1402| | /* djb-rwth: erroneous loop execution condition 1403| | 1404| | for (j = T_NUM_NO_ISOTOPIC; j < INCHI_T_NUM_MOVABLE; j++) 1405| | { 1406| | pINChI->nTautomer[len++] = 0; // should not happen 1407| | } 1408| | 1409| | */ 1410| | 1411| | /* tautomeric group endpoint canonical numbers, pre-sorted in ascending order */ 1412| | 1413| 3.56k| for (j = (int) t_group->nFirstEndpointAtNoPos, 1414| 12.1k| m = j + (int) t_group->nNumEndpoints; j < m; j++) ------------------ | Branch (1414:57): [True: 8.58k, False: 3.56k] ------------------ 1415| 8.58k| { 1416| 8.58k| pINChI->nTautomer[len++] = pCanonRank[(int) t_group_info->nEndpointAtomNumber[j]]; /* At[j] */ 1417| 8.58k| } 1418| 3.56k| } 1419| | 1420| 3.46k| pINChI->lenTautomer = len; 1421| 3.46k| pINChI_Aux->nNumberOfTGroups = n; 1422| 3.46k| } 1423| 284k| else 1424| 284k| { 1425| 284k| pINChI->lenTautomer = 0; 1426| 284k| pINChI_Aux->nNumberOfTGroups = 0; 1427| | 1428| 284k| if (t_group_info && ( ( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) || ------------------ | | 156| 248k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 146| 248k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 157| 248k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 248k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 158| 248k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 148| 248k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 159| 248k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 149| 248k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 160| 248k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 248k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 161| 248k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 151| 248k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 162| 248k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 153| 248k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 163| 248k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 152| 248k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (1428:13): [True: 248k, False: 36.3k] | Branch (1428:31): [True: 37.2k, False: 211k] ------------------ 1429| 211k| (t_group_info->nNumIsotopicEndpoints > 1 && ------------------ | Branch (1429:14): [True: 122, False: 211k] ------------------ 1430| 122| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) )) ) ------------------ | | 981| 122|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) )) ) ------------------ | | 982| 122|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (1430:13): [True: 122, False: 0] ------------------ 1431| 284k| ) /* djb-rwth: addressing LLVM warning */ 1432| 37.4k| { 1433| | /* only protons (re)moved or added */ 1434| 37.4k| pINChI->lenTautomer = 1; 1435| 37.4k| pINChI->nTautomer[0] = 0; 1436| 37.4k| } 1437| 284k| } 1438| | 1439| | /* Number of H (excluding tautomeric) */ 1440| 288k| if (pCS->nNum_H) ------------------ | Branch (1440:9): [True: 288k, False: 0] ------------------ 1441| 288k| { 1442| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1442:21): [True: 1.09M, False: 288k] ------------------ 1443| 1.09M| { 1444| 1.09M| pINChI->nNum_H[i] = pCS->nNum_H[i]; 1445| 1.09M| } 1446| 288k| } 1447| | 1448| | 1449| | /* Number of fixed H (tautomeric H in non-tautomeric representation) */ 1450| 288k| if (pCS->nNum_H_fixed && !pINChI->lenTautomer) ------------------ | Branch (1450:9): [True: 288k, False: 0] | Branch (1450:30): [True: 247k, False: 40.8k] ------------------ 1451| 247k| { 1452| 1.26M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1452:21): [True: 1.01M, False: 247k] ------------------ 1453| 1.01M| { 1454| 1.01M| pINChI->nNum_H_fixed[i] = pCS->nNum_H_fixed[i]; 1455| 1.01M| pINChI->nNum_H[i] += pCS->nNum_H_fixed[i]; 1456| 1.01M| } 1457| 247k| } 1458| | 1459| | 1460| | /*********************************************************** 1461| | * Tautomeric group(s) numbering and symmetry; 1462| | * should not depend on switching to rel. stereo numbering 1463| | */ 1464| 288k| if (pINChI->lenTautomer && ( n = pINChI_Aux->nNumberOfTGroups )) ------------------ | Branch (1464:9): [True: 40.8k, False: 247k] | Branch (1464:32): [True: 3.46k, False: 37.4k] ------------------ 1465| 3.46k| { 1466| 3.46k| pCanonOrdTaut = pCS->nLenCanonOrdStereoTaut > 0 ? pCS->nCanonOrdStereoTaut : ------------------ | Branch (1466:25): [True: 35, False: 3.43k] ------------------ 1467| 3.46k| pCS->nLenCanonOrdTaut > 0 ? pCS->nCanonOrdTaut : NULL; ------------------ | Branch (1467:13): [True: 3.43k, False: 0] ------------------ 1468| 3.46k| pConstitEquNumb = pINChI_Aux->nConstitEquTGroupNumbers; 1469| 3.46k| pSymmRank = pCS->nSymmRankTaut; 1470| | 1471| 3.46k| if (pCanonOrdTaut && pSymmRank && pConstitEquNumb) ------------------ | Branch (1471:13): [True: 3.46k, False: 0] | Branch (1471:30): [True: 3.46k, False: 0] | Branch (1471:43): [True: 3.46k, False: 0] ------------------ 1472| 3.46k| { 1473| 7.03k| for (i = 0; i < n; i++) ------------------ | Branch (1473:25): [True: 3.56k, False: 3.46k] ------------------ 1474| 3.56k| { 1475| 3.56k| pConstitEquNumb[i] = pSymmRank[pCanonOrdTaut[i]]; 1476| 3.56k| pSortOrd[i] = i; 1477| 3.56k| } 1478| 3.46k| pCG->m_pn_RankForSort = pConstitEquNumb; 1479| 3.46k| inchi_qsort( pCG, pSortOrd, n, sizeof( pSortOrd[0] ), CompRanksOrd ); 1480| 7.03k| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= n; j++) ------------------ | Branch (1480:55): [True: 3.56k, False: 3.46k] ------------------ 1481| 3.56k| { 1482| 3.56k| if (j == n || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1482:21): [True: 3.46k, False: 101] | Branch (1482:31): [True: 100, False: 1] ------------------ 1483| 3.56k| { 1484| 3.56k| nMinOrd++; /* make is start from 1, not from zero */ 1485| 3.56k| if (j - i > 1) ------------------ | Branch (1485:25): [True: 1, False: 3.56k] ------------------ 1486| 1| { 1487| | /* found a sequence of more than one equivalent t-groups: i..j-1 */ 1488| 3| while (i < j) ------------------ | Branch (1488:32): [True: 2, False: 1] ------------------ 1489| 2| { 1490| 2| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; 1491| 2| } 1492| 1| } 1493| 3.56k| else 1494| 3.56k| { 1495| 3.56k| pConstitEquNumb[pSortOrd[i++]] = 0; 1496| 3.56k| } 1497| 3.56k| nMinOrd = pSortOrd[j]; /* at the end j == n */ 1498| 3.56k| } 1499| 3.56k| } 1500| 3.46k| } 1501| 3.46k| } 1502| | 1503| | 1504| | /* Allocate and fill Hill formula */ 1505| | 1506| 288k| pINChI->szHillFormula = AllocateAndFillHillFormula( pINChI ); 1507| | 1508| 288k| if (!pINChI->szHillFormula) ------------------ | Branch (1508:9): [True: 14, False: 288k] ------------------ 1509| 14| { 1510| 14| nErrorCode = 0; 1511| 14| ret = CT_WRONG_FORMULA; /* CT_OUT_OF_RAM;*/ /* */ ------------------ | | 37| 14|#define CT_WRONG_FORMULA (CT_ERR_FIRST-18) /*(-30017) */ | | ------------------ | | | | 18| 14|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1512| 14| pINChI->nErrorCode = pINChI_Aux->nErrorCode = ret; 1513| 14| goto exit_function; 1514| 14| } 1515| | 1516| 288k| nStereoUnmarkMode = UnmarkAllUndefinedUnknownStereo( pINChI->Stereo, nUserMode ); 1517| | 1518| 288k| if (nStereoUnmarkMode) ------------------ | Branch (1518:9): [True: 186, False: 288k] ------------------ 1519| 186| { 1520| 186| pINChI->nFlags |= 1521| 186| ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_UU ------------------ | | 30| 186|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_UU ------------------ | | 123| 130|#define INCHI_FLAG_SC_IGN_ALL_UU 0x0008 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1521:13): [True: 130, False: 56] ------------------ 1522| 186| : 0; 1523| 186| pINChI->nFlags |= 1524| 186| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SB_IGN_ALL_UU ------------------ | | 32| 186|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SB_IGN_ALL_UU ------------------ | | 124| 56|#define INCHI_FLAG_SB_IGN_ALL_UU 0x0010 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1524:13): [True: 56, False: 130] ------------------ 1525| 186| : 0; 1526| | 1527| 186| if (( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) || ------------------ | | 30| 186|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (1527:13): [True: 130, False: 56] ------------------ 1528| 56| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU )) ------------------ | | 32| 56|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (1528:13): [True: 56, False: 0] ------------------ 1529| 186| { 1530| 186| if (!bNoWarnings) ------------------ | Branch (1530:17): [True: 186, False: 0] ------------------ 1531| 186| { 1532| 186| WarningMessage( pStrErrStruct, "Omitted undefined stereo" ); ------------------ | | 132| 186|#define WarningMessage AddErrorMessage ------------------ 1533| 186| } 1534| 186| } 1535| 186| } 1536| | 1537| | /*************************/ 1538| | /* Mark ambiguous stereo */ 1539| | /*************************/ 1540| | 1541| 288k| MarkAmbiguousStereo( at, norm_at, 0 /* non-isotopic */, pCanonOrd, 1542| 288k| pCS->LinearCTStereoCarb, pCS->nLenLinearCTStereoCarb, 1543| 288k| pCS->LinearCTStereoDble, pCS->nLenLinearCTStereoDble ); 1544| | 1545| | 1546| | /************************************************************************ 1547| | * 1548| | * Isotopic part 1549| | */ 1550| | 1551| | /* abs or rel stereo may establish one of two canonical numberings */ 1552| | 1553| 288k| if (( pCS->nLenLinearCTIsotopicStereoCarb > 0 || pCS->nLenLinearCTIsotopicStereoDble > 0 ) && ------------------ | Branch (1553:11): [True: 182, False: 288k] | Branch (1553:54): [True: 52, False: 288k] ------------------ 1554| 234| pCS->nLenCanonOrdIsotopicStereo > 0 && ------------------ | Branch (1554:11): [True: 219, False: 15] ------------------ 1555| 219| ( (pCS->LinearCTIsotopicStereoCarb && pCS->LinearCTIsotopicStereoCarbInv) || ------------------ | Branch (1555:14): [True: 167, False: 52] | Branch (1555:49): [True: 167, False: 0] ------------------ 1556| 52| (pCS->LinearCTIsotopicStereoDble && pCS->LinearCTIsotopicStereoDbleInv) ) && ------------------ | Branch (1556:16): [True: 52, False: 0] | Branch (1556:51): [True: 52, False: 0] ------------------ 1557| 219| pCS->nCanonOrdIsotopicStereo && pCS->nCanonOrdIsotopicStereoInv ------------------ | Branch (1557:11): [True: 219, False: 0] | Branch (1557:43): [True: 219, False: 0] ------------------ 1558| 288k| ) /* djb-rwth: addressing LLVM warning */ 1559| 219| { 1560| | /* found isotopic stereo */ 1561| | 1562| 219| pCanonRank = pCanonRankAtoms; 1563| 219| pCanonOrd = pCS->nCanonOrdIsotopicStereo; 1564| 219| pCanonRankInv = pSortOrd; 1565| 219| pCanonOrdInv = pCS->nCanonOrdIsotopicStereoInv; 1566| 219| Stereo = pINChI->StereoIsotopic; 1567| | 1568| 1.63k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (1568:21): [True: 1.41k, False: 219] ------------------ 1569| 1.41k| { 1570| 1.41k| pCanonRankInv[pCanonOrdInv[i]] = 1571| 1.41k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1572| 1.41k| } 1573| | 1574| | 1575| | /********************************************************************/ 1576| | /* copy stereo bonds and stereo centers; compare Inv and Abs stereo */ 1577| | /********************************************************************/ 1578| | 1579| 219| nErrorCode = CopyLinearCTStereoToINChIStereo( Stereo, 1580| 219| pCS->LinearCTIsotopicStereoCarb, 1581| 219| pCS->nLenLinearCTIsotopicStereoCarb, 1582| 219| pCS->LinearCTIsotopicStereoDble, 1583| 219| pCS->nLenLinearCTIsotopicStereoDble, 1584| 219| pCanonOrd, pCanonRank, at, 1 /* isotopic */, 1585| 219| pCS->LinearCTIsotopicStereoCarbInv, 1586| 219| pCS->LinearCTIsotopicStereoDbleInv, 1587| 219| pCanonOrdInv, pCanonRankInv ); 1588| | 1589| | /* djb-rwth: fixing oss-fuzz issue #68271 */ 1590| 219| if (nErrorCode == 1) ------------------ | Branch (1590:13): [True: 3, False: 216] ------------------ 1591| 3| { 1592| 3| nErrorCode = 0; 1593| 3| ret = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 3|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 3|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1594| 3| pINChI->nErrorCode = pINChI_Aux->nErrorCode = CT_OUT_OF_RAM; ------------------ | | 21| 3|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 3|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1595| 3| goto exit_function; 1596| 3| } 1597| | 1598| 216| if (Stereo->t_parityInv && Stereo->nNumberInv) ------------------ | Branch (1598:13): [True: 216, False: 0] | Branch (1598:36): [True: 216, False: 0] ------------------ 1599| 216| { 1600| 216| if (nUserMode & REQ_MODE_RELATIVE_STEREO) ------------------ | | 26| 216|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (1600:17): [True: 3, False: 213] ------------------ 1601| 3| { 1602| 3| pINChI->nFlags |= INCHI_FLAG_REL_STEREO; ------------------ | | 121| 3|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ 1603| 3| } 1604| | 1605| 216| if (nUserMode & REQ_MODE_RACEMIC_STEREO) ------------------ | | 28| 216|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (1605:17): [True: 3, False: 213] ------------------ 1606| 3| { 1607| 3| pINChI->nFlags |= INCHI_FLAG_RAC_STEREO; ------------------ | | 122| 3|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 1608| 3| } 1609| | 1610| 216| if (Stereo->nCompInv2Abs) ------------------ | Branch (1610:17): [True: 65, False: 151] ------------------ 1611| 65| { 1612| 65| if (Stereo->nCompInv2Abs == -1) ------------------ | Branch (1612:21): [True: 50, False: 15] ------------------ 1613| 50| { 1614| | /* switch pointers so that the stereo becomes the smallest (relative) */ 1615| | /* flag Stereo->nCompInv2Abs == -1 will keep track of this exchange */ 1616| 50| AT_NUMB *nNumberInv = Stereo->nNumberInv; 1617| 50| S_CHAR *t_parityInv = Stereo->t_parityInv; 1618| 50| Stereo->nNumberInv = Stereo->nNumber; 1619| 50| Stereo->t_parityInv = Stereo->t_parity; 1620| 50| Stereo->nNumber = nNumberInv; 1621| 50| Stereo->t_parity = t_parityInv; 1622| 50| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1623| 50| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1624| 50| bUseIsotopicNumberingInv = 1; 1625| 50| } 1626| 65| } 1627| 216| } 1628| | 1629| 1.58k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1629:21): [True: 1.37k, False: 216] ------------------ 1630| 1.37k| { 1631| 1.37k| pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv[i] = at[pCanonOrdInv[i]].orig_at_number; 1632| 1.37k| pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1633| 1.37k| } 1634| | 1635| 216| if (bUseIsotopicNumberingInv) ------------------ | Branch (1635:13): [True: 50, False: 166] ------------------ 1636| 50| { 1637| 50| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1638| 50| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1639| 50| memcpy(pCanonRank, pCanonRankInv, num_at_tg * sizeof(pCanonRank[0])); 1640| 50| memcpy(pCanonOrd, pCanonOrdInv, num_at_tg * sizeof(pCanonOrd[0])); 1641| 50| } 1642| | 1643| 216| pCanonRankInv = NULL; 1644| 216| pCanonOrdInv = NULL; 1645| 216| pOrigNosInCanonOrd = NULL; 1646| 216| } 1647| 288k| else 1648| 288k| { 1649| | /* no isotopic stereo */ 1650| | 1651| 288k| pCanonOrd = pCS->nLenCanonOrdIsotopicStereo > 0 ? pCS->nCanonOrdIsotopicStereo ------------------ | Branch (1651:21): [True: 11, False: 288k] ------------------ 1652| 288k| : pCS->nLenCanonOrdIsotopic > 0 ? pCS->nCanonOrdIsotopic ------------------ | Branch (1652:15): [True: 1.88k, False: 286k] ------------------ 1653| 288k| : NULL; 1654| 288k| pCanonRank = pCanonRankAtoms; 1655| 288k| pOrigNosInCanonOrd = pINChI_Aux->nIsotopicOrigAtNosInCanonOrd; 1656| | 1657| | /* djb-rwth: fixing oss-fuzz issue #30496 */ 1658| 288k| if (pCanonOrd && pCanonRank && pOrigNosInCanonOrd) ------------------ | Branch (1658:13): [True: 1.90k, False: 286k] | Branch (1658:26): [True: 1.90k, False: 0] | Branch (1658:40): [True: 1.88k, False: 16] ------------------ 1659| 1.88k| { 1660| 12.8k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1660:25): [True: 10.9k, False: 1.88k] ------------------ 1661| 10.9k| { 1662| | /* Fix13 -- out of bounds */ 1663| 10.9k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1664| 10.9k| pOrigNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1665| 10.9k| } 1666| 1.96k| for (; i < num_at_tg; i++) ------------------ | Branch (1666:20): [True: 76, False: 1.88k] ------------------ 1667| 76| { 1668| | /* Fix13 -- out of bounds */ 1669| 76| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1670| 76| } 1671| 1.88k| } 1672| 288k| } 1673| | /*pCanonOrdIso = pCanonOrd;*/ 1674| | 1675| | 1676| 288k| pConstitEquNumb = pINChI_Aux->nConstitEquIsotopicNumbers; 1677| 288k| pSymmRank = pCS->nSymmRankIsotopic; 1678| | 1679| 288k| if (pCanonOrd && pCanonRank && pConstitEquNumb && pSymmRank) ------------------ | Branch (1679:9): [True: 2.11k, False: 286k] | Branch (1679:22): [True: 2.11k, False: 0] | Branch (1679:36): [True: 2.10k, False: 16] | Branch (1679:55): [True: 2.10k, False: 0] ------------------ 1680| 2.10k| { 1681| 14.4k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1681:21): [True: 12.3k, False: 2.10k] ------------------ 1682| 12.3k| { 1683| 12.3k| pConstitEquNumb[i] = pSymmRank[pCanonOrd[i]]; 1684| 12.3k| pSortOrd[i] = i; 1685| 12.3k| } 1686| | 1687| 2.19k| for (; i < num_at_tg; i++) ------------------ | Branch (1687:16): [True: 98, False: 2.10k] ------------------ 1688| 98| { 1689| 98| pSortOrd[i] = i; 1690| 98| } 1691| | 1692| 2.10k| pCG->m_pn_RankForSort = pConstitEquNumb; 1693| 2.10k| inchi_qsort( pCG, pSortOrd, num_atoms, sizeof( pSortOrd[0] ), CompRanksOrd ); 1694| | 1695| 14.4k| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= num_atoms; j++) ------------------ | Branch (1695:51): [True: 12.3k, False: 2.10k] ------------------ 1696| 12.3k| { 1697| 12.3k| if (j == num_atoms || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1697:17): [True: 2.10k, False: 10.2k] | Branch (1697:35): [True: 3.44k, False: 6.80k] ------------------ 1698| 5.54k| { 1699| 5.54k| nMinOrd++; 1700| | 1701| 5.54k| if (j - i > 1) ------------------ | Branch (1701:21): [True: 858, False: 4.68k] ------------------ 1702| 858| { 1703| | /* found a sequence of equivalent atoms: i..j-1 */ 1704| 8.52k| while (i < j) ------------------ | Branch (1704:28): [True: 7.66k, False: 858] ------------------ 1705| 7.66k| { 1706| 7.66k| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; 1707| 7.66k| } 1708| 858| } 1709| 4.68k| else 1710| 4.68k| { 1711| 4.68k| pConstitEquNumb[pSortOrd[i++]] = 0; /* nMinOrd; */ 1712| 4.68k| } 1713| 5.54k| nMinOrd = pSortOrd[j]; 1714| 5.54k| } 1715| 12.3k| } 1716| 2.10k| } 1717| 286k| else 1718| 286k| { 1719| 286k| goto exit_function; /* no isotopic info available */ 1720| 286k| } 1721| | 1722| | 1723| | /* Isotopic atoms */ 1724| | 1725| 2.10k| n = pINChI->nNumberOfIsotopicAtoms = pCS->nLenLinearCTIsotopic; 1726| | 1727| 4.49k| for (i = 0; i < n; i++) ------------------ | Branch (1727:17): [True: 2.39k, False: 2.10k] ------------------ 1728| 2.39k| { 1729| 2.39k| pINChI->IsotopicAtom[i].nAtomNumber = pCS->LinearCTIsotopic[i].at_num; 1730| 2.39k| pINChI->IsotopicAtom[i].nIsoDifference = pCS->LinearCTIsotopic[i].iso_atw_diff; 1731| 2.39k| pINChI->IsotopicAtom[i].nNum_H = pCS->LinearCTIsotopic[i].num_1H; 1732| 2.39k| pINChI->IsotopicAtom[i].nNum_D = pCS->LinearCTIsotopic[i].num_D; 1733| 2.39k| pINChI->IsotopicAtom[i].nNum_T = pCS->LinearCTIsotopic[i].num_T; 1734| 2.39k| } 1735| | 1736| | /* Isotopic tautomeric groups */ 1737| | 1738| 2.10k| n = pINChI->nNumberOfIsotopicTGroups = pCS->nLenLinearCTIsotopicTautomer; 1739| | 1740| 2.10k| for (i = 0; i < n; i++) ------------------ | Branch (1740:17): [True: 0, False: 2.10k] ------------------ 1741| 0| { 1742| 0| pINChI->IsotopicTGroup[i].nTGroupNumber = pCS->LinearCTIsotopicTautomer[i].tgroup_num; 1743| 0| pINChI->IsotopicTGroup[i].nNum_H = pCS->LinearCTIsotopicTautomer[i].num[2]; 1744| 0| pINChI->IsotopicTGroup[i].nNum_D = pCS->LinearCTIsotopicTautomer[i].num[1]; 1745| 0| pINChI->IsotopicTGroup[i].nNum_T = pCS->LinearCTIsotopicTautomer[i].num[0]; 1746| 0| } 1747| | 1748| | /* Atoms that may exchange isotopic H-atoms */ 1749| | 1750| 2.10k| if (pCS->nExchgIsoH && pINChI->nPossibleLocationsOfIsotopicH) ------------------ | Branch (1750:9): [True: 2.10k, False: 0] | Branch (1750:28): [True: 2.10k, False: 0] ------------------ 1751| 2.10k| { 1752| 14.4k| for (i = 0, j = 1; i < num_atoms; i++) ------------------ | Branch (1752:28): [True: 12.3k, False: 2.10k] ------------------ 1753| 12.3k| { 1754| 12.3k| if (pCS->nExchgIsoH[i]) ------------------ | Branch (1754:17): [True: 254, False: 12.0k] ------------------ 1755| 254| { 1756| 254| pINChI->nPossibleLocationsOfIsotopicH[j++] = (AT_NUMB) ( i + 1 ); /* canonical number */ 1757| 254| } 1758| 12.3k| } 1759| 2.10k| pINChI->nPossibleLocationsOfIsotopicH[0] = (AT_NUMB) j; /* length including the 0th element */ 1760| 2.10k| } 1761| | 1762| 2.10k| if ((nStereoUnmarkMode = UnmarkAllUndefinedUnknownStereo( pINChI->StereoIsotopic, nUserMode ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1762:9): [True: 51, False: 2.04k] ------------------ 1763| 51| { 1764| 51| pINChI->nFlags |= 1765| 51| ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU ------------------ | | 30| 51|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU ------------------ | | 125| 31|#define INCHI_FLAG_SC_IGN_ALL_ISO_UU 0x0020 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1765:13): [True: 31, False: 20] ------------------ 1766| 51| : 0; 1767| 51| pINChI->nFlags |= 1768| 51| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU ------------------ | | 32| 51|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU ------------------ | | 125| 20|#define INCHI_FLAG_SC_IGN_ALL_ISO_UU 0x0020 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1768:13): [True: 20, False: 31] ------------------ 1769| 51| : 0; 1770| 51| if (( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) || ------------------ | | 30| 51|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (1770:13): [True: 31, False: 20] ------------------ 1771| 20| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU )) ------------------ | | 32| 20|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (1771:13): [True: 20, False: 0] ------------------ 1772| 51| { 1773| 51| if (!bNoWarnings) ------------------ | Branch (1773:17): [True: 51, False: 0] ------------------ 1774| 51| { 1775| 51| WarningMessage( pStrErrStruct, "Omitted undefined stereo" ); ------------------ | | 132| 51|#define WarningMessage AddErrorMessage ------------------ 1776| 51| } 1777| 51| } 1778| 51| } 1779| | 1780| | /* Mark ambiguous stereo */ 1781| | 1782| 2.10k| MarkAmbiguousStereo( at, norm_at, 1 /* isotopic */, pCanonOrd, 1783| 2.10k| pCS->LinearCTIsotopicStereoCarb, pCS->nLenLinearCTIsotopicStereoCarb, 1784| 2.10k| pCS->LinearCTIsotopicStereoDble, pCS->nLenLinearCTIsotopicStereoDble ); 1785| | 1786| | 1787| | /*********************************************************** 1788| | * Isotopic tautomeric group(s) numbering and symmetry; 1789| | * should not depend on switching to rel. stereo numbering 1790| | */ 1791| | 1792| 2.10k| if (pINChI->lenTautomer && ------------------ | Branch (1792:9): [True: 851, False: 1.24k] ------------------ 1793| 851| pINChI_Aux->nConstitEquIsotopicTGroupNumbers && ------------------ | Branch (1793:10): [True: 851, False: 0] ------------------ 1794| 851| pCS->nSymmRankIsotopicTaut && ------------------ | Branch (1794:10): [True: 85, False: 766] ------------------ 1795| 85| ( pCS->nLenLinearCTIsotopic || pCS->nLenLinearCTIsotopicTautomer ) && ------------------ | Branch (1795:12): [True: 81, False: 4] | Branch (1795:41): [True: 0, False: 4] ------------------ 1796| 81| t_group_info && t_group_info->num_t_groups > 0) ------------------ | Branch (1796:10): [True: 81, False: 0] | Branch (1796:26): [True: 81, False: 0] ------------------ 1797| 81| { 1798| | 1799| | /* djb-rwth: removing redundant code */ 1800| | 1801| 81| pCanonOrdTaut = 1802| 81| pCS->nLenCanonOrdIsotopicStereoTaut > 0 ? ( n = pCS->nLenCanonOrdIsotopicStereoTaut, pCS->nCanonOrdIsotopicStereoTaut ) ------------------ | Branch (1802:13): [True: 17, False: 64] ------------------ 1803| 81| : pCS->nLenCanonOrdIsotopicTaut > 0 ? ( n = pCS->nLenCanonOrdIsotopicTaut, pCS->nCanonOrdIsotopicTaut ) ------------------ | Branch (1803:15): [True: 64, False: 0] ------------------ 1804| 64| : ( n = 0, (AT_RANK*) NULL ); 1805| | 1806| 81| pConstitEquNumb = pINChI_Aux->nConstitEquIsotopicTGroupNumbers; 1807| | 1808| 81| pSymmRank = pCS->nSymmRankIsotopicTaut; 1809| | 1810| 81| if (pCanonOrdTaut && pSymmRank && pConstitEquNumb && n > 0) ------------------ | Branch (1810:13): [True: 81, False: 0] | Branch (1810:30): [True: 81, False: 0] | Branch (1810:43): [True: 81, False: 0] | Branch (1810:62): [True: 81, False: 0] ------------------ 1811| 81| { 1812| 175| for (i = 0; i < n; i++) ------------------ | Branch (1812:25): [True: 94, False: 81] ------------------ 1813| 94| { 1814| 94| pConstitEquNumb[i] = pSymmRank[pCanonOrdTaut[i]]; 1815| 94| pSortOrd[i] = i; 1816| 94| } 1817| | 1818| 81| pCG->m_pn_RankForSort = pConstitEquNumb; 1819| 81| inchi_qsort( pCG, pSortOrd, n, sizeof( pSortOrd[0] ), CompRanksOrd ); 1820| 175| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= n; j++) ------------------ | Branch (1820:55): [True: 94, False: 81] ------------------ 1821| 94| { 1822| 94| if (j == n || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1822:21): [True: 81, False: 13] | Branch (1822:31): [True: 13, False: 0] ------------------ 1823| 94| { 1824| 94| nMinOrd++; 1825| 94| if (j - i > 1) ------------------ | Branch (1825:25): [True: 0, False: 94] ------------------ 1826| 0| { 1827| | /* found a sequence of equivalent t-groups: i..j-1 */ 1828| 0| while (i < j) ------------------ | Branch (1828:32): [True: 0, False: 0] ------------------ 1829| 0| { 1830| 0| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; 1831| 0| } 1832| 0| } 1833| 94| else 1834| 94| { 1835| 94| pConstitEquNumb[pSortOrd[i++]] = 0; /* nMinOrd; */ 1836| 94| } 1837| 94| nMinOrd = pSortOrd[j]; /* at the end j = n */ 1838| 94| } 1839| 94| } 1840| 81| } 1841| 81| } 1842| | 1843| | 1844| 288k|exit_function: 1845| | 1846| 288k| if (pCanonRankAtoms) ------------------ | Branch (1846:9): [True: 288k, False: 0] ------------------ 1847| 288k| { 1848| 288k| inchi_free( pCanonRankAtoms ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 1849| 288k| } 1850| 288k| if (pSortOrd) ------------------ | Branch (1850:9): [True: 288k, False: 0] ------------------ 1851| 288k| { 1852| 288k| inchi_free( pSortOrd ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 1853| 288k| } 1854| | 1855| 288k| pINChI->nErrorCode |= nErrorCode; 1856| 288k| pINChI_Aux->nErrorCode |= nErrorCode; 1857| | 1858| 288k| return ret; 1859| 2.10k|} inp2spATOM: 85| 288k|{ 86| 288k| int i, j, val, elname_len; 87| | 88| 288k| memset(at, 0, sizeof(at[0]) * num_inp_at); /* djb-rwth: memset_s C11/Annex K variant? */ 89| | 90| 1.38M| for (i = 0; i < num_inp_at; i++) ------------------ | Branch (90:17): [True: 1.10M, False: 288k] ------------------ 91| 1.10M| { 92| 1.10M| elname_len = sizeof(at[0].elname) - 1; /* djb-rwth: fixing coverity ID #499609 */ 93| 1.10M| strncpy(at[i].elname, inp_at[i].elname, elname_len); 94| 1.10M| at[i].elname[elname_len] = '\0'; 95| 1.10M| at[i].el_number = (U_CHAR)get_periodic_table_number(at[i].elname); 96| 1.10M| val = at[i].valence = inp_at[i].valence; 97| 1.58M| for (j = 0; j < val; j++) ------------------ | Branch (97:21): [True: 486k, False: 1.10M] ------------------ 98| 486k| { 99| 486k| at[i].neighbor[j] = inp_at[i].neighbor[j]; 100| 486k| at[i].bond_type[j] = inp_at[i].bond_type[j]; 101| 486k| } 102| 1.10M| at[i].chem_bonds_valence = inp_at[i].chem_bonds_valence; 103| 1.10M| at[i].orig_at_number = inp_at[i].orig_at_number; 104| 1.10M| at[i].orig_compt_at_numb = inp_at[i].orig_compt_at_numb; 105| 1.10M| at[i].endpoint = inp_at[i].endpoint; 106| 1.10M| at[i].iso_atw_diff = inp_at[i].iso_atw_diff; 107| 1.10M| at[i].num_H = inp_at[i].num_H; 108| 1.10M| at[i].cFlags = inp_at[i].cFlags; 109| 4.40M| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 72| 4.40M|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (109:21): [True: 3.30M, False: 1.10M] ------------------ 110| 3.30M| { 111| 3.30M| at[i].num_iso_H[j] = inp_at[i].num_iso_H[j]; 112| 3.30M| } 113| 1.10M| at[i].charge = inp_at[i].charge; 114| 1.10M| at[i].radical = inp_at[i].radical; 115| | 116| 1.10M|#if ( FIND_RING_SYSTEMS == 1 ) 117| 1.10M| at[i].nBlockSystem = inp_at[i].nBlockSystem; 118| 1.10M| at[i].bCutVertex = inp_at[i].bCutVertex; 119| 1.10M| at[i].nRingSystem = inp_at[i].nRingSystem; 120| 1.10M| at[i].nNumAtInRingSystem = inp_at[i].nNumAtInRingSystem; 121| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 122| | at[i].nDistanceFromTerminal = inp_at[i].nDistanceFromTerminal; 123| |#endif 124| 1.10M|#endif 125| | 126| | /* 127| | at[i].x = inp_at[i].x; 128| | at[i].y = inp_at[i].y; 129| | at[i].z = inp_at[i].z; 130| | */ 131| 1.10M| } 132| | 133| 288k| return 0; 134| 288k|} GetElementAndCount: 139| 16.1M|{ 140| 16.1M| const char* p = *f; 141| 16.1M| char* q; 142| 16.1M| int i = 0; 143| | 144| | /* djb-rwth: fixing oss-fuzz issue #37224 */ 145| 16.1M| if (p && *p) ------------------ | Branch (145:9): [True: 14.4M, False: 1.64M] | Branch (145:14): [True: 9.83M, False: 4.63M] ------------------ 146| 9.83M| { 147| 9.83M| if (isupper(UCINT * p)) ------------------ | Branch (147:13): [True: 9.83M, False: 0] ------------------ 148| 9.83M| { 149| 9.83M| szEl[i++] = *p++; 150| 9.83M| if (*p && islower(UCINT * p)) ------------------ | Branch (150:17): [True: 5.87M, False: 3.96M] | Branch (150:23): [True: 1.74M, False: 4.12M] ------------------ 151| 1.74M| { 152| 1.74M| szEl[i++] = *p++; 153| 1.74M| } 154| 9.83M| szEl[i] = '\0'; 155| 9.83M| if (1 == i && szEl[0] == 'C') ------------------ | Branch (155:17): [True: 8.09M, False: 1.74M] | Branch (155:27): [True: 471k, False: 7.61M] ------------------ 156| 471k| { 157| 471k| szEl[0] = 'A'; /* less than any element: */ 158| | /* carbon-containing compounds should be first */ 159| 471k| } 160| 9.83M| if (*p && isdigit(UCINT * p)) ------------------ | Branch (160:17): [True: 5.67M, False: 4.16M] | Branch (160:23): [True: 2.09M, False: 3.58M] ------------------ 161| 2.09M| { 162| 2.09M| *count = strtol(p, &q, 10); 163| 2.09M| p = q; 164| 2.09M| } 165| 7.74M| else 166| 7.74M| { 167| 7.74M| *count = 1; 168| 7.74M| } 169| 9.83M| *f = p; /* next element; */ 170| 9.83M| return 1; 171| 9.83M| } 172| 0| return -1; /* not a chemical formula */ 173| 9.83M| } 174| | /* v. 1.06 Changed "Zz" to "Zzz" as "Zz" is valid symbol now */ 175| 6.28M| strcpy(szEl, "Zzz"); 176| | /*strcpy( szEl, "Zz" );*/ 177| | /* zero termination 'element' is larger than any other element */ 178| 6.28M| *count = 99999; /* zero termination 'element count' is larger than any other count */ 179| 6.28M| return 0; 180| 16.1M|} CompareHillFormulas: 207| 450k|{ 208| 450k| char szEl1[4], szEl2[4]; 209| 450k| int count1, count2, ret1, ret2, ret; 210| | 211| 450k| do 212| 900k| { 213| 900k| ret1 = GetElementAndCount(&f1, szEl1, &count1); 214| 900k| ret2 = GetElementAndCount(&f2, szEl2, &count2); 215| 900k| if (0 <= ret1 && 0 <= ret2) ------------------ | Branch (215:13): [True: 900k, False: 0] | Branch (215:26): [True: 900k, False: 0] ------------------ 216| 900k| { 217| 900k| if ((ret = strcmp(szEl1, szEl2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (217:17): [True: 0, False: 900k] ------------------ 218| 0| { 219| 0| return ret; /* lexicographic order, string termination > any character */ 220| 0| } 221| 900k| if ((ret = count2 - count1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (221:17): [True: 0, False: 900k] ------------------ 222| 0| { 223| 0| return ret; /* inverse atom count order */ 224| 0| } 225| 900k| } 226| 0| else 227| 0| { 228| 0| return 0; /* program error */ 229| 0| } 230| 900k| } while (0 < ret1 && 0 < ret2); ------------------ | Branch (230:14): [True: 450k, False: 450k] | Branch (230:26): [True: 450k, False: 0] ------------------ 231| | 232| 450k| return 0; 233| 450k|} CompareHillFormulasNoH: 241| 2.77M|{ 242| 2.77M| char szEl1[4], szEl2[4]; 243| 2.77M| int count1, count2, ret1, ret2, ret; 244| | 245| 2.77M| do 246| 5.88M| { 247| 5.88M| ret1 = GetElementAndCount(&f1, szEl1, &count1); 248| 5.88M| if (0 < ret1 && szEl1[0] == 'H' && !szEl1[1]) ------------------ | Branch (248:13): [True: 4.22M, False: 1.66M] | Branch (248:25): [True: 1.31M, False: 2.90M] | Branch (248:44): [True: 1.29M, False: 22.3k] ------------------ 249| 1.29M| { 250| 1.29M| *num_H1 += count1; 251| 1.29M| ret1 = GetElementAndCount(&f1, szEl1, &count1); 252| 1.29M| } 253| 5.88M| ret2 = GetElementAndCount(&f2, szEl2, &count2); 254| 5.88M| if (0 < ret2 && szEl2[0] == 'H' && !szEl2[1]) ------------------ | Branch (254:13): [True: 4.23M, False: 1.64M] | Branch (254:25): [True: 1.27M, False: 2.96M] | Branch (254:44): [True: 1.25M, False: 22.3k] ------------------ 255| 1.25M| { 256| 1.25M| *num_H2 += count2; 257| 1.25M| ret2 = GetElementAndCount(&f2, szEl2, &count2); 258| 1.25M| } 259| 5.88M| if (0 <= ret1 && 0 <= ret2) ------------------ | Branch (259:13): [True: 5.88M, False: 0] | Branch (259:26): [True: 5.88M, False: 0] ------------------ 260| 5.88M| { 261| 5.88M| if ((ret = strcmp(szEl1, szEl2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (261:17): [True: 77.2k, False: 5.80M] ------------------ 262| 77.2k| { 263| 77.2k| return ret; /* lexicographic order, string termination > any character */ 264| 77.2k| } 265| 5.80M| if ((ret = count2 - count1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (265:17): [True: 22.4k, False: 5.78M] ------------------ 266| 22.4k| { 267| 22.4k| return ret; /* inverse atom count order */ 268| 22.4k| } 269| 5.80M| } 270| 0| else 271| 0| { 272| 0| return 0; /* program error */ 273| 0| } 274| 5.88M| } while (0 < ret1 && 0 < ret2); ------------------ | Branch (274:14): [True: 3.11M, False: 2.67M] | Branch (274:26): [True: 3.11M, False: 0] ------------------ 275| | 276| 2.67M| return 0; 277| 2.77M|} CompareTautNonIsoPartOfINChI: 282| 2.56M|{ 283| 2.56M| int len1, len2, ret, i; 284| | 285| 2.56M| len1 = i1->lenTautomer > 0 && i1->nTautomer[0] ? i1->lenTautomer : 0; ------------------ | Branch (285:12): [True: 901k, False: 1.66M] | Branch (285:35): [True: 589, False: 900k] ------------------ 286| 2.56M| len2 = i2->lenTautomer > 0 && i2->nTautomer[0] ? i2->lenTautomer : 0; ------------------ | Branch (286:12): [True: 901k, False: 1.66M] | Branch (286:35): [True: 589, False: 900k] ------------------ 287| 2.56M| if ((ret = len2 - len1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (287:9): [True: 0, False: 2.56M] ------------------ 288| 0| { 289| 0| return ret; 290| 0| } 291| 2.57M| for (i = 0; i < len1; i++) ------------------ | Branch (291:17): [True: 14.0k, False: 2.56M] ------------------ 292| 14.0k| { 293| 14.0k| if ((ret = (int)i2->nTautomer[i] - (int)i1->nTautomer[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (293:13): [True: 0, False: 14.0k] ------------------ 294| 0| return ret; 295| 14.0k| } 296| 2.56M| return 0; 297| 2.56M|} CompINChITautVsNonTaut: 309| 97.5k|{ 310| 97.5k| int ret, num, i, num_H1, num_H2; 311| | 312| 97.5k| const INChI* i1 = NULL; /* Mobile-H layers in Mobile-H sorting order */ 313| 97.5k| const INChI* i2 = NULL; /* Fixed-H layers in Fixed-H sorting order */ 314| | 315| 97.5k| int n1; /* TAUT_YES if tautomeric i1 exists, otherwise TAUT_NON */ 316| | 317| | /* INChI_Stereo *Stereo1, *Stereo2; */ 318| | 319| 97.5k| n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (319:11): [True: 97.5k, False: 0] | Branch (319:35): [True: 97.5k, False: 0] ------------------ 320| | 321| 97.5k| i1 = p1->pINChI[n1]; 322| 97.5k| i2 = (n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 575| 195k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i2 = (n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (322:11): [True: 97.5k, False: 0] | Branch (322:29): [True: 0, False: 97.5k] ------------------ 323| 97.5k| p2->pINChI[TAUT_NON]->nNumberOfAtoms) ? p2->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p2->pINChI[TAUT_NON]->nNumberOfAtoms) ? p2->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (323:9): [True: 0, False: 0] ------------------ 324| | 325| | /* non-deleted-non-empty < deleted < empty */ 326| 97.5k| if (i1 && !i2) ------------------ | Branch (326:9): [True: 97.5k, False: 0] | Branch (326:15): [True: 97.5k, False: 0] ------------------ 327| 97.5k| return 0; /* non-empty is the smallest (first) */ 328| 0| if (!i1 && i2) ------------------ | Branch (328:9): [True: 0, False: 0] | Branch (328:16): [True: 0, False: 0] ------------------ 329| 0| return 0; 330| 0| if (!i1 && !i2) ------------------ | Branch (330:9): [True: 0, False: 0] | Branch (330:16): [True: 0, False: 0] ------------------ 331| 0| return 0; 332| 0| if (i1->bDeleted) ------------------ | Branch (332:9): [True: 0, False: 0] ------------------ 333| 0| return 1; /* deleted is the largest (last) among non-empty */ 334| 0| if (i2->bDeleted) ------------------ | Branch (334:9): [True: 0, False: 0] ------------------ 335| 0| return -1; 336| | 337| 0| if (i1->nNumberOfAtoms > 0 && !i2->nNumberOfAtoms) ------------------ | Branch (337:9): [True: 0, False: 0] | Branch (337:35): [True: 0, False: 0] ------------------ 338| 0| return 0; 339| | 340| | /* i2 = i2; djb-rwth: an obviously useless statement */ 341| | 342| 0| num_H1 = num_H2 = 0; 343| | 344| | /* do not compare terminal H */ 345| 0| if ((ret = CompareHillFormulasNoH(i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (345:9): [True: 0, False: 0] ------------------ 346| 0| { 347| 0| return ret; /* lexicographic order except the shorter one is greater (last): CH2O < CH2; C3XX < C2XX */ 348| 0| } 349| | 350| | /* 351| | compare non-isotopic non-tautomeric part 352| | */ 353| | 354| | /* compare number of atoms (excluding terminal H) */ 355| 0| if ((ret = i2->nNumberOfAtoms - i1->nNumberOfAtoms)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (355:9): [True: 0, False: 0] ------------------ 356| 0| return ret; /* more atoms first */ 357| | 358| | /* compare elements (excluding terminal H) */ 359| 0| num = i1->nNumberOfAtoms; 360| 0| for (i = 0; i < num; i++) ------------------ | Branch (360:17): [True: 0, False: 0] ------------------ 361| 0| { /* should always be equal if Hill formulas are same */ 362| 0| if ((ret = (int)i2->nAtom[i] - (int)i1->nAtom[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (362:13): [True: 0, False: 0] ------------------ 363| 0| return ret; /* greater periodic number first */ 364| 0| } 365| | /* 366| | compare connection tables 367| | */ 368| 0| if ((ret = i2->lenConnTable - i1->lenConnTable)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (368:9): [True: 0, False: 0] ------------------ 369| 0| return ret; /* longer connection table first */ 370| 0| num = i2->lenConnTable; 371| 0| for (i = 0; i < num; i++) ------------------ | Branch (371:17): [True: 0, False: 0] ------------------ 372| 0| { 373| 0| if ((ret = (int)i2->nConnTable[i] - (int)i1->nConnTable[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (373:13): [True: 0, False: 0] ------------------ 374| 0| return ret; /* greater connection table first */ 375| 0| } 376| | /* 377| | compare total number of H (inverse: H3 < H2 ) 378| | */ 379| 0| if ((ret = num_H2 - num_H1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (379:9): [True: 0, False: 0] ------------------ 380| 0| return ret; 381| | /* 382| | compare non-tautomeric num_H: N < NH3 < NH2 < NH 383| | */ 384| 0| num = i1->nNumberOfAtoms; 385| 0| for (i = 0; i < num; i++) ------------------ | Branch (385:17): [True: 0, False: 0] ------------------ 386| 0| { 387| 0| if (i2->nNum_H[i] != i1->nNum_H[i]) ------------------ | Branch (387:13): [True: 0, False: 0] ------------------ 388| 0| { 389| 0| return !i2->nNum_H[i] ? 1 : /* no H first */ ------------------ | Branch (389:20): [True: 0, False: 0] ------------------ 390| 0| !i1->nNum_H[i] ? -1 : ------------------ | Branch (390:17): [True: 0, False: 0] ------------------ 391| 0| (int)i2->nNum_H[i] - (int)i1->nNum_H[i]; 392| 0| } 393| 0| } 394| | /* 395| | compare non-isotopic tautomeric part 396| | */ 397| 0| if ((ret = CompareTautNonIsoPartOfINChI(i1, i2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (397:9): [True: 0, False: 0] ------------------ 398| 0| { 399| 0| return ret; 400| 0| } 401| | /* 402| | if ( ret = i2->lenTautomer - i1->lenTautomer ) 403| | return ret; 404| | num = inchi_min( i2->lenTautomer, i1->lenTautomer ); 405| | for ( i = 0; i < num; i ++ ) { 406| | if ( ret = (int)i2->nTautomer[i] - (int)i1->nTautomer[i] ) 407| | return ret; 408| | } 409| | */ 410| | 411| | /* 412| | at this point both components are either tautomeric 413| | or non-tautomeric 414| | */ 415| | 416| | /* 417| | non-tautomeric "fixed H" specific 418| | */ 419| 0| if ( /*TAUT_NON == bTaut && (i2 &&*/ i2->nNum_H_fixed) /* djb-rwth: fixing coverity ID #499493 */ ------------------ | Branch (419:42): [True: 0, False: 0] ------------------ 420| 0| { 421| | /* first, compare non-tautomeric chem. formulas -- they may be different */ 422| | /* secondly, compare fixed-H distribution */ 423| 0| if (i2->nNum_H_fixed) ------------------ | Branch (423:13): [True: 0, False: 0] ------------------ 424| 0| { 425| 0| num = i2->nNumberOfAtoms; 426| 0| for (i = 0; i < num; i++) ------------------ | Branch (426:25): [True: 0, False: 0] ------------------ 427| 0| { 428| 0| if (i2->nNum_H_fixed[i] != 0) ------------------ | Branch (428:21): [True: 0, False: 0] ------------------ 429| 0| { 430| 0| return 1; 431| 0| } 432| 0| } 433| 0| } 434| 0| } 435| | /* 436| | compare non-isotopic stereo 437| | */ 438| 0| ret = CompareInchiStereo(i1->Stereo, i1->nFlags, i2->Stereo, i2->nFlags); 439| 0| if (ret) ------------------ | Branch (439:9): [True: 0, False: 0] ------------------ 440| 0| { 441| 0| return ret; 442| 0| } 443| | 444| | /* 445| | do not switch back to tautomeric i1, i2 446| | */ 447| | 448| | /* -- how to switch back -- 449| | if ( i1t ) { 450| | i1 = i1t; 451| | i1t = NULL; 452| | } 453| | if ( i2t ) { 454| | i2 = i2t; 455| | i2t = NULL; 456| | } 457| | */ 458| | 459| | /* 460| | compare isotopic non-tautomeric part 461| | */ 462| 0| if (bCompareIsotopic) ------------------ | Branch (462:9): [True: 0, False: 0] ------------------ 463| 0| { 464| 0| if ((ret = i2->nNumberOfIsotopicAtoms - i1->nNumberOfIsotopicAtoms)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (464:13): [True: 0, False: 0] ------------------ 465| 0| return ret; 466| 0| num = i1->nNumberOfIsotopicAtoms; 467| | 468| | /* compare isotopic atoms */ 469| 0| for (i = 0; i < num; i++) ------------------ | Branch (469:21): [True: 0, False: 0] ------------------ 470| 0| { 471| 0| if ((ret = (int)i2->IsotopicAtom[i].nAtomNumber - (int)i1->IsotopicAtom[i].nAtomNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (471:17): [True: 0, False: 0] ------------------ 472| 0| return ret; 473| 0| if ((ret = (int)i2->IsotopicAtom[i].nIsoDifference - (int)i1->IsotopicAtom[i].nIsoDifference)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (473:17): [True: 0, False: 0] ------------------ 474| 0| return ret; 475| 0| } 476| | 477| | /* compare isotopic H */ 478| | /* if tautomeric comparison mode then here are compared only non-tautomeric H */ 479| 0| for (i = 0; i < num; i++) ------------------ | Branch (479:21): [True: 0, False: 0] ------------------ 480| 0| { 481| 0| if ((ret = (int)i2->IsotopicAtom[i].nNum_T - (int)i1->IsotopicAtom[i].nNum_T)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (481:17): [True: 0, False: 0] ------------------ 482| 0| return ret; 483| 0| if ((ret = (int)i2->IsotopicAtom[i].nNum_D - (int)i1->IsotopicAtom[i].nNum_D)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (483:17): [True: 0, False: 0] ------------------ 484| 0| return ret; 485| 0| if ((ret = (int)i2->IsotopicAtom[i].nNum_H - (int)i1->IsotopicAtom[i].nNum_H)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (485:17): [True: 0, False: 0] ------------------ 486| 0| return ret; 487| 0| } 488| | 489| | /* compare isotopic tautomeric part */ 490| 0| if ((ret = i2->nNumberOfIsotopicTGroups || i1->nNumberOfIsotopicTGroups)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (490:13): [True: 0, False: 0] | Branch (490:20): [True: 0, False: 0] | Branch (490:52): [True: 0, False: 0] ------------------ 491| 0| return ret; 492| | 493| | /* 494| | num = i1->nNumberOfIsotopicTGroups; 495| | for ( i = 0; i < num; i ++ ) { 496| | if ( ret = (int)i2->IsotopicTGroup[i].nTGroupNumber - (int)i1->IsotopicTGroup[i].nTGroupNumber ) 497| | return ret; 498| | if ( ret = (int)i2->IsotopicTGroup[i].nNum_T - (int)i1->IsotopicTGroup[i].nNum_T ) 499| | return ret; 500| | if ( ret = (int)i2->IsotopicTGroup[i].nNum_D - (int)i1->IsotopicTGroup[i].nNum_D ) 501| | return ret; 502| | if ( ret = (int)i2->IsotopicTGroup[i].nNum_H - (int)i1->IsotopicTGroup[i].nNum_H ) 503| | return ret; 504| | } 505| | */ 506| | 507| | /* compare isotopic stereo */ 508| 0| ret = CompareInchiStereo(i1->StereoIsotopic, i1->nFlags, 509| 0| i2->StereoIsotopic, i2->nFlags); 510| 0| if (ret) ------------------ | Branch (510:13): [True: 0, False: 0] ------------------ 511| 0| { 512| 0| return ret; 513| 0| } 514| 0| } 515| | 516| | /* 517| | compare charges: non-charged first, then in order of 518| | ascending charges (negative first) 519| | */ 520| | 521| 0| if (i2->nTotalCharge && i1->nTotalCharge) ------------------ | Branch (521:9): [True: 0, False: 0] | Branch (521:29): [True: 0, False: 0] ------------------ 522| 0| { 523| | /* both are charged; smaller charges first */ 524| 0| ret = (int)i1->nTotalCharge - (int)i2->nTotalCharge; 525| 0| return ret; 526| 0| } 527| 0| if ((ret = (i1->nTotalCharge ? 1 : 0) - (i2->nTotalCharge ? 1 : 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (527:9): [True: 0, False: 0] | Branch (527:17): [True: 0, False: 0] | Branch (527:46): [True: 0, False: 0] ------------------ 528| 0| { 529| | /* only one is charged; uncharged first */ 530| 0| return ret; 531| 0| } 532| | /* stable sort */ 533| | /*ret = p1->ord_number - p2->ord_number;*/ 534| | 535| 0| return ret; 536| 0|} GetSp3RelRacAbs: 559| 390k|{ 560| 390k| int nRet = SP3_NONE; 561| 390k| if (pINChI && !pINChI->bDeleted && Stereo && 0 < Stereo->nNumberOfStereoCenters) ------------------ | Branch (561:9): [True: 195k, False: 195k] | Branch (561:19): [True: 195k, False: 12] | Branch (561:40): [True: 10.3k, False: 184k] | Branch (561:50): [True: 508, False: 9.81k] ------------------ 562| 508| { 563| 508| if (0 != Stereo->nCompInv2Abs) ------------------ | Branch (563:13): [True: 41, False: 467] ------------------ 564| 41| { 565| 41| if (pINChI->nFlags & INCHI_FLAG_REL_STEREO) ------------------ | | 121| 41|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ | Branch (565:17): [True: 15, False: 26] ------------------ 566| 15| { 567| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 568| | if (1 < Stereo->nNumberOfStereoCenters) 569| | { 570| | nRet = SP3_REL; 571| | } 572| |#else 573| 15| nRet = SP3_REL; 574| 15|#endif 575| 15| } 576| 26| else if (pINChI->nFlags & INCHI_FLAG_RAC_STEREO) ------------------ | | 122| 26|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (576:22): [True: 21, False: 5] ------------------ 577| 21| { 578| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 579| | if (1 < Stereo->nNumberOfStereoCenters) 580| | { 581| | nRet = SP3_REL; 582| | } 583| |#else 584| 21| nRet = SP3_RAC; 585| 21|#endif 586| 21| } 587| 5| else 588| 5| { 589| 5| nRet = SP3_ABS; 590| 5| } 591| 41| } 592| 467| else 593| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 594| | if (!((pINChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && 1 == Stereo->nNumberOfStereoCenters)) 595| |#endif 596| 467| { 597| 467| nRet = SP3_ONLY; /* SP3_NONE if relative stereo and 1 stereocenter */ 598| 467| } 599| 508| } 600| 390k| return nRet; 601| 390k|} CompINChILayers: 613| 97.5k|{ 614| 97.5k| int ret = 0, num, i, num_H1, num_H2; 615| | 616| 97.5k| const INChI* i1 = NULL; /* Mobile-H layers in Mobile-H sorting order */ 617| 97.5k| const INChI* i2 = NULL; /* Fixed-H layers in Fixed-H sorting order */ 618| | 619| 97.5k| int n1; /* TAUT_YES if tautomeric i1 exists, otherwise TAUT_NON */ 620| | 621| 97.5k| INChI_Stereo* Stereo1, * Stereo2; 622| 97.5k| INChI_Stereo* IsoStereo1, * IsoStereo2; 623| 97.5k| int bRelRac[DIFL_LENGTH]; 624| 97.5k| char* psDifSegs; 625| | 626| 97.5k| n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (626:11): [True: 97.5k, False: 0] | Branch (626:35): [True: 97.5k, False: 0] ------------------ 627| | 628| 97.5k| i1 = p1->pINChI[n1]; 629| 97.5k| i2 = (n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 575| 195k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i2 = (n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (629:11): [True: 97.5k, False: 0] | Branch (629:29): [True: 0, False: 97.5k] ------------------ 630| 97.5k| p2->pINChI[TAUT_NON]->nNumberOfAtoms) ? p2->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p2->pINChI[TAUT_NON]->nNumberOfAtoms) ? p2->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (630:9): [True: 0, False: 0] ------------------ 631| | 632| 97.5k| num_H1 = num_H2 = 0; 633| 97.5k| memset(bRelRac, DIFV_BOTH_EMPTY, sizeof(bRelRac)); /* djb-rwth: memset_s C11/Annex K variant? */ 634| | /*=====================*/ 635| | /*==== /f ======*/ 636| | /*=====================*/ 637| 97.5k| if (i1 && !i1->bDeleted && i1->szHillFormula && i1->szHillFormula[0]) ------------------ | Branch (637:9): [True: 97.5k, False: 0] | Branch (637:15): [True: 97.5k, False: 6] | Branch (637:32): [True: 62.2k, False: 35.2k] | Branch (637:53): [True: 62.2k, False: 0] ------------------ 638| 62.2k| { 639| 62.2k| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 640| 62.2k| if (i2 && !i2->bDeleted && i2->szHillFormula && i2->szHillFormula[0]) ------------------ | Branch (640:13): [True: 0, False: 62.2k] | Branch (640:19): [True: 0, False: 0] | Branch (640:36): [True: 0, False: 0] | Branch (640:57): [True: 0, False: 0] ------------------ 641| 0| { 642| 0| if (!CompareHillFormulasNoH(i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2) && ------------------ | Branch (642:17): [True: 0, False: 0] ------------------ 643| 0| num_H1 == num_H2) ------------------ | Branch (643:17): [True: 0, False: 0] ------------------ 644| 0| { 645| 0| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_EQL2PRECED; 646| 0| } 647| 0| else 648| 0| { 649| 0| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 650| 0| } 651| 0| } 652| 62.2k| else 653| 62.2k| { 654| 62.2k| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (654:49): [True: 0, False: 62.2k] ------------------ 655| 62.2k| } 656| 62.2k| } 657| 35.3k| else 658| 35.3k| { 659| 35.3k| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_BOTH_EMPTY; 660| 35.3k| if (i2 && !i2->bDeleted && i2->szHillFormula && i2->szHillFormula[0]) ------------------ | Branch (660:13): [True: 0, False: 35.3k] | Branch (660:19): [True: 0, False: 0] | Branch (660:36): [True: 0, False: 0] | Branch (660:57): [True: 0, False: 0] ------------------ 661| 0| { 662| 0| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 663| 0| } 664| 35.3k| else 665| 35.3k| { 666| 35.3k| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_BOTH_EMPTY; 667| 35.3k| } 668| 35.3k| } 669| | /*=====================*/ 670| | /*==== /c ======*/ 671| | /*=====================*/ 672| 97.5k| if (i1 && !i1->bDeleted && i1->lenConnTable > 1) ------------------ | Branch (672:9): [True: 97.5k, False: 0] | Branch (672:15): [True: 97.5k, False: 6] | Branch (672:32): [True: 34.2k, False: 63.2k] ------------------ 673| 34.2k| { 674| 34.2k| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 675| 34.2k| } 676| 63.2k| else 677| 63.2k| { 678| 63.2k| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_BOTH_EMPTY; 679| 63.2k| } 680| | /*=====================*/ 681| | /*==== /h ======*/ 682| | /*=====================*/ 683| | /* M: H atoms */ 684| 97.5k| if (i1 && !i1->bDeleted) ------------------ | Branch (684:9): [True: 97.5k, False: 0] | Branch (684:15): [True: 97.5k, False: 6] ------------------ 685| 97.5k| { 686| 97.5k| num_H1 = (i1->lenTautomer > 0 && i1->nTautomer && i1->nTautomer[0]) ? 1 : 0; /* number of t-groups */ ------------------ | Branch (686:19): [True: 1.23k, False: 96.2k] | Branch (686:42): [True: 1.23k, False: 0] | Branch (686:59): [True: 1.23k, False: 0] ------------------ 687| 97.5k| if (!num_H1 && i1->nNum_H) ------------------ | Branch (687:13): [True: 96.2k, False: 1.23k] | Branch (687:24): [True: 96.2k, False: 0] ------------------ 688| 96.2k| { 689| 1.30M| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (689:25): [True: 1.21M, False: 95.5k] ------------------ 690| 1.21M| { /* immobile H */ 691| 1.21M| if (i1->nNum_H[i]) ------------------ | Branch (691:21): [True: 704, False: 1.21M] ------------------ 692| 704| { 693| 704| num_H1 = 1; 694| 704| break; 695| 704| } 696| 1.21M| } 697| 96.2k| } 698| 97.5k| sDifSegs[DIFL_M][DIFS_h_H_ATOMS] |= num_H1 ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (698:45): [True: 1.94k, False: 95.5k] ------------------ 699| 97.5k| } 700| 6| else 701| 6| { 702| 6| sDifSegs[DIFL_M][DIFS_h_H_ATOMS] |= DIFV_BOTH_EMPTY; 703| 6| } 704| | /* F: fixed mobile H */ 705| 97.5k| if (i2 && !i2->bDeleted && i2->nNum_H_fixed) ------------------ | Branch (705:9): [True: 0, False: 97.5k] | Branch (705:15): [True: 0, False: 0] | Branch (705:32): [True: 0, False: 0] ------------------ 706| 0| { 707| 0| num_H2 = 0; 708| 0| if (i1 && !i1->bDeleted) ------------------ | Branch (708:13): [True: 0, False: 0] | Branch (708:19): [True: 0, False: 0] ------------------ 709| 0| { 710| 0| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (710:25): [True: 0, False: 0] ------------------ 711| 0| { 712| 0| if (i2->nNum_H_fixed[i]) ------------------ | Branch (712:21): [True: 0, False: 0] ------------------ 713| 0| { 714| 0| num_H2 = 1; 715| 0| break; 716| 0| } 717| 0| } 718| 0| } 719| 0| sDifSegs[DIFL_F][DIFS_h_H_ATOMS] |= num_H2 ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (719:45): [True: 0, False: 0] ------------------ 720| 0| } 721| 97.5k| else 722| 97.5k| { 723| 97.5k| sDifSegs[DIFL_F][DIFS_h_H_ATOMS] |= DIFV_BOTH_EMPTY; 724| 97.5k| } 725| | /* MI: exchangable isotopic H: see OutputINChI1(), num_iso_H[] */ 726| | 727| | /*=====================*/ 728| | /*==== /q ======*/ 729| | /*=====================*/ 730| 97.5k| psDifSegs = &sDifSegs[DIFL_F][DIFS_q_CHARGE]; 731| 97.5k| if (i1 && !i1->bDeleted) ------------------ | Branch (731:9): [True: 97.5k, False: 0] | Branch (731:15): [True: 97.5k, False: 6] ------------------ 732| 97.5k| { 733| 97.5k| if (i1->nTotalCharge) ------------------ | Branch (733:13): [True: 253, False: 97.2k] ------------------ 734| 253| { 735| 253| sDifSegs[DIFL_M][DIFS_q_CHARGE] |= DIFV_NEQ2PRECED; 736| 253| } 737| 97.2k| else 738| 97.2k| { 739| 97.2k| sDifSegs[DIFL_M][DIFS_q_CHARGE] |= DIFV_BOTH_EMPTY; 740| 97.2k| } 741| 97.5k| if (i2 && !i2->bDeleted) ------------------ | Branch (741:13): [True: 0, False: 97.5k] | Branch (741:19): [True: 0, False: 0] ------------------ 742| 0| { 743| 0| if (i1->nTotalCharge) ------------------ | Branch (743:17): [True: 0, False: 0] ------------------ 744| 0| { 745| 0| if (i1->nTotalCharge == i2->nTotalCharge) ------------------ | Branch (745:21): [True: 0, False: 0] ------------------ 746| 0| { 747| 0| *psDifSegs |= DIFV_EQL2PRECED; 748| 0| } 749| 0| else 750| 0| { 751| 0| if (i2->nTotalCharge) ------------------ | Branch (751:25): [True: 0, False: 0] ------------------ 752| 0| { 753| 0| *psDifSegs |= DIFV_NEQ2PRECED; 754| 0| } 755| 0| else 756| 0| { 757| 0| *psDifSegs |= DIFV_IS_EMPTY; 758| 0| } 759| 0| } 760| 0| } 761| 0| else 762| 0| { 763| 0| if (i2->nTotalCharge) ------------------ | Branch (763:21): [True: 0, False: 0] ------------------ 764| 0| { 765| 0| *psDifSegs |= DIFV_NEQ2PRECED; 766| 0| } 767| 0| else 768| 0| { 769| 0| *psDifSegs |= DIFV_BOTH_EMPTY; 770| 0| } 771| 0| } 772| 0| } 773| 97.5k| else 774| 97.5k| { 775| 97.5k| if (!i2) ------------------ | Branch (775:17): [True: 97.5k, False: 0] ------------------ 776| 97.5k| { 777| 97.5k| if (bFixTranspChargeBug == 1) ------------------ | Branch (777:21): [True: 97.5k, False: 0] ------------------ 778| 97.5k| { 779| | /* bug explanation: 780| | 781| | component #1 is tautomeric, component #2 is not 782| | Mobile-H(#2) > Mobile-H(#1) 783| | Fixed-H(#2) = Mobile-H(#2) < Fixed-H(#1) 784| | 785| | Layer first_charge second_charge 786| | 787| | Mobile-H 0 (comp#1) -1 (comp#2) 788| | Fixed-H none (comp#2) -1 (comp#1) 789| | 790| | v1.01 charge compared decided that charge layers are same and omitted Fixed-H /q layer 791| | 792| | Solution: when component permutation is detected AND fixed-H component does not exist, 793| | compare Mobile-H charge [0 (comp#1) in the example] to the charge of Mobile-H [-1 (comp#2)] 794| | of the component that has none Fixed-H charge 795| | */ 796| | 797| | /* Fixed-H i2 is empty because Fixed-H struct is same as Mobile-H */ 798| 97.5k| if (p1->ord_number != p2->ord_number && /* component order in Fixed-H is different from Mobile-H */ ------------------ | Branch (798:25): [True: 0, False: 97.5k] ------------------ 799| 0| n1 == TAUT_YES && p2->pINChI[TAUT_YES] && !p2->pINChI[TAUT_YES]->bDeleted && ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 == TAUT_YES && p2->pINChI[TAUT_YES] && !p2->pINChI[TAUT_YES]->bDeleted && ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 == TAUT_YES && p2->pINChI[TAUT_YES] && !p2->pINChI[TAUT_YES]->bDeleted && ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (799:25): [True: 0, False: 0] | Branch (799:43): [True: 0, False: 0] | Branch (799:67): [True: 0, False: 0] ------------------ 800| 0| p2->pINChI[TAUT_YES]->nNumberOfAtoms) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (800:25): [True: 0, False: 0] ------------------ 801| 0| { 802| 0| int i2_nTotalCharge = p2->pINChI[TAUT_YES]->nTotalCharge; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 803| | 804| 0| if (i1->nTotalCharge) ------------------ | Branch (804:29): [True: 0, False: 0] ------------------ 805| 0| { 806| 0| if (i1->nTotalCharge == i2_nTotalCharge) ------------------ | Branch (806:33): [True: 0, False: 0] ------------------ 807| 0| { 808| 0| *psDifSegs |= DIFV_EQL2PRECED; 809| 0| } 810| 0| else 811| 0| { 812| 0| if (i2_nTotalCharge) ------------------ | Branch (812:37): [True: 0, False: 0] ------------------ 813| 0| { 814| 0| *psDifSegs |= DIFV_NEQ2PRECED; 815| 0| } 816| 0| else 817| 0| { 818| 0| *psDifSegs |= DIFV_IS_EMPTY; 819| 0| } 820| 0| } 821| 0| } 822| 0| else 823| 0| { 824| 0| if (i2_nTotalCharge) ------------------ | Branch (824:33): [True: 0, False: 0] ------------------ 825| 0| { 826| 0| *psDifSegs |= DIFV_NEQ2PRECED; 827| 0| } 828| 0| else 829| 0| { 830| 0| *psDifSegs |= DIFV_BOTH_EMPTY; 831| 0| } 832| 0| } 833| 0| } 834| 97.5k| else 835| 97.5k| { 836| 97.5k| *psDifSegs |= i1->nTotalCharge ? DIFV_EQL2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (836:39): [True: 253, False: 97.2k] ------------------ 837| 97.5k| } 838| 97.5k| } 839| 0| else /* if (bFixTranspChargeBug==1) */ 840| 0| { 841| 0| *psDifSegs |= i1->nTotalCharge ? DIFV_EQL2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (841:35): [True: 0, False: 0] ------------------ 842| 0| } 843| 97.5k| } 844| 0| else /* if ( !i2 ) { */ 845| 0| { 846| | /* i2 && i2->bDeleted */ 847| 0| *psDifSegs |= i1->nTotalCharge ? DIFV_IS_EMPTY : DIFV_BOTH_EMPTY; ------------------ | Branch (847:31): [True: 0, False: 0] ------------------ 848| 0| } 849| 97.5k| } 850| 97.5k| } 851| 6| else 852| 6| { 853| 6| sDifSegs[DIFL_M][DIFS_q_CHARGE] |= DIFV_BOTH_EMPTY; 854| 6| if (i2 && !i2->bDeleted) ------------------ | Branch (854:13): [True: 0, False: 6] | Branch (854:19): [True: 0, False: 0] ------------------ 855| 0| { 856| 0| if (i2->nTotalCharge) ------------------ | Branch (856:17): [True: 0, False: 0] ------------------ 857| 0| { 858| 0| sDifSegs[DIFL_F][DIFS_q_CHARGE] |= DIFV_NEQ2PRECED; 859| 0| } 860| 0| else 861| 0| { 862| 0| sDifSegs[DIFL_F][DIFS_q_CHARGE] |= DIFV_BOTH_EMPTY; 863| 0| } 864| 0| } 865| 6| } 866| | 867| | 868| | /*************** stereo *****************/ 869| | 870| 97.5k| if (i1 && !i1->bDeleted) ------------------ | Branch (870:9): [True: 97.5k, False: 0] | Branch (870:15): [True: 97.5k, False: 6] ------------------ 871| 97.5k| { 872| 97.5k| Stereo1 = i1->Stereo; 873| 97.5k| IsoStereo1 = i1->StereoIsotopic; 874| 97.5k| } 875| 6| else 876| 6| { 877| 6| Stereo1 = NULL; 878| 6| IsoStereo1 = NULL; 879| 6| } 880| 97.5k| if (i2 && !i2->bDeleted) ------------------ | Branch (880:9): [True: 0, False: 97.5k] | Branch (880:15): [True: 0, False: 0] ------------------ 881| 0| { 882| 0| Stereo2 = i2->Stereo; 883| 0| IsoStereo2 = i2->StereoIsotopic; 884| 0| } 885| 97.5k| else 886| 97.5k| { 887| 97.5k| Stereo2 = NULL; 888| 97.5k| IsoStereo2 = NULL; 889| 97.5k| } 890| | 891| | /*=====================*/ 892| | /*==== /b ======*/ 893| | /*=====================*/ 894| | /* M double bond stereo */ 895| 97.5k| psDifSegs = &sDifSegs[DIFL_M][DIFS_b_SBONDS]; 896| 97.5k| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (896:9): [True: 10.0k, False: 87.5k] | Branch (896:20): [True: 411, False: 9.59k] ------------------ 897| 411| { 898| 411| *psDifSegs |= DIFV_NEQ2PRECED; 899| 411| } 900| 97.0k| else 901| 97.0k| { 902| 97.0k| *psDifSegs |= DIFV_BOTH_EMPTY; 903| 97.0k| } 904| | /* F double bond stereo */ 905| 97.5k| psDifSegs = &sDifSegs[DIFL_F][DIFS_b_SBONDS]; 906| 97.5k| if (Stereo2 && Stereo2->nNumberOfStereoBonds) ------------------ | Branch (906:9): [True: 0, False: 97.5k] | Branch (906:20): [True: 0, False: 0] ------------------ 907| 0| { 908| 0| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (908:13): [True: 0, False: 0] | Branch (908:24): [True: 0, False: 0] ------------------ 909| 0| { 910| 0| if (Eql_INChI_Stereo(Stereo1, EQL_SP2, Stereo2, EQL_SP2, 0)) ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ if (Eql_INChI_Stereo(Stereo1, EQL_SP2, Stereo2, EQL_SP2, 0)) ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (910:17): [True: 0, False: 0] ------------------ 911| 0| { 912| 0| *psDifSegs |= DIFV_EQL2PRECED; 913| 0| } 914| 0| else 915| 0| { 916| 0| *psDifSegs |= DIFV_NEQ2PRECED; 917| 0| } 918| 0| } 919| 0| else 920| 0| { 921| 0| *psDifSegs |= DIFV_NEQ2PRECED; 922| 0| } 923| 0| } 924| 97.5k| else 925| 97.5k| { 926| 97.5k| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (926:13): [True: 10.0k, False: 87.5k] | Branch (926:24): [True: 411, False: 9.59k] ------------------ 927| 411| { 928| 411| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (928:27): [True: 0, False: 411] ------------------ 929| 411| } 930| 97.0k| else 931| 97.0k| { 932| 97.0k| *psDifSegs |= DIFV_BOTH_EMPTY; 933| 97.0k| } 934| 97.5k| } 935| | 936| | /* MI double bond stereo */ 937| 97.5k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_b_SBONDS]; 938| 97.5k| if (IsoStereo1 && IsoStereo1->nNumberOfStereoBonds) ------------------ | Branch (938:9): [True: 320, False: 97.1k] | Branch (938:23): [True: 81, False: 239] ------------------ 939| 81| { 940| 81| if (Eql_INChI_Stereo(IsoStereo1, EQL_SP2, Stereo1, EQL_SP2, 0)) ------------------ | | 477| 81|#define EQL_SP2 8 ------------------ if (Eql_INChI_Stereo(IsoStereo1, EQL_SP2, Stereo1, EQL_SP2, 0)) ------------------ | | 477| 81|#define EQL_SP2 8 ------------------ | Branch (940:13): [True: 41, False: 40] ------------------ 941| 41| { 942| 41| *psDifSegs |= DIFV_EQL2PRECED; 943| 41| } 944| 40| else 945| 40| { 946| 40| *psDifSegs |= DIFV_NEQ2PRECED; 947| 40| } 948| 81| } 949| 97.4k| else 950| 97.4k| { 951| 97.4k| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (951:13): [True: 9.96k, False: 87.4k] | Branch (951:24): [True: 368, False: 9.59k] ------------------ 952| 368| { 953| 368| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 954| 368| } 955| 97.0k| else 956| 97.0k| { 957| 97.0k| *psDifSegs |= DIFV_BOTH_EMPTY; 958| 97.0k| } 959| 97.4k| } 960| | 961| | /* FI double bond stereo */ 962| 97.5k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_b_SBONDS]; 963| 97.5k| if (IsoStereo2 && IsoStereo2->nNumberOfStereoBonds) ------------------ | Branch (963:9): [True: 0, False: 97.5k] | Branch (963:23): [True: 0, False: 0] ------------------ 964| 0| { 965| 0| if (Eql_INChI_Stereo(IsoStereo2, EQL_SP2, Stereo2, EQL_SP2, 0)) ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ if (Eql_INChI_Stereo(IsoStereo2, EQL_SP2, Stereo2, EQL_SP2, 0)) ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (965:13): [True: 0, False: 0] ------------------ 966| 0| { 967| 0| *psDifSegs |= DIFV_EQL2PRECED; 968| 0| } 969| 0| else 970| 0| { 971| 0| if (!(Stereo1 && Stereo1->nNumberOfStereoBonds) && ------------------ | Branch (971:19): [True: 0, False: 0] | Branch (971:30): [True: 0, False: 0] ------------------ 972| 0| !(Stereo2 && Stereo2->nNumberOfStereoBonds) && ------------------ | Branch (972:19): [True: 0, False: 0] | Branch (972:30): [True: 0, False: 0] ------------------ 973| 0| Eql_INChI_Stereo(IsoStereo2, EQL_SP2, IsoStereo1, EQL_SP2, 0)) ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo(IsoStereo2, EQL_SP2, IsoStereo1, EQL_SP2, 0)) ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (973:17): [True: 0, False: 0] ------------------ 974| 0| { 975| 0| *psDifSegs |= DIFV_FI_EQ_MI; 976| 0| } 977| 0| else 978| 0| { 979| 0| *psDifSegs |= DIFV_NEQ2PRECED; 980| 0| } 981| 0| } 982| 0| } 983| 97.5k| else 984| 97.5k| { 985| | /* the solution table for FI stereo, 986| | in case of FI stereo is empty 987| | E = segment is empty, NE = not empty 988| | +==============================+ 989| | | M | MI | F | result | 990| | +=====+=====+=====+============+ 991| | | E | E | E | both empty | 992| | +-----+-----+-----+------------+ 993| | | NE | E | E | both empty | 994| | +-----+-----+-----+------------+ 995| | | E | NE | E | is empty | 996| | +-----+-----+-----+------------+ 997| | | NE | NE | E | both empty | 998| | +-----+-----+-----+------------+ 999| | | E | E | NE | is empty | 1000| | +-----+-----+-----+------------+ 1001| | | NE | E | NE | is empty | 1002| | +-----+-----+-----+------------+ 1003| | | E | NE | NE | is empty | 1004| | +-----+-----+-----+------------+ 1005| | | NE | NE | ME | is empty | 1006| | +==============================+ 1007| | */ 1008| 97.5k| if (Stereo2 && Stereo2->nNumberOfStereoBonds) ------------------ | Branch (1008:13): [True: 0, False: 97.5k] | Branch (1008:24): [True: 0, False: 0] ------------------ 1009| 0| { 1010| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1011| 0| } 1012| 97.5k| else 1013| 97.5k| if (IsoStereo1 && IsoStereo1->nNumberOfStereoBonds && ------------------ | Branch (1013:17): [True: 320, False: 97.1k] | Branch (1013:31): [True: 81, False: 239] ------------------ 1014| 81| !(Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (1014:19): [True: 43, False: 38] | Branch (1014:30): [True: 43, False: 0] ------------------ 1015| 97.5k| ) 1016| 38| { 1017| 38| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1017:31): [True: 0, False: 38] ------------------ 1018| 38| } 1019| 97.4k| else 1020| 97.4k| { 1021| 97.4k| *psDifSegs |= DIFV_BOTH_EMPTY; 1022| 97.4k| } 1023| 97.5k| } 1024| | 1025| | /*==================================*/ 1026| | /*==== /t, /m, /s for M ======*/ 1027| | /*==================================*/ 1028| | /* M sp3 stereo */ 1029| 97.5k| bRelRac[DIFL_M] = GetSp3RelRacAbs(i1, Stereo1); /* Mobile-H */ 1030| 97.5k| bRelRac[DIFL_MI] = GetSp3RelRacAbs(i1, IsoStereo1); 1031| 97.5k| bRelRac[DIFL_F] = GetSp3RelRacAbs(i2, Stereo2); /* Fixed-H */ 1032| 97.5k| bRelRac[DIFL_FI] = GetSp3RelRacAbs(i2, IsoStereo2); 1033| 97.5k| if (SP3_NONE != bRelRac[DIFL_M]) ------------------ | Branch (1033:9): [True: 382, False: 97.1k] ------------------ 1034| 382| { 1035| 382| sDifSegs[DIFL_M][DIFS_t_SATOMS] |= (bRelRac[DIFL_M] & SP3_ANY) ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1035:44): [True: 382, False: 0] ------------------ 1036| 382| sDifSegs[DIFL_M][DIFS_m_SP3INV] |= (bRelRac[DIFL_M] & SP3_ABS) ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1036:44): [True: 3, False: 379] ------------------ 1037| 382| sDifSegs[DIFL_M][DIFS_s_STYPE] |= (bRelRac[DIFL_M] & SP3_TYPE) ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1037:43): [True: 15, False: 367] ------------------ 1038| 382| } 1039| 97.1k| else 1040| 97.1k| { 1041| 97.1k| sDifSegs[DIFL_M][DIFS_t_SATOMS] |= DIFV_BOTH_EMPTY; 1042| 97.1k| sDifSegs[DIFL_M][DIFS_m_SP3INV] |= DIFV_BOTH_EMPTY; 1043| 97.1k| sDifSegs[DIFL_M][DIFS_s_STYPE] |= DIFV_BOTH_EMPTY; 1044| 97.1k| } 1045| | 1046| | /*=====================*/ 1047| | /*==== /t ======*/ 1048| | /*=====================*/ 1049| | /* F sp3 stereo */ 1050| 97.5k| psDifSegs = &sDifSegs[DIFL_F][DIFS_t_SATOMS]; 1051| 97.5k| if (SP3_ANY & bRelRac[DIFL_F]) ------------------ | Branch (1051:9): [True: 0, False: 97.5k] ------------------ 1052| 0| { 1053| 0| if (Eql_INChI_Stereo(Stereo2, EQL_SP3, Stereo1, EQL_SP3, 0)) ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ if (Eql_INChI_Stereo(Stereo2, EQL_SP3, Stereo1, EQL_SP3, 0)) ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ | Branch (1053:13): [True: 0, False: 0] ------------------ 1054| 0| { 1055| 0| *psDifSegs |= DIFV_EQL2PRECED; 1056| 0| } 1057| 0| else 1058| 0| { 1059| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1060| 0| } 1061| 0| } 1062| 97.5k| else 1063| 97.5k| { 1064| 97.5k| if (SP3_ANY & bRelRac[DIFL_M]) ------------------ | Branch (1064:13): [True: 382, False: 97.1k] ------------------ 1065| 382| { 1066| 382| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1066:27): [True: 0, False: 382] ------------------ 1067| 382| } 1068| 97.1k| else 1069| 97.1k| { 1070| 97.1k| *psDifSegs |= DIFV_BOTH_EMPTY; 1071| 97.1k| } 1072| 97.5k| } 1073| | 1074| | /* MI sp3 stereo */ 1075| 97.5k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_t_SATOMS]; 1076| 97.5k| if (SP3_ANY & bRelRac[DIFL_MI]) ------------------ | Branch (1076:9): [True: 126, False: 97.3k] ------------------ 1077| 126| { 1078| 126| if (Eql_INChI_Stereo(IsoStereo1, EQL_SP3, Stereo1, EQL_SP3, 0)) ------------------ | | 475| 126|#define EQL_SP3 2 ------------------ if (Eql_INChI_Stereo(IsoStereo1, EQL_SP3, Stereo1, EQL_SP3, 0)) ------------------ | | 475| 126|#define EQL_SP3 2 ------------------ | Branch (1078:13): [True: 47, False: 79] ------------------ 1079| 47| { 1080| 47| *psDifSegs |= DIFV_EQL2PRECED; 1081| 47| } 1082| 79| else 1083| 79| { 1084| 79| *psDifSegs |= DIFV_NEQ2PRECED; 1085| 79| } 1086| 126| } 1087| 97.3k| else 1088| 97.3k| { 1089| 97.3k| if (SP3_ANY & bRelRac[DIFL_M]) ------------------ | Branch (1089:13): [True: 324, False: 97.0k] ------------------ 1090| 324| { 1091| 324| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1092| 324| } 1093| 97.0k| else 1094| 97.0k| { 1095| 97.0k| *psDifSegs |= DIFV_BOTH_EMPTY; 1096| 97.0k| } 1097| 97.3k| } 1098| | 1099| | /* FI sp3 stereo */ 1100| 97.5k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_t_SATOMS]; 1101| 97.5k| if (SP3_ANY & bRelRac[DIFL_FI]) ------------------ | Branch (1101:9): [True: 0, False: 97.5k] ------------------ 1102| 0| { 1103| 0| if (Eql_INChI_Stereo(IsoStereo2, EQL_SP3, Stereo2, EQL_SP3, 0)) ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ if (Eql_INChI_Stereo(IsoStereo2, EQL_SP3, Stereo2, EQL_SP3, 0)) ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ | Branch (1103:13): [True: 0, False: 0] ------------------ 1104| 0| { 1105| 0| *psDifSegs |= DIFV_EQL2PRECED; 1106| 0| } 1107| 0| else 1108| 0| { 1109| 0| if (!(SP3_ANY & bRelRac[DIFL_M]) && ------------------ | Branch (1109:17): [True: 0, False: 0] ------------------ 1110| 0| !(SP3_ANY & bRelRac[DIFL_F]) && ------------------ | Branch (1110:17): [True: 0, False: 0] ------------------ 1111| 0| Eql_INChI_Stereo(IsoStereo2, EQL_SP3, IsoStereo1, EQL_SP3, 0)) ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo(IsoStereo2, EQL_SP3, IsoStereo1, EQL_SP3, 0)) ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ | Branch (1111:17): [True: 0, False: 0] ------------------ 1112| 0| { 1113| 0| *psDifSegs |= DIFV_FI_EQ_MI; 1114| 0| } 1115| 0| else 1116| 0| { 1117| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1118| 0| } 1119| 0| } 1120| 0| } 1121| 97.5k| else /* similar to /b */ 1122| 97.5k| if ((SP3_ANY & bRelRac[DIFL_F])) ------------------ | Branch (1122:13): [True: 0, False: 97.5k] ------------------ 1123| 0| { 1124| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1125| 0| } 1126| 97.5k| else 1127| 97.5k| { 1128| 97.5k| if ((SP3_ANY & bRelRac[DIFL_MI]) && !(SP3_ANY & bRelRac[DIFL_M])) ------------------ | Branch (1128:17): [True: 126, False: 97.3k] | Branch (1128:49): [True: 68, False: 58] ------------------ 1129| 68| { 1130| 68| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1130:31): [True: 0, False: 68] ------------------ 1131| 68| } 1132| 97.4k| else 1133| 97.4k| { 1134| 97.4k| *psDifSegs |= DIFV_BOTH_EMPTY; 1135| 97.4k| } 1136| 97.5k| } 1137| | 1138| | /*=====================*/ 1139| | /*==== /m ======*/ 1140| | /*=====================*/ 1141| | /* F sp3 abs stereo inversion */ 1142| 97.5k| psDifSegs = &sDifSegs[DIFL_F][DIFS_m_SP3INV]; 1143| 97.5k| if (bRelRac[DIFL_F] & SP3_ABS) ------------------ | Branch (1143:9): [True: 0, False: 97.5k] ------------------ 1144| 0| { 1145| | /* the order of || operands below is critically important: || is not a commutative operation */ 1146| 0| if (!(bRelRac[DIFL_M] & SP3_ABS) || Stereo2->nCompInv2Abs != Stereo1->nCompInv2Abs) ------------------ | Branch (1146:13): [True: 0, False: 0] | Branch (1146:45): [True: 0, False: 0] ------------------ 1147| 0| { 1148| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1149| 0| } 1150| 0| else 1151| 0| { 1152| 0| *psDifSegs |= DIFV_EQL2PRECED; 1153| 0| } 1154| 0| } 1155| 97.5k| else 1156| 97.5k| { 1157| 97.5k| if (bRelRac[DIFL_M] & SP3_ABS) ------------------ | Branch (1157:13): [True: 3, False: 97.5k] ------------------ 1158| 3| { 1159| 3| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1159:27): [True: 0, False: 3] ------------------ 1160| 3| } 1161| 97.5k| else 1162| 97.5k| { 1163| 97.5k| *psDifSegs |= DIFV_BOTH_EMPTY; 1164| 97.5k| } 1165| 97.5k| } 1166| | 1167| | /* MI sp3 abs stereo inversion */ 1168| 97.5k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_m_SP3INV]; 1169| 97.5k| if (SP3_ABS & bRelRac[DIFL_MI]) ------------------ | Branch (1169:9): [True: 2, False: 97.5k] ------------------ 1170| 2| { 1171| 2| if ((SP3_ABS & bRelRac[DIFL_M]) && IsoStereo1->nCompInv2Abs == Stereo1->nCompInv2Abs) ------------------ | Branch (1171:13): [True: 0, False: 2] | Branch (1171:44): [True: 0, False: 0] ------------------ 1172| 0| { 1173| 0| *psDifSegs |= DIFV_EQL2PRECED; 1174| 0| } 1175| 2| else 1176| 2| { 1177| 2| *psDifSegs |= DIFV_NEQ2PRECED; 1178| 2| } 1179| 2| } 1180| 97.5k| else 1181| 97.5k| { 1182| 97.5k| if (SP3_ABS & bRelRac[DIFL_M]) ------------------ | Branch (1182:13): [True: 3, False: 97.5k] ------------------ 1183| 3| { 1184| 3| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1185| 3| } 1186| 97.5k| else 1187| 97.5k| { 1188| 97.5k| *psDifSegs |= DIFV_BOTH_EMPTY; 1189| 97.5k| } 1190| 97.5k| } 1191| | 1192| | /* FI sp3 abs stereo inversion */ 1193| 97.5k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_m_SP3INV]; 1194| 97.5k| if (SP3_ABS & bRelRac[DIFL_FI]) ------------------ | Branch (1194:9): [True: 0, False: 97.5k] ------------------ 1195| 0| { 1196| 0| if ((SP3_ABS & bRelRac[DIFL_F]) && IsoStereo2->nCompInv2Abs == Stereo2->nCompInv2Abs) ------------------ | Branch (1196:13): [True: 0, False: 0] | Branch (1196:44): [True: 0, False: 0] ------------------ 1197| 0| { 1198| 0| *psDifSegs |= DIFV_EQL2PRECED; 1199| 0| } 1200| 0| else 1201| 0| { 1202| 0| if (!(SP3_ABS & bRelRac[DIFL_M]) && ------------------ | Branch (1202:17): [True: 0, False: 0] ------------------ 1203| 0| !(SP3_ABS & bRelRac[DIFL_F]) && ------------------ | Branch (1203:17): [True: 0, False: 0] ------------------ 1204| 0| (SP3_ABS & bRelRac[DIFL_MI]) && /* make sure IsoStereo1 != NULL */ ------------------ | Branch (1204:17): [True: 0, False: 0] ------------------ 1205| 0| IsoStereo2->nCompInv2Abs == IsoStereo1->nCompInv2Abs) ------------------ | Branch (1205:17): [True: 0, False: 0] ------------------ 1206| 0| { 1207| 0| *psDifSegs |= DIFV_FI_EQ_MI; 1208| 0| } 1209| 0| else 1210| 0| { 1211| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1212| 0| } 1213| 0| } 1214| 0| } 1215| | 1216| 97.5k| else 1217| 97.5k| { 1218| | /* similar to /b */ 1219| | /* the order of || operands below is critically important: || is no a commutative operation */ 1220| 97.5k| if ((SP3_ABS & bRelRac[DIFL_F])) ------------------ | Branch (1220:13): [True: 0, False: 97.5k] ------------------ 1221| 0| { 1222| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1223| 0| } 1224| 97.5k| else 1225| 97.5k| { 1226| 97.5k| if ((SP3_ABS & bRelRac[DIFL_MI]) && !(SP3_ABS & bRelRac[DIFL_M])) ------------------ | Branch (1226:17): [True: 2, False: 97.5k] | Branch (1226:49): [True: 2, False: 0] ------------------ 1227| 2| { 1228| 2| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1228:31): [True: 0, False: 2] ------------------ 1229| 2| } 1230| 97.5k| else 1231| 97.5k| { 1232| 97.5k| *psDifSegs |= DIFV_BOTH_EMPTY; 1233| 97.5k| } 1234| 97.5k| } 1235| 97.5k| } 1236| | 1237| | /*=====================*/ 1238| | /*==== /s ======*/ 1239| | /*=====================*/ 1240| | /* F sp3 stereo type */ 1241| 97.5k| psDifSegs = &sDifSegs[DIFL_F][DIFS_s_STYPE]; 1242| 97.5k| if (bRelRac[DIFL_F] & SP3_TYPE) ------------------ | Branch (1242:9): [True: 0, False: 97.5k] ------------------ 1243| 0| { 1244| 0| if ((bRelRac[DIFL_F] & SP3_TYPE) == (bRelRac[DIFL_M] & SP3_TYPE)) ------------------ | Branch (1244:13): [True: 0, False: 0] ------------------ 1245| 0| { 1246| 0| *psDifSegs |= DIFV_EQL2PRECED; 1247| 0| } 1248| 0| else 1249| 0| { 1250| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1251| 0| } 1252| 0| } 1253| 97.5k| else 1254| 97.5k| { 1255| 97.5k| if (bRelRac[DIFL_M] & SP3_TYPE) ------------------ | Branch (1255:13): [True: 15, False: 97.4k] ------------------ 1256| 15| { 1257| 15| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1257:27): [True: 0, False: 15] ------------------ 1258| 15| } 1259| 97.4k| else 1260| 97.4k| { 1261| 97.4k| *psDifSegs |= DIFV_BOTH_EMPTY; 1262| 97.4k| } 1263| 97.5k| } 1264| | 1265| | /* MI sp3 stereo type */ 1266| 97.5k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_s_STYPE]; 1267| 97.5k| if (SP3_TYPE & bRelRac[DIFL_MI]) ------------------ | Branch (1267:9): [True: 26, False: 97.4k] ------------------ 1268| 26| { 1269| 26| if ((SP3_TYPE & bRelRac[DIFL_MI]) == (SP3_TYPE & bRelRac[DIFL_M])) ------------------ | Branch (1269:13): [True: 0, False: 26] ------------------ 1270| 0| { 1271| 0| *psDifSegs |= DIFV_EQL2PRECED; 1272| 0| } 1273| 26| else 1274| 26| { 1275| 26| *psDifSegs |= DIFV_NEQ2PRECED; 1276| 26| } 1277| 26| } 1278| 97.4k| else 1279| 97.4k| { 1280| 97.4k| if (SP3_TYPE & bRelRac[DIFL_M]) ------------------ | Branch (1280:13): [True: 15, False: 97.4k] ------------------ 1281| 15| { 1282| 15| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1283| 15| } 1284| 97.4k| else 1285| 97.4k| { 1286| 97.4k| *psDifSegs |= DIFV_BOTH_EMPTY; 1287| 97.4k| } 1288| 97.4k| } 1289| | 1290| | /* FI sp3 stereo type */ 1291| 97.5k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_s_STYPE]; 1292| 97.5k| if (SP3_TYPE & bRelRac[DIFL_FI]) ------------------ | Branch (1292:9): [True: 0, False: 97.5k] ------------------ 1293| 0| { 1294| 0| if ((SP3_TYPE & bRelRac[DIFL_FI]) == (SP3_TYPE & bRelRac[DIFL_F])) ------------------ | Branch (1294:13): [True: 0, False: 0] ------------------ 1295| 0| { 1296| 0| *psDifSegs |= DIFV_EQL2PRECED; 1297| 0| } 1298| 0| else 1299| 0| { 1300| 0| if (!(SP3_TYPE & bRelRac[DIFL_M]) && ------------------ | Branch (1300:17): [True: 0, False: 0] ------------------ 1301| 0| !(SP3_TYPE & bRelRac[DIFL_F]) && ------------------ | Branch (1301:17): [True: 0, False: 0] ------------------ 1302| 0| (SP3_TYPE & bRelRac[DIFL_MI])) ------------------ | Branch (1302:17): [True: 0, False: 0] ------------------ 1303| 0| { 1304| 0| *psDifSegs |= DIFV_FI_EQ_MI; 1305| 0| } 1306| 0| else 1307| 0| { 1308| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1309| 0| } 1310| 0| } 1311| 0| } 1312| 97.5k| else 1313| 97.5k| { 1314| | /* similar to /b */ 1315| | /* the order of || operands below is critically important: || is not a commutative operation */ 1316| 97.5k| if ((SP3_TYPE & bRelRac[DIFL_F])) ------------------ | Branch (1316:13): [True: 0, False: 97.5k] ------------------ 1317| 0| { 1318| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1319| 0| } 1320| 97.5k| else 1321| 97.5k| { 1322| 97.5k| if ((SP3_TYPE & bRelRac[DIFL_MI]) && !(SP3_TYPE & bRelRac[DIFL_M])) ------------------ | Branch (1322:17): [True: 26, False: 97.4k] | Branch (1322:50): [True: 26, False: 0] ------------------ 1323| 26| { 1324| 26| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1324:31): [True: 0, False: 26] ------------------ 1325| 26| } 1326| 97.4k| else 1327| 97.4k| { 1328| 97.4k| *psDifSegs |= DIFV_BOTH_EMPTY; 1329| 97.4k| } 1330| 97.5k| } 1331| 97.5k| } 1332| | 1333| | /*=====================*/ 1334| | /*==== /o ======*/ 1335| | /*=====================*/ 1336| 97.5k| if (p1 && p2 && p1->ord_number != p2->ord_number) ------------------ | Branch (1336:9): [True: 97.5k, False: 0] | Branch (1336:15): [True: 97.5k, False: 0] | Branch (1336:21): [True: 0, False: 97.5k] ------------------ 1337| 0| { 1338| 0| sDifSegs[DIFL_F][DIFS_o_TRANSP] |= DIFV_NEQ2PRECED; 1339| 0| } 1340| | /*=====================*/ 1341| | /*==== /i ======*/ 1342| | /*=====================*/ 1343| | 1344| | /* M isotopic atoms */ 1345| 97.5k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_i_IATOMS]; 1346| 97.5k| if (i1 && !i1->bDeleted && (i1->nNumberOfIsotopicAtoms || i1->nNumberOfIsotopicTGroups)) ------------------ | Branch (1346:9): [True: 97.5k, False: 0] | Branch (1346:15): [True: 97.5k, False: 6] | Branch (1346:33): [True: 628, False: 96.8k] | Branch (1346:63): [True: 0, False: 96.8k] ------------------ 1347| 628| { 1348| 628| *psDifSegs |= DIFV_NEQ2PRECED; 1349| 628| } 1350| 96.8k| else 1351| 96.8k| { 1352| 96.8k| *psDifSegs |= DIFV_BOTH_EMPTY; 1353| 96.8k| } 1354| | /* F isotopic atoms */ 1355| 97.5k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_i_IATOMS]; 1356| 97.5k| if (i2 && !i2->bDeleted) ------------------ | Branch (1356:9): [True: 0, False: 97.5k] | Branch (1356:15): [True: 0, False: 0] ------------------ 1357| 0| { 1358| 0| if (i2->nNumberOfIsotopicAtoms || i2->nNumberOfIsotopicTGroups) ------------------ | Branch (1358:13): [True: 0, False: 0] | Branch (1358:43): [True: 0, False: 0] ------------------ 1359| 0| { 1360| 0| if (!i1 || i1->bDeleted || ------------------ | Branch (1360:17): [True: 0, False: 0] | Branch (1360:24): [True: 0, False: 0] ------------------ 1361| 0| i2->nNumberOfIsotopicAtoms != i1->nNumberOfIsotopicAtoms || ------------------ | Branch (1361:17): [True: 0, False: 0] ------------------ 1362| 0| i2->nNumberOfIsotopicTGroups != i1->nNumberOfIsotopicTGroups) ------------------ | Branch (1362:17): [True: 0, False: 0] ------------------ 1363| 0| { 1364| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1365| 0| } 1366| 0| else 1367| 0| { 1368| 0| int diff; 1369| 0| num = i1->nNumberOfIsotopicAtoms; 1370| 0| diff = 0; 1371| 0| for (i = 0; i < num; i++) ------------------ | Branch (1371:29): [True: 0, False: 0] ------------------ 1372| 0| { 1373| | /* compare isotopic atoms */ 1374| 0| if ((diff = (int)i2->IsotopicAtom[i].nAtomNumber - (int)i1->IsotopicAtom[i].nAtomNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1374:25): [True: 0, False: 0] ------------------ 1375| 0| { 1376| 0| break; 1377| 0| } 1378| 0| if ((diff = (int)i2->IsotopicAtom[i].nIsoDifference - (int)i1->IsotopicAtom[i].nIsoDifference)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1378:25): [True: 0, False: 0] ------------------ 1379| 0| { 1380| 0| break; 1381| 0| } 1382| | /* compare isotopic H */ 1383| 0| if ((diff = (int)i2->IsotopicAtom[i].nNum_T - (int)i1->IsotopicAtom[i].nNum_T)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1383:25): [True: 0, False: 0] ------------------ 1384| 0| { 1385| 0| break; 1386| 0| } 1387| 0| if ((diff = (int)i2->IsotopicAtom[i].nNum_D - (int)i1->IsotopicAtom[i].nNum_D)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1387:25): [True: 0, False: 0] ------------------ 1388| 0| { 1389| 0| break; 1390| 0| } 1391| 0| if ((diff = (int)i2->IsotopicAtom[i].nNum_H - (int)i1->IsotopicAtom[i].nNum_H)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1391:25): [True: 0, False: 0] ------------------ 1392| 0| { 1393| 0| break; 1394| 0| } 1395| 0| } 1396| 0| if (!diff) ------------------ | Branch (1396:21): [True: 0, False: 0] ------------------ 1397| 0| { 1398| 0| num = i1->nNumberOfIsotopicTGroups; 1399| 0| for (i = 0; i < num; i++) ------------------ | Branch (1399:33): [True: 0, False: 0] ------------------ 1400| 0| { 1401| 0| if ((diff = (int)i2->IsotopicTGroup[i].nTGroupNumber - (int)i1->IsotopicTGroup[i].nTGroupNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1401:29): [True: 0, False: 0] ------------------ 1402| 0| { 1403| 0| break; 1404| 0| } 1405| 0| if ((diff = (int)i2->IsotopicTGroup[i].nNum_T - (int)i1->IsotopicTGroup[i].nNum_T)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1405:29): [True: 0, False: 0] ------------------ 1406| 0| { 1407| 0| break; 1408| 0| } 1409| 0| if ((diff = (int)i2->IsotopicTGroup[i].nNum_D - (int)i1->IsotopicTGroup[i].nNum_D)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1409:29): [True: 0, False: 0] ------------------ 1410| 0| { 1411| 0| return diff; 1412| 0| } 1413| 0| if ((diff = (int)i2->IsotopicTGroup[i].nNum_H - (int)i1->IsotopicTGroup[i].nNum_H)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1413:29): [True: 0, False: 0] ------------------ 1414| 0| { 1415| 0| break; 1416| 0| } 1417| 0| } 1418| 0| } 1419| 0| *psDifSegs |= diff ? DIFV_NEQ2PRECED : DIFV_FI_EQ_MI; ------------------ | Branch (1419:31): [True: 0, False: 0] ------------------ 1420| 0| } 1421| 0| } 1422| 0| else 1423| 0| { 1424| 0| if (i1 && !i1->bDeleted && (i1->nNumberOfIsotopicAtoms || i1->nNumberOfIsotopicTGroups)) ------------------ | Branch (1424:17): [True: 0, False: 0] | Branch (1424:23): [True: 0, False: 0] | Branch (1424:41): [True: 0, False: 0] | Branch (1424:71): [True: 0, False: 0] ------------------ 1425| 0| { 1426| 0| *psDifSegs |= DIFV_IS_EMPTY; 1427| 0| } 1428| 0| } 1429| 0| } 1430| 97.5k| else 1431| 97.5k| { 1432| 97.5k| if (!i2) ------------------ | Branch (1432:13): [True: 97.5k, False: 0] ------------------ 1433| 97.5k| { 1434| 97.5k| if (i1 && !i1->bDeleted && (i1->nNumberOfIsotopicAtoms || i1->nNumberOfIsotopicTGroups)) ------------------ | Branch (1434:17): [True: 97.5k, False: 0] | Branch (1434:23): [True: 97.5k, False: 6] | Branch (1434:41): [True: 628, False: 96.8k] | Branch (1434:71): [True: 0, False: 96.8k] ------------------ 1435| 628| { 1436| 628| *psDifSegs |= DIFV_EQL2PRECED; 1437| 628| } 1438| 96.8k| else 1439| 96.8k| { 1440| 96.8k| *psDifSegs |= DIFV_BOTH_EMPTY; 1441| 96.8k| } 1442| 97.5k| } 1443| 97.5k| } 1444| | 1445| 97.5k| return ret; 1446| 97.5k|} INChI_SegmentAction: 1451| 44.8k|{ 1452| 44.8k| if (!(cDifSegs & DIFV_OUTPUT_OMIT_F)) ------------------ | Branch (1452:9): [True: 39.6k, False: 5.20k] ------------------ 1453| 39.6k| { 1454| 39.6k| return INCHI_SEGM_OMIT; 1455| 39.6k| } 1456| 5.20k| if ((cDifSegs & DIFV_OUTPUT_EMPTY_T) && !(cDifSegs & DIFV_OUTPUT_EMPTY_F)) ------------------ | Branch (1456:9): [True: 188, False: 5.01k] | Branch (1456:45): [True: 188, False: 0] ------------------ 1457| 188| { 1458| 188| return INCHI_SEGM_EMPTY; 1459| 188| } 1460| 5.01k| if ((cDifSegs & DIFV_OUTPUT_FILL_T)) ------------------ | Branch (1460:9): [True: 5.01k, False: 0] ------------------ 1461| 5.01k| { 1462| 5.01k| return INCHI_SEGM_FILL; 1463| 5.01k| } 1464| | 1465| 0| return INCHI_SEGM_OMIT; /* the control flow shoul never reach this point */ 1466| 5.01k|} MarkUnusedAndEmptyLayers: 1490| 5.02k|{ 1491| 5.02k| int i, nLayer, sBits, nFirstSegm; 1492| 5.02k|#define nFirstFmlSegm DIFS_f_FORMULA 1493| 5.02k|#define nFirstIsoSegm DIFS_i_IATOMS 1494| | /* FI */ 1495| 5.02k| nLayer = DIFL_FI; 1496| 5.02k| nFirstSegm = nFirstIsoSegm; ------------------ | | 1493| 5.02k|#define nFirstIsoSegm DIFS_i_IATOMS ------------------ 1497| 5.02k| sBits = 0; 1498| 60.3k| for (i = 0; i < DIFS_idf_LENGTH; i++) ------------------ | Branch (1498:17): [True: 55.2k, False: 5.02k] ------------------ 1499| 55.2k| { 1500| 55.2k| sBits |= sDifSegs[nLayer][i]; 1501| 55.2k| } 1502| 5.02k| if (!(sBits & DIFV_OUTPUT_OMIT_F)) ------------------ | Branch (1502:9): [True: 5.02k, False: 0] ------------------ 1503| 5.02k| { 1504| | /* Omit the FI layer */ 1505| 5.02k| memset(sDifSegs[nLayer], DIFV_BOTH_EMPTY, DIFS_idf_LENGTH); /* djb-rwth: memset_s C11/Annex K variant? */ 1506| 5.02k| } 1507| 0| else 1508| 0| { 1509| 0| if (sDifSegs[nLayer][nFirstSegm] == DIFV_BOTH_EMPTY || ------------------ | Branch (1509:13): [True: 0, False: 0] ------------------ 1510| 0| !(sDifSegs[nLayer][nFirstSegm] & DIFV_OUTPUT_OMIT_F)) ------------------ | Branch (1510:13): [True: 0, False: 0] ------------------ 1511| 0| { 1512| 0| sDifSegs[nLayer][nFirstSegm] = DIFV_IS_EMPTY; 1513| 0| } 1514| 0| } 1515| | 1516| | /* MI */ 1517| 5.02k| nLayer = DIFL_MI; 1518| 5.02k| nFirstSegm = nFirstIsoSegm; ------------------ | | 1493| 5.02k|#define nFirstIsoSegm DIFS_i_IATOMS ------------------ 1519| 5.02k| sBits = 0; 1520| 60.3k| for (i = 0; i < DIFS_idf_LENGTH; i++) ------------------ | Branch (1520:17): [True: 55.2k, False: 5.02k] ------------------ 1521| 55.2k| { 1522| 55.2k| sBits |= sDifSegs[nLayer][i]; 1523| 55.2k| } 1524| 5.02k| if (!(sBits & DIFV_OUTPUT_OMIT_F)) ------------------ | Branch (1524:9): [True: 4.48k, False: 545] ------------------ 1525| 4.48k| { 1526| | /* Omit the MI layer */ 1527| 4.48k| memset(sDifSegs[nLayer], DIFV_BOTH_EMPTY, DIFS_idf_LENGTH); /* djb-rwth: memset_s C11/Annex K variant? */ 1528| 4.48k| } 1529| 545| else 1530| 545| { 1531| 545| if (sDifSegs[nLayer][nFirstSegm] == DIFV_BOTH_EMPTY || ------------------ | Branch (1531:13): [True: 94, False: 451] ------------------ 1532| 451| !(sDifSegs[nLayer][nFirstSegm] & DIFV_OUTPUT_OMIT_F)) ------------------ | Branch (1532:13): [True: 0, False: 451] ------------------ 1533| 94| { 1534| 94| sDifSegs[nLayer][nFirstSegm] = DIFV_IS_EMPTY; 1535| 94| } 1536| 545| } 1537| | 1538| | /* F */ 1539| 5.02k| nLayer = DIFL_F; 1540| 5.02k| nFirstSegm = nFirstFmlSegm; ------------------ | | 1492| 5.02k|#define nFirstFmlSegm DIFS_f_FORMULA ------------------ 1541| 5.02k| sBits = 0; 1542| 60.3k| for (i = 0; i < DIFS_idf_LENGTH; i++) ------------------ | Branch (1542:17): [True: 55.2k, False: 5.02k] ------------------ 1543| 55.2k| { 1544| 55.2k| sBits |= sDifSegs[nLayer][i]; 1545| 55.2k| } 1546| 5.02k| if (!(sBits & DIFV_OUTPUT_OMIT_F) && ------------------ | Branch (1546:9): [True: 5.02k, False: 0] ------------------ 1547| 5.02k| sDifSegs[DIFL_FI][nFirstIsoSegm] == DIFV_BOTH_EMPTY) ------------------ | | 1493| 5.02k|#define nFirstIsoSegm DIFS_i_IATOMS ------------------ | Branch (1547:9): [True: 5.02k, False: 0] ------------------ 1548| 5.02k| { 1549| | /* Omit the F layer: no non-iotopic and no isotopic segments */ 1550| 5.02k| memset(sDifSegs[nLayer], DIFV_BOTH_EMPTY, DIFS_idf_LENGTH); /* djb-rwth: memset_s C11/Annex K variant? */ 1551| 5.02k| } 1552| 0| else 1553| 0| { /* do not omit fixed-H layer */ 1554| 0| if (sDifSegs[nLayer][nFirstSegm] == DIFV_BOTH_EMPTY || ------------------ | Branch (1554:13): [True: 0, False: 0] ------------------ 1555| 0| !(sDifSegs[nLayer][nFirstSegm] & DIFV_OUTPUT_OMIT_F)) ------------------ | Branch (1555:13): [True: 0, False: 0] ------------------ 1556| 0| { 1557| 0| sDifSegs[nLayer][nFirstSegm] = DIFV_IS_EMPTY; 1558| 0| } 1559| 0| } 1560| | 1561| | /* M -- leave as it is */ 1562| | 1563| 5.02k| return 0; 1564| | 1565| 5.02k|#undef nFirstFmlSegm 1566| 5.02k|#undef nFirstIsoSegm 1567| 5.02k|} CompareInchiStereo: 1575| 5.12M|{ 1576| 5.12M| int i, num, ret; 1577| 5.12M| if (Stereo2 && Stereo1) ------------------ | Branch (1577:9): [True: 1.16M, False: 3.96M] | Branch (1577:20): [True: 1.16M, False: 0] ------------------ 1578| 1.16M| { 1579| | /* compare stereogenic bonds */ 1580| 1.16M| num = inchi_min(Stereo2->nNumberOfStereoBonds, Stereo1->nNumberOfStereoBonds); ------------------ | | 139| 1.16M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 1.16M] | | ------------------ ------------------ 1581| 1.16M| for (i = 0; i < num; i++) ------------------ | Branch (1581:21): [True: 4, False: 1.16M] ------------------ 1582| 4| { 1583| 4| if ((ret = (int)Stereo2->nBondAtom1[i] - (int)Stereo1->nBondAtom1[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1583:17): [True: 0, False: 4] ------------------ 1584| 0| { 1585| 0| return ret; 1586| 0| } 1587| 4| if ((ret = (int)Stereo2->nBondAtom2[i] - (int)Stereo1->nBondAtom2[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1587:17): [True: 0, False: 4] ------------------ 1588| 0| { 1589| 0| return ret; 1590| 0| } 1591| 4| if ((ret = (int)Stereo2->b_parity[i] - (int)Stereo1->b_parity[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1591:17): [True: 0, False: 4] ------------------ 1592| 0| { 1593| 0| return ret; 1594| 0| } 1595| 4| } 1596| 1.16M| if ((ret = (int)Stereo2->nNumberOfStereoBonds - (int)Stereo1->nNumberOfStereoBonds)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1596:13): [True: 0, False: 1.16M] ------------------ 1597| 0| { 1598| 0| return ret; 1599| 0| } 1600| | 1601| | /* compare stereogenic atoms */ 1602| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1603| | if (((nFlags1 | nFlags2) & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && 1604| | 1 == Stereo2->nNumberOfStereoCenters && 1605| | 1 == Stereo1->nNumberOfStereoCenters) 1606| | { 1607| | ; /* do not compare single stereocenters in case of relative stereo */ 1608| | } 1609| | else 1610| |#endif 1611| 1.16M| { 1612| 1.16M| num = inchi_min(Stereo2->nNumberOfStereoCenters, Stereo1->nNumberOfStereoCenters); ------------------ | | 139| 1.16M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 18, False: 1.16M] | | ------------------ ------------------ 1613| 1.16M| for (i = 0; i < num; i++) ------------------ | Branch (1613:25): [True: 78, False: 1.16M] ------------------ 1614| 78| { 1615| 78| if ((ret = (int)Stereo2->nNumber[i] - (int)Stereo1->nNumber[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1615:21): [True: 48, False: 30] ------------------ 1616| 48| { 1617| 48| return ret; 1618| 48| } 1619| 30| if ((ret = (int)Stereo2->t_parity[i] - (int)Stereo1->t_parity[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1619:21): [True: 16, False: 14] ------------------ 1620| 16| { 1621| 16| return ret; 1622| 16| } 1623| 30| } 1624| 1.16M| if ((ret = (int)Stereo2->nNumberOfStereoCenters - (int)Stereo1->nNumberOfStereoCenters)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1624:17): [True: 20, False: 1.16M] ------------------ 1625| 20| return ret; 1626| | /* compare stereo-abs-is-inverted flags for non-relative, non-racemic */ 1627| 1.16M| if (!((nFlags1 | nFlags2) & (INCHI_FLAG_RAC_STEREO | INCHI_FLAG_REL_STEREO))) ------------------ | | 122| 1.16M|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ if (!((nFlags1 | nFlags2) & (INCHI_FLAG_RAC_STEREO | INCHI_FLAG_REL_STEREO))) ------------------ | | 121| 1.16M|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ | Branch (1627:17): [True: 1.16M, False: 6] ------------------ 1628| 1.16M| { 1629| 1.16M| if ((ret = (Stereo2->nCompInv2Abs < 0) - (Stereo1->nCompInv2Abs < 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1629:21): [True: 0, False: 1.16M] ------------------ 1630| 0| { 1631| 0| return ret; 1632| 0| } 1633| 1.16M| } 1634| 1.16M| } 1635| 1.16M| } 1636| 3.96M| else 1637| 3.96M| { 1638| 3.96M| if (Stereo2 && (Stereo2->nNumberOfStereoBonds > 0 || Stereo2->nNumberOfStereoCenters > 0 ------------------ | Branch (1638:13): [True: 0, False: 3.96M] | Branch (1638:25): [True: 0, False: 0] | Branch (1638:62): [True: 0, False: 0] ------------------ 1639| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1640| | && /* do not compare single stereocenters in case of relative stereo */ 1641| | !((nFlags2 & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && 1642| | 1 == Stereo2->nNumberOfStereoCenters 1643| | ) 1644| |#endif 1645| 0| )) 1646| 0| { 1647| 0| return 1; 1648| 0| } 1649| 3.96M| else 1650| 3.96M| { 1651| 3.96M| if (Stereo1 && (Stereo1->nNumberOfStereoBonds > 0 || Stereo1->nNumberOfStereoCenters > 0 ------------------ | Branch (1651:17): [True: 0, False: 3.96M] | Branch (1651:29): [True: 0, False: 0] | Branch (1651:66): [True: 0, False: 0] ------------------ 1652| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1653| | && /* do not compare single stereocenters in case of relative stereo */ 1654| | !((nFlags1 & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && 1655| | 1 == Stereo1->nNumberOfStereoCenters 1656| | ) 1657| |#endif 1658| 0| )) 1659| 0| { 1660| 0| return -1; 1661| 0| } 1662| 3.96M| } 1663| 3.96M| } 1664| | 1665| 5.12M| return 0; 1666| 5.12M|} CompINChI2: 1680| 2.67M|{ 1681| 2.67M| int ret, num, i, num_H1, num_H2; 1682| | 1683| 2.67M| const INChI* i1 = NULL; /* tautomeric if exists, otherwise non-tautomeric */ 1684| 2.67M| const INChI* i2 = NULL; /* tautomeric if exists, otherwise non-tautomeric */ 1685| | 1686| 2.67M| int n1; /* TAUT_YES if tautomeric i1 exists, otherwise TAUT_NON */ 1687| 2.67M| int n2; /* TAUT_YES if tautomeric i2 exists, otherwise TAUT_NON */ 1688| | 1689| 2.67M| const INChI* i1n = NULL; /* non-tautomeric if both tautomeric AND non-tautomeric exist */ 1690| 2.67M| const INChI* i2n = NULL; /* non-tautomeric if both tautomeric AND non-tautomeric exist */ 1691| | 1692| | /*const INChI *i1t = NULL;*/ /* temp for i1 if both tautomeric AND non-tautomeric exist */ 1693| | /*const INChI *i2t = NULL;*/ /* temp for i2 if both tautomeric AND non-tautomeric exist */ 1694| | 1695| | /* INChI_Stereo *Stereo1, *Stereo2; */ 1696| | 1697| 2.67M| n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 2.67M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 2.67M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 2.67M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = (p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 574| 2.67M|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1697:11): [True: 2.67M, False: 0] | Branch (1697:35): [True: 2.67M, False: 0] ------------------ 1698| 2.67M| n2 = (p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 2.67M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n2 = (p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 2.67M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n2 = (p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 575| 2.67M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n2 = (p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms) ? TAUT_YES : TAUT_NON; ------------------ | | 574| 2.67M|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1698:11): [True: 2.67M, False: 0] | Branch (1698:35): [True: 2.67M, False: 0] ------------------ 1699| | 1700| 2.67M| i1 = p1->pINChI[n1]; 1701| 2.67M| i1n = (n1 == TAUT_YES && p1->pINChI[TAUT_NON] && ------------------ | | 575| 5.34M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i1n = (n1 == TAUT_YES && p1->pINChI[TAUT_NON] && ------------------ | | 574| 2.67M|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1701:12): [True: 2.67M, False: 0] | Branch (1701:30): [True: 900k, False: 1.77M] ------------------ 1702| 1.77M| p1->pINChI[TAUT_NON]->nNumberOfAtoms) ? p1->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 900k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p1->pINChI[TAUT_NON]->nNumberOfAtoms) ? p1->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 900k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1702:9): [True: 900k, False: 24] ------------------ 1703| | 1704| 2.67M| i2 = p2->pINChI[n2]; 1705| 2.67M| i2n = (n2 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 575| 5.34M|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i2n = (n2 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 574| 2.67M|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1705:12): [True: 2.67M, False: 0] | Branch (1705:30): [True: 900k, False: 1.77M] ------------------ 1706| 1.77M| p2->pINChI[TAUT_NON]->nNumberOfAtoms) ? p2->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 900k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p2->pINChI[TAUT_NON]->nNumberOfAtoms) ? p2->pINChI[TAUT_NON] : (const INChI*)NULL; ------------------ | | 574| 900k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1706:9): [True: 900k, False: 42] ------------------ 1707| | 1708| | /* non-deleted-non-empty < deleted < empty */ 1709| 2.67M| if (i1 && !i2) ------------------ | Branch (1709:9): [True: 2.67M, False: 0] | Branch (1709:15): [True: 0, False: 2.67M] ------------------ 1710| 0| return -1; /* non-empty is the smallest (first) */ 1711| 2.67M| if (!i1 && i2) ------------------ | Branch (1711:9): [True: 0, False: 2.67M] | Branch (1711:16): [True: 0, False: 0] ------------------ 1712| 0| return 1; 1713| 2.67M| if (!i1 && !i2) ------------------ | Branch (1713:9): [True: 0, False: 2.67M] | Branch (1713:16): [True: 0, False: 0] ------------------ 1714| 0| return 0; 1715| 2.67M| if (i1->bDeleted && !i2->bDeleted) ------------------ | Branch (1715:9): [True: 900k, False: 1.77M] | Branch (1715:25): [True: 0, False: 900k] ------------------ 1716| 0| return 1; /* deleted is the largest (last) among non-empty */ 1717| 2.67M| if (!i1->bDeleted && i2->bDeleted) ------------------ | Branch (1717:9): [True: 1.77M, False: 900k] | Branch (1717:26): [True: 0, False: 1.77M] ------------------ 1718| 0| return -1; 1719| | 1720| 2.67M| num_H1 = num_H2 = 0; 1721| | 1722| | /* do not compare terminal H */ 1723| 2.67M| if ((ret = CompareHillFormulasNoH(i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1723:9): [True: 88.0k, False: 2.58M] ------------------ 1724| 88.0k| { 1725| 88.0k| return ret; /* lexicographic order except the shorter one is greater (last): CH2O < CH2; C3XX < C2XX */ 1726| 88.0k| } 1727| | 1728| | /********************************************************* 1729| | compare non-isotopic non-tautomeric part 1730| | *********************************************************/ 1731| | 1732| | /* compare number of atoms (excluding terminal H) */ 1733| 2.58M| if ((ret = i2->nNumberOfAtoms - i1->nNumberOfAtoms)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1733:9): [True: 20.1k, False: 2.56M] ------------------ 1734| 20.1k| return ret; /* more atoms first */ 1735| | 1736| | /* compare elements (excluding terminal H) */ 1737| 2.56M| num = i1->nNumberOfAtoms; 1738| 18.6M| for (i = 0; i < num; i++) ------------------ | Branch (1738:17): [True: 16.1M, False: 2.56M] ------------------ 1739| 16.1M| { 1740| | /* should always be equal if Hill formulas are same */ 1741| 16.1M| if ((ret = (int)i2->nAtom[i] - (int)i1->nAtom[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1741:13): [True: 1.18k, False: 16.1M] ------------------ 1742| 1.18k| return ret; /* greater periodic number first */ 1743| 16.1M| } 1744| | 1745| | /********************************************************** 1746| | compare connection tables 1747| | ***********************************************************/ 1748| 2.56M| if ((ret = i2->lenConnTable - i1->lenConnTable)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1748:9): [True: 140, False: 2.56M] ------------------ 1749| 140| return ret; /* longer connection table first */ 1750| 2.56M| num = i2->lenConnTable; 1751| 8.54M| for (i = 0; i < num; i++) ------------------ | Branch (1751:17): [True: 5.98M, False: 2.56M] ------------------ 1752| 5.98M| { 1753| 5.98M| if ((ret = (int)i2->nConnTable[i] - (int)i1->nConnTable[i])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1753:13): [True: 208, False: 5.98M] ------------------ 1754| 208| return ret; /* greater connection table first */ 1755| 5.98M| } 1756| | 1757| | /********************************************************* 1758| | compare compare total number of H (inverse: H3 < H2 ) 1759| | **********************************************************/ 1760| 2.56M| if ((ret = num_H2 - num_H1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1760:9): [True: 0, False: 2.56M] ------------------ 1761| 0| { 1762| 0| return ret; 1763| 0| } 1764| | 1765| | /********************************************************* 1766| | compare non-tautomeric num_H: N < NH3 < NH2 < NH 1767| | **********************************************************/ 1768| 2.56M| num = i1->nNumberOfAtoms; 1769| 18.6M| for (i = 0; i < num; i++) ------------------ | Branch (1769:17): [True: 16.1M, False: 2.56M] ------------------ 1770| 16.1M| { 1771| 16.1M| if (i2->nNum_H[i] != i1->nNum_H[i]) ------------------ | Branch (1771:13): [True: 0, False: 16.1M] ------------------ 1772| 0| { 1773| 0| return !i2->nNum_H[i] ? 1 : /* no H first */ ------------------ | Branch (1773:20): [True: 0, False: 0] ------------------ 1774| 0| !i1->nNum_H[i] ? -1 : ------------------ | Branch (1774:17): [True: 0, False: 0] ------------------ 1775| 0| (int)i2->nNum_H[i] - (int)i1->nNum_H[i]; 1776| 0| } 1777| 16.1M| } 1778| | 1779| | /********************************************************* 1780| | compare non-isotopic tautomeric part 1781| | *********************************************************/ 1782| 2.56M| if ((ret = CompareTautNonIsoPartOfINChI(i1, i2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1782:9): [True: 0, False: 2.56M] ------------------ 1783| 0| { 1784| 0| return ret; 1785| 0| } 1786| | /* 1787| | if ( ret = i2->lenTautomer - i1->lenTautomer ) 1788| | return ret; 1789| | num = inchi_min( i2->lenTautomer, i1->lenTautomer ); 1790| | for ( i = 0; i < num; i ++ ) { 1791| | if ( ret = (int)i2->nTautomer[i] - (int)i1->nTautomer[i] ) 1792| | return ret; 1793| | } 1794| | */ 1795| | 1796| | /********************************************************* 1797| | * * 1798| | * at this point both components are either tautomeric * 1799| | * or non-tautomeric * 1800| | * * 1801| | *********************************************************/ 1802| | 1803| | /********************************************************* 1804| | non-tautomeric "fixed H" specific 1805| | *********************************************************/ 1806| 2.56M| if (TAUT_NON == bTaut && ((i1n && i1n->nNum_H_fixed) || (i2n && i2n->nNum_H_fixed))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 2.56M|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1806:9): [True: 1.28M, False: 1.28M] | Branch (1806:32): [True: 450k, False: 831k] | Branch (1806:39): [True: 450k, False: 0] | Branch (1806:62): [True: 0, False: 831k] | Branch (1806:69): [True: 0, False: 0] ------------------ 1807| 450k| { 1808| | /* first, compare non-tautomeric chem. formulas -- they may be different */ 1809| 450k| const char* f1 = (i1n /*&& i1n->nNum_H_fixed*/) ? i1n->szHillFormula : i1->szHillFormula; ------------------ | Branch (1809:26): [True: 450k, False: 0] ------------------ 1810| 450k| const char* f2 = (i2n /*&& i2n->nNum_H_fixed*/) ? i2n->szHillFormula : i2->szHillFormula; ------------------ | Branch (1810:26): [True: 450k, False: 0] ------------------ 1811| 450k| if (f1 && f2 && (ret = CompareHillFormulas(f1, f2))) ------------------ | Branch (1811:13): [True: 450k, False: 0] | Branch (1811:19): [True: 450k, False: 0] | Branch (1811:25): [True: 0, False: 450k] ------------------ 1812| 0| { 1813| 0| return ret; 1814| 0| } 1815| | /* secondly, compare fixed-H distribution */ 1816| 450k| if (i1n && i1n->nNum_H_fixed && i2n && i2n->nNum_H_fixed) ------------------ | Branch (1816:13): [True: 450k, False: 0] | Branch (1816:20): [True: 450k, False: 0] | Branch (1816:41): [True: 450k, False: 0] | Branch (1816:48): [True: 450k, False: 0] ------------------ 1817| 450k| { 1818| 450k| num = inchi_min(i1n->nNumberOfAtoms, i2n->nNumberOfAtoms); ------------------ | | 139| 450k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 450k] | | ------------------ ------------------ 1819| 900k| for (i = 0; i < num; i++) ------------------ | Branch (1819:25): [True: 450k, False: 450k] ------------------ 1820| 450k| { 1821| 450k| if (i2n->nNum_H_fixed[i] != i1n->nNum_H_fixed[i]) ------------------ | Branch (1821:21): [True: 0, False: 450k] ------------------ 1822| 0| { 1823| 0| return !i2n->nNum_H_fixed[i] ? 1 : /* no fixed H first */ ------------------ | Branch (1823:28): [True: 0, False: 0] ------------------ 1824| 0| !i1n->nNum_H_fixed[i] ? -1 : ------------------ | Branch (1824:25): [True: 0, False: 0] ------------------ 1825| 0| (int)i2n->nNum_H_fixed[i] - (int)i1n->nNum_H_fixed[i]; 1826| 0| } 1827| 450k| } 1828| 450k| if ((ret = (int)i2n->nNumberOfAtoms - (int)i1n->nNumberOfAtoms)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1828:17): [True: 0, False: 450k] ------------------ 1829| 0| { 1830| 0| return ret; /* should not happen */ 1831| 0| } 1832| 450k| } 1833| 0| else 1834| 0| { 1835| 0| if (i1n && i1n->nNum_H_fixed) ------------------ | Branch (1835:17): [True: 0, False: 0] | Branch (1835:24): [True: 0, False: 0] ------------------ 1836| 0| { 1837| 0| num = i1n->nNumberOfAtoms; 1838| 0| for (i = 0; i < num; i++) ------------------ | Branch (1838:29): [True: 0, False: 0] ------------------ 1839| 0| { 1840| | /* added 2004-05-04 */ 1841| 0| if (i1n->nNum_H_fixed[i]) ------------------ | Branch (1841:25): [True: 0, False: 0] ------------------ 1842| 0| { 1843| 0| return -1; /* i1n->nNum_H_fixed[i] > 0? -1:1;*/ 1844| 0| } 1845| 0| } 1846| | /* p1 is tautomeric, p2 is not tautomeric; this must have been detected earlier */ 1847| | /*return -1;*/ /* has fixed H first *//* */ /* removed 2004-05-04 */ 1848| 0| } 1849| 0| else 1850| 0| { 1851| 0| num = i2n->nNumberOfAtoms; 1852| 0| for (i = 0; i < num; i++) ------------------ | Branch (1852:29): [True: 0, False: 0] ------------------ 1853| 0| { 1854| | /* added 2004-05-04 */ 1855| 0| if (i2n->nNum_H_fixed[i]) ------------------ | Branch (1855:25): [True: 0, False: 0] ------------------ 1856| 0| { 1857| 0| return 1; /* i2n->nNum_H_fixed[i] > 0? 1:-1;*/ 1858| 0| } 1859| 0| } 1860| | /* p2 is tautomeric, p1 is not tautomeric; this must have been detected earlier */ 1861| | /*return 1; */ /* has fixed H first *//* */ /* removed 2004-05-04 */ 1862| 0| } 1863| 0| } 1864| 450k| } 1865| | 1866| | /************************************************************************* 1867| | if requested non-tautomeric comparison then 1868| | prepare to compare non-taut non-isotopic stereo, etc. 1869| | *************************************************************************/ 1870| 2.56M| if (TAUT_NON == bTaut) ------------------ | | 574| 2.56M|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1870:9): [True: 1.28M, False: 1.28M] ------------------ 1871| 1.28M| { 1872| 1.28M| if (i1n) ------------------ | Branch (1872:13): [True: 450k, False: 831k] ------------------ 1873| 450k| { 1874| | /*i1t = i1;*/ 1875| 450k| i1 = i1n; 1876| 450k| } 1877| 1.28M| if (i2n) ------------------ | Branch (1877:13): [True: 450k, False: 831k] ------------------ 1878| 450k| { 1879| | /*i2t = i2;*/ 1880| 450k| i2 = i2n; 1881| 450k| } 1882| 1.28M| } 1883| | 1884| | /********************************************************* 1885| | compare non-isotopic stereo 1886| | *********************************************************/ 1887| 2.56M| ret = CompareInchiStereo(i1->Stereo, i1->nFlags, i2->Stereo, i2->nFlags); 1888| 2.56M| if (ret) ------------------ | Branch (1888:9): [True: 62, False: 2.56M] ------------------ 1889| 62| { 1890| 62| return ret; 1891| 62| } 1892| | /******************************************************* 1893| | do not switch back to tautomeric i1, i2 1894| | *******************************************************/ 1895| | /* -- how to switch back -- 1896| | if ( i1t ) { 1897| | i1 = i1t; 1898| | i1t = NULL; 1899| | } 1900| | if ( i2t ) { 1901| | i2 = i2t; 1902| | i2t = NULL; 1903| | } 1904| | */ 1905| | 1906| | /****************************************************** 1907| | compare isotopic non-tautomeric part 1908| | ******************************************************/ 1909| 2.56M| if (bCompareIsotopic) ------------------ | Branch (1909:9): [True: 2.56M, False: 0] ------------------ 1910| 2.56M| { 1911| 2.56M| if ((ret = i2->nNumberOfIsotopicAtoms - i1->nNumberOfIsotopicAtoms)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1911:13): [True: 196, False: 2.56M] ------------------ 1912| 196| { 1913| 196| return ret; 1914| 196| } 1915| 2.56M| num = i1->nNumberOfIsotopicAtoms; 1916| | /* compare isotopic atoms */ 1917| 2.57M| for (i = 0; i < num; i++) ------------------ | Branch (1917:21): [True: 10.7k, False: 2.56M] ------------------ 1918| 10.7k| { 1919| 10.7k| if ((ret = (int)i2->IsotopicAtom[i].nAtomNumber - (int)i1->IsotopicAtom[i].nAtomNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1919:17): [True: 8, False: 10.7k] ------------------ 1920| 8| { 1921| 8| return ret; 1922| 8| } 1923| 10.7k| if ((ret = (int)i2->IsotopicAtom[i].nIsoDifference - (int)i1->IsotopicAtom[i].nIsoDifference)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1923:17): [True: 24, False: 10.7k] ------------------ 1924| 24| { 1925| 24| return ret; 1926| 24| } 1927| 10.7k| } 1928| | 1929| | /* compare isotopic H */ 1930| | /* if tautomeric comparison mode then here are compared only non-tautomeric H */ 1931| 2.57M| for (i = 0; i < num; i++) ------------------ | Branch (1931:21): [True: 10.7k, False: 2.56M] ------------------ 1932| 10.7k| { 1933| 10.7k| if ((ret = (int)i2->IsotopicAtom[i].nNum_T - (int)i1->IsotopicAtom[i].nNum_T)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1933:17): [True: 0, False: 10.7k] ------------------ 1934| 0| { 1935| 0| return ret; 1936| 0| } 1937| 10.7k| if ((ret = (int)i2->IsotopicAtom[i].nNum_D - (int)i1->IsotopicAtom[i].nNum_D)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1937:17): [True: 0, False: 10.7k] ------------------ 1938| 0| { 1939| 0| return ret; 1940| 0| } 1941| 10.7k| if ((ret = (int)i2->IsotopicAtom[i].nNum_H - (int)i1->IsotopicAtom[i].nNum_H)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1941:17): [True: 0, False: 10.7k] ------------------ 1942| 0| { 1943| 0| return ret; 1944| 0| } 1945| 10.7k| } 1946| | 1947| | /***************************************************** 1948| | compare isotopic tautomeric part 1949| | *****************************************************/ 1950| 2.56M| if ((ret = i2->nNumberOfIsotopicTGroups - i1->nNumberOfIsotopicTGroups)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1950:13): [True: 0, False: 2.56M] ------------------ 1951| 0| return ret; 1952| 2.56M| num = i1->nNumberOfIsotopicTGroups; 1953| 2.56M| for (i = 0; i < num; i++) ------------------ | Branch (1953:21): [True: 0, False: 2.56M] ------------------ 1954| 0| { 1955| 0| if ((ret = (int)i2->IsotopicTGroup[i].nTGroupNumber - (int)i1->IsotopicTGroup[i].nTGroupNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1955:17): [True: 0, False: 0] ------------------ 1956| 0| { 1957| 0| return ret; 1958| 0| } 1959| 0| if ((ret = (int)i2->IsotopicTGroup[i].nNum_T - (int)i1->IsotopicTGroup[i].nNum_T)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1959:17): [True: 0, False: 0] ------------------ 1960| 0| { 1961| 0| return ret; 1962| 0| } 1963| 0| if ((ret = (int)i2->IsotopicTGroup[i].nNum_D - (int)i1->IsotopicTGroup[i].nNum_D)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1963:17): [True: 0, False: 0] ------------------ 1964| 0| { 1965| 0| return ret; 1966| 0| } 1967| 0| if ((ret = (int)i2->IsotopicTGroup[i].nNum_H - (int)i1->IsotopicTGroup[i].nNum_H)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1967:17): [True: 0, False: 0] ------------------ 1968| 0| { 1969| 0| return ret; 1970| 0| } 1971| 0| } 1972| | 1973| | /**************************************************** 1974| | compare isotopic stereo 1975| | ****************************************************/ 1976| 2.56M| ret = CompareInchiStereo(i1->StereoIsotopic, i1->nFlags, i2->StereoIsotopic, i2->nFlags); 1977| 2.56M| if (ret) ------------------ | Branch (1977:13): [True: 22, False: 2.56M] ------------------ 1978| 22| { 1979| 22| return ret; 1980| 22| } 1981| 2.56M| } 1982| | 1983| | /********************************************************** 1984| | compare charges: non-charged first, then in order of 1985| | ascending charges (negative first) 1986| | ***********************************************************/ 1987| 2.56M| if (i2->nTotalCharge && i1->nTotalCharge) ------------------ | Branch (1987:9): [True: 900k, False: 1.66M] | Branch (1987:29): [True: 900k, False: 0] ------------------ 1988| 900k| { 1989| | /* both are charged; smaller charges first */ 1990| 900k| ret = (int)i1->nTotalCharge - (int)i2->nTotalCharge; 1991| 900k| return ret; 1992| 900k| } 1993| 1.66M| if ((ret = (i1->nTotalCharge ? 1 : 0) - (i2->nTotalCharge ? 1 : 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1993:9): [True: 6, False: 1.66M] | Branch (1993:17): [True: 6, False: 1.66M] | Branch (1993:46): [True: 0, False: 1.66M] ------------------ 1994| 6| { 1995| | /* only one is charged; uncharged first */ 1996| 6| return ret; 1997| 6| } 1998| | /* stable sort */ 1999| | /*ret = p1->ord_number - p2->ord_number;*/ 2000| | 2001| 1.66M| return ret; 2002| 1.66M|} CompINChINonTaut2: 2007| 695k|{ 2008| 695k| int ret; 2009| 695k| ret = CompINChI2((const INCHI_SORT*)p1, (const INCHI_SORT*)p2, TAUT_NON, 1); ------------------ | | 574| 695k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2010| 695k|#if ( CANON_FIXH_TRANS == 1 ) 2011| 695k| if (!ret) ------------------ | Branch (2011:9): [True: 640k, False: 55.0k] ------------------ 2012| 640k| { 2013| | /* to obtain canonical transposition 2004-05-10 */ 2014| 640k| ret = CompINChI2((const INCHI_SORT*)p1, (const INCHI_SORT*)p2, TAUT_YES, 1); ------------------ | | 575| 640k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2015| 640k| } 2016| 695k|#endif 2017| 695k| if (!ret) ------------------ | Branch (2017:9): [True: 640k, False: 55.0k] ------------------ 2018| 640k| { 2019| | /* stable sort */ 2020| 640k| ret = ((const INCHI_SORT*)p1)->ord_number - ((const INCHI_SORT*)p2)->ord_number; 2021| 640k| } 2022| | 2023| 695k| return ret; 2024| 695k|} CompINChITaut2: 2029| 695k|{ 2030| 695k| int ret; 2031| 695k| ret = CompINChI2((const INCHI_SORT*)p1, (const INCHI_SORT*)p2, TAUT_YES, 1); ------------------ | | 575| 695k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2032| 695k|#if ( CANON_FIXH_TRANS == 1 ) 2033| 695k| if (!ret) ------------------ | Branch (2033:9): [True: 640k, False: 55.0k] ------------------ 2034| 640k| { 2035| | /* to obtain canonical transposition 2004-05-10 */ 2036| 640k| ret = CompINChI2((const INCHI_SORT*)p1, (const INCHI_SORT*)p2, TAUT_NON, 1); ------------------ | | 574| 640k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2037| 640k| } 2038| 695k|#endif 2039| 695k| if (!ret) ------------------ | Branch (2039:9): [True: 640k, False: 55.0k] ------------------ 2040| 640k| { 2041| | /* stable sort */ 2042| 640k| ret = ((const INCHI_SORT*)p1)->ord_number - ((const INCHI_SORT*)p2)->ord_number; 2043| 640k| } 2044| | 2045| 695k| return ret; 2046| 695k|} mystrrev: 2055| 56.9k|{ 2056| 56.9k| char c, * q = p; 2057| 121k| while (*q++) ------------------ | Branch (2057:12): [True: 64.6k, False: 56.9k] ------------------ 2058| 64.6k| { 2059| 64.6k| ; 2060| 64.6k| } 2061| 56.9k| q -= 2; /* pointer to the last character */ 2062| 62.1k| while (p < q) ------------------ | Branch (2062:12): [True: 5.27k, False: 56.9k] ------------------ 2063| 5.27k| { 2064| 5.27k| c = *q; /* swap */ 2065| 5.27k| *q-- = *p; 2066| 5.27k| *p++ = c; 2067| 5.27k| } 2068| 56.9k|} GetDfsOrder4CT: 2124| 4.30k|{ 2125| 4.30k| AT_NUMB* nStackAtom = NULL; 2126| 4.30k| int nTopStackAtom = -1; 2127| 4.30k| AT_NUMB* nNumDescendants = NULL; /* number of descendants incl. closures and the atom itself */ 2128| 4.30k| AT_NUMB* nDfsNumber = NULL; 2129| 4.30k| S_CHAR* cNeighNumb = NULL; 2130| 4.30k| NEIGH_LIST* nl = NULL; 2131| 4.30k| AT_NUMB nDfs; 2132| 4.30k| int i, j, u, k, start, num_rings, nTotOutputStringLen; 2133| 4.30k| AT_NUMB* nOutputString = NULL, cDelim; 2134| 4.30k| int bCtPredecessors = (nCtMode & CT_MODE_PREDECESSORS); ------------------ | | 28| 4.30k|#define CT_MODE_PREDECESSORS 8 ------------------ 2135| 4.30k| OrderStruct os; 2136| | 2137| | /* allocate arrays */ 2138| 4.30k| nStackAtom = (AT_NUMB*)inchi_malloc(num_atoms * sizeof(nStackAtom[0])); ------------------ | | 1143| 4.30k|#define inchi_malloc malloc ------------------ 2139| 4.30k| nNumDescendants = (AT_NUMB*)inchi_malloc(num_atoms * sizeof(nNumDescendants[0])); ------------------ | | 1143| 4.30k|#define inchi_malloc malloc ------------------ 2140| 4.30k| nDfsNumber = (AT_NUMB*)inchi_malloc(num_atoms * sizeof(nDfsNumber[0])); ------------------ | | 1143| 4.30k|#define inchi_malloc malloc ------------------ 2141| 4.30k| cNeighNumb = (S_CHAR*)inchi_malloc(num_atoms * sizeof(cNeighNumb[0])); ------------------ | | 1143| 4.30k|#define inchi_malloc malloc ------------------ 2142| 4.30k| nl = CreateNeighListFromLinearCT(LinearCT, nLenCT, num_atoms); 2143| | 2144| | /* check allocation */ 2145| 4.30k| if (!nStackAtom || !nNumDescendants || !nDfsNumber || !cNeighNumb || !nl) ------------------ | Branch (2145:9): [True: 0, False: 4.30k] | Branch (2145:24): [True: 0, False: 4.30k] | Branch (2145:44): [True: 0, False: 4.30k] | Branch (2145:59): [True: 0, False: 4.30k] | Branch (2145:74): [True: 0, False: 4.30k] ------------------ 2146| 0| { 2147| | /* ret = CT_OUT_OF_RAM; */ /* program error */ /* */ 2148| 0| goto exit_function; 2149| 0| } 2150| 4.30k| if (bCtPredecessors) ------------------ | Branch (2150:9): [True: 0, False: 4.30k] ------------------ 2151| 0| { 2152| 0| start = 0; 2153| 0| } 2154| 4.30k| else 2155| 4.30k| { 2156| | /* find DFS start vertex (atom) */ 2157| 26.7k| for (i = 1, start = 0; i < num_atoms; i++) ------------------ | Branch (2157:32): [True: 22.4k, False: 4.30k] ------------------ 2158| 22.4k| { 2159| 22.4k| if (nl[i][0] < nl[start][0]) ------------------ | Branch (2159:17): [True: 2.93k, False: 19.4k] ------------------ 2160| 2.93k| { /* index = nRank-1 */ 2161| 2.93k| start = i; 2162| 2.93k| } 2163| 22.4k| } 2164| 4.30k| } 2165| | 2166| | /* 2167| | vertex information: 2168| | 1. Number of (forward edges) + (back edges, first visit -- ring closures): nl[i][0] 2169| | 2. Number of vertices traversed from this vertex, including the vertex: nNumDescendants[i] 2170| | 3. Each edge information: 2171| | a. forward edge (0) or back edge (1) indicator: nDfsNumber[i] > nDfsNumber[neigh] 2172| | b. neighbor at another end of the edge neigh = nl[i][k+1], k < i 2173| | 2174| | Total per edge: 2 + 2*(number of edges) 2175| | */ 2176| | 2177| | /* DFS initiation */ 2178| 4.30k| u = start; /* start atom */ 2179| 4.30k| nDfs = 0; 2180| 4.30k| nTopStackAtom = -1; 2181| 4.30k| memset(nDfsNumber, 0, num_atoms * sizeof(nDfsNumber[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 2182| 4.30k| memset(nNumDescendants, 0, num_atoms * sizeof(nNumDescendants[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 2183| 4.30k| memset(cNeighNumb, 0, num_atoms * sizeof(cNeighNumb[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 2184| | /* push the start atom on the stack */ 2185| 4.30k| nDfsNumber[u] = ++nDfs; 2186| 4.30k| if (bCtPredecessors) ------------------ | Branch (2186:9): [True: 0, False: 4.30k] ------------------ 2187| 0| { 2188| 0| nNumDescendants[u] = 0; /* atom #1 has no predecessor */ 2189| 0| } 2190| 4.30k| else 2191| 4.30k| { 2192| 4.30k| nNumDescendants[u] = 1; /* count itself as a descendant */ 2193| 4.30k| } 2194| 4.30k| nStackAtom[++nTopStackAtom] = (AT_NUMB)u; 2195| | /* nNumStartChildren = 0; */ 2196| 4.30k| num_rings = 0; 2197| | 2198| | /* DFS */ 2199| 4.30k| do 2200| 26.7k| { 2201| | /* advance */ 2202| 79.2k| while (i = (int)nStackAtom[nTopStackAtom], j = (int)cNeighNumb[i] + 1, (int)nl[i][0] >= j) ------------------ | Branch (2202:16): [True: 52.5k, False: 26.7k] ------------------ 2203| | /*while ( (int)nl[i=nStackAtom[nTopStackAtom]][0] >= (j = (int)cNeighNumb[i]+1) )*/ 2204| | 2205| | /* replaced due to missing sequence point; undefined behavior, pointed by Geoffrey Hutchison */ 2206| 52.5k| { 2207| 52.5k| cNeighNumb[i]++; 2208| 52.5k| u = (int)nl[i][j]; /* jth neighbor of the vertex i */ 2209| 52.5k| if (!nDfsNumber[u]) ------------------ | Branch (2209:17): [True: 22.4k, False: 30.1k] ------------------ 2210| 22.4k| { 2211| | /* tree edge, 1st visit -- advance */ 2212| | /* put unexplored vertex u on the stack for further examination */ 2213| 22.4k| nStackAtom[++nTopStackAtom] = (AT_NUMB)u; 2214| 22.4k| nDfsNumber[u] = ++nDfs; 2215| 22.4k| if (bCtPredecessors) ------------------ | Branch (2215:21): [True: 0, False: 22.4k] ------------------ 2216| 0| { 2217| 0| nNumDescendants[u] = i + 1; /* predecessor's rank */ 2218| 0| } 2219| 22.4k| else 2220| 22.4k| { 2221| 22.4k| nNumDescendants[u]++; /* count atom u as its descendant */ 2222| 22.4k| } 2223| 22.4k| } 2224| 30.1k| else 2225| 30.1k| { 2226| 30.1k| if (nTopStackAtom && u != (int)nStackAtom[nTopStackAtom - 1] && ------------------ | Branch (2226:21): [True: 29.2k, False: 964] | Branch (2226:38): [True: 6.79k, False: 22.4k] ------------------ 2227| | /* back edge: u is not a predecessor of i */ 2228| 6.79k| nDfsNumber[u] < nDfsNumber[i]) ------------------ | Branch (2228:21): [True: 3.87k, False: 2.91k] ------------------ 2229| 3.87k| { 2230| | /* Back edge, 1st visit: u is an ancestor of i (ring closure) */ 2231| 3.87k| if (!bCtPredecessors) ------------------ | Branch (2231:25): [True: 3.87k, False: 0] ------------------ 2232| 3.87k| { 2233| 3.87k| nNumDescendants[i]++; /* count closures as descendants */ 2234| 3.87k| } 2235| 3.87k| num_rings++; /* count ring closures */ 2236| 3.87k| } 2237| 26.2k| else 2238| 26.2k| { 2239| 26.2k| nl[i][j] = MAX_ATOMS + 1; /* back edge, 2nd visit: mark as deleted */ ------------------ | | 15| 26.2k|#define MAX_ATOMS 32766 ------------------ 2240| 26.2k| } 2241| 30.1k| } 2242| 52.5k| } 2243| 26.7k| cNeighNumb[i] = 0; /* all neighbors of the ith atom have been 2244| | traversed; resore the neighbor counter */ 2245| | /* back up */ 2246| 26.7k| if (!bCtPredecessors && nTopStackAtom /* that is, i != start */) ------------------ | Branch (2246:13): [True: 26.7k, False: 0] | Branch (2246:33): [True: 22.4k, False: 4.30k] ------------------ 2247| 22.4k| { 2248| 22.4k| u = (int)nStackAtom[nTopStackAtom - 1]; /* predecessor of i */ 2249| 22.4k| nNumDescendants[u] += nNumDescendants[i]; /* add descendants */ 2250| 22.4k| } 2251| 26.7k| } while (--nTopStackAtom >= 0); ------------------ | Branch (2251:14): [True: 22.4k, False: 4.30k] ------------------ 2252| | 2253| | /* Sort the neighbors in ascending order so that: 2254| | primary key = number of descendants in the DFS tree; closure neighbor is 0 2255| | secondary key = canonical number (here vertex number = canonical number - 1) 2256| | */ 2257| | 2258| 4.30k| os.m_gDfs4CT_nDfsNumber = nDfsNumber; 2259| 4.30k| os.m_gDfs4CT_nNumDescendants = nNumDescendants; 2260| 4.30k| os.m_gDfs4CT_nCurrentAtom = -1; 2261| | 2262| | /* sorting; deleted will be the last neighbors */ 2263| 31.0k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (2263:17): [True: 26.7k, False: 4.30k] ------------------ 2264| 26.7k| { 2265| 26.7k| if (nl[i][0] > 1) ------------------ | Branch (2265:13): [True: 17.3k, False: 9.39k] ------------------ 2266| 17.3k| { 2267| 17.3k| os.m_gDfs4CT_nCurrentAtom = i; 2268| 17.3k| insertions_sort(&os, &nl[i][1], nl[i][0], sizeof(nl[i][1]), CompareDfsDescendants4CT); 2269| 17.3k| } 2270| | /* reduce number of neighbors to exclude deleted */ 2271| 53.0k| for (k = 0; k < nl[i][0] && nl[i][k + 1] <= MAX_ATOMS; k++) ------------------ | | 15| 49.4k|#define MAX_ATOMS 32766 ------------------ | Branch (2271:21): [True: 49.4k, False: 3.52k] | Branch (2271:37): [True: 26.2k, False: 23.1k] ------------------ 2272| 26.2k| { 2273| 26.2k| ; 2274| 26.2k| } 2275| 26.7k| nl[i][0] = k; 2276| 26.7k| } 2277| | 2278| 4.30k| nTotOutputStringLen = 3 * (num_atoms + num_rings + 1); /* last 3 elements are a 'zero termination' */ 2279| | 2280| 4.30k| if (bCtPredecessors) ------------------ | Branch (2280:9): [True: 0, False: 4.30k] ------------------ 2281| 0| { 2282| 0| if ((nOutputString = (AT_RANK*)inchi_calloc(nTotOutputStringLen, sizeof(nOutputString[0])))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ | Branch (2282:13): [True: 0, False: 0] ------------------ 2283| 0| { 2284| 0| cDelim = '-'; 2285| 0| for (u = 0, k = -3; u < num_atoms; u++) ------------------ | Branch (2285:33): [True: 0, False: 0] ------------------ 2286| 0| { 2287| 0| k += 3; 2288| 0| if (k + 6 > nTotOutputStringLen) ------------------ | Branch (2288:21): [True: 0, False: 0] ------------------ 2289| 0| { 2290| 0| goto exit_error; /* program error */ 2291| 0| } 2292| 0| nOutputString[k] = nNumDescendants[u] ? nNumDescendants[u] : MAX_ATOMS + 1; ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ | Branch (2292:36): [True: 0, False: 0] ------------------ 2293| 0| nOutputString[k + 1] = nNum_H ? 16 + nNum_H[u] : 0; ------------------ | Branch (2293:40): [True: 0, False: 0] ------------------ 2294| 0| nOutputString[k + 2] = k ? ',' : '\0'; ------------------ | Branch (2294:40): [True: 0, False: 0] ------------------ 2295| 0| for (j = 1; j <= nl[u][0] && nDfsNumber[u] > nDfsNumber[i = nl[u][j]]; j++) ------------------ | Branch (2295:29): [True: 0, False: 0] | Branch (2295:46): [True: 0, False: 0] ------------------ 2296| 0| { 2297| | /* closures */ 2298| 0| k += 3; 2299| 0| if (k + 6 > nTotOutputStringLen) ------------------ | Branch (2299:25): [True: 0, False: 0] ------------------ 2300| 0| { 2301| 0| goto exit_error; /* program error */ 2302| 0| } 2303| 0| nOutputString[k] = i + 1; /* closure */ 2304| 0| nOutputString[k + 1] = 0; 2305| 0| nOutputString[k + 2] = cDelim; 2306| 0| } 2307| 0| } 2308| 0| } 2309| 0| } 2310| 4.30k| else 2311| 4.30k| { 2312| 4.30k| if (nNumDescendants) ------------------ | Branch (2312:13): [True: 4.30k, False: 0] ------------------ 2313| 4.30k| { /* do not need anymore */ 2314| 4.30k| inchi_free(nNumDescendants); ------------------ | | 1152| 4.30k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 4.30k, False: 0] | | | Branch (1152:50): [Folded, False: 4.30k] | | ------------------ ------------------ 2315| 4.30k| nNumDescendants = NULL; 2316| 4.30k| } 2317| | 2318| | /* 2319| | the output string contains: 2320| | (num_atoms) atoms for the DFS (spanning) tree 2321| | (num_atoms-1) delimiters for the DFS (spanning) tree 2322| | 1 character for each atom that has 1 terminal hydrogen atoms 2323| | 2 characters for each atom that has 2-9 terminal hydrogen atoms 2324| | 3 characters for each atom that has 10-99 terminal hydrogen atoms, etc. 2325| | (num_rings) atoms for the ring closures 2326| | (num_rings) delimiters for the ring closures 2327| | */ 2328| | 2329| 4.30k| if ((nOutputString = (AT_RANK*)inchi_calloc(nTotOutputStringLen, sizeof(nOutputString[0])))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1146| 4.30k|#define inchi_calloc calloc ------------------ | Branch (2329:13): [True: 4.30k, False: 0] ------------------ 2330| 4.30k| { 2331| 4.30k| u = start; /* start atom */ 2332| 4.30k| nTopStackAtom = -1; 2333| 4.30k| memset(cNeighNumb, 0, num_atoms * sizeof(cNeighNumb[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 2334| | /* push the start atom on the stack */ 2335| 4.30k| nStackAtom[++nTopStackAtom] = (AT_NUMB)u; 2336| | /* output the starting atom */ 2337| 4.30k| k = 0; 2338| 4.30k| nOutputString[k] = u + 1; 2339| 4.30k| nOutputString[k + 1] = nNum_H ? 16 + nNum_H[u] : 0; ------------------ | Branch (2339:36): [True: 0, False: 4.30k] ------------------ 2340| 4.30k| nOutputString[k + 2] = '\0'; 2341| | 2342| 4.30k| do 2343| 26.7k| { 2344| | /* advance */ 2345| 53.0k| while (i = (int)nStackAtom[nTopStackAtom], j = (int)cNeighNumb[i] + 1, i < num_atoms && (int)nl[i][0] >= j) /* djb-rwth: additional condition to avoid buffer overruns */ ------------------ | Branch (2345:24): [True: 26.2k, False: 26.7k] | Branch (2345:88): [True: 53.0k, False: 0] | Branch (2345:105): [True: 26.2k, False: 26.7k] ------------------ 2346| | /*while ( (int)nl[i=nStackAtom[nTopStackAtom]][0] >= (j = (int)cNeighNumb[i]+1) )*/ 2347| | /* replaced due to missing sequence point; undefined behavior, reported by Geoffrey Hutchison */ 2348| 26.2k| { 2349| 26.2k| k += 3; 2350| 26.2k| if (k + 6 > nTotOutputStringLen) ------------------ | Branch (2350:25): [True: 0, False: 26.2k] ------------------ 2351| 0| { 2352| 0| goto exit_error; /* program error */ 2353| 0| } 2354| 26.2k| cNeighNumb[i]++; 2355| 26.2k| u = (int)nl[i][j]; /* neighbor */ 2356| | 2357| | /* output neighbor's canonical number */ 2358| 26.2k| nOutputString[k] = u + 1; 2359| | 2360| 26.2k| if (nDfsNumber[u] > nDfsNumber[i]) ------------------ | Branch (2360:25): [True: 22.4k, False: 3.87k] ------------------ 2361| 22.4k| { 2362| | /* tree edge, 1st visit -- advance */ 2363| | /* put 'unexplored' vertex u on the stack */ 2364| 22.4k| nStackAtom[++nTopStackAtom] = (AT_NUMB)u; 2365| | 2366| | /* output neighbor's number of H */ 2367| 22.4k| nOutputString[k + 1] = nNum_H ? 16 + nNum_H[u] : 0; ------------------ | Branch (2367:48): [True: 0, False: 22.4k] ------------------ 2368| 22.4k| } 2369| 3.87k| else 2370| 3.87k| { 2371| 3.87k| nOutputString[k + 1] = 0; 2372| 3.87k| } 2373| | /* output a delimiter preceding the neighbor */ 2374| 26.2k| if (1 < nl[i][0]) ------------------ | Branch (2374:25): [True: 9.58k, False: 16.7k] ------------------ 2375| 9.58k| { 2376| 9.58k| if (j == 1) ------------------ | Branch (2376:29): [True: 4.12k, False: 5.45k] ------------------ 2377| 4.12k| { 2378| 4.12k| cDelim = '('; 2379| 4.12k| } 2380| 5.45k| else 2381| 5.45k| { 2382| 5.45k| if (j == nl[i][0]) ------------------ | Branch (2382:33): [True: 4.12k, False: 1.32k] ------------------ 2383| 4.12k| { 2384| 4.12k| cDelim = ')'; 2385| 4.12k| } 2386| 1.32k| else 2387| 1.32k| { 2388| 1.32k| cDelim = ','; 2389| 1.32k| } 2390| 5.45k| } 2391| 9.58k| } 2392| 16.7k| else 2393| 16.7k| { 2394| 16.7k| cDelim = '-'; 2395| 16.7k| } 2396| 26.2k| nOutputString[k + 2] = cDelim; 2397| 26.2k| } 2398| | 2399| 26.7k| if ((i >= 0) && (i < num_atoms)) /* djb-rwth: fixing coverity ID #499483 */ ------------------ | Branch (2399:21): [True: 26.7k, False: 0] | Branch (2399:33): [True: 26.7k, False: 0] ------------------ 2400| 26.7k| { 2401| 26.7k| cNeighNumb[i] = 0; 2402| 26.7k| } 2403| | 2404| | /* back up: nothing else to do */ 2405| 26.7k| } while (--nTopStackAtom >= 0); ------------------ | Branch (2405:22): [True: 22.4k, False: 4.30k] ------------------ 2406| 4.30k| } 2407| 4.30k| } 2408| 4.30k| goto exit_function; 2409| | 2410| 4.30k|exit_error: 2411| 0| if (nOutputString) ------------------ | Branch (2411:9): [True: 0, False: 0] ------------------ 2412| 0| { 2413| 0| inchi_free(nOutputString); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2414| 0| nOutputString = NULL; 2415| 0| } 2416| | 2417| 4.30k|exit_function: 2418| 4.30k| if (nStackAtom) ------------------ | Branch (2418:9): [True: 4.30k, False: 0] ------------------ 2419| 4.30k| { 2420| 4.30k| inchi_free(nStackAtom); ------------------ | | 1152| 4.30k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 4.30k, False: 0] | | | Branch (1152:50): [Folded, False: 4.30k] | | ------------------ ------------------ 2421| 4.30k| } 2422| 4.30k| if (nNumDescendants) ------------------ | Branch (2422:9): [True: 0, False: 4.30k] ------------------ 2423| 0| { 2424| 0| inchi_free(nNumDescendants); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2425| 0| } 2426| 4.30k| if (nDfsNumber) ------------------ | Branch (2426:9): [True: 4.30k, False: 0] ------------------ 2427| 4.30k| { 2428| 4.30k| inchi_free(nDfsNumber); ------------------ | | 1152| 4.30k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 4.30k, False: 0] | | | Branch (1152:50): [Folded, False: 4.30k] | | ------------------ ------------------ 2429| 4.30k| } 2430| 4.30k| if (cNeighNumb) ------------------ | Branch (2430:9): [True: 4.30k, False: 0] ------------------ 2431| 4.30k| { 2432| 4.30k| inchi_free(cNeighNumb); ------------------ | | 1152| 4.30k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 4.30k, False: 0] | | | Branch (1152:50): [Folded, False: 4.30k] | | ------------------ ------------------ 2433| 4.30k| } 2434| 4.30k| if (nl) ------------------ | Branch (2434:9): [True: 4.30k, False: 0] ------------------ 2435| 4.30k| { 2436| 4.30k| FreeNeighList(nl); 2437| 4.30k| } 2438| | 2439| 4.30k| return nOutputString; 2440| 0|} CompareReversedStereoINChI: 2522| 61.0k|{ 2523| 61.0k| if (s1 == NULL && s2 == NULL) ------------------ | Branch (2523:9): [True: 60.7k, False: 344] | Branch (2523:23): [True: 30.4k, False: 30.2k] ------------------ 2524| 30.4k| { 2525| 30.4k| return 0; 2526| 30.4k| } 2527| 30.5k| if ((s1 == NULL) ^ (s2 == NULL)) ------------------ | Branch (2527:9): [True: 30.2k, False: 306] ------------------ 2528| 30.2k| { 2529| 30.2k| INChI_Stereo* s = s1 ? s1 : s2; ------------------ | Branch (2529:27): [True: 38, False: 30.2k] ------------------ 2530| 30.2k| if (s->nNumberOfStereoCenters || s->nNumberOfStereoBonds) ------------------ | Branch (2530:13): [True: 63, False: 30.2k] | Branch (2530:42): [True: 33, False: 30.1k] ------------------ 2531| 96| { 2532| 96| return 20; /* Diff: Missing Stereo */ 2533| 96| } 2534| 30.1k| else 2535| 30.1k| { 2536| 30.1k| return 0; 2537| 30.1k| } 2538| 30.2k| } 2539| | 2540| 306| if (s1->nNumberOfStereoCenters != s2->nNumberOfStereoCenters) ------------------ | Branch (2540:9): [True: 81, False: 225] ------------------ 2541| 81| { 2542| 81| return 21; /* Diff: Number of sp3 stereocenters */ 2543| 81| } 2544| 225| if (s1->nNumberOfStereoCenters > 0) ------------------ | Branch (2544:9): [True: 89, False: 136] ------------------ 2545| 89| { 2546| 89| if (memcmp(s1->nNumber, s2->nNumber, s1->nNumberOfStereoCenters * sizeof(s1->nNumber[0]))) ------------------ | Branch (2546:13): [True: 27, False: 62] ------------------ 2547| 27| { 2548| 27| return 22; /* Diff: sp3 stereocenter locations */ 2549| 27| } 2550| 62| if (memcmp(s1->t_parity, s2->t_parity, s1->nNumberOfStereoCenters * sizeof(s1->t_parity[0]))) ------------------ | Branch (2550:13): [True: 11, False: 51] ------------------ 2551| 11| { 2552| 11| return 23; /* Diff: sp3 stereocenter parities */ 2553| 11| } 2554| 51| if (s1->nCompInv2Abs != s2->nCompInv2Abs && s1->nCompInv2Abs && s2->nCompInv2Abs) ------------------ | Branch (2554:13): [True: 8, False: 43] | Branch (2554:53): [True: 2, False: 6] | Branch (2554:73): [True: 0, False: 2] ------------------ 2555| 0| { 2556| 0| return 24; /* Diff: sp3 inversion */ 2557| 0| } 2558| | /* 2559| | if ( s1->nNumberInv && s2->nNumberInv ) { 2560| | if ( memcmp( s1->nNumberInv, s2->nNumberInv, s1->nNumberOfStereoCenters*sizeof(s1->nNumber[0]) ) ) 2561| | return 25; 2562| | if ( memcmp( s1->t_parityInv, s2->t_parityInv, s1->nNumberOfStereoCenters*sizeof(s1->t_parity[0]) ) ) 2563| | return 26; 2564| | if ( s1->nCompInv2Abs != s2->nCompInv2Abs || 2565| | s1->bTrivialInv != s2->bTrivialInv ) { 2566| | return 27; 2567| | } 2568| | } else 2569| | if ( s1->nNumberInv || s2->nNumberInv ) { 2570| | return 28; 2571| | } 2572| | */ 2573| 51| } 2574| 187| if (s1->nNumberOfStereoBonds != s2->nNumberOfStereoBonds) ------------------ | Branch (2574:9): [True: 60, False: 127] ------------------ 2575| 60| { 2576| 60| return 25; /* Diff: Number of stereobonds */ 2577| 60| } 2578| 127| if (s1->nNumberOfStereoBonds > 0) ------------------ | Branch (2578:9): [True: 12, False: 115] ------------------ 2579| 12| { 2580| 12| if (memcmp(s1->nBondAtom1, s2->nBondAtom1, s1->nNumberOfStereoBonds * sizeof(s1->nBondAtom1[0]))) ------------------ | Branch (2580:13): [True: 0, False: 12] ------------------ 2581| 0| { 2582| 0| return 26; /* Diff: Stereobond 1st atom locations */ 2583| 0| } 2584| 12| if (memcmp(s1->nBondAtom2, s2->nBondAtom2, s1->nNumberOfStereoBonds * sizeof(s1->nBondAtom2[0]))) ------------------ | Branch (2584:13): [True: 0, False: 12] ------------------ 2585| 0| { 2586| 0| return 27; /* Diff: Stereobond 2nd atom locations */ 2587| 0| } 2588| 12| if (memcmp(s1->b_parity, s2->b_parity, s1->nNumberOfStereoBonds * sizeof(s1->b_parity[0]))) ------------------ | Branch (2588:13): [True: 0, False: 12] ------------------ 2589| 0| { 2590| 0| return 28; /* Diff: Stereobond parities */ 2591| 0| } 2592| 12| } 2593| | 2594| 127| return 0; 2595| 127|} CompareReversedStereoINChI2: 2602| 41.3k|{ 2603| 41.3k| int ret = 0; 2604| 41.3k| int j1, j2, num_dif, num_extra_undf, num_miss_undf, num_in1_only, num_in2_only; /* djb-rwth: removing redundant variables */ 2605| 41.3k| int bAddSb = !(picr->num_sb_undef_in1_only + picr->num_sb_in1_only + picr->num_sb_in2_only); 2606| 41.3k| int bAddSc = !(picr->num_sc_undef_in1_only + picr->num_sc_in1_only + picr->num_sc_in2_only); 2607| | 2608| 41.3k| int nNumSc1 = s1 ? s1->nNumberOfStereoCenters : 0; ------------------ | Branch (2608:19): [True: 41.3k, False: 0] ------------------ 2609| 41.3k| int nNumSc2 = s2 ? s2->nNumberOfStereoCenters : 0; ------------------ | Branch (2609:19): [True: 1.84k, False: 39.4k] ------------------ 2610| 41.3k| int nNumSb1 = s1 ? s1->nNumberOfStereoBonds : 0; ------------------ | Branch (2610:19): [True: 41.3k, False: 0] ------------------ 2611| 41.3k| int nNumSb2 = s2 ? s2->nNumberOfStereoBonds : 0; ------------------ | Branch (2611:19): [True: 1.84k, False: 39.4k] ------------------ 2612| | 2613| | /* djb-rwth: redundant part of the condition corrected; fixing a NULL pointer dereference */ 2614| 41.3k| if (s1 && s2 && (nNumSc1 || nNumSc2) && (nNumSc1 != nNumSc2 || ------------------ | Branch (2614:9): [True: 41.3k, False: 0] | Branch (2614:15): [True: 1.84k, False: 39.4k] | Branch (2614:22): [True: 338, False: 1.51k] | Branch (2614:33): [True: 186, False: 1.32k] | Branch (2614:46): [True: 433, False: 91] ------------------ 2615| 91| memcmp(s1->nNumber, s2->nNumber, nNumSc1 * sizeof(s1->nNumber[0])) || ------------------ | Branch (2615:9): [True: 16, False: 75] ------------------ 2616| 75| memcmp(s1->t_parity, s2->t_parity, nNumSc1 * sizeof(s1->t_parity[0])))) ------------------ | Branch (2616:9): [True: 36, False: 39] ------------------ 2617| 485| { 2618| 485| num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; 2619| 1.19k| for (j1 = j2 = 0; j1 < nNumSc1 && j2 < nNumSc2; ) ------------------ | Branch (2619:27): [True: 883, False: 311] | Branch (2619:43): [True: 709, False: 174] ------------------ 2620| 709| { 2621| 709| if (s1->nNumber[j1] == s2->nNumber[j2]) ------------------ | Branch (2621:17): [True: 433, False: 276] ------------------ 2622| 433| { 2623| 433| if (s1->t_parity[j1] != s2->t_parity[j2]) /* djb-rwth: removing redundant code */ ------------------ | Branch (2623:21): [True: 267, False: 166] ------------------ 2624| 267| { 2625| 267| num_dif++; 2626| 267| } 2627| 433| j1++; 2628| 433| j2++; 2629| 433| } 2630| 276| else 2631| 276| { 2632| 276| if (s1->nNumber[j1] < s2->nNumber[j2]) ------------------ | Branch (2632:21): [True: 254, False: 22] ------------------ 2633| 254| { 2634| 254| num_in1_only++; 2635| 254| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 254|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2635:25): [True: 168, False: 86] ------------------ 2636| 168| { 2637| 168| num_extra_undf++; 2638| 168| } 2639| 254| if (bAddSc) ------------------ | Branch (2639:25): [True: 254, False: 0] ------------------ 2640| 254| { 2641| 254| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 375| 254|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2641:29): [True: 254, False: 0] ------------------ 2642| 254| { 2643| 254| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2644| 254| } 2645| 254| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 254|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2645:29): [True: 168, False: 86] ------------------ 2646| 168| { 2647| 168| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 378| 168|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2647:33): [True: 168, False: 0] ------------------ 2648| 168| { 2649| 168| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2650| 168| } 2651| 168| } 2652| 254| } 2653| 254| j1++; 2654| 254| } 2655| 22| else 2656| 22| { 2657| 22| num_in2_only++; 2658| 22| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 22|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2658:25): [True: 4, False: 18] ------------------ 2659| 4| { 2660| 4| num_miss_undf++; 2661| 4| } 2662| 22| if (bAddSc) ------------------ | Branch (2662:25): [True: 22, False: 0] ------------------ 2663| 22| { 2664| 22| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 376| 22|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2664:29): [True: 22, False: 0] ------------------ 2665| 22| { 2666| 22| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2667| 22| } 2668| 22| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 22|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2668:29): [True: 4, False: 18] ------------------ 2669| 4| { 2670| 4| if (picr->num_sc_undef_in2_only < ICR_MAX_SC_UNDF) ------------------ | | 378| 4|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2670:33): [True: 4, False: 0] ------------------ 2671| 4| { 2672| 4| picr->sc_undef_in2_only[picr->num_sc_undef_in2_only++] = j1; 2673| 4| } 2674| 4| } 2675| 22| } 2676| 22| j2++; 2677| 22| } 2678| 276| } 2679| 709| } 2680| 734| while (j1 < nNumSc1) ------------------ | Branch (2680:16): [True: 249, False: 485] ------------------ 2681| 249| { 2682| 249| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 249|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2682:17): [True: 233, False: 16] ------------------ 2683| 233| { 2684| 233| num_extra_undf++; 2685| 233| } 2686| 249| num_in1_only++; 2687| 249| if (bAddSc) ------------------ | Branch (2687:17): [True: 249, False: 0] ------------------ 2688| 249| { 2689| 249| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 375| 249|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2689:21): [True: 249, False: 0] ------------------ 2690| 249| { 2691| 249| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2692| 249| } 2693| 249| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 249|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2693:21): [True: 233, False: 16] ------------------ 2694| 233| { 2695| 233| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 378| 233|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2695:25): [True: 233, False: 0] ------------------ 2696| 233| { 2697| 233| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2698| 233| } 2699| 233| } 2700| 249| } 2701| 249| j1++; 2702| 249| } 2703| 790| while (j2 < nNumSc2) ------------------ | Branch (2703:16): [True: 305, False: 485] ------------------ 2704| 305| { 2705| 305| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 305|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2705:17): [True: 43, False: 262] ------------------ 2706| 43| { 2707| 43| num_miss_undf++; 2708| 43| } 2709| 305| num_in2_only++; 2710| 305| if (bAddSc) ------------------ | Branch (2710:17): [True: 305, False: 0] ------------------ 2711| 305| { 2712| 305| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 376| 305|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2712:21): [True: 305, False: 0] ------------------ 2713| 305| { 2714| 305| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2715| 305| } 2716| 305| } 2717| 305| j2++; 2718| 305| } 2719| 485| if (num_dif) ------------------ | Branch (2719:13): [True: 216, False: 269] ------------------ 2720| 216| { 2721| 216| ret |= IDIF_SC_PARITY; 2722| 216| } 2723| 485| if (num_in1_only) ------------------ | Branch (2723:13): [True: 246, False: 239] ------------------ 2724| 246| { 2725| 246| if (num_extra_undf) ------------------ | Branch (2725:17): [True: 200, False: 46] ------------------ 2726| 200| { 2727| 200| ret |= IDIF_SC_EXTRA_UNDF; 2728| 200| } 2729| 246| if (num_in1_only != num_extra_undf) ------------------ | Branch (2729:17): [True: 95, False: 151] ------------------ 2730| 95| { 2731| 95| ret |= IDIF_SC_EXTRA; 2732| 95| } 2733| 246| } 2734| 485| if (num_in2_only) ------------------ | Branch (2734:13): [True: 240, False: 245] ------------------ 2735| 240| { 2736| 240| if (num_miss_undf) ------------------ | Branch (2736:17): [True: 44, False: 196] ------------------ 2737| 44| { 2738| 44| ret |= IDIF_SC_MISS_UNDF; 2739| 44| } 2740| 240| if (num_in2_only != num_miss_undf) ------------------ | Branch (2740:17): [True: 206, False: 34] ------------------ 2741| 206| { 2742| 206| ret |= IDIF_SC_MISS; 2743| 206| } 2744| 240| } 2745| 485| } 2746| 41.3k| if (s1 && s2 && s1->nCompInv2Abs != s2->nCompInv2Abs && s1->nCompInv2Abs && s2->nCompInv2Abs) ------------------ | Branch (2746:9): [True: 41.3k, False: 0] | Branch (2746:15): [True: 1.84k, False: 39.4k] | Branch (2746:21): [True: 156, False: 1.69k] | Branch (2746:61): [True: 148, False: 8] | Branch (2746:81): [True: 5, False: 143] ------------------ 2747| 5| { 2748| 5| ret |= IDIF_SC_INV; 2749| 5| } 2750| | 2751| 41.3k| if ((nNumSb1 || nNumSb2) && ------------------ | Branch (2751:10): [True: 317, False: 41.0k] | Branch (2751:21): [True: 570, False: 40.4k] ------------------ 2752| 887| (nNumSb1 != nNumSb2 || ------------------ | Branch (2752:10): [True: 760, False: 127] ------------------ 2753| 127| memcmp(s1->nBondAtom1, s2->nBondAtom1, nNumSb1 * sizeof(s1->nBondAtom1[0])) || ------------------ | Branch (2753:13): [True: 41, False: 86] ------------------ 2754| 86| memcmp(s1->nBondAtom2, s2->nBondAtom2, nNumSb1 * sizeof(s1->nBondAtom2[0])) || ------------------ | Branch (2754:13): [True: 0, False: 86] ------------------ 2755| 86| memcmp(s1->b_parity, s2->b_parity, nNumSb1 * sizeof(s1->b_parity[0])))) ------------------ | Branch (2755:13): [True: 6, False: 80] ------------------ 2756| 807| { 2757| 807| num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; /* djb-rwth: removing redundant code */ 2758| 1.39k| for (j1 = j2 = 0; j1 < nNumSb1 && j2 < nNumSb2; ) ------------------ | Branch (2758:27): [True: 747, False: 652] | Branch (2758:43): [True: 592, False: 155] ------------------ 2759| 592| { 2760| 592| if (s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && ------------------ | Branch (2760:17): [True: 225, False: 367] ------------------ 2761| 225| s1->nBondAtom2[j1] == s2->nBondAtom2[j2]) ------------------ | Branch (2761:17): [True: 195, False: 30] ------------------ 2762| 195| { 2763| 195| if (s1->b_parity[j1] != s2->b_parity[j2]) /* djb-rwth: removing redundant code */ ------------------ | Branch (2763:21): [True: 78, False: 117] ------------------ 2764| 78| { 2765| 78| num_dif++; 2766| 78| } 2767| 195| j1++; 2768| 195| j2++; 2769| 195| } 2770| 397| else 2771| 397| { 2772| 397| if (s1->nBondAtom1[j1] < s2->nBondAtom1[j2] || ------------------ | Branch (2772:21): [True: 337, False: 60] ------------------ 2773| 60| (s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && s1->nBondAtom2[j1] < s2->nBondAtom2[j2])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2773:22): [True: 30, False: 30] | Branch (2773:66): [True: 30, False: 0] ------------------ 2774| 367| { 2775| 367| num_in1_only++; 2776| 367| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 367|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2776:25): [True: 282, False: 85] ------------------ 2777| 282| { 2778| 282| num_extra_undf++; 2779| 282| } 2780| 367| if (bAddSb) ------------------ | Branch (2780:25): [True: 367, False: 0] ------------------ 2781| 367| { 2782| 367| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 373| 367|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2782:29): [True: 367, False: 0] ------------------ 2783| 367| { 2784| 367| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2785| 367| } 2786| 367| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 367|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2786:29): [True: 282, False: 85] ------------------ 2787| 282| { 2788| 282| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 282|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2788:33): [True: 282, False: 0] ------------------ 2789| 282| { 2790| 282| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2791| 282| } 2792| 282| } 2793| 367| } 2794| 367| j1++; 2795| 367| } 2796| 30| else 2797| 30| { 2798| 30| num_in2_only++; 2799| 30| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 30|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2799:25): [True: 24, False: 6] ------------------ 2800| 24| { 2801| 24| num_miss_undf++; 2802| 24| } 2803| 30| if (bAddSb) ------------------ | Branch (2803:25): [True: 30, False: 0] ------------------ 2804| 30| { 2805| 30| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 374| 30|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2805:29): [True: 30, False: 0] ------------------ 2806| 30| { 2807| 30| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2808| 30| } 2809| 30| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 30|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2809:29): [True: 24, False: 6] ------------------ 2810| 24| { 2811| 24| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 24|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2811:33): [True: 24, False: 0] ------------------ 2812| 24| { 2813| 24| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2814| 24| } 2815| 24| } 2816| 30| } 2817| 30| j2++; 2818| 30| } 2819| 397| } 2820| 592| } 2821| 1.40k| while (j1 < nNumSb1) ------------------ | Branch (2821:16): [True: 597, False: 807] ------------------ 2822| 597| { 2823| 597| num_in1_only++; 2824| 597| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 597|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2824:17): [True: 549, False: 48] ------------------ 2825| 549| { 2826| 549| num_extra_undf++; 2827| 549| } 2828| 597| if (bAddSb) ------------------ | Branch (2828:17): [True: 597, False: 0] ------------------ 2829| 597| { 2830| 597| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 373| 597|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2830:21): [True: 597, False: 0] ------------------ 2831| 597| { 2832| 597| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2833| 597| } 2834| 597| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 597|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2834:21): [True: 549, False: 48] ------------------ 2835| 549| { 2836| 549| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 549|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2836:25): [True: 549, False: 0] ------------------ 2837| 549| { 2838| 549| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2839| 549| } 2840| 549| } 2841| 597| } 2842| 597| j1++; 2843| 597| } 2844| 1.69k| while (j2 < nNumSb2) ------------------ | Branch (2844:16): [True: 885, False: 807] ------------------ 2845| 885| { 2846| 885| num_in2_only++; 2847| 885| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 885|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2847:17): [True: 148, False: 737] ------------------ 2848| 148| { 2849| 148| num_miss_undf++; 2850| 148| } 2851| 885| if (bAddSb) ------------------ | Branch (2851:17): [True: 885, False: 0] ------------------ 2852| 885| { 2853| 885| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 374| 885|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2853:21): [True: 885, False: 0] ------------------ 2854| 885| { 2855| 885| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2856| 885| } 2857| 885| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 885|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2857:21): [True: 148, False: 737] ------------------ 2858| 148| { 2859| 148| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 148|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2859:25): [True: 148, False: 0] ------------------ 2860| 148| { 2861| 148| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2862| 148| } 2863| 148| } 2864| 885| } 2865| 885| j2++; 2866| 885| } 2867| 807| if (num_dif) ------------------ | Branch (2867:13): [True: 60, False: 747] ------------------ 2868| 60| { 2869| 60| ret |= IDIF_SB_PARITY; 2870| 60| } 2871| 807| if (num_in1_only) ------------------ | Branch (2871:13): [True: 225, False: 582] ------------------ 2872| 225| { 2873| 225| if (num_extra_undf) ------------------ | Branch (2873:17): [True: 208, False: 17] ------------------ 2874| 208| { 2875| 208| ret |= IDIF_SB_EXTRA_UNDF; 2876| 208| } 2877| 225| if (num_in1_only != num_extra_undf) ------------------ | Branch (2877:17): [True: 102, False: 123] ------------------ 2878| 102| { 2879| 102| ret |= IDIF_SB_EXTRA; 2880| 102| } 2881| 225| } 2882| 807| if (num_in2_only) ------------------ | Branch (2882:13): [True: 637, False: 170] ------------------ 2883| 637| { 2884| 637| if (num_miss_undf) ------------------ | Branch (2884:17): [True: 151, False: 486] ------------------ 2885| 151| { 2886| 151| ret |= IDIF_SB_MISS_UNDF; 2887| 151| } 2888| 637| if (num_in2_only != num_miss_undf) ------------------ | Branch (2888:17): [True: 541, False: 96] ------------------ 2889| 541| { 2890| 541| ret |= IDIF_SB_MISS; 2891| 541| } 2892| 637| } 2893| 807| } 2894| | 2895| 41.3k| return ret; 2896| 41.3k|} CompareReversedINChI: 2904| 31.7k|{ 2905| 31.7k| int ret; 2906| | 2907| 31.7k| if (i1 == NULL && i2 == NULL) ------------------ | Branch (2907:9): [True: 0, False: 31.7k] | Branch (2907:23): [True: 0, False: 0] ------------------ 2908| 0| { 2909| 0| return 0; 2910| 0| } 2911| 31.7k| if ((i1 == NULL) ^ (i2 == NULL)) ------------------ | Branch (2911:9): [True: 0, False: 31.7k] ------------------ 2912| 0| { 2913| 0| return 1; /* Diff: Missing InChI */ 2914| 0| } 2915| | 2916| 31.7k| if (i1->nErrorCode == i2->nErrorCode) ------------------ | Branch (2916:9): [True: 31.7k, False: 0] ------------------ 2917| 31.7k| { 2918| 31.7k| if (i1->nErrorCode) ------------------ | Branch (2918:13): [True: 0, False: 31.7k] ------------------ 2919| 0| { 2920| 0| return 0; 2921| 0| } 2922| 31.7k| } 2923| 0| else 2924| 0| { 2925| 0| return 2; /* Diff: Error codes */ 2926| 0| } 2927| 31.7k| if (i1->bDeleted != i2->bDeleted) ------------------ | Branch (2927:9): [True: 0, False: 31.7k] ------------------ 2928| 0| { 2929| 0| return 1; /* Diff: Missing InChI */ 2930| 0| } 2931| 31.7k| if (i1->nNumberOfAtoms != i2->nNumberOfAtoms) ------------------ | Branch (2931:9): [True: 0, False: 31.7k] ------------------ 2932| 0| { 2933| 0| return 3; /* Diff: Num. atoms */ 2934| 0| } 2935| | 2936| 31.7k| if (i1->nNumberOfAtoms > 0) ------------------ | Branch (2936:9): [True: 31.7k, False: 0] ------------------ 2937| 31.7k| { 2938| 31.7k| if (memcmp(i1->nAtom, i2->nAtom, i1->nNumberOfAtoms * sizeof(i1->nAtom[0]))) ------------------ | Branch (2938:13): [True: 0, False: 31.7k] ------------------ 2939| 0| { 2940| 0| return 4; /* Diff: Elements */ 2941| 0| } 2942| 31.7k| if (strcmp(i1->szHillFormula, i2->szHillFormula)) ------------------ | Branch (2942:13): [True: 286, False: 31.4k] ------------------ 2943| 286| { 2944| 286| return 7; /* Diff: Hill Formulas */ 2945| 286| } 2946| 31.4k| if (memcmp(i1->nNum_H, i2->nNum_H, i1->nNumberOfAtoms * sizeof(i1->nNum_H[0]))) ------------------ | Branch (2946:13): [True: 554, False: 30.8k] ------------------ 2947| 554| { 2948| 554| if (i1->lenConnTable > 1 || i2->lenConnTable > 1) ------------------ | Branch (2948:17): [True: 547, False: 7] | Branch (2948:41): [True: 0, False: 7] ------------------ 2949| 547| { 2950| 547| return 5; /* Diff: H Locations (mobile H present) */ 2951| 547| } 2952| 7| else 2953| 7| { 2954| 7| return 6; /* Diff: H Locations (no mobile H) */ 2955| 7| } 2956| 554| } 2957| | 2958| | /* fixed H */ 2959| 30.8k| if (i1->nNum_H_fixed || i2->nNum_H_fixed) ------------------ | Branch (2959:13): [True: 0, False: 30.8k] | Branch (2959:33): [True: 108, False: 30.7k] ------------------ 2960| 108| { 2961| 108| int bHasFixedH1 = 0, bHasFixedH2 = 0, i, j1, j2; 2962| 108| if (i1->nNum_H_fixed) ------------------ | Branch (2962:17): [True: 0, False: 108] ------------------ 2963| 0| { 2964| 0| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2964:29): [True: 0, False: 0] ------------------ 2965| 0| { 2966| 0| if (i1->nNum_H_fixed[i]) ------------------ | Branch (2966:25): [True: 0, False: 0] ------------------ 2967| 0| { 2968| 0| bHasFixedH1++; 2969| 0| } 2970| 0| } 2971| 0| } 2972| 108| if (i2->nNum_H_fixed) ------------------ | Branch (2972:17): [True: 108, False: 0] ------------------ 2973| 108| { 2974| 650| for (i = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (2974:29): [True: 542, False: 108] ------------------ 2975| 542| { 2976| 542| if (i2->nNum_H_fixed[i]) ------------------ | Branch (2976:25): [True: 0, False: 542] ------------------ 2977| 0| { 2978| 0| bHasFixedH2++; 2979| 0| } 2980| 542| } 2981| 108| } 2982| | 2983| | /* count the differences */ 2984| 108| j1 = j2 = 0; 2985| 108| if (bHasFixedH1 && !bHasFixedH2) ------------------ | Branch (2985:17): [True: 0, False: 108] | Branch (2985:32): [True: 0, False: 0] ------------------ 2986| 0| { 2987| 0| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2987:29): [True: 0, False: 0] ------------------ 2988| 0| { 2989| 0| if (i1->nNum_H_fixed[i] > 0) ------------------ | Branch (2989:25): [True: 0, False: 0] ------------------ 2990| 0| { 2991| 0| j1++; 2992| 0| } 2993| 0| else 2994| 0| if (i1->nNum_H_fixed[i] < 0) ------------------ | Branch (2994:29): [True: 0, False: 0] ------------------ 2995| 0| { 2996| 0| j2++; 2997| 0| } 2998| 0| } 2999| 0| return 18; /* Diff: Extra Fixed-H */ 3000| 0| } 3001| 108| else 3002| 108| { 3003| 108| if (!bHasFixedH1 && bHasFixedH2) ------------------ | Branch (3003:21): [True: 108, False: 0] | Branch (3003:37): [True: 0, False: 108] ------------------ 3004| 0| { 3005| 0| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3005:43): [True: 0, False: 0] ------------------ 3006| 0| { 3007| 0| if (0 > i2->nNum_H_fixed[i]) ------------------ | Branch (3007:29): [True: 0, False: 0] ------------------ 3008| 0| { 3009| 0| j1++; 3010| 0| } 3011| 0| else 3012| 0| if (0 < i2->nNum_H_fixed[i]) ------------------ | Branch (3012:33): [True: 0, False: 0] ------------------ 3013| 0| { 3014| 0| j2++; 3015| 0| } 3016| 0| } 3017| 0| return 19; /* Diff: Missed Fixed-H */ 3018| 0| } 3019| 108| else 3020| 108| { 3021| 108| if (bHasFixedH1 && bHasFixedH2 && ------------------ | Branch (3021:25): [True: 0, False: 108] | Branch (3021:40): [True: 0, False: 0] ------------------ 3022| 0| memcmp(i1->nNum_H_fixed, i2->nNum_H_fixed, i1->nNumberOfAtoms * sizeof(i1->nNum_H_fixed[0]))) ------------------ | Branch (3022:25): [True: 0, False: 0] ------------------ 3023| 0| { 3024| 0| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3024:47): [True: 0, False: 0] ------------------ 3025| 0| { 3026| 0| if (i1->nNum_H_fixed[i] > i2->nNum_H_fixed[i]) ------------------ | Branch (3026:33): [True: 0, False: 0] ------------------ 3027| 0| { 3028| 0| j1++; 3029| 0| } 3030| 0| else 3031| 0| { 3032| 0| if (i1->nNum_H_fixed[i] < i2->nNum_H_fixed[i]) ------------------ | Branch (3032:37): [True: 0, False: 0] ------------------ 3033| 0| { 3034| 0| j2++; 3035| 0| } 3036| 0| } 3037| 0| } 3038| 0| } 3039| 108| } 3040| 108| } 3041| 108| ret = (j1 && j2) ? 20 : j1 ? 18 : j2 ? 19 : 0; ------------------ | Branch (3041:20): [True: 0, False: 108] | Branch (3041:26): [True: 0, False: 0] | Branch (3041:37): [True: 0, False: 108] | Branch (3041:47): [True: 0, False: 108] ------------------ 3042| 108| if (ret) ------------------ | Branch (3042:17): [True: 0, False: 108] ------------------ 3043| 0| { 3044| 0| return ret; /* 20 => Diff: NotEql Fixed-H */ 3045| | /* 19 => Diff: Missed Fixed-H (i1 has less) */ 3046| | /* 18 => Diff: Extra Fixed-H (i1 has more) */ 3047| 0| } 3048| 108| } 3049| 30.8k| } 3050| | 3051| 30.8k| if (i1->lenConnTable != i2->lenConnTable) ------------------ | Branch (3051:9): [True: 0, False: 30.8k] ------------------ 3052| 0| { 3053| 0| return 8; /* Diff: Connections length */ 3054| 0| } 3055| 30.8k| if (i1->lenConnTable > 0 && memcmp(i1->nConnTable, i2->nConnTable, i1->lenConnTable * sizeof(i1->nConnTable[0]))) ------------------ | Branch (3055:9): [True: 30.8k, False: 0] | Branch (3055:33): [True: 1, False: 30.8k] ------------------ 3056| 1| { 3057| 1| return 9; /* Diff: Connections */ 3058| 1| } 3059| | 3060| | /* output special cases: different number of t-groups, different sizes of t-groups, different endpoints */ 3061| 30.8k| if (i1->lenTautomer != i2->lenTautomer && (i1->lenTautomer > 1 || i2->lenTautomer > 1)) ------------------ | Branch (3061:9): [True: 150, False: 30.7k] | Branch (3061:48): [True: 150, False: 0] | Branch (3061:71): [True: 0, False: 0] ------------------ 3062| 150| { 3063| 150| return 10; /* Diff: Mobile groups length */ /* in isotopic or deprotonated cases i1->lenTautomer == 1 && i1->nTautomer[0] = 0 */ 3064| 150| } 3065| 30.7k| if ((i1->lenTautomer > 1 && i2->lenTautomer > 1) && ------------------ | Branch (3065:10): [True: 0, False: 30.7k] | Branch (3065:33): [True: 0, False: 0] ------------------ 3066| 0| memcmp(i1->nTautomer, i2->nTautomer, i1->lenTautomer * sizeof(i1->nTautomer[0]))) ------------------ | Branch (3066:9): [True: 0, False: 0] ------------------ 3067| 0| { 3068| 0| return 11; /* Diff: Mobile groups */ 3069| 0| } 3070| | 3071| 30.7k| if (i1->nNumberOfIsotopicAtoms != i2->nNumberOfIsotopicAtoms) ------------------ | Branch (3071:9): [True: 67, False: 30.6k] ------------------ 3072| 67| { 3073| 67| return 12; /* Diff: Isotopic atoms number */ 3074| 67| } 3075| 30.6k| if (i1->nNumberOfIsotopicAtoms > 0 && memcmp(i1->IsotopicAtom, i2->IsotopicAtom, i1->nNumberOfIsotopicAtoms * sizeof(i1->IsotopicAtom[0]))) ------------------ | Branch (3075:9): [True: 49, False: 30.5k] | Branch (3075:43): [True: 1, False: 48] ------------------ 3076| 1| { 3077| 1| return 13; /* Diff: Isotopic atoms */ 3078| 1| } 3079| 30.6k| if (i1->nTotalCharge != i2->nTotalCharge) ------------------ | Branch (3079:9): [True: 0, False: 30.6k] ------------------ 3080| 0| { 3081| 0| return 14; /* Diff: Charge */ 3082| 0| } 3083| | 3084| | /* 3085| | if ( i1->nNumberOfIsotopicTGroups != i2->nNumberOfIsotopicTGroups ) 3086| | { 3087| | return 14; 3088| | } 3089| | if ( i1->nNumberOfIsotopicTGroups > 0 && memcmp( i1->IsotopicTGroup, i2->IsotopicTGroup, i1->nNumberOfIsotopicTGroups*sizeof(i1->IsotopicTGroup[0]) ) ) 3090| | { 3091| | return 15; 3092| | } 3093| | */ 3094| | 3095| 30.6k| if (a1 && a2) ------------------ | Branch (3095:9): [True: 0, False: 30.6k] | Branch (3095:15): [True: 0, False: 0] ------------------ 3096| 0| { 3097| 0| if (a1->nNumRemovedProtons != a2->nNumRemovedProtons) ------------------ | Branch (3097:13): [True: 0, False: 0] ------------------ 3098| 0| { 3099| 0| return 16; /* Diff: Number of removed protons */ 3100| 0| } 3101| 0| if (memcmp(a1->nNumRemovedIsotopicH, a2->nNumRemovedIsotopicH, sizeof(a1->nNumRemovedIsotopicH))) ------------------ | Branch (3101:13): [True: 0, False: 0] ------------------ 3102| 0| { 3103| 0| return 17; /* Diff: Removed isotopic H */ 3104| 0| } 3105| 0| } 3106| | 3107| | /* 3108| | if ( i1->nPossibleLocationsOfIsotopicH && i2->nPossibleLocationsOfIsotopicH ) { 3109| | { 3110| | if ( i1->nPossibleLocationsOfIsotopicH[0] != i2->nPossibleLocationsOfIsotopicH[0] || 3111| | memcmp(i1->nPossibleLocationsOfIsotopicH, i2->nPossibleLocationsOfIsotopicH, 3112| | sizeof(i1->nPossibleLocationsOfIsotopicH[0])*i1->nPossibleLocationsOfIsotopicH[0]) ) 3113| | { 3114| | return 18; 3115| | } 3116| | } 3117| | } else 3118| | { 3119| | if ( !i1->nPossibleLocationsOfIsotopicH != !i2->nPossibleLocationsOfIsotopicH ) { 3120| | { 3121| | return 19;} 3122| | } 3123| | } 3124| | */ 3125| | 3126| | /* ret = 20..31 => 40..51 */ 3127| 30.6k| if ((ret = CompareReversedStereoINChI(i1->Stereo, i2->Stereo))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3127:9): [True: 238, False: 30.4k] ------------------ 3128| 238| { 3129| 238| return ret + 20; 3130| 238| } 3131| | /* ret = 40..51 => 60..71 */ 3132| | 3133| 30.4k| if (!i2->StereoIsotopic && i2->Stereo && i1->StereoIsotopic && ------------------ | Branch (3133:9): [True: 202, False: 30.2k] | Branch (3133:32): [True: 84, False: 118] | Branch (3133:46): [True: 23, False: 61] ------------------ 3134| 23| 0 < (i1->StereoIsotopic->nNumberOfStereoBonds + i1->StereoIsotopic->nNumberOfStereoCenters) && ------------------ | Branch (3134:9): [True: 10, False: 13] ------------------ 3135| 10| 0 == CompareReversedStereoINChI(i1->StereoIsotopic, i2->Stereo)) ------------------ | Branch (3135:9): [True: 6, False: 4] ------------------ 3136| 6| { 3137| | /* InChI from reversed structure does not contain fully duplicated isotopic stereo */ 3138| 6| ; 3139| 6| } 3140| 30.3k| else 3141| 30.3k| { 3142| 30.3k| if ((ret = CompareReversedStereoINChI(i1->StereoIsotopic, i2->StereoIsotopic))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3142:13): [True: 33, False: 30.3k] ------------------ 3143| 33| { 3144| 33| return ret + 40; 3145| 33| } 3146| 30.3k| } 3147| | 3148| 30.3k| return 0; 3149| 30.4k|} CompareIcr: 3158| 76|{ 3159| 76| int nNumExtraBits1 = 0, nNumExtraBits2 = 0, bit1, bit2; 3160| 76| INCHI_MODE Flg1 = picr1->flags, Flg2 = picr2->flags, cur_bit = 1, in1, in2; 3161| 76| int i, ret; 3162| | 3163| | /* compare flags */ 3164| 76| in1 = in2 = 0; 3165| 2.04k| for (i = 0; Flg1 || Flg2; i++, Flg1 >>= 1, Flg2 >>= 1, cur_bit <<= 1) ------------------ | Branch (3165:17): [True: 1.83k, False: 218] | Branch (3165:25): [True: 142, False: 76] ------------------ 3166| 1.97k| { 3167| 1.97k| if (!(mask & cur_bit)) ------------------ | Branch (3167:13): [True: 1.02k, False: 948] ------------------ 3168| 1.02k| { 3169| 1.02k| continue; 3170| 1.02k| } 3171| 948| bit1 = Flg1 & 1; 3172| 948| bit2 = Flg2 & 1; 3173| 948| if (bit1 && !bit2) ------------------ | Branch (3173:13): [True: 114, False: 834] | Branch (3173:21): [True: 21, False: 93] ------------------ 3174| 21| { 3175| 21| in1 |= 1 << i; 3176| 21| nNumExtraBits1++; 3177| 21| } 3178| 927| else 3179| 927| { 3180| 927| if (!bit1 && bit2) ------------------ | Branch (3180:17): [True: 834, False: 93] | Branch (3180:26): [True: 24, False: 810] ------------------ 3181| 24| { 3182| 24| in2 |= 1 << i; 3183| 24| nNumExtraBits2++; 3184| 24| } 3185| 927| } 3186| 948| } 3187| 76| if (nNumExtraBits1 && !nNumExtraBits2) ------------------ | Branch (3187:9): [True: 8, False: 68] | Branch (3187:27): [True: 6, False: 2] ------------------ 3188| 6| { 3189| 6| ret = 1; 3190| 6| } 3191| 70| else 3192| 70| { 3193| 70| if (!nNumExtraBits1 && nNumExtraBits2) ------------------ | Branch (3193:13): [True: 68, False: 2] | Branch (3193:32): [True: 7, False: 61] ------------------ 3194| 7| { 3195| 7| ret = -1; 3196| 7| } 3197| 63| else 3198| 63| { 3199| 63| if (!in1 && !in2) ------------------ | Branch (3199:17): [True: 61, False: 2] | Branch (3199:25): [True: 61, False: 0] ------------------ 3200| 61| { 3201| 61| ret = 0; 3202| 61| } 3203| 2| else 3204| 2| { 3205| 2| ret = 2; /* compare produced undefined results */ 3206| 2| } 3207| 63| } 3208| 70| } 3209| | 3210| 76| if (pin1) ------------------ | Branch (3210:9): [True: 0, False: 76] ------------------ 3211| 0| { 3212| 0| *pin1 = in1; 3213| 0| } 3214| 76| if (pin2) ------------------ | Branch (3214:9): [True: 0, False: 76] ------------------ 3215| 0| { 3216| 0| *pin2 = in2; 3217| 0| } 3218| | 3219| | /* more detailed compare not implemented */ 3220| | 3221| 76| return ret; 3222| 76|} CompareReversedINChI2: 3232| 115k|{ 3233| 115k| INCHI_MODE ret = 0; 3234| 115k| INChI_Stereo* Stereo1 = NULL, * Stereo2 = NULL; 3235| 115k| int n1, n2, m, j, j1, j2, ret2, num_H1, num_H2; 3236| | 3237| 115k| *err = 0; 3238| | 3239| 115k| memset(picr, 0, sizeof(*picr)); /* djb-rwth: memset_s C11/Annex K variant? */ 3240| | 3241| 115k| if (i1 == NULL && i2 == NULL) ------------------ | Branch (3241:9): [True: 22, False: 115k] | Branch (3241:23): [True: 0, False: 22] ------------------ 3242| 0| { 3243| 0| return 0; 3244| 0| } 3245| 115k| if ((i1 == NULL) ^ (i2 == NULL)) ------------------ | Branch (3245:9): [True: 22, False: 115k] ------------------ 3246| 22| { 3247| 22| ret |= IDIF_PROBLEM; /* one InChI exists while another doesn't */ 3248| 22| goto exit_function; 3249| 22| } 3250| | 3251| 115k| if (i1->nErrorCode == i2->nErrorCode) ------------------ | Branch (3251:9): [True: 115k, False: 0] ------------------ 3252| 115k| { 3253| 115k| if (i1->nErrorCode) ------------------ | Branch (3253:13): [True: 0, False: 115k] ------------------ 3254| 0| { 3255| 0| ret |= IDIF_PROBLEM; /* both InChI have same error codes */ 3256| 0| goto exit_function; 3257| 0| } 3258| 115k| } 3259| 0| else 3260| 0| { 3261| 0| ret |= IDIF_PROBLEM; /* at least one InChI has an error code */ 3262| 0| goto exit_function; 3263| 0| } 3264| | 3265| 115k| if (i1->nNumberOfAtoms != i2->nNumberOfAtoms) ------------------ | Branch (3265:9): [True: 0, False: 115k] ------------------ 3266| 0| { 3267| 0| ret |= IDIF_NUM_AT; 3268| 0| goto exit_function; 3269| 0| } 3270| 115k| if (i1->nNumberOfAtoms > 0) ------------------ | Branch (3270:9): [True: 115k, False: 0] ------------------ 3271| 115k| { 3272| 115k| if (memcmp(i1->nAtom, i2->nAtom, i1->nNumberOfAtoms * sizeof(i1->nAtom[0]))) ------------------ | Branch (3272:13): [True: 57.4k, False: 58.3k] ------------------ 3273| 57.4k| { 3274| 57.4k| ret |= IDIF_ATOMS; 3275| 57.4k| goto exit_function; 3276| 57.4k| } 3277| | /* IDIF_NON_TAUT_H, IDIF_MORE_FH, IDIF_LESS_FH */ 3278| 58.3k| if (memcmp(i1->nNum_H, i2->nNum_H, i1->nNumberOfAtoms * sizeof(i1->nNum_H[0]))) ------------------ | Branch (3278:13): [True: 3.51k, False: 54.8k] ------------------ 3279| 3.51k| { 3280| 3.51k| ret |= IDIF_POSITION_H; 3281| 26.0k| for (j1 = 0; j1 < i1->nNumberOfAtoms; j1++) ------------------ | Branch (3281:26): [True: 22.4k, False: 3.51k] ------------------ 3282| 22.4k| { 3283| 22.4k| if (i1->nNum_H[j1] != i2->nNum_H[j1] && picr->num_diff_pos_H < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 5.03k|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3283:21): [True: 5.03k, False: 17.4k] | Branch (3283:57): [True: 5.03k, False: 0] ------------------ 3284| 5.03k| { 3285| 5.03k| picr->diff_pos_H_at[picr->num_diff_pos_H] = j1; 3286| 5.03k| picr->diff_pos_H_nH[picr->num_diff_pos_H] = i1->nNum_H[j1] - i2->nNum_H[j1]; 3287| 5.03k| picr->num_diff_pos_H++; 3288| 5.03k| } 3289| 22.4k| } 3290| 3.51k| } 3291| | /* fixed H */ 3292| 58.3k| if (i1->nNum_H_fixed || i2->nNum_H_fixed) ------------------ | Branch (3292:13): [True: 58.3k, False: 0] | Branch (3292:33): [True: 0, False: 0] ------------------ 3293| 58.3k| { 3294| 58.3k| int bHasFixedH1 = 0, bHasFixedH2 = 0, i; 3295| 58.3k| if (i1->nNum_H_fixed) ------------------ | Branch (3295:17): [True: 58.3k, False: 0] ------------------ 3296| 58.3k| { 3297| 358k| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3297:29): [True: 300k, False: 58.3k] ------------------ 3298| 300k| { 3299| 300k| if (i1->nNum_H_fixed[i]) ------------------ | Branch (3299:25): [True: 655, False: 299k] ------------------ 3300| 655| { 3301| 655| bHasFixedH1++; 3302| 655| } 3303| 300k| } 3304| 58.3k| } 3305| 58.3k| if (i2->nNum_H_fixed) ------------------ | Branch (3305:17): [True: 888, False: 57.5k] ------------------ 3306| 888| { 3307| 7.27k| for (i = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (3307:29): [True: 6.38k, False: 888] ------------------ 3308| 6.38k| { 3309| 6.38k| if (i2->nNum_H_fixed[i]) ------------------ | Branch (3309:25): [True: 1.64k, False: 4.74k] ------------------ 3310| 1.64k| { 3311| 1.64k| bHasFixedH2++; 3312| 1.64k| } 3313| 6.38k| } 3314| 888| } 3315| 58.3k| if (bHasFixedH1 && !bHasFixedH2) ------------------ | Branch (3315:17): [True: 532, False: 57.8k] | Branch (3315:32): [True: 135, False: 397] ------------------ 3316| 135| { 3317| 846| for (i = j = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3317:33): [True: 711, False: 135] ------------------ 3318| 711| { 3319| 711| if (i1->nNum_H_fixed[i]) ------------------ | Branch (3319:25): [True: 170, False: 541] ------------------ 3320| 170| { 3321| 170| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 170|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3321:29): [True: 170, False: 0] ------------------ 3322| 170| { 3323| 170| picr->fixed_H_at1_more[j] = i; 3324| 170| picr->fixed_H_nH1_more[j] = i1->nNum_H_fixed[i]; 3325| 170| j++; 3326| 170| } 3327| 170| } 3328| 711| } 3329| 135| picr->num_fixed_H1_more = j; 3330| 135| ret |= IDIF_MORE_FH; /* Extra Fixed-H */ 3331| 135| } 3332| 58.2k| else 3333| 58.2k| { 3334| 58.2k| if (!bHasFixedH1 && bHasFixedH2) ------------------ | Branch (3334:21): [True: 57.8k, False: 397] | Branch (3334:37): [True: 360, False: 57.4k] ------------------ 3335| 360| { 3336| 3.00k| for (i = j = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (3336:37): [True: 2.64k, False: 360] ------------------ 3337| 2.64k| { 3338| 2.64k| if (i2->nNum_H_fixed[i]) ------------------ | Branch (3338:29): [True: 768, False: 1.87k] ------------------ 3339| 768| { 3340| 768| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 768|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3340:33): [True: 768, False: 0] ------------------ 3341| 768| { 3342| 768| picr->fixed_H_at2_more[j] = i; 3343| 768| picr->fixed_H_nH2_more[j] = i2->nNum_H_fixed[i]; 3344| 768| j++; 3345| 768| } 3346| 768| } 3347| 2.64k| } 3348| 360| picr->num_fixed_H2_more = j; 3349| 360| ret |= IDIF_LESS_FH; /* Missed Fixed-H */ 3350| 360| } 3351| 57.8k| else 3352| 57.8k| { 3353| 57.8k| if (bHasFixedH1 && bHasFixedH2 && ------------------ | Branch (3353:25): [True: 397, False: 57.4k] | Branch (3353:40): [True: 397, False: 0] ------------------ 3354| 397| memcmp(i1->nNum_H_fixed, i2->nNum_H_fixed, i1->nNumberOfAtoms * sizeof(i1->nNum_H_fixed[0]))) ------------------ | Branch (3354:25): [True: 385, False: 12] ------------------ 3355| 385| { 3356| 3.25k| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3356:47): [True: 2.87k, False: 385] ------------------ 3357| 2.87k| { 3358| 2.87k| if (i1->nNum_H_fixed[i] > i2->nNum_H_fixed[i]) ------------------ | Branch (3358:33): [True: 503, False: 2.36k] ------------------ 3359| 503| { 3360| 503| if (j1 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 503|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3360:37): [True: 503, False: 0] ------------------ 3361| 503| { 3362| 503| picr->fixed_H_at1_more[j1] = i; 3363| 503| picr->fixed_H_nH1_more[j1] = i1->nNum_H_fixed[i] - i2->nNum_H_fixed[i]; 3364| 503| j1++; 3365| 503| } 3366| 503| } 3367| 2.36k| else 3368| 2.36k| { 3369| 2.36k| if (i1->nNum_H_fixed[i] < i2->nNum_H_fixed[i]) ------------------ | Branch (3369:37): [True: 239, False: 2.13k] ------------------ 3370| 239| { 3371| 239| if (j2 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 239|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3371:41): [True: 239, False: 0] ------------------ 3372| 239| { 3373| 239| picr->fixed_H_at2_more[j2] = i; 3374| 239| picr->fixed_H_nH2_more[j2] = i2->nNum_H_fixed[i] - i1->nNum_H_fixed[i]; 3375| 239| j2++; 3376| 239| } 3377| 239| } 3378| 2.36k| } 3379| 2.87k| } 3380| 385| ret |= (j1 ? IDIF_MORE_FH : 0) | (j2 ? IDIF_LESS_FH : 0); ------------------ | Branch (3380:33): [True: 363, False: 22] | Branch (3380:59): [True: 191, False: 194] ------------------ 3381| 385| picr->num_fixed_H1_more = j1; 3382| 385| picr->num_fixed_H2_more = j2; 3383| 385| } 3384| 57.8k| } 3385| 58.2k| } 3386| 58.3k| } 3387| 58.3k| } 3388| | 3389| | /* compare formulas and H */ 3390| 58.3k| num_H1 = 0; 3391| 58.3k| num_H2 = 0; 3392| 58.3k| ret2 = CompareHillFormulasNoH(i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2); 3393| 58.3k| picr->tot_num_H1 = num_H1; 3394| 58.3k| picr->tot_num_H2 = num_H2; 3395| 58.3k| if (ret2) ------------------ | Branch (3395:9): [True: 8.62k, False: 49.7k] ------------------ 3396| 8.62k| { 3397| 8.62k| ret |= IDIF_NUM_EL; 3398| 8.62k| goto exit_function; 3399| 8.62k| } 3400| 49.7k| if (num_H1 > num_H2) ------------------ | Branch (3400:9): [True: 31.1k, False: 18.6k] ------------------ 3401| 31.1k| { 3402| 31.1k| ret |= IDIF_MORE_H; 3403| 31.1k| } 3404| 49.7k| if (num_H1 < num_H2) ------------------ | Branch (3404:9): [True: 1.07k, False: 48.6k] ------------------ 3405| 1.07k| { 3406| 1.07k| ret |= IDIF_LESS_H; 3407| 1.07k| } 3408| 49.7k| if (i1->lenConnTable != i2->lenConnTable) ------------------ | Branch (3408:9): [True: 1.18k, False: 48.5k] ------------------ 3409| 1.18k| { 3410| 1.18k| ret |= IDIF_CON_LEN; 3411| 1.18k| goto exit_function; 3412| 1.18k| } 3413| 48.5k| else 3414| 48.5k| { 3415| 48.5k| if (i1->lenConnTable > 0 && memcmp(i1->nConnTable, i2->nConnTable, i1->lenConnTable * sizeof(i1->nConnTable[0]))) ------------------ | Branch (3415:13): [True: 48.5k, False: 0] | Branch (3415:37): [True: 7.26k, False: 41.3k] ------------------ 3416| 7.26k| { 3417| 7.26k| ret |= IDIF_CON_TBL; 3418| 7.26k| goto exit_function; 3419| 7.26k| } 3420| 48.5k| } 3421| | 3422| | /* output special cases: different number of t-groups, different sizes of t-groups, different endpoints */ 3423| | /* in isotopic or deprotonated cases i1->lenTautomer == 1 && i1->nTautomer[0] = 0 */ 3424| | 3425| | /* 3426| | if ( i1->lenTautomer != i2->lenTautomer && (i1->lenTautomer > 1 || i2->lenTautomer > 1) ) { 3427| | ret |= IDIF_TAUT_LEN; 3428| | } 3429| | */ 3430| | 3431| | /* compare number of t-groups */ 3432| 41.3k| n1 = i1->lenTautomer ? i1->nTautomer[0] : 0; ------------------ | Branch (3432:10): [True: 3.35k, False: 37.9k] ------------------ 3433| 41.3k| n2 = i2->lenTautomer ? i2->nTautomer[0] : 0; ------------------ | Branch (3433:10): [True: 1.68k, False: 39.6k] ------------------ 3434| 41.3k| if (!n1 && n2) ------------------ | Branch (3434:9): [True: 39.7k, False: 1.59k] | Branch (3434:16): [True: 1.12k, False: 38.6k] ------------------ 3435| 1.12k| { 3436| 1.12k| ret |= IDIF_NO_TAUT; 3437| 1.12k| } 3438| 40.1k| else 3439| 40.1k| { 3440| 40.1k| if (n1 && !n2) ------------------ | Branch (3440:13): [True: 1.59k, False: 38.6k] | Branch (3440:19): [True: 1.02k, False: 562] ------------------ 3441| 1.02k| { 3442| 1.02k| ret |= IDIF_WRONG_TAUT; 3443| 1.02k| } 3444| 39.1k| else 3445| 39.1k| { 3446| 39.1k| if (n1 == 1 && n2 > 1) ------------------ | Branch (3446:17): [True: 526, False: 38.6k] | Branch (3446:28): [True: 46, False: 480] ------------------ 3447| 46| { 3448| 46| ret |= IDIF_SINGLE_TG; 3449| 46| } 3450| 39.1k| else 3451| 39.1k| { 3452| 39.1k| if (n1 > 1 && n2 == 1) ------------------ | Branch (3452:21): [True: 36, False: 39.0k] | Branch (3452:31): [True: 21, False: 15] ------------------ 3453| 21| { 3454| 21| ret |= IDIF_MULTIPLE_TG; 3455| 21| } 3456| 39.1k| else 3457| 39.1k| { 3458| 39.1k| if (n1 != n2) ------------------ | Branch (3458:25): [True: 6, False: 39.0k] ------------------ 3459| 6| { 3460| 6| ret |= IDIF_NUM_TG; 3461| 6| } 3462| 39.1k| } 3463| 39.1k| } 3464| 39.1k| } 3465| 40.1k| } 3466| | 3467| 41.3k| if (n1 || n2) ------------------ | Branch (3467:9): [True: 1.59k, False: 39.7k] | Branch (3467:15): [True: 1.12k, False: 38.6k] ------------------ 3468| 2.71k| { 3469| | /* number of endpoints */ 3470| 2.71k| int num1 = 0, num2 = 0, num_M1 = 0, num_M2 = 0; 3471| 2.71k| int len, num_eq, num_in1_only, num_in2_only; 3472| 2.71k| AT_NUMB* pe1 = (AT_NUMB*)inchi_malloc(((long long)i1->lenTautomer + 1) * sizeof(pe1[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 2.71k|#define inchi_malloc malloc ------------------ 3473| 2.71k| AT_NUMB* pe2 = (AT_NUMB*)inchi_malloc(((long long)i2->lenTautomer + 1) * sizeof(pe2[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 2.71k|#define inchi_malloc malloc ------------------ 3474| 2.71k| num_H1 = num_H2 = 0; 3475| | /* collect endpoints, H, (-) */ 3476| 2.71k| if (!pe1 || !pe2) ------------------ | Branch (3476:13): [True: 0, False: 2.71k] | Branch (3476:21): [True: 0, False: 2.71k] ------------------ 3477| 0| { 3478| 0| if (pe1) ------------------ | Branch (3478:17): [True: 0, False: 0] ------------------ 3479| 0| { 3480| 0| inchi_free(pe1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3481| 0| } 3482| 0| if (pe2) ------------------ | Branch (3482:17): [True: 0, False: 0] ------------------ 3483| 0| { 3484| 0| inchi_free(pe2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3485| 0| } 3486| 0| *err = -1; /* allocation error */ 3487| 0| goto exit_function; 3488| 0| } 3489| 4.39k| for (m = 1; m < i1->lenTautomer; m += len) ------------------ | Branch (3489:21): [True: 1.68k, False: 2.71k] ------------------ 3490| 1.68k| { 3491| 1.68k| len = i1->nTautomer[m++]; 3492| 1.68k| num_H1 += i1->nTautomer[m]; 3493| 1.68k| num_M1 += i1->nTautomer[m + 1]; 3494| 5.85k| for (j = 2; j < len; j++) ------------------ | Branch (3494:25): [True: 4.16k, False: 1.68k] ------------------ 3495| 4.16k| { 3496| 4.16k| pe1[num1++] = i1->nTautomer[m + j]; 3497| 4.16k| } 3498| 1.68k| } 3499| 4.49k| for (m = 1; m < i2->lenTautomer; m += len) ------------------ | Branch (3499:21): [True: 1.78k, False: 2.71k] ------------------ 3500| 1.78k| { 3501| 1.78k| len = i2->nTautomer[m++]; 3502| 1.78k| num_H2 += i2->nTautomer[m]; 3503| 1.78k| num_M2 += i2->nTautomer[m + 1]; 3504| 5.78k| for (j = 2; j < len; j++) ------------------ | Branch (3504:25): [True: 4.00k, False: 1.78k] ------------------ 3505| 4.00k| { 3506| 4.00k| pe2[num2++] = i2->nTautomer[m + j]; 3507| 4.00k| } 3508| 1.78k| } 3509| 2.71k| picr->num_taut_H1 = num_H1; 3510| 2.71k| picr->num_taut_H2 = num_H2; 3511| 2.71k| picr->num_taut_M1 = num_M1; 3512| 2.71k| picr->num_taut_M2 = num_M2; 3513| | /* sort endpoints */ 3514| 2.71k| insertions_sort_AT_RANK(pe1, num1); 3515| 2.71k| insertions_sort_AT_RANK(pe2, num2); 3516| | /* compare */ 3517| | /* 3518| | if ( num1 < num2 ) { 3519| | ret |= IDIF_LESS_TG_ENDP; 3520| | } else 3521| | if ( num1 > num2 ) { 3522| | ret |= IDIF_MORE_TG_ENDP; 3523| | } 3524| | */ 3525| | /* compare all */ 3526| 2.71k| num_eq = num_in1_only = num_in2_only = 0; 3527| 4.55k| for (j1 = j2 = 0; j1 < num1 && j2 < num2; ) ------------------ | Branch (3527:27): [True: 3.06k, False: 1.48k] | Branch (3527:40): [True: 1.83k, False: 1.22k] ------------------ 3528| 1.83k| { 3529| 1.83k| if (pe1[j1] == pe2[j2]) ------------------ | Branch (3529:17): [True: 611, False: 1.22k] ------------------ 3530| 611| { 3531| 611| j1++; 3532| 611| j2++; 3533| 611| num_eq++; 3534| 611| } 3535| 1.22k| else 3536| 1.22k| { 3537| 1.22k| if (pe1[j1] < pe2[j2]) ------------------ | Branch (3537:21): [True: 464, False: 763] ------------------ 3538| 464| { /* BC: fixed, was pe2[j1] 2006-03-27 */ 3539| 464| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 370| 464|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (3539:25): [True: 464, False: 0] ------------------ 3540| 464| { 3541| 464| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 3542| 464| } 3543| 464| j1++; 3544| 464| num_in1_only++; 3545| 464| } 3546| 763| else 3547| 763| { 3548| 763| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 371| 763|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (3548:25): [True: 763, False: 0] ------------------ 3549| 763| { 3550| 763| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 3551| 763| } 3552| 763| j2++; 3553| 763| num_in2_only++; 3554| 763| } 3555| 1.22k| } 3556| 1.83k| } 3557| 5.80k| while (j1 < num1) ------------------ | Branch (3557:16): [True: 3.08k, False: 2.71k] ------------------ 3558| 3.08k| { 3559| 3.08k| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 370| 3.08k|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (3559:17): [True: 3.08k, False: 0] ------------------ 3560| 3.08k| { 3561| 3.08k| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 3562| 3.08k| } 3563| 3.08k| j1++; 3564| 3.08k| num_in1_only++; 3565| 3.08k| } 3566| 5.34k| while (j2 < num2) ------------------ | Branch (3566:16): [True: 2.63k, False: 2.71k] ------------------ 3567| 2.63k| { 3568| 2.63k| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 371| 2.63k|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (3568:17): [True: 2.63k, False: 0] ------------------ 3569| 2.63k| { 3570| 2.63k| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 3571| 2.63k| } 3572| 2.63k| j2++; 3573| 2.63k| num_in2_only++; 3574| 2.63k| } 3575| 2.71k| if (num_in1_only) ------------------ | Branch (3575:13): [True: 1.51k, False: 1.20k] ------------------ 3576| 1.51k| { 3577| 1.51k| ret |= IDIF_EXTRA_TG_ENDP; 3578| 1.51k| } 3579| 2.71k| if (num_in2_only) ------------------ | Branch (3579:13): [True: 1.55k, False: 1.15k] ------------------ 3580| 1.55k| { 3581| 1.55k| ret |= IDIF_MISS_TG_ENDP; 3582| 1.55k| } 3583| 2.71k| if (!num_in1_only && !num_in2_only && num_eq) ------------------ | Branch (3583:13): [True: 1.20k, False: 1.51k] | Branch (3583:30): [True: 31, False: 1.17k] | Branch (3583:47): [True: 31, False: 0] ------------------ 3584| 31| { 3585| 31| ; /* same t-groups endpoints */ 3586| 31| } 3587| 2.68k| else 3588| 2.68k| { 3589| 2.68k| ret |= IDIF_DIFF_TG_ENDP; 3590| 2.68k| } 3591| 2.71k| inchi_free(pe1); ------------------ | | 1152| 2.71k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 2.71k, False: 0] | | | Branch (1152:50): [Folded, False: 2.71k] | | ------------------ ------------------ 3592| 2.71k| inchi_free(pe2); ------------------ | | 1152| 2.71k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 2.71k, False: 0] | | | Branch (1152:50): [Folded, False: 2.71k] | | ------------------ ------------------ 3593| 2.71k| } 3594| | 3595| 41.3k| if ((i1->lenTautomer > 1 && i2->lenTautomer > 1) && ------------------ | Branch (3595:10): [True: 1.59k, False: 39.7k] | Branch (3595:33): [True: 562, False: 1.02k] ------------------ 3596| 562| (i1->lenTautomer != i2->lenTautomer || ------------------ | Branch (3596:10): [True: 416, False: 146] ------------------ 3597| 146| memcmp(i1->nTautomer, i2->nTautomer, i1->lenTautomer * sizeof(i1->nTautomer[0])))) ------------------ | Branch (3597:13): [True: 143, False: 3] ------------------ 3598| 559| { 3599| 559| ret |= IDIF_TG; 3600| 559| } 3601| | 3602| 41.3k| if (i1->nNumberOfIsotopicAtoms != i2->nNumberOfIsotopicAtoms) ------------------ | Branch (3602:9): [True: 127, False: 41.1k] ------------------ 3603| 127| { 3604| 127| ret |= IDIF_NUM_ISO_AT; 3605| 127| } 3606| 41.1k| else 3607| 41.1k| { 3608| 41.1k| if (i1->nNumberOfIsotopicAtoms > 0 && memcmp(i1->IsotopicAtom, i2->IsotopicAtom, i1->nNumberOfIsotopicAtoms * sizeof(i1->IsotopicAtom[0]))) ------------------ | Branch (3608:13): [True: 516, False: 40.6k] | Branch (3608:47): [True: 310, False: 206] ------------------ 3609| 310| { 3610| 310| ret |= IDIF_ISO_AT; 3611| 310| } 3612| 41.1k| } 3613| 41.3k| if (i1->nTotalCharge != i2->nTotalCharge) ------------------ | Branch (3613:9): [True: 3.26k, False: 38.0k] ------------------ 3614| 3.26k| { 3615| 3.26k| ret |= IDIF_CHARGE; 3616| 3.26k| } 3617| 41.3k| if (a1 && a1->nNumRemovedProtons && (!a2 || a2->nNumRemovedProtons != a1->nNumRemovedProtons)) ------------------ | Branch (3617:9): [True: 41.3k, False: 0] | Branch (3617:15): [True: 2.71k, False: 38.6k] | Branch (3617:42): [True: 2.71k, False: 0] | Branch (3617:49): [True: 0, False: 0] ------------------ 3618| 2.71k| { 3619| 2.71k| ret |= IDIF_REM_PROT; 3620| 2.71k| } 3621| 41.3k| if (a1 && (!a2 || ------------------ | Branch (3621:9): [True: 41.3k, False: 0] | Branch (3621:16): [True: 41.3k, False: 0] ------------------ 3622| 0| a2->nNumRemovedIsotopicH[0] != a1->nNumRemovedIsotopicH[0] || ------------------ | Branch (3622:9): [True: 0, False: 0] ------------------ 3623| 0| a2->nNumRemovedIsotopicH[1] != a1->nNumRemovedIsotopicH[1] || ------------------ | Branch (3623:9): [True: 0, False: 0] ------------------ 3624| 0| a2->nNumRemovedIsotopicH[2] != a1->nNumRemovedIsotopicH[2])) ------------------ | Branch (3624:9): [True: 0, False: 0] ------------------ 3625| 41.3k| { 3626| 41.3k| ret |= IDIF_REM_ISO_H; 3627| 41.3k| } 3628| | 3629| | /* 3630| | if ( i1->nPossibleLocationsOfIsotopicH && i2->nPossibleLocationsOfIsotopicH ) { 3631| | if ( i1->nPossibleLocationsOfIsotopicH[0] != i2->nPossibleLocationsOfIsotopicH[0] || 3632| | memcmp(i1->nPossibleLocationsOfIsotopicH, i2->nPossibleLocationsOfIsotopicH, 3633| | sizeof(i1->nPossibleLocationsOfIsotopicH[0])*i1->nPossibleLocationsOfIsotopicH[0]) ) 3634| | return 18; 3635| | } else 3636| | if ( !i1->nPossibleLocationsOfIsotopicH != !i2->nPossibleLocationsOfIsotopicH ) { 3637| | return 19; 3638| | } 3639| | */ 3640| | 3641| 41.3k| if (i1->StereoIsotopic && ------------------ | Branch (3641:9): [True: 619, False: 40.7k] ------------------ 3642| 619| i1->StereoIsotopic->nNumberOfStereoBonds + i1->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3642:9): [True: 170, False: 449] ------------------ 3643| 170| { 3644| 170| Stereo1 = i1->StereoIsotopic; 3645| 170| } 3646| 41.1k| else 3647| 41.1k| { 3648| 41.1k| Stereo1 = i1->Stereo; 3649| 41.1k| } 3650| 41.3k| if (i2->StereoIsotopic && ------------------ | Branch (3650:9): [True: 552, False: 40.7k] ------------------ 3651| 552| i2->StereoIsotopic->nNumberOfStereoBonds + i2->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3651:9): [True: 313, False: 239] ------------------ 3652| 313| { 3653| 313| Stereo2 = i2->StereoIsotopic; 3654| 313| } 3655| 41.0k| else 3656| 41.0k| { 3657| 41.0k| Stereo2 = i2->Stereo; 3658| 41.0k| } 3659| 41.3k| ret |= CompareReversedStereoINChI2(Stereo1, Stereo2, picr); 3660| | 3661| 115k|exit_function: 3662| | 3663| 115k| picr->flags = ret; 3664| | 3665| 115k| return ret; 3666| 41.3k|} Create_INChI: 3687| 252k|{ 3688| | /* 3689| | #define NON_TAUT 0 3690| | #define TAUT 1 3691| | */ 3692| 252k| int nebend = 0, * ebend = NULL; 3693| | 3694| 252k| sp_ATOM* at[TAUT_NUM]; /* at[0]=>non-tautomeric, at[1]=>tautomeric */ 3695| 252k| int i, n1, n2, num_atoms, num_at_tg, num_removed_H, num_removed_H_taut = 0, ret = 0, ret2 = 0; 3696| 252k| INCHI_MODE nMode = 0; 3697| 252k| T_GROUP_INFO vt_group_info; 3698| 252k| T_GROUP_INFO vt_group_info_orig; 3699| 252k| T_GROUP_INFO* /*const*/ t_group_info = &vt_group_info; 3700| 252k| T_GROUP_INFO* /*const*/ t_group_info_orig = &vt_group_info_orig; 3701| | 3702| 252k| CANON_STAT CS, CS2; 3703| 252k| CANON_STAT* pCS = &CS; 3704| 252k| CANON_STAT* pCS2 = &CS2; /* save all allocations to avoid memory leaks in case Canon_INChI() removes the pointer */ 3705| | 3706| 252k| ATOM_SIZES s[TAUT_NUM]; 3707| | 3708| 252k| BCN Bcn; 3709| 252k| BCN* pBCN = &Bcn; 3710| | 3711| 252k| int bHasIsotopicAtoms = 0; 3712| 252k| int bMayHaveStereo = 0; 3713| 252k| int num_taut_at = 0; 3714| | 3715| 252k| inp_ATOM* out_at = NULL; /*, *norm_at_fixed_bonds[TAUT_NUM]; */ /* = {out_norm_nontaut_at, out_norm_taut_at} ; */ 3716| 252k| INChI* pINChI = NULL; /* added initialization 2006-03 */ 3717| 252k| INChI_Aux* pINChI_Aux = NULL; /* added initialization 2006-03 */ 3718| 252k| int bPointedEdgeStereo = ((TG_FLAG_POINTED_EDGE_STEREO & *pbTautFlags) ? PES_BIT_POINT_EDGE_STEREO : 0) ------------------ | | 937| 252k|#define TG_FLAG_POINTED_EDGE_STEREO 0x00002000 /* only pointed edge of stereo bond defines stereo */ ------------------ int bPointedEdgeStereo = ((TG_FLAG_POINTED_EDGE_STEREO & *pbTautFlags) ? PES_BIT_POINT_EDGE_STEREO : 0) ------------------ | | 44| 252k|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ | Branch (3718:38): [True: 252k, False: 0] ------------------ 3719| 252k| | ((TG_FLAG_PHOSPHINE_STEREO & *pbTautFlags) ? PES_BIT_PHOSPHINE_STEREO : 0) ------------------ | | 941| 252k|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ | ((TG_FLAG_PHOSPHINE_STEREO & *pbTautFlags) ? PES_BIT_PHOSPHINE_STEREO : 0) ------------------ | | 45| 116|#define PES_BIT_PHOSPHINE_STEREO 2 ------------------ | Branch (3719:12): [True: 116, False: 252k] ------------------ 3720| 252k| | ((TG_FLAG_ARSINE_STEREO & *pbTautFlags) ? PES_BIT_ARSINE_STEREO : 0) ------------------ | | 942| 252k|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ | ((TG_FLAG_ARSINE_STEREO & *pbTautFlags) ? PES_BIT_ARSINE_STEREO : 0) ------------------ | | 46| 3|#define PES_BIT_ARSINE_STEREO 4 ------------------ | Branch (3720:12): [True: 3, False: 252k] ------------------ 3721| 252k| | ((TG_FLAG_FIX_SP3_BUG & *pbTautFlags) ? PES_BIT_FIX_SP3_BUG : 0); ------------------ | | 944| 252k|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ | ((TG_FLAG_FIX_SP3_BUG & *pbTautFlags) ? PES_BIT_FIX_SP3_BUG : 0); ------------------ | | 47| 0|#define PES_BIT_FIX_SP3_BUG 8 ------------------ | Branch (3721:12): [True: 0, False: 252k] ------------------ 3722| 252k| INCHI_MODE bTautFlags = (*pbTautFlags & (~(INCHI_MODE)TG_FLAG_ALL_TAUTOMERIC)); ------------------ | | 926| 252k|#define TG_FLAG_ALL_TAUTOMERIC (TG_FLAG_TEST_TAUT__ATOMS| \ | | ------------------ | | | | 918| 252k|#define TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */ | | ------------------ | | 927| 252k| TG_FLAG_TEST_TAUT__SALTS| \ | | ------------------ | | | | 920| 252k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ | | ------------------ | | 928| 252k| TG_FLAG_TEST_TAUT2_SALTS| \ | | ------------------ | | | | 922| 252k|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ | | ------------------ | | 929| 252k| TG_FLAG_MERGE_TAUT_SALTS) | | ------------------ | | | | 924| 252k|#define TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */ | | ------------------ ------------------ 3723| 252k| INCHI_MODE bTautFlagsDone = (*pbTautFlagsDone /*& (~(INCHI_MODE)TG_FLAG_ALL_TAUTOMERIC) */); 3724| |#if ( bRELEASE_VERSION == 0 ) 3725| | int bExtract = 0; /* EXTR_HAS_ATOM_WITH_DEFINED_PARITY; */ 3726| |#endif 3727| | 3728| |#ifdef GHI100_FIX 3729| |#if ((SPRINTF_FLAG != 1) && (SPRINTF_FLAG != 2)) 3730| | setlocale(LC_ALL, "en-US"); /* djb-rwth: setting all locales to "en-US" */ 3731| |#endif 3732| |#endif 3733| | 3734| | /* */ 3735| 252k| int bFixIsoFixedH = 0; 3736| 252k| int bFixTermHChrg = 0; 3737| | 3738| 252k| int LargeMolecules = ip->bLargeMolecules; 3739| | /* djb-rwth: removing redundant variables */ 3740| | 3741| | /* vABParityUnknown holds actual value of an internal constant signifying 3742| | unknown parity: either the same as for undefined parity (default==standard) 3743| | or a specific one (non-std; requested by SLUUD switch). */ 3744| 252k| int vABParityUnknown = AB_PARITY_UNDF; ------------------ | | 222| 252k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 3745| 252k| if (0 != (nUserMode & REQ_MODE_DIFF_UU_STEREO)) ------------------ | | 40| 252k|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (3745:9): [True: 0, False: 252k] ------------------ 3746| 0| { 3747| | /* Make labels for unknown and undefined stereo different */ 3748| 0| vABParityUnknown = AB_PARITY_UNKN; ------------------ | | 221| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ 3749| 0| } 3750| | 3751| | /* djb-rwth: removing redundant code */ 3752| | 3753| 252k|#if ( FIX_ISO_FIXEDH_BUG == 1 ) 3754| 252k| if (TG_FLAG_FIX_ISO_FIXEDH_BUG & *pbTautFlags) ------------------ | | 950| 252k|#define TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */ ------------------ | Branch (3754:9): [True: 252k, False: 0] ------------------ 3755| 252k| bFixIsoFixedH = 1; 3756| 252k|#endif 3757| 252k|#if ( FIX_TERM_H_CHRG_BUG == 1 ) 3758| 252k| if (TG_FLAG_FIX_TERM_H_CHRG_BUG & *pbTautFlags) ------------------ | | 951| 252k|#define TG_FLAG_FIX_TERM_H_CHRG_BUG 0x00400000 /* fix bug found after v.102b (moving H charge in 'remove_terminal_HDT') */ ------------------ | Branch (3758:9): [True: 252k, False: 0] ------------------ 3759| 252k| bFixTermHChrg = 1; 3760| 252k|#endif 3761| | 3762| |#ifdef FIX_SRU_CYCLIZING_PS_BONDS_IN_BNS 3763| | /* Polymer related */ 3764| | if (orig_inp_data && orig_inp_data->polymer && orig_inp_data->polymer->n > 0 && orig_inp_data->polymer->valid) 3765| | { 3766| | int j, jj; 3767| | nebend = 0; 3768| | for (j = 0; j < orig_inp_data->polymer->n; j++) 3769| | if (orig_inp_data->polymer->units[j]->cyclized == 1) 3770| | nebend++; 3771| | if (nebend) 3772| | { 3773| | nebend *= 2; 3774| | ebend = inchi_calloc(2 * nebend, sizeof(int)); 3775| | if (!ebend) 3776| | { 3777| | ret = CT_OUT_OF_RAM; goto exit_function; 3778| | } 3779| | jj = 0; 3780| | for (j = 0; j < orig_inp_data->polymer->n; j++) 3781| | { 3782| | if (orig_inp_data->polymer->units[j]->cyclized == 1) 3783| | { 3784| | ebend[jj] = orig_inp_data->polymer->units[j]->end_atom1; 3785| | ebend[jj + 1] = orig_inp_data->polymer->units[j]->end_atom2; 3786| | jj += 2; 3787| | } 3788| | } 3789| | } 3790| | } 3791| |#endif 3792| | 3793| 252k| memset(s, 0, sizeof(s)); /* djb-rwth: memset_s C11/Annex K variant? */ 3794| 252k| if (pBCN) ------------------ | Branch (3794:9): [True: 252k, False: 0] ------------------ 3795| 252k| { 3796| 252k| memset(pBCN, 0, sizeof(pBCN[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 3797| 252k| } 3798| 252k| memset(t_group_info, 0, sizeof(*t_group_info)); /* djb-rwth: memset_s C11/Annex K variant? */ 3799| 252k| memset(t_group_info_orig, 0, sizeof(*t_group_info_orig)); /* djb-rwth: memset_s C11/Annex K variant? */ 3800| | /*norm_at[TAUT_NON] = out_norm_data[TAUT_NON]->at; *//* output normalized non-tautomeric component */ 3801| | /*norm_at[TAUT_YES] = out_norm_data[TAUT_YES]->at; *//* output normalized tautomeric component */ 3802| | /*norm_at_fixed_bonds[TAUT_NON] = NULL;*/ 3803| | /*norm_at_fixed_bonds[TAUT_YES] = out_norm_data[TAUT_YES]->at_fixed_bonds;*/ 3804| 756k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 756k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3804:17): [True: 504k, False: 252k] ------------------ 3805| 504k| { 3806| 504k| if (out_norm_data[i]->at) ------------------ | Branch (3806:13): [True: 289k, False: 214k] ------------------ 3807| 289k| { 3808| 289k| if (!(at[i] = (sp_ATOM*)inchi_malloc(num_inp_at * sizeof(*at[0])))) ------------------ | | 1143| 289k|#define inchi_malloc malloc ------------------ | Branch (3808:17): [True: 0, False: 289k] ------------------ 3809| 0| { 3810| 0| ret = -1; 3811| 0| } 3812| 289k| } 3813| 214k| else 3814| 214k| { 3815| 214k| at[i] = NULL; 3816| 214k| } 3817| 504k| } 3818| | 3819| 252k| if ((!out_norm_data[TAUT_NON]->at && !out_norm_data[TAUT_YES]->at) ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if ((!out_norm_data[TAUT_NON]->at && !out_norm_data[TAUT_YES]->at) ------------------ | | 575| 214k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3819:10): [True: 214k, False: 37.6k] | Branch (3819:42): [True: 0, False: 214k] ------------------ 3820| 252k| || !inp_at || ret) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3820:12): [True: 0, False: 252k] | Branch (3820:23): [True: 0, False: 252k] ------------------ 3821| 0| { 3822| 0| ret = -1; 3823| 0| goto exit_function; 3824| 0| } 3825| | 3826| | /* the first struct to process: tautomeric if exists else non-tautomeric */ 3827| 252k| out_at = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES]->at : out_norm_data[TAUT_NON]->at; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ out_at = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES]->at : out_norm_data[TAUT_NON]->at; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ out_at = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES]->at : out_norm_data[TAUT_NON]->at; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3827:14): [True: 252k, False: 0] ------------------ 3828| | /* copy the input structure to be normalized to the buffer for the normalization data */ 3829| 252k| memcpy(out_at, inp_at, num_inp_at * sizeof(out_at[0])); 3830| | /* tautomeric groups setting */ 3831| 252k| t_group_info->bIgnoreIsotopic = 0; /* include tautomeric group isotopic info in MarkTautomerGroups() */ 3832| 252k| t_group_info->bTautFlags = *pbTautFlags; 3833| 252k| t_group_info->bTautFlagsDone = *pbTautFlagsDone; 3834| 252k| t_group_info->t_group = NULL; /* djb-rwth: fixing oss-fuzz issue #70475 */ 3835| | 3836| | /* 3837| | Preprocess the structure 3838| | (here THE NUMBER OF ATOMS MAY BE REDUCED) 3839| | */ 3840| | 3841| | /* ??? Ambiguity: H-D may become HD or DH 3842| | (that is, H+implicit D or D+implicit H) */ 3843| 252k| if (TG_FLAG_H_ALREADY_REMOVED & bTautFlags) ------------------ | | 943| 252k|#define TG_FLAG_H_ALREADY_REMOVED 0x00020000 /* processing structure restored from InChI */ ------------------ | Branch (3843:9): [True: 146k, False: 106k] ------------------ 3844| 146k| { 3845| 146k| INP_ATOM_DATA* out_norm_data1 = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES] : ------------------ | | 575| 146k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ INP_ATOM_DATA* out_norm_data1 = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES] : ------------------ | | 575| 146k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3845:41): [True: 146k, False: 0] ------------------ 3846| 146k| out_norm_data[TAUT_NON]->at ? out_norm_data[TAUT_NON] : NULL; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ out_norm_data[TAUT_NON]->at ? out_norm_data[TAUT_NON] : NULL; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3846:13): [True: 0, False: 0] ------------------ 3847| 146k| if (out_norm_data1) ------------------ | Branch (3847:13): [True: 146k, False: 0] ------------------ 3848| 146k| { 3849| 146k| num_at_tg = 3850| 146k| num_atoms = out_norm_data1->num_at - out_norm_data1->num_removed_H; 3851| 146k| num_removed_H = out_norm_data1->num_removed_H; 3852| 146k| t_group_info->tni.nNumRemovedExplicitH = num_removed_H; 3853| 146k| } 3854| 0| else 3855| 0| { 3856| 0| ret = -1; 3857| 0| goto exit_function; 3858| 0| } 3859| 146k| } 3860| 106k| else 3861| 106k| { 3862| 106k| num_at_tg = num_atoms = remove_terminal_HDT(num_inp_at, out_at, bFixTermHChrg, keep_explicit_HDT); 3863| 106k| num_removed_H = num_inp_at - num_atoms; 3864| 106k| t_group_info->tni.nNumRemovedExplicitH = num_removed_H; 3865| 106k| add_DT_to_num_H(num_atoms, out_at); 3866| 106k| } 3867| | /*fix_odd_things( num_atoms, out_at );*/ 3868| 252k|#if ( FIND_RING_SYSTEMS == 1 ) 3869| 252k| MarkRingSystemsInp(out_at, num_atoms, 0); 3870| 252k|#endif 3871| | /* duplicate the preprocessed structure so that all supplied out_norm_data[]->at buffers are filled */ 3872| 252k| if (out_at != out_norm_data[TAUT_YES]->at && out_norm_data[TAUT_YES]->at) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (out_at != out_norm_data[TAUT_YES]->at && out_norm_data[TAUT_YES]->at) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3872:9): [True: 0, False: 252k] | Branch (3872:50): [True: 0, False: 0] ------------------ 3873| 0| { 3874| 0| memcpy(out_norm_data[TAUT_YES]->at, out_at, num_inp_at * sizeof(out_at[0])); ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3875| 0| } 3876| 252k| if (out_norm_data[TAUT_YES]->at_fixed_bonds && out_norm_data[TAUT_YES]->at) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (out_norm_data[TAUT_YES]->at_fixed_bonds && out_norm_data[TAUT_YES]->at) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3876:9): [True: 252k, False: 0] | Branch (3876:52): [True: 252k, False: 0] ------------------ 3877| 252k| { 3878| 252k| memcpy(out_norm_data[TAUT_YES]->at_fixed_bonds, out_at, num_inp_at * sizeof(out_at[0])); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3879| 252k| } 3880| 252k| if (out_at != out_norm_data[TAUT_NON]->at && out_norm_data[TAUT_NON]->at) ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (out_at != out_norm_data[TAUT_NON]->at && out_norm_data[TAUT_NON]->at) ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3880:9): [True: 252k, False: 0] | Branch (3880:50): [True: 37.6k, False: 214k] ------------------ 3881| 37.6k| { 3882| 37.6k| memcpy(out_norm_data[TAUT_NON]->at, out_at, num_inp_at * sizeof(out_at[0])); ------------------ | | 574| 37.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3883| 37.6k| } 3884| | 3885| | /* 3886| | ??? not true ??? duplicate inp_at and keep inp_at[] unchanged after terminal hydrogens removal 3887| | set stereo parities in taut_at[], non_taut_at[] 3888| | obtain max. lenghts of the name stereo parts 3889| | Ignore absence/presence of isotopic stereo for now 3890| | mark isotopic atoms 3891| | */ 3892| 252k| if (out_norm_data[TAUT_YES]->at && at[TAUT_YES]) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (out_norm_data[TAUT_YES]->at && at[TAUT_YES]) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3892:9): [True: 252k, False: 0] | Branch (3892:40): [True: 252k, False: 0] ------------------ 3893| 252k| { 3894| | /* final normalization of possibly tautomeric structure */ 3895| 252k| ret = mark_alt_bonds_and_taut_groups(ic, pCG, 3896| 252k| out_norm_data[TAUT_YES]->at, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3897| 252k| out_norm_data[TAUT_YES]->at_fixed_bonds, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3898| 252k| num_atoms, ulMaxTime, t_group_info, 3899| 252k| NULL, NULL, 3900| 252k| nebend, ebend); 3901| 252k| if (ret < 0) ------------------ | Branch (3901:13): [True: 12, False: 252k] ------------------ 3902| 12| { 3903| 12| goto exit_function;/* out of RAM or other normalization problem */ 3904| 12| } 3905| 252k| num_taut_at = ret; /* number of atoms without removed H? */ 3906| 252k| num_removed_H_taut = t_group_info->tni.nNumRemovedExplicitH; 3907| 252k| out_norm_data[TAUT_YES]->num_at = num_atoms + num_removed_H_taut; /* protons might have been removed */ ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3908| 252k| out_norm_data[TAUT_YES]->num_removed_H = num_removed_H_taut; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3909| 252k| out_norm_data[TAUT_YES]->nNumRemovedProtons += t_group_info->tni.nNumRemovedProtons; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3910| 1.00M| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 72| 1.00M|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3910:21): [True: 756k, False: 252k] ------------------ 3911| 756k| { 3912| 756k| out_norm_data[TAUT_YES]->nNumRemovedProtonsIsotopic[i] += ------------------ | | 575| 756k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3913| 756k| t_group_info->tni.nNumRemovedProtonsIsotopic[i] /*+ t_group_info->num_iso_H[i]*/; 3914| 756k| out_norm_data[TAUT_YES]->num_iso_H[i] += ------------------ | | 575| 756k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3915| 756k| t_group_info->num_iso_H[i]; 3916| 756k| } 3917| | /* mark deleted isolated tautomeric H(+) */ 3918| 252k| if (num_taut_at == 1 && ------------------ | Branch (3918:13): [True: 149k, False: 102k] ------------------ 3919| 149k| out_norm_data[TAUT_YES]->at[0].at_type == ATT_PROTON && ------------------ | | 575| 149k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ out_norm_data[TAUT_YES]->at[0].at_type == ATT_PROTON && ------------------ | | 43| 401k|#define ATT_PROTON 0x1000 ------------------ | Branch (3919:13): [True: 35.0k, False: 114k] ------------------ 3920| 35.0k| t_group_info && t_group_info->tni.nNumRemovedProtons == 1) ------------------ | Branch (3920:13): [True: 35.0k, False: 0] | Branch (3920:29): [True: 35.0k, False: 0] ------------------ 3921| 35.0k| { 3922| 35.0k| out_norm_data[TAUT_YES]->bDeleted = 1; ------------------ | | 575| 35.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3923| 35.0k| FreeInpAtom(&out_norm_data[TAUT_YES]->at_fixed_bonds); ------------------ | | 575| 35.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3924| 35.0k| } 3925| 217k| else 3926| 217k| { 3927| 217k| if ((t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT) && ------------------ | | 156| 217k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 146| 217k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 157| 217k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 217k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 158| 217k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 148| 217k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 159| 217k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 149| 217k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 160| 217k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 217k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 161| 217k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 151| 217k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 162| 217k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 153| 217k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 163| 217k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 152| 217k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (3927:17): [True: 4.59k, False: 212k] ------------------ 3928| 4.59k| out_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 575| 4.59k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3928:17): [True: 4.59k, False: 0] ------------------ 3929| 4.59k| { 3930| 4.59k| out_norm_data[TAUT_YES]->bTautPreprocessed = 1; ------------------ | | 575| 4.59k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3931| 4.59k| } 3932| 217k| } 3933| | 3934| | /* 3935| | if ( !(t_group_info->tni.bNormalizationFlags & (FLAG_NORM_CONSIDER_TAUT & ~FLAG_PROTON_SINGLE_REMOVED)) && 3936| | out_norm_data[TAUT_YES]->at_fixed_bonds) { 3937| | FreeInpAtom( &out_norm_data[TAUT_YES]->at_fixed_bonds ); 3938| | } 3939| | */ 3940| | 3941| | /*out_norm_data[TAUT_YES]->num_removed_H = num_removed_H_taut;*/ 3942| | 3943| 252k| out_norm_data[TAUT_YES]->bTautFlags = *pbTautFlags = t_group_info->bTautFlags; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3944| 252k| out_norm_data[TAUT_YES]->bTautFlagsDone = *pbTautFlagsDone = t_group_info->bTautFlagsDone; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3945| 252k| out_norm_data[TAUT_YES]->bNormalizationFlags = t_group_info->tni.bNormalizationFlags; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3946| | 3947| | /* create internal sp_ATOM at[] out of out_norm_data[]->at */ 3948| 252k| inp2spATOM(out_norm_data[TAUT_YES]->at, num_inp_at, at[TAUT_YES]); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ inp2spATOM(out_norm_data[TAUT_YES]->at, num_inp_at, at[TAUT_YES]); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3949| | 3950| | /* set stereo parities to at[]; nUserMode: accept alt. stereo bonds, min ring size */ 3951| 252k| ret = set_stereo_parity(pCG, out_norm_data[TAUT_YES]->at, at[TAUT_YES], ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ ret = set_stereo_parity(pCG, out_norm_data[TAUT_YES]->at, at[TAUT_YES], ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3952| 252k| num_taut_at, num_removed_H_taut, 3953| 252k| &s[TAUT_YES].nMaxNumStereoAtoms, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3954| 252k| &s[TAUT_YES].nMaxNumStereoBonds, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3955| 252k| nUserMode, bPointedEdgeStereo, 3956| 252k| vABParityUnknown, ip->bLooseTSACheck, ip->bStereoAtZz); 3957| | 3958| |#if ( bRELEASE_VERSION == 0 ) 3959| | if (0 < ret) 3960| | { 3961| | bExtract |= EXTR_HAS_ATOM_WITH_DEFINED_PARITY; 3962| | } 3963| | if (t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT) 3964| | { 3965| | bExtract |= EXTR_TAUT_TREATMENT_CHARGES; 3966| | } 3967| |#endif 3968| | 3969| 252k| if (RETURNED_ERROR(ret)) ------------------ | | 44| 252k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 252k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 252k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 252k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 252k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 252k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 252k, False: 0] | | | Branch (44:53): [True: 16, False: 252k] | | ------------------ ------------------ 3970| 16| { 3971| 16| goto exit_function; /* stereo bond error */ 3972| 16| } 3973| | 3974| 252k| s[TAUT_YES].bMayHaveStereo = ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3975| 252k| (s[TAUT_YES].nMaxNumStereoAtoms || ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3975:14): [True: 6.77k, False: 245k] ------------------ 3976| 245k| s[TAUT_YES].nMaxNumStereoBonds); ------------------ | | 575| 245k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3976:17): [True: 3.86k, False: 241k] ------------------ 3977| | 3978| | /* 3979| | mark isotopic atoms and atoms that have non-tautomeric 3980| | isotopic terminal hydrogen atoms 1H, 2H(D), 3H(T) 3981| | */ 3982| | 3983| 252k| s[TAUT_YES].num_isotopic_atoms = ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3984| 252k| set_atom_iso_sort_keys(num_taut_at, 3985| 252k| at[TAUT_YES], ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3986| 252k| t_group_info, 3987| 252k| &s[TAUT_YES].bHasIsotopicTautGroups); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3988| | 3989| | /* 3990| | Prepare tautomeric (if no tautomerism found then prepare non-tautomeric) 3991| | structure for canonicalizaton: 3992| | 3993| | remove t-groups that have no H, 3994| | remove charges from t-groups if requested 3995| | renumber t-groups and find final t_group_info->num_t_groups 3996| | add to t-groups lists of endpoints tgroup->nEndpointAtomNumber[] 3997| | calculate length of the t-group part of the connection table 3998| | */ 3999| | 4000| 252k| s[TAUT_YES].nLenLinearCTTautomer = CountTautomerGroups(at[TAUT_YES], num_taut_at, t_group_info); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTTautomer = CountTautomerGroups(at[TAUT_YES], num_taut_at, t_group_info); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4001| | 4002| 252k| if (RETURNED_ERROR(s[TAUT_YES].nLenLinearCTTautomer)) ------------------ | | 44| 252k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 252k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 252k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 252k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 252k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 252k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 252k, False: 0] | | | Branch (44:53): [True: 0, False: 252k] | | ------------------ ------------------ 4003| 0| { 4004| | /* added error treatment 9-11-2003 */ 4005| 0| ret = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4006| 0| goto exit_function; 4007| | /* error has happened; no breakpoint here 4008| | s[TAUT_YES].nLenLinearCTTautomer = 0; 4009| | */ 4010| 0| } 4011| | 4012| 252k| else if (s[TAUT_YES].nLenLinearCTTautomer > 0) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4012:18): [True: 40.8k, False: 211k] ------------------ 4013| 40.8k| { 4014| 40.8k| num_at_tg = num_taut_at + t_group_info->num_t_groups; 4015| | /* ??? -not true- create t_group_info_orig for multiple calls with atom renumbering */ 4016| 40.8k| make_a_copy_of_t_group_info(t_group_info_orig /* dest*/, t_group_info /* source*/); /* djb-rwth: addressing coverity ID #499544 -- properly used sequence of arguments according to the comment in previous line */ 4017| | /* mark isotopic tautomer groups: calculate t_group->iWeight */ 4018| 40.8k| s[TAUT_YES].nLenLinearCTIsotopicTautomer = set_tautomer_iso_sort_keys(t_group_info); ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4019| 40.8k| if (s[TAUT_YES].nLenLinearCTIsotopicTautomer < 0) ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4019:17): [True: 0, False: 40.8k] ------------------ 4020| 0| { 4021| | /* ??? -error cannot happen- error has happened; no breakpoint here */ 4022| 0| s[TAUT_YES].nLenLinearCTIsotopicTautomer = 0; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4023| 0| } 4024| 40.8k| out_norm_data[TAUT_YES]->bTautomeric = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ out_norm_data[TAUT_YES]->bTautomeric = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 575| 40.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4025| 40.8k| } 4026| | 4027| | /* new variable: s[TAUT_YES].nLenCT introduced 7-22-2002 */ 4028| 252k| GetCanonLengths(num_taut_at, at[TAUT_YES], &s[TAUT_YES], t_group_info); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ GetCanonLengths(num_taut_at, at[TAUT_YES], &s[TAUT_YES], t_group_info); ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4029| 252k| } 4030| | 4031| 252k| if (out_norm_data[TAUT_NON]->at && ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4031:9): [True: 37.6k, False: 214k] ------------------ 4032| 37.6k| out_norm_data[TAUT_YES]->at && ------------------ | | 575| 37.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4032:9): [True: 37.6k, False: 0] ------------------ 4033| 37.6k| at[TAUT_NON] && ------------------ | | 574| 37.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4033:9): [True: 37.6k, False: 0] ------------------ 4034| 37.6k| !s[TAUT_YES].nLenLinearCTTautomer) ------------------ | | 575| 37.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4034:9): [True: 1.23k, False: 36.3k] ------------------ 4035| 1.23k| { 4036| | /* the structure is non-tautomeric: use tautomeric treatment results only for it */ 4037| 1.23k| inchi_free(at[TAUT_NON]); ------------------ | | 1152| 1.23k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.23k, False: 0] | | | Branch (1152:50): [Folded, False: 1.23k] | | ------------------ ------------------ 4038| 1.23k| at[TAUT_NON] = NULL; ------------------ | | 574| 1.23k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4039| 1.23k| } 4040| | 4041| 250k| else if (!out_norm_data[TAUT_NON]->at && ------------------ | | 574| 250k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4041:14): [True: 214k, False: 36.3k] ------------------ 4042| 214k| out_norm_data[TAUT_YES]->at && ------------------ | | 575| 214k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4042:9): [True: 214k, False: 0] ------------------ 4043| 214k| !at[TAUT_NON] && ------------------ | | 574| 214k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4043:9): [True: 214k, False: 0] ------------------ 4044| 214k| at[TAUT_YES] && ------------------ | | 575| 214k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4044:9): [True: 214k, False: 0] ------------------ 4045| 214k| !s[TAUT_YES].nLenLinearCTTautomer) ------------------ | | 575| 214k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4045:9): [True: 209k, False: 4.50k] ------------------ 4046| 209k| { 4047| | /* requested tautomeric; found non-tautomeric; it is located in out_norm_data[TAUT_YES]->at */ 4048| 209k| out_norm_data[TAUT_YES]->bTautomeric = 0; ------------------ | | 575| 209k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4049| 209k| } 4050| | 4051| 40.8k| else if (out_norm_data[TAUT_NON]->at && at[TAUT_NON]) ------------------ | | 574| 40.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ else if (out_norm_data[TAUT_NON]->at && at[TAUT_NON]) ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4051:14): [True: 36.3k, False: 4.50k] | Branch (4051:45): [True: 36.3k, False: 0] ------------------ 4052| 36.3k| { 4053| | /* the structure needs non-tautomeric treatment: 4054| | final normalization of non-tautomeric structure */ 4055| 36.3k| ret = mark_alt_bonds_and_taut_groups(ic, pCG, 4056| 36.3k| out_norm_data[TAUT_NON]->at, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4057| 36.3k| NULL, 4058| 36.3k| num_atoms, 4059| 36.3k| ulMaxTime, 4060| 36.3k| NULL, 4061| 36.3k| &bTautFlags, 4062| 36.3k| &bTautFlagsDone, 4063| 36.3k| nebend, ebend); 4064| 36.3k| if (ret < 0) ------------------ | Branch (4064:13): [True: 0, False: 36.3k] ------------------ 4065| 0| { 4066| 0| goto exit_function; /* out of RAM or other normalization problem */ 4067| 0| } 4068| 36.3k| out_norm_data[TAUT_NON]->num_at = num_atoms + num_removed_H; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4069| 36.3k| out_norm_data[TAUT_NON]->num_removed_H = num_removed_H; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4070| 36.3k| out_norm_data[TAUT_NON]->bTautFlags = *pbTautFlags; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4071| 36.3k| out_norm_data[TAUT_NON]->bTautFlagsDone = *pbTautFlagsDone; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4072| 36.3k| out_norm_data[TAUT_NON]->bNormalizationFlags = 0; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4073| | 4074| | /* create internal sp_ATOM at[] out of out_norm_data[]->at */ 4075| 36.3k| inp2spATOM(out_norm_data[TAUT_NON]->at, num_inp_at, at[TAUT_NON]); ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ inp2spATOM(out_norm_data[TAUT_NON]->at, num_inp_at, at[TAUT_NON]); ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4076| | 4077| | /* set stereo parities to at[]; nUserMode: accept alt. stereo bonds, min ring size */ 4078| 36.3k| ret = set_stereo_parity(pCG, out_norm_data[TAUT_NON]->at, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4079| 36.3k| at[TAUT_NON], num_atoms, num_removed_H, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4080| 36.3k| &s[TAUT_NON].nMaxNumStereoAtoms, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4081| 36.3k| &s[TAUT_NON].nMaxNumStereoBonds, nUserMode, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4082| 36.3k| bPointedEdgeStereo, vABParityUnknown, 4083| 36.3k| ip->bLooseTSACheck, ip->bStereoAtZz); 4084| |#if ( bRELEASE_VERSION == 0 ) 4085| | if (0 < ret) 4086| | { 4087| | bExtract |= EXTR_HAS_ATOM_WITH_DEFINED_PARITY; 4088| | } 4089| |#endif 4090| 36.3k| if (RETURNED_ERROR(ret)) ------------------ | | 44| 36.3k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 36.3k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 36.3k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 36.3k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 36.3k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 36.3k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 36.3k, False: 0] | | | Branch (44:53): [True: 10, False: 36.3k] | | ------------------ ------------------ 4091| 10| { 4092| 10| goto exit_function; /* stereo bond error */ 4093| 10| } 4094| 36.3k| s[TAUT_NON].bMayHaveStereo = (s[TAUT_NON].nMaxNumStereoAtoms || ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ s[TAUT_NON].bMayHaveStereo = (s[TAUT_NON].nMaxNumStereoAtoms || ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4094:39): [True: 306, False: 36.0k] ------------------ 4095| 36.0k| s[TAUT_NON].nMaxNumStereoBonds); ------------------ | | 574| 36.0k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4095:13): [True: 259, False: 35.8k] ------------------ 4096| | 4097| | /* 4098| | * mark isotopic atoms and atoms that have non-tautomeric 4099| | * isotopic terminal hydrogen atoms 1H, 2H(D), 3H(T) 4100| | */ 4101| 36.3k| s[TAUT_NON].num_isotopic_atoms = set_atom_iso_sort_keys(num_atoms, at[TAUT_NON], NULL, NULL); ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ s[TAUT_NON].num_isotopic_atoms = set_atom_iso_sort_keys(num_atoms, at[TAUT_NON], NULL, NULL); ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4102| 36.3k| GetCanonLengths(num_atoms, at[TAUT_NON], &s[TAUT_NON], NULL); ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ GetCanonLengths(num_atoms, at[TAUT_NON], &s[TAUT_NON], NULL); ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4103| 36.3k| out_norm_data[TAUT_NON]->bTautomeric = 0; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4104| 36.3k| } 4105| | 4106| | /* common */ 4107| 252k| bMayHaveStereo = s[TAUT_YES].bMayHaveStereo || s[TAUT_NON].bMayHaveStereo; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ bMayHaveStereo = s[TAUT_YES].bMayHaveStereo || s[TAUT_NON].bMayHaveStereo; ------------------ | | 574| 241k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4107:22): [True: 10.6k, False: 241k] | Branch (4107:52): [True: 118, False: 241k] ------------------ 4108| 252k| bHasIsotopicAtoms = s[TAUT_NON].num_isotopic_atoms > 0 || s[TAUT_NON].bHasIsotopicTautGroups > 0 || ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ bHasIsotopicAtoms = s[TAUT_NON].num_isotopic_atoms > 0 || s[TAUT_NON].bHasIsotopicTautGroups > 0 || ------------------ | | 574| 251k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4108:25): [True: 666, False: 251k] | Branch (4108:63): [True: 0, False: 251k] ------------------ 4109| 251k| s[TAUT_YES].num_isotopic_atoms > 0 || s[TAUT_YES].bHasIsotopicTautGroups > 0; ------------------ | | 575| 251k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].num_isotopic_atoms > 0 || s[TAUT_YES].bHasIsotopicTautGroups > 0; ------------------ | | 575| 250k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4109:9): [True: 751, False: 250k] | Branch (4109:47): [True: 73, False: 250k] ------------------ 4110| 252k| if (bFixIsoFixedH) ------------------ | Branch (4110:9): [True: 252k, False: 0] ------------------ 4111| 252k| { 4112| | /* 2008-03-21 DT */ 4113| 252k| bHasIsotopicAtoms = bHasIsotopicAtoms ------------------ | Branch (4113:29): [True: 1.49k, False: 250k] ------------------ 4114| 250k| || 4115| 250k| (s[TAUT_YES].nLenLinearCTTautomer > 0 && t_group_info && ------------------ | | 575| 250k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4115:14): [True: 39.9k, False: 210k] | Branch (4115:54): [True: 39.9k, False: 0] ------------------ 4116| 39.9k| ((0 < NUM_H_ISOTOPES && t_group_info->tni.nNumRemovedProtonsIsotopic[0]) || ------------------ | | 72| 79.9k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (4116:19): [True: 39.9k, Folded] | Branch (4116:41): [True: 2, False: 39.9k] ------------------ 4117| 39.9k| (1 < NUM_H_ISOTOPES && t_group_info->tni.nNumRemovedProtonsIsotopic[1]) || ------------------ | | 72| 79.9k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (4117:22): [True: 39.9k, Folded] | Branch (4117:44): [True: 3, False: 39.9k] ------------------ 4118| 39.9k| (2 < NUM_H_ISOTOPES && t_group_info->tni.nNumRemovedProtonsIsotopic[2]) ------------------ | | 72| 79.9k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (4118:22): [True: 39.9k, Folded] | Branch (4118:44): [True: 3, False: 39.9k] ------------------ 4119| 39.9k| )); /* djb-rwth: addressing LLVM warning */ 4120| 252k| } 4121| 252k| bHasIsotopicAtoms = bHasIsotopicAtoms ------------------ | Branch (4121:25): [True: 1.49k, False: 250k] ------------------ 4122| 250k| || 4123| 250k| (s[TAUT_YES].nLenIsotopicEndpoints > 1 && t_group_info && ------------------ | | 575| 250k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4123:10): [True: 0, False: 250k] | Branch (4123:51): [True: 0, False: 0] ------------------ 4124| 0| (t_group_info->bTautFlagsDone & (TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE))); /* djb-rwth: addressing LLVM warning */ ------------------ | | 981| 0|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ (t_group_info->bTautFlagsDone & (TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE))); /* djb-rwth: addressing LLVM warning */ ------------------ | | 982| 0|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (4124:13): [True: 0, False: 0] ------------------ 4125| | 4126| | /* default mode */ 4127| 252k| if (!(nUserMode & REQ_MODE_DEFAULT)) ------------------ | | 46| 252k|#define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 15| 252k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 16| 252k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 17| 252k|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 18| 252k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 19| 252k|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ ------------------ | Branch (4127:9): [True: 0, False: 252k] ------------------ 4128| 0| { 4129| | /* default */ 4130| 0| nUserMode |= REQ_MODE_DEFAULT; ------------------ | | 46| 0|#define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 18| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ | | ------------------ | | #define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ ------------------ 4131| 0| } 4132| | 4133| | /* adjust the mode to the reality */ 4134| 252k| if ((nUserMode & REQ_MODE_ISO) && !bHasIsotopicAtoms) ------------------ | | 17| 252k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4134:9): [True: 252k, False: 0] | Branch (4134:39): [True: 250k, False: 1.49k] ------------------ 4135| 250k| { 4136| 250k| nUserMode ^= REQ_MODE_ISO; ------------------ | | 17| 250k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 4137| 250k| nUserMode |= REQ_MODE_NON_ISO; /* at least one is needed */ ------------------ | | 18| 250k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 4138| 250k| } 4139| 252k| if ((nUserMode & REQ_MODE_STEREO) && (nUserMode & REQ_MODE_ISO)) ------------------ | | 19| 252k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ if ((nUserMode & REQ_MODE_STEREO) && (nUserMode & REQ_MODE_ISO)) ------------------ | | 17| 8.26k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4139:9): [True: 8.26k, False: 243k] | Branch (4139:42): [True: 363, False: 7.90k] ------------------ 4140| 363| { 4141| 363| nUserMode |= REQ_MODE_ISO_STEREO; ------------------ | | 20| 363|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 4142| 363| } 4143| 252k| if ((nUserMode & REQ_MODE_STEREO) && !(nUserMode & REQ_MODE_NON_ISO)) ------------------ | | 19| 252k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ if ((nUserMode & REQ_MODE_STEREO) && !(nUserMode & REQ_MODE_NON_ISO)) ------------------ | | 18| 8.26k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (4143:9): [True: 8.26k, False: 243k] | Branch (4143:42): [True: 0, False: 8.26k] ------------------ 4144| 0| { 4145| 0| nUserMode ^= REQ_MODE_STEREO; ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 4146| 0| } 4147| 252k| if (!bMayHaveStereo) ------------------ | Branch (4147:9): [True: 241k, False: 10.7k] ------------------ 4148| 241k| { 4149| 241k| if (nUserMode & REQ_MODE_STEREO) ------------------ | | 19| 241k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (4149:13): [True: 7.35k, False: 233k] ------------------ 4150| 7.35k| nUserMode ^= REQ_MODE_STEREO; ------------------ | | 19| 7.35k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 4151| 241k| if (nUserMode & REQ_MODE_ISO_STEREO) ------------------ | | 20| 241k|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ | Branch (4151:13): [True: 7.35k, False: 233k] ------------------ 4152| 7.35k| nUserMode ^= REQ_MODE_ISO_STEREO; ------------------ | | 20| 7.35k|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 4153| 241k| } 4154| | 4155| 252k| if ((nUserMode & REQ_MODE_BASIC) && ------------------ | | 15| 252k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (4155:9): [True: 37.6k, False: 214k] ------------------ 4156| 37.6k| (!out_norm_data[TAUT_NON]->at || !ppINChI[TAUT_NON] || ------------------ | | 574| 37.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ (!out_norm_data[TAUT_NON]->at || !ppINChI[TAUT_NON] || ------------------ | | 574| 37.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4156:10): [True: 0, False: 37.6k] | Branch (4156:42): [True: 0, False: 37.6k] ------------------ 4157| 37.6k| !ppINChI_Aux[TAUT_NON] || !at[TAUT_NON])) ------------------ | | 574| 37.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ !ppINChI_Aux[TAUT_NON] || !at[TAUT_NON])) ------------------ | | 574| 37.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4157:13): [True: 0, False: 37.6k] | Branch (4157:39): [True: 1.23k, False: 36.3k] ------------------ 4158| 1.23k| { 4159| 1.23k| nUserMode ^= REQ_MODE_BASIC; ------------------ | | 15| 1.23k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 4160| 1.23k| } 4161| 252k| if ((nUserMode & REQ_MODE_TAUT) && ------------------ | | 16| 252k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (4161:9): [True: 252k, False: 0] ------------------ 4162| 252k| (!out_norm_data[TAUT_YES]->at || !ppINChI[TAUT_YES] || ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ (!out_norm_data[TAUT_YES]->at || !ppINChI[TAUT_YES] || ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4162:10): [True: 0, False: 252k] | Branch (4162:42): [True: 0, False: 252k] ------------------ 4163| 252k| !ppINChI_Aux[TAUT_YES] || !at[TAUT_YES])) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ !ppINChI_Aux[TAUT_YES] || !at[TAUT_YES])) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4163:13): [True: 0, False: 252k] | Branch (4163:39): [True: 0, False: 252k] ------------------ 4164| 0| { 4165| 0| nUserMode ^= REQ_MODE_TAUT; ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 4166| 0| } 4167| | 4168| 252k| switch ((int)nUserMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) ------------------ | | 15| 252k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ switch ((int)nUserMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) ------------------ | | 16| 252k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 4169| 252k| { 4170| 0| case REQ_MODE_BASIC: ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (4170:5): [True: 0, False: 252k] ------------------ 4171| 0| n1 = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4172| 0| n2 = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4173| 0| break; 4174| 215k| case REQ_MODE_TAUT: ------------------ | | 16| 215k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (4174:5): [True: 215k, False: 36.3k] ------------------ 4175| 215k| n1 = TAUT_YES; ------------------ | | 575| 215k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4176| 215k| n2 = TAUT_YES; ------------------ | | 575| 215k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4177| 215k| break; 4178| 36.3k| case (REQ_MODE_BASIC | REQ_MODE_TAUT): ------------------ | | 15| 36.3k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ case (REQ_MODE_BASIC | REQ_MODE_TAUT): ------------------ | | 16| 36.3k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (4178:5): [True: 36.3k, False: 215k] ------------------ 4179| 36.3k| n1 = TAUT_NON; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4180| 36.3k| n2 = TAUT_YES; ------------------ | | 575| 36.3k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4181| 36.3k| break; 4182| 0| default: ------------------ | Branch (4182:5): [True: 0, False: 252k] ------------------ 4183| 0| ret = -3; 4184| 0| goto exit_function; /* program error: inconsistent nUserMode or missing taut/non-taut allocation */ /* */ 4185| 252k| } 4186| | 4187| | /* 4188| | Obtain all non-stereo canonical numberings 4189| | */ 4190| | 4191| 252k| if ((nUserMode & REQ_MODE_NON_ISO) && !(nUserMode & REQ_MODE_ISO)) ------------------ | | 18| 252k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ if ((nUserMode & REQ_MODE_NON_ISO) && !(nUserMode & REQ_MODE_ISO)) ------------------ | | 17| 252k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4191:9): [True: 252k, False: 0] | Branch (4191:43): [True: 250k, False: 1.49k] ------------------ 4192| 250k| { 4193| | /* added for special non-isotopic test mode 2004-10-04 */ 4194| 250k| if (t_group_info) ------------------ | Branch (4194:13): [True: 250k, False: 0] ------------------ 4195| 250k| { 4196| 250k| t_group_info->bIgnoreIsotopic = 1; 4197| 250k| if (t_group_info->nIsotopicEndpointAtomNumber) ------------------ | Branch (4197:17): [True: 0, False: 250k] ------------------ 4198| 0| { 4199| 0| t_group_info->nIsotopicEndpointAtomNumber[0] = inchi_min(1, t_group_info->nIsotopicEndpointAtomNumber[0]); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 4200| 0| } 4201| 250k| memset(t_group_info->num_iso_H, 0, sizeof(t_group_info->num_iso_H)); /* djb-rwth: memset_s C11/Annex K variant? */ 4202| 250k| memset(t_group_info->tni.nNumRemovedProtonsIsotopic, 0, sizeof(t_group_info->tni.nNumRemovedProtonsIsotopic)); /* djb-rwth: memset_s C11/Annex K variant? */ 4203| 250k| t_group_info->bTautFlagsDone &= ~(TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE); ------------------ | | 981| 250k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ t_group_info->bTautFlagsDone &= ~(TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE); ------------------ | | 982| 250k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 4204| 250k| } 4205| 751k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 751k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (4205:21): [True: 501k, False: 250k] ------------------ 4206| 501k| { 4207| 501k| s[i].bHasIsotopicTautGroups = 0; 4208| 501k| s[i].bIgnoreIsotopic = 1; 4209| 501k| s[i].nLenIsotopic = 0; 4210| 501k| s[i].nLenIsotopicEndpoints = 0; 4211| 501k| s[i].nLenLinearCTIsotopicTautomer = 0; 4212| 501k| s[i].num_isotopic_atoms = 0; 4213| 501k| } 4214| 250k| bHasIsotopicAtoms = 0; 4215| 250k| } 4216| | 4217| 252k| ret = GetBaseCanonRanking(ic, num_atoms, num_at_tg, at, 4218| 252k| t_group_info, s, pBCN, ulMaxTime, 4219| 252k| pCG, bFixIsoFixedH, LargeMolecules); 4220| | 4221| 252k| if (ret < 0) ------------------ | Branch (4221:9): [True: 0, False: 252k] ------------------ 4222| 0| { 4223| 0| goto exit_function; /* program error */ 4224| 0| } 4225| |#if ( bRELEASE_VERSION == 0 && FIND_CANON_NE_EQUITABLE == 1 ) 4226| | /* Debug only: find whether canonical equivalence is different from equitable partition */ 4227| | if (bCanonIsFinerThanEquitablePartition(num_atoms, at[n1], pBCN->ftcn[TAUT_NON].nSymmRankCt)) 4228| | { 4229| | bExtract |= EXTR_CANON_NE_EQUITABLE; 4230| | } 4231| |#endif 4232| | 4233| | /* added for special non-isotopic test mode 2004-10-04 */ 4234| 252k| if (!pBCN->ftcn[n1].PartitionCt.Rank) ------------------ | Branch (4234:9): [True: 0, False: 252k] ------------------ 4235| 0| { 4236| 0| n1 = ALT_TAUT(n1); ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 4237| 0| } 4238| 252k| if (!pBCN->ftcn[n2].PartitionCt.Rank) ------------------ | Branch (4238:9): [True: 0, False: 252k] ------------------ 4239| 0| { 4240| 0| n2 = ALT_TAUT(n2); ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 4241| 0| } 4242| 252k| if (n1 > n2) ------------------ | Branch (4242:9): [True: 0, False: 252k] ------------------ 4243| 0| { 4244| 0| ret = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4245| 0| goto exit_function; /* program error */ 4246| 0| } 4247| | 4248| | /* 4249| | Obtain stereo canonical numberings 4250| | */ 4251| | 4252| 540k| for (i = n2; i >= n1 && !RETURNED_ERROR(ret); i--) ------------------ | | 44| 288k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 288k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 288k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 288k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 288k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 288k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 288k, False: 0] | | | Branch (44:53): [True: 14, False: 288k] | | ------------------ ------------------ | Branch (4252:18): [True: 288k, False: 252k] ------------------ 4253| 288k| { 4254| 288k| memset(pCS, 0, sizeof(*pCS)); /* djb-rwth: memset_s C11/Annex K variant? */ 4255| | 4256| 288k| switch (i) ------------------ | Branch (4256:17): [True: 288k, False: 0] ------------------ 4257| 288k| { 4258| 36.3k| case TAUT_NON: ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4258:9): [True: 36.3k, False: 252k] ------------------ 4259| | /* non-tautomeric */ 4260| | /* djb-rwth: removing redundant code */ 4261| 36.3k| nMode = (s[i].nLenLinearCTTautomer == 0) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 786| 36.3k|#define CANON_MODE_CT (CMODE_CT) | | ------------------ | | | | 769| 36.3k|#define CMODE_CT 0x000001 | | ------------------ ------------------ nMode = (s[i].nLenLinearCTTautomer == 0) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 787| 36.3k|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 769| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 774| 0|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (4261:21): [True: 36.3k, False: 0] ------------------ 4262| 36.3k| nMode |= (bHasIsotopicAtoms && (nUserMode & REQ_MODE_ISO)) ? CANON_MODE_ISO : 0; ------------------ | | 17| 666|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= (bHasIsotopicAtoms && (nUserMode & REQ_MODE_ISO)) ? CANON_MODE_ISO : 0; ------------------ | | 788| 666|#define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 769| 666|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 770| 666|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 771| 666|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ ------------------ | Branch (4262:23): [True: 666, False: 35.6k] | Branch (4262:44): [True: 666, False: 0] ------------------ 4263| 36.3k| nMode |= (s[TAUT_NON].bMayHaveStereo && (nUserMode & REQ_MODE_STEREO)) ? CANON_MODE_STEREO : 0; ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nMode |= (s[TAUT_NON].bMayHaveStereo && (nUserMode & REQ_MODE_STEREO)) ? CANON_MODE_STEREO : 0; ------------------ | | 19| 563|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nMode |= (s[TAUT_NON].bMayHaveStereo && (nUserMode & REQ_MODE_STEREO)) ? CANON_MODE_STEREO : 0; ------------------ | | 789| 86|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 769| 86|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 86|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4263:23): [True: 563, False: 35.7k] | Branch (4263:53): [True: 86, False: 477] ------------------ 4264| 36.3k| nMode |= (bHasIsotopicAtoms && s[TAUT_NON].bMayHaveStereo && (nUserMode & REQ_MODE_ISO_STEREO)) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 574| 666|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nMode |= (bHasIsotopicAtoms && s[TAUT_NON].bMayHaveStereo && (nUserMode & REQ_MODE_ISO_STEREO)) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 20| 54|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nMode |= (bHasIsotopicAtoms && s[TAUT_NON].bMayHaveStereo && (nUserMode & REQ_MODE_ISO_STEREO)) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 790| 39|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 769| 39|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 770| 39|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 771| 39|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 39|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4264:23): [True: 666, False: 35.6k] | Branch (4264:44): [True: 54, False: 612] | Branch (4264:74): [True: 39, False: 15] ------------------ 4265| 36.3k| nMode |= (nUserMode & REQ_MODE_NOEQ_STEREO) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 21| 36.3k|#define REQ_MODE_NOEQ_STEREO 0x000040 /* SS */ ------------------ nMode |= (nUserMode & REQ_MODE_NOEQ_STEREO) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 775| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (4265:22): [True: 0, False: 36.3k] ------------------ 4266| 36.3k| nMode |= (nUserMode & REQ_MODE_REDNDNT_STEREO) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 22| 36.3k|#define REQ_MODE_REDNDNT_STEREO 0x000080 /* RS */ ------------------ nMode |= (nUserMode & REQ_MODE_REDNDNT_STEREO) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 776| 0|#define CMODE_REDNDNT_STEREO 0x000080 /* 6-11-2002: do not check for redundant stereo elements */ ------------------ | Branch (4266:22): [True: 0, False: 36.3k] ------------------ 4267| 36.3k| nMode |= (nUserMode & REQ_MODE_NO_ALT_SBONDS) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 23| 36.3k|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ nMode |= (nUserMode & REQ_MODE_NO_ALT_SBONDS) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 777| 0|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (4267:22): [True: 0, False: 36.3k] ------------------ 4268| 36.3k| if ((nMode & CANON_MODE_STEREO) == CANON_MODE_STEREO || ------------------ | | 789| 36.3k|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 769| 36.3k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 36.3k|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ if ((nMode & CANON_MODE_STEREO) == CANON_MODE_STEREO || ------------------ | | 789| 72.7k|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 769| 36.3k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 36.3k|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4268:17): [True: 86, False: 36.2k] ------------------ 4269| 36.2k| (nMode & CANON_MODE_ISO_STEREO) == CANON_MODE_ISO_STEREO) ------------------ | | 790| 36.2k|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 769| 36.2k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 770| 36.2k|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 771| 36.2k|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 36.2k|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ (nMode & CANON_MODE_ISO_STEREO) == CANON_MODE_ISO_STEREO) ------------------ | | 790| 36.2k|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 769| 36.2k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 770| 36.2k|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 771| 36.2k|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 36.2k|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4269:17): [True: 0, False: 36.2k] ------------------ 4270| 86| { 4271| 86| nMode |= (nUserMode & REQ_MODE_RELATIVE_STEREO) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 26| 86|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ nMode |= (nUserMode & REQ_MODE_RELATIVE_STEREO) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 779| 0|#define CMODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (4271:26): [True: 0, False: 86] ------------------ 4272| 86| nMode |= (nUserMode & REQ_MODE_RACEMIC_STEREO) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 28| 86|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ nMode |= (nUserMode & REQ_MODE_RACEMIC_STEREO) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 780| 0|#define CMODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (4272:26): [True: 0, False: 86] ------------------ 4273| 86| nMode |= (nUserMode & REQ_MODE_SC_IGN_ALL_UU) ? CMODE_SC_IGN_ALL_UU : 0; ------------------ | | 30| 86|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ nMode |= (nUserMode & REQ_MODE_SC_IGN_ALL_UU) ? CMODE_SC_IGN_ALL_UU : 0; ------------------ | | 781| 78|#define CMODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (4273:26): [True: 78, False: 8] ------------------ 4274| 86| nMode |= (nUserMode & REQ_MODE_SB_IGN_ALL_UU) ? CMODE_SB_IGN_ALL_UU : 0; ------------------ | | 32| 86|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ nMode |= (nUserMode & REQ_MODE_SB_IGN_ALL_UU) ? CMODE_SB_IGN_ALL_UU : 0; ------------------ | | 782| 72|#define CMODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (4274:26): [True: 72, False: 14] ------------------ 4275| 86| } 4276| 36.3k| if ((ret = AllocateCS(pCS, num_atoms, num_atoms, s[TAUT_NON].nLenCT, s[TAUT_NON].nLenCTAtOnly, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if ((ret = AllocateCS(pCS, num_atoms, num_atoms, s[TAUT_NON].nLenCT, s[TAUT_NON].nLenCTAtOnly, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4276:17): [True: 0, False: 36.3k] ------------------ 4277| 36.3k| s[TAUT_NON].nLenLinearCTStereoDble, s[TAUT_NON].nMaxNumStereoBonds, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ s[TAUT_NON].nLenLinearCTStereoDble, s[TAUT_NON].nMaxNumStereoBonds, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4278| 36.3k| s[TAUT_NON].nLenLinearCTStereoCarb, s[TAUT_NON].nMaxNumStereoAtoms, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ s[TAUT_NON].nLenLinearCTStereoCarb, s[TAUT_NON].nMaxNumStereoAtoms, ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4279| 36.3k| 0, 0, s[TAUT_NON].nLenIsotopic, nMode, pBCN))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 36.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4280| 0| { 4281| 0| goto exit_function; 4282| 0| } 4283| 36.3k| *pCS2 = *pCS; 4284| 36.3k| break; 4285| 252k| case TAUT_YES: /* tautomeric */ ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4285:9): [True: 252k, False: 36.3k] ------------------ 4286| | /* djb-rwth: removing redundant code */ 4287| 252k| nMode = (s[i].nLenLinearCTTautomer == 0) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 786| 211k|#define CANON_MODE_CT (CMODE_CT) | | ------------------ | | | | 769| 211k|#define CMODE_CT 0x000001 | | ------------------ ------------------ nMode = (s[i].nLenLinearCTTautomer == 0) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 787| 292k|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 769| 40.8k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 774| 40.8k|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (4287:21): [True: 211k, False: 40.8k] ------------------ 4288| 252k| nMode |= (bHasIsotopicAtoms && (nUserMode & REQ_MODE_ISO)) ? CANON_MODE_ISO : 0; ------------------ | | 17| 1.49k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= (bHasIsotopicAtoms && (nUserMode & REQ_MODE_ISO)) ? CANON_MODE_ISO : 0; ------------------ | | 788| 1.49k|#define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 769| 1.49k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 770| 1.49k|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 771| 1.49k|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ ------------------ | Branch (4288:23): [True: 1.49k, False: 250k] | Branch (4288:44): [True: 1.49k, False: 0] ------------------ 4289| 252k| nMode |= (s[TAUT_YES].bMayHaveStereo && (nUserMode & REQ_MODE_STEREO)) ? CANON_MODE_STEREO : 0; ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nMode |= (s[TAUT_YES].bMayHaveStereo && (nUserMode & REQ_MODE_STEREO)) ? CANON_MODE_STEREO : 0; ------------------ | | 19| 10.6k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nMode |= (s[TAUT_YES].bMayHaveStereo && (nUserMode & REQ_MODE_STEREO)) ? CANON_MODE_STEREO : 0; ------------------ | | 789| 903|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 769| 903|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 903|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4289:23): [True: 10.6k, False: 241k] | Branch (4289:53): [True: 903, False: 9.74k] ------------------ 4290| 252k| nMode |= (bHasIsotopicAtoms && s[TAUT_YES].bMayHaveStereo && (nUserMode & REQ_MODE_ISO_STEREO)) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 575| 1.49k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nMode |= (bHasIsotopicAtoms && s[TAUT_YES].bMayHaveStereo && (nUserMode & REQ_MODE_ISO_STEREO)) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 20| 319|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nMode |= (bHasIsotopicAtoms && s[TAUT_YES].bMayHaveStereo && (nUserMode & REQ_MODE_ISO_STEREO)) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 790| 227|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 769| 227|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 770| 227|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 771| 227|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 227|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4290:23): [True: 1.49k, False: 250k] | Branch (4290:44): [True: 319, False: 1.17k] | Branch (4290:74): [True: 227, False: 92] ------------------ 4291| 252k| nMode |= (nUserMode & REQ_MODE_NOEQ_STEREO) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 21| 252k|#define REQ_MODE_NOEQ_STEREO 0x000040 /* SS */ ------------------ nMode |= (nUserMode & REQ_MODE_NOEQ_STEREO) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 775| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (4291:22): [True: 0, False: 252k] ------------------ 4292| 252k| nMode |= (nUserMode & REQ_MODE_REDNDNT_STEREO) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 22| 252k|#define REQ_MODE_REDNDNT_STEREO 0x000080 /* RS */ ------------------ nMode |= (nUserMode & REQ_MODE_REDNDNT_STEREO) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 776| 0|#define CMODE_REDNDNT_STEREO 0x000080 /* 6-11-2002: do not check for redundant stereo elements */ ------------------ | Branch (4292:22): [True: 0, False: 252k] ------------------ 4293| 252k| nMode |= (nUserMode & REQ_MODE_NO_ALT_SBONDS) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 23| 252k|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ nMode |= (nUserMode & REQ_MODE_NO_ALT_SBONDS) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 777| 0|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (4293:22): [True: 0, False: 252k] ------------------ 4294| 252k| if ((nMode & CANON_MODE_STEREO) == CANON_MODE_STEREO || ------------------ | | 789| 252k|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 769| 252k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 252k|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ if ((nMode & CANON_MODE_STEREO) == CANON_MODE_STEREO || ------------------ | | 789| 504k|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 769| 252k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 252k|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4294:17): [True: 903, False: 251k] ------------------ 4295| 251k| (nMode & CANON_MODE_ISO_STEREO) == CANON_MODE_ISO_STEREO) ------------------ | | 790| 251k|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 769| 251k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 770| 251k|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 771| 251k|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 251k|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ (nMode & CANON_MODE_ISO_STEREO) == CANON_MODE_ISO_STEREO) ------------------ | | 790| 251k|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 769| 251k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 770| 251k|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 771| 251k|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 251k|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4295:17): [True: 0, False: 251k] ------------------ 4296| 903| { 4297| 903| nMode |= (nUserMode & REQ_MODE_RELATIVE_STEREO) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 26| 903|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ nMode |= (nUserMode & REQ_MODE_RELATIVE_STEREO) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 779| 36|#define CMODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (4297:26): [True: 36, False: 867] ------------------ 4298| 903| nMode |= (nUserMode & REQ_MODE_RACEMIC_STEREO) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 28| 903|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ nMode |= (nUserMode & REQ_MODE_RACEMIC_STEREO) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 780| 43|#define CMODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (4298:26): [True: 43, False: 860] ------------------ 4299| 903| nMode |= (nUserMode & REQ_MODE_SC_IGN_ALL_UU) ? CMODE_SC_IGN_ALL_UU : 0; ------------------ | | 30| 903|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ nMode |= (nUserMode & REQ_MODE_SC_IGN_ALL_UU) ? CMODE_SC_IGN_ALL_UU : 0; ------------------ | | 781| 838|#define CMODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (4299:26): [True: 838, False: 65] ------------------ 4300| 903| nMode |= (nUserMode & REQ_MODE_SB_IGN_ALL_UU) ? CMODE_SB_IGN_ALL_UU : 0; ------------------ | | 32| 903|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ nMode |= (nUserMode & REQ_MODE_SB_IGN_ALL_UU) ? CMODE_SB_IGN_ALL_UU : 0; ------------------ | | 782| 799|#define CMODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (4300:26): [True: 799, False: 104] ------------------ 4301| 903| } 4302| 252k| if ((ret = AllocateCS(pCS, num_atoms, num_at_tg, s[TAUT_YES].nLenCT, s[TAUT_YES].nLenCTAtOnly, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if ((ret = AllocateCS(pCS, num_atoms, num_at_tg, s[TAUT_YES].nLenCT, s[TAUT_YES].nLenCTAtOnly, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4302:17): [True: 0, False: 252k] ------------------ 4303| 252k| s[TAUT_YES].nLenLinearCTStereoDble, s[TAUT_YES].nMaxNumStereoBonds, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTStereoDble, s[TAUT_YES].nMaxNumStereoBonds, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4304| 252k| s[TAUT_YES].nLenLinearCTStereoCarb, s[TAUT_YES].nMaxNumStereoAtoms, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTStereoCarb, s[TAUT_YES].nMaxNumStereoAtoms, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4305| 252k| s[TAUT_YES].nLenLinearCTTautomer, s[TAUT_YES].nLenLinearCTIsotopicTautomer, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTTautomer, s[TAUT_YES].nLenLinearCTIsotopicTautomer, ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4306| 252k| s[TAUT_YES].nLenIsotopic, nMode, pBCN))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4307| 0| { 4308| 0| goto exit_function; 4309| 0| } 4310| 252k| *pCS2 = *pCS; 4311| 252k| break; 4312| 288k| } 4313| | 4314| | /* 2009-12-05 */ 4315| 288k| nMode |= (nUserMode & REQ_MODE_DIFF_UU_STEREO) ? REQ_MODE_DIFF_UU_STEREO : 0; ------------------ | | 40| 288k|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ nMode |= (nUserMode & REQ_MODE_DIFF_UU_STEREO) ? REQ_MODE_DIFF_UU_STEREO : 0; ------------------ | | 40| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (4315:18): [True: 0, False: 288k] ------------------ 4316| | /* 2009-12-05 */ 4317| | 4318| | /* settings */ 4319| 288k| pCS->lNumDecreasedCT = -1; 4320| 288k| pCS->bDoubleBondSquare = DOUBLE_BOND_NEIGH_LIST ? 2 : 0; /* 2 => special mode */ ------------------ | | 810| 288k|#define DOUBLE_BOND_NEIGH_LIST 0 /* 1 => include double bond neighbor in NeighList 2 times */ | | ------------------ | | | Branch (810:35): [Folded, False: 288k] | | ------------------ ------------------ 4321| 288k| pCS->bIgnoreIsotopic = !((s[TAUT_NON].num_isotopic_atoms || ------------------ | | 574| 288k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4321:35): [True: 1.33k, False: 287k] ------------------ 4322| 287k| s[TAUT_YES].num_isotopic_atoms || ------------------ | | 575| 287k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4322:13): [True: 751, False: 286k] ------------------ 4323| 286k| s[TAUT_YES].bHasIsotopicTautGroups) || ------------------ | | 575| 286k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4323:13): [True: 74, False: 286k] ------------------ 4324| 286k| (nUserMode & REQ_MODE_NON_ISO) || ------------------ | | 18| 286k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (4324:13): [True: 286k, False: 0] ------------------ 4325| 0| !(nUserMode & REQ_MODE_ISO)); ------------------ | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4325:13): [True: 0, False: 0] ------------------ 4326| | 4327| 288k| if ((nUserMode & REQ_MODE_NON_ISO) && !(nUserMode & REQ_MODE_ISO)) ------------------ | | 18| 288k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ if ((nUserMode & REQ_MODE_NON_ISO) && !(nUserMode & REQ_MODE_ISO)) ------------------ | | 17| 288k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4327:13): [True: 288k, False: 0] | Branch (4327:47): [True: 286k, False: 2.16k] ------------------ 4328| 286k| { 4329| 286k| pCS->bIgnoreIsotopic = 1; /* 10-04-2004 */ 4330| 286k| } 4331| | 4332| 288k| if (i == TAUT_YES) ------------------ | | 575| 288k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4332:13): [True: 252k, False: 36.3k] ------------------ 4333| 252k| { 4334| | /* tautomeric */ 4335| 252k| pCS->t_group_info = t_group_info; /* ??? make a copy or reuse ??? */ 4336| 252k| pCS->t_group_info->bIgnoreIsotopic = !(s[TAUT_YES].bHasIsotopicTautGroups || ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4336:52): [True: 269, False: 251k] ------------------ 4337| 251k| (nUserMode & REQ_MODE_NON_ISO) || ------------------ | | 18| 251k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (4337:17): [True: 251k, False: 0] ------------------ 4338| 0| !(nUserMode & REQ_MODE_ISO)); ------------------ | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4338:17): [True: 0, False: 0] ------------------ 4339| 252k| if ((nUserMode & REQ_MODE_NON_ISO) && !(nUserMode & REQ_MODE_ISO)) ------------------ | | 18| 252k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ if ((nUserMode & REQ_MODE_NON_ISO) && !(nUserMode & REQ_MODE_ISO)) ------------------ | | 17| 252k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4339:17): [True: 252k, False: 0] | Branch (4339:51): [True: 250k, False: 1.49k] ------------------ 4340| 250k| { 4341| 250k| pCS->t_group_info->bIgnoreIsotopic = 1; /* 10-04-2004 */ 4342| 250k| } 4343| 252k| } 4344| | 4345| 288k| pCS->ulTimeOutTime = pBCN->ulTimeOutTime; 4346| | /*=========== Obsolete Mode Bits (bit 0 is Least Significant Bit) =========== 4347| | * 4348| | * Mode Bits Description 4349| | * '0' c 0 Only one connection table canonicalization 4350| | * '1' C 1 Recalculate CT using fixed nSymmRank 4351| | * '2' i 1|2 Isotopic canonicalization (internal) 4352| | * '3' I 1|2|4 Isotopic canonicalization (output) 4353| | * '4' s 1|8 Stereo canonicalization 4354| | * '5' S 1|2|4|16 Stereo isotopic canonicalization 4355| | * '6' A 1|2|4|8|16 Output All 4356| | */ 4357| | 4358| | /* 4359| | The last canonicalization step 4360| | */ 4361| | 4362| 288k| if (pBCN) ------------------ | Branch (4362:13): [True: 288k, False: 0] ------------------ 4363| 288k| { 4364| | /* USE_CANON2 == 1 */ 4365| 288k| pCS->NeighList = NULL; 4366| 288k| pCS->pBCN = pBCN; 4367| | 4368| 288k| ret = Canon_INChI(ic, 4369| 288k| num_atoms, 4370| 288k| i ? num_at_tg : num_atoms, ------------------ | Branch (4370:17): [True: 252k, False: 36.3k] ------------------ 4371| 288k| at[i], pCS, 4372| 288k| pCG, 4373| 288k| nMode, i); 4374| 288k| } 4375| 0| else 4376| 0| { 4377| | /* old way */ 4378| 0| pCS->NeighList = CreateNeighList(num_atoms, 4379| 0| i ? num_at_tg : num_atoms, ------------------ | Branch (4379:17): [True: 0, False: 0] ------------------ 4380| 0| at[i], 4381| 0| pCS->bDoubleBondSquare, 4382| 0| pCS->t_group_info); 4383| 0| pCS->pBCN = NULL; 4384| | 4385| 0| ret = Canon_INChI(ic, 4386| 0| num_atoms, 4387| 0| i ? num_at_tg : num_atoms, ------------------ | Branch (4387:17): [True: 0, False: 0] ------------------ 4388| 0| at[i], pCS, 4389| 0| pCG, 4390| 0| nMode, i); 4391| 0| } 4392| | 4393| 288k| pINChI = ppINChI[i]; /* pointers to already allocated still empty InChI */ 4394| 288k| pINChI_Aux = ppINChI_Aux[i]; 4395| | 4396| 288k| if (ret <= 0) ------------------ | Branch (4396:13): [True: 1, False: 288k] ------------------ 4397| 1| { 4398| | /* 4399| | Failure in Canon_INChI() 4400| | */ 4401| 1| pINChI->nErrorCode = ret; 4402| 1| pINChI_Aux->nErrorCode = ret; 4403| 1| } 4404| 288k| else 4405| 288k| { 4406| | /* 4407| | Success Canon_INChI() 4408| | 4409| | save canonicalization results in 4410| | pINChI and pINChI_Aux 4411| | */ 4412| 288k| pINChI->nErrorCode = 0; 4413| 288k| pINChI_Aux->nErrorCode = 0; 4414| 288k| pINChI->bDeleted = pINChI_Aux->bDeleted = out_norm_data[i]->bDeleted; 4415| 288k| pINChI_Aux->nCanonFlags = pCS->nCanonFlags; 4416| 288k| pINChI_Aux->bTautFlags = out_norm_data[i]->bTautFlags; 4417| 288k| pINChI_Aux->bTautFlagsDone = out_norm_data[i]->bTautFlagsDone; 4418| 288k| pINChI_Aux->bNormalizationFlags = out_norm_data[i]->bNormalizationFlags; 4419| | 4420| | /* may return an error or a warning */ 4421| 288k| ret = FillOutINChI(pINChI, pINChI_Aux, 4422| 288k| num_atoms, i ? num_at_tg : num_atoms, ------------------ | Branch (4422:28): [True: 252k, False: 36.3k] ------------------ 4423| 288k| i ? num_removed_H_taut : num_removed_H, at[i], ------------------ | Branch (4423:17): [True: 252k, False: 36.3k] ------------------ 4424| 288k| out_norm_data[i]->at, pCS, 4425| 288k| pCG, 4426| 288k| i, nUserMode, 4427| 288k| pStrErrStruct, ip->bNoWarnings); 4428| | 4429| 288k| if (RETURNED_ERROR(ret)) ------------------ | | 44| 288k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 288k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 288k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 288k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 288k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 288k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 288k, False: 0] | | | Branch (44:53): [True: 17, False: 288k] | | ------------------ ------------------ 4430| 17| { 4431| | /* Failure in FillOutINChI() */ 4432| 17| pINChI->nErrorCode = ret; 4433| 17| pINChI_Aux->nErrorCode = ret; 4434| 17| } 4435| 288k| else 4436| 288k| { 4437| | /* Success in FillOutINChI() */ 4438| | 4439| |#if ( bRELEASE_VERSION == 0 ) 4440| | if (pINChI->Stereo && 4441| | (pINChI->Stereo->nCompInv2Abs && !pINChI->Stereo->bTrivialInv) || 4442| | pINChI->StereoIsotopic && 4443| | (pINChI->StereoIsotopic->nCompInv2Abs && !pINChI->StereoIsotopic->bTrivialInv)) 4444| | { 4445| | bExtract |= EXTR_NON_TRIVIAL_STEREO; 4446| | } 4447| |#endif 4448| | /* Mark non-tautomeric representation as having 4449| | another, tautomeric representation */ 4450| 288k| if (pINChI_Aux && s[TAUT_YES].nLenLinearCTTautomer) ------------------ | | 575| 288k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4450:21): [True: 288k, False: 0] | Branch (4450:35): [True: 77.2k, False: 211k] ------------------ 4451| 77.2k| { 4452| 77.2k| pINChI_Aux->bIsTautomeric = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 575| 77.2k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4453| 77.2k| } 4454| |#if ( bRELEASE_VERSION == 0 ) 4455| | pCS->bExtract |= bExtract; 4456| | pINChI->bExtract |= pCS->bExtract; 4457| |#endif 4458| | 4459| 288k| ret2 = CheckCanonNumberingCorrectness(num_atoms, 4460| 288k| i ? num_at_tg : num_atoms, ------------------ | Branch (4460:21): [True: 252k, False: 36.3k] ------------------ 4461| 288k| at[i], pCS, 4462| 288k| pCG, 4463| 288k| i, pStrErrStruct); 4464| 288k| if (ret2 && pINChI_Aux) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (4464:21): [True: 0, False: 288k] | Branch (4464:29): [True: 0, False: 0] ------------------ 4465| 0| { 4466| 0| pINChI->nErrorCode = ret2; 4467| 0| pINChI_Aux->nErrorCode = ret2; 4468| 0| ret = ret2; 4469| 0| } 4470| 288k| } 4471| 288k| } 4472| | 4473| 288k| FreeNeighList(pCS->NeighList); 4474| 288k| DeAllocateCS(pCS2); 4475| | 4476| 288k| pINChI = NULL; /* avoid dangling pointers */ 4477| 288k| pINChI_Aux = NULL; /* avoid dangling pointers */ 4478| 288k| } 4479| | 4480| 252k| if (ret == 0) ------------------ | Branch (4480:9): [True: 252k, False: 18] ------------------ 4481| 252k| { 4482| 252k| ret = num_atoms; 4483| 252k| } 4484| | /* treat the results later */ 4485| | 4486| 252k|exit_function: 4487| | 4488| 252k| DeAllocBCN(pBCN); 4489| 252k| if (at[TAUT_YES]) ------------------ | | 575| 252k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4489:9): [True: 252k, False: 0] ------------------ 4490| 252k| { 4491| 252k| inchi_free(at[TAUT_YES]); ------------------ | | 1152| 252k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 252k, False: 0] | | | Branch (1152:50): [Folded, False: 252k] | | ------------------ ------------------ 4492| 252k| } 4493| 252k| if (at[TAUT_NON]) ------------------ | | 574| 252k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4493:9): [True: 36.4k, False: 215k] ------------------ 4494| 36.4k| { 4495| 36.4k| inchi_free(at[TAUT_NON]); ------------------ | | 1152| 36.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 36.4k, False: 0] | | | Branch (1152:50): [Folded, False: 36.4k] | | ------------------ ------------------ 4496| 36.4k| } 4497| 252k| if (ti_out) ------------------ | Branch (4497:9): [True: 146k, False: 106k] ------------------ 4498| 146k| { 4499| 146k| *ti_out = *t_group_info; 4500| 146k| } 4501| 106k| else 4502| 106k| { 4503| | /* free_t_group_info(t_group_info); */ 4504| 106k| if (t_group_info) /* djb-rwth: fixing oss-fuzz issue #42537161/70475 */ ------------------ | Branch (4504:13): [True: 106k, False: 0] ------------------ 4505| 106k| { 4506| 106k| if (t_group_info->nEndpointAtomNumber) ------------------ | Branch (4506:17): [True: 1.02k, False: 105k] ------------------ 4507| 1.02k| { 4508| 1.02k| inchi_free(t_group_info->nEndpointAtomNumber); ------------------ | | 1152| 1.02k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.02k, False: 0] | | | Branch (1152:50): [Folded, False: 1.02k] | | ------------------ ------------------ 4509| 1.02k| } 4510| 106k| if (t_group_info->tGroupNumber) ------------------ | Branch (4510:17): [True: 1.02k, False: 105k] ------------------ 4511| 1.02k| { 4512| 1.02k| inchi_free(t_group_info->tGroupNumber); ------------------ | | 1152| 1.02k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.02k, False: 0] | | | Branch (1152:50): [Folded, False: 1.02k] | | ------------------ ------------------ 4513| 1.02k| } 4514| 106k| if (t_group_info->nIsotopicEndpointAtomNumber) ------------------ | Branch (4514:17): [True: 81, False: 105k] ------------------ 4515| 81| { 4516| 81| inchi_free(t_group_info->nIsotopicEndpointAtomNumber); ------------------ | | 1152| 81|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 81, False: 0] | | | Branch (1152:50): [Folded, False: 81] | | ------------------ ------------------ 4517| 81| } 4518| 106k| if (t_group_info->t_group) ------------------ | Branch (4518:17): [True: 106k, False: 1] ------------------ 4519| 106k| { 4520| 106k| inchi_free(t_group_info->t_group); ------------------ | | 1152| 106k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 106k, False: 0] | | | Branch (1152:50): [Folded, False: 106k] | | ------------------ ------------------ 4521| 106k| } 4522| 106k| memset(t_group_info, 0, sizeof(*t_group_info)); /* djb-rwth: memset_s C11/Annex K variant? */ 4523| 106k| } 4524| 106k| } 4525| 252k| free_t_group_info(t_group_info_orig); 4526| | 4527| 252k| if (ebend) ------------------ | Branch (4527:9): [True: 0, False: 252k] ------------------ 4528| 0| { 4529| 0| inchi_free(ebend); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4530| 0| } 4531| | 4532| 252k| return ret; 4533| 252k|} CheckCanonNumberingCorrectness: 6206| 288k|{ 6207| 288k| int i, ret = 0; 6208| 288k| AT_NUMB* pCanonOrd = NULL; 6209| 288k| int nErrorCode = 0; 6210| 288k| AT_NUMB* pCanonRank; /* canonical ranks of the atoms or tautomeric groups */ 6211| 288k| AT_NUMB* pCanonRankAtoms = NULL; 6212| | 6213| | /* djb-rwth: removing redundant code */ 6214| | 6215| 288k| pCanonRankAtoms = (AT_NUMB*)inchi_calloc((long long)num_at_tg + 1, sizeof(pCanonRankAtoms[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ 6216| | 6217| | /* 6218| | Non-isotopic part 6219| | */ 6220| | 6221| 288k| pCanonOrd = pCS->nLenCanonOrdStereo > 0 ? pCS->nCanonOrdStereo : ------------------ | Branch (6221:17): [True: 892, False: 287k] ------------------ 6222| 288k| pCS->nLenCanonOrd > 0 ? pCS->nCanonOrd : NULL; ------------------ | Branch (6222:9): [True: 287k, False: 0] ------------------ 6223| 288k| pCanonRank = pCanonRankAtoms; 6224| 288k| if (pCanonOrd && pCanonRank) ------------------ | Branch (6224:9): [True: 288k, False: 0] | Branch (6224:22): [True: 288k, False: 0] ------------------ 6225| 288k| { 6226| 1.38M| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6226:21): [True: 1.09M, False: 288k] ------------------ 6227| 1.09M| { 6228| 1.09M| pCanonRank[pCanonOrd[i]] = (AT_NUMB)(i + 1); 6229| 1.09M| } 6230| 288k| ret = UpdateFullLinearCT(num_atoms, num_at_tg, at, pCanonRank, pCanonOrd, pCS, 6231| 288k| pCG, 6232| 288k| 0); 6233| 288k| if (ret /*|| memcmp(pCS->LinearCT, pCS->LinearCT2, sizeof(AT_RANK) * pCS->nLenLinearCT )*/) ------------------ | Branch (6233:13): [True: 0, False: 288k] ------------------ 6234| 0| { 6235| 0| nErrorCode |= WARN_FAILED_STEREO; ------------------ | | 48| 0|#define WARN_FAILED_STEREO 0x0001 ------------------ 6236| 0| } 6237| 288k| } 6238| 0| else 6239| 0| { 6240| 0| nErrorCode |= ERR_NO_CANON_RESULTS; ------------------ | | 51| 0|#define ERR_NO_CANON_RESULTS 0x0008 ------------------ 6241| 0| goto exit_function; 6242| 0| } 6243| | 6244| | /* 6245| | Isotopic part 6246| | */ 6247| | 6248| 288k| pCanonOrd = pCS->nLenCanonOrdIsotopicStereo > 0 ? pCS->nCanonOrdIsotopicStereo : ------------------ | Branch (6248:17): [True: 227, False: 288k] ------------------ 6249| 288k| pCS->nLenCanonOrdIsotopic > 0 ? pCS->nCanonOrdIsotopic : NULL; ------------------ | Branch (6249:9): [True: 1.88k, False: 286k] ------------------ 6250| 288k| pCanonRank = pCanonRankAtoms; 6251| | 6252| 288k| if (pCanonOrd && pCanonRank) ------------------ | Branch (6252:9): [True: 2.11k, False: 286k] | Branch (6252:22): [True: 2.11k, False: 0] ------------------ 6253| 2.11k| { 6254| 14.6k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6254:21): [True: 12.5k, False: 2.11k] ------------------ 6255| 12.5k| { 6256| 12.5k| pCanonRank[pCanonOrd[i]] = (AT_NUMB)(i + 1); 6257| 12.5k| } 6258| 2.11k| ret = UpdateFullLinearCT(num_atoms, num_at_tg, at, pCanonRank, pCanonOrd, pCS, 6259| 2.11k| pCG, 6260| 2.11k| 0); 6261| 2.11k| if (ret /*|| memcmp(pCS->LinearCT, pCS->LinearCT2, sizeof(AT_RANK) * pCS->nLenLinearCT )*/) ------------------ | Branch (6261:13): [True: 0, False: 2.11k] ------------------ 6262| 0| { 6263| 0| nErrorCode |= (pCS->nLenCanonOrdIsotopicStereo ? WARN_FAILED_ISOTOPIC_STEREO : WARN_FAILED_ISOTOPIC); ------------------ | | 50| 0|#define WARN_FAILED_ISOTOPIC_STEREO 0x0004 ------------------ nErrorCode |= (pCS->nLenCanonOrdIsotopicStereo ? WARN_FAILED_ISOTOPIC_STEREO : WARN_FAILED_ISOTOPIC); ------------------ | | 49| 0|#define WARN_FAILED_ISOTOPIC 0x0002 ------------------ | Branch (6263:28): [True: 0, False: 0] ------------------ 6264| 0| } 6265| 2.11k| } 6266| | 6267| 288k|exit_function: 6268| 288k| if (pCanonRankAtoms) ------------------ | Branch (6268:9): [True: 288k, False: 0] ------------------ 6269| 288k| { 6270| 288k| inchi_free(pCanonRankAtoms); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 6271| 288k| } 6272| | 6273| 288k| if (nErrorCode) ------------------ | Branch (6273:9): [True: 0, False: 288k] ------------------ 6274| 0| { 6275| 0| return CT_CANON_ERR; ------------------ | | 35| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6276| 0| } 6277| | 6278| 288k| return 0; 6279| 288k|} ichimake.c:CompareDfsDescendants4CT: 2084| 31.5k|{ 2085| 31.5k| OrderStruct* os = (OrderStruct*)p; 2086| 31.5k| int neigh1 = (int)*(const AT_RANK*)a1; 2087| 31.5k| int neigh2 = (int)*(const AT_RANK*)a2; 2088| 31.5k| if (neigh1 > MAX_ATOMS) ------------------ | | 15| 31.5k|#define MAX_ATOMS 32766 ------------------ | Branch (2088:9): [True: 17.3k, False: 14.2k] ------------------ 2089| 17.3k| { 2090| 17.3k| if (neigh2 > MAX_ATOMS) ------------------ | | 15| 17.3k|#define MAX_ATOMS 32766 ------------------ | Branch (2090:13): [True: 3.09k, False: 14.2k] ------------------ 2091| 3.09k| { 2092| 3.09k| return 0; 2093| 3.09k| } 2094| 14.2k| return 1; 2095| 17.3k| } 2096| 14.2k| else if (neigh2 > MAX_ATOMS) ------------------ | | 15| 14.2k|#define MAX_ATOMS 32766 ------------------ | Branch (2096:14): [True: 8.03k, False: 6.16k] ------------------ 2097| 8.03k| { 2098| 8.03k| return -1; 2099| 8.03k| } 2100| 6.16k| else 2101| 6.16k| { 2102| 6.16k| AT_RANK nCurDfsNumber = os->m_gDfs4CT_nDfsNumber[os->m_gDfs4CT_nCurrentAtom]; 2103| 6.16k| int nDesc1 = nCurDfsNumber > os->m_gDfs4CT_nDfsNumber[neigh1] ? ------------------ | Branch (2103:22): [True: 1.37k, False: 4.79k] ------------------ 2104| 4.79k| 0 : (int)os->m_gDfs4CT_nNumDescendants[neigh1]; 2105| 6.16k| int nDesc2 = nCurDfsNumber > os->m_gDfs4CT_nDfsNumber[neigh2] ? ------------------ | Branch (2105:22): [True: 850, False: 5.31k] ------------------ 2106| 5.31k| 0 : (int)os->m_gDfs4CT_nNumDescendants[neigh2]; 2107| 6.16k| int ret; 2108| 6.16k| if ((ret = nDesc1 - nDesc2)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2108:13): [True: 3.84k, False: 2.32k] ------------------ 2109| 3.84k| { 2110| 3.84k| return ret; 2111| 3.84k| } 2112| 2.32k| return (int)neigh1 - (int)neigh2; /* canon. numbers difference */ 2113| 6.16k| } 2114| 31.5k|} All_SC_Same: 23| 2.06k|{ 24| 2.06k| int n1 = (int) nAtomNumberCanonFrom[(int) canon_rank1 - 1]; 25| 2.06k| AT_RANK r1 = pRankStack1[0][n1]; 26| 2.06k| int iMax1 = (int) r1; 27| 2.06k| int i1, s1; 28| 2.06k| int bFound = 0, stereo_atom_parity = -1; 29| | 30| | /* find one stereo atom such that canon_rank1 can be mapped on it */ 31| 4.10k| for (i1 = 1; i1 <= iMax1 && r1 == pRankStack2[0][s1 = (int) pRankStack2[1][iMax1 - i1]]; i1++) ------------------ | Branch (31:18): [True: 4.08k, False: 22] | Branch (31:33): [True: 2.29k, False: 1.79k] ------------------ 32| 2.29k| { 33| 2.29k| if (at[s1].stereo_bond_neighbor[0]) ------------------ | Branch (33:13): [True: 0, False: 2.29k] ------------------ 34| 0| { 35| 0| bFound = 0; /* at[s1] is not sp3-stereogenic: it belongs to a stereobond */ 36| 0| break; 37| 0| } 38| 2.29k| else 39| 2.29k| if (i1 == 1) ------------------ | Branch (39:17): [True: 2.06k, False: 235] ------------------ 40| 2.06k| { 41| 2.06k| stereo_atom_parity = PARITY_VAL( at[s1].stereo_atom_parity ); ------------------ | | 262| 2.06k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 2.06k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 42| 2.06k| if (!ATOM_PARITY_KNOWN( stereo_atom_parity )) ------------------ | | 258| 2.06k|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 2.06k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 1.93k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (258:38): [True: 1.93k, False: 127] | | | Branch (258:68): [True: 1.93k, False: 0] | | ------------------ ------------------ 43| 127| { 44| 127| bFound = 0; /* at[s1] does not have a KNOWN parity */ 45| 127| break; 46| 127| } 47| 2.06k| } 48| 235| else 49| 235| if (stereo_atom_parity != PARITY_VAL( at[s1].stereo_atom_parity )) ------------------ | | 262| 235|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 235|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ | Branch (49:21): [True: 119, False: 116] ------------------ 50| 119| { 51| 119| bFound = 0; /* two equivalent atoms have different parities */ 52| 119| break; 53| 119| } 54| 2.04k| bFound++; 55| 2.04k| } 56| | 57| 2.06k| return bFound; 58| 2.06k|} Next_SC_At_CanonRank2: 73| 6.15k|{ 74| 6.15k| AT_RANK canon_rank1_inp = *canon_rank1; 75| 6.15k| AT_RANK cr1; /* canonical rank (canonical number) */ 76| 6.15k| AT_RANK r1; /* mapping rank */ 77| 6.15k| int n1; /* ord. number of an atom with the canon. number */ 78| 6.15k| int s1; /* ord. number of an atom with stereo */ 79| 6.15k| int i1, bFound = 0; 80| 6.15k| int iMax1; 81| | 82| 6.15k| if (canon_rank1_inp < *canon_rank1_min) ------------------ | Branch (82:9): [True: 0, False: 6.15k] ------------------ 83| 0| { 84| 0| canon_rank1_inp = *canon_rank1_min; 85| 0| } 86| 6.15k| else 87| 6.15k| { 88| 6.15k| if (canon_rank1_inp < 1) ------------------ | Branch (88:13): [True: 1.25k, False: 4.89k] ------------------ 89| 1.25k| { 90| 1.25k| canon_rank1_inp = 1; 91| 1.25k| } 92| 4.89k| else 93| 4.89k| { 94| 4.89k| canon_rank1_inp++; /* next canonical rank */ 95| 4.89k| } 96| 6.15k| } 97| 6.15k| cr1 = canon_rank1_inp; 98| | 99| 8.26k| while ((int) cr1 <= num_atoms) ------------------ | Branch (99:12): [True: 8.26k, False: 0] ------------------ 100| 8.26k| { 101| 8.26k| n1 = (int) nAtomNumberCanonFrom[(int) cr1 - 1]; /* atom1 (which has canon. rank cr1) ord. number */ 102| 8.26k| iMax1 = (int) ( r1 = pRankStack1[0][n1] ); /* mapping rank of atom1 */ 103| | /* find atoms "to" to which the canon. number can be mapped; they have mapping rank r1, number s1 */ 104| 10.8k| for (i1 = 1; i1 <= iMax1 && r1 == pRankStack2[0][s1 = (int) pRankStack2[1][iMax1 - i1]]; i1++) ------------------ | Branch (104:22): [True: 9.97k, False: 894] | Branch (104:37): [True: 8.76k, False: 1.21k] ------------------ 105| 8.76k| { 106| | /* looking for a stereo center atom that has mapping rank r1 */ 107| 8.76k| if (bAtomUsedForStereo[s1] == STEREO_AT_MARK) ------------------ | | 878| 8.76k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ | Branch (107:17): [True: 6.15k, False: 2.61k] ------------------ 108| 6.15k| { 109| | /* found a sterogenic atom that has not been mapped yet */ 110| 6.15k| bFound = 1; 111| 6.15k| break; 112| 6.15k| } 113| 8.76k| } 114| 8.26k| if (bFound) ------------------ | Branch (114:13): [True: 6.15k, False: 2.10k] ------------------ 115| 6.15k| { 116| | /* one sterogenic not mapped yet atom "to" has been found */ 117| 6.15k| if (*bFirstTime) ------------------ | Branch (117:17): [True: 6.15k, False: 0] ------------------ 118| 6.15k| { 119| 6.15k| *canon_rank1_min = cr1; 120| 6.15k| *bFirstTime = 0; 121| 6.15k| } 122| 6.15k| break; 123| 6.15k| } 124| 2.10k| else 125| 2.10k| { 126| | /* a not mapped yet stereogenic atom has not found */ 127| | /* for the mapping rank r1 defined by the canonical rank cr1; try next cr1 */ 128| 2.10k| cr1++; 129| 2.10k| } 130| 8.26k| } 131| 6.15k| if (bFound) ------------------ | Branch (131:9): [True: 6.15k, False: 0] ------------------ 132| 6.15k| { 133| | /* success */ 134| 6.15k| *canon_rank1 = cr1; 135| 6.15k| return 1; 136| 6.15k| } 137| | 138| 0| return 0; 139| 6.15k|} CompareLinCtStereoDble: 147| 1.73k|{ 148| 1.73k| int i, num, ret = 0; 149| | 150| | /* compare double bonds */ 151| 1.73k| if (LinearCTStereoDble1 && LinearCTStereoDble2) ------------------ | Branch (151:9): [True: 1.31k, False: 419] | Branch (151:32): [True: 1.31k, False: 0] ------------------ 152| 1.31k| { 153| 1.31k| num = inchi_min( nLenLinearCTStereoDble1, nLenLinearCTStereoDble2 ); ------------------ | | 139| 1.31k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 1.31k] | | ------------------ ------------------ 154| 2.62k| for (i = 0; i < num; i++) ------------------ | Branch (154:21): [True: 1.30k, False: 1.31k] ------------------ 155| 1.30k| { 156| 1.30k| if ((ret = (int) LinearCTStereoDble1[i].at_num1 - (int) LinearCTStereoDble2[i].at_num1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (156:17): [True: 0, False: 1.30k] ------------------ 157| 0| break; 158| 1.30k| if ((ret = (int) LinearCTStereoDble1[i].at_num2 - (int) LinearCTStereoDble2[i].at_num2)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (158:17): [True: 0, False: 1.30k] ------------------ 159| 0| break; 160| 1.30k| if ((ret = (int) LinearCTStereoDble1[i].parity - (int) LinearCTStereoDble2[i].parity)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (160:17): [True: 2, False: 1.30k] ------------------ 161| 2| break; 162| 1.30k| } 163| 1.31k| if (!ret) ------------------ | Branch (163:13): [True: 1.31k, False: 2] ------------------ 164| 1.31k| { 165| 1.31k| ret = nLenLinearCTStereoDble1 - nLenLinearCTStereoDble2; 166| 1.31k| } 167| 1.31k| } 168| 419| else 169| 419| { 170| 419| if (LinearCTStereoDble1 && nLenLinearCTStereoDble1 > 0) ------------------ | Branch (170:13): [True: 0, False: 419] | Branch (170:36): [True: 0, False: 0] ------------------ 171| 0| { 172| 0| ret = 1; 173| 0| } 174| 419| else 175| 419| { 176| 419| if (LinearCTStereoDble2 && nLenLinearCTStereoDble2 > 0) ------------------ | Branch (176:17): [True: 0, False: 419] | Branch (176:40): [True: 0, False: 0] ------------------ 177| 0| { 178| 0| ret = -1; 179| 0| } 180| 419| } 181| 419| } 182| | 183| 1.73k| return ret; 184| 1.73k|} CompareLinCtStereoCarb: 192| 434|{ 193| 434| int i, num, ret = 0; 194| | 195| | /* compare stereocenters */ 196| 434| if (LinearCTStereoCarb1 && LinearCTStereoCarb2) ------------------ | Branch (196:9): [True: 434, False: 0] | Branch (196:32): [True: 434, False: 0] ------------------ 197| 434| { 198| 434| num = inchi_min( nLenLinearCTStereoCarb1, nLenLinearCTStereoCarb2 ); ------------------ | | 139| 434|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 434] | | ------------------ ------------------ 199| 1.33k| for (i = 0; i < num; i++) ------------------ | Branch (199:21): [True: 1.14k, False: 191] ------------------ 200| 1.14k| { 201| 1.14k| if ((ret = (int) LinearCTStereoCarb1[i].at_num - (int) LinearCTStereoCarb2[i].at_num)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (201:17): [True: 27, False: 1.11k] ------------------ 202| 27| break; 203| 1.11k| if ((ret = (int) LinearCTStereoCarb1[i].parity - (int) LinearCTStereoCarb2[i].parity)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (203:17): [True: 216, False: 900] ------------------ 204| 216| break; 205| 1.11k| } 206| 434| if (!ret) ------------------ | Branch (206:13): [True: 191, False: 243] ------------------ 207| 191| { 208| 191| ret = nLenLinearCTStereoCarb1 - nLenLinearCTStereoCarb2; 209| 191| } 210| 434| } 211| 0| else 212| 0| if (LinearCTStereoCarb1 && nLenLinearCTStereoCarb1 > 0) ------------------ | Branch (212:13): [True: 0, False: 0] | Branch (212:36): [True: 0, False: 0] ------------------ 213| 0| { 214| 0| ret = 1; 215| 0| } 216| 0| else 217| 0| if (LinearCTStereoCarb2 && nLenLinearCTStereoCarb2 > 0) ------------------ | Branch (217:17): [True: 0, False: 0] | Branch (217:40): [True: 0, False: 0] ------------------ 218| 0| { 219| 0| ret = -1; 220| 0| } 221| | 222| 434| return ret; 223| 434|} CompareLinCtStereo: 235| 436|{ 236| 436| int ret; 237| | 238| | /* compare double bonds */ 239| 436| ret = CompareLinCtStereoDble( LinearCTStereoDble1, nLenLinearCTStereoDble1, 240| 436| LinearCTStereoDble2, nLenLinearCTStereoDble2 ); 241| 436| if (!ret) ------------------ | Branch (241:9): [True: 434, False: 2] ------------------ 242| 434| { 243| 434| ret = CompareLinCtStereoCarb( LinearCTStereoCarb1, nLenLinearCTStereoCarb1, 244| | 245| 434| LinearCTStereoCarb2, nLenLinearCTStereoCarb2 ); 246| 434| } 247| 436| return ret; 248| 436|} CompareLinCtStereoAtomToValues: 255| 14.4k|{ 256| 14.4k| if (LinearCTStereoCarb->at_num CT_GREATER_THAN at_rank_canon1) ------------------ | Branch (256:9): [True: 409, False: 14.0k] ------------------ 257| 409| { 258| 409| return 1; 259| 409| } 260| 14.0k| if (LinearCTStereoCarb->at_num != at_rank_canon1) ------------------ | Branch (260:9): [True: 172, False: 13.8k] ------------------ 261| 172| { 262| 172| return -1; 263| 172| } 264| 13.8k| if (LinearCTStereoCarb->parity CT_GREATER_THAN parity) ------------------ | Branch (264:9): [True: 1.91k, False: 11.9k] ------------------ 265| 1.91k| { 266| 1.91k| return 1; 267| 1.91k| } 268| 11.9k| if (LinearCTStereoCarb->parity != parity) ------------------ | Branch (268:9): [True: 3.69k, False: 8.27k] ------------------ 269| 3.69k| { 270| 3.69k| return -1; 271| 3.69k| } 272| | 273| 8.27k| return 0; 274| 11.9k|} bUniqueAtNbrFromMappingRank: 282| 3.33k|{ 283| 3.33k| int r = (int) nAtRank - 1; 284| 3.33k| AT_NUMB i = pRankStack[1][r]; 285| 3.33k| if (nAtRank == pRankStack[0][(int) i] && ------------------ | Branch (285:9): [True: 3.33k, False: 5] ------------------ 286| 3.33k| ( !r || nAtRank != pRankStack[0][pRankStack[1][r - 1]] ) ------------------ | Branch (286:11): [True: 560, False: 2.77k] | Branch (286:17): [True: 2.76k, False: 5] ------------------ 287| 3.33k| ) 288| 3.32k| { 289| 3.32k| *nAtNumber = i; 290| 3.32k| return 1; 291| 3.32k| } 292| | 293| 10| return 0; 294| 3.33k|} nGetMcr: 302| 4.69k|{ 303| 4.69k| AT_RANK n1, n2, mcr; /* recursive version is much shorter. */ 304| | 305| 4.69k| n1 = nEqArray[(int) n]; 306| 4.69k| if (n == n1) ------------------ | Branch (306:9): [True: 3.11k, False: 1.57k] ------------------ 307| 3.11k| { 308| 3.11k| return n; 309| 3.11k| } 310| | /* 1st pass: find mcr */ 311| 1.67k| while (n1 != ( n2 = nEqArray[(int) n1] )) ------------------ | Branch (311:12): [True: 96, False: 1.57k] ------------------ 312| 96| { 313| 96| n1 = n2; 314| 96| } 315| | /* 2nd pass: copy mcr to each element of the set starting from nEqArray[n] */ 316| 1.57k| mcr = n1; 317| 1.57k| n1 = n; 318| 1.67k| while ( /*n1*/ mcr != ( n2 = nEqArray[(int) n1] )) ------------------ | Branch (318:20): [True: 96, False: 1.57k] ------------------ 319| 96| { 320| 96| nEqArray[(int) n1] = mcr; 321| 96| n1 = n2; 322| 96| } 323| | 324| 1.57k| return ( mcr ); 325| 4.69k|} nJoin2Mcrs: 332| 1.66k|{ 333| 1.66k| n1 = nGetMcr( nEqArray, n1 ); 334| 1.66k| n2 = nGetMcr( nEqArray, n2 ); 335| 1.66k| if (n1 < n2) ------------------ | Branch (335:9): [True: 93, False: 1.57k] ------------------ 336| 93| { 337| 93| nEqArray[n2] = n1; 338| 93| return 1; /* a change has been made */ 339| 93| } 340| 1.57k| if (n2 < n1) ------------------ | Branch (340:9): [True: 508, False: 1.06k] ------------------ 341| 508| { 342| 508| nEqArray[n1] = n2; 343| 508| return 1; /* a change has been made */ 344| 508| } 345| | 346| 1.06k| return 0; /* no changes */ 347| 1.57k|} All_SB_Same: 364| 2.10k|{ 365| 2.10k| int n1 = (int) nAtomNumberCanonFrom[(int) canon_rank1 - 1]; /* at1 has canon_rank1 */ 366| 2.10k| int n2 = (int) nAtomNumberCanonFrom[(int) canon_rank2 - 1]; /* at2 has canon_rank2 */ 367| 2.10k| AT_RANK r1 = pRankStack1[0][n1]; /* at1 mapping rank */ 368| 2.10k| AT_RANK r2 = pRankStack1[0][n2]; /* at2 mapping rank */ 369| 2.10k| AT_RANK rNeigh1, rNeigh2; 370| 2.10k| int iMax1 = (int) r1; 371| | /* int iMax2 = (int)r2; */ 372| 2.10k| int i1, i2, s1 = 0, s2 = 0, k1 = 0, k2, m, k, num_equal; 373| 2.10k| int bNotFound = 1, cumulene_len, stereo_bond_parity; 374| | 375| | /* at the first atom that possibly may have canon_rank1 find one stereo bond such that */ 376| | /* canon_rank1-canon_rank2 possibly may be mapped on it */ 377| 2.19k| for (i1 = 1; i1 <= iMax1 && r1 == pRankStack2[0][s1 = (int) pRankStack2[1][iMax1 - i1]]; i1++) ------------------ | Branch (377:18): [True: 2.19k, False: 0] | Branch (377:33): [True: 2.19k, False: 0] ------------------ 378| 2.19k| { 379| | /* at[n1] may be possible to map on at[s1] */ 380| 2.19k| for (k1 = 0, s2 = 0, bNotFound = 1; 381| 2.76k| k1 < MAX_NUM_STEREO_BONDS && ( s2 = (int) at[s1].stereo_bond_neighbor[k1] ) && ------------------ | | 873| 5.53k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (381:15): [True: 2.76k, False: 0] | Branch (381:44): [True: 2.67k, False: 94] ------------------ 382| 2.67k| ( bNotFound = ( r2 != pRankStack2[0][--s2] ) ); k1++) ------------------ | Branch (382:15): [True: 569, False: 2.10k] ------------------ 383| 569| ; /* continue until the 1st at[s2] (to which at[n2] may be mapped) have been found */ 384| 2.19k| if (!bNotFound) ------------------ | Branch (384:13): [True: 2.10k, False: 94] ------------------ 385| 2.10k| { 386| 2.10k| break; /* stop at 1st found */ 387| 2.10k| } 388| 2.19k| } 389| 2.10k| if (bNotFound) ------------------ | Branch (389:9): [True: 0, False: 2.10k] ------------------ 390| 0| { 391| 0| return -1; /* error: no mapping exists */ 392| 0| } 393| 3.24k| for (k2 = 0, m = 0; k2 < MAX_NUM_STEREO_BONDS && ( m = (int) at[s2].stereo_bond_neighbor[k2] ) && m - 1 != s1; k2++) ------------------ | | 873| 6.48k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (393:25): [True: 3.24k, False: 0] | Branch (393:54): [True: 3.24k, False: 0] | Branch (393:103): [True: 1.13k, False: 2.10k] ------------------ 394| 1.13k| ; 395| 2.10k| if (m - 1 != s1) ------------------ | Branch (395:9): [True: 0, False: 2.10k] ------------------ 396| 0| { 397| 0| return -1; /* program error: stereo bond in opposite direction not found */ 398| 0| } 399| 2.10k| stereo_bond_parity = at[s1].stereo_bond_parity[k1]; 400| 2.10k| if (!PARITY_KNOWN( stereo_bond_parity )) ------------------ | | 265| 2.10k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 2.10k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 4.21k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 2.10k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 2.10k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 2.10k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 2.10k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 2.10k, False: 0] | | | Branch (265:78): [True: 2.10k, False: 3] | | ------------------ ------------------ 401| 3| { 402| 3| return 0; 403| 3| } 404| 2.10k| cumulene_len = BOND_CHAIN_LEN( stereo_bond_parity ); ------------------ | | 214| 2.10k|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 2.10k|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 2.10k|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 2.10k|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 405| 2.10k| rNeigh1 = pRankStack2[0][(int) at[s1].neighbor[(int) at[s1].stereo_bond_ord[k1]]]; 406| 2.10k| rNeigh2 = pRankStack2[0][(int) at[s2].neighbor[(int) at[s2].stereo_bond_ord[k2]]]; 407| | 408| 2.10k| num_equal = 0; 409| | /* Search among ALL neighbors because sometimes a stereo bond may be mapped on a non-stereo bond. */ 410| | /* If is so then return 0: not all mappings are stereo-equivalent */ 411| 4.02k| for (s1 = 1; s1 <= iMax1 && r1 == pRankStack2[0][i1 = (int) pRankStack2[1][iMax1 - s1]]; s1++) ------------------ | Branch (411:18): [True: 3.93k, False: 87] | Branch (411:33): [True: 2.38k, False: 1.55k] ------------------ 412| 2.38k| { 413| 6.49k| for (k = 0; k < at[i1].valence; k++) ------------------ | Branch (413:21): [True: 4.57k, False: 1.92k] ------------------ 414| 4.57k| { 415| 4.57k| n1 = at[i1].neighbor[k]; 416| 4.57k| if (rNeigh1 != pRankStack2[0][n1]) ------------------ | Branch (416:17): [True: 1.73k, False: 2.83k] ------------------ 417| 1.73k| { 418| 1.73k| continue; /* wrong neighbor */ 419| 1.73k| } 420| 2.83k| if (cumulene_len) ------------------ | Branch (420:17): [True: 0, False: 2.83k] ------------------ 421| 0| { 422| 0| int prev, next, len, j; 423| 0| for (prev = i1, len = 0, next = n1; len < cumulene_len; len++) ------------------ | Branch (423:53): [True: 0, False: 0] ------------------ 424| 0| { 425| 0| if (at[next].valence == 2 && !at[next].num_H) ------------------ | Branch (425:25): [True: 0, False: 0] | Branch (425:50): [True: 0, False: 0] ------------------ 426| 0| { 427| 0| j = ( (int) at[next].neighbor[0] == prev ); 428| 0| prev = next; 429| 0| next = at[next].neighbor[j]; 430| 0| } 431| 0| else 432| 0| { 433| 0| break; /* cannot continue */ 434| 0| } 435| 0| } 436| 0| if (len != cumulene_len || ------------------ | Branch (436:21): [True: 0, False: 0] ------------------ 437| 0| r2 != pRankStack2[0][next] || ------------------ | Branch (437:22): [True: 0, False: 0] ------------------ 438| 0| rNeigh2 != pRankStack2[0][prev]) ------------------ | Branch (438:22): [True: 0, False: 0] ------------------ 439| 0| { 440| | /* cumulene chain not found */ 441| 0| continue; 442| 0| } 443| 0| i2 = next; 444| 0| } 445| 2.83k| else 446| 2.83k| { 447| 2.83k| i2 = n1; 448| 2.83k| } 449| | /* find if a stereogenic bond between at[i1]-at[i2] exists */ 450| 4.04k| for (k1 = 0; k1 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 8.08k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (450:26): [True: 4.04k, False: 0] ------------------ 451| 4.04k| ( m = (int) at[i1].stereo_bond_neighbor[k1] ) && m - 1 != i2; k1++) ------------------ | Branch (451:17): [True: 3.75k, False: 286] | Branch (451:66): [True: 1.20k, False: 2.54k] ------------------ 452| 1.20k| ; 453| 2.83k| if (m - 1 != i2) ------------------ | Branch (453:17): [True: 286, False: 2.54k] ------------------ 454| 286| { 455| 286| return 0; 456| 286| } 457| 3.83k| for (k2 = 0; k2 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 7.67k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (457:26): [True: 3.83k, False: 0] ------------------ 458| 3.83k| ( m = (int) at[i2].stereo_bond_neighbor[k2] ) && m - 1 != i1; k2++) ------------------ | Branch (458:17): [True: 3.83k, False: 0] | Branch (458:66): [True: 1.28k, False: 2.54k] ------------------ 459| 1.28k| ; 460| 2.54k| if (m - 1 != i1) ------------------ | Branch (460:17): [True: 0, False: 2.54k] ------------------ 461| 0| { 462| 0| return 0; 463| 0| } 464| 2.54k| if (at[i1].stereo_bond_parity[k1] != at[i2].stereo_bond_parity[k2]) ------------------ | Branch (464:17): [True: 0, False: 2.54k] ------------------ 465| 0| { 466| 0| return -1; /* program error */ 467| 0| } 468| 2.54k| if (stereo_bond_parity != at[i1].stereo_bond_parity[k1]) ------------------ | Branch (468:17): [True: 179, False: 2.36k] ------------------ 469| 179| { 470| 179| return 0; 471| 179| } 472| 2.36k| num_equal++; 473| 2.36k| } 474| 2.38k| } 475| | 476| 1.63k| return num_equal; 477| 2.10k|} Next_SB_At_CanonRanks2: 496| 2.38k|{ 497| 2.38k| AT_RANK canon_rank1_inp = *canon_rank1; 498| 2.38k| AT_RANK canon_rank2_inp = *canon_rank2; 499| 2.38k| AT_RANK cr1, cr2; /* canonical ranks (canonical numbers) */ 500| 2.38k| AT_RANK r1, r2; /* mapping ranks */ 501| 2.38k| int n1, n2; /* ord. numbers of atoms with stereo */ 502| 2.38k| int s1, s2; /* ord. numbers of atoms with canon. numbers */ 503| 2.38k| int i1, i2, k, m; 504| 2.38k| int iMax1, iMax2; 505| | 506| 2.38k| if (canon_rank1_inp < *canon_rank1_min || ------------------ | Branch (506:9): [True: 0, False: 2.38k] ------------------ 507| 2.38k| (canon_rank1_inp == *canon_rank1_min && ------------------ | Branch (507:11): [True: 413, False: 1.97k] ------------------ 508| 413| canon_rank2_inp < *canon_rank2_min)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (508:10): [True: 0, False: 413] ------------------ 509| 0| { 510| | 511| 0| canon_rank1_inp = *canon_rank1_min; 512| 0| canon_rank2_inp = *canon_rank2_min; 513| 0| } 514| 2.38k| else 515| 2.38k| if (canon_rank1_inp < 2) ------------------ | Branch (515:13): [True: 409, False: 1.97k] ------------------ 516| 409| { 517| 409| canon_rank1_inp = 2; 518| 409| canon_rank2_inp = 0; 519| 409| } 520| 2.38k| cr1 = canon_rank1_inp; 521| 2.38k| cr2 = num_atoms; /* initialize. 1/8/2002 */ 522| 4.84k| while ((int) cr1 <= num_atoms) ------------------ | Branch (522:12): [True: 4.80k, False: 34] ------------------ 523| 4.80k| { 524| 4.80k| cr2 = cr1; 525| 4.80k| n1 = (int) nAtomNumberCanonFrom[(int) cr1 - 1]; /* atom1=at[n1] (which has canon. rank) ord. number */ 526| 4.80k| iMax1 = (int) ( r1 = pRankStack1[0][n1] ); /* mapping rank of atom1 */ 527| 11.6k| for (i1 = 1; i1 <= iMax1 && r1 == pRankStack2[0][s1 = (int) pRankStack2[1][iMax1 - i1]]; i1++) ------------------ | Branch (527:22): [True: 11.0k, False: 565] | Branch (527:37): [True: 6.81k, False: 4.24k] ------------------ 528| 6.81k| { 529| | /* looking for a stereo bond atom that has mapping rank r1 */ 530| | /* found at[s1] such that rank cr1 can be mapped on at[s1] because cr1 and s1 have equal */ 531| | /* mapping rank = r1. Check at[s1] stereo bonds */ 532| 6.81k| if (bAtomUsedForStereo[s1] && bAtomUsedForStereo[s1] < STEREO_AT_MARK) ------------------ | | 878| 6.14k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ | Branch (532:17): [True: 6.14k, False: 670] | Branch (532:43): [True: 6.14k, False: 0] ------------------ 533| 6.14k| { 534| 17.0k| for (k = 0; k < MAX_NUM_STEREO_BONDS && ( s2 = (int) at[s1].stereo_bond_neighbor[k] ); k++) /* djb-rwth: removing redundant code */ ------------------ | | 873| 34.0k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (534:29): [True: 17.0k, False: 0] | Branch (534:57): [True: 10.9k, False: 6.14k] ------------------ 535| 10.9k| { 536| | /* stereo bond at[s1]-at[s2] has been found */ 537| 10.9k| if (bAtomUsedForStereo[--s2]) ------------------ | Branch (537:25): [True: 10.8k, False: 59] ------------------ 538| 10.8k| { 539| | /* stereo bonds have not been mapped. however, this check is not needed */ 540| 10.8k| int cumulene_len = BOND_CHAIN_LEN( at[s1].stereo_bond_parity[k] ); ------------------ | | 214| 10.8k|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 10.8k|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 10.8k|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 10.8k|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 541| 10.8k| if ((cumulene_len % 2 && !bAllene) || /* 09-26-2003 */ ------------------ | Branch (541:30): [True: 70, False: 10.7k] | Branch (541:50): [True: 35, False: 35] ------------------ 542| 10.8k| (!( cumulene_len % 2 ) && bAllene)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (542:31): [True: 10.7k, False: 35] | Branch (542:56): [True: 67, False: 10.7k] ------------------ 543| 102| { /* 08-17-2003 Fix05 */ 544| 102| continue; 545| 102| } 546| 10.7k| iMax2 = (int) ( r2 = pRankStack2[0][s2] ); /* mapping rank of atom2 */ 547| | /* Go back to canonical ranks and find an atom that has mapping rank r2 */ 548| | /* and is connected to the atom with canonical rank cr1 (possibly by cumulene chain) */ 549| | /* These cr1-cr2 canon. ranks possibly can be mapped on at[s1]-at[s2] stereo bond */ 550| 40.4k| for (i2 = 1; i2 <= iMax2 && r2 == pRankStack1[0][n2 = (int) pRankStack1[1][iMax2 - i2]]; i2++) ------------------ | Branch (550:38): [True: 36.9k, False: 3.42k] | Branch (550:53): [True: 29.6k, False: 7.31k] ------------------ 551| 29.6k| { 552| 29.6k| if (cumulene_len) ------------------ | Branch (552:33): [True: 59, False: 29.6k] ------------------ 553| 59| { 554| 59| int prev, next, len, j; 555| 145| for (m = 0; m < at[n1].valence; m++) ------------------ | Branch (555:45): [True: 121, False: 24] ------------------ 556| 121| { 557| 242| for (prev = n1, len = 0, next = (int) at[n1].neighbor[m]; len < cumulene_len; len++) ------------------ | Branch (557:95): [True: 121, False: 121] ------------------ 558| 121| { 559| 121| if (at[next].valence == 2 && !at[next].num_H) ------------------ | Branch (559:45): [True: 121, False: 0] | Branch (559:70): [True: 121, False: 0] ------------------ 560| 121| { 561| 121| j = ( (int) at[next].neighbor[0] == prev ); 562| 121| prev = next; 563| 121| next = at[next].neighbor[j]; 564| 121| } 565| 0| else 566| 0| { 567| 0| break; /* cannot continue */ 568| 0| } 569| 121| } 570| 121| if (len == cumulene_len && n2 == next) ------------------ | Branch (570:41): [True: 121, False: 0] | Branch (570:64): [True: 35, False: 86] ------------------ 571| 35| { 572| 35| break; 573| 35| } 574| 121| } 575| 59| } 576| 29.6k| else 577| 29.6k| { 578| 68.6k| for (m = 0; m < at[n1].valence && n2 != (int) at[n1].neighbor[m]; m++) ------------------ | Branch (578:45): [True: 52.3k, False: 16.2k] | Branch (578:67): [True: 39.0k, False: 13.3k] ------------------ 579| 39.0k| ; 580| 29.6k| } 581| 29.6k| if (m < at[n1].valence && ------------------ | Branch (581:33): [True: 13.3k, False: 16.3k] ------------------ 582| 13.3k| nCanonRankFrom[n2] < cr2 && ------------------ | Branch (582:34): [True: 5.13k, False: 8.22k] ------------------ 583| 5.13k| nCanonRankFrom[n2] > canon_rank2_inp) ------------------ | Branch (583:34): [True: 2.44k, False: 2.68k] ------------------ 584| 2.44k| { 585| | 586| 2.44k| cr2 = nCanonRankFrom[n2]; /* found a candidate for cr2 */ 587| 2.44k| } 588| 29.6k| } 589| 10.7k| } 590| 10.9k| } 591| 6.14k| } 592| 6.81k| } 593| 4.80k| if (cr2 >= cr1) ------------------ | Branch (593:13): [True: 2.45k, False: 2.35k] ------------------ 594| 2.45k| { 595| | /* not found for this r1 */ 596| 2.45k| cr1++; 597| 2.45k| canon_rank2_inp = 0; 598| 2.45k| } 599| 2.35k| else 600| 2.35k| { 601| | /* found cr2 < cr1 */ 602| 2.35k| if (*bFirstTime) ------------------ | Branch (602:17): [True: 2.34k, False: 4] ------------------ 603| 2.34k| { 604| 2.34k| *canon_rank1_min = cr1; 605| 2.34k| *canon_rank2_min = cr2; 606| 2.34k| *bFirstTime = 0; 607| 2.34k| } 608| 2.35k| break; 609| 2.35k| } 610| 4.80k| } 611| 2.38k| if (cr1 > cr2 && cr1 <= num_atoms) ------------------ | Branch (611:9): [True: 2.38k, False: 0] | Branch (611:22): [True: 2.35k, False: 34] ------------------ 612| 2.35k| { 613| | /* success */ 614| 2.35k| *canon_rank1 = cr1; 615| 2.35k| *canon_rank2 = cr2; 616| 2.35k| return 1; 617| 2.35k| } 618| | 619| 34| return 0; 620| 2.38k|} NextStereoParity2Test: 632| 2.38k|{ 633| | /* sequence of (stereo_bond_parity, sb_parity_calc) pairs: 634| | 635| | (BEST_PARITY, BEST_PARITY) 636| | | 637| | (BEST_PARITY, WORSE_PARITY) 638| | | 639| | (WORSE_PARITY, WORSE_PARITY) (BEST_PARITY, 0) 640| | \___________________________________________/ 641| | | 642| | (WORSE_PARITY, 0) 643| | | 644| | (AB_PARITY_UNKN, 0) 645| | | 646| | (AB_PARITY_UNDF, 0) 647| | | 648| | 649| | Meaning: 650| | stereo_bond_parity is the parity we are looking for 651| | stereo_bond_parity==sb_parity_calc => parity to be calculated from canonical numbers 652| | stereo_bond_parity!=sb_parity_calc => parity is already known 653| | */ 654| 4.71k|get_next_parity: 655| 4.71k| switch (*stereo_bond_parity) ------------------ | Branch (655:13): [True: 4.71k, False: 0] ------------------ 656| 4.71k| { 657| 3.11k| case BEST_PARITY: ------------------ | | 828| 3.11k|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (657:9): [True: 3.11k, False: 1.59k] ------------------ 658| 3.11k| switch (*sb_parity_calc) ------------------ | Branch (658:21): [True: 3.11k, False: 0] ------------------ 659| 3.11k| { 660| 7| case 0: /* BEST_PARITY(known) : (BEST_PARITY, 0) -> */ ------------------ | Branch (660:17): [True: 7, False: 3.11k] ------------------ 661| 7| *stereo_bond_parity = WORSE_PARITY; /* WORSE_PARITY(known): (WORSE_PARITY, 0) */ ------------------ | | 829| 7|#define WORSE_PARITY 2 ------------------ 662| 7| if (!nNumWorse) ------------------ | Branch (662:25): [True: 7, False: 0] ------------------ 663| 7| { 664| 7| goto get_next_parity; 665| 7| } 666| 0| break; 667| 1.55k| case BEST_PARITY: /* BEST_PARITY(calc) : (BEST_PARITY, BEST_PARITY) -> */ ------------------ | | 828| 1.55k|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (667:17): [True: 1.55k, False: 1.56k] ------------------ 668| 1.55k| *sb_parity_calc = WORSE_PARITY; /* BEST_PARITY(known): (BEST_PARITY, WORSE_PARITY) */ ------------------ | | 829| 1.55k|#define WORSE_PARITY 2 ------------------ 669| 1.55k| if (!nNumBest) ------------------ | Branch (669:25): [True: 1.55k, False: 0] ------------------ 670| 1.55k| { 671| 1.55k| goto get_next_parity; 672| 1.55k| } 673| 0| break; 674| 1.55k| case WORSE_PARITY: /* BEST_PARITY(known): (BEST_PARITY, WORSE_PARITY)-> */ ------------------ | | 829| 1.55k|#define WORSE_PARITY 2 ------------------ | Branch (674:17): [True: 1.55k, False: 1.56k] ------------------ 675| 1.55k| *stereo_bond_parity = WORSE_PARITY; /* WORSE_PARITY(calc): (WORSE_PARITY,WORSE_PARITY) */ ------------------ | | 829| 1.55k|#define WORSE_PARITY 2 ------------------ 676| 1.55k| if (!nNumCalc) ------------------ | Branch (676:25): [True: 0, False: 1.55k] ------------------ 677| 0| { /* added 12-17-2003 */ 678| 0| goto get_next_parity; 679| 0| } 680| 1.55k| break; 681| 3.11k| } 682| 1.55k| break; 683| 1.55k| case WORSE_PARITY: ------------------ | | 829| 773|#define WORSE_PARITY 2 ------------------ | Branch (683:9): [True: 773, False: 3.94k] ------------------ 684| 773| switch (*sb_parity_calc) ------------------ | Branch (684:21): [True: 773, False: 0] ------------------ 685| 773| { 686| 390| case 0: /* WORSE_PARITY(known) : (WORSE_PARITY, 0) -> */ ------------------ | Branch (686:17): [True: 390, False: 383] ------------------ 687| 390| *stereo_bond_parity = vABParityUnknown /* AB_PARITY_UNKN */;/* AB_PARITY_UNKN(known): (AB_PARITY_UNKN, 0) */ 688| 390| if (!nNumUnkn) ------------------ | Branch (688:25): [True: 389, False: 1] ------------------ 689| 389| { 690| 389| goto get_next_parity; 691| 389| } 692| 1| break; 693| 1| case BEST_PARITY: /* error */ ------------------ | | 828| 0|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (693:17): [True: 0, False: 773] ------------------ 694| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 695| 383| case WORSE_PARITY: /* WORSE_PARITY(calc) : (WORSE_PARITY,WORSE_PARITY)-> */ ------------------ | | 829| 383|#define WORSE_PARITY 2 ------------------ | Branch (695:17): [True: 383, False: 390] ------------------ 696| 383| *sb_parity_calc = 0; /* WORSE_PARITY(known): (WORSE_PARITY, 0) */ 697| 383| if (!nNumWorse) ------------------ | Branch (697:25): [True: 383, False: 0] ------------------ 698| 383| { 699| 383| goto get_next_parity; 700| 383| } 701| 0| break; 702| 773| } 703| 1| break; 704| | 705| 28| case AB_PARITY_UNKN: /* AB_PARITY_UNKN(known): (AB_PARITY_UNKN, 0) -> */ ------------------ | | 221| 28|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (705:9): [True: 28, False: 4.69k] ------------------ 706| 28| if (*sb_parity_calc) /* error */ ------------------ | Branch (706:17): [True: 0, False: 28] ------------------ 707| 0| { 708| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 709| 0| } 710| 28| *stereo_bond_parity = AB_PARITY_UNDF; /* AB_PARITY_UNDF(known): (AB_PARITY_UNDF, 0) */ ------------------ | | 222| 28|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 711| 28| if (!nNumUndf) ------------------ | Branch (711:17): [True: 28, False: 0] ------------------ 712| 28| { 713| 28| return 1; /*goto next_canon_ranks;*/ 714| 28| } 715| 0| break; 716| | 717| 798| case AB_PARITY_UNDF: /* AB_PARITY_UNDF(known): (AB_PARITY_UNDF, 0) -> */ ------------------ | | 222| 798|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (717:9): [True: 798, False: 3.92k] ------------------ 718| 798| if (*sb_parity_calc) ------------------ | Branch (718:17): [True: 0, False: 798] ------------------ 719| 0| { /* error */ 720| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 721| 0| } 722| 798| return 1; /*goto next_canon_ranks;*/ /* next canon ranks */ 723| 4.71k| } 724| 1.55k| return 0; 725| 4.71k|} CompareLinCtStereoDoubleToValues: 733| 4.23k|{ 734| 4.23k| if (LinearCTStereoDble->at_num1 CT_GREATER_THAN at_rank_canon1) ------------------ | Branch (734:9): [True: 163, False: 4.07k] ------------------ 735| 163| { 736| 163| return 1; 737| 163| } 738| 4.07k| if (LinearCTStereoDble->at_num1 != at_rank_canon1) ------------------ | Branch (738:9): [True: 34, False: 4.03k] ------------------ 739| 34| { 740| 34| return -1; 741| 34| } 742| 4.03k| if (LinearCTStereoDble->at_num2 CT_GREATER_THAN at_rank_canon2) ------------------ | Branch (742:9): [True: 14, False: 4.02k] ------------------ 743| 14| { 744| 14| return 1; 745| 14| } 746| 4.02k| if (LinearCTStereoDble->at_num2 != at_rank_canon2) ------------------ | Branch (746:9): [True: 10, False: 4.01k] ------------------ 747| 10| { 748| 10| return -1; 749| 10| } 750| 4.01k| if (LinearCTStereoDble->parity CT_GREATER_THAN bond_parity) ------------------ | Branch (750:9): [True: 183, False: 3.83k] ------------------ 751| 183| { 752| 183| return 1; 753| 183| } 754| 3.83k| if (LinearCTStereoDble->parity != bond_parity) ------------------ | Branch (754:9): [True: 141, False: 3.69k] ------------------ 755| 141| { 756| 141| return -1; 757| 141| } 758| | 759| 3.69k| return 0; 760| 3.83k|} SetUseAtomForStereo: 770| 1.73k|{ 771| 1.73k| int i, k; 772| 1.73k| memset( bAtomUsedForStereo, 0, sizeof( bAtomUsedForStereo[0] )*num_atoms ); /* djb-rwth: memset_s C11/Annex K variant? */ 773| 12.0k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (773:17): [True: 10.3k, False: 1.73k] ------------------ 774| 10.3k| { 775| 10.3k| if (at[i].parity) ------------------ | Branch (775:13): [True: 4.99k, False: 5.35k] ------------------ 776| 4.99k| { 777| 7.64k| for (k = 0; k < MAX_NUM_STEREO_BONDS && at[i].stereo_bond_neighbor[k]; k++) ------------------ | | 873| 15.2k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (777:25): [True: 7.64k, False: 0] | Branch (777:53): [True: 2.65k, False: 4.99k] ------------------ 778| 2.65k| { 779| 2.65k| ; 780| 2.65k| } 781| 4.99k| bAtomUsedForStereo[i] = k ? k : STEREO_AT_MARK; ------------------ | | 878| 8.27k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ | Branch (781:37): [True: 1.71k, False: 3.28k] ------------------ 782| 4.99k| } 783| 10.3k| } 784| 1.73k|} CurTreeAlloc: 789| 1.14k|{ 790| 1.14k| if (cur_tree) ------------------ | Branch (790:9): [True: 1.14k, False: 0] ------------------ 791| 1.14k| { 792| 1.14k| if (cur_tree->tree && cur_tree->max_len > 0 && !( cur_tree->max_len % num_atoms )) ------------------ | Branch (792:13): [True: 221, False: 926] | Branch (792:31): [True: 221, False: 0] | Branch (792:56): [True: 221, False: 0] ------------------ 793| 221| { 794| | /* do not reallocate */ 795| 221| cur_tree->cur_len = 0; 796| 221| cur_tree->incr_len = num_atoms; 797| 221| memset( cur_tree->tree, 0, cur_tree->max_len * sizeof( cur_tree->tree[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 798| 221| return 0; /* ok */ 799| 221| } 800| 926| inchi_free( cur_tree->tree ); ------------------ | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 926] | | | Branch (1152:50): [Folded, False: 926] | | ------------------ ------------------ 801| 926| memset( cur_tree, 0, sizeof( *cur_tree ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 802| 926| if ((cur_tree->tree = (AT_NUMB *) inchi_calloc( num_atoms, sizeof( cur_tree->tree[0] ) ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1146| 926|#define inchi_calloc calloc ------------------ | Branch (802:13): [True: 926, False: 0] ------------------ 803| 926| { 804| 926| cur_tree->incr_len = 805| 926| cur_tree->max_len = num_atoms; 806| 926| return 0; /* ok */ 807| 926| } 808| 926| } 809| | 810| 0| return -1; /* error */ /* */ 811| 1.14k|} CurTreeReAlloc: 816| 201|{ 817| 201| if (cur_tree) ------------------ | Branch (817:9): [True: 201, False: 0] ------------------ 818| 201| { 819| 201| if (cur_tree->tree && cur_tree->max_len > 0 && cur_tree->incr_len > 0) ------------------ | Branch (819:13): [True: 201, False: 0] | Branch (819:31): [True: 201, False: 0] | Branch (819:56): [True: 201, False: 0] ------------------ 820| 201| { 821| 201| void *p = cur_tree->tree; 822| 201| if ((cur_tree->tree = (AT_NUMB *) inchi_calloc( (long long)cur_tree->max_len + (long long)cur_tree->incr_len, sizeof( cur_tree->tree[0] ) ))) /* djb-rwth: cast operators added; addressing LLVM warning */ ------------------ | | 1146| 201|#define inchi_calloc calloc ------------------ | Branch (822:17): [True: 201, False: 0] ------------------ 823| 201| { 824| 201| memcpy(cur_tree->tree, p, cur_tree->cur_len * sizeof(cur_tree->tree[0])); 825| 201| inchi_free( p ); ------------------ | | 1152| 201|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 201, False: 0] | | | Branch (1152:50): [Folded, False: 201] | | ------------------ ------------------ 826| 201| cur_tree->max_len += cur_tree->incr_len; 827| 201| return 0; /* ok */ 828| 201| } 829| 201| } 830| 201| } 831| | 832| 0| return -1; /* error */ /* */ 833| 201|} CurTreeFree: 837| 288k|{ 838| 288k| if (cur_tree) ------------------ | Branch (838:9): [True: 926, False: 287k] ------------------ 839| 926| { 840| 926| inchi_free( cur_tree->tree ); ------------------ | | 1152| 926|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 926, False: 0] | | | Branch (1152:50): [Folded, False: 926] | | ------------------ ------------------ 841| 926| memset( cur_tree, 0, sizeof( *cur_tree ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 842| 926| } 843| 288k|} CurTreeAddRank: 847| 6.15k|{ 848| 6.15k| if (cur_tree) ------------------ | Branch (848:9): [True: 6.15k, False: 0] ------------------ 849| 6.15k| { 850| 6.15k| if (cur_tree->cur_len + 2 > cur_tree->max_len) ------------------ | Branch (850:13): [True: 47, False: 6.10k] ------------------ 851| 47| { 852| 47| if (CurTreeReAlloc( cur_tree )) ------------------ | Branch (852:17): [True: 0, False: 47] ------------------ 853| 0| { 854| 0| return -1; /* error */ /* */ 855| 0| } 856| 47| } 857| 6.15k| cur_tree->tree[cur_tree->cur_len++] = rank; 858| 6.15k| cur_tree->tree[cur_tree->cur_len++] = 1; 859| 6.15k| return 0; 860| 6.15k| } 861| | 862| 0| return -1; /* error */ /* */ 863| 6.15k|} CurTreeIsLastRank: 868| 16.8k|{ 869| 16.8k| if (cur_tree && cur_tree->cur_len > 0) ------------------ | Branch (869:9): [True: 16.8k, False: 0] | Branch (869:21): [True: 16.8k, False: 0] ------------------ 870| 16.8k| { 871| 16.8k| int rank_pos; 872| 16.8k| rank_pos = cur_tree->cur_len - 1; 873| 16.8k| rank_pos -= cur_tree->tree[rank_pos]; 874| 16.8k| if (rank_pos >= 0) ------------------ | Branch (874:13): [True: 16.8k, False: 0] ------------------ 875| 16.8k| { 876| 16.8k| return ( rank == cur_tree->tree[rank_pos] ); 877| 16.8k| } 878| 16.8k| } 879| | 880| 0| return 0; /* not found */ 881| 16.8k|} CurTreeRemoveLastRankIfNoAtoms: 886| 2.98k|{ 887| 2.98k| if (cur_tree && cur_tree->tree && cur_tree->cur_len >= 2) ------------------ | Branch (887:9): [True: 2.98k, False: 0] | Branch (887:21): [True: 2.98k, False: 0] | Branch (887:39): [True: 2.98k, False: 0] ------------------ 888| 2.98k| { 889| 2.98k| if (1 == cur_tree->tree[cur_tree->cur_len - 1]) ------------------ | Branch (889:13): [True: 2.60k, False: 379] ------------------ 890| 2.60k| { 891| 2.60k| return CurTreeRemoveLastRank( cur_tree ); /* 0=> success, -1=>failed */ 892| 2.60k| } 893| 379| return 1; /* cannot remove */ 894| 2.98k| } 895| 0| return -1; /* error */ /* */ 896| 2.98k|} CurTreeAddAtom: 901| 7.19k|{ 902| 7.19k| if (cur_tree) ------------------ | Branch (902:9): [True: 7.19k, False: 0] ------------------ 903| 7.19k| { 904| 7.19k| if (cur_tree->cur_len + 1 > cur_tree->max_len) ------------------ | Branch (904:13): [True: 154, False: 7.03k] ------------------ 905| 154| { 906| 154| if (CurTreeReAlloc( cur_tree )) ------------------ | Branch (906:17): [True: 0, False: 154] ------------------ 907| 0| { 908| 0| return -1; /* error */ /* */ 909| 0| } 910| 154| } 911| 7.19k| if (cur_tree->cur_len > 0) ------------------ | Branch (911:13): [True: 7.19k, False: 0] ------------------ 912| 7.19k| { 913| 7.19k| AT_NUMB new_len = cur_tree->tree[--cur_tree->cur_len] + 1; 914| 7.19k| cur_tree->tree[cur_tree->cur_len++] = (AT_NUMB) at_no; 915| 7.19k| cur_tree->tree[cur_tree->cur_len++] = new_len; 916| 7.19k| return 0; 917| 7.19k| } 918| 7.19k| } 919| | 920| 0| return -1; 921| 7.19k|} CurTreeKeepLastAtomsOnly: 926| 4.44k|{ /* on first entry: shift = 1; other values may occur in subsequent recursion */ 927| | /* cur_tree[cur_tree->cur_len - shift] is the length of a segment */ 928| | /* action: remove all atoms except the last from all segments 929| | that have length value positon to the right from tpos */ 930| 4.44k| int cur_length_pos; 931| 4.44k| if (cur_tree && cur_tree->tree && ( cur_length_pos = cur_tree->cur_len - shift ) > tpos) ------------------ | Branch (931:9): [True: 4.44k, False: 0] | Branch (931:21): [True: 4.44k, False: 0] | Branch (931:39): [True: 1.95k, False: 2.49k] ------------------ 932| 1.95k| { 933| 1.95k| if (cur_tree->tree[cur_length_pos] > 2) ------------------ | Branch (933:13): [True: 155, False: 1.79k] ------------------ 934| 155| { 935| | /* current segment contains more than 1 atom. Leave in the segment: rank, the last atom, length value */ 936| | /* subtract (old segment length)-(new segment length) from the tree length */ 937| | /* actual segment length including segment length value = (cur_tree->tree[cur_length_pos]+1) */ 938| 155| cur_tree->cur_len -= (int) cur_tree->tree[cur_length_pos] - 2; 939| 155| memmove(cur_tree->tree + cur_length_pos - cur_tree->tree[cur_length_pos] + 1, /* 1st atom pos */ 940| 155| cur_tree->tree + cur_length_pos - 1, /* last atom in the current segment position */ 941| 155| ((long long)shift + 1) * sizeof(cur_tree->tree[0])); /* djb-rwth: cast operator added */ 942| | /* (current segment length) distance from the last tree element has not changed */ 943| 155| cur_tree->tree[cur_tree->cur_len - shift] = 2; 944| | /* add 3 to move to the previous segment length position */ 945| 155| shift += 3; /* lenghth = 3 accounts for 3 currently present. segment items: 946| | (1) the last atom, (2) rank, (3) length value */ 947| 155| } 948| 1.79k| else 949| 1.79k| { 950| 1.79k| shift += (int) cur_tree->tree[cur_length_pos] + 1; /* cur_tree->cur_len - (previous segment length position) */ 951| 1.79k| } 952| 1.95k| CurTreeKeepLastAtomsOnly( cur_tree, tpos, shift ); 953| 1.95k| } 954| 4.44k|} CurTreeRemoveIfLastAtom: 959| 2.98k|{ 960| 2.98k| if (cur_tree && cur_tree->tree && cur_tree->cur_len > 2) ------------------ | Branch (960:9): [True: 2.98k, False: 0] | Branch (960:21): [True: 2.98k, False: 0] | Branch (960:39): [True: 2.98k, False: 0] ------------------ 961| 2.98k| { 962| 2.98k| AT_NUMB len = cur_tree->tree[cur_tree->cur_len - 1]; 963| 2.98k| if (len >= 2 && (int) cur_tree->tree[cur_tree->cur_len - 2] == at_no) ------------------ | Branch (963:13): [True: 2.98k, False: 0] | Branch (963:25): [True: 2.79k, False: 182] ------------------ 964| 2.79k| { 965| 2.79k| cur_tree->tree[--cur_tree->cur_len - 1] = len - 1; 966| 2.79k| return 0; 967| 2.79k| } 968| 182| return 1; /* not found */ 969| 2.98k| } 970| | 971| 0| return -1; /* error */ /* */ 972| 2.98k|} CurTreeGetPos: 977| 56.2k|{ 978| 56.2k| if (cur_tree) ------------------ | Branch (978:9): [True: 56.2k, False: 0] ------------------ 979| 56.2k| { 980| 56.2k| return cur_tree->cur_len; 981| 56.2k| } 982| | 983| 0| return -1; 984| 56.2k|} CurTreeSetPos: 989| 21.1k|{ 990| 21.1k| if (cur_tree) ------------------ | Branch (990:9): [True: 21.1k, False: 0] ------------------ 991| 21.1k| { 992| 21.1k| cur_tree->cur_len = len; 993| 21.1k| return 0; 994| 21.1k| } 995| | 996| 0| return -1; 997| 21.1k|} CurTreeRemoveLastRank: 1002| 5.95k|{ 1003| 5.95k| if (cur_tree && cur_tree->cur_len > 0) ------------------ | Branch (1003:9): [True: 5.95k, False: 0] | Branch (1003:21): [True: 5.95k, False: 0] ------------------ 1004| 5.95k| { 1005| 5.95k| cur_tree->cur_len -= cur_tree->tree[cur_tree->cur_len - 1] + 1; 1006| 5.95k| if (cur_tree->cur_len >= 0) ------------------ | Branch (1006:13): [True: 5.95k, False: 0] ------------------ 1007| 5.95k| { 1008| 5.95k| return 0; 1009| 5.95k| } 1010| 5.95k| } 1011| | 1012| 0| return -1; 1013| 5.95k|} CurTreeIsLastAtomEqu: 1020| 1.50k|{ 1021| 1.50k| if (cur_tree && cur_tree->tree && nSymmStereo && cur_tree->cur_len > 1) ------------------ | Branch (1021:9): [True: 1.50k, False: 0] | Branch (1021:21): [True: 1.50k, False: 0] | Branch (1021:39): [True: 1.50k, False: 0] | Branch (1021:54): [True: 1.50k, False: 0] ------------------ 1022| 1.50k| { 1023| 1.50k| AT_NUMB nEq = nSymmStereo[at_no]; 1024| 1.50k| int end = cur_tree->cur_len - 1; 1025| 1.50k| int len = cur_tree->tree[end] - 1; 1026| 2.82k| for (; len > 0; len--) ------------------ | Branch (1026:16): [True: 1.60k, False: 1.21k] ------------------ 1027| 1.60k| { 1028| 1.60k| if (nSymmStereo[(int) cur_tree->tree[end - len]] == nEq) ------------------ | Branch (1028:17): [True: 286, False: 1.32k] ------------------ 1029| 286| return 1; 1030| 1.60k| } 1031| 1.21k| return 0; 1032| 1.50k| } 1033| | 1034| 0| return -1; /* error */ /* */ 1035| 1.50k|} SortedEquInfoToRanks: 114| 262k|{ 115| | /* v. 1.05 - changed declaration of nNumDiffRanks as suggested by Burt Leland 116| | to avoid the problem arising on compilation with VS2015 117| | 118| | AT_RANK rNew, rOld, nNumDiffRanks;*/ 119| 262k| AT_RANK rNew, rOld; 120| 262k| int nNumDiffRanks = 1; 121| | 122| | 123| 262k| int i, j, nNumChanges = 0, i_init; 124| | 125| 262k| i_init = num_atoms - 1; 126| | /* djb-rwth: fixing oss-fuzz issue #69965 */ 127| 262k| if (i_init >= 0) ------------------ | Branch (127:9): [True: 262k, False: 0] ------------------ 128| 262k| { 129| 262k| j = (int)nAtomNumber[i_init]; 130| 262k| rOld = nSymmRank[j]; 131| 262k| rNew = (AT_RANK)num_atoms; 132| 262k| nRank[j] = (AT_RANK)num_atoms; 133| 262k| nNumDiffRanks = 1; 134| 1.10M| for (i = i_init; i > 0; i--) ------------------ | Branch (134:26): [True: 843k, False: 262k] ------------------ 135| 843k| { 136| 843k| j = (int)nAtomNumber[i - 1]; 137| | 138| 843k| if (nSymmRank[j] != rOld) ------------------ | Branch (138:17): [True: 440k, False: 403k] ------------------ 139| 440k| { 140| 440k| nNumDiffRanks++; 141| 440k| rNew = (AT_RANK)i; 142| 440k| nNumChanges += (rOld != rNew + 1); 143| 440k| rOld = nSymmRank[j]; 144| 440k| } 145| | 146| 843k| nRank[j] = rNew; 147| 843k| } 148| 262k| } 149| 262k| if (bChanged) ------------------ | Branch (149:9): [True: 253k, False: 9.73k] ------------------ 150| 253k| { 151| 253k| *bChanged = ( 0 != nNumChanges ); 152| 253k| } 153| | 154| 262k| return nNumDiffRanks; 155| 262k|} SortedRanksToEquInfo: 165| 7|{ 166| | /* v. 1.05 - changed declaration of nNumDiffRanks as suggested by Burt Leland 167| | to avoid the problem arising on compilation with VS2015 168| | 169| | AT_RANK rNew, rOld, nNumDiffRanks;*/ 170| 7| AT_RANK rNew, rOld; 171| 7| int nNumDiffRanks = 1; 172| | 173| 7| int i, j; 174| 7| for (i = 1, j = (int) nAtomNumber[0], 175| 7| rOld = nRank[j], rNew = nSymmRank[j] = 1, 176| 7| nNumDiffRanks = 1; 177| 56| i < num_atoms; ------------------ | Branch (177:13): [True: 49, False: 7] ------------------ 178| 49| i++) 179| 49| { 180| 49| j = (int) nAtomNumber[i]; 181| 49| if (nRank[j] != rOld) ------------------ | Branch (181:13): [True: 16, False: 33] ------------------ 182| 16| { 183| 16| nNumDiffRanks++; 184| 16| rNew = (AT_RANK) ( i + 1 ); 185| 16| rOld = nRank[j]; 186| 16| } 187| 49| nSymmRank[j] = rNew; 188| 49| } 189| | 190| 7| return nNumDiffRanks; 191| 7|} switch_ptrs: 196| 6.71M|{ 197| 6.71M| AT_RANK *tmp = *p1; 198| 6.71M| *p1 = *p2; 199| 6.71M| *p2 = tmp; 200| 6.71M|} SetNewRanksFromNeighLists3: 212| 4.99M|{ 213| 4.99M| int i, j, k, nNumDiffRanks, nNumNewRanks; 214| 4.99M| AT_RANK r1, r2; 215| | 216| | /* -- nAtomNumber[] is already properly set -- 217| | for ( i = 0; i < num_atoms; i++ ) { 218| | nAtomNumber[i] = (AT_RANK)i; 219| | } 220| | */ 221| | /* set globals for qsort */ 222| | 223| 4.99M| pCG->m_pNeighList_RankForSort = NeighList; 224| 4.99M| pCG->m_pn_RankForSort = nRank; 225| 4.99M| nNumDiffRanks = 0; 226| 4.99M| nNumNewRanks = 0; 227| | 228| 4.99M| memset( nNewRank, 0, num_atoms * sizeof( nNewRank[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 229| | 230| | /* sorting */ 231| 524M| for (i = 0, r1 = 1; i < num_atoms; r1++) ------------------ | Branch (231:25): [True: 519M, False: 4.99M] ------------------ 232| 519M| { 233| 519M| j = (int)nAtomNumber[i]; 234| 519M| r2 = nRank[j]; 235| 519M| if (r1 == r2) ------------------ | Branch (235:13): [True: 508M, False: 10.5M] ------------------ 236| 508M| { 237| 508M| nNewRank[j] = r2; 238| 508M| nNumDiffRanks++; 239| 508M| i++; 240| 508M| continue; 241| 508M| } 242| 10.5M| r1 = r2; 243| 10.5M| insertions_sort_AT_NUMBERS( pCG, nAtomNumber + i, (int) r2 - i, CompNeighLists ); 244| | /*insertions_sort( nAtomNumber+i, r2-i, sizeof( nAtomNumber[0] ), CompNeighLists );*/ 245| 10.5M| j = r2 - 1; 246| 10.5M| k = (int)nAtomNumber[j]; 247| 10.5M| nNewRank[k] = r2; 248| 10.5M| nNumDiffRanks++; 249| 254M| while (j > i) ------------------ | Branch (249:16): [True: 243M, False: 10.5M] ------------------ 250| 243M| { 251| 243M| if (CompareNeighListLex( NeighList[(int) nAtomNumber[j - 1]], ------------------ | Branch (251:17): [True: 11.1k, False: 243M] ------------------ 252| 243M| NeighList[(int) nAtomNumber[j]], nRank )) 253| 11.1k| { 254| 11.1k| r2 = j; 255| 11.1k| nNumDiffRanks++; 256| 11.1k| nNumNewRanks++; 257| 11.1k| } 258| 243M| j--; 259| 243M| nNewRank[(int) nAtomNumber[j]] = r2; 260| 243M| } 261| 10.5M| i = r1; 262| 10.5M| } 263| | 264| 4.99M| return nNumNewRanks ? -nNumDiffRanks : nNumDiffRanks; ------------------ | Branch (264:12): [True: 11.0k, False: 4.98M] ------------------ 265| 4.99M|} SetNewRanksFromNeighLists4: 280| 1.30M|{ 281| 1.30M| int i, j, nNumDiffRanks, nNumNewRanks; 282| 1.30M| AT_RANK r1, r2; 283| | /* -- nAtomNumber[] is already properly set -- 284| | for ( i = 0; i < num_atoms; i++ ) { 285| | nAtomNumber[i] = (AT_RANK)i; 286| | } 287| | */ 288| | 289| | /* set globals for CompNeighListsUpToMaxRank */ 290| 1.30M| pCG->m_pNeighList_RankForSort = NeighList; 291| 1.30M| pCG->m_pn_RankForSort = nRank; 292| 1.30M| nNumDiffRanks = 0; 293| 1.30M| nNumNewRanks = 0; 294| 1.30M| pCG->m_nMaxAtNeighRankForSort = nMaxAtRank; 295| | 296| 1.30M| memset( nNewRank, 0, num_atoms * sizeof( nNewRank[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 297| | 298| | /* sorting */ 299| 131M| for (i = 0, r1 = 1; i < num_atoms; r1++) ------------------ | Branch (299:25): [True: 129M, False: 1.30M] ------------------ 300| 129M| { 301| 129M| if (r1 == ( r2 = nRank[j = (int) nAtomNumber[i]] )) ------------------ | Branch (301:13): [True: 126M, False: 2.82M] ------------------ 302| 126M| { 303| | /* non-tied rank: singleton */ 304| 126M| nNewRank[j] = r2; 305| 126M| nNumDiffRanks++; 306| 126M| i++; 307| 126M| continue; 308| 126M| } 309| | /* tied rank r2 310| | r2-i atoms have rank r2 311| | next atom after them is in position r2 312| | */ 313| 2.82M| r1 = r2; 314| | 315| 2.82M| insertions_sort_AT_NUMBERS( pCG, nAtomNumber + i, 316| 2.82M| (int) r2 - i, CompNeighListsUpToMaxRank ); 317| | /*insertions_sort( nAtomNumber+i, r2-i, sizeof( nAtomNumber[0] ), CompNeighListsUpToMaxRank );*/ 318| | 319| 2.82M| j = r2 - 1; /* prepare cycle backward, from j to i step -1 */ 320| 2.82M| nNewRank[(int) nAtomNumber[j]] = r2; 321| 2.82M| nNumDiffRanks++; 322| 62.6M| while (j > i) ------------------ | Branch (322:16): [True: 59.7M, False: 2.82M] ------------------ 323| 59.7M| { 324| 59.7M| if (CompareNeighListLexUpToMaxRank( NeighList[nAtomNumber[j - 1]], ------------------ | Branch (324:17): [True: 3.74k, False: 59.7M] ------------------ 325| 59.7M| NeighList[nAtomNumber[j]], nRank, nMaxAtRank )) 326| 3.74k| { 327| 3.74k| r2 = j; 328| 3.74k| nNumDiffRanks++; 329| 3.74k| nNumNewRanks++; 330| 3.74k| } 331| 59.7M| j--; 332| 59.7M| nNewRank[(int) nAtomNumber[j]] = r2; 333| 59.7M| } 334| 2.82M| i = r1; 335| 2.82M| } 336| | 337| 1.30M| return nNumNewRanks ? -nNumDiffRanks : nNumDiffRanks; ------------------ | Branch (337:12): [True: 3.73k, False: 1.30M] ------------------ 338| 1.30M|} SetNewRanksFromNeighLists: 353| 406k|{ 354| 406k| int i, nNumDiffRanks, j; 355| 406k| AT_RANK nCurrentRank; 356| | /* -- nAtomNumber[] is already properly set -- 357| | for ( i = 0; i < num_atoms; i++ ) { 358| | nAtomNumber[i] = (AT_RANK)i; 359| | } 360| | */ 361| | 362| | /* set globals for qsort */ 363| 406k| pCG->m_pNeighList_RankForSort = NeighList; 364| 406k| pCG->m_pn_RankForSort = nRank; 365| | 366| | /* sorting */ 367| 406k| if (bUseAltSort & 1) ------------------ | Branch (367:9): [True: 406k, False: 0] ------------------ 368| 406k| tsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), comp /*CompNeighListRanksOrd*/ ); ------------------ | | 18| 406k|#define tsort insertions_sort ------------------ 369| 0| else 370| 0| inchi_qsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), comp /*CompNeighListRanksOrd*/ ); 371| | 372| | /* djb-rwth: fixing oss-fuzz issue #69315 */ 373| 406k| nNumDiffRanks = 1; 374| 406k| if (num_atoms > 0) ------------------ | Branch (374:9): [True: 406k, False: 0] ------------------ 375| 406k| { 376| 406k| nCurrentRank = (AT_RANK)num_atoms; 377| 406k| j = num_atoms - 1; 378| 406k| nNewRank[(int)nAtomNumber[j]] = nCurrentRank; 379| | 380| 1.73M| for (i = num_atoms - 1; i > 0; i--) ------------------ | Branch (380:33): [True: 1.33M, False: 406k] ------------------ 381| 1.33M| { 382| | /* Note: CompNeighListRanks() in following line implicitly reads nRank pointed by pn_RankForSort */ 383| 1.33M| if (CompNeighListRanks(&nAtomNumber[i - 1], &nAtomNumber[i], pCG)) ------------------ | Branch (383:17): [True: 799k, False: 531k] ------------------ 384| 799k| { 385| 799k| nNumDiffRanks++; 386| 799k| nCurrentRank = (AT_RANK)i; 387| 799k| } 388| 1.33M| nNewRank[(int)nAtomNumber[i - 1]] = nCurrentRank; 389| 1.33M| } 390| 406k| } 391| | 392| 406k| return nNumDiffRanks; 393| 406k|} SortNeighListsBySymmAndCanonRank: 403| 25.2k|{ 404| 25.2k| int i; 405| 159k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (405:17): [True: 134k, False: 25.2k] ------------------ 406| 134k| { 407| 134k| insertions_sort_NeighListBySymmAndCanonRank( NeighList[i], nSymmRank, nCanonRank ); 408| 134k| } 409| 25.2k|} SortNeighLists2: 417| 406k|{ 418| 406k| int k, i; 419| 406k| AT_RANK nPrevRank = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 420| | /* 421| | * on entry nRank[nAtomNumber[k]] <= nRank[nAtomNumber[k+1]] ( k < num_atoms-1 ) 422| | * nRank[nAtomNumber[k]] >= k+1 ( k < num_atoms ) 423| | * nRank[nAtomNumber[k]] == k+1 if this nRank value is not tied OR if 424| | * nRank[nAtomNumber[k]] < nRank[nAtomNumber[k+1]] OR if k = num_atoms-1. 425| | * 426| | */ 427| 2.14M| for (k = 0; k < num_atoms; k++) ------------------ | Branch (427:17): [True: 1.73M, False: 406k] ------------------ 428| 1.73M| { 429| 1.73M| i = nAtomNumber[k]; 430| 1.73M|#ifdef FIX_STEREOCOUNT_ERR 431| 1.73M| if (NeighList[i][0] > 1) ------------------ | Branch (431:13): [True: 730k, False: 1.00M] ------------------ 432| |#else 433| | if (( nRank[i] != k + 1 || nRank[i] == nPrevRank ) && NeighList[i][0] > 1) 434| |#endif 435| 730k| { 436| | /* nRank[i] is tied (duplicated) */ 437| 730k| insertions_sort_NeighList_AT_NUMBERS( NeighList[i], nRank ); 438| 730k| } 439| 1.73M| nPrevRank = nRank[i]; /* djb-rwth: ignoring LLVM warning: variable used */ 440| 1.73M| } 441| | 442| 406k| return 0; 443| 406k|} SortNeighLists3: 451| 6.30M|{ 452| 6.30M| int k, i; 453| 6.30M| AT_RANK nPrevRank = 0; 454| | /* 455| | * on entry nRank[nAtomNumber[k]] <= nRank[nAtomNumber[k+1]] ( k < num_atoms-1 ) 456| | * nRank[nAtomNumber[k]] >= k+1 ( k < num_atoms ) 457| | * nRank[nAtomNumber[k]] == k+1 if this nRank value is not tied OR if 458| | * nRank[nAtomNumber[k]] < nRank[nAtomNumber[k+1]] OR if k = num_atoms-1. 459| | * 460| | */ 461| 958M| for (k = 0; k < num_atoms; k++) ------------------ | Branch (461:17): [True: 952M, False: 6.30M] ------------------ 462| 952M| { 463| 952M| i = nAtomNumber[k]; 464| 952M| if (( nRank[i] != k + 1 || nRank[i] == nPrevRank ) && NeighList[i][0] > 1) ------------------ | Branch (464:15): [True: 303M, False: 648M] | Branch (464:36): [True: 13.3M, False: 635M] | Branch (464:63): [True: 77.8k, False: 316M] ------------------ 465| 77.8k| { 466| | /* nRank[i] is tied (duplicated) */ 467| 77.8k| insertions_sort_NeighList_AT_NUMBERS3( NeighList[i], nRank ); 468| 77.8k| } 469| 952M| nPrevRank = nRank[i]; 470| 952M| } 471| 6.30M| return 0; 472| 6.30M|} DifferentiateRanks2: 492| 304k|{ 493| | /*int nNumPrevRanks;*/ 494| | 495| | /* SortNeighLists2 needs sorted ranks */ 496| 304k| pCG->m_pn_RankForSort = pnCurrRank; 497| 304k| if (bUseAltSort & 1) ------------------ | Branch (497:9): [True: 14.5k, False: 289k] ------------------ 498| 14.5k| tsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompRank /* CompRanksOrd*/ ); ------------------ | | 18| 14.5k|#define tsort insertions_sort ------------------ 499| 289k| else 500| 289k| inchi_qsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompRanksOrd ); 501| | 502| 304k| do 503| 327k| { 504| 327k| *lNumIter += 1; 505| | /*nNumPrevRanks = nNumCurrRanks;*/ 506| 327k| switch_ptrs( &pnCurrRank, &pnPrevRank ); 507| 327k| SortNeighLists2( num_atoms, pnPrevRank, NeighList, nAtomNumber ); 508| | /* the following call creates pnCurrRank out of pnPrevRank */ 509| 327k| nNumCurrRanks = SetNewRanksFromNeighLists( pCG, num_atoms, NeighList, pnPrevRank, pnCurrRank, nAtomNumber, 510| 327k| 1, CompNeighListRanksOrd ); 511| 327k| } 512| 327k| while ( /*nNumPrevRanks != nNumCurrRanks ||*/ memcmp( pnPrevRank, pnCurrRank, num_atoms * sizeof( pnCurrRank[0] ) )); ------------------ | Branch (512:51): [True: 23.1k, False: 304k] ------------------ 513| | 514| 304k| return nNumCurrRanks; 515| 304k|} DifferentiateRanks3: 534| 4.98M|{ 535| | /* 536| | static long count = 0; 537| | count ++; 538| | if ( count == 103 ) { 539| | int stop=1; 540| | } 541| | */ 542| | 543| | /* SortNeighLists3 needs sorted ranks: ranks/atnumbers must have been already sorted */ 544| 4.98M| do 545| 4.99M| { 546| 4.99M| *lNumIter += 1; 547| 4.99M| switch_ptrs( &pnCurrRank, &pnPrevRank ); 548| 4.99M| SortNeighLists3( num_atoms, pnPrevRank, NeighList, nAtomNumber ); 549| | /* the following call creates pnCurrRank out of pnPrevRank */ 550| 4.99M| nNumCurrRanks = SetNewRanksFromNeighLists3( pCG, num_atoms, NeighList, pnPrevRank, 551| 4.99M| pnCurrRank, nAtomNumber ); 552| 4.99M| } 553| 4.99M| while (nNumCurrRanks < 0 /* memcmp( pnPrevRank, pnCurrRank, num_atoms*sizeof(pnCurrRank[0]) )*/); ------------------ | Branch (553:12): [True: 11.0k, False: 4.98M] ------------------ 554| | 555| 4.98M| return nNumCurrRanks; 556| 4.98M|} DifferentiateRanks4: 570| 1.30M|{ 571| | /* 572| | static long count = 0; 573| | count ++; 574| | if ( count == 103 ) { 575| | int stop=1; 576| | } 577| | */ 578| | /* SortNeighLists4 needs sorted ranks: ranks/atnumbers must have been already sorted */ 579| 1.30M| do 580| 1.30M| { 581| 1.30M| *lNumIter += 1; 582| 1.30M| switch_ptrs( &pnCurrRank, &pnPrevRank ); 583| 1.30M| SortNeighLists3( num_atoms, pnPrevRank, NeighList, nAtomNumber ); 584| | /* the following call creates pnCurrRank out of pnPrevRank */ 585| 1.30M| nNumCurrRanks = SetNewRanksFromNeighLists4( pCG, num_atoms, NeighList, pnPrevRank, 586| 1.30M| pnCurrRank, nAtomNumber, nMaxAtRank ); 587| 1.30M| } 588| 1.30M| while (nNumCurrRanks < 0 /* memcmp( pnPrevRank, pnCurrRank, num_atoms*sizeof(pnCurrRank[0]) )*/); ------------------ | Branch (588:12): [True: 3.73k, False: 1.30M] ------------------ 589| | 590| 1.30M| return nNumCurrRanks; 591| 1.30M|} DifferentiateRanksBasic: 605| 39.2k|{ 606| 39.2k| int nNumPrevRanks; 607| | 608| | /* SortNeighLists2 needs sorted ranks */ 609| 39.2k| pCG->m_pn_RankForSort = pnCurrRank; 610| 39.2k| if (bUseAltSort & 1) ------------------ | Branch (610:9): [True: 39.2k, False: 0] ------------------ 611| 39.2k| { 612| 39.2k| tsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompRank ); ------------------ | | 18| 39.2k|#define tsort insertions_sort ------------------ 613| 39.2k| } 614| 0| else 615| 0| { 616| 0| inchi_qsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompRank ); 617| 0| } 618| | 619| 39.2k| do 620| 78.6k| { 621| 78.6k| *lNumIter += 1; 622| 78.6k| nNumPrevRanks = nNumCurrRanks; 623| 78.6k| switch_ptrs( &pnCurrRank, &pnPrevRank ); 624| 78.6k| SortNeighLists2( num_atoms, pnPrevRank, NeighList, nAtomNumber ); 625| | /* the following call creates pnCurrRank out of pnPrevRank */ 626| 78.6k| nNumCurrRanks = SetNewRanksFromNeighLists( pCG, num_atoms, NeighList, pnPrevRank, pnCurrRank, nAtomNumber, bUseAltSort, CompNeighListRanks ); 627| 78.6k| } 628| 78.6k| while (nNumPrevRanks != nNumCurrRanks || memcmp( pnPrevRank, pnCurrRank, num_atoms * sizeof( pnCurrRank[0] ) )); ------------------ | Branch (628:12): [True: 39.4k, False: 39.2k] | Branch (628:46): [True: 0, False: 39.2k] ------------------ 629| 39.2k| return nNumCurrRanks; 630| 39.2k|} NumberOfTies: 653| 8.98k|{ 654| | 655| 8.98k| AT_RANK *nRank1 = *pRankStack1++; 656| 8.98k| AT_RANK *nAtomNumber1 = *pRankStack1++; /* ranks for mapping "1", "from" */ 657| | 658| 8.98k| AT_RANK *nRank2 = *pRankStack2++; 659| 8.98k| AT_RANK *nAtomNumber2 = *pRankStack2++; /* ranks for mapping "2", "to" */ 660| | 661| 8.98k| AT_RANK r, *pTempArray; 662| | 663| 8.98k| int iMax, i, i1, i2; 664| | 665| 8.98k| *bAddStack = 0; 666| 8.98k| *bMapped1 = 0; 667| 8.98k| *nNewRank = 0; 668| 8.98k| r = nRank1[at_no1]; 669| | 670| 8.98k| if (r != nRank2[at_no2]) ------------------ | Branch (670:9): [True: 0, False: 8.98k] ------------------ 671| 0| { 672| 0| return CT_MAPCOUNT_ERR; /* atoms cannot be mapped onto each other: they have different ranks */ /* */ ------------------ | | 26| 0|#define CT_MAPCOUNT_ERR (CT_ERR_FIRST- 7) /*(-30007) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 673| 0| } 674| 8.98k| iMax = r - 1; 675| | /* find i1 and i2 = numbers of ranks in nRank1[] and nRank2[] equal to r: */ 676| 21.1k| for (i1 = 1; i1 <= iMax && r == nRank1[nAtomNumber1[iMax - i1]]; i1++) ------------------ | Branch (676:18): [True: 20.3k, False: 851] | Branch (676:32): [True: 12.1k, False: 8.13k] ------------------ 677| 12.1k| { 678| 12.1k| ; 679| 12.1k| } 680| 21.1k| for (i2 = 1; i2 <= iMax && r == nRank2[nAtomNumber2[iMax - i2]]; i2++) ------------------ | Branch (680:18): [True: 20.3k, False: 851] | Branch (680:32): [True: 12.1k, False: 8.13k] ------------------ 681| 12.1k| { 682| 12.1k| ; 683| 12.1k| } 684| 8.98k| if (i2 != i1) ------------------ | Branch (684:9): [True: 0, False: 8.98k] ------------------ 685| 0| return CT_MAPCOUNT_ERR; /* program error: must be identical number of equal ranks */ /* */ ------------------ | | 26| 0|#define CT_MAPCOUNT_ERR (CT_ERR_FIRST- 7) /*(-30007) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 686| | /* found i1 equal rank(s); preceding (smaller) non-equal rank is r-i1 */ 687| | /* To break the tie we have to reduce the rank r to r-i1+1 */ 688| | 689| | /************ Note ******************************* 690| | * IF ( i=r-1 && 0 <= i && i < num_atoms AND 691| | * nRank[nAtomNumber1[i]] == r ) 692| | * THEN: 693| | * nRank[nAtomNumber1[i+1]] > r; (if i+1 < num_atoms) 694| | * nRank[nAtomNumber1[i-1]] <= r; (if i > 0) 695| | * 696| | * IF r = nRank[i] THEN 697| | * nRank[nAtomNumber1[r-1]] == r 698| | * nRank[nAtomNumber1[r-i-1]] <= nRank[nAtomNumber1[r-i]] (for 1 <= i < r ) 699| | */ 700| 8.98k| if (i1 > 1) ------------------ | Branch (700:9): [True: 7.20k, False: 1.78k] ------------------ 701| 7.20k| { 702| | /* int bAtFromHasAlreadyBeenMapped = 0; */ 703| 7.20k| *nNewRank = r - i1 + 1; 704| | /* grab an existing or allocate a new array */ 705| | /* we need 4 arrays: 2 for ranks + 2 for numbers */ 706| 36.0k| for (i = 0; i < 4; i++) ------------------ | Branch (706:21): [True: 28.8k, False: 7.20k] ------------------ 707| 28.8k| { 708| 28.8k| if (i < 2) ------------------ | Branch (708:17): [True: 14.4k, False: 14.4k] ------------------ 709| 14.4k| { 710| 14.4k| pTempArray = *pRankStack1; 711| 14.4k| *bMapped1 += ( pTempArray && pTempArray[0] ); ------------------ | Branch (711:32): [True: 14.0k, False: 395] | Branch (711:46): [True: 4.97k, False: 9.03k] ------------------ 712| 14.4k| } 713| 14.4k| else 714| 14.4k| { 715| 14.4k| pTempArray = *pRankStack2; 716| 14.4k| } 717| 28.8k| if (!pTempArray && !( pTempArray = (AT_RANK *) inchi_malloc( length ) )) ------------------ | | 1143| 790|#define inchi_malloc malloc ------------------ | Branch (717:17): [True: 790, False: 28.0k] | Branch (717:32): [True: 0, False: 790] ------------------ 718| 0| return CT_OUT_OF_RAM; /* out of RAM */ /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 719| | /* copy "to" contents */ 720| 28.8k| switch (i) ------------------ | Branch (720:21): [True: 14.4k, False: 14.4k] ------------------ 721| 28.8k| { 722| 7.20k| case 2: ------------------ | Branch (722:17): [True: 7.20k, False: 21.6k] ------------------ 723| 7.20k| memcpy(pTempArray, nRank2, length); 724| 7.20k| break; 725| 7.20k| case 3: ------------------ | Branch (725:17): [True: 7.20k, False: 21.6k] ------------------ 726| 7.20k| memcpy(pTempArray, nAtomNumber2, length); 727| 7.20k| break; 728| 28.8k| } 729| 28.8k| if (i < 2) ------------------ | Branch (729:17): [True: 14.4k, False: 14.4k] ------------------ 730| 14.4k| *pRankStack1++ = pTempArray; 731| 14.4k| else 732| 14.4k| { 733| 14.4k| *pRankStack2++ = pTempArray; 734| 14.4k| } 735| 28.8k| } 736| 7.20k| *bAddStack = 2; /* to break the tie we added 2 more arrays to pRankStack1 and pRankStack2 */ 737| 7.20k| } 738| | 739| 8.98k| return i1; 740| 8.98k|} HalfStereoBondParity: 771| 538|{ 772| | /* 773| | Suppose neighbors #0,#1,#2 have ranks a, b, c. Remove rank of the neighbor connected 774| | by the stereogenic bond (NCSB) from the a, b, c list and denote the two left as r[0], r[1], 775| | in the same order. Let iNCSB be an ordering number (0,1,or 2) of the NCSB. 776| | Assume the neighbor connected by the stereogenic bond has infinite positive rank. 777| | Position the half-bond so that the stereogenic bond neighbor is to the right from the atom (see below) 778| | 779| | Definition. 780| | =========== 781| | if rank(X) != rank(Y) then Half-bond parity = (rank(X) > rank(Y)), that is, 782| | Y 783| | \ if ( rank(X) < rank(Y) ) then Half-bond parity is Even 784| | C==NCSB if ( rank(X) > rank(Y) ) then Half-bond parity is Odd 785| | / if ( rank(X) = rank(Y) ) then Half-bond parity cannot be defined 786| | X 787| | 788| | 1 2 1 789| | \ \ \ 790| | C==NCSB C==NCSB C==NCSB C==NCSB 791| | / / / 792| | 2 1 1 793| | 794| | Parity = 1 Parity = 1 Parity = 2 Parity = 2 795| | (Odd) (Odd) (Even) or 0 (Even) or 0 796| | 797| | Half-bond parity = (iNCSB + (r[0] > r[1]) + (Atom C geometric parity))%2 798| | 799| | Consider the following cases to prove the formula: 800| | 801| | Case 1: 3 explicit neighbors 802| | ============================ 803| | If (1) atom's geometric parity = even (which means neighbors #0, #1, #2 are located clockwise), 804| | and (2) neighbors other than NCSB have different ranks, then, 805| | assuming that NCSB always has the largest (infinite) rank (this is consistent with 806| | the assumption that implicit hydrogens have smallest ranks), we have 3 possibilities: 807| | 808| | c a b 809| | \ \ \ 810| | C==a C==b C==c 811| | / / / 812| | b c a 813| | 814| | iNCSB = 0 1 2 815| | Half-bond parity = b>c ab (0=even, 1=odd) 816| | r[0]>r[1] r[0]r[1] 817| | Half-bond parity 818| | for all 3 cases = (iNCSB + (r[0] > r[1]))%2 819| | 820| | The following slight modification will work for both odd and even geometric parity: 821| | 822| | Half-bond parity = (iNCSB + (r[0] > r[1]) + (Atom C geometric parity))%2 823| | 824| | even parity (0) => atom above the bond has lower rank than the atom below the bond. 825| | 826| | 827| | Case 2: 2 explicit neighbors 828| | ============================ 829| | One implicit hydrogen atom H or hydrogen isotope (implicit rank=0). Assume r[1]=0 830| | 831| | H a Note. The same method 832| | \ \ works for 833| | C==a C==b 834| | / / N==a and a 835| | b H / \ 836| | b N==b 837| | iNCSB = 0 1 838| | Half-bond parity = b>0 a<0 839| | (r[1]=0, r[0]>0) r[0]>r[1] r[0] r[1]) + (Atom C geometric parity))%2 842| | 843| | Case 3: 1 explicit neighbor (NCSB) 844| | ================================== 845| | Two implicit hydrogens, (number of neighbors on non-streogenic bonds)==0: 846| | 847| | Atom C geometric parity: Even Odd Note. The same method 848| | works for 849| | D H 850| | \ \ Even and Odd 851| | C==a C==a 852| | / / H N==a 853| | H D \ / 854| | N==a H 855| | iNCSB = 0 0 856| | Half-bond parity = (0<0)=0 (0<0)+1 = 1 857| | (r[1]=0, r[0]=0) r[1] r[1]) + (Atom C geometric parity))%2 861| | 862| | */ 863| 538| int i, j, k, iNeigh, parity, at1_parity, at_no2; 864| 538| AT_RANK r[MAX_NUM_STEREO_BOND_NEIGH]; 865| | 866| 538| if (at[at_no1].valence > MAX_NUM_STEREO_BOND_NEIGH || ( at1_parity = at[at_no1].parity ) <= 0) ------------------ | | 874| 1.07k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (866:9): [True: 0, False: 538] | Branch (866:59): [True: 0, False: 538] ------------------ 867| 0| { 868| 0| return 0; 869| 0| } 870| 538| if (!PARITY_WELL_DEF( at1_parity )) ------------------ | | 266| 538|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 538|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 1.07k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 538|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 538|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 538|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 538|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 538, False: 0] | | | Branch (266:85): [True: 538, False: 0] | | ------------------ ------------------ 871| 0| { 872| 0| if (PARITY_KNOWN( at1_parity )) ------------------ | | 265| 0|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 0|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 0, False: 0] | | | Branch (265:78): [True: 0, False: 0] | | ------------------ ------------------ 873| 0| { 874| 0| return at1_parity; 875| 0| } 876| 0| return -at1_parity; 877| 0| } 878| 538| if (0 > i_sb_neigh || i_sb_neigh >= MAX_NUM_STEREO_BOND_NEIGH) ------------------ | | 874| 538|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (878:9): [True: 0, False: 538] | Branch (878:27): [True: 0, False: 538] ------------------ 879| 0| { 880| 0| return CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 881| 0| } 882| 1.21k| for (i = 0; i <= i_sb_neigh; i++) ------------------ | Branch (882:17): [True: 677, False: 538] ------------------ 883| 677| { 884| 677| if (!at[at_no1].stereo_bond_neighbor[i]) ------------------ | Branch (884:13): [True: 0, False: 677] ------------------ 885| 0| { 886| 0| return CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 887| 0| } 888| 677| } 889| 538| at_no2 = at[at_no1].neighbor[(int) at[at_no1].stereo_bond_ord[i_sb_neigh]]; 890| 538| memset( r, 0, sizeof( r ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 891| 1.64k| for (i = j = 0, iNeigh = -1; i < at[at_no1].valence; i++) ------------------ | Branch (891:34): [True: 1.11k, False: 538] ------------------ 892| 1.11k| { 893| 1.11k| if (( k = (int) at[at_no1].neighbor[i] ) == at_no2) ------------------ | Branch (893:13): [True: 538, False: 573] ------------------ 894| 538| { 895| 538| iNeigh = i; 896| 538| } 897| 573| else 898| 573| { 899| 573| r[j++] = nRank[k]; 900| 573| } 901| 1.11k| } 902| 538| if (iNeigh < 0 || iNeigh != at[at_no1].stereo_bond_ord[i_sb_neigh]) ------------------ | Branch (902:9): [True: 0, False: 538] | Branch (902:23): [True: 0, False: 538] ------------------ 903| 0| { 904| 0| return CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 905| 0| } 906| 538| if ((j > 0 && !r[0]) || (j > 1 && !r[1])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (906:10): [True: 511, False: 27] | Branch (906:19): [True: 0, False: 511] | Branch (906:30): [True: 62, False: 476] | Branch (906:39): [True: 0, False: 62] ------------------ 907| 0| return 0; /* undefined ranks */ 908| | 909| 538| if ((j == 2 && r[0] == r[1]) || iNeigh < 0) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (909:10): [True: 62, False: 476] | Branch (909:20): [True: 0, False: 62] | Branch (909:37): [True: 0, False: 538] ------------------ 910| 0| { 911| 0| parity = AB_PARITY_CALC; /* cannot calculate bond parity without additional breaking ties. */ ------------------ | | 224| 0|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ 912| 0| } 913| 538| else 914| 538| { 915| 538| parity = 2 - ( at[at_no1].parity + iNeigh + ( r[1] < r[0] ) ) % 2; 916| 538| } 917| | 918| 538| return parity; 919| 538|} parity_of_mapped_half_bond: 932| 27|{ 933| 27| int i, j, k, num_neigh; 934| 27| int to_sb_neigh_ord, from_sb_neigh_ord, parity; 935| 27| AT_RANK r_to[MAX_NUM_STEREO_BOND_NEIGH], at_no_to[MAX_NUM_STEREO_BOND_NEIGH]; 936| 27| AT_RANK r_canon_from[MAX_NUM_STEREO_BOND_NEIGH], at_no_from[MAX_NUM_STEREO_BOND_NEIGH]; 937| 27| AT_RANK r, r_sb_neigh; 938| | 939| 108| for (i = 0; i < MAX_NUM_STEREO_BOND_NEIGH; i++) ------------------ | | 874| 108|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (939:17): [True: 81, False: 27] ------------------ 940| 81| { 941| 81| r_to[i] = r_canon_from[i] = 0; 942| 81| } 943| | 944| 27| if (pEN) ------------------ | Branch (944:9): [True: 27, False: 0] ------------------ 945| 27| { 946| 27| memset( pEN, 0, sizeof( *pEN ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 947| 27| } 948| | 949| | /* for debug only */ 950| 27| if (nRankFrom[from_at] != nRankTo[to_at] || ------------------ | Branch (950:9): [True: 0, False: 27] ------------------ 951| 27| nRankFrom[from_neigh] != nRankTo[to_neigh] || ------------------ | Branch (951:10): [True: 0, False: 27] ------------------ 952| 27| at[to_at].valence != at[from_at].valence) ------------------ | Branch (952:10): [True: 0, False: 27] ------------------ 953| 0| { 954| 0| return 0; /* program error: both atoms must be mapped */ /* */ 955| 0| } 956| | 957| 27| parity = PARITY_VAL( at[to_at].parity ); ------------------ | | 262| 27|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 27|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 958| 27| num_neigh = at[to_at].valence; 959| | 960| 27| if (num_neigh > MAX_NUM_STEREO_BOND_NEIGH || num_neigh < MIN_NUM_STEREO_BOND_NEIGH) ------------------ | | 874| 54|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ if (num_neigh > MAX_NUM_STEREO_BOND_NEIGH || num_neigh < MIN_NUM_STEREO_BOND_NEIGH) ------------------ | | 875| 27|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (960:9): [True: 0, False: 27] | Branch (960:50): [True: 0, False: 27] ------------------ 961| 0| { 962| | /* 2 neighbors are possible in case of stereo bond with implicit H */ 963| | /* or a stereocenter -CHD- with an implicit H */ 964| 0| if (num_neigh == 1 && at[to_at].stereo_bond_neighbor[0]) ------------------ | Branch (964:13): [True: 0, False: 0] | Branch (964:31): [True: 0, False: 0] ------------------ 965| 0| { 966| | /* 1 neighbor can happen in case of a terminal =CHD */ 967| 0| if (PARITY_WELL_DEF( parity )) ------------------ | | 266| 0|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 0, False: 0] | | | Branch (266:85): [True: 0, False: 0] | | ------------------ ------------------ 968| 0| { 969| 0| return 2 - parity % 2; 970| 0| } 971| 0| else 972| 0| { 973| 0| if (parity) ------------------ | Branch (973:21): [True: 0, False: 0] ------------------ 974| 0| { 975| 0| return parity; 976| 0| } 977| 0| else 978| 0| { 979| 0| return AB_PARITY_UNDF; /* undefined parity */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 980| 0| } 981| 0| } 982| 0| } 983| 0| return 0; /* program error */ /* */ 984| 0| } 985| | 986| 27| if (ATOM_PARITY_KNOWN( parity )) ------------------ | | 258| 27|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 27|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 27|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (258:38): [True: 27, False: 0] | | | Branch (258:68): [True: 27, False: 0] | | ------------------ ------------------ 987| 27| { 988| 27| if (!ATOM_PARITY_WELL_DEF( parity )) ------------------ | | 259| 27|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 27|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 27|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 27, False: 0] | | | Branch (259:75): [True: 27, False: 0] | | ------------------ ------------------ 989| 0| { 990| 0| return parity; 991| 0| } 992| 27| } 993| 0| else 994| 0| { 995| 0| if (parity) ------------------ | Branch (995:13): [True: 0, False: 0] ------------------ 996| 0| { 997| 0| return 0; /* parity; */ 998| 0| } 999| 0| else 1000| 0| { 1001| 0| return 0; /* AB_PARITY_UNDF; */ /* possibly program error: undefined parity */ 1002| 0| } 1003| 0| } 1004| | 1005| | /* locate at[to_at].stereo_bond_neighbor[] ordering numbers */ 1006| 27| for (i = 0, to_sb_neigh_ord = -1; i < MAX_NUM_STEREO_BONDS && ( k = (int) at[to_at].stereo_bond_neighbor[i] ); i++) ------------------ | | 873| 54|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1006:39): [True: 27, False: 0] | Branch (1006:67): [True: 27, False: 0] ------------------ 1007| 27| { 1008| 27| if (k == to_neigh + 1) ------------------ | Branch (1008:13): [True: 27, False: 0] ------------------ 1009| 27| { 1010| 27| to_sb_neigh_ord = i; 1011| 27| break; 1012| 27| } 1013| 27| } 1014| 27| if (to_sb_neigh_ord < 0) ------------------ | Branch (1014:9): [True: 0, False: 27] ------------------ 1015| 0| { 1016| 0| return 0; /* program error: not a stereo bond */ /* */ 1017| 0| } 1018| 27| to_sb_neigh_ord = (int) at[to_at].stereo_bond_ord[to_sb_neigh_ord]; 1019| 27| r_sb_neigh = nRankTo[(int) at[to_at].neighbor[to_sb_neigh_ord]]; 1020| 107| for (i = j = 0; i < num_neigh; i++) ------------------ | Branch (1020:21): [True: 80, False: 27] ------------------ 1021| 80| { 1022| 80| if (i != to_sb_neigh_ord) ------------------ | Branch (1022:13): [True: 53, False: 27] ------------------ 1023| 53| { 1024| 53| r_to[j] = nRankTo[(int) ( at_no_to[j] = at[to_at].neighbor[i] )]; 1025| 53| if (r_sb_neigh == r_to[j]) ------------------ | Branch (1025:17): [True: 0, False: 53] ------------------ 1026| 0| { 1027| 0| return 0; /* stereo bond atoms are not fully mapped */ 1028| 0| } 1029| 53| j++; 1030| 53| } 1031| 80| } 1032| 27| if (j + 1 != num_neigh) ------------------ | Branch (1032:9): [True: 0, False: 27] ------------------ 1033| 0| { 1034| 0| return 0; /* program error */ /* */ 1035| 0| } 1036| 27| if (j == 1) ------------------ | Branch (1036:9): [True: 1, False: 26] ------------------ 1037| 1| { 1038| | /* only one neighbor; no mapping needed */ 1039| 1| return 2 - ( parity + 1 + to_sb_neigh_ord ) % 2; 1040| 1| } 1041| 26| if (j != 2) ------------------ | Branch (1041:9): [True: 0, False: 26] ------------------ 1042| 0| { 1043| 0| return 0; /* program error: j can be only 0, 1, or 2 */ /* */ /* djb-rwth: addressing coverity ID #499526 -- refer to the first comment in this line */ 1044| 0| } 1045| | 1046| 26| if (r_to[0] == r_to[1]) ------------------ | Branch (1046:9): [True: 10, False: 16] ------------------ 1047| 10| { 1048| | /* double bond neighbors need to be mapped */ 1049| 10| j = 0; 1050| 10| from_sb_neigh_ord = -1; 1051| 40| for (i = 0; i < num_neigh; i++) ------------------ | Branch (1051:21): [True: 30, False: 10] ------------------ 1052| 30| { 1053| 30| k = at[from_at].neighbor[i]; 1054| 30| r = nRankFrom[k]; 1055| 30| if (r == r_sb_neigh) ------------------ | Branch (1055:17): [True: 10, False: 20] ------------------ 1056| 10| { 1057| 10| from_sb_neigh_ord = i; /* we need this value only for error-checking */ 1058| 10| } 1059| 20| else 1060| 20| { 1061| 20| if (r == r_to[0]) ------------------ | Branch (1061:21): [True: 20, False: 0] ------------------ 1062| 20| { 1063| 20| r_canon_from[j] = nCanonRankFrom[k]; 1064| 20| at_no_from[j] = (AT_RANK) k; 1065| 20| j++; 1066| 20| } 1067| 0| else 1068| 0| { 1069| 0| return 0; /* program error: unexpected rank, not fully mapped adjacent to the stereo bond atoms */ /* */ 1070| 0| } 1071| 20| } 1072| 30| } 1073| 10| if (from_sb_neigh_ord < 0 || j != 2) ------------------ | Branch (1073:13): [True: 0, False: 10] | Branch (1073:38): [True: 0, False: 10] ------------------ 1074| 0| { 1075| 0| return 0; /* program error: rank of a neighbor not found */ /* */ 1076| 0| } 1077| 10| if (pEN) ------------------ | Branch (1077:13): [True: 10, False: 0] ------------------ 1078| 10| { 1079| | /* j == 2 */ 1080| 10| pEN->to_at[0] = at_no_to[0]; 1081| 10| pEN->to_at[1] = at_no_to[1]; 1082| 10| pEN->num_to = 2; /* number of stored in pEN->to_at[] central atom neighbors */ 1083| 10| pEN->rank = r_to[0]; /* mapping rank of the tied neighbors */ 1084| | /* i := index of the smaller out of r_canon_from[1] and r_canon_from[0] */ 1085| 10| i = ( r_canon_from[1] < r_canon_from[0] ); 1086| 10| pEN->from_at = at_no_from[i]; 1087| 10| pEN->canon_rank = r_canon_from[i]; 1088| 10| } 1089| 10| return -( (int) r_to[0] ); 1090| 10| } 1091| | /* double bond neighbors a mapped: r_to[0] != r_to[1] */ 1092| 16| from_sb_neigh_ord = -1; 1093| 64| for (i = 0; i < num_neigh; i++) ------------------ | Branch (1093:17): [True: 48, False: 16] ------------------ 1094| 48| { 1095| 48| k = at[from_at].neighbor[i]; 1096| 48| r = nRankFrom[k]; 1097| 48| if (r == r_sb_neigh) ------------------ | Branch (1097:13): [True: 16, False: 32] ------------------ 1098| 16| { 1099| 16| from_sb_neigh_ord = i; /* we need this value only for error-checking */ 1100| 16| } 1101| 32| else 1102| 32| { 1103| 32| if (r == r_to[0]) ------------------ | Branch (1103:17): [True: 16, False: 16] ------------------ 1104| 16| { 1105| 16| r_canon_from[0] = nCanonRankFrom[k]; 1106| | /* at_no_from[0] = (AT_RANK)k; */ 1107| 16| } 1108| 16| else 1109| 16| { 1110| 16| if (r == r_to[1]) ------------------ | Branch (1110:21): [True: 16, False: 0] ------------------ 1111| 16| { 1112| 16| r_canon_from[1] = nCanonRankFrom[k]; 1113| | /* at_no_from[1] = (AT_RANK)k; */ 1114| 16| } 1115| 0| else 1116| 0| { 1117| 0| return 0; /* program error: unexpected rank, not fully mapped adjacent to the stereo bond atoms */ /* */ 1118| 0| } 1119| 16| } 1120| 32| } 1121| 48| } 1122| | 1123| 16| if (!r_canon_from[0] || !r_canon_from[1] || from_sb_neigh_ord < 0) ------------------ | Branch (1123:9): [True: 0, False: 16] | Branch (1123:29): [True: 0, False: 16] | Branch (1123:49): [True: 0, False: 16] ------------------ 1124| 0| { 1125| 0| return 0; /* program error: neighbor rank not found */ /* */ 1126| 0| } 1127| | 1128| 16| return 2 - ( parity + to_sb_neigh_ord + ( r_canon_from[1] < r_canon_from[0] ) ) % 2; 1129| 16|} parity_of_mapped_atom2: 1141| 7.96k|{ 1142| 7.96k| AT_RANK nNeighRankFrom[4], nNeighNumberFrom[4], nNeighRankTo[4], nNeighNumberTo[4]; 1143| 7.96k| AT_RANK nNeighRankFromCanon[4], nNeighRankToCanon[4]; 1144| 7.96k| int i, j, k, num_neigh; 1145| 7.96k| int r1, r2, r, r_canon_from_min, neigh_canon_from_min = 0, r_canon_from; /* djb-rwth: proper initialisation required */ 1146| 7.96k| int num_trans_to, num_trans_from, neigh1, neigh2; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1147| | 1148| 7.96k| num_neigh = at[to_at].valence; 1149| | 1150| 7.96k| if (pEN) ------------------ | Branch (1150:9): [True: 7.96k, False: 0] ------------------ 1151| 7.96k| { 1152| 7.96k| memset( pEN, 0, sizeof( *pEN ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1153| 7.96k| } 1154| | 1155| | /* for debug only */ 1156| 7.96k| if (nRankFrom[from_at] != nRankTo[to_at]) ------------------ | Branch (1156:9): [True: 0, False: 7.96k] ------------------ 1157| 0| { 1158| 0| return 0; /* program error */ /* */ 1159| 0| } 1160| 7.96k| if (num_neigh > MAX_NUM_STEREO_ATOM_NEIGH || num_neigh < 2) ------------------ | | 877| 15.9k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1160:9): [True: 0, False: 7.96k] | Branch (1160:50): [True: 0, False: 7.96k] ------------------ 1161| 0| { 1162| | /* 2 neighbors are possible in case of stereo bond with implicit H */ 1163| | /* or a stereocenter >CHD with two implicit H */ 1164| 0| if (num_neigh == 1) ------------------ | Branch (1164:13): [True: 0, False: 0] ------------------ 1165| 0| { 1166| | /* 1 neighbor can happen in case of a terminal -CHDT or =CHD */ 1167| 0| if (at[to_at].parity) ------------------ | Branch (1167:17): [True: 0, False: 0] ------------------ 1168| 0| { 1169| 0| return at[to_at].parity; 1170| 0| } 1171| 0| else 1172| 0| { 1173| 0| return AB_PARITY_UNDF; /* undefined parity */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 1174| 0| } 1175| 0| } 1176| 0| return 0; /* program error */ /* */ 1177| 0| } 1178| 38.7k| for (i = 0; i < num_neigh; i++) ------------------ | Branch (1178:17): [True: 30.7k, False: 7.96k] ------------------ 1179| 30.7k| { /* initialization of locals */ 1180| 30.7k| nNeighNumberTo[i] = 1181| 30.7k| nNeighNumberFrom[i] = i; 1182| 30.7k| nNeighRankTo[i] = nRankTo[(int) at[to_at].neighbor[i]]; /* mapping rank */ 1183| 30.7k| nNeighRankFrom[i] = nRankFrom[j = (int) at[from_at].neighbor[i]]; /* mapping rank */ 1184| 30.7k| nNeighRankFromCanon[i] = nCanonRankFrom[j]; /* canonical number */ 1185| 30.7k| } 1186| | 1187| 7.96k| pCG->m_pn_RankForSort = nNeighRankFrom; 1188| 7.96k| pCG->m_nNumCompNeighborsRanksCountEql = 0; /* sort mapping ranks-from */ 1189| 7.96k| num_trans_from = insertions_sort( pCG, nNeighNumberFrom, num_neigh, sizeof( nNeighNumberFrom[0] ), CompNeighborsRanksCountEql ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1190| | 1191| 7.96k| if (pCG->m_nNumCompNeighborsRanksCountEql) ------------------ | Branch (1191:9): [True: 2.66k, False: 5.30k] ------------------ 1192| 2.66k| { 1193| | /* At least 2 neighbors have equal mapping ranks (are tied). */ 1194| | /* Find tied from-neighbors with minimal canonical rank (nCanonRankFrom[]) */ 1195| 2.66k| r_canon_from_min = MAX_ATOMS + 1; /* max possible rank + 1 */ ------------------ | | 15| 2.66k|#define MAX_ATOMS 32766 ------------------ 1196| 10.2k| for (i = 1, r = 0, r1 = nNeighRankFrom[neigh1 = nNeighNumberFrom[0]]; i < num_neigh; i++, r1 = r2, neigh1 = neigh2) ------------------ | Branch (1196:79): [True: 7.61k, False: 2.66k] ------------------ 1197| 7.61k| { 1198| 7.61k| r2 = nNeighRankFrom[neigh2 = nNeighNumberFrom[i]]; 1199| 7.61k| if (r2 == r1) ------------------ | Branch (1199:17): [True: 3.50k, False: 4.10k] ------------------ 1200| 3.50k| { 1201| | /* found neighbors with tied ranks */ 1202| 3.50k| if (r != r2) ------------------ | Branch (1202:21): [True: 2.71k, False: 795] ------------------ 1203| 2.71k| { 1204| | /* the 1st pair of neighbor with this rank */ 1205| 2.71k| r = r2; 1206| 2.71k| if (( r_canon_from = nNeighRankFromCanon[neigh1] ) < r_canon_from_min) ------------------ | Branch (1206:25): [True: 2.66k, False: 52] ------------------ 1207| 2.66k| { 1208| 2.66k| r_canon_from_min = r_canon_from; /* min canon rank */ 1209| 2.66k| neigh_canon_from_min = neigh1; /* neighbor number */ 1210| 2.66k| } 1211| 2.71k| } 1212| 3.50k| if (( r_canon_from = nNeighRankFromCanon[neigh2] ) < r_canon_from_min) ------------------ | Branch (1212:21): [True: 1, False: 3.50k] ------------------ 1213| 1| { 1214| 1| r_canon_from_min = r_canon_from; 1215| 1| neigh_canon_from_min = neigh2; 1216| 1| } 1217| 3.50k| } 1218| 7.61k| } 1219| 2.66k| if (r) ------------------ | Branch (1219:13): [True: 2.66k, False: 0] ------------------ 1220| 2.66k| { 1221| | /* neighbors with tied ranks have been found => parity cannot be determined without additional mapping */ 1222| | /* find to-neighbors on which neigh_canon_from_min can be mapped */ 1223| 2.66k| r1 = nNeighRankFrom[neigh_canon_from_min]; 1224| 2.66k| if (pEN) ------------------ | Branch (1224:17): [True: 2.66k, False: 0] ------------------ 1225| 2.66k| { 1226| 12.9k| for (i = j = 0; i < num_neigh; i++) ------------------ | Branch (1226:33): [True: 10.2k, False: 2.66k] ------------------ 1227| 10.2k| { 1228| 10.2k| if (r1 == nNeighRankTo[i]) ------------------ | Branch (1228:25): [True: 6.11k, False: 4.15k] ------------------ 1229| 6.11k| { 1230| 6.11k| pEN->to_at[j++] = at[to_at].neighbor[i]; 1231| 6.11k| } 1232| 10.2k| } 1233| 2.66k| insertions_sort( pCG, pEN->to_at, j, sizeof( pEN->to_at[0] ), CompRanksInvOrd ); 1234| 2.66k| pEN->num_to = j; /* number of stored in pEN->to_at[] central atom neighbors */ 1235| 2.66k| pEN->from_at = at[from_at].neighbor[neigh_canon_from_min]; /* neighbor with min. canon number */ 1236| 2.66k| pEN->rank = r1; /* mapping rank of the tied neighbors */ 1237| 2.66k| pEN->canon_rank = r_canon_from_min; /* canon. rank of the pEN->from_at */ 1238| 2.66k| } 1239| 0| else 1240| 0| { 1241| | /* debug only */ 1242| 0| for (i = j = 0; i < num_neigh; i++) ------------------ | Branch (1242:33): [True: 0, False: 0] ------------------ 1243| 0| { 1244| 0| if (r1 == nNeighRankTo[i]) ------------------ | Branch (1244:25): [True: 0, False: 0] ------------------ 1245| 0| { 1246| 0| j++; 1247| 0| } 1248| 0| } 1249| 0| } 1250| | /* debug only */ 1251| 2.66k| if (j <= 1 || !r1 || r_canon_from_min > MAX_ATOMS) ------------------ | | 15| 2.66k|#define MAX_ATOMS 32766 ------------------ | Branch (1251:17): [True: 0, False: 2.66k] | Branch (1251:27): [True: 0, False: 2.66k] | Branch (1251:34): [True: 0, False: 2.66k] ------------------ 1252| 0| { 1253| 0| return 0; /* program error */ /* */ 1254| 0| } 1255| 2.66k| return -r; /* means parity cannot be determined */ 1256| 2.66k| } 1257| 0| return 0; /* program error */ 1258| 2.66k| } 1259| | 1260| | /* All neighbors have different mapping ranks; */ 1261| | /* therefore no additional mapping of the neighbors is necessary */ 1262| 5.30k| if (!ATOM_PARITY_WELL_DEF( at[to_at].parity )) ------------------ | | 259| 5.30k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 5.30k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 5.30k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 5.30k, False: 0] | | | Branch (259:75): [True: 5.30k, False: 0] | | ------------------ ------------------ 1263| 0| { 1264| 0| return at[to_at].parity; /* unknown parity or cannot be determined */ 1265| 0| } 1266| | 1267| 5.30k| pCG->m_pn_RankForSort = nNeighRankTo; 1268| 5.30k| num_trans_to = insertions_sort( pCG, nNeighNumberTo, num_neigh, sizeof( nNeighNumberTo[0] ), CompNeighborsRanksCountEql ); 1269| | 1270| | /* Map canonical ranks of neighbors. Mapped on each other "to" and "from" atoms have equal mapping ranks */ 1271| 25.7k| for (i = 0; i < num_neigh; i++) ------------------ | Branch (1271:17): [True: 20.4k, False: 5.30k] ------------------ 1272| 20.4k| { 1273| 20.4k| if (nNeighRankTo[j = nNeighNumberTo[i]] != nNeighRankFrom[k = nNeighNumberFrom[i]]) ------------------ | Branch (1273:13): [True: 0, False: 20.4k] ------------------ 1274| 0| { 1275| 0| return 0; /* program error: mapping ranks not equal, from_at neigborhood cannot be mapped on to_at neighbood. */ /* */ 1276| 0| } 1277| 20.4k| nNeighRankToCanon[j] = nNeighRankFromCanon[k]; /* potential problem: other atom(s) may have same mapping rank and */ 1278| | /* different canon. rank(s). */ 1279| | /* we may save some memory by eliminating nNeighRankFromCanon[]: */ 1280| | /* nNeighRankToCanon[j] = nCanonRankFrom[at[from_at].neighbor[k]] */ 1281| 20.4k| } 1282| | 1283| 5.30k| pCG->m_pn_RankForSort = nNeighRankToCanon; 1284| 5.30k| num_trans_to += insertions_sort( pCG, nNeighNumberTo, num_neigh, sizeof( nNeighNumberTo[0] ), CompNeighborsRanksCountEql ); 1285| |#ifndef CT_NEIGH_INCREASE 1286| | num_trans_to += ( ( num_neigh*( num_neigh - 1 ) ) / 2 ) % 2; /* get correct parity for ascending order of canon. numbers */ 1287| |#endif 1288| | 1289| 5.30k| return 2 - ( num_trans_to + at[to_at].parity ) % 2; 1290| 5.30k|} ClearPreviousMappings: 1300| 5.59k|{ 1301| 5.59k| int i; 1302| 16.4k| for (i = 0; pRankStack1[i]; i++) ------------------ | Branch (1302:17): [True: 10.8k, False: 5.59k] ------------------ 1303| 10.8k| { 1304| 10.8k| pRankStack1[i][0] = 0; 1305| 10.8k| } 1306| | 1307| 5.59k| return i; 1308| 5.59k|} map_an_atom2: 1328| 8.98k|{ 1329| 8.98k| AT_RANK *nRank1, *nAtomNumber1; /* ranks for mapping "1", "from" */ 1330| 8.98k| AT_RANK *nRank2, *nAtomNumber2; /* ranks for mapping "2", "to" */ 1331| 8.98k| AT_RANK *nNewRank1 = NULL, *nNewAtomNumber1 = NULL; /* ranks for mapping "1", "from" */ 1332| 8.98k| AT_RANK *nNewRank2 = NULL, *nNewAtomNumber2 = NULL; /* ranks for mapping "2", "to" */ 1333| 8.98k| int length = num_max * sizeof( AT_RANK ); 1334| 8.98k| int nNewNumRanks2, nNewNumRanks1; 1335| 8.98k| int i, bAtFromHasAlreadyBeenMapped, nNumTies; 1336| 8.98k| AT_RANK nNewRank; 1337| | 1338| 8.98k| nNumTies = NumberOfTies( pRankStack1, pRankStack2, length, at_no1, at_no2, &nNewRank, bAddStack, &bAtFromHasAlreadyBeenMapped ); 1339| | 1340| 8.98k| if (RETURNED_ERROR( nNumTies )) ------------------ | | 44| 8.98k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 8.98k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 8.98k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 8.98k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 8.98k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 8.98k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 8.98k, False: 0] | | | Branch (44:53): [True: 0, False: 8.98k] | | ------------------ ------------------ 1341| 0| { 1342| 0| return nNumTies; /* error */ 1343| 0| } 1344| | 1345| 8.98k| nRank1 = *pRankStack1++; 1346| 8.98k| nAtomNumber1 = *pRankStack1++; /* ranks for mapping "1", "from" */ 1347| | 1348| 8.98k| nRank2 = *pRankStack2++; 1349| 8.98k| nAtomNumber2 = *pRankStack2++; /* ranks for mapping "2", "to" */ 1350| | 1351| 8.98k| if (nNumTies > 1) ------------------ | Branch (1351:9): [True: 7.20k, False: 1.78k] ------------------ 1352| 7.20k| { 1353| | 1354| 7.20k| nNewRank1 = *pRankStack1++; 1355| 7.20k| nNewAtomNumber1 = *pRankStack1++; /* ranks for mapping "1", "from" */ 1356| | 1357| 7.20k| nNewRank2 = *pRankStack2++; 1358| 7.20k| nNewAtomNumber2 = *pRankStack2++; /* ranks for mapping "2", "to" */ 1359| | /* break a tie for "to" */ 1360| 7.20k| memcpy(nNewRank2, nRank2, length); 1361| 7.20k| memcpy(nNewAtomNumber2, nAtomNumber2, length); 1362| 7.20k| nNewRank2[at_no2] = nNewRank; 1363| 7.20k| nNewNumRanks2 = DifferentiateRanks2( pCG, num_atoms, NeighList, 1364| 7.20k| nNumMappedRanks, nNewRank2, nTempRank, 1365| 7.20k| nNewAtomNumber2, &pCS->lNumNeighListIter, 1 ); 1366| 7.20k| pCS->lNumBreakTies++; 1367| | 1368| | /* Check whether the old mapping can be reused */ 1369| 7.20k| if (2 == bAtFromHasAlreadyBeenMapped && nNewRank == nNewRank1[at_no1]) ------------------ | Branch (1369:13): [True: 1.05k, False: 6.14k] | Branch (1369:49): [True: 1.05k, False: 2] ------------------ 1370| 1.05k| { 1371| 7.64k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1371:25): [True: 6.59k, False: 1.05k] ------------------ 1372| 6.59k| { 1373| 6.59k| if (nNewRank1[nNewAtomNumber1[i]] != nNewRank2[nNewAtomNumber2[i]]) ------------------ | Branch (1373:21): [True: 0, False: 6.59k] ------------------ 1374| 0| { 1375| 0| bAtFromHasAlreadyBeenMapped = 0; /* It cannot. */ 1376| 0| break; 1377| 0| } 1378| 6.59k| } 1379| 1.05k| } 1380| 6.15k| else 1381| 6.15k| { 1382| 6.15k| bAtFromHasAlreadyBeenMapped = 0; 1383| 6.15k| } 1384| 7.20k| if (2 != bAtFromHasAlreadyBeenMapped) ------------------ | Branch (1384:13): [True: 6.15k, False: 1.05k] ------------------ 1385| 6.15k| { 1386| | /* break a tie for "from" */ 1387| 21.4k| for (i = 0; pRankStack1[i]; i++) ------------------ | Branch (1387:25): [True: 15.2k, False: 6.15k] ------------------ 1388| 15.2k| { 1389| 15.2k| pRankStack1[i][0] = 0; 1390| 15.2k| } 1391| 6.15k| memcpy(nNewRank1, nRank1, length); 1392| 6.15k| memcpy(nNewAtomNumber1, nAtomNumber1, length); /* GPF: bad nAtomNumber1 */ 1393| 6.15k| nNewRank1[at_no1] = nNewRank; 1394| 6.15k| nNewNumRanks1 = DifferentiateRanks2( pCG, num_atoms, NeighList, 1395| 6.15k| nNumMappedRanks, nNewRank1, nTempRank, 1396| 6.15k| nNewAtomNumber1, &pCS->lNumNeighListIter, 1 ); 1397| 6.15k| pCS->lNumBreakTies++; 1398| 6.15k| } 1399| 1.05k| else 1400| 1.05k| { 1401| 1.05k| nNewNumRanks1 = nNewNumRanks2; 1402| 1.05k| } 1403| | 1404| 7.20k| if (nNewNumRanks1 != nNewNumRanks2) ------------------ | Branch (1404:13): [True: 0, False: 7.20k] ------------------ 1405| 0| return CT_MAPCOUNT_ERR; /* program error */ /* */ ------------------ | | 26| 0|#define CT_MAPCOUNT_ERR (CT_ERR_FIRST- 7) /*(-30007) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1406| 7.20k| *pnNewNumMappedRanks = nNewNumRanks2; 1407| | /* debug only */ 1408| 46.2k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1408:21): [True: 39.0k, False: 7.20k] ------------------ 1409| 39.0k| { 1410| 39.0k| if (nNewRank1[nNewAtomNumber1[i]] != nNewRank2[nNewAtomNumber2[i]]) ------------------ | Branch (1410:17): [True: 0, False: 39.0k] ------------------ 1411| 0| { 1412| 0| return CT_MAPCOUNT_ERR; /* program error */ /* */ ------------------ | | 26| 0|#define CT_MAPCOUNT_ERR (CT_ERR_FIRST- 7) /*(-30007) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1413| 0| } 1414| 39.0k| } 1415| 7.20k| } 1416| 1.78k| else 1417| 1.78k| { 1418| 1.78k| *pnNewNumMappedRanks = nNumMappedRanks; 1419| 1.78k| } 1420| | 1421| 8.98k| return ( nNewRank1 ) ? nNewRank1[at_no1] : nRank1[at_no1]; /* mapping rank value */ ------------------ | Branch (1421:12): [True: 7.20k, False: 1.78k] ------------------ 1422| 8.98k|} DeAllocateForNonStereoRemoval: 1476| 4.02k|{ 1477| 4.02k| if (*nAtomNumberCanon1) ------------------ | Branch (1477:9): [True: 2.01k, False: 2.01k] ------------------ 1478| 2.01k| { 1479| 2.01k| inchi_free( *nAtomNumberCanon1 ); ------------------ | | 1152| 2.01k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 2.01k, False: 0] | | | Branch (1152:50): [Folded, False: 2.01k] | | ------------------ ------------------ 1480| 2.01k| *nAtomNumberCanon1 = NULL; 1481| 2.01k| } 1482| 4.02k| if (*nAtomNumberCanon2) ------------------ | Branch (1482:9): [True: 2.01k, False: 2.01k] ------------------ 1483| 2.01k| { 1484| 2.01k| inchi_free( *nAtomNumberCanon2 ); ------------------ | | 1152| 2.01k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 2.01k, False: 0] | | | Branch (1152:50): [Folded, False: 2.01k] | | ------------------ ------------------ 1485| 2.01k| *nAtomNumberCanon2 = NULL; 1486| 2.01k| } 1487| 4.02k| if (*nl) ------------------ | Branch (1487:9): [True: 2.01k, False: 2.01k] ------------------ 1488| 2.01k| { 1489| 2.01k| FreeNeighList( *nl ); 1490| 2.01k| *nl = 0; 1491| 2.01k| } 1492| 4.02k| if (*nl1) ------------------ | Branch (1492:9): [True: 2.01k, False: 2.01k] ------------------ 1493| 2.01k| { 1494| 2.01k| FreeNeighList( *nl1 ); 1495| 2.01k| *nl1 = 0; 1496| 2.01k| } 1497| 4.02k| if (*nl2) ------------------ | Branch (1497:9): [True: 2.01k, False: 2.01k] ------------------ 1498| 2.01k| { 1499| 2.01k| FreeNeighList( *nl2 ); 1500| 2.01k| *nl2 = 0; 1501| 2.01k| } 1502| 4.02k| if (*nVisited1) ------------------ | Branch (1502:9): [True: 2.01k, False: 2.01k] ------------------ 1503| 2.01k| { 1504| 2.01k| inchi_free( *nVisited1 ); ------------------ | | 1152| 2.01k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 2.01k, False: 0] | | | Branch (1152:50): [Folded, False: 2.01k] | | ------------------ ------------------ 1505| 2.01k| *nVisited1 = NULL; 1506| 2.01k| } 1507| 4.02k| if (*nVisited2) ------------------ | Branch (1507:9): [True: 2.01k, False: 2.01k] ------------------ 1508| 2.01k| { 1509| 2.01k| inchi_free( *nVisited2 ); ------------------ | | 1152| 2.01k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 2.01k, False: 0] | | | Branch (1152:50): [Folded, False: 2.01k] | | ------------------ ------------------ 1510| | *nVisited2 = NULL; 1511| 2.01k| } 1512| 4.02k|} AllocateForNonStereoRemoval: 1527| 2.01k|{ 1528| 2.01k| DeAllocateForNonStereoRemoval( nAtomNumberCanon1, nAtomNumberCanon2, nl, nl1, nl2, nVisited1, nVisited2 ); 1529| 2.01k| *nAtomNumberCanon1 = (AT_RANK *) inchi_malloc( num_atoms * sizeof( **nAtomNumberCanon1 ) ); ------------------ | | 1143| 2.01k|#define inchi_malloc malloc ------------------ 1530| 2.01k| *nAtomNumberCanon2 = (AT_RANK *) inchi_malloc( num_atoms * sizeof( **nAtomNumberCanon2 ) ); ------------------ | | 1143| 2.01k|#define inchi_malloc malloc ------------------ 1531| 2.01k| *nl = CreateNeighList( num_atoms, num_atoms, at, 0, NULL ); 1532| 2.01k| *nl1 = CreateNeighList( num_atoms, num_atoms, at, 0, NULL ); 1533| 2.01k| *nl2 = CreateNeighList( num_atoms, num_atoms, at, 0, NULL ); 1534| 2.01k| *nVisited1 = (AT_RANK *) inchi_malloc( num_atoms * sizeof( **nVisited1 ) ); ------------------ | | 1143| 2.01k|#define inchi_malloc malloc ------------------ 1535| 2.01k| *nVisited2 = (AT_RANK *) inchi_malloc( num_atoms * sizeof( **nVisited2 ) ); ------------------ | | 1143| 2.01k|#define inchi_malloc malloc ------------------ 1536| | 1537| 2.01k| if (!*nl || !*nl1 || !*nl2 || !*nVisited1 || !*nVisited2 || !*nAtomNumberCanon1 || !*nAtomNumberCanon2) ------------------ | Branch (1537:9): [True: 0, False: 2.01k] | Branch (1537:17): [True: 0, False: 2.01k] | Branch (1537:26): [True: 0, False: 2.01k] | Branch (1537:35): [True: 0, False: 2.01k] | Branch (1537:50): [True: 0, False: 2.01k] | Branch (1537:65): [True: 0, False: 2.01k] | Branch (1537:88): [True: 0, False: 2.01k] ------------------ 1538| 0| { 1539| 0| DeAllocateForNonStereoRemoval( nAtomNumberCanon1, nAtomNumberCanon2, nl, nl1, nl2, nVisited1, nVisited2 ); 1540| 0| return 0; 1541| 0| } 1542| | /* Sort neighbors according to symm. ranks (primary key) and canon. ranks (secondary key), in descending order */ 1543| 2.01k| SortNeighListsBySymmAndCanonRank( num_atoms, *nl, nSymmRank, nCanonRank ); 1544| 2.01k| SortNeighListsBySymmAndCanonRank( num_atoms, *nl1, nSymmRank, nCanonRank ); 1545| 2.01k| SortNeighListsBySymmAndCanonRank( num_atoms, *nl2, nSymmRank, nCanonRank ); 1546| | 1547| 2.01k| return 1; 1548| 2.01k|} GetMinNewRank: 1553| 9.61k|{ 1554| 9.61k| int i; 1555| 9.61k| AT_RANK nRank2 = 0; 1556| 42.2k| for (i = (int) nRank1 - 1; 0 <= i && nRank1 == ( nRank2 = nAtomRank[(int) nAtomNumb[i]] ); i--) ------------------ | Branch (1556:32): [True: 41.8k, False: 429] | Branch (1556:42): [True: 32.6k, False: 9.18k] ------------------ 1557| 32.6k| { 1558| 32.6k| ; 1559| 32.6k| } 1560| 9.61k| if (i >= 0) ------------------ | Branch (1560:9): [True: 9.18k, False: 429] ------------------ 1561| 9.18k| { 1562| 9.18k| nRank2++; 1563| 9.18k| } 1564| 429| else 1565| 429| { 1566| 429| nRank2 = 1; 1567| 429| } 1568| | 1569| 9.61k| return nRank2; 1570| 9.61k|} BreakNeighborsTie: 1593| 9.73k|{ 1594| 9.73k| AT_RANK nRank1, nRank2; 1595| 9.73k| int nNumDiffRanks, nNumDiffRanks1, nNumDiffRanks2, i; 1596| 9.73k| int n1 = (int) neigh_num[in1]; 1597| 9.73k| int n2 = (int) neigh_num[in2]; 1598| 9.73k| int other_neigh[2] = {0}, other_neig_ord[2] = {0}, num_other_neigh; /* djb-rwth: initialisations added */ 1599| | 1600| | /* asymmetric calculation */ 1601| | 1602| 9.73k| if ((mode == MAP_MODE_S4 && in1) || /* for S4 we need only (in1,in2) = (0,1) (0,2) (0,3) pairs of neighbors */ ------------------ | | 17| 19.4k|#define MAP_MODE_S4 3 /* Check for S4 rotation/reflection leading to parity inversion */ ------------------ | Branch (1602:10): [True: 0, False: 9.73k] | Branch (1602:34): [True: 0, False: 0] ------------------ 1603| 9.73k| (mode != MAP_MODE_STD && at[ia].valence != MAX_NUM_STEREO_ATOM_NEIGH) || ------------------ | | 14| 19.4k|#define MAP_MODE_STD 0 /* Standard approach: switch 2 neighbors */ ------------------ (mode != MAP_MODE_STD && at[ia].valence != MAX_NUM_STEREO_ATOM_NEIGH) || ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1603:11): [True: 0, False: 9.73k] | Branch (1603:35): [True: 0, False: 0] ------------------ 1604| 9.73k| (mode != MAP_MODE_STD && nSymmRank[n1] != nSymmRank[n2])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 14| 19.4k|#define MAP_MODE_STD 0 /* Standard approach: switch 2 neighbors */ ------------------ | Branch (1604:11): [True: 0, False: 9.73k] | Branch (1604:35): [True: 0, False: 0] ------------------ 1605| 0| { 1606| 0| return 0; 1607| 0| } 1608| | 1609| | /* 1. Create initial ranks from equivalence information stored in nSymmRank */ 1610| 9.73k| memcpy(pRankStack1[0], nSymmRank, num_at_tg * sizeof(pRankStack1[0][0])); 1611| 9.73k| pCG->m_pn_RankForSort = pRankStack1[0]; 1612| 9.73k| tsort( pCG, pRankStack1[1], num_at_tg, sizeof( pRankStack1[1][0] ), CompRanksOrd ); ------------------ | | 18| 9.73k|#define tsort insertions_sort ------------------ 1613| 9.73k| nNumDiffRanks = SortedEquInfoToRanks( pRankStack1[0]/*inp*/, pRankStack1[0]/*out*/, pRankStack1[1], num_at_tg, NULL ); 1614| | 1615| | /* other neighbors */ 1616| 9.73k| num_other_neigh = 0; 1617| 9.73k| if (at[ia].valence <= MAX_NUM_STEREO_ATOM_NEIGH && mode) ------------------ | | 877| 19.4k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1617:9): [True: 9.73k, False: 0] | Branch (1617:56): [True: 0, False: 9.73k] ------------------ 1618| 0| { 1619| 0| for (i = 0; i < at[ia].valence; i++) ------------------ | Branch (1619:21): [True: 0, False: 0] ------------------ 1620| 0| { 1621| 0| if (i != in1 && i != in2) ------------------ | Branch (1621:17): [True: 0, False: 0] | Branch (1621:29): [True: 0, False: 0] ------------------ 1622| 0| { 1623| 0| other_neigh[num_other_neigh] = (int) neigh_num[i]; 1624| 0| other_neig_ord[num_other_neigh] = i; 1625| 0| num_other_neigh++; 1626| 0| } 1627| 0| } 1628| 0| } 1629| 9.73k| if ((mode != MAP_MODE_STD && nSymmRank[other_neigh[0]] != nSymmRank[other_neigh[1]]) || ------------------ | | 14| 19.4k|#define MAP_MODE_STD 0 /* Standard approach: switch 2 neighbors */ ------------------ | Branch (1629:10): [True: 0, False: 9.73k] | Branch (1629:34): [True: 0, False: 0] ------------------ 1630| 9.73k| (mode == MAP_MODE_S4 && nSymmRank[n1] != nSymmRank[other_neigh[1]])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 17| 19.4k|#define MAP_MODE_S4 3 /* Check for S4 rotation/reflection leading to parity inversion */ ------------------ | Branch (1630:11): [True: 0, False: 9.73k] | Branch (1630:34): [True: 0, False: 0] ------------------ 1631| 0| { 1632| 0| return 0; 1633| 0| } 1634| | 1635| | /* 2. Fix at[ia] */ 1636| 9.73k| if (pRankStack1[0][ia] != nSymmRank[ia]) ------------------ | Branch (1636:9): [True: 8.48k, False: 1.25k] ------------------ 1637| 8.48k| { 1638| | /* at[ia] is constitutionally equivalent to some other atom. Fix at[ia]. */ 1639| 8.48k| pRankStack1[0][ia] = nSymmRank[ia]; 1640| 8.48k| nNumDiffRanks = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1641| 8.48k| nNumDiffRanks, pRankStack1[0], nTempRank, 1642| 8.48k| pRankStack1[1], lNumIter, 1 ); 1643| 8.48k| } 1644| | /* 3. In case of a double bond/cumulene only: */ 1645| | /* fix at[ib] -- the opposite double bond/cumulene atom */ 1646| 9.73k| if (ib < num_atoms) ------------------ | Branch (1646:9): [True: 14, False: 9.71k] ------------------ 1647| 14| { 1648| | /* find the smallest possible rank */ 1649| 14| nRank1 = pRankStack1[0][ib]; 1650| 14| nRank2 = GetMinNewRank( pRankStack1[0], pRankStack1[1], nRank1 ); 1651| | /* if the rank is smaller than pRankStack1[0][ib] then fix at[ib] */ 1652| 14| if (nRank2 != nRank1) ------------------ | Branch (1652:13): [True: 0, False: 14] ------------------ 1653| 0| { 1654| 0| pRankStack1[0][ib] = nRank2; 1655| 0| nNumDiffRanks = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1656| 0| nNumDiffRanks, pRankStack1[0], nTempRank, 1657| 0| pRankStack1[1], lNumIter, 1 ); 1658| 0| } 1659| 14| } 1660| | 1661| | /************************************************************************************** 1662| | * Note: It may (or may not?) make sense to fix "other neighbors": 1663| | * in case of a stereo center fix neighbors other than n1, n2 1664| | * in case of a double bond/cumulene fix the opposite atom neighbors 1665| | * The ranks assigned to the other neighbors in case of their equivalence 1666| | * should be in the ascending order of their canonical ranks ???? 1667| | * *** For now we do not fix other neighbors *** 1668| | **************************************************************************************/ 1669| | 1670| | /* 4. Check whether the neighbors still have equal ranks */ 1671| 9.73k| if (pRankStack1[0][n1] != pRankStack1[0][n2]) ------------------ | Branch (1671:9): [True: 127, False: 9.60k] ------------------ 1672| 127| { 1673| 127| return 0; /* the two neighbors are not constitutionally equivalent */ 1674| 127| } 1675| | /* 5. Find new smallest possible rank for n1 and n2 */ 1676| 9.60k| nRank1 = pRankStack1[0][n1]; 1677| 9.60k| nRank2 = GetMinNewRank( pRankStack1[0], pRankStack1[1], nRank1 ); 1678| | 1679| | /* 6. Copy the results to the 2nd eq. rank arrays */ 1680| 9.60k| memcpy(pRankStack2[0], pRankStack1[0], num_at_tg * sizeof(pRankStack2[0][0])); 1681| 9.60k| memcpy(pRankStack2[1], pRankStack1[1], num_at_tg * sizeof(pRankStack2[0][0])); 1682| | /* 7. Break neighbor tie: map n1(1) <--> n2(2) */ 1683| | /* 7. Break neighbor tie: map n1(1) <--> n2(2) */ 1684| 9.60k| pRankStack1[0][n1] = nRank2; 1685| 9.60k| nNumDiffRanks1 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1686| 9.60k| nNumDiffRanks, pRankStack1[0], nTempRank, 1687| 9.60k| pRankStack1[1], lNumIter, 1 ); 1688| | 1689| 9.60k| pRankStack2[0][n2] = nRank2; 1690| 9.60k| nNumDiffRanks2 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1691| 9.60k| nNumDiffRanks, pRankStack2[0], nTempRank, 1692| 9.60k| pRankStack2[1], lNumIter, 1 ); 1693| | 1694| 9.60k| if (nNumDiffRanks1 != nNumDiffRanks2) ------------------ | Branch (1694:9): [True: 0, False: 9.60k] ------------------ 1695| 0| { 1696| 0| return -1; /* */ 1697| 0| } 1698| | 1699| 9.60k| if (mode == MAP_MODE_C2v || mode == MAP_MODE_C2) ------------------ | | 15| 19.2k|#define MAP_MODE_C2v 1 /* Check for C2v reflection leading to parity inversion */ ------------------ if (mode == MAP_MODE_C2v || mode == MAP_MODE_C2) ------------------ | | 16| 9.60k|#define MAP_MODE_C2 2 /* Check for C2 rotation preserving parities */ ------------------ | Branch (1699:9): [True: 0, False: 9.60k] | Branch (1699:33): [True: 0, False: 9.60k] ------------------ 1700| 0| { 1701| | /* Check for C2v reflection leading to parity inversion (mode=1) or C2 rotation (mode=2) */ 1702| 0| AT_RANK nRank10, nRank20; 1703| 0| int nn1, nn2; 1704| | /* 1705| | * C2v & C2: map 1706| | * n1(1) <--> n2(2) -- at this point already done 1707| | * n1(2) <--> n2(1) --> do at i = 0 1708| | * 1709| | * C2v: other neighbors must be unmoved: map 1710| | * other_neigh[0](1) <--> other_neigh[0](2) 1711| | * other_neigh[1](1) <--> other_neigh[1](2) 1712| | * 1713| | * C2: other neighbors should be mapped on each other 1714| | * other_neigh[0](1) <--> other_neigh[1](2) 1715| | * other_neigh[1](1) <--> other_neigh[0](2) 1716| | */ 1717| 0| for (i = 0; i <= 2; i++) ------------------ | Branch (1717:21): [True: 0, False: 0] ------------------ 1718| 0| { 1719| 0| if (i == 0) ------------------ | Branch (1719:17): [True: 0, False: 0] ------------------ 1720| 0| { 1721| | /* C2v & C2. Map n2(1) <--> n1(2) */ 1722| 0| nn1 = n2; 1723| 0| nn2 = n1; 1724| 0| } 1725| 0| else 1726| 0| { 1727| 0| if (mode == MAP_MODE_C2v) ------------------ | | 15| 0|#define MAP_MODE_C2v 1 /* Check for C2v reflection leading to parity inversion */ ------------------ | Branch (1727:21): [True: 0, False: 0] ------------------ 1728| 0| { /* was '=', pointed by WDI */ 1729| | /* i = 1 or 2 1730| | * C2v. Other neighbors must be unmoved: map 1731| | * i=1: other_neigh[0](1) <--> other_neigh[0](2) 1732| | * i=2: other_neigh[1](1) <--> other_neigh[1](2) 1733| | */ 1734| 0| nn1 = other_neigh[i - 1]; /* 0 or 1 */ 1735| 0| nn2 = other_neigh[i - 1]; /* 0 or 1 */ 1736| 0| } 1737| 0| else 1738| 0| { 1739| 0| if (mode == MAP_MODE_C2) ------------------ | | 16| 0|#define MAP_MODE_C2 2 /* Check for C2 rotation preserving parities */ ------------------ | Branch (1739:25): [True: 0, False: 0] ------------------ 1740| 0| { 1741| | /* was '=', pointed by WDI */ 1742| | /* i = 1 or 2 1743| | * C2. Other neighbors should be mapped on each other 1744| | * i=1: other_neigh[0](1) <--> other_neigh[1](2) 1745| | * i=2: other_neigh[1](1) <--> other_neigh[0](2) 1746| | */ 1747| 0| nn1 = other_neigh[i - 1]; /* 0 or 1 */ 1748| 0| nn2 = other_neigh[2 - i]; /* 1 or 0 */ 1749| 0| } 1750| 0| else 1751| 0| { 1752| 0| return -1; /* program error */ 1753| 0| } 1754| 0| } 1755| 0| } 1756| | 1757| | /* map nn1(1) <--> nn2(2) */ 1758| 0| nRank10 = pRankStack1[0][nn1]; 1759| 0| nRank20 = pRankStack2[0][nn2]; 1760| 0| nRank1 = GetMinNewRank( pRankStack1[0], pRankStack1[1], nRank10 ); 1761| 0| nRank2 = GetMinNewRank( pRankStack2[0], pRankStack2[1], nRank20 ); 1762| 0| if (nRank10 == nRank20 && nRank1 == nRank2) ------------------ | Branch (1762:17): [True: 0, False: 0] | Branch (1762:39): [True: 0, False: 0] ------------------ 1763| 0| { 1764| 0| if (nRank10 == nRank1) ------------------ | Branch (1764:21): [True: 0, False: 0] ------------------ 1765| 0| { 1766| 0| ; /* atoms are already mapped */ 1767| 0| } 1768| 0| else 1769| 0| { 1770| | /* need additional mapping: ranks are not fixed yet */ 1771| 0| pRankStack1[0][nn1] = nRank1; 1772| 0| nNumDiffRanks1 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1773| 0| nNumDiffRanks, pRankStack1[0], nTempRank, 1774| 0| pRankStack1[1], lNumIter, 1 ); 1775| 0| pRankStack2[0][nn2] = nRank2; 1776| 0| nNumDiffRanks2 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1777| 0| nNumDiffRanks, pRankStack2[0], nTempRank, 1778| 0| pRankStack2[1], lNumIter, 1 ); 1779| 0| if (nNumDiffRanks1 != nNumDiffRanks2) ------------------ | Branch (1779:25): [True: 0, False: 0] ------------------ 1780| 0| { 1781| 0| return -1; /* */ 1782| 0| } 1783| 0| } 1784| 0| } 1785| 0| else 1786| 0| { 1787| 0| return 0; /* mapping is not possible */ 1788| 0| } 1789| 0| } 1790| 0| } 1791| | 1792| 9.60k| if (mode == MAP_MODE_S4) ------------------ | | 17| 9.60k|#define MAP_MODE_S4 3 /* Check for S4 rotation/reflection leading to parity inversion */ ------------------ | Branch (1792:9): [True: 0, False: 9.60k] ------------------ 1793| 0| { 1794| | /* 1795| | * Check for S4 reflection/rotation leading to parity inversion (mode=3) 1796| | * 1797| | * At this point n1(1) <--> n2(2) have been mapped and n1 has index in1 = 0 1798| | * Below indexes in neigh_num[] are in brackets; [i] means neigh_num[i]. 1799| | * Numbers (#) in parentheses refer to pRankStack# 1800| | * 1801| | * in2=1: [0](1) <--> [1](2) mapping has been done; add more mappings: 1802| | * [1](1) <--> [2](2) [x]=[2] 1803| | * [2](1) <--> [3](2) [y]=[3] 1804| | * [3](1) <--> [0](2) 1805| | * this will succeed if C2 axis crosses middle of [0]-[2] and [1]-[3] lines 1806| | * 1807| | * in2=2: [0](1) <--> [2](2) mapping has been done; add more mappings: 1808| | * [2](1) <--> [3](2) [x]=[3] 1809| | * [3](1) <--> [1](2) [y]=[1] 1810| | * [1](1) <--> [0](2) 1811| | * this will succeed if C2 axis crosses middle of [0]-[3] and [1]-[2] lines 1812| | * 1813| | * in2=3: [0](1) <--> [3](2) mapping has been done; add more mappings: 1814| | * [3](1) <--> [1](2) [x]=[1] 1815| | * [1](1) <--> [2](2) [y]=[2] 1816| | * [2](1) <--> [0](2) 1817| | * this will succeed if C2 axis crosses middle of [0]-[1] and [2]-[3] lines 1818| | * 1819| | * In general: 1820| | * [in1](1) <--> [in2](2) 1821| | * [in2](1) <--> [x] (2) i=0 1822| | * [x] (1) <--> [y] (2) i=1 1823| | * [y] (1) <--> [in1](2) i=2 1824| | * 1825| | * in1=0 always 1826| | * ===== how to find x, y from in2 ==== 1827| | * in2=1 => x,y = 2, 3 or [x] = other_neigh[0], [y] = other_neigh[1] 1828| | * in2=2 => x,y = 3, 1 or [x] = other_neigh[1], [y] = other_neigh[0] 1829| | * in2=3 => x,y = 1, 2 or [x] = other_neigh[0], [y] = other_neigh[1] 1830| | * ==================================== 1831| | */ 1832| 0| AT_RANK nRank10, nRank20; 1833| 0| int nn1, nn2; 1834| 0| for (i = 0; i <= 2; i++) ------------------ | Branch (1834:21): [True: 0, False: 0] ------------------ 1835| 0| { 1836| 0| switch (i) 1837| 0| { 1838| 0| case 0: /* [in2](1) <--> [x](2); */ ------------------ | Branch (1838:17): [True: 0, False: 0] ------------------ 1839| 0| nn1 = n2; /* [in2] */ 1840| 0| nn2 = other_neigh[1 - in2 % 2]; /* [x] */ 1841| 0| break; 1842| 0| case 1: /* [x](1) <--> [y](2) */ ------------------ | Branch (1842:17): [True: 0, False: 0] ------------------ 1843| 0| nn1 = other_neigh[1 - in2 % 2]; /* [x] */ 1844| 0| nn2 = other_neigh[in2 % 2]; /* [y] */ 1845| 0| break; 1846| 0| case 2: ------------------ | Branch (1846:17): [True: 0, False: 0] ------------------ 1847| 0| nn1 = other_neigh[in2 % 2]; /* [y] */ 1848| 0| nn2 = n1; /* [in1] */ 1849| 0| break; 1850| 0| default: ------------------ | Branch (1850:17): [True: 0, False: 0] ------------------ 1851| 0| return -1; /* program error */ 1852| 0| } 1853| | /* map nn1(1) <--> nn2(2) */ 1854| 0| nRank10 = pRankStack1[0][nn1]; 1855| 0| nRank20 = pRankStack2[0][nn2]; 1856| 0| nRank1 = GetMinNewRank( pRankStack1[0], pRankStack1[1], nRank10 ); 1857| 0| nRank2 = GetMinNewRank( pRankStack2[0], pRankStack2[1], nRank20 ); 1858| 0| if (nRank10 == nRank20 && nRank1 == nRank2) ------------------ | Branch (1858:17): [True: 0, False: 0] | Branch (1858:39): [True: 0, False: 0] ------------------ 1859| 0| { 1860| 0| if (nRank10 == nRank1) ------------------ | Branch (1860:21): [True: 0, False: 0] ------------------ 1861| 0| { 1862| 0| ;/* atoms are already mapped */ 1863| 0| } 1864| 0| else 1865| 0| { 1866| | /* need additional mapping: ranks are not fixed yet */ 1867| 0| pRankStack1[0][nn1] = nRank1; 1868| 0| nNumDiffRanks1 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1869| 0| nNumDiffRanks, pRankStack1[0], nTempRank, 1870| 0| pRankStack1[1], lNumIter, 1 ); 1871| 0| pRankStack2[0][nn2] = nRank2; 1872| 0| nNumDiffRanks2 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1873| 0| nNumDiffRanks, pRankStack2[0], nTempRank, 1874| 0| pRankStack2[1], lNumIter, 1 ); 1875| | 1876| 0| if (nNumDiffRanks1 != nNumDiffRanks2) ------------------ | Branch (1876:25): [True: 0, False: 0] ------------------ 1877| 0| { 1878| 0| return -1; /* */ 1879| 0| } 1880| 0| } 1881| 0| } 1882| 0| else 1883| 0| { 1884| 0| return 0; /* mapping is not possible */ 1885| 0| } 1886| 0| } 1887| 0| } 1888| | 1889| 9.60k|#if ( BREAK_ONE_MORE_SC_TIE == 1 ) /* { */ 1890| | /* Check for a very highly symmetrical stereo center 12-06-2002 */ 1891| 9.60k| if (ib >= num_atoms && at[ia].valence == MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 9.59k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1891:9): [True: 9.59k, False: 14] | Branch (1891:28): [True: 8.63k, False: 955] ------------------ 1892| 8.63k| { 1893| 8.63k| int num_eq; 1894| 8.63k| nRank1 = pRankStack1[0][n2]; 1895| 43.1k| for (i = 0, num_eq = 0; i < at[ia].valence; i++) ------------------ | Branch (1895:33): [True: 34.5k, False: 8.63k] ------------------ 1896| 34.5k| { 1897| 34.5k| num_eq += ( nRank1 == pRankStack1[0][at[ia].neighbor[i]] ); 1898| 34.5k| } 1899| 8.63k| if (num_eq == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 877| 8.63k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1899:13): [True: 5.76k, False: 2.87k] ------------------ 1900| 5.76k| { 1901| 23.0k| for (i = (int) nRank1 - 1; 0 <= i && nRank1 == ( nRank2 = pRankStack1[0][(int) pRankStack1[1][i]] ); i--) ------------------ | Branch (1901:40): [True: 23.0k, False: 0] | Branch (1901:50): [True: 17.2k, False: 5.76k] ------------------ 1902| 17.2k| { 1903| 17.2k| ; 1904| 17.2k| } 1905| 5.76k| if (i >= 0) ------------------ | Branch (1905:17): [True: 5.76k, False: 0] ------------------ 1906| 5.76k| { 1907| 5.76k| nRank2++; 1908| 5.76k| } 1909| 0| else 1910| 0| { 1911| 0| nRank2 = 1; 1912| 0| } 1913| | 1914| | /* 7a. Break another neighbor tie */ 1915| 5.76k| nNumDiffRanks = nNumDiffRanks1; 1916| | 1917| 5.76k| pRankStack1[0][n2] = nRank2; 1918| 5.76k| nNumDiffRanks1 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1919| 5.76k| nNumDiffRanks, pRankStack1[0], nTempRank, 1920| 5.76k| pRankStack1[1], lNumIter, 1 ); 1921| | 1922| 5.76k| pRankStack2[0][n1] = nRank2; 1923| 5.76k| nNumDiffRanks2 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1924| 5.76k| nNumDiffRanks, pRankStack2[0], nTempRank, 1925| 5.76k| pRankStack2[1], lNumIter, 1 ); 1926| 5.76k| } 1927| 8.63k| } 1928| | 1929| 9.60k| if (nNumDiffRanks1 != nNumDiffRanks2) ------------------ | Branch (1929:9): [True: 0, False: 9.60k] ------------------ 1930| 0| { 1931| 0| return -1; /* */ 1932| 0| } 1933| 9.60k|#endif /* } BREAK_ONE_MORE_SC_TIE */ 1934| | 1935| |#if ( BREAK_ALSO_NEIGH_TIE == 1 ) 1936| | /* check whether neighbor's neighbors are tied and untie them */ 1937| | if (at[n1].nRingSystem == at[n2].nRingSystem && ib >= num_atoms) 1938| | { 1939| | AT_RANK NeighNeighList[MAX_NUM_STEREO_ATOM_NEIGH + 1]; 1940| | int m, neigh1 = -1, neigh2 = -1; 1941| | nRank1 = nRank2 = 0; 1942| | /* n1 */ 1943| | NeighNeighList[0] = at[n1].valence - 1; /* for insertions_sort_NeighListBySymmAndCanonRank() */ 1944| | for (i = 0, m = 1; i < at[n1].valence; i++) 1945| | { 1946| | int neigh = at[n1].neighbor[i]; 1947| | if (neigh != ia) 1948| | { 1949| | NeighNeighList[m++] = neigh; 1950| | } 1951| | } 1952| | insertions_sort_NeighListBySymmAndCanonRank( NeighNeighList, pRankStack1[0], nCanonRank ); 1953| | for (m = 2; m < at[n1].valence; m++) 1954| | { 1955| | if (pRankStack1[0][NeighNeighList[m]] == pRankStack1[0][NeighNeighList[m - 1]]) 1956| | { 1957| | neigh1 = NeighNeighList[m - 1]; 1958| | break; 1959| | } 1960| | } 1961| | /* n2 */ 1962| | NeighNeighList[0] = at[n2].valence - 1; /* for insertions_sort_NeighListBySymmAndCanonRank() */ 1963| | for (i = 0, m = 1; i < at[n2].valence; i++) 1964| | { 1965| | int neigh = at[n2].neighbor[i]; 1966| | if (neigh != ia) 1967| | { 1968| | NeighNeighList[m++] = neigh; 1969| | } 1970| | } 1971| | insertions_sort_NeighListBySymmAndCanonRank( NeighNeighList, pRankStack2[0], nCanonRank ); 1972| | for (m = 2; m < at[n2].valence; m++) 1973| | { 1974| | if (pRankStack2[0][NeighNeighList[m]] == pRankStack2[0][NeighNeighList[m - 1]]) 1975| | { 1976| |#if ( BREAK_ALSO_NEIGH_TIE_ROTATE == 1 ) 1977| | neigh2 = NeighNeighList[m]; /* [m] to obtain same axis orientation around ia= 0 && neigh2 >= 0 && pRankStack1[0][neigh1] == pRankStack2[0][neigh2]) 1985| | { 1986| | /* neighbors' neighbors are tied */ 1987| | nRank1 = pRankStack1[0][neigh1]; 1988| | nRank2 = GetMinNewRank( pRankStack1[0], pRankStack1[1], nRank1 ); 1989| | 1990| | /* Break neighbor's neighbor tie */ 1991| | 1992| | nNumDiffRanks = nNumDiffRanks1; 1993| | 1994| | pRankStack1[0][neigh1] = nRank2; 1995| | nNumDiffRanks1 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 1996| | nNumDiffRanks, pRankStack1[0], nTempRank, 1997| | pRankStack1[1], lNumIter, 1 ); 1998| | 1999| | pRankStack2[0][neigh2] = nRank2; 2000| | nNumDiffRanks2 = DifferentiateRanksBasic( pCG, num_at_tg, NeighList, 2001| | nNumDiffRanks, pRankStack2[0], nTempRank, 2002| | pRankStack2[1], lNumIter, 1 ); 2003| | } 2004| | } 2005| |#endif 2006| | 2007| | /* for debug only */ 2008| 58.8k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (2008:17): [True: 49.2k, False: 9.60k] ------------------ 2009| 49.2k| { 2010| 49.2k| if (pRankStack1[0][(int) pRankStack1[1][i]] != pRankStack2[0][(int) pRankStack2[1][i]]) ------------------ | Branch (2010:13): [True: 0, False: 49.2k] ------------------ 2011| 0| { 2012| 0| return -1; /* */ 2013| 0| } 2014| 49.2k| } 2015| | 2016| | /* Resort lists of neighbors */ 2017| 9.60k| SortNeighListsBySymmAndCanonRank( num_atoms, nl1, pRankStack1[0], nCanonRank ); 2018| 9.60k| SortNeighListsBySymmAndCanonRank( num_atoms, nl2, pRankStack2[0], nCanonRank ); 2019| | 2020| 9.60k| return nNumDiffRanks1 + 1; 2021| 9.60k|} CheckNextSymmNeighborsAndBonds: 2037| 75.5k|{ 2038| 75.5k| AT_RANK s1 = 0, s2 = 0; 2039| 75.5k| int i1, i2, k1, k2; 2040| 75.5k| if (nRank1[n1] != nRank2[n2]) ------------------ | Branch (2040:9): [True: 0, False: 75.5k] ------------------ 2041| 0| { 2042| 0| return -1; /* parallel traversal in stereo removal failed */ /* */ 2043| 0| } 2044| 75.5k| switch (!nVisited1[n1] + !nVisited2[n2]) ------------------ | Branch (2044:13): [True: 55.0k, False: 20.5k] ------------------ 2045| 75.5k| { 2046| 55.0k| case 0: ------------------ | Branch (2046:9): [True: 55.0k, False: 20.5k] ------------------ 2047| 55.0k| if (nVisited1[n1] != n2 + 1 || nVisited2[n2] != n1 + 1) ------------------ | Branch (2047:17): [True: 0, False: 55.0k] | Branch (2047:44): [True: 0, False: 55.0k] ------------------ 2048| 0| { 2049| 0| return -1; /* 0; */ /* possibly error???: we have come to an alreardy traversed pair and */ 2050| | /* found that the pair previously has not been traversed synchroneously. */ 2051| 0| } /* -- Happens in C60. */ 2052| 55.0k| break; 2053| 55.0k| case 1: ------------------ | Branch (2053:9): [True: 0, False: 75.5k] ------------------ 2054| 0| return -1; /* 0; */ /* possibly error: one is zero, another is not a zero. Happens in C60 */ 2055| | 2056| | /* case 2: */ 2057| | /* both are zero, OK. */ 2058| 75.5k| } 2059| | 2060| 75.5k| if (nVisitOrd1[n1] != nVisitOrd2[n2]) ------------------ | Branch (2060:9): [True: 0, False: 75.5k] ------------------ 2061| 0| { 2062| 0| return -1; /* 0; */ /* different DFS trees */ 2063| 0| } 2064| | /* at[n1] and at[n2] are next to at[cur1] and at[cur2] respectively */ 2065| | /* Even though the bond might have already been checked, check whether */ 2066| | /* it is a stereo bond/cumulene. If it is, check the bond/cumulene parity. */ 2067| | 2068| | /* Even though the bond or cumulene might have already been checked, check it: this is */ 2069| | /* the only place we can check stereo bonds and cumulenes that are not edges of the DFS tree */ 2070| | /* The code works both for a stereo bond and a stereogenic cumulene. */ 2071| | 2072| 75.5k| for (i1 = 0, k1 = 0; i1 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 151k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2072:26): [True: 75.5k, False: 0] ------------------ 2073| 75.5k| ( s1 = at[cur1].stereo_bond_neighbor[i1] ) && ------------------ | Branch (2073:9): [True: 64, False: 75.5k] ------------------ 2074| 64| !( k1 = ( at[cur1].neighbor[(int) at[cur1].stereo_bond_ord[i1]] == n1 ) ); i1++) ------------------ | Branch (2074:26): [True: 22, False: 42] ------------------ 2075| 22| { 2076| 22| ; 2077| 22| } 2078| 75.5k| for (i2 = 0, k2 = 0; i2 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 151k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2078:26): [True: 75.5k, False: 0] ------------------ 2079| 75.5k| ( s2 = at[cur2].stereo_bond_neighbor[i2] ) && ------------------ | Branch (2079:9): [True: 63, False: 75.5k] ------------------ 2080| 63| !( k2 = ( at[cur2].neighbor[(int) at[cur2].stereo_bond_ord[i2]] == n2 ) ); i2++) ------------------ | Branch (2080:26): [True: 21, False: 42] ------------------ 2081| 21| { 2082| 21| ; 2083| 21| } 2084| | 2085| | /* -- this does not work in case of cumulenes -- 2086| | for ( i1 = 0, k1 = 0; i1 < MAX_NUM_STEREO_BONDS && (s1=at[cur1].stereo_bond_neighbor[i1]) && !(k1=(s1-1 == n1)); i1 ++ ) 2087| | ; 2088| | for ( i2 = 0, k2 = 0; i2 < MAX_NUM_STEREO_BONDS && (s2=at[cur2].stereo_bond_neighbor[i2]) && !(k2=(s2-1 == n2)); i2 ++ ) 2089| | ; 2090| | */ 2091| | 2092| 75.5k| if (k1 != k2) ------------------ | Branch (2092:9): [True: 0, False: 75.5k] ------------------ 2093| 0| { 2094| 0| return 0; /* not an error: a stereo bond and not a stereo bond */ 2095| 0| } 2096| 75.5k| if (k1) ------------------ | Branch (2096:9): [True: 42, False: 75.5k] ------------------ 2097| 42| { 2098| | /* here k1 == k2 */ 2099| 42| int bCheckBond1, bCheckBond2; 2100| 42| s1--; 2101| 42| s2--; 2102| | 2103| 42| bCheckBond1 = ( cur1 != nAvoidCheckAtom[0] || s1 != nAvoidCheckAtom[1] ) && ------------------ | Branch (2103:25): [True: 42, False: 0] | Branch (2103:55): [True: 0, False: 0] ------------------ 2104| 42| ( cur1 != nAvoidCheckAtom[1] || s1 != nAvoidCheckAtom[0] ); ------------------ | Branch (2104:15): [True: 42, False: 0] | Branch (2104:45): [True: 0, False: 0] ------------------ 2105| 42| bCheckBond2 = ( cur2 != nAvoidCheckAtom[0] || s2 != nAvoidCheckAtom[1] ) && ------------------ | Branch (2105:25): [True: 42, False: 0] | Branch (2105:55): [True: 0, False: 0] ------------------ 2106| 42| ( cur2 != nAvoidCheckAtom[1] || s2 != nAvoidCheckAtom[0] ); ------------------ | Branch (2106:15): [True: 42, False: 0] | Branch (2106:45): [True: 0, False: 0] ------------------ 2107| | 2108| 42| if (bCheckBond1 != bCheckBond2) ------------------ | Branch (2108:13): [True: 0, False: 42] ------------------ 2109| 0| return 0; 2110| | 2111| 42| if (!bCheckBond1 && !bCheckBond2) ------------------ | Branch (2111:13): [True: 0, False: 42] | Branch (2111:29): [True: 0, False: 0] ------------------ 2112| 0| { 2113| 0| return 1; /* do not go any further in this direction */ 2114| 0| } 2115| | 2116| 42| if (at[cur1].stereo_bond_parity[i1] != at[cur2].stereo_bond_parity[i2]) ------------------ | Branch (2116:13): [True: 5, False: 37] ------------------ 2117| 5| { 2118| | /* different values of at[].stereo_bond_parity: definitely different bonds */ 2119| | /* known parities */ 2120| 5| if (PARITY_KNOWN( at[cur1].stereo_bond_parity[i1] ) && ------------------ | | 265| 10|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 5|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 10|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 5|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 5|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 5|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 5|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 5, False: 0] | | | Branch (265:78): [True: 5, False: 0] | | ------------------ ------------------ 2121| 5| PARITY_KNOWN( at[cur2].stereo_bond_parity[i2] )) ------------------ | | 265| 5|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 5|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 10|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 5|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 5|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 5|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 5|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 5, False: 0] | | | Branch (265:78): [True: 5, False: 0] | | ------------------ ------------------ 2122| 5| { 2123| 5| return 0; /* different currently known stereo bond parities */ 2124| 5| } 2125| |#if ( PROPAGATE_ILL_DEF_STEREO != 1 ) 2126| | /* well defined and to be calculated from the ranks */ 2127| | if (!( PARITY_CALCULATE( at[cur1].stereo_bond_parity[i1] ) && PARITY_WELL_DEF( at[cur2].stereo_bond_parity[i2] ) || 2128| | PARITY_WELL_DEF( at[cur1].stereo_bond_parity[i1] ) && PARITY_CALCULATE( at[cur2].stereo_bond_parity[i2] ) || 2129| | PARITY_CALCULATE( at[cur1].stereo_bond_parity[i1] ) && PARITY_CALCULATE( at[cur2].stereo_bond_parity[i2] ) )) 2130| | { 2131| |/* do not reject if: "well defined" and "calculate" or "calculate" and "calculate" */ 2132| | return 0; 2133| | } 2134| |#endif 2135| 5| } 2136| | 2137| |#if ( PROPAGATE_ILL_DEF_STEREO != 1 ) 2138| | if (( cur1 != cur2 || s1 != s2 ) && ( cur1 != s2 || cur2 != s1 )) 2139| | { 2140| |/* two different stereo bonds */ 2141| | if (PARITY_ILL_DEF( at[cur1].stereo_bond_parity[i1] ) || 2142| | PARITY_ILL_DEF( at[cur2].stereo_bond_parity[i2] )) 2143| | { 2144| | return 0; 2145| | } 2146| | } 2147| |#endif 2148| 42| } 2149| | 2150| 75.5k| return 1; /* stereo bonds to n1 and n2 have same known parities or are not stereo bonds */ 2151| 75.5k|} CreateCheckSymmPaths: 2174| 30.1k|{ 2175| 30.1k| int k, k1, k2, ret = 0, bParitiesInvertedZero = 0, *pbParitiesInverted; 2176| 30.1k| AT_RANK n1, n2; 2177| | 2178| 30.1k| nVisited1[cur1] = cur2 + 1; /* symmetrically exchange atom numbers */ 2179| 30.1k| nVisited2[cur2] = cur1 + 1; 2180| | 2181| 30.1k| ( *nLength )++; 2182| | 2183| 30.1k| nVisitOrd1[cur1] = *nLength; /* save DFS visit order */ 2184| 30.1k| nVisitOrd2[cur2] = *nLength; 2185| | 2186| | /* new version allows all inverted parities */ 2187| 30.1k| if (PARITY_WELL_DEF( at[cur1].stereo_atom_parity ) && ------------------ | | 266| 60.2k|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 30.1k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 60.2k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 30.1k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 23.0k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 23.0k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 23.0k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 23.0k, False: 7.10k] | | | Branch (266:85): [True: 72, False: 22.9k] | | ------------------ ------------------ 2188| 72| PARITY_WELL_DEF( at[cur2].stereo_atom_parity )) ------------------ | | 266| 72|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 72|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 144|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 72|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 68|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 68|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 68|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 68, False: 4] | | | Branch (266:85): [True: 58, False: 10] | | ------------------ ------------------ 2189| 58| { 2190| 58| if (*bParitiesInverted < 0) ------------------ | Branch (2190:13): [True: 0, False: 58] ------------------ 2191| 0| { 2192| 0| *bParitiesInverted = ( at[cur1].stereo_atom_parity + at[cur2].stereo_atom_parity ) % 2; 2193| 0| } 2194| 58| else 2195| 58| { 2196| 58| if (*bParitiesInverted != ( at[cur1].stereo_atom_parity + at[cur2].stereo_atom_parity ) % 2) ------------------ | Branch (2196:17): [True: 31, False: 27] ------------------ 2197| 31| { 2198| 31| return 0; /* Different known in advance parities have wrong "inverted" relation */ 2199| 31| } 2200| 58| } 2201| 58| } 2202| 30.0k| else 2203| 30.0k| { 2204| 30.0k| if (PARITY_KNOWN( at[cur1].stereo_atom_parity ) && ------------------ | | 265| 60.1k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 30.0k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 60.1k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 30.0k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 22.9k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 22.9k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 22.9k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 22.9k, False: 7.10k] | | | Branch (265:78): [True: 13.1k, False: 9.84k] | | ------------------ ------------------ 2205| 13.1k| PARITY_KNOWN( at[cur2].stereo_atom_parity ) && ------------------ | | 265| 43.1k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 13.1k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 26.2k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 13.1k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 12.3k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 12.3k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 12.3k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 12.3k, False: 714] | | | Branch (265:78): [True: 9.13k, False: 3.26k] | | ------------------ ------------------ 2206| 9.13k| at[cur1].stereo_atom_parity != at[cur2].stereo_atom_parity) ------------------ | Branch (2206:13): [True: 295, False: 8.83k] ------------------ 2207| 295| { 2208| 295| return 0; /* Different known in advance parities */ 2209| 295| } 2210| 30.0k| } 2211| | 2212| 29.7k| if (cur1 != cur2 && ------------------ | Branch (2212:9): [True: 16.3k, False: 13.4k] ------------------ 2213| 16.3k| !at[cur1].stereo_bond_neighbor[0] && !at[cur2].stereo_bond_neighbor[0] && ------------------ | Branch (2213:10): [True: 16.3k, False: 44] | Branch (2213:47): [True: 16.3k, False: 0] ------------------ 2214| 16.3k| PARITY_KNOWN( at[cur1].parity ) != PARITY_KNOWN( at[cur2].parity )) ------------------ | | 265| 16.3k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 16.3k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 32.6k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 16.3k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 13.4k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 13.4k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 13.4k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 13.4k, False: 2.83k] | | | Branch (265:78): [True: 13.4k, False: 0] | | ------------------ ------------------ PARITY_KNOWN( at[cur1].parity ) != PARITY_KNOWN( at[cur2].parity )) ------------------ | | 265| 16.3k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 16.3k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 32.6k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 16.3k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 14.3k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 14.3k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 14.3k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 14.3k, False: 1.92k] | | | Branch (265:78): [True: 14.3k, False: 0] | | ------------------ ------------------ | Branch (2214:10): [True: 2.69k, False: 13.6k] ------------------ 2215| 2.69k| { 2216| 2.69k| return 0; /* one atom is stereogenic, another (presumably equivalent) is not. 9-11-2002 */ 2217| 2.69k| } 2218| |#if ( PROPAGATE_ILL_DEF_STEREO != 1 ) 2219| | if (cur1 != cur2 && 2220| | ( PARITY_ILL_DEF( at[cur1].stereo_atom_parity ) || 2221| | PARITY_ILL_DEF( at[cur2].stereo_atom_parity ) ) 2222| | ) 2223| | { 2224| | return 0; /* Cannot detect whether the paths are same or different */ 2225| | } 2226| |#endif 2227| | 2228| 27.1k| if (at[cur1].valence != at[cur2].valence) ------------------ | Branch (2228:9): [True: 0, False: 27.1k] ------------------ 2229| 0| { 2230| 0| return CT_REMOVE_STEREO_ERR; /* program error */ /* */ ------------------ | | 33| 0|#define CT_REMOVE_STEREO_ERR (CT_ERR_FIRST-14) /*(-30014) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2231| 0| } 2232| 27.1k| if (at[cur1].valence == 1) ------------------ | Branch (2232:9): [True: 261, False: 26.8k] ------------------ 2233| 261| { 2234| 261| return 1; /* so far success */ 2235| 261| } 2236| | 2237| 26.8k| if (nl1[(int) cur1][0] != nl2[(int) cur2][0] || nl1[(int) cur1][0] != at[cur1].valence) ------------------ | Branch (2237:9): [True: 0, False: 26.8k] | Branch (2237:53): [True: 0, False: 26.8k] ------------------ 2238| 0| { 2239| 0| return CT_REMOVE_STEREO_ERR; /* error: different valences */ /* */ ------------------ | | 33| 0|#define CT_REMOVE_STEREO_ERR (CT_ERR_FIRST-14) /*(-30014) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2240| 0| } 2241| | 2242| | 2243| 102k| for (k = 1, k1 = 1, k2 = 1; k < at[cur1].valence; k++, k1++, k2++) ------------------ | Branch (2243:33): [True: 75.5k, False: 26.6k] ------------------ 2244| 75.5k| { 2245| 75.5k| if (( n1 = nl1[(int) cur1][k1] ) == prev1) ------------------ | Branch (2245:13): [True: 20.1k, False: 55.3k] ------------------ 2246| 20.1k| { 2247| 20.1k| n1 = nl1[(int) cur1][++k1]; /* don't go back */ 2248| 20.1k| } 2249| 75.5k| if (( n2 = nl2[(int) cur2][k2] ) == prev2) ------------------ | Branch (2249:13): [True: 20.1k, False: 55.3k] ------------------ 2250| 20.1k| { 2251| 20.1k| n2 = nl2[(int) cur2][++k2]; /* don't go back */ 2252| 20.1k| } 2253| | 2254| 75.5k| if (0 >= ( ret = CheckNextSymmNeighborsAndBonds( at, cur1, cur2, n1, n2, nAvoidCheckAtom, ------------------ | Branch (2254:13): [True: 5, False: 75.5k] ------------------ 2255| 75.5k| nVisited1, nVisited2, nVisitOrd1, nVisitOrd2, nRank1, nRank2 ) )) 2256| 5| { 2257| 5| return ret; /* different neighbors or bonds */ 2258| 5| } 2259| | 2260| 75.5k| if (!nVisited1[n1]) ------------------ | Branch (2260:13): [True: 20.5k, False: 55.0k] ------------------ 2261| 20.5k| { 2262| | /* recursion */ 2263| | /* allow all inverted parities only inside a single ring system containing the starting point */ 2264| 20.5k| pbParitiesInverted = ( at[cur1].nRingSystem == at[n1].nRingSystem ) ? bParitiesInverted : &bParitiesInvertedZero; ------------------ | Branch (2264:34): [True: 20.2k, False: 303] ------------------ 2265| 20.5k| if (0 >= ( ret = CreateCheckSymmPaths( at, cur1, n1, cur2, n2, nAvoidCheckAtom, ------------------ | Branch (2265:17): [True: 143, False: 20.3k] ------------------ 2266| 20.5k| nVisited1, nVisited2, nVisitOrd1, nVisitOrd2, 2267| 20.5k| nl1, nl2, nRank1, nRank2, nCanonRank, nLength, pbParitiesInverted, mode ) )) 2268| 143| { 2269| 143| return ret; 2270| 143| } 2271| 20.5k| } 2272| 75.5k| } 2273| | 2274| 26.6k| return 1; /* Success */ 2275| 26.8k|} CalculatedPathsParitiesAreIdentical: 2382| 9.60k|{ 2383| 9.60k| int i, i01, i02, i11, i12, i21, i22, k, parity, parity1, parity2, parity12, num_other_neigh; 2384| 9.60k| int nNumEqStereogenic, nCheckingMode, not_well_def_parities; 2385| 9.60k| AT_RANK other_neigh[MAX_NUM_STEREO_ATOM_NEIGH], neigh, r1, r2; 2386| 9.60k| int nNumComparedCenters = 0, nNumComparedBonds = 0, bCurParityInv1 = 0 /*, bCurParityInv2=0*/; 2387| 9.60k| int bCurRotated = 0, nNumDiff = 0, nNumInv = 0; 2388| 9.60k| int s1, s2; 2389| | 2390| 9.60k| nCheckingMode = ( prev_sb_neigh < num_atoms ) ? CHECKING_STEREOBOND : CHECKING_STEREOCENTER; ------------------ | | 2286| 14|#define CHECKING_STEREOBOND 2 ------------------ nCheckingMode = ( prev_sb_neigh < num_atoms ) ? CHECKING_STEREOBOND : CHECKING_STEREOCENTER; ------------------ | | 2285| 19.1k|#define CHECKING_STEREOCENTER 1 ------------------ | Branch (2390:21): [True: 14, False: 9.59k] ------------------ 2391| 9.60k| not_well_def_parities = 0; 2392| 9.60k| nNumEqStereogenic = 0; 2393| | 2394| 9.60k| if ((nNeighMode != NEIGH_MODE_RING && ------------------ | | 2282| 19.2k|#define NEIGH_MODE_RING 1 ------------------ | Branch (2394:10): [True: 0, False: 9.60k] ------------------ 2395| 9.60k| bParitiesInverted != 0) || abs( bParitiesInverted ) != 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2395:10): [True: 0, False: 0] | Branch (2395:37): [True: 9.60k, False: 0] ------------------ 2396| 9.60k| { 2397| 9.60k| bParitiesInverted = 0; 2398| 9.60k| } 2399| | 2400| 9.60k| if (bParitiesInverted) ------------------ | Branch (2400:9): [True: 0, False: 9.60k] ------------------ 2401| 0| { 2402| 0| for (i = 0, i11 = i22 = 0; i < num_atoms; i++) ------------------ | Branch (2402:36): [True: 0, False: 0] ------------------ 2403| 0| { 2404| | /* count number of atoms that have not been visited */ 2405| 0| i11 += !nVisited1[i]; 2406| 0| i22 += !nVisited2[i]; 2407| 0| nAtomNumberCanon1[i] = MAX_ATOMS + 1; /* mark unchanged */ ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ 2408| 0| nAtomNumberCanon2[i] = MAX_ATOMS + 1; /* mark unchanged */ ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ 2409| 0| } 2410| 0| if (i11 || i22) ------------------ | Branch (2410:13): [True: 0, False: 0] | Branch (2410:20): [True: 0, False: 0] ------------------ 2411| 0| { 2412| 0| if (bParitiesInverted == 1) ------------------ | Branch (2412:17): [True: 0, False: 0] ------------------ 2413| 0| { 2414| 0| return 0; /* only a part of the structure has been inverted */ 2415| 0| } 2416| 0| else 2417| 0| { 2418| 0| bParitiesInverted = 0; 2419| 0| } 2420| 0| } 2421| 0| } 2422| 9.60k| else 2423| 9.60k| { 2424| 58.8k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (2424:21): [True: 49.2k, False: 9.60k] ------------------ 2425| 49.2k| { 2426| 49.2k| nAtomNumberCanon1[i] = MAX_ATOMS + 1; /* mark unchanged */ ------------------ | | 15| 49.2k|#define MAX_ATOMS 32766 ------------------ 2427| 49.2k| nAtomNumberCanon2[i] = MAX_ATOMS + 1; /* mark unchanged */ ------------------ | | 15| 49.2k|#define MAX_ATOMS 32766 ------------------ 2428| 49.2k| } 2429| 9.60k| } 2430| 9.60k| if ((bParitiesInverted > 0 && !( mode == MAP_MODE_C2v || mode == MAP_MODE_S4 )) || ------------------ | | 15| 0|#define MAP_MODE_C2v 1 /* Check for C2v reflection leading to parity inversion */ ------------------ if ((bParitiesInverted > 0 && !( mode == MAP_MODE_C2v || mode == MAP_MODE_S4 )) || ------------------ | | 17| 0|#define MAP_MODE_S4 3 /* Check for S4 rotation/reflection leading to parity inversion */ ------------------ | Branch (2430:10): [True: 0, False: 9.60k] | Branch (2430:38): [True: 0, False: 0] | Branch (2430:62): [True: 0, False: 0] ------------------ 2431| 9.60k| (bParitiesInverted == 0 && !( mode == MAP_MODE_C2 || mode == MAP_MODE_STD ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 16| 19.2k|#define MAP_MODE_C2 2 /* Check for C2 rotation preserving parities */ ------------------ (bParitiesInverted == 0 && !( mode == MAP_MODE_C2 || mode == MAP_MODE_STD ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 14| 9.60k|#define MAP_MODE_STD 0 /* Standard approach: switch 2 neighbors */ ------------------ | Branch (2431:11): [True: 9.60k, False: 0] | Branch (2431:40): [True: 0, False: 9.60k] | Branch (2431:63): [True: 9.60k, False: 0] ------------------ 2432| 0| { 2433| 0| return 0; 2434| 0| } 2435| | /************************************************************************************** 2436| | * The following discussion assumes that the canonical numbers are 2437| | * switched for some pairs of constitutionally identical atoms 2438| | * in such a way that the new numbering is an equivalent to the 2439| | * nCanonRank[] canonical numbering (the transposition belongs to the 2440| | * automorphism group of the chemical structure having no stereo). 2441| | * At this point non-zero elements of nVisited1[] and nVisited2[] 2442| | * together contain transposition P of the atom numbers. 2443| | * and P2 respectively of the ordering atom numbers: nVisitedi[k] = Pi(k)+1; 2444| | * In this implementation: 2445| | * P1(k)=k for all k 2446| | * P2(cur)=cur, P2(next1)=next2, P2(next2)=next1 2447| | * 2448| | * Below we call one of the numberings "old", another "new". 2449| | * 2450| | * *IF* the old and the new canonical numberings produce same parities for stereogenic 2451| | * elements for the same canonical number(s) 2452| | * (that is, old_parity(canon_number) == new_parity(canon_number) 2453| | * *except* the currently being tested stereocenter at[cur] or stereobond/cumulene 2454| | * at[cur]=at[prev_sb_neigh], whose parity MUST be inverted 2455| | * 2456| | * *THEN* the stereocenter or stereobond/cumulene is not stereogenic with one 2457| | * 2458| | * *EXCEPTION* If the currently tested stereogenic element is constitutionally 2459| | * equivalent to two or more other stereogenic elements that have been 2460| | * permuted then the currently tested one is still stereogenic. 2461| | **************************************************************************************/ 2462| | 2463| | /* 2464| | * 1. replace the assigned in each of the parallel traversals atom numbers 2465| | * with the canon. ranks corresponding to the atom numbers in the 2466| | * currently numbered atoms at[]. 2467| | * One of obtained this way canonical numberings (probably nVisited1[]) 2468| | * is same as the nCanonRank[] because usually nVisited1[i] = i+1 or 0 2469| | */ 2470| 58.8k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (2470:17): [True: 49.2k, False: 9.60k] ------------------ 2471| 49.2k| { 2472| 49.2k| if (nVisited1[i]) ------------------ | Branch (2472:13): [True: 39.7k, False: 9.53k] ------------------ 2473| 39.7k| { 2474| | /* canonical number of the atom mapped on atom #i in 'left' path */ 2475| 39.7k| nVisited1[i] = nCanonRank[(int) nVisited1[i] - 1]; 2476| | /* reverse: atom # from the mapped canonical rank in 'left' path */ 2477| 39.7k| nAtomNumberCanon1[nVisited1[i] - 1] = i; 2478| 39.7k| } 2479| 49.2k| if (nVisited2[i]) ------------------ | Branch (2479:13): [True: 39.7k, False: 9.53k] ------------------ 2480| 39.7k| { 2481| | /* canonical number of the atom mapped on atom #i in 'right' path */ 2482| 39.7k| nVisited2[i] = nCanonRank[(int) nVisited2[i] - 1]; 2483| | /* reverse: atom # from the mapped canonical rank in 'right' path */ 2484| 39.7k| nAtomNumberCanon2[nVisited2[i] - 1] = i; 2485| 39.7k| } 2486| | /* if 'left' and 'right' path do not have atoms in common except the 2487| | starting atom (and in case of stereobond, the end atom) some of 2488| | nVisitedi[i] elements may be zero. 2489| | */ 2490| 49.2k| } 2491| | 2492| | /* 2493| | * if started with a stereobond then check whether its parity has changed. 2494| | * If yes then continue, otherwise parities are different 2495| | * 2496| | * if started with a stereo center then prev_sb_neigh = MAX_ATOMS+1 2497| | * 2498| | * If the transposition of next1 and next2 changes only the parity of the starting stereo atom or stereo bond 2499| | * then the stereo bond or stereo atom is not stereogenic 2500| | * 2501| | * The exception: the stereogenic elememt in question is equivalent 2502| | * to two or more traversed other stereogenic elememts 2503| | * (see nNumEqStereogenic below, case similar to trimethylcyclopropane: 2504| | * 3 or more constitutionally equivalent stereogenic elements) 2505| | */ 2506| 9.60k| if (nCheckingMode == CHECKING_STEREOBOND) ------------------ | | 2286| 9.60k|#define CHECKING_STEREOBOND 2 ------------------ | Branch (2506:9): [True: 14, False: 9.59k] ------------------ 2507| 14| { 2508| | /****************************************************************************** 2509| | * 2510| | * Possibly stereogenic starting bond or cumulene at[cur]-at[prev_sb_neigh] 2511| | * 2512| | *******************************************************************************/ 2513| | /* checking the starting stereo bond */ 2514| 14| if (nVisited1[prev_sb_neigh] || nVisited2[prev_sb_neigh]) ------------------ | Branch (2514:13): [True: 0, False: 14] | Branch (2514:41): [True: 0, False: 14] ------------------ 2515| 0| { 2516| | /* the bond or cumulene is in the ring and the opposite atom has been visited */ 2517| 0| if (nVisited1[prev_sb_neigh] != nVisited2[prev_sb_neigh] || ------------------ | Branch (2517:17): [True: 0, False: 0] ------------------ 2518| 0| nCanonRank[prev_sb_neigh] != nVisited2[prev_sb_neigh]) ------------------ | Branch (2518:18): [True: 0, False: 0] ------------------ 2519| 0| { 2520| 0| return 0; /* error: we came back to the same bond/cumulene and */ /* */ 2521| | /* assigned different canon. ranks to the opposite atom. */ 2522| 0| } 2523| 0| if (at[prev_sb_neigh].valence + at[prev_sb_neigh].num_H > 3) ------------------ | Branch (2523:17): [True: 0, False: 0] ------------------ 2524| 0| { 2525| 0| return 0; /* at[prev_sb_neigh] atom can not be adjacent to a stereo bond/cumulene */ 2526| | /* or does not have 3 attachments (hydrogens are not considered here) */ 2527| 0| } 2528| 0| for (i = 0, k = 0; i < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2528:32): [True: 0, False: 0] ------------------ 2529| 0| ( neigh = at[prev_sb_neigh].stereo_bond_neighbor[i] ) && !( k = ( neigh - 1 == cur ) ); ------------------ | Branch (2529:17): [True: 0, False: 0] | Branch (2529:74): [True: 0, False: 0] ------------------ 2530| 0| i++) 2531| 0| { 2532| 0| ; 2533| 0| } 2534| 0| if (!k) ------------------ | Branch (2534:17): [True: 0, False: 0] ------------------ 2535| 0| { 2536| 0| return -1; /* program error: could not locate stereogenic bond mark on the opposite atom */ 2537| 0| } 2538| 0| k = (int) at[prev_sb_neigh].stereo_bond_ord[i]; /* seq. number of the double or cumulene bond on at[prev_sb_neigh] */ 2539| | 2540| 0| for (i = 0, num_other_neigh = 0; i < at[prev_sb_neigh].valence && num_other_neigh <= MAX_OTHER_NEIGH; i++) ------------------ | | 2280| 0|#define MAX_OTHER_NEIGH 2 ------------------ | Branch (2540:46): [True: 0, False: 0] | Branch (2540:79): [True: 0, False: 0] ------------------ 2541| 0| { 2542| 0| if (i != k) ------------------ | Branch (2542:21): [True: 0, False: 0] ------------------ 2543| 0| { 2544| | /* do not include the double or cumulene bond */ 2545| 0| other_neigh[num_other_neigh++] = at[prev_sb_neigh].neighbor[i]; 2546| 0| } 2547| 0| } 2548| 0| if (num_other_neigh + at[prev_sb_neigh].num_H > MAX_OTHER_NEIGH) ------------------ | | 2280| 0|#define MAX_OTHER_NEIGH 2 ------------------ | Branch (2548:17): [True: 0, False: 0] ------------------ 2549| 0| { 2550| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2551| 0| } 2552| 0| for (i = 0; i < num_other_neigh; i++) ------------------ | Branch (2552:25): [True: 0, False: 0] ------------------ 2553| 0| { 2554| 0| k = (int) other_neigh[i]; 2555| 0| if (nVisited1[k] && nVisited1[k] != nCanonRank[k]) ------------------ | Branch (2555:21): [True: 0, False: 0] | Branch (2555:37): [True: 0, False: 0] ------------------ 2556| 0| { 2557| 0| return 0; /* parity of the statring stereo bond/cumulene has not changed. */ 2558| 0| } 2559| 0| if (nVisited2[k] && nVisited2[k] != nCanonRank[k]) ------------------ | Branch (2559:21): [True: 0, False: 0] | Branch (2559:37): [True: 0, False: 0] ------------------ 2560| 0| { 2561| 0| return 0; /* parity of the statring stereo bond/cumulene has not changed. */ 2562| 0| } 2563| 0| } 2564| 0| } 2565| 14| } 2566| | 2567| 9.60k| if (nCheckingMode == CHECKING_STEREOCENTER) ------------------ | | 2285| 9.60k|#define CHECKING_STEREOCENTER 1 ------------------ | Branch (2567:9): [True: 9.59k, False: 14] ------------------ 2568| 9.59k| { 2569| | /************************************************** 2570| | * 2571| | * Possibly stereogenic starting atom at[cur] 2572| | * 2573| | **************************************************/ 2574| | /* checking the starting stereo center */ 2575| 46.9k| for (i = 0, num_other_neigh = 0; i < at[cur].valence && num_other_neigh <= MAX_OTHER_NEIGH; i++) ------------------ | | 2280| 37.4k|#define MAX_OTHER_NEIGH 2 ------------------ | Branch (2575:42): [True: 37.4k, False: 9.59k] | Branch (2575:65): [True: 37.4k, False: 0] ------------------ 2576| 37.4k| { 2577| 37.4k| neigh = at[cur].neighbor[i]; 2578| 37.4k| if (neigh != next1 && neigh != next2) ------------------ | Branch (2578:17): [True: 27.8k, False: 9.59k] | Branch (2578:35): [True: 18.2k, False: 9.59k] ------------------ 2579| 18.2k| { 2580| 18.2k| other_neigh[num_other_neigh++] = neigh; 2581| 18.2k| } 2582| 37.4k| } 2583| 9.59k| if (num_other_neigh + at[cur].num_H > MAX_OTHER_NEIGH) ------------------ | | 2280| 9.59k|#define MAX_OTHER_NEIGH 2 ------------------ | Branch (2583:13): [True: 0, False: 9.59k] ------------------ 2584| 0| { 2585| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2586| 0| } 2587| | /* 2588| | if ( bParitiesInverted && at[cur].valence == MAX_NUM_STEREO_ATOM_NEIGH ) { 2589| | if ( nVisited1[other_neigh[0]] == nCanonRank[other_neigh[0]] || 2590| | nVisited2[other_neigh[0]] == nCanonRank[other_neigh[0]] || 2591| | nVisited1[other_neigh[1]] == nCanonRank[other_neigh[1]] || 2592| | nVisited2[other_neigh[1]] == nCanonRank[other_neigh[1]] ) { 2593| | bParitiesInverted = 0; 2594| | bCurRotated = 1; 2595| | } 2596| | } 2597| | */ 2598| | /* bParitiesInverted = -1 means no predefined stereocenter has been checked */ 2599| 9.59k| if (bParitiesInverted && at[cur].valence == MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2599:13): [True: 0, False: 9.59k] | Branch (2599:34): [True: 0, False: 0] ------------------ 2600| 0| { 2601| | /* special case: 4 canonically eq. neighbors */ 2602| 0| int canon_parity, parity_vis_1, parity_vis_2; 2603| 0| canon_parity = GetPermutationParity( pCG, at + cur, MAX_ATOMS + 1, nCanonRank ); ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ 2604| 0| parity_vis_1 = GetPermutationParity( pCG, at + cur, MAX_ATOMS + 1, nVisited1 ); ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ 2605| 0| parity_vis_2 = GetPermutationParity( pCG, at + cur, MAX_ATOMS + 1, nVisited2 ); ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ 2606| 0| if (parity_vis_1 != parity_vis_2) ------------------ | Branch (2606:17): [True: 0, False: 0] ------------------ 2607| 0| { 2608| 0| return 0; 2609| 0| } 2610| 0| if (bParitiesInverted == 1 && parity_vis_1 == canon_parity) ------------------ | Branch (2610:17): [True: 0, False: 0] | Branch (2610:43): [True: 0, False: 0] ------------------ 2611| 0| { 2612| 0| return 0; /* not a typical case of inversion during the mapping of D4h stereocenter */ 2613| 0| } 2614| 0| else 2615| 0| { 2616| 0| if (bParitiesInverted == -1) ------------------ | Branch (2616:21): [True: 0, False: 0] ------------------ 2617| 0| { 2618| 0| if (parity_vis_1 == canon_parity) ------------------ | Branch (2618:25): [True: 0, False: 0] ------------------ 2619| 0| { 2620| 0| bParitiesInverted = 0; 2621| 0| } 2622| 0| else 2623| 0| { 2624| 0| bParitiesInverted = 1; 2625| 0| } 2626| 0| } 2627| 0| } 2628| 0| } 2629| | /* at this point bParitiesInverted >= 0 */ 2630| 9.59k| if (!bParitiesInverted && !bCurRotated) ------------------ | Branch (2630:13): [True: 9.59k, False: 0] | Branch (2630:35): [True: 9.59k, False: 0] ------------------ 2631| 9.59k| { 2632| 27.1k| for (i = 0; i < num_other_neigh; i++) ------------------ | Branch (2632:25): [True: 17.9k, False: 9.16k] ------------------ 2633| 17.9k| { 2634| 17.9k| k = (int) other_neigh[i]; 2635| 17.9k| if (nVisited1[k] && nVisited1[k] != nCanonRank[k]) ------------------ | Branch (2635:21): [True: 12.3k, False: 5.58k] | Branch (2635:37): [True: 418, False: 11.9k] ------------------ 2636| 418| { 2637| 418| return 0; /* parity of the statring stereo center has not changed. */ 2638| 418| } 2639| 17.5k| if (nVisited2[k] && nVisited2[k] != nCanonRank[k]) ------------------ | Branch (2639:21): [True: 11.9k, False: 5.57k] | Branch (2639:37): [True: 12, False: 11.9k] ------------------ 2640| 12| { 2641| 12| return 0; /* parity of the statring stereo center has not changed. */ 2642| 12| } 2643| 17.5k| } 2644| 9.59k| } 2645| 9.59k| } 2646| | 2647| | /***************************************************** 2648| | * Check other (non-starting) stereo centers 2649| | ******************************************************/ 2650| 21.6k| for (i = 0; i < pCS->nLenLinearCTStereoCarb; i++, nNumComparedCenters += ( k > 0 )) ------------------ | Branch (2650:17): [True: 21.1k, False: 519] ------------------ 2651| 21.1k| { 2652| 21.1k| r1 = pCS->LinearCTStereoCarb[i].at_num; 2653| 21.1k| i01 = nAtomNumberCanon[r1 - 1]; /* ord. number of the atom that has canon rank r1 */ 2654| | 2655| 21.1k| i11 = nAtomNumberCanon1[r1 - 1]; /* = (MAX_ATOMS+1) > num_atoms if the atom has not been traversed */ 2656| 21.1k| i12 = nAtomNumberCanon2[r1 - 1]; /* = otherwise < num_atoms */ 2657| | 2658| 21.1k| s1 = ( i11 < num_atoms ); /* 1 => the center was traversed on path #1 */ 2659| 21.1k| s2 = ( i12 < num_atoms ); /* 1 => the center was traversed on path #2 */ 2660| | 2661| 21.1k| bCurParityInv1 = ( bParitiesInverted && ------------------ | Branch (2661:28): [True: 0, False: 21.1k] ------------------ 2662| 0| at[cur].nRingSystem == at[i11].nRingSystem && ------------------ | Branch (2662:27): [True: 0, False: 0] ------------------ 2663| 0| at[cur].nRingSystem == at[i12].nRingSystem ); ------------------ | Branch (2663:27): [True: 0, False: 0] ------------------ 2664| | 2665| | 2666| 21.1k| k = 0; 2667| | 2668| | /* check whether the two stereo centers (they can be one and the same atom) have been traversed */ 2669| 21.1k| if (!s1 && !s2) ------------------ | Branch (2669:13): [True: 3.95k, False: 17.1k] | Branch (2669:20): [True: 3.06k, False: 895] ------------------ 2670| 3.06k| { 2671| 3.06k| continue; /* Both stereo centers have not been traversed; check the next pair. */ 2672| 3.06k| } 2673| | 2674| 18.0k| if (nCheckingMode == CHECKING_STEREOCENTER) ------------------ | | 2285| 18.0k|#define CHECKING_STEREOCENTER 1 ------------------ | Branch (2674:13): [True: 18.0k, False: 0] ------------------ 2675| 18.0k| { 2676| | /* check whether the stereocenters are the starting stereocenter */ 2677| 18.0k| switch (( cur == i11 ) + ( cur == i12 )) ------------------ | Branch (2677:21): [True: 4.51k, False: 13.5k] ------------------ 2678| 18.0k| { 2679| 4.51k| case 2: ------------------ | Branch (2679:17): [True: 4.51k, False: 13.5k] ------------------ 2680| 4.51k| continue; /* do not recheck the starting atom */ 2681| 0| case 1: ------------------ | Branch (2681:17): [True: 0, False: 18.0k] ------------------ 2682| 0| return -1; /* possibly program error */ /* */ 2683| | /* case 0: */ 2684| | /* break; */ /* the stereo centers are not the sarting stereo center */ 2685| 18.0k| } 2686| 13.5k| if (cur == i01) ------------------ | Branch (2686:17): [True: 0, False: 13.5k] ------------------ 2687| 0| { 2688| 0| return -1; /* program error: in this case at least one of the i11, i12 must be == cur */ /* */ 2689| 0| } 2690| 13.5k| } 2691| | 2692| 13.5k| if (nNeighMode == NEIGH_MODE_RING) ------------------ | | 2282| 13.5k|#define NEIGH_MODE_RING 1 ------------------ | Branch (2692:13): [True: 13.5k, False: 0] ------------------ 2693| 13.5k| { 2694| 13.5k| if (i11 != i12 && !bCurParityInv1) ------------------ | Branch (2694:17): [True: 2.91k, False: 10.6k] | Branch (2694:31): [True: 2.91k, False: 0] ------------------ 2695| 2.91k| { 2696| 2.91k| return -1; /* failed: the two stereo atoms have not been traversed synchronously */ 2697| 2.91k| } 2698| 10.6k| if (!at[i11].parity || !at[i12].parity) ------------------ | Branch (2698:17): [True: 0, False: 10.6k] | Branch (2698:36): [True: 0, False: 10.6k] ------------------ 2699| 0| { 2700| 0| return 0; /* another atom does not have parity (it might have been removed) 9-11-2002 */ 2701| 0| } 2702| 10.6k| } 2703| 10.6k| if (nNeighMode == NEIGH_MODE_CHAIN) ------------------ | | 2283| 10.6k|#define NEIGH_MODE_CHAIN 2 ------------------ | Branch (2703:13): [True: 0, False: 10.6k] ------------------ 2704| 0| { 2705| 0| if (s1 + s2 != 1) ------------------ | Branch (2705:17): [True: 0, False: 0] ------------------ 2706| 0| { 2707| 0| return -1; /* program error: only one out of s1 and s2 must be 1, another must be 0. */ 2708| 0| } 2709| 0| if ((s1 && !at[i11].parity) || (s2 && !at[i12].parity)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2709:18): [True: 0, False: 0] | Branch (2709:24): [True: 0, False: 0] | Branch (2709:45): [True: 0, False: 0] | Branch (2709:51): [True: 0, False: 0] ------------------ 2710| 0| { 2711| 0| return 0; /* another atom does not have parity (it might have been removed) 9-11-2002 */ 2712| 0| } 2713| 0| } 2714| | 2715| 10.6k| parity = pCS->LinearCTStereoCarb[i].parity; 2716| 10.6k| if (nNeighMode == (NEIGH_MODE_RING && ( i11 != i01 ) && ( i12 != i01 )) || ------------------ | | 2282| 21.3k|#define NEIGH_MODE_RING 1 | | ------------------ | | | Branch (2282:32): [True: 10.6k, Folded] | | ------------------ ------------------ | Branch (2716:13): [True: 5.04k, False: 5.62k] | Branch (2716:47): [True: 5.04k, False: 5.62k] | Branch (2716:65): [True: 5.04k, False: 0] ------------------ 2717| | /* in NEIGH_MODE_RING case we know that i11 == i12 except bCurParityInv1 == 1 */ 2718| 5.62k| nNeighMode == NEIGH_MODE_CHAIN ------------------ | | 2283| 5.62k|#define NEIGH_MODE_CHAIN 2 ------------------ | Branch (2718:14): [True: 0, False: 5.62k] ------------------ 2719| | /* in NEIGH_MODE_CHAIN case here we always have 2 different atoms */ 2720| 10.6k| ) /* djb-rwth: addressing LLVM warning */ 2721| 5.04k| { 2722| | /**************************************************************** 2723| | * Case of two transposed atoms or a circular permutation in D4h 2724| | */ 2725| 5.04k| parity1 = s1 ? GetStereoCenterParity( pCG, at, i11, nVisited1 ) : PARITY_IMPOSSIBLE; ------------------ | | 2292| 5.04k|#define PARITY_IMPOSSIBLE 999 ------------------ | Branch (2725:23): [True: 5.04k, False: 0] ------------------ 2726| 5.04k| parity2 = s2 ? GetStereoCenterParity( pCG, at, i12, nVisited2 ) : PARITY_IMPOSSIBLE; ------------------ | | 2292| 5.04k|#define PARITY_IMPOSSIBLE 999 ------------------ | Branch (2726:23): [True: 5.04k, False: 0] ------------------ 2727| 5.04k| if (!ATOM_PARITY_KNOWN( parity1 ) && !ATOM_PARITY_KNOWN( parity2 )) ------------------ | | 258| 10.0k|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 5.04k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 5.04k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (258:38): [True: 5.04k, False: 0] | | | Branch (258:68): [True: 5.04k, False: 0] | | ------------------ ------------------ if (!ATOM_PARITY_KNOWN( parity1 ) && !ATOM_PARITY_KNOWN( parity2 )) ------------------ | | 258| 0|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 0|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (258:38): [True: 0, False: 0] | | | Branch (258:68): [True: 0, False: 0] | | ------------------ ------------------ 2728| 0| { 2729| 0| return -1; /* should not happen: must have been detected at the time of the traversal */ 2730| 0| } 2731| 5.04k| if (s1 && s2) ------------------ | Branch (2731:17): [True: 5.04k, False: 0] | Branch (2731:23): [True: 5.04k, False: 0] ------------------ 2732| 5.04k| { 2733| 5.04k| if (bCurParityInv1) ------------------ | Branch (2733:21): [True: 0, False: 5.04k] ------------------ 2734| 0| { 2735| 0| int parity1orig = GetStereoCenterParity( pCG, at, i11, nCanonRank ); 2736| 0| int parity2orig = GetStereoCenterParity( pCG, at, i12, nCanonRank ); 2737| 0| if (i11 == i12 || ------------------ | Branch (2737:25): [True: 0, False: 0] ------------------ 2738| 0| (( parity1 == parity1orig || parity2 == parity2orig || parity1 != parity2 ) && ------------------ | Branch (2738:28): [True: 0, False: 0] | Branch (2738:54): [True: 0, False: 0] | Branch (2738:80): [True: 0, False: 0] ------------------ 2739| 0| ATOM_PARITY_WELL_DEF( parity1 )) || ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2740| 0| ((parity1 != parity2 && ( !ATOM_PARITY_WELL_DEF( parity1 ))) || ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2740:28): [True: 0, False: 0] ------------------ 2741| 0| !ATOM_PARITY_WELL_DEF( parity2 ) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2742| | /*return -1; */ /* should be different atoms with inverted parities */ 2743| 0| nNumDiff++; 2744| 0| } 2745| 5.04k| else 2746| 5.04k| { 2747| 5.04k| if (i11 != i12 || parity1 != parity2) ------------------ | Branch (2747:25): [True: 0, False: 5.04k] | Branch (2747:39): [True: 0, False: 5.04k] ------------------ 2748| 0| { 2749| 0| return -1; /* program error: must be the same atom */ 2750| 0| } 2751| 5.04k| } 2752| 5.04k| } 2753| 5.04k| parity12 = s1 ? parity1 : parity2; ------------------ | Branch (2753:24): [True: 5.04k, False: 0] ------------------ 2754| | 2755| 5.04k| if (ATOM_PARITY_WELL_DEF( parity ) && parity == parity12) ------------------ | | 259| 10.0k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 5.04k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 5.04k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 5.04k, False: 0] | | | Branch (259:75): [True: 2.96k, False: 2.08k] | | ------------------ ------------------ | Branch (2755:51): [True: 585, False: 2.37k] ------------------ 2756| 585| { 2757| | /* symmetrical neighbors have well-defined equal parities */ 2758| 585| k++; 2759| 585| if (nCheckingMode == CHECKING_STEREOCENTER && nNeighMode == NEIGH_MODE_RING) ------------------ | | 2285| 1.17k|#define CHECKING_STEREOCENTER 1 ------------------ if (nCheckingMode == CHECKING_STEREOCENTER && nNeighMode == NEIGH_MODE_RING) ------------------ | | 2282| 585|#define NEIGH_MODE_RING 1 ------------------ | Branch (2759:21): [True: 585, False: 0] | Branch (2759:63): [True: 585, False: 0] ------------------ 2760| 585| { 2761| | /* all 3: cur, i01, i11 are different atoms (here i11==i12) */ 2762| | /* here nSymmRank[i01]==nSymmRank[i11] due to the parallel traversal */ 2763| 585| if (nSymmRank[cur] == nSymmRank[i01]) ------------------ | Branch (2763:25): [True: 480, False: 105] ------------------ 2764| 480| { 2765| 480| nNumEqStereogenic++; /* all 3 are equ */ 2766| 480| } 2767| 585| } 2768| 585| } 2769| 4.45k| else 2770| 4.45k| { 2771| 4.45k| if (ATOM_PARITY_WELL_DEF( parity ) && ATOM_PARITY_WELL_DEF( parity12 )) ------------------ | | 259| 8.91k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 4.45k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 4.45k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 4.45k, False: 0] | | | Branch (259:75): [True: 2.37k, False: 2.08k] | | ------------------ ------------------ if (ATOM_PARITY_WELL_DEF( parity ) && ATOM_PARITY_WELL_DEF( parity12 )) ------------------ | | 259| 2.37k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 2.37k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 2.37k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 2.37k, False: 0] | | | Branch (259:75): [True: 590, False: 1.78k] | | ------------------ ------------------ 2772| 590| { 2773| | /* apparently different well-defined parities */ 2774| 590| if (!bCurParityInv1) ------------------ | Branch (2774:25): [True: 590, False: 0] ------------------ 2775| 590| { 2776| 590| nNumInv++; 2777| | /* return 0; */ 2778| 590| } 2779| 590| } 2780| 3.86k| else 2781| 3.86k| { 2782| 3.86k|#if ( PROPAGATE_ILL_DEF_STEREO == 1 ) 2783| | /* at least one parity is ill-defined. Use parity1 and parity2 to temporarily save bitmaps */ 2784| 3.86k| parity1 = ( parity == vABParityUnknown /*AB_PARITY_UNKN*/ ) ------------------ | Branch (2784:31): [True: 2.08k, False: 1.78k] ------------------ 2785| 3.86k| ? NOT_WELL_DEF_UNKN ------------------ | | 2289| 2.08k|#define NOT_WELL_DEF_UNKN 2 ------------------ 2786| 3.86k| : ( parity == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 222| 1.78k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ : ( parity == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 2290| 0|#define NOT_WELL_DEF_UNDF 4 ------------------ | Branch (2786:27): [True: 0, False: 1.78k] ------------------ 2787| 3.86k| parity2 = ( parity12 == vABParityUnknown /*AB_PARITY_UNKN*/ ) ------------------ | Branch (2787:31): [True: 2.86k, False: 1.00k] ------------------ 2788| 3.86k| ? NOT_WELL_DEF_UNKN : ( parity12 == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 2289| 2.86k|#define NOT_WELL_DEF_UNKN 2 ------------------ ? NOT_WELL_DEF_UNKN : ( parity12 == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 222| 1.00k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ ? NOT_WELL_DEF_UNKN : ( parity12 == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 2290| 0|#define NOT_WELL_DEF_UNDF 4 ------------------ | Branch (2788:47): [True: 0, False: 1.00k] ------------------ 2789| 3.86k| if (parity1 | parity2) ------------------ | Branch (2789:25): [True: 3.69k, False: 178] ------------------ 2790| 3.69k| { 2791| 3.69k| not_well_def_parities |= ( parity1 | parity2 ); 2792| 3.69k| k++; 2793| 3.69k| } 2794| 178| else 2795| 178| { 2796| 178| return -1; /* program error */ /* */ 2797| 178| } 2798| |#else 2799| | return 0; 2800| |#endif 2801| 3.86k| } 2802| 4.45k| } 2803| 5.04k| } 2804| 5.62k| else 2805| 5.62k| { 2806| 5.62k| if (i11 == i01 && i12 == i01) ------------------ | Branch (2806:17): [True: 5.62k, False: 0] | Branch (2806:31): [True: 5.62k, False: 0] ------------------ 2807| 5.62k| { 2808| | /********************************************************************/ 2809| | /* i11 == i12 are same atom as i01, nNeighMode == NEIGH_MODE_RING */ 2810| 5.62k| if (!s1 || !s2) ------------------ | Branch (2810:21): [True: 0, False: 5.62k] | Branch (2810:28): [True: 0, False: 5.62k] ------------------ 2811| 0| { 2812| 0| return -1; 2813| 0| } 2814| | /* the parity of the new neighbors permutation must be same as the old one */ 2815| | /* this must work for well-defined and ill-defined parities. */ 2816| | /* actual parity (that includes the geometry) is not important here. */ 2817| | /* old permutation */ 2818| 5.62k| parity = GetPermutationParity( pCG, at + i01, MAX_ATOMS + 1, nCanonRank ); ------------------ | | 15| 5.62k|#define MAX_ATOMS 32766 ------------------ 2819| | /* new parmutation */ 2820| 5.62k| parity1 = GetPermutationParity( pCG, at + i01, MAX_ATOMS + 1, nVisited1 ); ------------------ | | 15| 5.62k|#define MAX_ATOMS 32766 ------------------ 2821| 5.62k| parity2 = GetPermutationParity( pCG, at + i01, MAX_ATOMS + 1, nVisited2 ); ------------------ | | 15| 5.62k|#define MAX_ATOMS 32766 ------------------ 2822| 5.62k| if (parity != parity1 || parity != parity2) ------------------ | Branch (2822:21): [True: 5.56k, False: 55] | Branch (2822:42): [True: 0, False: 55] ------------------ 2823| 5.56k| { 2824| 5.56k| return 0; 2825| 5.56k| } 2826| 55| k++; 2827| 55| } 2828| 0| else 2829| 0| { 2830| | /* nNeighMode == NEIGH_MODE_RING and only one out of the two (i11 == i01) (i12 == i01) is true */ 2831| 0| return -1; 2832| 0| } 2833| 5.62k| } 2834| | /* nNumComparedCenters += (k > 0); */ 2835| 10.6k| } 2836| 519| if (bCurRotated || nNumDiff || nNumInv) ------------------ | Branch (2836:9): [True: 0, False: 519] | Branch (2836:24): [True: 0, False: 519] | Branch (2836:36): [True: 13, False: 506] ------------------ 2837| 13| { 2838| 13| return 0; 2839| 13| } 2840| | 2841| | /* !!!! Add here bParitiesInverted == 1 case !!!! */ 2842| | /******************************************************/ 2843| | /* Check other (non-starting) stereo bonds/cumulenes */ 2844| | /******************************************************/ 2845| 578| for (i = 0; i < pCS->nLenLinearCTStereoDble; i++, nNumComparedBonds += ( k > 0 )) ------------------ | Branch (2845:17): [True: 74, False: 504] ------------------ 2846| 74| { 2847| 74| r1 = pCS->LinearCTStereoDble[i].at_num1; 2848| 74| r2 = pCS->LinearCTStereoDble[i].at_num2; 2849| 74| i01 = nAtomNumberCanon[r1 - 1]; /* ord. number of the atom that originally has canon rank r1 */ 2850| 74| i02 = nAtomNumberCanon[r2 - 1]; /* ord. number of the atom that originally has canon rank r2 */ 2851| | 2852| 74| i11 = nAtomNumberCanon1[r1 - 1]; /* ord. number of the atom that got canon rank r1 during the parallel traversal */ 2853| 74| i12 = nAtomNumberCanon1[r2 - 1]; /* ord. number of the atom that got canon rank r2 during the parallel traversal */ 2854| | 2855| 74| i21 = nAtomNumberCanon2[r1 - 1]; 2856| 74| i22 = nAtomNumberCanon2[r2 - 1]; 2857| | 2858| | 2859| 74| s1 = ( i11 < num_atoms && i12 < num_atoms ); ------------------ | Branch (2859:16): [True: 42, False: 32] | Branch (2859:35): [True: 36, False: 6] ------------------ 2860| 74| s2 = ( i21 < num_atoms && i22 < num_atoms ); ------------------ | Branch (2860:16): [True: 40, False: 34] | Branch (2860:35): [True: 34, False: 6] ------------------ 2861| | 2862| 74| k = 0; 2863| | 2864| | /* check whether the two stereo bonds/allenes (they can be one and the same) have been traversed */ 2865| 74| if (!s1 && !s2) ------------------ | Branch (2865:13): [True: 38, False: 36] | Branch (2865:20): [True: 38, False: 0] ------------------ 2866| 38| { 2867| 38| continue; /* Both stereo bonds/cumulenes have not been traversed; check the next pair. */ 2868| 38| } 2869| | 2870| 36| if (nCheckingMode == CHECKING_STEREOBOND) ------------------ | | 2286| 36|#define CHECKING_STEREOBOND 2 ------------------ | Branch (2870:13): [True: 0, False: 36] ------------------ 2871| 0| { 2872| 0| switch (( (i11 == cur && i12 == prev_sb_neigh) || (i12 == cur && i11 == prev_sb_neigh) ) + ------------------ | Branch (2872:21): [True: 0, False: 0] | Branch (2872:24): [True: 0, False: 0] | Branch (2872:38): [True: 0, False: 0] | Branch (2872:64): [True: 0, False: 0] | Branch (2872:78): [True: 0, False: 0] ------------------ 2873| 0| ( (i21 == cur && i22 == prev_sb_neigh) || (i22 == cur && i21 == prev_sb_neigh) )) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2873:20): [True: 0, False: 0] | Branch (2873:34): [True: 0, False: 0] | Branch (2873:60): [True: 0, False: 0] | Branch (2873:74): [True: 0, False: 0] ------------------ 2874| 0| { 2875| 0| case 2: ------------------ | Branch (2875:17): [True: 0, False: 0] ------------------ 2876| 0| continue; /* do not recheck the starting bond/cumulene */ 2877| 0| case 1: ------------------ | Branch (2877:17): [True: 0, False: 0] ------------------ 2878| 0| return -1; /* possibly program error */ /* */ 2879| | /* case 0: */ 2880| | /* break; */ /* the stereo centers are not the sarting stereo center */ 2881| 0| } 2882| 0| if (( i01 == cur && i02 == prev_sb_neigh ) || ( i02 == cur && i01 == prev_sb_neigh )) ------------------ | Branch (2882:19): [True: 0, False: 0] | Branch (2882:33): [True: 0, False: 0] | Branch (2882:61): [True: 0, False: 0] | Branch (2882:75): [True: 0, False: 0] ------------------ 2883| 0| { 2884| 0| return -1; /* program error: in this case at least one of the i1x, i2x must be == cur */ /* */ 2885| 0| } 2886| 0| } 2887| | 2888| 36| if (nNeighMode == NEIGH_MODE_RING) ------------------ | | 2282| 36|#define NEIGH_MODE_RING 1 ------------------ | Branch (2888:13): [True: 36, False: 0] ------------------ 2889| 36| { 2890| 36| if (( i11 != i21 || i12 != i22 ) && ( i11 != i22 || i12 != i21 )) ------------------ | Branch (2890:19): [True: 2, False: 34] | Branch (2890:33): [True: 0, False: 34] | Branch (2890:51): [True: 2, False: 0] | Branch (2890:65): [True: 0, False: 0] ------------------ 2891| 2| { 2892| 2| return -1; /* failed: the two bonds/cumulenes have not been traversed synchronously */ 2893| 2| } 2894| 34| if (0 > GetStereoNeighborPos( at, i11, i12 )) ------------------ | Branch (2894:17): [True: 0, False: 34] ------------------ 2895| 0| { 2896| 0| return 0; /* another bond is not stereo (the stereo might have been removed) 9-11-2002 */ 2897| 0| } 2898| 34| } 2899| 34| if (nNeighMode == NEIGH_MODE_CHAIN) ------------------ | | 2283| 34|#define NEIGH_MODE_CHAIN 2 ------------------ | Branch (2899:13): [True: 0, False: 34] ------------------ 2900| 0| { 2901| 0| if (s1 + s2 != 1) ------------------ | Branch (2901:17): [True: 0, False: 0] ------------------ 2902| 0| { 2903| 0| return -1; /* program error: only one out of s1 and s2 must be 1, another must be 0. */ 2904| 0| } 2905| 0| if ((s1 && 0 > GetStereoNeighborPos( at, i11, i12 )) || ------------------ | Branch (2905:18): [True: 0, False: 0] | Branch (2905:24): [True: 0, False: 0] ------------------ 2906| 0| (s2 && 0 > GetStereoNeighborPos( at, i21, i22 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2906:19): [True: 0, False: 0] | Branch (2906:25): [True: 0, False: 0] ------------------ 2907| 0| { 2908| 0| return 0; /* another bond is not stereo (the stereo might have been removed) 9-11-2002 */ 2909| 0| } 2910| 0| } 2911| | 2912| 34| parity = pCS->LinearCTStereoDble[i].parity; 2913| | /* bMustBeIdentical = ATOM_PARITY_ILL_DEF(parity); */ 2914| | /* nNumEqStereogenic = 0; */ 2915| | 2916| 34| if ((nNeighMode == NEIGH_MODE_RING && ( i11 != i01 || i12 != i02 ) && ( i11 != i02 || i12 != i01 )) || ------------------ | | 2282| 68|#define NEIGH_MODE_RING 1 ------------------ | Branch (2916:14): [True: 34, False: 0] | Branch (2916:49): [True: 34, False: 0] | Branch (2916:63): [True: 0, False: 0] | Branch (2916:81): [True: 34, False: 0] | Branch (2916:95): [True: 0, False: 0] ------------------ 2917| 0| nNeighMode == NEIGH_MODE_CHAIN /* in NEIGH_MODE_CHAIN case here we always have 2 different atoms */ ------------------ | | 2283| 0|#define NEIGH_MODE_CHAIN 2 ------------------ | Branch (2917:14): [True: 0, False: 0] ------------------ 2918| 34| ) /* djb-rwth: addressing LLVM warning */ 2919| 34| { 2920| | /*******************************************/ 2921| | /* case of two transposed bonds/cumulenes */ 2922| 34| parity1 = s1 ? GetStereoBondParity( at, i11, i12, nVisited1 ) : PARITY_IMPOSSIBLE; ------------------ | | 2292| 34|#define PARITY_IMPOSSIBLE 999 ------------------ | Branch (2922:23): [True: 34, False: 0] ------------------ 2923| 34| parity2 = s2 ? GetStereoBondParity( at, i21, i22, nVisited2 ) : PARITY_IMPOSSIBLE; ------------------ | | 2292| 34|#define PARITY_IMPOSSIBLE 999 ------------------ | Branch (2923:23): [True: 34, False: 0] ------------------ 2924| 34| if (!ATOM_PARITY_KNOWN( parity1 ) && !ATOM_PARITY_KNOWN( parity2 )) ------------------ | | 258| 68|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 34|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 34|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (258:38): [True: 34, False: 0] | | | Branch (258:68): [True: 34, False: 0] | | ------------------ ------------------ if (!ATOM_PARITY_KNOWN( parity1 ) && !ATOM_PARITY_KNOWN( parity2 )) ------------------ | | 258| 0|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 0|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (258:38): [True: 0, False: 0] | | | Branch (258:68): [True: 0, False: 0] | | ------------------ ------------------ 2925| 0| { 2926| 0| return -1; /* should not happen: must have been detected at the time of traversal */ 2927| 0| } 2928| 34| if (s1 && s2 && ( (( i11 != i21 || i12 != i22 ) && ( i11 != i22 || i12 != i21 )) || parity1 != parity2 )) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2928:17): [True: 34, False: 0] | Branch (2928:23): [True: 34, False: 0] | Branch (2928:34): [True: 0, False: 34] | Branch (2928:48): [True: 0, False: 34] | Branch (2928:66): [True: 0, False: 0] | Branch (2928:80): [True: 0, False: 0] | Branch (2928:97): [True: 0, False: 34] ------------------ 2929| 0| { 2930| 0| return -1; /* program error: must be the same bond/cumulene */ 2931| 0| } 2932| 34| parity12 = s1 ? parity1 : parity2; ------------------ | Branch (2932:24): [True: 34, False: 0] ------------------ 2933| 34| if (ATOM_PARITY_WELL_DEF( parity ) && parity == parity12) ------------------ | | 259| 68|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 34|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 34|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 34, False: 0] | | | Branch (259:75): [True: 2, False: 32] | | ------------------ ------------------ | Branch (2933:51): [True: 2, False: 0] ------------------ 2934| 2| { 2935| | /* symmetrical neighbors have well-defined equal parities */ 2936| 2| k++; 2937| 2| if (nCheckingMode == CHECKING_STEREOBOND && nNeighMode == NEIGH_MODE_RING) ------------------ | | 2286| 4|#define CHECKING_STEREOBOND 2 ------------------ if (nCheckingMode == CHECKING_STEREOBOND && nNeighMode == NEIGH_MODE_RING) ------------------ | | 2282| 0|#define NEIGH_MODE_RING 1 ------------------ | Branch (2937:21): [True: 0, False: 2] | Branch (2937:61): [True: 0, False: 0] ------------------ 2938| 0| { 2939| | /* all 3 bonds: cur-prev_sb_neigh, i01-i02, i11-i12 are different */ 2940| | /* (here == compared as unordered pairs) */ 2941| 0| if ((nSymmRank[cur] == nSymmRank[i01] && nSymmRank[prev_sb_neigh] == nSymmRank[i02]) || ------------------ | Branch (2941:26): [True: 0, False: 0] | Branch (2941:62): [True: 0, False: 0] ------------------ 2942| 0| (nSymmRank[cur] == nSymmRank[i02] && nSymmRank[prev_sb_neigh] == nSymmRank[i01])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2942:27): [True: 0, False: 0] | Branch (2942:63): [True: 0, False: 0] ------------------ 2943| 0| { 2944| 0| nNumEqStereogenic++; 2945| 0| } 2946| 0| } 2947| 2| } 2948| 32| else 2949| 32| { 2950| 32| if (ATOM_PARITY_WELL_DEF( parity ) && ATOM_PARITY_WELL_DEF( parity12 )) ------------------ | | 259| 64|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 32|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 32|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 32, False: 0] | | | Branch (259:75): [True: 0, False: 32] | | ------------------ ------------------ if (ATOM_PARITY_WELL_DEF( parity ) && ATOM_PARITY_WELL_DEF( parity12 )) ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2951| 0| { 2952| | /* apparently different well-defined parities */ 2953| 0| return 0; 2954| 0| } 2955| 32| else 2956| 32| { 2957| | /* at least one parity is ill-defined. Use parity1 and parity2 to temporarily save bitmaps */ 2958| 32|#if ( PROPAGATE_ILL_DEF_STEREO == 1 ) 2959| 32| parity1 = ( parity == vABParityUnknown /*AB_PARITY_UNKN*/ ) ? NOT_WELL_DEF_UNKN : ------------------ | | 2289| 32|#define NOT_WELL_DEF_UNKN 2 ------------------ | Branch (2959:31): [True: 32, False: 0] ------------------ 2960| 32| ( parity == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ ( parity == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 2290| 0|#define NOT_WELL_DEF_UNDF 4 ------------------ | Branch (2960:25): [True: 0, False: 0] ------------------ 2961| 32| parity2 = ( parity12 == vABParityUnknown /*AB_PARITY_UNKN*/ ) ? NOT_WELL_DEF_UNKN : ------------------ | | 2289| 32|#define NOT_WELL_DEF_UNKN 2 ------------------ | Branch (2961:31): [True: 32, False: 0] ------------------ 2962| 32| ( parity12 == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ ( parity12 == AB_PARITY_UNDF ) ? NOT_WELL_DEF_UNDF : 0; ------------------ | | 2290| 0|#define NOT_WELL_DEF_UNDF 4 ------------------ | Branch (2962:25): [True: 0, False: 0] ------------------ 2963| 32| if (parity1 | parity2) ------------------ | Branch (2963:25): [True: 32, False: 0] ------------------ 2964| 32| { 2965| 32| not_well_def_parities |= ( parity1 | parity2 ); 2966| 32| k++; 2967| 32| } 2968| 0| else 2969| 0| { 2970| 0| return -1; /* program error */ 2971| 0| } 2972| |#else 2973| | return 0; 2974| |#endif 2975| 32| } 2976| 32| } 2977| 34| } 2978| 0| else 2979| 0| { 2980| | /*****************************************************************************************/ 2981| | /* i11-i12 and i21-i22 are same as i01-i02 bond/cumulene, nNeighMode == NEIGH_MODE_RING */ 2982| 0| AT_NUMB n1, n2; 2983| 0| int j; 2984| 0| if (!s1 || !s2) ------------------ | Branch (2984:17): [True: 0, False: 0] | Branch (2984:24): [True: 0, False: 0] ------------------ 2985| 0| { 2986| 0| return -1; 2987| 0| } 2988| | /* find neighbors along the stereo bond/cumulene */ 2989| 0| for (j = 0, n1 = MAX_ATOMS + 1; j < MAX_NUM_STEREO_BOND_NEIGH && at[i01].stereo_bond_neighbor[j]; j++) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ for (j = 0, n1 = MAX_ATOMS + 1; j < MAX_NUM_STEREO_BOND_NEIGH && at[i01].stereo_bond_neighbor[j]; j++) ------------------ | | 874| 0|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2989:45): [True: 0, False: 0] | Branch (2989:78): [True: 0, False: 0] ------------------ 2990| 0| { 2991| 0| if ((int) at[i01].stereo_bond_neighbor[j] == i02 + 1) ------------------ | Branch (2991:21): [True: 0, False: 0] ------------------ 2992| 0| { 2993| 0| n1 = at[i01].neighbor[(int) at[i01].stereo_bond_ord[j]]; 2994| 0| break; 2995| 0| } 2996| 0| } 2997| 0| for (j = 0, n2 = MAX_ATOMS + 1; j < MAX_NUM_STEREO_BOND_NEIGH && at[i02].stereo_bond_neighbor[j]; j++) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ for (j = 0, n2 = MAX_ATOMS + 1; j < MAX_NUM_STEREO_BOND_NEIGH && at[i02].stereo_bond_neighbor[j]; j++) ------------------ | | 874| 0|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2997:45): [True: 0, False: 0] | Branch (2997:78): [True: 0, False: 0] ------------------ 2998| 0| { 2999| 0| if ((int) at[i02].stereo_bond_neighbor[j] == i01 + 1) ------------------ | Branch (2999:21): [True: 0, False: 0] ------------------ 3000| 0| { 3001| 0| n2 = at[i02].neighbor[(int) at[i02].stereo_bond_ord[j]]; 3002| 0| break; 3003| 0| } 3004| 0| } 3005| 0| if (n1 > MAX_ATOMS || n2 > MAX_ATOMS) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ if (n1 > MAX_ATOMS || n2 > MAX_ATOMS) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ | Branch (3005:17): [True: 0, False: 0] | Branch (3005:35): [True: 0, False: 0] ------------------ 3006| 0| { 3007| 0| return CT_REMOVE_STEREO_ERR; ------------------ | | 33| 0|#define CT_REMOVE_STEREO_ERR (CT_ERR_FIRST-14) /*(-30014) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3008| 0| } 3009| | /* the parity of the new neighbors permutation must be same as the old one */ 3010| | /* this must work for well-defined and ill-defined parities. */ 3011| | /* actual parity (that includes the geometry) is not important here. */ 3012| | /* old permutation */ 3013| 0| parity = GetPermutationParity( pCG, at + i01, n1, nCanonRank ) + GetPermutationParity( pCG, at + i02, n2, nCanonRank ); 3014| | /* new parmutation */ 3015| 0| parity1 = GetPermutationParity( pCG, at + i01, n1, nVisited1 ) + GetPermutationParity( pCG, at + i02, n2, nVisited1 ); 3016| 0| parity2 = GetPermutationParity( pCG, at + i01, n1, nVisited2 ) + GetPermutationParity( pCG, at + i02, n2, nVisited2 ); 3017| 0| if (parity % 2 != parity1 % 2 || parity1 % 2 != parity2 % 2) ------------------ | Branch (3017:17): [True: 0, False: 0] | Branch (3017:46): [True: 0, False: 0] ------------------ 3018| 0| { 3019| 0| return 0; 3020| 0| } 3021| 0| k++; 3022| 0| } 3023| | 3024| | /* nNumComparedBonds += ( k > 0 ); */ 3025| 34| } 3026| | 3027| 504| if (nNumEqStereogenic > 0) ------------------ | Branch (3027:9): [True: 19, False: 485] ------------------ 3028| 19| { 3029| |/* case similar to trimethylcyclopropane: 3 constitutionally equivalent stereogenic elements */ 3030| |/* the transposition does not change the parities */ 3031| |#if ( bRELEASE_VERSION == 0 ) 3032| | pCS->bExtract |= EXTR_2EQL2CENTER_TO_REMOVE_PARITY; 3033| |#endif 3034| | 3035| 19| return 0; 3036| 19| } 3037| | 3038| | 3039| |/* ========================================================================================= 3040| | Note 3041| | ==== 3042| | At this point the comparison is complete and no difference sufficient to establish 3043| | absence of stereo parity has been found. 3044| | However, non-zero not_well_def_parities means that an ill-defined parity was 3045| | compared to an ill-defined or well-defined parity. This means that the parity 3046| | of the atom or bond being checked cannot be well-defined anymore. 3047| |========================================================================================*/ 3048| | 3049| | 3050| 485| not_well_def_parities |= COMP_STEREO_SUCCESS; ------------------ | | 2288| 485|#define COMP_STEREO_SUCCESS 1 ------------------ 3051| | 3052| 485| return not_well_def_parities; 3053| | 3054| | /* Add 1 to indicate success. The stereogenic elements might have been */ 3055| | /* removed while checking existence of the previous atom/bond stereo */ 3056| | /* return (nNumComparedCenters + nNumComparedBonds + 1); */ 3057| 504|} RemoveCalculatedNonStereoBondParities: 3083| 2.18k|{ 3084| 2.18k| int j, n, m, ret, ret1, ret2, ret_failed = 0; 3085| | 3086| 2.18k| int i1, n1, s2; /* n1 must be SIGNED integer */ 3087| 2.18k| AT_RANK nAtomRank1, nAtomRank2, neigh[3] = { 0 }, nAvoidCheckAtom[2], opposite_atom, nLength; /* djb-rwth: initialisation of neigh required to avoid undefined array subscript */ 3088| 2.18k| int nNeighMode = NEIGH_MODE_CHAIN; ------------------ | | 2283| 2.18k|#define NEIGH_MODE_CHAIN 2 ------------------ 3089| 2.18k| int nNumEqRingNeigh = 0, bRingNeigh, bSymmNeigh, bParitiesInverted; 3090| 2.18k| NEIGH_LIST *nl01, *nl02; 3091| 2.18k| const AT_RANK *nSymmRank1, *nSymmRank2; 3092| | 3093| 2.18k| ret = 0; 3094| | 3095| 2.19k|second_pass: 3096| | 3097| 15.0k| for (i1 = 0; i1 < num_atoms && !RETURNED_ERROR(ret_failed); i1++) ------------------ | | 44| 12.8k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 12.8k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 12.8k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 12.8k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 12.8k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 12.8k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 12.8k, False: 0] | | | Branch (44:53): [True: 0, False: 12.8k] | | ------------------ ------------------ | Branch (3097:18): [True: 12.8k, False: 2.19k] ------------------ 3098| 12.8k| { 3099| 12.8k| if (at[i1].valence != 3 || !at[i1].stereo_bond_neighbor[0]) ------------------ | Branch (3099:13): [True: 10.7k, False: 2.12k] | Branch (3099:36): [True: 2.00k, False: 124] ------------------ 3100| 12.7k| { 3101| 12.7k| continue; 3102| 12.7k| } 3103| 251| for (n1 = 0; n1 < MAX_NUM_STEREO_BONDS && !RETURNED_ERROR(ret_failed) && (s2 = at[i1].stereo_bond_neighbor[n1]); n1++) ------------------ | | 873| 502|#define MAX_NUM_STEREO_BONDS 3 ------------------ for (n1 = 0; n1 < MAX_NUM_STEREO_BONDS && !RETURNED_ERROR(ret_failed) && (s2 = at[i1].stereo_bond_neighbor[n1]); n1++) ------------------ | | 44| 502|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 251|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 251|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 251|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 251|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 251|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 251, False: 0] | | | Branch (44:53): [True: 0, False: 251] | | ------------------ ------------------ | Branch (3103:22): [True: 251, False: 0] | Branch (3103:82): [True: 127, False: 124] ------------------ 3104| 127| { 3105| 127| if (!PARITY_CALCULATE(at[i1].stereo_bond_parity[n1]) && PARITY_WELL_DEF(at[i1].stereo_bond_parity[n1])) ------------------ | | 267| 254|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 127|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 127|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 127|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ ------------------ if (!PARITY_CALCULATE(at[i1].stereo_bond_parity[n1]) && PARITY_WELL_DEF(at[i1].stereo_bond_parity[n1])) ------------------ | | 266| 104|#define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 104|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 208|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 104|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 262| 104|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 104|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 104|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (266:38): [True: 104, False: 0] | | | Branch (266:85): [True: 39, False: 65] | | ------------------ ------------------ | Branch (3105:17): [True: 104, False: 23] ------------------ 3106| 39| { 3107| 39| continue; 3108| 39| } 3109| 88| opposite_atom = (AT_RANK)(s2 - 1); 3110| 88| s2 = at[i1].neighbor[(int)at[i1].stereo_bond_ord[n1]]; /* different from opposite_atom in case of a cumulene */ 3111| 352| for (j = 1, n = 0; j <= (int)at[i1].valence; j++) ------------------ | Branch (3111:32): [True: 264, False: 88] ------------------ 3112| 264| { 3113| 264| if (nl[i1][j] != s2) ------------------ | Branch (3113:21): [True: 176, False: 88] ------------------ 3114| 176| { 3115| 176| neigh[n++] = nl[i1][j]; /* sorting guarantees that canon. rank of neigh[0] is greater or equal */ 3116| 176| } 3117| 264| } 3118| 88| if (n != 2) ------------------ | Branch (3118:17): [True: 0, False: 88] ------------------ 3119| 0| { 3120| 0| ret = CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3121| 0| goto exit_function; 3122| 0| } 3123| 88| if (nSymmRank[(int)neigh[0]] != nSymmRank[(int)neigh[1]]) ------------------ | Branch (3123:17): [True: 56, False: 32] ------------------ 3124| 56| { 3125| 56| continue; /* may happen if another half-bond has not a defined parity */ 3126| 56| } 3127| | 3128| 32| bRingNeigh = (at[(int)neigh[0]].nRingSystem == at[(int)neigh[1]].nRingSystem); 3129| 32| switch (nNeighMode) 3130| 32| { 3131| 18| case NEIGH_MODE_CHAIN: ------------------ | | 2283| 18|#define NEIGH_MODE_CHAIN 2 ------------------ | Branch (3131:13): [True: 18, False: 14] ------------------ 3132| 18| if (bRingNeigh) ------------------ | Branch (3132:21): [True: 18, False: 0] ------------------ 3133| 18| { 3134| 18| nNumEqRingNeigh++; 3135| 18| continue; 3136| 18| } 3137| 0| nl01 = nl; 3138| 0| nl02 = nl; 3139| 0| nSymmRank1 = nSymmRank; 3140| 0| nSymmRank2 = nSymmRank; 3141| 0| break; 3142| | 3143| 14| case NEIGH_MODE_RING: ------------------ | | 2282| 14|#define NEIGH_MODE_RING 1 ------------------ | Branch (3143:13): [True: 14, False: 18] ------------------ 3144| 14| if (!bRingNeigh) ------------------ | Branch (3144:21): [True: 0, False: 14] ------------------ 3145| 0| continue; 3146| | /* break a tie between the two contitutionally equivalent neighbors, */ 3147| | /* refine the two partitions, sort neighbors lists nl1, nl2 */ 3148| | 3149| 14| bSymmNeigh = BreakNeighborsTie(pCG, 3150| 14| at, num_atoms, num_at_tg, 3151| 14| opposite_atom, i1, 3152| 14| neigh, 0, 1, 0, 3153| 14| pRankStack1, pRankStack2, nTempRank, 3154| 14| NeighList, nSymmRank, nCanonRank, 3155| 14| nl1, nl2, &pCS->lNumNeighListIter); 3156| | 3157| 14| if (bSymmNeigh <= 0) ------------------ | Branch (3157:21): [True: 0, False: 14] ------------------ 3158| 0| { 3159| 0| if (ret_failed > bSymmNeigh) ------------------ | Branch (3159:25): [True: 0, False: 0] ------------------ 3160| 0| ret_failed = bSymmNeigh; 3161| 0| continue; 3162| 0| } 3163| 14| nl01 = nl1; 3164| 14| nl02 = nl2; 3165| 14| nSymmRank1 = pRankStack1[0]; 3166| 14| nSymmRank2 = pRankStack2[0]; 3167| 14| break; 3168| 0| default: ------------------ | Branch (3168:13): [True: 0, False: 32] ------------------ 3169| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3170| 32| } 3171| | 3172| | /* initialize arrays */ 3173| 14| memset(nVisited1, 0, sizeof(nVisited1[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3174| 14| memset(nVisited2, 0, sizeof(nVisited2[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3175| 14| memset(nAtomNumberCanon1, 0, sizeof(nAtomNumberCanon1[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3176| 14| memset(nAtomNumberCanon2, 0, sizeof(nAtomNumberCanon2[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3177| 14| nLength = 1; 3178| 14| nVisited1[i1] = i1 + 1; /* start atoms are the same */ 3179| 14| nVisited2[i1] = i1 + 1; 3180| 14| nAtomNumberCanon1[i1] = nLength; 3181| 14| nAtomNumberCanon2[i1] = nLength; 3182| 14| nAvoidCheckAtom[0] = i1; 3183| 14| nAvoidCheckAtom[1] = opposite_atom; 3184| 14| bParitiesInverted = (nNeighMode == NEIGH_MODE_RING && ------------------ | | 2282| 28|#define NEIGH_MODE_RING 1 ------------------ | Branch (3184:34): [True: 14, False: 0] ------------------ 3185| 14| IS_ALLENE_CHAIN(at[i1].stereo_bond_parity[n1]) && ------------------ | | 215| 28|#define IS_ALLENE_CHAIN(X) ((GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND)%2) | | ------------------ | | | | 213| 14|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 14|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define IS_ALLENE_CHAIN(X) ((GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND)%2) | | ------------------ | | | | 209| 14|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ | | | Branch (215:37): [True: 7, False: 7] | | ------------------ ------------------ 3186| 7| PARITY_CALCULATE(at[i1].stereo_bond_parity[n1]) && ------------------ | | 267| 21|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 7|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 7|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 7|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | | Branch (267:37): [True: 6, False: 1] | | ------------------ ------------------ 3187| 6| at[i1].nRingSystem == at[opposite_atom].nRingSystem && ------------------ | Branch (3187:17): [True: 0, False: 6] ------------------ 3188| 14| at[opposite_atom].valence == MAX_NUM_STEREO_BONDS) ? -1 : 0; ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3188:17): [True: 0, False: 0] ------------------ 3189| | /* djb-rwth: removing redundant code */ 3190| | 3191| | /* djb-rwth: restructuring code to avoid garbage values -- discussion required */ 3192| | 3193| 14| ret1 = CreateCheckSymmPaths(at, (AT_RANK)i1, neigh[0], (AT_RANK)i1, neigh[1], nAvoidCheckAtom, 3194| 14| nVisited1, nVisited2, nAtomNumberCanon1, nAtomNumberCanon2, 3195| 14| nl01, nl02, nSymmRank1, nSymmRank2, nCanonRank, &nLength, &bParitiesInverted, 0); 3196| 14| ret2 = CalculatedPathsParitiesAreIdentical(pCG, at, num_atoms, nSymmRank, 3197| 14| nCanonRank, nAtomNumberCanon, nAtomNumberCanon1, nAtomNumberCanon2, 3198| 14| nVisited1, nVisited2, opposite_atom, (AT_RANK)i1, 3199| 14| neigh[0], neigh[1], nNeighMode, bParitiesInverted, 0, 3200| 14| pCS, vABParityUnknown); 3201| | 3202| 14| if (0 < ret1) /* djb-rwth: or is this (0 < ret1) && (0 < ret2) ? */ ------------------ | Branch (3202:17): [True: 14, False: 0] ------------------ 3203| 14| { 3204| 14| if (0 < ret2) ------------------ | Branch (3204:21): [True: 14, False: 0] ------------------ 3205| 14| { 3206| 14| { 3207| 14| if (ret2 & (NOT_WELL_DEF_UNKN | NOT_WELL_DEF_UNDF)) ------------------ | | 2289| 14|#define NOT_WELL_DEF_UNKN 2 ------------------ if (ret2 & (NOT_WELL_DEF_UNKN | NOT_WELL_DEF_UNDF)) ------------------ | | 2290| 14|#define NOT_WELL_DEF_UNDF 4 ------------------ | Branch (3207:29): [True: 0, False: 14] ------------------ 3208| 0| { 3209| | /* possibly change the parity to unknown or undefined */ 3210| 0| int new_parity = (ret2 & NOT_WELL_DEF_UNKN) ? vABParityUnknown /*AB_PARITY_UNKN*/ : AB_PARITY_UNDF; ------------------ | | 2289| 0|#define NOT_WELL_DEF_UNKN 2 ------------------ int new_parity = (ret2 & NOT_WELL_DEF_UNKN) ? vABParityUnknown /*AB_PARITY_UNKN*/ : AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (3210:46): [True: 0, False: 0] ------------------ 3211| 0| if ((PARITY_ILL_DEF(at[i1].stereo_bond_parity[n1]) && PARITY_VAL(at[i1].stereo_bond_parity[n1]) > new_parity) || ------------------ | | 264| 0|#define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 239| 0|#define AB_MIN_ILL_DEFINED_PARITY 3 | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 240| 0|#define AB_MAX_ILL_DEFINED_PARITY 4 | | ------------------ | | | Branch (264:38): [True: 0, False: 0] | | | Branch (264:84): [True: 0, False: 0] | | ------------------ ------------------ if ((PARITY_ILL_DEF(at[i1].stereo_bond_parity[n1]) && PARITY_VAL(at[i1].stereo_bond_parity[n1]) > new_parity) || ------------------ | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ | Branch (3211:83): [True: 0, False: 0] ------------------ 3212| 0| PARITY_CALCULATE(at[i1].stereo_bond_parity[n1])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 267| 0|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 0|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 0|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 0|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | | Branch (267:37): [True: 0, False: 0] | | ------------------ ------------------ 3213| 0| { 3214| | /* set new unknown or undefined parity */ 3215| 0| SetOneStereoBondIllDefParity(at, i1, /* atom number*/ n1 /* stereo bond ord. number*/, new_parity); 3216| | /* change in pCS */ 3217| 0| nAtomRank1 = inchi_max(nCanonRank[i1], nCanonRank[opposite_atom]); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 3218| 0| nAtomRank2 = inchi_min(nCanonRank[i1], nCanonRank[opposite_atom]); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 3219| 0| for (n = 0, m = pCS->nLenLinearCTStereoDble - 1; n <= m; n++) ------------------ | Branch (3219:82): [True: 0, False: 0] ------------------ 3220| 0| { 3221| 0| if (pCS->LinearCTStereoDble[n].at_num1 == nAtomRank1 && ------------------ | Branch (3221:41): [True: 0, False: 0] ------------------ 3222| 0| pCS->LinearCTStereoDble[n].at_num2 == nAtomRank2) ------------------ | Branch (3222:41): [True: 0, False: 0] ------------------ 3223| 0| { 3224| 0| pCS->LinearCTStereoDble[n].parity = new_parity; 3225| |#if ( bRELEASE_VERSION == 0 ) 3226| | pCS->bExtract |= EXTR_CALC_USED_TO_REMOVE_PARITY; 3227| |#endif 3228| 0| m = -1; 3229| 0| break; 3230| 0| } 3231| 0| } 3232| 0| if (m >= 0) ------------------ | Branch (3232:37): [True: 0, False: 0] ------------------ 3233| 0| { 3234| 0| ret = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3235| 0| goto exit_function; 3236| 0| } 3237| 0| ret++; 3238| 0| } 3239| 0| } 3240| 14| else 3241| 14| { 3242| | /* remove the parity */ 3243| 14| if (!RemoveOneStereoBond(at, i1, /* atom number*/ n1 /* stereo bond ord. number*/)) ------------------ | Branch (3243:33): [True: 0, False: 14] ------------------ 3244| 0| { 3245| 0| ret = CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3246| 0| goto exit_function; 3247| 0| } 3248| 14| n1--; /* cycle counter may temporarily become negative */ 3249| | /* Remove from the pCS */ 3250| 14| nAtomRank1 = inchi_max(nCanonRank[i1], nCanonRank[opposite_atom]); ------------------ | | 138| 14|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 1, False: 13] | | ------------------ ------------------ 3251| 14| nAtomRank2 = inchi_min(nCanonRank[i1], nCanonRank[opposite_atom]); ------------------ | | 139| 14|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 13, False: 1] | | ------------------ ------------------ 3252| 14| for (n = 0, m = pCS->nLenLinearCTStereoDble - 1; n <= m; n++) ------------------ | Branch (3252:78): [True: 14, False: 0] ------------------ 3253| 14| { 3254| 14| if (pCS->LinearCTStereoDble[n].at_num1 == nAtomRank1 && ------------------ | Branch (3254:37): [True: 14, False: 0] ------------------ 3255| 14| pCS->LinearCTStereoDble[n].at_num2 == nAtomRank2) ------------------ | Branch (3255:37): [True: 14, False: 0] ------------------ 3256| 14| { 3257| 14| if (n < m) ------------------ | Branch (3257:41): [True: 0, False: 14] ------------------ 3258| 0| { 3259| | /* remove pCS->LinearCTStereoDble[n] */ 3260| 0| memmove(pCS->LinearCTStereoDble + n, 3261| 0| pCS->LinearCTStereoDble + n + 1, 3262| 0| ((long long)m - (long long)n) * sizeof(pCS->LinearCTStereoDble[0])); /* djb-rwth: cast operators added */ 3263| 0| } 3264| 14| pCS->nLenLinearCTStereoDble--; 3265| |#if ( bRELEASE_VERSION == 0 ) 3266| | pCS->bExtract |= EXTR_CALC_USED_TO_REMOVE_PARITY; 3267| |#endif 3268| 14| m = -1; 3269| 14| break; 3270| 14| } 3271| 14| } 3272| 14| if (m >= 0) ------------------ | Branch (3272:33): [True: 0, False: 14] ------------------ 3273| 0| { 3274| 0| ret = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3275| 0| goto exit_function; 3276| 0| } 3277| 14| ret++; 3278| 14| } 3279| 14| } 3280| 14| } 3281| 0| else 3282| 0| { 3283| 0| if (!ret_failed) ------------------ | Branch (3283:25): [True: 0, False: 0] ------------------ 3284| 0| { 3285| 0| ret_failed = (ret1 < 0) ? ret1 : (ret2 < 0) ? ret2 : 0; ------------------ | Branch (3285:38): [True: 0, False: 0] | Branch (3285:58): [True: 0, False: 0] ------------------ 3286| 0| } 3287| 0| if (!RETURNED_ERROR(ret_failed)) ------------------ | | 44| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 0, False: 0] | | | Branch (44:53): [True: 0, False: 0] | | ------------------ ------------------ 3288| 0| { 3289| 0| if (RETURNED_ERROR(ret1)) ------------------ | | 44| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 0, False: 0] | | | Branch (44:53): [True: 0, False: 0] | | ------------------ ------------------ 3290| 0| { 3291| 0| ret_failed = ret1; 3292| 0| } 3293| 0| else 3294| 0| { 3295| 0| if (RETURNED_ERROR(ret2)) ------------------ | | 44| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 0, False: 0] | | | Branch (44:53): [True: 0, False: 0] | | ------------------ ------------------ 3296| 0| { 3297| 0| ret_failed = ret2; 3298| 0| } 3299| 0| } 3300| 0| } 3301| 0| } 3302| 14| } 3303| 14| } 3304| 124| } 3305| | 3306| 2.19k| if (nNeighMode == NEIGH_MODE_CHAIN && nNumEqRingNeigh && !RETURNED_ERROR( ret_failed )) ------------------ | | 2283| 4.39k|#define NEIGH_MODE_CHAIN 2 ------------------ if (nNeighMode == NEIGH_MODE_CHAIN && nNumEqRingNeigh && !RETURNED_ERROR( ret_failed )) ------------------ | | 44| 14|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 14|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 14|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 14|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 14|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 14|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 14, False: 0] | | | Branch (44:53): [True: 0, False: 14] | | ------------------ ------------------ | Branch (3306:9): [True: 2.18k, False: 14] | Branch (3306:43): [True: 14, False: 2.16k] ------------------ 3307| 14| { 3308| 14| nNeighMode = NEIGH_MODE_RING; ------------------ | | 2282| 14|#define NEIGH_MODE_RING 1 ------------------ 3309| 14| goto second_pass; 3310| 14| } 3311| | 3312| 2.18k|exit_function: 3313| | 3314| 2.18k| return RETURNED_ERROR( ret_failed ) ? ret_failed : ret_failed ? -( ret_failed + 1 ) : ret; ------------------ | | 44| 2.18k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.18k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.18k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.18k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.18k, False: 0] | | | Branch (44:53): [True: 0, False: 2.18k] | | ------------------ ------------------ | Branch (3314:56): [True: 0, False: 2.18k] ------------------ 3315| 2.19k|} RemoveCalculatedNonStereoCenterParities: 3341| 2.18k|{ 3342| 2.18k| int j, n, m, ret; 3343| | 3344| 2.18k| int i, k, ret1, ret2, ret_failed = 0, mode, max_mode; 3345| 2.18k| AT_RANK nAtomRank1, neigh[MAX_NUM_STEREO_ATOM_NEIGH] = { 0 }, nAvoidCheckAtom[2], nLength; /* djb-rwth: initialisation of neigh required to avoid undefined array subscript */ 3346| 2.18k| int nNeighMode = NEIGH_MODE_CHAIN; ------------------ | | 2283| 2.18k|#define NEIGH_MODE_CHAIN 2 ------------------ 3347| 2.18k| int nNumEqRingNeigh = 0, bRingNeigh, bSymmNeigh, bParitiesInverted; 3348| 2.18k| NEIGH_LIST *nl01, *nl02; 3349| 2.18k| const AT_RANK *nSymmRank1, *nSymmRank2; 3350| | 3351| 2.18k| ret = 0; 3352| | 3353| 3.29k|second_pass: 3354| | 3355| 22.1k| for (i = 0; i < num_atoms && !RETURNED_ERROR( ret_failed ); i++) ------------------ | | 44| 18.8k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 18.8k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 18.8k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 18.8k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 18.8k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 18.8k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 18.8k, False: 0] | | | Branch (44:53): [True: 0, False: 18.8k] | | ------------------ ------------------ | Branch (3355:17): [True: 18.8k, False: 3.29k] ------------------ 3356| 18.8k| { 3357| 18.8k| if (!at[i].parity || at[i].stereo_bond_neighbor[0]) ------------------ | Branch (3357:13): [True: 8.50k, False: 10.3k] | Branch (3357:30): [True: 2.03k, False: 8.34k] ------------------ 3358| 10.5k| { 3359| 10.5k| continue; 3360| 10.5k| } 3361| | 3362| 8.34k| if (at[i].valence > MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 8.34k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3362:13): [True: 0, False: 8.34k] ------------------ 3363| 0| { 3364| 0| continue; /* error: stereo center cannot have more than 4 neighbors */ /* */ 3365| 0| } 3366| | 3367| | /* at[i1] is a stereo center */ 3368| 8.34k| if (!PARITY_CALCULATE( at[i].stereo_atom_parity ) && !PARITY_ILL_DEF( at[i].stereo_atom_parity )) ------------------ | | 267| 16.6k|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 8.34k|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 8.34k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 8.34k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ ------------------ if (!PARITY_CALCULATE( at[i].stereo_atom_parity ) && !PARITY_ILL_DEF( at[i].stereo_atom_parity )) ------------------ | | 264| 5.61k|#define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 239| 5.61k|#define AB_MIN_ILL_DEFINED_PARITY 3 | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 262| 11.2k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 5.61k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 262| 5.11k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 5.11k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 240| 5.11k|#define AB_MAX_ILL_DEFINED_PARITY 4 | | ------------------ | | | Branch (264:38): [True: 5.11k, False: 505] | | | Branch (264:84): [True: 5.11k, False: 0] | | ------------------ ------------------ | Branch (3368:13): [True: 5.61k, False: 2.72k] ------------------ 3369| 505| { 3370| 505| continue; 3371| 505| } 3372| | 3373| | /* neighbors sorted according to symm. ranks (primary key) and canon. ranks (secondary key), in descending order */ 3374| | /* sorting guarantees that for two constit. equ. neighbors canon. ranks of the first is greater */ 3375| | /* !!! previously (but not anymore) the canon. rank of neigh[0] was greater than the others !!! */ 3376| 37.7k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (3376:21): [True: 29.9k, False: 7.83k] ------------------ 3377| 29.9k| { 3378| 29.9k| neigh[j] = nl[i][j + 1]; /* sorting does NOT guarantee that canon. rank of neigh[0] is greater than others */ 3379| 29.9k| } 3380| | 3381| | /* 3382| | * mode = 0 => Standard approach: switch 2 neighbors 3383| | * 1 => Check for C2v reflection leading to parity inversion 3384| | * 2 => Check for C2 rotation preserving parities 3385| | * 3 => Check for S4 rotation/reflection leading to parity inversion 3386| | */ 3387| | 3388| |#if ( CHECK_C2v_S4_SYMM == 1 ) 3389| | if (nNeighMode = NEIGH_MODE_RING && at[i].valence == 4 && 3390| | nSymmRank[(int) neigh[0]] == nSymmRank[(int) neigh[1]] && 3391| | nSymmRank[(int) neigh[2]] == nSymmRank[(int) neigh[3]] && 3392| | !at[i].bCutVertex 3393| | ) 3394| | { 3395| | if (nSymmRank[(int) neigh[1]] == nSymmRank[(int) neigh[2]]) 3396| | { 3397| | max_mode = MAP_MODE_S4; 3398| | } 3399| | else 3400| | { 3401| | max_mode = inchi_max( MAP_MODE_C2v, MAP_MODE_C2 ); 3402| | } 3403| | } 3404| | else 3405| | { 3406| | max_mode = MAP_MODE_STD; 3407| | } 3408| |#else 3409| 7.83k| max_mode = MAP_MODE_STD; ------------------ | | 14| 7.83k|#define MAP_MODE_STD 0 /* Standard approach: switch 2 neighbors */ ------------------ 3410| 7.83k|#endif 3411| | 3412| 37.6k| for (j = 0; j < at[i].valence && at[i].parity && !RETURNED_ERROR( ret_failed ); j++) ------------------ | | 44| 29.7k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 29.7k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 29.7k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 29.7k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 29.7k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 29.7k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 29.7k, False: 0] | | | Branch (44:53): [True: 0, False: 29.7k] | | ------------------ ------------------ | Branch (3412:21): [True: 29.8k, False: 7.75k] | Branch (3412:42): [True: 29.7k, False: 89] ------------------ 3413| 29.7k| { 3414| 72.4k| for (k = j + 1; k < at[i].valence && at[i].parity && !RETURNED_ERROR( ret_failed ); k++) ------------------ | | 44| 42.6k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 42.6k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 42.6k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 42.6k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 42.6k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 42.6k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 42.6k, False: 0] | | | Branch (44:53): [True: 0, False: 42.6k] | | ------------------ ------------------ | Branch (3414:29): [True: 42.7k, False: 29.7k] | Branch (3414:50): [True: 42.6k, False: 43] ------------------ 3415| 42.6k| { 3416| 85.3k| for (mode = 0; mode <= max_mode && at[i].parity && !RETURNED_ERROR(ret_failed); mode++) ------------------ | | 44| 42.6k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 42.6k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 42.6k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 42.6k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 42.6k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 42.6k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 42.6k, False: 0] | | | Branch (44:53): [True: 0, False: 42.6k] | | ------------------ ------------------ | Branch (3416:32): [True: 42.6k, False: 42.6k] | Branch (3416:52): [True: 42.6k, False: 0] ------------------ 3417| 42.6k| { 3418| 42.6k| if (nSymmRank[(int)neigh[j]] != nSymmRank[(int)neigh[k]]) ------------------ | Branch (3418:25): [True: 23.1k, False: 19.5k] ------------------ 3419| 23.1k| { 3420| 23.1k| continue; /* the two neighbors are not constitutionally identical */ 3421| 23.1k| } 3422| 19.5k| bRingNeigh = (at[(int)neigh[j]].nRingSystem == at[(int)neigh[k]].nRingSystem); 3423| 19.5k| switch (nNeighMode) 3424| 19.5k| { 3425| 9.79k| case NEIGH_MODE_CHAIN: ------------------ | | 2283| 9.79k|#define NEIGH_MODE_CHAIN 2 ------------------ | Branch (3425:21): [True: 9.79k, False: 9.71k] ------------------ 3426| 9.79k| if (bRingNeigh) ------------------ | Branch (3426:29): [True: 9.79k, False: 0] ------------------ 3427| 9.79k| { 3428| 9.79k| nNumEqRingNeigh++; 3429| 9.79k| continue; 3430| 9.79k| } 3431| 0| nl01 = nl; 3432| 0| nl02 = nl; 3433| 0| nSymmRank1 = nSymmRank; 3434| 0| nSymmRank2 = nSymmRank; 3435| 0| break; 3436| 9.71k| case NEIGH_MODE_RING: ------------------ | | 2282| 9.71k|#define NEIGH_MODE_RING 1 ------------------ | Branch (3436:21): [True: 9.71k, False: 9.79k] ------------------ 3437| 9.71k| if (!bRingNeigh) ------------------ | Branch (3437:29): [True: 0, False: 9.71k] ------------------ 3438| 0| continue; 3439| | /* break a tie between the two contitutionally equivalent neighbors, */ 3440| | /* refine the two partitions, sort neighbors lists nl1, nl2 */ 3441| 9.71k| bSymmNeigh = BreakNeighborsTie(pCG, at, num_atoms, num_at_tg, MAX_ATOMS + 1, i, ------------------ | | 15| 9.71k|#define MAX_ATOMS 32766 ------------------ 3442| 9.71k| neigh, j, k, mode, 3443| 9.71k| pRankStack1, pRankStack2, nTempRank, NeighList, nSymmRank, nCanonRank, 3444| 9.71k| nl1, nl2, &pCS->lNumNeighListIter); 3445| 9.71k| if (bSymmNeigh <= 0) ------------------ | Branch (3445:29): [True: 127, False: 9.59k] ------------------ 3446| 127| { 3447| 127| if (ret_failed > bSymmNeigh) ------------------ | Branch (3447:33): [True: 0, False: 127] ------------------ 3448| 0| ret_failed = bSymmNeigh; 3449| 127| continue; 3450| 127| } 3451| 9.59k| nl01 = nl1; 3452| 9.59k| nl02 = nl2; 3453| 9.59k| nSymmRank1 = pRankStack1[0]; 3454| 9.59k| nSymmRank2 = pRankStack2[0]; 3455| 9.59k| break; 3456| 0| default: ------------------ | Branch (3456:21): [True: 0, False: 19.5k] ------------------ 3457| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3458| 19.5k| } 3459| | 3460| | /* initialize arrays */ 3461| 9.59k| memset(nVisited1, 0, sizeof(nVisited1[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3462| 9.59k| memset(nVisited2, 0, sizeof(nVisited2[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3463| 9.59k| memset(nAtomNumberCanon1, 0, sizeof(nAtomNumberCanon1[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3464| 9.59k| memset(nAtomNumberCanon2, 0, sizeof(nAtomNumberCanon2[0]) * num_atoms); /* djb-rwth: memset_s C11/Annex K variant? */ 3465| 9.59k| nLength = 1; 3466| 9.59k| nVisited1[i] = i + 1; /* start atom is same */ 3467| 9.59k| nVisited2[i] = i + 1; 3468| 9.59k| nAtomNumberCanon1[i] = nLength; 3469| 9.59k| nAtomNumberCanon2[i] = nLength; 3470| 9.59k| nAvoidCheckAtom[0] = i; 3471| 9.59k| nAvoidCheckAtom[1] = MAX_ATOMS + 1; ------------------ | | 15| 9.59k|#define MAX_ATOMS 32766 ------------------ 3472| | 3473| 9.59k| bParitiesInverted = (mode == MAP_MODE_C2v || mode == MAP_MODE_S4) ? -1 : 0; ------------------ | | 15| 19.1k|#define MAP_MODE_C2v 1 /* Check for C2v reflection leading to parity inversion */ ------------------ bParitiesInverted = (mode == MAP_MODE_C2v || mode == MAP_MODE_S4) ? -1 : 0; ------------------ | | 17| 9.59k|#define MAP_MODE_S4 3 /* Check for S4 rotation/reflection leading to parity inversion */ ------------------ | Branch (3473:42): [True: 0, False: 9.59k] | Branch (3473:66): [True: 0, False: 9.59k] ------------------ 3474| | 3475| | /* 3476| | if (nNeighMode==NEIGH_MODE_RING && at[i].valence==MAX_NUM_STEREO_ATOM_NEIGH) { 3477| | AT_RANK other_neigh[2]; 3478| | int n; 3479| | for ( m = n = 0; m < MAX_NUM_STEREO_ATOM_NEIGH; m ++ ) { 3480| | if ( at[i].neighbor[m] != neigh[j] && at[i].neighbor[m] != neigh[k] ) 3481| | other_neigh[n++] = at[i].neighbor[m]; 3482| | } 3483| | if ( nSymmRank[(int)other_neigh[0]] == nSymmRank[(int)other_neigh[1]] ) 3484| | bParitiesInverted = -1; 3485| | } 3486| | */ 3487| | 3488| | /* allow matching inverted centers only in case all equivalent neighbors in same ring system */ 3489| | 3490| | /* djb-rwth: restructuring code to avoid undefined array subscripts; removing unnecessary code; discussion required */ 3491| | 3492| 9.59k| ret1 = CreateCheckSymmPaths(at, (AT_RANK)i, neigh[j], (AT_RANK)i, neigh[k], nAvoidCheckAtom, 3493| 9.59k| nVisited1, nVisited2, nAtomNumberCanon1, nAtomNumberCanon2, 3494| 9.59k| nl01, nl02, nSymmRank1, nSymmRank2, nCanonRank, &nLength, 3495| 9.59k| &bParitiesInverted, mode); 3496| 9.59k| ret2 = CalculatedPathsParitiesAreIdentical(pCG, at, num_atoms, nSymmRank, 3497| 9.59k| nCanonRank, nAtomNumberCanon, nAtomNumberCanon1, nAtomNumberCanon2, 3498| 9.59k| nVisited1, nVisited2, (AT_RANK)MAX_ATOMS, (AT_RANK)i, ------------------ | | 15| 9.59k|#define MAX_ATOMS 32766 ------------------ 3499| 9.59k| neigh[j], neigh[k], nNeighMode, 3500| 9.59k| bParitiesInverted, mode, pCS, vABParityUnknown); 3501| | 3502| 9.59k| if (0 < ret1) /* djb-rwth: or is this (0 < ret1) && (0 < ret2) ? */ ------------------ | Branch (3502:25): [True: 6.56k, False: 3.02k] ------------------ 3503| 6.56k| { 3504| 6.56k| if (0 < ret2) ------------------ | Branch (3504:29): [True: 468, False: 6.09k] ------------------ 3505| 468| { 3506| 468| { 3507| 468| if (ret2 & (NOT_WELL_DEF_UNKN | NOT_WELL_DEF_UNDF)) ------------------ | | 2289| 468|#define NOT_WELL_DEF_UNKN 2 ------------------ if (ret2 & (NOT_WELL_DEF_UNKN | NOT_WELL_DEF_UNDF)) ------------------ | | 2290| 468|#define NOT_WELL_DEF_UNDF 4 ------------------ | Branch (3507:37): [True: 379, False: 89] ------------------ 3508| 379| { 3509| | /* possibly change the parity to unknown or undefined */ 3510| 379| int new_parity = (ret2 & NOT_WELL_DEF_UNKN) ? vABParityUnknown /*AB_PARITY_UNKN*/ : AB_PARITY_UNDF; ------------------ | | 2289| 379|#define NOT_WELL_DEF_UNKN 2 ------------------ int new_parity = (ret2 & NOT_WELL_DEF_UNKN) ? vABParityUnknown /*AB_PARITY_UNKN*/ : AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (3510:54): [True: 379, False: 0] ------------------ 3511| 379| if ((PARITY_ILL_DEF(at[i].stereo_atom_parity) && ------------------ | | 264| 758|#define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 239| 379|#define AB_MIN_ILL_DEFINED_PARITY 3 | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 262| 758|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 379|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 262| 379|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 379|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 240| 379|#define AB_MAX_ILL_DEFINED_PARITY 4 | | ------------------ | | | Branch (264:38): [True: 379, False: 0] | | | Branch (264:84): [True: 303, False: 76] | | ------------------ ------------------ 3512| 303| PARITY_VAL(at[i].stereo_atom_parity) > new_parity) || ------------------ | | 262| 303|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 303|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ | Branch (3512:41): [True: 0, False: 303] ------------------ 3513| 379| PARITY_CALCULATE(at[i].stereo_atom_parity)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 267| 379|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 379|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 379|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 379|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | | Branch (267:37): [True: 76, False: 303] | | ------------------ ------------------ 3514| 76| { 3515| | /* set new unknown or undefined parity */ 3516| 76| at[i].stereo_atom_parity = (at[i].stereo_atom_parity ^ PARITY_VAL(at[i].stereo_atom_parity)) | PARITY_VAL(new_parity); ------------------ | | 262| 76|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 76|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ at[i].stereo_atom_parity = (at[i].stereo_atom_parity ^ PARITY_VAL(at[i].stereo_atom_parity)) | PARITY_VAL(new_parity); ------------------ | | 262| 76|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 76|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 3517| 76| at[i].parity = PARITY_VAL(new_parity); ------------------ | | 262| 76|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 76|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 3518| | /* Remove from pCS */ 3519| 76| nAtomRank1 = nCanonRank[i]; 3520| 151| for (n = 0, m = pCS->nLenLinearCTStereoCarb - 1; n <= m; n++) ------------------ | Branch (3520:90): [True: 151, False: 0] ------------------ 3521| 151| { 3522| 151| if (pCS->LinearCTStereoCarb[n].at_num == nAtomRank1) ------------------ | Branch (3522:49): [True: 76, False: 75] ------------------ 3523| 76| { 3524| 76| pCS->LinearCTStereoCarb[n].parity = PARITY_VAL(new_parity); ------------------ | | 262| 76|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 76|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 3525| |#if ( bRELEASE_VERSION == 0 ) 3526| | pCS->bExtract |= EXTR_CALC_USED_TO_REMOVE_PARITY; 3527| |#endif 3528| 76| m = -1; 3529| 76| break; 3530| 76| } 3531| 151| } 3532| 76| if (m >= 0) ------------------ | Branch (3532:45): [True: 0, False: 76] ------------------ 3533| 0| { 3534| 0| ret = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3535| 0| goto exit_function; 3536| 0| } 3537| 76| ret++; /* number of removed or set unknown/undefined parities */ 3538| 76| } 3539| 379| } 3540| 89| else 3541| 89| { 3542| 89|#ifdef FIX_STEREOCOUNT_ERR 3543| 89| if (at[i].stereo_atom_parity & KNOWN_PARITIES_EQL) ------------------ | | 206| 89|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ | Branch (3543:41): [True: 44, False: 45] ------------------ 3544| 44| { 3545| 44| int jj; 3546| 44| AT_RANK EqRank = pCS->nSymmRank[i]; 3547| 268| for (jj = 0; jj < num_atoms; jj++) ------------------ | Branch (3547:54): [True: 224, False: 44] ------------------ 3548| 224| { 3549| 224| if (pCS->nSymmRank[jj] == EqRank) ------------------ | Branch (3549:49): [True: 46, False: 178] ------------------ 3550| 46| { 3551| 46| at[jj].stereo_atom_parity &= ~KNOWN_PARITIES_EQL; ------------------ | | 206| 46|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ 3552| 46| } 3553| 224| } 3554| 44| } 3555| 89|#endif 3556| 89| RemoveOneStereoCenter(at, i /* atom number*/); 3557| | /* Remove from pCS */ 3558| 89| nAtomRank1 = nCanonRank[i]; 3559| 101| for (n = 0, m = pCS->nLenLinearCTStereoCarb - 1; n <= m; n++) ------------------ | Branch (3559:86): [True: 101, False: 0] ------------------ 3560| 101| { 3561| 101| if (pCS->LinearCTStereoCarb[n].at_num == nAtomRank1) ------------------ | Branch (3561:45): [True: 89, False: 12] ------------------ 3562| 89| { 3563| 89| if (n < m) ------------------ | Branch (3563:49): [True: 4, False: 85] ------------------ 3564| 4| { 3565| | /* remove pCS->LinearCTStereoDble[n] */ 3566| 4| memmove(pCS->LinearCTStereoCarb + n, 3567| 4| pCS->LinearCTStereoCarb + n + 1, 3568| 4| ((long long)m - (long long)n) * sizeof(pCS->LinearCTStereoCarb[0])); /* djb-rwth: cast operators added */ 3569| 4| } 3570| 89| pCS->nLenLinearCTStereoCarb--; 3571| |#if ( bRELEASE_VERSION == 0 ) 3572| | pCS->bExtract |= EXTR_CALC_USED_TO_REMOVE_PARITY; 3573| |#endif 3574| 89| m = -1; 3575| 89| break; 3576| 89| } 3577| 101| } 3578| 89| if (m >= 0) ------------------ | Branch (3578:41): [True: 0, False: 89] ------------------ 3579| 0| { 3580| 0| ret = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3581| 0| goto exit_function; 3582| 0| } 3583| 89| ret++; /* number of removed or set unknown/undefined parities */ 3584| 89| } 3585| 468| } 3586| 468| } 3587| 6.09k| else 3588| 6.09k| { 3589| 6.09k| if (!ret_failed) ------------------ | Branch (3589:33): [True: 5.70k, False: 396] ------------------ 3590| 5.70k| { 3591| 5.70k| if (ret1 < 0) ------------------ | Branch (3591:37): [True: 0, False: 5.70k] ------------------ 3592| 0| { 3593| 0| ret_failed = ret1; 3594| 0| } 3595| 5.70k| else 3596| 5.70k| { 3597| 5.70k| if (ret2 < 0) ------------------ | Branch (3597:41): [True: 78, False: 5.62k] ------------------ 3598| 78| { 3599| 78| ret_failed = ret2; 3600| 78| } 3601| 5.70k| } 3602| 5.70k| } 3603| 6.09k| if (!RETURNED_ERROR(ret_failed)) ------------------ | | 44| 6.09k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 6.09k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 6.09k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 6.09k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 6.09k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 6.09k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 6.09k, False: 0] | | | Branch (44:53): [True: 0, False: 6.09k] | | ------------------ ------------------ 3604| 6.09k| { 3605| 6.09k| if (RETURNED_ERROR(ret1)) ------------------ | | 44| 6.09k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 6.09k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 6.09k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 6.09k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 6.09k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 6.09k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 6.09k, False: 0] | | | Branch (44:53): [True: 0, False: 6.09k] | | ------------------ ------------------ 3606| 0| { 3607| 0| ret_failed = ret1; 3608| 0| } 3609| 6.09k| else 3610| 6.09k| { 3611| 6.09k| if (RETURNED_ERROR(ret2)) ------------------ | | 44| 6.09k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 6.09k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 6.09k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 6.09k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 6.09k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 6.09k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 6.09k, False: 0] | | | Branch (44:53): [True: 0, False: 6.09k] | | ------------------ ------------------ 3612| 0| { 3613| 0| ret_failed = ret2; 3614| 0| } 3615| 6.09k| } 3616| 6.09k| } 3617| 6.09k| } 3618| 6.56k| } 3619| 9.59k| } 3620| 42.6k| } 3621| 29.7k| } 3622| 7.83k| } 3623| | 3624| 3.29k| if (nNeighMode == NEIGH_MODE_CHAIN && nNumEqRingNeigh && !RETURNED_ERROR( ret_failed )) ------------------ | | 2283| 6.58k|#define NEIGH_MODE_CHAIN 2 ------------------ if (nNeighMode == NEIGH_MODE_CHAIN && nNumEqRingNeigh && !RETURNED_ERROR( ret_failed )) ------------------ | | 44| 1.11k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 1.11k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 1.11k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 1.11k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 1.11k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 1.11k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 1.11k, False: 0] | | | Branch (44:53): [True: 0, False: 1.11k] | | ------------------ ------------------ | Branch (3624:9): [True: 2.18k, False: 1.11k] | Branch (3624:43): [True: 1.11k, False: 1.07k] ------------------ 3625| 1.11k| { 3626| 1.11k| nNeighMode = NEIGH_MODE_RING; ------------------ | | 2282| 1.11k|#define NEIGH_MODE_RING 1 ------------------ 3627| 1.11k| goto second_pass; 3628| 1.11k| } 3629| | 3630| 2.18k|exit_function: 3631| | 3632| 2.18k| return RETURNED_ERROR( ret_failed ) ? ret_failed : ret_failed ? -( ret + 1 ) : ret; ------------------ | | 44| 2.18k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.18k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.18k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.18k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.18k, False: 0] | | | Branch (44:53): [True: 0, False: 2.18k] | | ------------------ ------------------ | Branch (3632:56): [True: 78, False: 2.10k] ------------------ 3633| 3.29k|} RemoveCalculatedNonStereo: 3650| 2.01k|{ 3651| 2.01k| NEIGH_LIST *nl = NULL, *nl1 = NULL, *nl2 = NULL; 3652| 2.01k| AT_RANK *nVisited1 = NULL, *nVisited2 = NULL, *nAtomNumberCanon1 = NULL, *nAtomNumberCanon2 = NULL; 3653| 2.01k| int nNumRemoved = 0, nTotRemoved = 0, ret = 0, ret1 = 0, ret2 = 0; 3654| | 3655| 2.01k| if (!AllocateForNonStereoRemoval( at, num_atoms, nSymmRank, nCanonRank, ------------------ | Branch (3655:9): [True: 0, False: 2.01k] ------------------ 3656| 2.01k| &nAtomNumberCanon1, &nAtomNumberCanon2, 3657| 2.01k| &nl, &nl1, &nl2, &nVisited1, &nVisited2 )) 3658| 0| { 3659| 0| return CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3660| 0| } 3661| | 3662| 2.01k| do 3663| 2.18k| { 3664| 2.18k| nNumRemoved = 0; 3665| | /* bonds */ 3666| 2.18k| ret = RemoveCalculatedNonStereoBondParities( pCG, at, num_atoms, num_at_tg, 3667| 2.18k| pRankStack1, pRankStack2, nTempRank, NeighList, 3668| 2.18k| nCanonRank, nSymmRank, 3669| 2.18k| nAtomNumberCanon, nAtomNumberCanon1, nAtomNumberCanon2, 3670| 2.18k| nl, nl1, nl2, nVisited1, nVisited2, pCS, 3671| 2.18k| vABParityUnknown ); 3672| 2.18k| if (RETURNED_ERROR( ret )) ------------------ | | 44| 2.18k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.18k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.18k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.18k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.18k, False: 0] | | | Branch (44:53): [True: 0, False: 2.18k] | | ------------------ ------------------ 3673| 0| { 3674| 0| goto exit_function; 3675| 0| } 3676| 2.18k| if (ret < 0) ------------------ | Branch (3676:13): [True: 0, False: 2.18k] ------------------ 3677| 0| { 3678| 0| if (ret < ret1) ------------------ | Branch (3678:17): [True: 0, False: 0] ------------------ 3679| 0| { /* */ 3680| 0| ret1 = ret; 3681| 0| } 3682| 0| ret = -( ret + 1 ); /* number of removed */ 3683| 0| } 3684| 2.18k| nNumRemoved += ret; 3685| | 3686| | /* centers */ 3687| 2.18k| ret = RemoveCalculatedNonStereoCenterParities( pCG, at, num_atoms, num_at_tg, 3688| 2.18k| pRankStack1, pRankStack2, nTempRank, NeighList, 3689| 2.18k| nCanonRank, nSymmRank, 3690| 2.18k| nAtomNumberCanon, nAtomNumberCanon1, nAtomNumberCanon2, 3691| 2.18k| nl, nl1, nl2, nVisited1, nVisited2, pCS, 3692| 2.18k| vABParityUnknown ); 3693| 2.18k| if (RETURNED_ERROR( ret )) ------------------ | | 44| 2.18k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.18k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.18k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.18k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.18k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.18k, False: 0] | | | Branch (44:53): [True: 0, False: 2.18k] | | ------------------ ------------------ 3694| 0| { 3695| 0| goto exit_function; 3696| 0| } 3697| 2.18k| if (ret < 0) ------------------ | Branch (3697:13): [True: 78, False: 2.10k] ------------------ 3698| 78| { 3699| 78| if (ret < ret2) ------------------ | Branch (3699:17): [True: 78, False: 0] ------------------ 3700| 78| { /* */ 3701| 78| ret2 = ret; 3702| 78| } 3703| 78| ret = -( ret + 1 ); /* number of removed */ 3704| 78| } 3705| 2.18k| nNumRemoved += ret; 3706| | 3707| 2.18k| nTotRemoved += nNumRemoved; 3708| 2.18k| } 3709| 2.18k| while (nNumRemoved); ------------------ | Branch (3709:12): [True: 171, False: 2.01k] ------------------ 3710| | 3711| 2.01k| if (!RETURNED_ERROR( ret1 ) && !RETURNED_ERROR( ret2 )) ------------------ | | 44| 4.02k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.01k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.01k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.01k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.01k, False: 0] | | | Branch (44:53): [True: 0, False: 2.01k] | | ------------------ ------------------ if (!RETURNED_ERROR( ret1 ) && !RETURNED_ERROR( ret2 )) ------------------ | | 44| 2.01k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.01k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.01k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.01k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.01k, False: 0] | | | Branch (44:53): [True: 0, False: 2.01k] | | ------------------ ------------------ 3712| 2.01k| { 3713| 2.01k| ret = inchi_min( ret1, ret2 ); ------------------ | | 139| 2.01k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 2.01k] | | ------------------ ------------------ 3714| 2.01k| ret = ( ret >= 0 ) ? nTotRemoved : -( 1 + nTotRemoved ); ------------------ | Branch (3714:15): [True: 1.93k, False: 78] ------------------ 3715| 2.01k| } 3716| | 3717| 2.01k|exit_function: 3718| | 3719| 2.01k| DeAllocateForNonStereoRemoval( &nAtomNumberCanon1, &nAtomNumberCanon2, &nl, &nl1, &nl2, &nVisited1, &nVisited2 ); 3720| | 3721| 2.01k| return ret; 3722| 2.01k|} map_stereo_bonds4: 69| 4.03k|{ 70| 4.03k| int nTotSuccess = 0; /* 1=>full mapping has been completed; 71| | * 2=>obtained a better stereo; 72| | * 4=>restart (stereo bond or atom removed from the stereo CT) 73| | */ 74| 4.03k| int tpos1 = 0; 75| 4.03k| AT_STEREO_DBLE prevBond; 76| 4.03k| memset( &prevBond, 0, sizeof( prevBond ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 77| 4.03k| tpos1 = CurTreeGetPos( cur_tree ); 78| | 79| 4.20k|total_restart: 80| | 81| 4.20k| if (!nNumMappedBonds) ------------------ | Branch (81:9): [True: 1.73k, False: 2.47k] ------------------ 82| 1.73k| { 83| | 84| 1.73k| memset( pCS->bRankUsedForStereo, 0, sizeof( pCS->bRankUsedForStereo[0] )*num_atoms ); /* djb-rwth: memset_s C11/Annex K variant? */ 85| 1.73k| SetUseAtomForStereo( pCS->bAtomUsedForStereo, at, num_atoms ); 86| | 87| 1.73k| if (pCS->bFirstCT && nSymmStereo && !pCS->bKeepSymmRank) ------------------ | Branch (87:13): [True: 1.73k, False: 0] | Branch (87:30): [True: 1.73k, False: 0] | Branch (87:45): [True: 1.73k, False: 0] ------------------ 88| 1.73k| { 89| 1.73k| int i; 90| 12.1k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (90:25): [True: 10.4k, False: 1.73k] ------------------ 91| 10.4k| { 92| | /* nSymmStereo[i] = min. {k | at[k] stereo eq. to at[i]} */ 93| 10.4k| nSymmStereo[i] = i; /* for union-join to keep track of stereo-equivalent atoms */ 94| 10.4k| } 95| 1.73k| } 96| 1.73k|#ifdef FIX_STEREOCOUNT_ERR 97| 1.73k| if (pCS->bFirstCT) ------------------ | Branch (97:13): [True: 1.73k, False: 0] ------------------ 98| 1.73k| { 99| 1.73k| CurTreeSetPos( cur_tree, tpos1 = 0 ); 100| 1.73k| } 101| 1.73k|#endif 102| 1.73k| } 103| | 104| 4.20k| if (nNumMappedBonds < pCS->nLenLinearCTStereoDble) ------------------ | Branch (104:9): [True: 2.36k, False: 1.84k] ------------------ 105| 2.36k| { 106| | 107| 2.36k| int at_rank1, at_rank2, bStereoIsBetterWasSetHere; 108| | /* AT_RANK *nRankFrom=*pRankStack1++, AT_RANK *nAtomNumberFrom=pRankStack1++; */ 109| | /* AT_RANK *nRankTo =*pRankStack2++, AT_RANK *nAtomNumberTo =pRankStack2++; */ 110| 2.36k| AT_RANK canon_min1, canon_min2; 111| 2.36k| int bFirstCanonRank; 112| 2.36k| int i, j, j1, j2, at_from1, at_from2, at_to1, at_to2, iMax, c; 113| 2.36k| int nStackPtr[SB_DEPTH], nNumMappedRanks[SB_DEPTH], LastMappedTo1; 114| 2.36k| int istk, istk2, istk3, bAddStack, nNumAtTo1Success; 115| 2.36k| int ret1, ret2, parity1, parity2; 116| | 117| 2.36k| AT_RANK at_rank_canon1; /* = pCS->LinearCTStereoDble[nNumMappedBonds].at_num1; */ /* canonical numbers of atoms */ 118| 2.36k| AT_RANK at_rank_canon2; /* = pCS->LinearCTStereoDble[nNumMappedBonds].at_num2; */ /* adjacent to the stereogenic bond */ 119| 2.36k| int nNumChoices, nNumUnkn, nNumUndf, nNumBest, nNumWorse, nNumCalc, sb_parity_calc; 120| 2.36k| int stereo_bond_parity = 0, prev_stereo_bond_parity, pass, bAllParitiesIdentical, bAllParitiesIdentical2; 121| 2.36k| AT_STEREO_DBLE prevBond2; 122| | 123| 2.36k| prevBond = pCS->LinearCTStereoDble[nNumMappedBonds]; 124| 2.36k| bFirstCanonRank = 1; 125| 2.36k| canon_min1 = canon_min2 = 0; 126| | /* 127| | // find candidates for atom_from1, atom_to1; they must have identical mapping ranks 128| | at_rank1=pRankStack1[0][at_from1=nAtomNumberCanonFrom[(int)at_rank_canon1 - 1]]; // rank "from" for mapping 129| | at_rank2=pRankStack1[0][at_from2=nAtomNumberCanonFrom[(int)at_rank_canon2 - 1]]; // rank "from" for mapping 130| | */ 131| 2.36k| if (nNumMappedBonds) ------------------ | Branch (131:13): [True: 1.97k, False: 386] ------------------ 132| 1.97k| { 133| 1.97k| at_rank_canon1 = pCS->LinearCTStereoDble[nNumMappedBonds - 1].at_num1; 134| 1.97k| at_rank_canon2 = pCS->LinearCTStereoDble[nNumMappedBonds - 1].at_num2; 135| 1.97k| } 136| 386| else 137| 386| { 138| 386| at_rank_canon1 = 0; 139| 386| at_rank_canon2 = 0; 140| 386| } 141| 2.36k| goto bypass_next_canon_ranks_check; 142| | 143| 212| next_canon_ranks: 144| | 145| | /* Save time: avoid calling Next_SB_At_CanonRanks2() */ 146| 212| if ((!pCS->bStereoIsBetter /* ??? && !pCS->bFirstCT ???*/ && ------------------ | Branch (146:14): [True: 182, False: 30] ------------------ 147| 182| at_rank_canon1 > pCS->LinearCTStereoDble[nNumMappedBonds].at_num1) || ------------------ | Branch (147:15): [True: 0, False: 182] ------------------ 148| 212| (at_rank_canon1 == pCS->LinearCTStereoDble[nNumMappedBonds].at_num1 && ------------------ | Branch (148:16): [True: 208, False: 4] ------------------ 149| 208| at_rank_canon2 >= pCS->LinearCTStereoDble[nNumMappedBonds].at_num2)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (149:15): [True: 208, False: 0] ------------------ 150| 208| { 151| | 152| 208| if (!nTotSuccess) ------------------ | Branch (152:17): [True: 208, False: 0] ------------------ 153| 208| { 154| 208| pCS->LinearCTStereoDble[nNumMappedBonds] = prevBond; 155| 208| } 156| 208| CurTreeSetPos( cur_tree, tpos1 ); 157| 208| return nTotSuccess; 158| 208| } 159| | 160| 2.36k| bypass_next_canon_ranks_check: 161| | 162| 2.36k| CurTreeSetPos( cur_tree, tpos1 ); 163| | 164| | /* find next available canon. numbers for a stereogenic bond pair of atoms */ 165| | /* process allenes AFTER all double bonds and odd-number-of-double-bonds cumulenes */ 166| 2.36k| if (!( ret1 = Next_SB_At_CanonRanks2( &at_rank_canon1, &at_rank_canon2, /* canonical numbers */ ------------------ | Branch (166:13): [True: 23, False: 2.34k] ------------------ 167| 2.36k| &canon_min1, &canon_min2, 168| 2.36k| &bFirstCanonRank, pCS->bAtomUsedForStereo, 169| 2.36k| pRankStack1, pRankStack2, 170| 2.36k| nCanonRankFrom, nAtomNumberCanonFrom, 171| 2.36k| at, num_atoms, bAllene ) )) 172| 23| { 173| | /* failed to find next stereo bond to assign parity */ 174| 23| if (!bAllene && bFirstCanonRank) ------------------ | Branch (174:17): [True: 23, False: 0] | Branch (174:29): [True: 23, False: 0] ------------------ 175| 23| { 176| | /* all stereobond have been processed; try to find allene to continue */ 177| 23| AT_RANK at_rank_canon1_Allene = 0, canon_min1_Allene = 0; 178| 23| AT_RANK at_rank_canon2_Allene = 0, canon_min2_Allene = 0; 179| 23| if ((ret1 = Next_SB_At_CanonRanks2( &at_rank_canon1_Allene, &at_rank_canon2_Allene, ------------------ | Branch (179:21): [True: 12, False: 11] ------------------ 180| 23| &canon_min1_Allene, &canon_min2_Allene, 181| 23| &bFirstCanonRank, pCS->bAtomUsedForStereo, 182| 23| pRankStack1, pRankStack2, 183| 23| nCanonRankFrom, nAtomNumberCanonFrom, 184| 23| at, num_atoms, 1 ))) /* djb-rwth: addressing LLVM warning */ 185| 12| { 186| 12| at_rank_canon1 = at_rank_canon1_Allene; 187| 12| at_rank_canon2 = at_rank_canon2_Allene; 188| 12| canon_min1 = canon_min1_Allene; 189| 12| canon_min2 = canon_min2_Allene; 190| 12| bAllene = 1; /* switch to allenes */ 191| 12| } 192| 23| } 193| 23| } 194| | 195| 2.36k| if (!ret1 || (!pCS->bStereoIsBetter && ------------------ | Branch (195:13): [True: 11, False: 2.35k] | Branch (195:23): [True: 1.82k, False: 524] ------------------ 196| 1.82k| ( at_rank_canon1 > pCS->LinearCTStereoDble[nNumMappedBonds].at_num1 || ------------------ | Branch (196:15): [True: 65, False: 1.76k] ------------------ 197| 1.76k| (at_rank_canon1 == pCS->LinearCTStereoDble[nNumMappedBonds].at_num1 && ------------------ | Branch (197:18): [True: 1.71k, False: 51] ------------------ 198| 1.71k| at_rank_canon2 > pCS->LinearCTStereoDble[nNumMappedBonds].at_num2) ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (198:17): [True: 7, False: 1.70k] ------------------ 199| 83| { 200| | /* new ranks provide greater pCS->LinearCTStereoDble[nNumMappedBonds] and therefore rejected */ 201| 83| if (!nTotSuccess) ------------------ | Branch (201:17): [True: 83, False: 0] ------------------ 202| 83| { 203| 83| pCS->LinearCTStereoDble[nNumMappedBonds] = prevBond; /* restore stereo bond CT for the current bond */ 204| 83| } 205| 83| return nTotSuccess; 206| 83| } 207| | 208| | /* current stereo bond initialization */ 209| 2.28k| nNumChoices = 0; 210| 2.28k| nNumUnkn = 0; 211| 2.28k| nNumUndf = 0; 212| 2.28k| nNumBest = 0; 213| 2.28k| nNumWorse = 0; 214| 2.28k| nNumCalc = 0; 215| 2.28k| pass = 0; 216| 2.28k| prev_stereo_bond_parity = 0; 217| | 218| 2.28k| at_rank1 = pRankStack1[0][at_from1 = nAtomNumberCanonFrom[(int) at_rank_canon1 - 1]]; /* atom 1 rank "from" for mapping */ 219| 2.28k| at_rank2 = pRankStack1[0][at_from2 = nAtomNumberCanonFrom[(int) at_rank_canon2 - 1]]; /* atom 2 rank "from" for mapping */ 220| | /* we are going to map bond (at[at_from1], at[at_from2]) and 221| | canonical ranks of its atoms (at_rank_canon1, at_rank_canon2) 222| | onto a stereogenic bond (at[at_to1], at[at_to2]) 223| | */ 224| 2.28k| iMax = at_rank1 - 1; 225| | /* test correctness: sorted pRankStack2[0][] and pRankStack1[0][] should have same ranks for both atoms */ 226| 2.28k| if (at_rank1 != pRankStack2[0][pRankStack2[1][at_rank1 - 1]] || ------------------ | Branch (226:13): [True: 0, False: 2.28k] ------------------ 227| 2.28k| at_rank2 != pRankStack2[0][pRankStack2[1][at_rank2 - 1]]) ------------------ | Branch (227:14): [True: 0, False: 2.28k] ------------------ 228| 0| { 229| | /* program error: "from" and "to" mapping ranks are not equal */ 230| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 231| 0| } 232| | /* -- do not check stereo features of "from" atoms: 233| | -- in case of "bond/charge isomerism" they may be missing. 234| | if ( !at[at_from1].stereo_bond_neighbor[0] || 235| | !at[at_from2].stereo_bond_neighbor[0] ) 236| | return CT_STEREOCOUNT_ERR; // program error 237| | */ 238| | 239| | /* find out if we have a choice in mapping: check all possible pairs (at_to1, at_to2) 240| | such that at_from1 is possibly constitutionally equivalent to at_to1, at_from2 to at_to2 */ 241| 5.89k| for (j1 = 0; j1 <= iMax && at_rank1 == pRankStack2[0][at_to1 = pRankStack2[1][iMax - j1]]; j1++) ------------------ | Branch (241:22): [True: 5.73k, False: 152] | Branch (241:36): [True: 3.61k, False: 2.12k] ------------------ 242| 3.61k| { 243| 3.61k| if (!at[at_to1].stereo_bond_neighbor[0]) ------------------ | Branch (243:17): [True: 86, False: 3.52k] ------------------ 244| 86| continue; /* at_to1 does not belong to a stereo bond */ 245| 9.82k| for (j2 = 0; j2 < MAX_NUM_STEREO_BONDS && ------------------ | | 873| 19.6k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (245:26): [True: 9.82k, False: 0] ------------------ 246| 9.82k| ( at_to2 = at[at_to1].stereo_bond_neighbor[j2] ); j2++) ------------------ | Branch (246:17): [True: 6.29k, False: 3.52k] ------------------ 247| 6.29k| { 248| 6.29k| at_to2--; 249| 6.29k| if (pRankStack1[0][at_from2] != pRankStack2[0][at_to2]) ------------------ | Branch (249:21): [True: 1.86k, False: 4.43k] ------------------ 250| 1.86k| continue; /* at_from2 cannot be mapped on at_to2 */ 251| 4.43k| stereo_bond_parity = PARITY_VAL( at[at_to1].stereo_bond_parity[j2] ); ------------------ | | 262| 4.43k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 4.43k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 252| 4.43k| i = 0; 253| 4.43k| switch (stereo_bond_parity) ------------------ | Branch (253:25): [True: 4.43k, False: 0] ------------------ 254| 4.43k| { 255| | 256| 3.90k| case AB_PARITY_UNDF: nNumUndf++; ------------------ | | 222| 3.90k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (256:21): [True: 3.90k, False: 534] ------------------ 257| 3.90k| break; /* 4 */ 258| 0| case AB_PARITY_UNKN: nNumUnkn++; ------------------ | | 221| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (258:21): [True: 0, False: 4.43k] ------------------ 259| 0| break; /* 3 (occurs if forced different to UNDF)*/ 260| | 261| 399| case BEST_PARITY: nNumBest++; break; /* 1 */ ------------------ | | 828| 399|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (261:21): [True: 399, False: 4.03k] ------------------ 262| 125| case WORSE_PARITY: nNumWorse++; break; /* 2 */ ------------------ | | 829| 125|#define WORSE_PARITY 2 ------------------ | Branch (262:21): [True: 125, False: 4.30k] ------------------ 263| 10| case AB_PARITY_CALC: nNumCalc++; break; /* 6 */ ------------------ | | 224| 10|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ | Branch (263:21): [True: 10, False: 4.42k] ------------------ 264| 0| case AB_PARITY_NONE: i++; break; /* 0 */ ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (264:21): [True: 0, False: 4.43k] ------------------ 265| 4.43k| } 266| 4.43k| nNumChoices += !i; 267| 4.43k| } 268| 3.52k| } 269| 2.28k| if (nNumChoices != nNumCalc + nNumUndf + nNumUnkn + nNumBest + nNumWorse) ------------------ | Branch (269:13): [True: 0, False: 2.28k] ------------------ 270| 0| { 271| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 272| 0| } 273| 2.28k| if (!nNumChoices) ------------------ | Branch (273:13): [True: 0, False: 2.28k] ------------------ 274| 0| { 275| 0| goto next_canon_ranks; 276| 0| } 277| | /* Determine the first parity to search */ 278| 2.28k| sb_parity_calc = ( nNumCalc > 0 ) ? BEST_PARITY : 0; ------------------ | | 828| 7|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (278:26): [True: 7, False: 2.27k] ------------------ 279| | 280| | /* ============================================================== 281| | Search sequence: sb_parity_calc stereo_bond_parity 282| | ============================================================== 283| | BEST_PARITY (calc) BEST_PARITY BEST_PARITY 284| | BEST_PARITY (known) BEST_PARITY WORSE_PARITY or 0 285| | WORSE_PARITY (calc) WORSE_PARITY WORSE_PARITY 286| | WORSE_PARITY (known) WORSE_PARITY 0 287| | AB_PARITY_UNKN(known) AB_PARITY_UNKN 0 288| | AB_PARITY_UNDF(known) AB_PARITY_UNDF 0 289| | 290| | if (sb_parity_calc==stereo_bond_parity) then "calc" else "known" 291| | */ 292| | 293| 2.49k| repeat_all: 294| | 295| 2.49k| if (!nNumMappedBonds) ------------------ | Branch (295:13): [True: 386, False: 2.10k] ------------------ 296| 386| pCS->bStereoIsBetter = 0; /* the first stereo feature in the canonical CT; moved here 7-13-2002 */ 297| | 298| 2.49k| if (!pass++) ------------------ | Branch (298:13): [True: 2.28k, False: 212] ------------------ 299| 2.28k| { 300| | /* select the smallest (best) parity to search */ 301| 2.28k| if (sb_parity_calc) ------------------ | Branch (301:17): [True: 7, False: 2.27k] ------------------ 302| 7| { 303| 7| stereo_bond_parity = BEST_PARITY; ------------------ | | 828| 7|#define BEST_PARITY 1 /* odd */ ------------------ 304| 7| } 305| 2.27k| else 306| 2.27k| { 307| 2.27k| stereo_bond_parity = nNumBest ? BEST_PARITY : ------------------ | | 828| 248|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (307:38): [True: 248, False: 2.02k] ------------------ 308| 2.27k| nNumWorse ? WORSE_PARITY : ------------------ | | 829| 80|#define WORSE_PARITY 2 ------------------ | Branch (308:21): [True: 80, False: 1.94k] ------------------ 309| 2.02k| nNumUnkn ? AB_PARITY_UNKN : ------------------ | | 221| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (309:21): [True: 0, False: 1.94k] ------------------ 310| 1.94k| nNumUndf ? AB_PARITY_UNDF : AB_PARITY_NONE; ------------------ | | 222| 1.94k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ nNumUndf ? AB_PARITY_UNDF : AB_PARITY_NONE; ------------------ | | 218| 2.27k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (310:21): [True: 1.94k, False: 0] ------------------ 311| 2.27k| } 312| 2.28k| } 313| 212| else 314| 212| { 315| | /* second pass: since the first pass failed, search for a worse result */ 316| 212| prev_stereo_bond_parity = stereo_bond_parity; 317| 212| i = NextStereoParity2Test( &stereo_bond_parity, &sb_parity_calc, 318| 212| nNumBest, nNumWorse, nNumUnkn, nNumUndf, nNumCalc, vABParityUnknown ); 319| 212| switch (i) 320| 212| { 321| 0| case 0: ------------------ | Branch (321:17): [True: 0, False: 212] ------------------ 322| 0| break; /* obtained next parity to test */ 323| 212| case 1: ------------------ | Branch (323:17): [True: 212, False: 0] ------------------ 324| 212| goto next_canon_ranks; 325| 0| default: ------------------ | Branch (325:17): [True: 0, False: 212] ------------------ 326| 0| return i; /* program error */ 327| 212| } 328| 212| } 329| 2.28k| if (stereo_bond_parity == AB_PARITY_NONE) ------------------ | | 218| 2.28k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (329:13): [True: 0, False: 2.28k] ------------------ 330| 0| { 331| | /* error? */ 332| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 333| 0| } 334| | /* check if the new requested parity is good (small) enough */ 335| 2.28k| if (!pCS->bStereoIsBetter) ------------------ | Branch (335:13): [True: 1.75k, False: 524] ------------------ 336| 1.75k| { 337| 1.75k| c = CompareLinCtStereoDoubleToValues( nTotSuccess ? pCS->LinearCTStereoDble + nNumMappedBonds : &prevBond, ------------------ | Branch (337:51): [True: 0, False: 1.75k] ------------------ 338| 1.75k| at_rank_canon1, at_rank_canon2, (U_CHAR) stereo_bond_parity ); 339| 1.75k| if (c < 0) ------------------ | Branch (339:17): [True: 43, False: 1.71k] ------------------ 340| 43| { 341| 43| if (!nTotSuccess) ------------------ | Branch (341:21): [True: 43, False: 0] ------------------ 342| 43| { 343| 43| pCS->LinearCTStereoDble[nNumMappedBonds] = prevBond; 344| 43| } 345| 43| CurTreeSetPos( cur_tree, tpos1 ); 346| 43| return nTotSuccess; 347| 43| } 348| 1.75k| } 349| | 350| 2.23k| bAllParitiesIdentical = 0; 351| | /* djb-rwth: removing redundant code */ 352| 2.23k| LastMappedTo1 = -1; 353| 2.23k| bStereoIsBetterWasSetHere = 0; 354| | /* djb-rwth: removing redundant code */ 355| | 356| 2.23k| if (!nNumMappedBonds && prev_stereo_bond_parity != stereo_bond_parity) ------------------ | Branch (356:13): [True: 386, False: 1.85k] | Branch (356:33): [True: 386, False: 0] ------------------ 357| 386| pCS->bStereoIsBetter = 0; /* the first stereo feature in the canonical CT; moved here 5-24-2002 */ 358| | 359| 2.23k| if (prev_stereo_bond_parity != stereo_bond_parity) ------------------ | Branch (359:13): [True: 2.23k, False: 0] ------------------ 360| 2.23k| { 361| 2.23k| CurTreeSetPos( cur_tree, tpos1 ); /* start over */ 362| 2.23k| } 363| | 364| | /* Mapping: here at_rank1 = nRankTo, at_to1 = nAtomNumberTo */ 365| 3.21k| for (j1 = 0; j1 <= iMax && at_rank1 == pRankStack2[0][at_to1 = pRankStack2[1][iMax - j1]]; j1++) ------------------ | Branch (365:22): [True: 3.11k, False: 93] | Branch (365:36): [True: 2.99k, False: 125] ------------------ 366| 2.99k| { 367| 2.99k| nNumAtTo1Success = 0; 368| 2.99k| if (!at[at_to1].stereo_bond_neighbor[0]) ------------------ | Branch (368:17): [True: 86, False: 2.90k] ------------------ 369| 86| continue; /* at_to1 does not belong to a stereo bond */ 370| 2.90k| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (370:17): [True: 409, False: 2.49k] ------------------ 371| 409| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 ) && ------------------ | Branch (371:18): [True: 409, False: 0] ------------------ 372| 409| 1 == CurTreeIsLastAtomEqu( cur_tree, at_to1, nSymmStereo )) ------------------ | Branch (372:18): [True: 11, False: 398] ------------------ 373| 11| { 374| | /* at_to1 is known to be stereogenically equivalent to another atom tried with at_rank_canon1 */ 375| 11| continue; 376| 11| } 377| 2.89k| bAllParitiesIdentical2 = 0; 378| 4.73k| for (j2 = 0; j2 < MAX_NUM_STEREO_BONDS && ( at_to2 = at[at_to1].stereo_bond_neighbor[j2] ); j2++) ------------------ | | 873| 9.47k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (378:26): [True: 4.73k, False: 0] | Branch (378:55): [True: 4.05k, False: 682] ------------------ 379| 4.05k| { 380| 4.05k| EQ_NEIGH EN1[2], EN2[2]; 381| 4.05k| int bond_parity, num1, num2; 382| 4.05k| AT_RANK at_rank_canon_n1, at_rank_canon_n2; 383| | 384| 4.05k| at_to2--; 385| 4.05k| if (pRankStack1[0][at_from2] != pRankStack2[0][at_to2]) ------------------ | Branch (385:21): [True: 677, False: 3.37k] ------------------ 386| 677| continue; /* at_from2 cannot be mapped on at_to2 even without mapping at_from1 to at_to1 */ 387| | 388| | /* check whether the bond parity corresponds to the requested bond parity */ 389| 3.37k| if (PARITY_KNOWN( at[at_to1].stereo_bond_parity[j2] )) ------------------ | | 265| 3.37k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 3.37k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 6.75k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 3.37k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 3.37k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 3.37k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 3.37k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 3.37k, False: 0] | | | Branch (265:78): [True: 3.37k, False: 7] | | ------------------ ------------------ 390| 3.37k| { 391| 3.37k| if (stereo_bond_parity == sb_parity_calc) ------------------ | Branch (391:25): [True: 0, False: 3.37k] ------------------ 392| 0| { 393| 0| continue; /* requested parity to be calculated, found known parity */ 394| 0| } 395| 3.37k| if (stereo_bond_parity != PARITY_VAL( at[at_to1].stereo_bond_parity[j2] )) ------------------ | | 262| 3.37k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 3.37k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ | Branch (395:25): [True: 902, False: 2.46k] ------------------ 396| 902| { 397| 902| continue; /* parity differs from the requested parity */ 398| 902| } 399| 3.37k| } 400| 7| else 401| 7| if (PARITY_CALCULATE( at[at_to1].stereo_bond_parity[j2] )) ------------------ | | 267| 7|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 7|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 7|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 7|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | | Branch (267:37): [True: 7, False: 0] | | ------------------ ------------------ 402| 7| { 403| 7| if (stereo_bond_parity != sb_parity_calc) ------------------ | Branch (403:29): [True: 0, False: 7] ------------------ 404| 0| { 405| 0| continue; /* requested known parity, found parity to be calculated */ 406| 0| } 407| 7| } 408| 0| else 409| 0| { 410| 0| return CT_STEREOCOUNT_ERR; /* unknown parity type */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 411| 0| } 412| | /* initialize stack pointer nStackPtr[istk] for "hand-made" recursion */ 413| | /* stacks are pRankStack1[], pRankStack2[], nNumMappedRanks[] */ 414| 2.47k| istk = 0; 415| 2.47k| nStackPtr[0] = 0; 416| 2.47k| nNumMappedRanks[0] = nNumMappedRanksInput; 417| 2.47k| bAddStack = 0; 418| 2.47k| bAllParitiesIdentical = ( ( at[at_to1].stereo_bond_parity[j2] & KNOWN_PARITIES_EQL ) ) && ------------------ | | 206| 2.47k|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ | Branch (418:41): [True: 570, False: 1.90k] ------------------ 419| 570| PARITY_KNOWN( at[at_to1].stereo_bond_parity[j2] ); ------------------ | | 265| 3.04k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 570|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 1.14k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 570|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 570|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 570|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 570|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 570, False: 0] | | | Branch (265:78): [True: 570, False: 0] | | ------------------ ------------------ 420| | 421| 2.47k| if (!bAllParitiesIdentical && !nNumCalc && ------------------ | Branch (421:21): [True: 1.90k, False: 570] | Branch (421:47): [True: 1.89k, False: 7] ------------------ 422| 1.89k| ( !nNumUndf + !nNumUnkn + !nNumBest + !nNumWorse ) == 3) ------------------ | Branch (422:21): [True: 1.66k, False: 234] ------------------ 423| 1.66k| { 424| | /* only one kind of bond parity is present; check whether all parities are really same */ 425| 1.66k| bAllParitiesIdentical = All_SB_Same( at_rank_canon1, at_rank_canon2, /* canonical numbers */ 426| 1.66k| pRankStack1, pRankStack2, 427| 1.66k| nAtomNumberCanonFrom, at ); 428| 1.66k| if (bAllParitiesIdentical < 0) ------------------ | Branch (428:25): [True: 0, False: 1.66k] ------------------ 429| 0| { 430| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 431| 0| } 432| 1.66k| } 433| | 434| | /***************************************************************** 435| | * do the mapping only if parities are not same 436| | */ 437| 2.47k| if (!bAllParitiesIdentical) ------------------ | Branch (437:21): [True: 462, False: 2.01k] ------------------ 438| 462| { 439| | /* map atom 1 or reuse previous mapping */ 440| 462| if (LastMappedTo1 != at_to1) ------------------ | Branch (440:25): [True: 462, False: 0] ------------------ 441| 462| { 442| | /* avoid repetitve mapping to the same first at_to1 using LastMappedTo1 variable */ 443| | /* map atom 1 */ 444| 462| ret1 = map_an_atom2( pCG, num_at_tg, num_max, at_from1, at_to1, 445| 462| nTempRank, nNumMappedRanks[istk], &nNumMappedRanks[istk + 1], pCS, 446| 462| NeighList, pRankStack1 + nStackPtr[istk], pRankStack2 + nStackPtr[istk], 447| 462| &bAddStack ); 448| 462| if (RETURNED_ERROR( ret1 )) ------------------ | | 44| 462|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 462|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 462|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 462|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 462|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 462|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 462, False: 0] | | | Branch (44:53): [True: 0, False: 462] | | ------------------ ------------------ 449| 0| { 450| 0| return ret1; /* error */ 451| 0| } 452| 462| nStackPtr[istk + 1] = nStackPtr[istk] + bAddStack; 453| 462| LastMappedTo1 = at_to1; 454| 462| if (bAddStack) ------------------ | Branch (454:29): [True: 441, False: 21] ------------------ 455| 441| { 456| 441| if (tpos1 == CurTreeGetPos( cur_tree ) || ------------------ | Branch (456:33): [True: 225, False: 216] ------------------ 457| 216| 0 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (457:34): [True: 0, False: 216] ------------------ 458| 225| { 459| 225| CurTreeAddRank( cur_tree, at_rank_canon1 ); 460| 225| } 461| 441| CurTreeAddAtom( cur_tree, at_to1 ); 462| 441| } 463| 462| } 464| 462| istk++; /* = 1 */ 465| | /* check if we can map atom 2 */ 466| 462| if (pRankStack1[nStackPtr[istk]][at_from2] != pRankStack2[nStackPtr[istk]][at_to2]) ------------------ | Branch (466:25): [True: 0, False: 462] ------------------ 467| 0| { 468| | /* 469| | * This may happen when: 470| | * A) Charge/bond isomerism, for example cyclopentadiene(-), or 471| | * B) possibly stereogenic bond in an alternating ring has heighbors 472| | * in 2 symmetrically attached rings. 473| | * Such an alternating bond cannot be mapped on possibly stereogenic bond 474| | * that has neighbors belonging to 1 of the symmetrically attached rings only. 475| | * For example: 476| | * A---B---C---D If all atoms are Carbons then B, C, F, G are constitutionally 477| | * || || || || equivalent. However, bonds B-C, F-G are not equivalent to 478| | * || || || || B-F and C-G and cannot be mapped on them. 479| | * E---F---G---H If at_from1=B, at_from2=F, at_to1=B, then at_from2 cannot be mapped on at_to2=C 480| | * If at_from1=B, at_from2=F, at_to1=C, then at_from2 cannot be mapped on at_to2=B 481| | * etc. 482| | */ 483| 0| if (sb_parity_calc != stereo_bond_parity) ------------------ | Branch (483:29): [True: 0, False: 0] ------------------ 484| 0| { 485| | /* can be passed only once for each bond */ 486| 0| nNumChoices--; 487| 0| nNumUndf -= ( stereo_bond_parity == AB_PARITY_UNDF ); ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 488| 0| nNumUnkn -= ( stereo_bond_parity == AB_PARITY_UNKN ); ------------------ | | 221| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ 489| 0| nNumBest -= ( stereo_bond_parity == BEST_PARITY ); ------------------ | | 828| 0|#define BEST_PARITY 1 /* odd */ ------------------ 490| 0| nNumWorse -= ( stereo_bond_parity == WORSE_PARITY ); ------------------ | | 829| 0|#define WORSE_PARITY 2 ------------------ 491| | /* nNumCalc = nNumChoices - (nNumUndf + nNumUnkn + nNumBest + nNumWorse); */ 492| 0| } 493| 0| else 494| 0| if (sb_parity_calc == BEST_PARITY) ------------------ | | 828| 0|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (494:33): [True: 0, False: 0] ------------------ 495| 0| { 496| | /* can be passed 2 times: for BEST_PARITY and WORSE_PARITY in this order */ 497| 0| nNumChoices--; /* do not repeate for WORSE_PARITY */ 498| 0| nNumCalc--; 499| 0| } 500| 0| continue; /* Happens for ID=80036,80253,91354,95532,101532,103788 */ 501| 0| } 502| 462| if (nStackPtr[istk] > nStackPtr[istk - 1]) ------------------ | Branch (502:25): [True: 441, False: 21] ------------------ 503| 441| { 504| 441| bAllParitiesIdentical2 = All_SB_Same( at_rank_canon1, at_rank_canon2, 505| 441| pRankStack1 + nStackPtr[istk], pRankStack2 + nStackPtr[istk], 506| 441| nAtomNumberCanonFrom, at ); 507| 441| if (bAllParitiesIdentical2 < 0) ------------------ | Branch (507:29): [True: 0, False: 441] ------------------ 508| 0| { 509| 0| return CT_STEREOBOND_ERROR; /* */ ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 510| 0| } 511| 441| } 512| 21| else 513| 21| { 514| 21| bAllParitiesIdentical2 = 0; 515| 21| } 516| 462| if (bAllParitiesIdentical2) ------------------ | Branch (516:25): [True: 194, False: 268] ------------------ 517| 194| { 518| | /* do no mapping when all equivalent bonds have same parity */ 519| | /* stereo_bond_parity = PARITY_VAL(at[at_to1].stereo_bond_parity[j2]); */ 520| 194| ClearPreviousMappings( pRankStack1 + nStackPtr[istk] + 2 ); 521| 194| } 522| 268| else 523| 268| { 524| 268| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (524:29): [True: 247, False: 21] ------------------ 525| 247| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon2 ) && ------------------ | Branch (525:30): [True: 0, False: 247] ------------------ 526| 0| 1 == CurTreeIsLastAtomEqu( cur_tree, at_to2, nSymmStereo )) ------------------ | Branch (526:30): [True: 0, False: 0] ------------------ 527| 0| { 528| 0| continue; 529| 0| } 530| | /* map atom 2 */ 531| 268| ret2 = map_an_atom2( pCG, num_at_tg, num_max, at_from2, at_to2, 532| 268| nTempRank, nNumMappedRanks[istk], &nNumMappedRanks[istk + 1], pCS, 533| 268| NeighList, pRankStack1 + nStackPtr[istk], pRankStack2 + nStackPtr[istk], 534| 268| &bAddStack ); 535| 268| if (RETURNED_ERROR( ret2 )) ------------------ | | 44| 268|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 268|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 268|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 268|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 268|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 268|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 268, False: 0] | | | Branch (44:53): [True: 0, False: 268] | | ------------------ ------------------ 536| 0| { 537| 0| return ret2; /* program error */ 538| 0| } 539| 268| nStackPtr[istk + 1] = nStackPtr[istk] + bAddStack; 540| 268| istk++; /* = 2 */ 541| 268| if (bAddStack) ------------------ | Branch (541:29): [True: 261, False: 7] ------------------ 542| 261| { 543| 261| if (tpos1 == CurTreeGetPos( cur_tree ) || ------------------ | Branch (543:33): [True: 17, False: 244] ------------------ 544| 244| 0 == CurTreeIsLastRank( cur_tree, at_rank_canon2 )) ------------------ | Branch (544:34): [True: 244, False: 0] ------------------ 545| 261| { 546| 261| CurTreeAddRank( cur_tree, at_rank_canon2 ); 547| 261| } 548| 261| CurTreeAddAtom( cur_tree, at_to2 ); 549| 261| } 550| 268| } 551| 462| } 552| 2.01k| else 553| 2.01k| { 554| | /* do no mapping when all equivalent bonds have same parity */ 555| | /* stereo_bond_parity = PARITY_VAL(at[at_to1].stereo_bond_parity[j2]); */ 556| 2.01k| ClearPreviousMappings( pRankStack1 + 2 ); 557| 2.01k| } 558| | 559| | /* we have a precalculated (known) bond parity */ 560| | 561| | /************************************************************ 562| | * 563| | * Known Bond Parity case: do not map stereo bond neighbors 564| | */ 565| 2.47k| if (stereo_bond_parity != sb_parity_calc) /* parity is known */ ------------------ | Branch (565:21): [True: 2.46k, False: 7] ------------------ 566| 2.46k| { 567| | /* accept bond parity and do not map the neighbors */ 568| 2.46k| bond_parity = stereo_bond_parity; 569| | /* same code as under " make a decision to accept current mapping" comment below */ 570| | /* with one exception: istk instead of istk3 */ 571| 2.46k| c = CompareLinCtStereoDoubleToValues( pCS->LinearCTStereoDble + nNumMappedBonds, 572| 2.46k| at_rank_canon1, at_rank_canon2, (U_CHAR) bond_parity ); 573| 2.46k| if (c < 0 && !pCS->bStereoIsBetter) ------------------ | Branch (573:25): [True: 142, False: 2.32k] | Branch (573:34): [True: 0, False: 142] ------------------ 574| 0| { 575| | /* reject */ 576| | 577| 0| pCS->lNumRejectedCT++; 578| | /* remove failed atom2 from the tree */ 579| 0| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (579:29): [True: 0, False: 0] ------------------ 580| 0| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon2 )) ------------------ | Branch (580:30): [True: 0, False: 0] ------------------ 581| 0| { 582| 0| CurTreeRemoveIfLastAtom( cur_tree, at_to2 ); 583| 0| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 584| 0| } 585| 0| continue; /* to next at_to2; Reject this at_to2: not a minimal CT. */ 586| 0| } 587| 2.46k| else 588| 2.46k| { 589| | /* accept */ 590| | 591| 2.46k| if (c > 0 && !pCS->bStereoIsBetter) ------------------ | Branch (591:29): [True: 223, False: 2.24k] | Branch (591:38): [True: 137, False: 86] ------------------ 592| 137| { 593| | /* bond entry is less than the previusly found */ 594| 137| pCS->bStereoIsBetter = bStereoIsBetterWasSetHere = 1; 595| 137| prevBond2 = pCS->LinearCTStereoDble[nNumMappedBonds]; 596| 137| } 597| 2.46k| pCS->LinearCTStereoDble[nNumMappedBonds].at_num1 = at_rank_canon1; 598| 2.46k| pCS->LinearCTStereoDble[nNumMappedBonds].at_num2 = at_rank_canon2; 599| 2.46k| pCS->LinearCTStereoDble[nNumMappedBonds].parity = bond_parity; 600| | /* recursive call */ 601| 2.46k| pCS->bRankUsedForStereo[at_from1] ++; 602| 2.46k| pCS->bRankUsedForStereo[at_from2] ++; 603| 2.46k| if (!bAllParitiesIdentical) ------------------ | Branch (603:29): [True: 455, False: 2.01k] ------------------ 604| 455| { 605| 455| pCS->bAtomUsedForStereo[at_to1] --; 606| 455| pCS->bAtomUsedForStereo[at_to2] --; 607| 455| } 608| 2.46k| ret2 = map_stereo_bonds4( ic, pCG, at, num_atoms, num_at_tg, num_max, bAllene, nCanonRankFrom, nAtomNumberCanonFrom, nCanonRankTo, 609| 2.46k| nSymmRank, pRankStack1 + nStackPtr[istk], pRankStack2 + nStackPtr[istk], 610| 2.46k| nTempRank, nNumMappedRanks[istk], nSymmStereo, NeighList, 611| 2.46k| pCS, cur_tree, nNumMappedBonds + 1, 612| 2.46k| vABParityUnknown ); 613| 2.46k| if (!bAllParitiesIdentical) ------------------ | Branch (613:29): [True: 455, False: 2.01k] ------------------ 614| 455| { 615| 455| pCS->bAtomUsedForStereo[at_to1] ++; 616| 455| pCS->bAtomUsedForStereo[at_to2] ++; 617| 455| } 618| 2.46k| pCS->bRankUsedForStereo[at_from1] --; 619| 2.46k| pCS->bRankUsedForStereo[at_from2] --; 620| 2.46k| if (ret2 == 4) ------------------ | Branch (620:29): [True: 7, False: 2.46k] ------------------ 621| 7| { 622| 7| if (nNumMappedBonds) ------------------ | Branch (622:33): [True: 0, False: 7] ------------------ 623| 0| { 624| 0| return ret2; 625| 0| } 626| 7| else 627| 7| { 628| 7| pCS->bFirstCT = 1; 629| 7| goto total_restart; 630| 7| } 631| 7| } 632| | 633| 2.46k| if (RETURNED_ERROR( ret2 )) ------------------ | | 44| 2.46k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.46k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.46k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.46k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.46k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.46k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.46k, False: 0] | | | Branch (44:53): [True: 0, False: 2.46k] | | ------------------ ------------------ 634| 0| { 635| 0| if (ret2 == CT_TIMEOUT_ERR) ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (635:33): [True: 0, False: 0] ------------------ 636| 0| return ret2; 637| 0| else 638| 0| return ret2; /* program error */ 639| 0| } 640| 2.46k| if (ret2 > 0) ------------------ | Branch (640:29): [True: 2.12k, False: 334] ------------------ 641| 2.12k| { 642| 2.12k| nTotSuccess |= 1; 643| 2.12k| nNumAtTo1Success++; 644| 2.12k| if (bStereoIsBetterWasSetHere || ( ret2 & 2 )) ------------------ | Branch (644:33): [True: 127, False: 2.00k] | Branch (644:62): [True: 156, False: 1.84k] ------------------ 645| 283| { 646| 283| CurTreeKeepLastAtomsOnly( cur_tree, tpos1, 1 ); /* start over */ 647| 283| nTotSuccess |= 2; /* Obtained a smaller CT */ 648| 283| } 649| 2.12k| } 650| 334| else 651| 334| { 652| 334| if (bStereoIsBetterWasSetHere) ------------------ | Branch (652:33): [True: 10, False: 324] ------------------ 653| 10| { /* rollback */ 654| 10| pCS->bStereoIsBetter = 0; 655| 10| pCS->LinearCTStereoDble[nNumMappedBonds] = prevBond2; 656| 10| } 657| | /* remove failed atom2 from the tree */ 658| 334| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (658:33): [True: 155, False: 179] ------------------ 659| 155| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon2 )) ------------------ | Branch (659:34): [True: 82, False: 73] ------------------ 660| 82| { 661| 82| CurTreeRemoveIfLastAtom( cur_tree, at_to2 ); 662| 82| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 663| 82| } 664| | /* 665| | if ( 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 ) ) { 666| | CurTreeRemoveLastAtom( cur_tree, at_to1 ); 667| | CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 668| | } 669| | */ 670| 334| } 671| 2.46k| bStereoIsBetterWasSetHere = 0; 672| 2.46k| } 673| 2.46k| if (bAllParitiesIdentical || bAllParitiesIdentical2) ------------------ | Branch (673:25): [True: 2.00k, False: 455] | Branch (673:50): [True: 194, False: 261] ------------------ 674| 2.20k| { 675| 2.20k| break; /* j2 cycle, at_to2 (no need to repeat) */ 676| 2.20k| } 677| 261| continue; /* to next at_to2 */ 678| 2.46k| } 679| | /*************************************************************************** 680| | * 681| | * Unknown Bond Parity case: may need to map stereo bond neighbors 682| | * 683| | **************************************************************************** 684| | * Ranks are not known in advance 685| | * check if at_from1/at_to1 half-bond has neighbors with equal mapping ranks 686| | */ 687| | 688| 7| parity1 = parity_of_mapped_half_bond( at_from1, at_to1, at_from2, at_to2, at, &EN1[0], 689| 7| nCanonRankFrom, pRankStack1[nStackPtr[istk]], pRankStack2[nStackPtr[istk]] ); 690| | /* old approach -- before E/Z parities 691| | parity1 = parity_of_mapped_atom2( pCG, at_from1, at_to1, at, &EN1[0], 692| | nCanonRankFrom, pRankStack1[nStackPtr[istk]], pRankStack2[nStackPtr[istk]] ); 693| | */ 694| | /* the following commented out statement is not needed here. */ 695| | /* parity2 = parity_of_mapped_atom2( pCG, at_from2, at_to2, at, &EN2[0], 696| | nCanonRankFrom, pRankStack1[nStackPtr[istk]], 697| | pRankStack2[nStackPtr[istk]] ); 698| | */ 699| 7| if (!parity1) ------------------ | Branch (699:21): [True: 0, False: 7] ------------------ 700| 0| { 701| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 702| 0| } 703| 7| num1 = parity1 > 0 ? 1 : 2; /* parity < 0 means additional mapping is needed to set parity */ ------------------ | Branch (703:24): [True: 4, False: 3] ------------------ 704| | 705| | /* --- try all possible mappings of the stereo bond ending atoms' neighbors --- */ 706| 7| at_rank_canon_n1 = 0; 707| | /* djb-rwth: removing redundant code */ 708| 7| for (i = 0; i < num1; i++) ------------------ | Branch (708:29): [True: 7, False: 0] ------------------ 709| 7| { 710| 7| int at_from_n1, at_to_n1, at_no_n1_num_success = 0; 711| 7| istk2 = istk; 712| 7| if (num1 == 2) ------------------ | Branch (712:25): [True: 3, False: 4] ------------------ 713| 3| { 714| 3| at_rank_canon_n1 = nCanonRankFrom[EN1[0].from_at]; 715| | /* an additional neighbor mapping is necessary; */ 716| | /* we need to map only one at_from1 neighbor to make all neighbors have different ranks */ 717| | 718| 3| at_from_n1 = EN1[0].from_at; 719| 3| at_to_n1 = EN1[0].to_at[i]; 720| | 721| 3| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (721:29): [True: 3, False: 0] ------------------ 722| 3| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 ) && ------------------ | Branch (722:30): [True: 0, False: 3] ------------------ 723| 0| 1 == CurTreeIsLastAtomEqu( cur_tree, at_to_n1, nSymmStereo )) ------------------ | Branch (723:30): [True: 0, False: 0] ------------------ 724| 0| continue; 725| | /* 726| | if ( nSymmStereo && !pCS->bFirstCT ) { 727| | if ( i && nSymmStereo[at_to_n1] == nSymmStereo[(int)EN1[0].to_at[0]] ) { 728| | continue; // do not test stereo equivalent atoms except the first one 729| | } 730| | } 731| | */ 732| | /* neighbors are tied. Untie them by breaking a tie on ONE of them. */ 733| 3| ret1 = map_an_atom2( pCG, num_at_tg, num_max, at_from_n1, at_to_n1, 734| 3| nTempRank, nNumMappedRanks[istk2], &nNumMappedRanks[istk2 + 1], pCS, 735| 3| NeighList, pRankStack1 + nStackPtr[istk2], pRankStack2 + nStackPtr[istk2], 736| 3| &bAddStack ); 737| 3| if (RETURNED_ERROR( ret1 )) ------------------ | | 44| 3|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 3|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 3|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 3|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 3|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 3|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 3, False: 0] | | | Branch (44:53): [True: 0, False: 3] | | ------------------ ------------------ 738| 0| { 739| 0| return ret1; /* program error */ /* */ 740| 0| } 741| 3| nStackPtr[istk2 + 1] = nStackPtr[istk2] + bAddStack; 742| 3| istk2++; /* <= 3 */ 743| | /* debug */ 744| 3| if (istk2 >= SB_DEPTH) ------------------ | | 13| 3|#define SB_DEPTH 6 ------------------ | Branch (744:29): [True: 0, False: 3] ------------------ 745| 0| { 746| 0| return CT_OVERFLOW; /* program error */ /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 747| 0| } 748| 3| if (bAddStack) ------------------ | Branch (748:29): [True: 3, False: 0] ------------------ 749| 3| { 750| 3| if (tpos1 == CurTreeGetPos( cur_tree ) || ------------------ | Branch (750:33): [True: 0, False: 3] ------------------ 751| 3| 0 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 )) ------------------ | Branch (751:34): [True: 3, False: 0] ------------------ 752| 3| { 753| 3| CurTreeAddRank( cur_tree, at_rank_canon_n1 ); 754| 3| } 755| 3| CurTreeAddAtom( cur_tree, at_to_n1 ); 756| 3| } 757| | 758| | 759| | /* now that all at_from1 neighbors have been mapped the parity must be defined */ 760| 3| parity1 = parity_of_mapped_half_bond( at_from1, at_to1, at_from2, at_to2, at, &EN1[1], 761| 3| nCanonRankFrom, pRankStack1[nStackPtr[istk2]], pRankStack2[nStackPtr[istk2]] ); 762| 3| if (parity1 <= 0) ------------------ | Branch (762:29): [True: 0, False: 3] ------------------ 763| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 764| 3| } 765| 4| else 766| 4| { 767| 4| nNumMappedRanks[istk2 + 1] = nNumMappedRanks[istk2]; 768| 4| nStackPtr[istk2 + 1] = nStackPtr[istk2]; 769| 4| istk2++; /* <= 3 */ 770| 4| } 771| | 772| | /* check if at_from2/at_to2 half-bond has neighbors with equal mapping ranks */ 773| 7| parity2 = parity_of_mapped_half_bond( at_from2, at_to2, at_from1, at_to1, at, &EN2[0], 774| 7| nCanonRankFrom, pRankStack1[nStackPtr[istk2]], pRankStack2[nStackPtr[istk2]] ); 775| 7| if (!parity2) ------------------ | Branch (775:25): [True: 0, False: 7] ------------------ 776| 0| { 777| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 778| 0| } 779| 7| num2 = parity2 > 0 ? 1 : 2; ------------------ | Branch (779:28): [True: 0, False: 7] ------------------ 780| 7| at_rank_canon_n2 = 0; 781| 10| for (j = 0; j < num2; j++) ------------------ | Branch (781:33): [True: 10, False: 0] ------------------ 782| 10| { 783| 10| int at_from_n2, at_to_n2 = 0; 784| 10| istk3 = istk2; 785| 10| if (num2 == 2) ------------------ | Branch (785:29): [True: 10, False: 0] ------------------ 786| 10| { 787| 10| at_rank_canon_n2 = nCanonRankFrom[EN2[0].from_at]; 788| | /* we need to map only one at_from2 neighbor to make its neighbors have different ranks */ 789| 10| at_from_n2 = EN2[0].from_at; 790| 10| at_to_n2 = EN2[0].to_at[j]; 791| | 792| 10| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (792:33): [True: 5, False: 5] ------------------ 793| 5| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 ) && ------------------ | Branch (793:34): [True: 0, False: 5] ------------------ 794| 0| 1 == CurTreeIsLastAtomEqu( cur_tree, at_to_n2, nSymmStereo )) ------------------ | Branch (794:34): [True: 0, False: 0] ------------------ 795| 0| continue; 796| | 797| | /* 798| | if ( nSymmStereo && !pCS->bFirstCT ) { 799| | if ( j && nSymmStereo[at_to_n2] == nSymmStereo[(int)EN2[0].to_at[0]] ) { 800| | continue; // do not test stereo equivalent atoms except the first one 801| | } 802| | } 803| | */ 804| | /* neighbors are tied. Untie them by breaking a tie on ONE of them. */ 805| 10| ret1 = map_an_atom2( pCG, num_at_tg, num_max, at_from_n2, at_to_n2, 806| 10| nTempRank, nNumMappedRanks[istk3], &nNumMappedRanks[istk3 + 1], pCS, 807| 10| NeighList, pRankStack1 + nStackPtr[istk3], 808| 10| pRankStack2 + nStackPtr[istk3], 809| 10| &bAddStack ); 810| 10| if (RETURNED_ERROR( ret1 )) ------------------ | | 44| 10|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 10|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 10|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 10|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 10|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 10|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 10, False: 0] | | | Branch (44:53): [True: 0, False: 10] | | ------------------ ------------------ 811| 0| { 812| 0| return ret1; /* program error */ 813| 0| } 814| 10| nStackPtr[istk3 + 1] = nStackPtr[istk3] + bAddStack; 815| 10| istk3++; /* <= 4 */ 816| | 817| 10| if (bAddStack) ------------------ | Branch (817:33): [True: 10, False: 0] ------------------ 818| 10| { 819| 10| if (tpos1 == CurTreeGetPos( cur_tree ) || ------------------ | Branch (819:37): [True: 5, False: 5] ------------------ 820| 5| 0 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 )) ------------------ | Branch (820:38): [True: 5, False: 0] ------------------ 821| 10| { 822| 10| CurTreeAddRank( cur_tree, at_rank_canon_n2 ); 823| 10| } 824| 10| CurTreeAddAtom( cur_tree, at_to_n2 ); 825| 10| } 826| | 827| 10| parity2 = parity_of_mapped_half_bond( at_from2, at_to2, at_from1, at_to1, at, &EN2[1], 828| 10| nCanonRankFrom, pRankStack1[nStackPtr[istk3]], pRankStack2[nStackPtr[istk3]] ); 829| 10| if (parity2 <= 0) ------------------ | Branch (829:33): [True: 0, False: 10] ------------------ 830| 0| { 831| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 832| 0| } 833| 10| } 834| 0| else 835| 0| { 836| | /* no additional mapping is needed to set atom's parity */ 837| 0| nNumMappedRanks[istk3 + 1] = nNumMappedRanks[istk3]; 838| 0| nStackPtr[istk3 + 1] = nStackPtr[istk3]; 839| 0| istk3++; /* <= 4 */ 840| 0| } 841| | 842| | /******************************************************************* 843| | * at this point the stereo bond is fully mapped to find its parity 844| | *******************************************************************/ 845| | 846| 10| if (parity1 <= 0 || parity2 <= 0) ------------------ | Branch (846:29): [True: 0, False: 10] | Branch (846:45): [True: 0, False: 10] ------------------ 847| 0| { 848| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 849| 0| } 850| | 851| | /* find current bond parity AB_PARITY_ODD */ 852| 10| if (ATOM_PARITY_WELL_DEF( parity1 ) && ATOM_PARITY_WELL_DEF( parity2 )) ------------------ | | 259| 20|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 10|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 10|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 10, False: 0] | | | Branch (259:75): [True: 10, False: 0] | | ------------------ ------------------ if (ATOM_PARITY_WELL_DEF( parity1 ) && ATOM_PARITY_WELL_DEF( parity2 )) ------------------ | | 259| 10|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 10|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 10|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 10, False: 0] | | | Branch (259:75): [True: 10, False: 0] | | ------------------ ------------------ 853| 10| { 854| 10| bond_parity = 2 - ( parity1 + parity2 ) % 2; 855| 10| } 856| 0| else 857| 0| { 858| 0| bond_parity = inchi_max( parity1, parity2 ); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 859| 0| } 860| 10| if (ATOM_PARITY_WELL_DEF( bond_parity ) && at[at_to1].stereo_bond_z_prod[j2] < 0) ------------------ | | 259| 20|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 10|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 10|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 10, False: 0] | | | Branch (259:75): [True: 10, False: 0] | | ------------------ ------------------ | Branch (860:68): [True: 0, False: 10] ------------------ 861| 0| bond_parity = 2 - ( bond_parity + 1 ) % 2; /* invert the bond parity */ 862| | 863| | 864| | /******************************************************** 865| | * make a decision whether to accept the current mapping 866| | */ 867| 10| c = CompareLinCtStereoDoubleToValues( pCS->LinearCTStereoDble + nNumMappedBonds, 868| 10| at_rank_canon1, at_rank_canon2, (U_CHAR) bond_parity ); 869| 10| if (sb_parity_calc != bond_parity || ------------------ | Branch (869:29): [True: 3, False: 7] ------------------ 870| 7| (c < 0 && !pCS->bStereoIsBetter)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (870:31): [True: 0, False: 7] | Branch (870:40): [True: 0, False: 0] ------------------ 871| 3| { 872| | /* reject */ 873| 3| pCS->lNumRejectedCT++; 874| | /* remove failed atom2 from the tree */ 875| 3| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (875:33): [True: 3, False: 0] ------------------ 876| 3| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 )) ------------------ | Branch (876:34): [True: 3, False: 0] ------------------ 877| 3| { 878| 3| CurTreeRemoveIfLastAtom( cur_tree, at_to_n2 ); 879| 3| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 880| 3| } 881| 3| continue; /* Reject: not a minimal CT. */ 882| 3| } 883| 7| else 884| 7| { 885| | 886| | /* try to accept */ 887| | 888| 7| if (c > 0 && !pCS->bStereoIsBetter) ------------------ | Branch (888:33): [True: 3, False: 4] | Branch (888:42): [True: 3, False: 0] ------------------ 889| 3| { 890| | /* bond_parity is less than the previusly found */ 891| 3| pCS->bStereoIsBetter = bStereoIsBetterWasSetHere = 1; 892| 3| prevBond2 = pCS->LinearCTStereoDble[nNumMappedBonds]; 893| 3| } 894| | /* accept */ 895| 7| pCS->LinearCTStereoDble[nNumMappedBonds].at_num1 = at_rank_canon1; 896| 7| pCS->LinearCTStereoDble[nNumMappedBonds].at_num2 = at_rank_canon2; 897| 7| pCS->LinearCTStereoDble[nNumMappedBonds].parity = bond_parity; 898| | /* recursive call */ 899| 7| pCS->bRankUsedForStereo[at_from1] ++; 900| 7| pCS->bRankUsedForStereo[at_from2] ++; 901| 7| pCS->bAtomUsedForStereo[at_to1] --; 902| 7| pCS->bAtomUsedForStereo[at_to2] --; 903| 7| ret2 = map_stereo_bonds4( ic, pCG, at, num_atoms, num_at_tg, num_max, bAllene, nCanonRankFrom, nAtomNumberCanonFrom, nCanonRankTo, 904| 7| nSymmRank, pRankStack1 + nStackPtr[istk3], pRankStack2 + nStackPtr[istk3], 905| 7| nTempRank, nNumMappedRanks[istk3], nSymmStereo, NeighList, 906| 7| pCS, cur_tree, nNumMappedBonds + 1, 907| 7| vABParityUnknown ); 908| 7| pCS->bRankUsedForStereo[at_from1] --; 909| 7| pCS->bRankUsedForStereo[at_from2] --; 910| 7| pCS->bAtomUsedForStereo[at_to1] ++; 911| 7| pCS->bAtomUsedForStereo[at_to2] ++; 912| 7| if (ret2 == 4) ------------------ | Branch (912:33): [True: 7, False: 0] ------------------ 913| 7| { 914| 7| if (nNumMappedBonds) ------------------ | Branch (914:37): [True: 0, False: 7] ------------------ 915| 0| { 916| 0| return ret2; 917| 0| } 918| 7| else 919| 7| { 920| 7| pCS->bFirstCT = 1; 921| 7| goto total_restart; 922| 7| } 923| 7| } 924| 0| if (RETURNED_ERROR( ret2 )) ------------------ | | 44| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 0, False: 0] | | | Branch (44:53): [True: 0, False: 0] | | ------------------ ------------------ 925| 0| { 926| 0| return ret2; /* program error */ /* djb-rwth: fixing coverity ID #499569 */ 927| 0| } 928| 0| if (ret2 > 0) ------------------ | Branch (928:33): [True: 0, False: 0] ------------------ 929| 0| { 930| 0| nTotSuccess |= 1; 931| 0| nNumAtTo1Success++; 932| 0| if (bStereoIsBetterWasSetHere || ( ret2 & 2 )) ------------------ | Branch (932:37): [True: 0, False: 0] | Branch (932:66): [True: 0, False: 0] ------------------ 933| 0| { 934| 0| CurTreeKeepLastAtomsOnly( cur_tree, tpos1, 1 ); /* start over */ 935| 0| nTotSuccess |= 2; /* Obtained a smaller CT */ 936| 0| } 937| 0| at_no_n1_num_success++; 938| 0| } 939| 0| else 940| 0| { 941| 0| if (bStereoIsBetterWasSetHere) ------------------ | Branch (941:37): [True: 0, False: 0] ------------------ 942| 0| { /* rollback */ 943| 0| pCS->bStereoIsBetter = 0; 944| 0| pCS->LinearCTStereoDble[nNumMappedBonds] = prevBond2; 945| 0| } 946| 0| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (946:37): [True: 0, False: 0] ------------------ 947| 0| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 )) ------------------ | Branch (947:38): [True: 0, False: 0] ------------------ 948| 0| { 949| 0| CurTreeRemoveIfLastAtom( cur_tree, at_to_n2 ); 950| 0| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 951| 0| } 952| 0| } 953| 0| bStereoIsBetterWasSetHere = 0; 954| 0| } 955| 10| } /* end choices in mapping neighbors of the 2nd half-bond */ 956| 0| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (956:25): [True: 0, False: 0] ------------------ 957| 0| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n2 )) ------------------ | Branch (957:26): [True: 0, False: 0] ------------------ 958| 0| { 959| 0| CurTreeRemoveLastRank( cur_tree ); 960| 0| } 961| | /* added 2006-07-20 */ 962| 0| if (!at_no_n1_num_success && tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (962:25): [True: 0, False: 0] | Branch (962:50): [True: 0, False: 0] ------------------ 963| 0| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 )) ------------------ | Branch (963:25): [True: 0, False: 0] ------------------ 964| 0| { 965| 0| CurTreeRemoveIfLastAtom( cur_tree, at_to_n1 ); 966| 0| } 967| 0| } /* end choices in mapping neighbors of the 1st half-bond */ 968| 0| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (968:21): [True: 0, False: 0] ------------------ 969| 0| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon_n1 )) ------------------ | Branch (969:23): [True: 0, False: 0] ------------------ 970| 0| { 971| 0| CurTreeRemoveLastRank( cur_tree ); 972| 0| } 973| 0| } /* end of choices in mapping at_from2 */ 974| 2.88k| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (974:17): [True: 637, False: 2.24k] ------------------ 975| 637| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon2 )) ------------------ | Branch (975:18): [True: 179, False: 458] ------------------ 976| 179| { 977| 179| CurTreeRemoveLastRank( cur_tree ); 978| 179| } 979| 2.88k| if (!nNumAtTo1Success) ------------------ | Branch (979:17): [True: 755, False: 2.12k] ------------------ 980| 755| { 981| 755| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (981:21): [True: 337, False: 418] ------------------ 982| 337| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (982:22): [True: 337, False: 0] ------------------ 983| 337| { 984| 337| CurTreeRemoveIfLastAtom( cur_tree, at_to1 ); 985| 337| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 986| 337| } 987| 755| } 988| 2.88k| if (bAllParitiesIdentical /*&& !nSymmStereo*/) ------------------ | Branch (988:17): [True: 2.00k, False: 876] ------------------ 989| 2.00k| { 990| 2.00k| break; 991| 2.00k| } 992| 2.88k| } /* end of choices in mapping at_from1 */ 993| | 994| 2.22k| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (994:13): [True: 168, False: 2.05k] ------------------ 995| 168| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (995:14): [True: 168, False: 0] ------------------ 996| 168| { 997| 168| CurTreeRemoveLastRank( cur_tree ); 998| 168| } 999| 2.05k| else 1000| 2.05k| { 1001| | /* CurTree consistecy check (debug only) */ 1002| 2.05k| if (tpos1 != CurTreeGetPos( cur_tree )) ------------------ | Branch (1002:17): [True: 0, False: 2.05k] ------------------ 1003| 0| { 1004| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1005| 0| } 1006| 2.05k| } 1007| | 1008| 2.22k| if (!nTotSuccess || stereo_bond_parity == sb_parity_calc) ------------------ | Branch (1008:13): [True: 212, False: 2.01k] | Branch (1008:29): [True: 0, False: 2.01k] ------------------ 1009| 212| { 1010| 212| goto repeat_all; /* repeat with next parity if no success or with the same parity, now known */ 1011| 212| } 1012| | 1013| | /* Previously the control flow never came here... */ 1014| 2.01k| if (!nTotSuccess) ------------------ | Branch (1014:13): [True: 0, False: 2.01k] ------------------ 1015| 0| { 1016| 0| pCS->LinearCTStereoDble[nNumMappedBonds] = prevBond; 1017| 0| CurTreeSetPos( cur_tree, tpos1 ); 1018| | /* Occurs when atoms are not really equvalent ( -O= without positive charge in "aromatic" ring) */ 1019| 0| return 0; /* Happens for ID=92439,100318,100319 when EXCL_ALL_AROM_BOND_PARITY=0 and 1020| | * nNumChoices=0. 1021| | * Results from impossible previous mapping of symmetric relatively 1022| | * to a central ring aromatic circles while central ring is not symmetrical due to 1023| | * alternate bonds (in the central ring number of pi-electrons, atoms and bonds 1024| | * are symmetrical). 1025| | * Does not happen when alternate bonds of the central ring 1026| | * are treated as aromatic by attaching a (+) charge to the oxygen. 1027| | */ 1028| 0| } 1029| 2.01k| } 1030| 1.84k| else 1031| 1.84k| { 1032| 1.84k| int ret; 1033| | 1034| 1.84k| if (!nNumMappedBonds) ------------------ | Branch (1034:13): [True: 1.34k, False: 501] ------------------ 1035| 1.34k| { 1036| 1.34k| pCS->bStereoIsBetter = 0; /* the first stereo feature in the canonical CT has not been processed yet */ 1037| 1.34k| } 1038| | 1039| 1.84k| if (nNumMappedBonds < pCS->nLenLinearCTStereoDble) ------------------ | Branch (1039:13): [True: 0, False: 1.84k] ------------------ 1040| 0| { 1041| 0| prevBond = pCS->LinearCTStereoDble[nNumMappedBonds]; 1042| 0| } 1043| | 1044| | /*deep_map_stereo_atoms4=0;*/ 1045| | 1046| | /* all stereo bonds have been mapped; now start processing stereo atoms... */ 1047| 1.84k| ret = map_stereo_atoms4( ic, pCG, at, num_atoms, num_at_tg, num_max, nCanonRankFrom, nAtomNumberCanonFrom, nCanonRankTo, 1048| 1.84k| nSymmRank, pRankStack1, pRankStack2, nTempRank, nNumMappedRanksInput, 1049| 1.84k| nSymmStereo, NeighList, pCS, cur_tree, 0, vABParityUnknown ); 1050| | 1051| 1.84k| if (ret == 4) ------------------ | Branch (1051:13): [True: 171, False: 1.67k] ------------------ 1052| 171| { 1053| 171| if (nNumMappedBonds) ------------------ | Branch (1053:17): [True: 14, False: 157] ------------------ 1054| 14| { 1055| 14| return ret; 1056| 14| } 1057| 157| else 1058| 157| { 1059| 157| pCS->bFirstCT = 1; 1060| 157| goto total_restart; 1061| 157| } 1062| 171| } 1063| 1.67k| if (RETURNED_ERROR( ret )) ------------------ | | 44| 1.67k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 1.67k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 1.67k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 1.67k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 1.67k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 1.67k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 1.67k, False: 0] | | | Branch (44:53): [True: 0, False: 1.67k] | | ------------------ ------------------ 1064| 0| { 1065| 0| if (ret == CT_TIMEOUT_ERR) ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1065:17): [True: 0, False: 0] ------------------ 1066| 0| return ret; 1067| 0| else 1068| 0| return ret; /* program error */ 1069| 0| } 1070| 1.67k| if (ret > 0) ------------------ | Branch (1070:13): [True: 1.67k, False: 0] ------------------ 1071| 1.67k| { 1072| 1.67k| nTotSuccess |= 1; 1073| 1.67k| if (ret & 2) ------------------ | Branch (1073:17): [True: 588, False: 1.09k] ------------------ 1074| 588| { 1075| 588| CurTreeKeepLastAtomsOnly( cur_tree, tpos1, 1 ); /* start over */ 1076| 588| nTotSuccess |= 2; /* Obtained a smaller CT */ 1077| 588| } 1078| 1.67k| } 1079| 1.67k| } 1080| 3.69k| if (!nTotSuccess && pCS->nLenLinearCTStereoDble && ------------------ | Branch (1080:9): [True: 0, False: 3.69k] | Branch (1080:25): [True: 0, False: 0] ------------------ 1081| 0| nNumMappedBonds < pCS->nLenLinearCTStereoDble) ------------------ | Branch (1081:10): [True: 0, False: 0] ------------------ 1082| 0| { 1083| 0| pCS->LinearCTStereoDble[nNumMappedBonds] = prevBond; 1084| 0| } 1085| | 1086| 3.69k| return nTotSuccess; /* ok */ 1087| 4.20k|} map_stereo_atoms4: 1111| 8.44k|{ 1112| | /* 1113| | * Do not check whether "from" atoms have any stereo features. 1114| | */ 1115| 8.44k| int nTotSuccess = 0; 1116| 8.44k| AT_STEREO_CARB prevAtom; 1117| 8.44k| int tpos1; 1118| | 1119| 8.44k| memset( &prevAtom, 0, sizeof( prevAtom ) ); 1120| | 1121| 8.44k| tpos1 = CurTreeGetPos( cur_tree ); 1122| | 1123| 8.44k| if (nNumMappedAtoms < pCS->nLenLinearCTStereoCarb) ------------------ | Branch (1123:9): [True: 6.15k, False: 2.29k] ------------------ 1124| 6.15k| { 1125| | /* AT_RANK *nRankFrom=*pRankStack1++, AT_RANK *nAtomNumberFrom=pRankStack1++; */ 1126| | /* AT_RANK *nRankTo =*pRankStack2++, AT_RANK *nAtomNumberTo =pRankStack2++; */ 1127| 6.15k| int j1, at_from1, at_to1, /*at_from2, at_to2,*/ iMax, lvl, bStereoIsBetterWasSetHere; 1128| 6.15k| int istk, bAddStack, nNumAtTo1Success, c, bFirstTime = 1, bAllParitiesIdentical; /* djb-rwth: removing redundant variables */ 1129| 6.15k| EQ_NEIGH EN[5], *pEN; 1130| 6.15k| int nStackPtr[5], nMappedRanks[5], j[5], *nSP, *nMR, bLastLvlFailed; 1131| | 1132| 6.15k| AT_RANK at_rank_canon1, cr[5], at_to[5]; 1133| 6.15k| AT_RANK canon_rank1_min = 0; 1134| 6.15k| int at_rank1; /* rank for mapping */ 1135| 6.15k| int nNumChoices, nNumUnkn, nNumUndf, nNumWorse, nNumBest, nNumCalc; 1136| 6.15k| int stereo_center_parity = 0, sb_parity_calc, pass; /* djb-rwth: removing redundant variable */ 1137| 6.15k| AT_STEREO_CARB prevAtom2; 1138| | 1139| 6.15k| prevAtom = pCS->LinearCTStereoCarb[nNumMappedAtoms]; /* save to restore in case of failure */ 1140| 6.15k| at_rank_canon1 = nNumMappedAtoms ? pCS->LinearCTStereoCarb[nNumMappedAtoms - 1].at_num : 0; ------------------ | Branch (1140:26): [True: 4.89k, False: 1.25k] ------------------ 1141| | 1142| 6.15k| goto bypass_next_canon_rank_check; 1143| | 1144| 614| next_canon_rank: 1145| | 1146| 614| if (!pCS->bStereoIsBetter /*??? && !pCS->bFirstCT ???*/ && ------------------ | Branch (1146:13): [True: 614, False: 0] ------------------ 1147| 614| at_rank_canon1 >= pCS->LinearCTStereoCarb[nNumMappedAtoms].at_num) ------------------ | Branch (1147:15): [True: 614, False: 0] ------------------ 1148| 614| { 1149| | /* cannot find next available canonical number */ 1150| 614| if (!nTotSuccess) ------------------ | Branch (1150:17): [True: 291, False: 323] ------------------ 1151| 291| { 1152| 291| pCS->LinearCTStereoCarb[nNumMappedAtoms] = prevAtom; /* restore because of failure */ 1153| 291| } 1154| 614| CurTreeSetPos( cur_tree, tpos1 ); 1155| 614| return nTotSuccess; 1156| 614| } 1157| | 1158| 6.15k|bypass_next_canon_rank_check: 1159| | 1160| 6.15k| CurTreeSetPos( cur_tree, tpos1 ); 1161| | 1162| | /* find next available canon. number for a stereogenic atom */ 1163| 6.15k| if (!Next_SC_At_CanonRank2( &at_rank_canon1, &canon_rank1_min, &bFirstTime, ------------------ | Branch (1163:13): [True: 0, False: 6.15k] ------------------ 1164| 6.15k| pCS->bAtomUsedForStereo, pRankStack1, pRankStack2, 1165| 6.15k| nAtomNumberCanonFrom, num_atoms ) || 1166| 6.15k| (!pCS->bStereoIsBetter && ------------------ | Branch (1166:16): [True: 4.79k, False: 1.35k] ------------------ 1167| 4.79k| at_rank_canon1 > pCS->LinearCTStereoCarb[nNumMappedAtoms].at_num)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1167:15): [True: 209, False: 4.58k] ------------------ 1168| 209| { 1169| | /* cannot find next available canonical number */ 1170| 209| if (!nTotSuccess) ------------------ | Branch (1170:17): [True: 209, False: 0] ------------------ 1171| 209| { 1172| 209| pCS->LinearCTStereoCarb[nNumMappedAtoms] = prevAtom; /* restore because of failure */ 1173| 209| } 1174| 209| return nTotSuccess; 1175| 209| } 1176| | 1177| 5.94k| nNumChoices = 0; 1178| 5.94k| nNumUnkn = 0; 1179| 5.94k| nNumUndf = 0; 1180| 5.94k| nNumBest = 0; 1181| 5.94k| nNumWorse = 0; 1182| 5.94k| nNumCalc = 0; 1183| 5.94k| pass = 0; 1184| | /* djb-rwth: removing redundant code */ 1185| | 1186| | /* get mapping rank for the canon. number */ 1187| 5.94k| at_rank1 = pRankStack1[0][at_from1 = (int) nAtomNumberCanonFrom[at_rank_canon1 - 1]]; 1188| 5.94k| iMax = at_rank1 - 1; 1189| | /* for debug only */ 1190| 5.94k| if (at_rank1 != pRankStack2[0][pRankStack2[1][at_rank1 - 1]]) ------------------ | Branch (1190:13): [True: 0, False: 5.94k] ------------------ 1191| 0| { 1192| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1193| 0| } 1194| | 1195| | /* count special parities of the not mapped yet "to" atoms */ 1196| 13.3k| for (j1 = 0; j1 <= iMax && at_rank1 == pRankStack2[0][at_to1 = pRankStack2[1][iMax - j1]]; j1++) ------------------ | Branch (1196:22): [True: 12.9k, False: 476] | Branch (1196:36): [True: 7.44k, False: 5.46k] ------------------ 1197| 7.44k| { 1198| 7.44k| if (!at[at_to1].stereo_bond_neighbor[0] && pCS->bAtomUsedForStereo[at_to1] == STEREO_AT_MARK) ------------------ | | 878| 7.44k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ | Branch (1198:17): [True: 7.44k, False: 0] | Branch (1198:56): [True: 7.19k, False: 249] ------------------ 1199| 7.19k| { 1200| 7.19k| int no_choice = 0; 1201| 7.19k| stereo_center_parity = PARITY_VAL( at[at_to1].stereo_atom_parity ); ------------------ | | 262| 7.19k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 7.19k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 1202| 7.19k| switch (stereo_center_parity) ------------------ | Branch (1202:25): [True: 7.19k, False: 0] ------------------ 1203| 7.19k| { 1204| | 1205| 4.65k| case AB_PARITY_UNDF: nNumUndf++; break; /* 4 */ ------------------ | | 222| 4.65k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (1205:21): [True: 4.65k, False: 2.53k] ------------------ 1206| | 1207| 244| case AB_PARITY_UNKN: nNumUnkn++; ------------------ | | 221| 244|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (1207:21): [True: 244, False: 6.95k] ------------------ 1208| 244| break; /* 3 */ 1209| | 1210| 227| case BEST_PARITY: nNumBest++; break; /* 1 */ ------------------ | | 828| 227|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (1210:21): [True: 227, False: 6.96k] ------------------ 1211| 242| case WORSE_PARITY: nNumWorse++; break; /* 2 */ ------------------ | | 829| 242|#define WORSE_PARITY 2 ------------------ | Branch (1211:21): [True: 242, False: 6.95k] ------------------ 1212| 1.82k| case AB_PARITY_CALC: nNumCalc++; break; ------------------ | | 224| 1.82k|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ | Branch (1212:21): [True: 1.82k, False: 5.37k] ------------------ 1213| 0| case AB_PARITY_NONE: no_choice++; break; /* 0 */ ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (1213:21): [True: 0, False: 7.19k] ------------------ 1214| 7.19k| } 1215| 7.19k| nNumChoices += !no_choice; 1216| 7.19k| } 1217| 7.44k| } 1218| | 1219| 5.94k| if (nNumChoices != nNumCalc + nNumUndf + nNumUnkn + nNumBest + nNumWorse) ------------------ | Branch (1219:13): [True: 0, False: 5.94k] ------------------ 1220| 0| { 1221| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1222| 0| } 1223| 5.94k| if (!nNumChoices) ------------------ | Branch (1223:13): [True: 0, False: 5.94k] ------------------ 1224| 0| { 1225| 0| goto next_canon_rank; 1226| 0| } 1227| | /* Determine the first parity to search */ 1228| 5.94k| sb_parity_calc = ( nNumCalc > 0 ) ? BEST_PARITY : 0; ------------------ | | 828| 1.66k|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (1228:26): [True: 1.66k, False: 4.27k] ------------------ 1229| | 1230| | /* ============================================================== 1231| | Search sequence: sb_parity_calc stereo_center_parity 1232| | ============================================================== 1233| | BEST_PARITY (calc) BEST_PARITY BEST_PARITY 1234| | BEST_PARITY (known) BEST_PARITY WORSE_PARITY or 0 1235| | WORSE_PARITY (calc) WORSE_PARITY WORSE_PARITY 1236| | WORSE_PARITY (known) WORSE_PARITY 0 1237| | AB_PARITY_UNKN(known) AB_PARITY_UNKN 0 1238| | AB_PARITY_UNDF(known) AB_PARITY_UNDF 0 1239| | 1240| | if (sb_parity_calc==stereo_center_parity) then "calc" else "known" 1241| | */ 1242| | 1243| 8.11k| repeat_all: 1244| | 1245| 8.11k| if (!pass++) ------------------ | Branch (1245:13): [True: 5.94k, False: 2.17k] ------------------ 1246| 5.94k| { 1247| | /* select the smallest parity to search */ 1248| 5.94k| if (sb_parity_calc) ------------------ | Branch (1248:17): [True: 1.66k, False: 4.27k] ------------------ 1249| 1.66k| { 1250| 1.66k| stereo_center_parity = BEST_PARITY; ------------------ | | 828| 1.66k|#define BEST_PARITY 1 /* odd */ ------------------ 1251| 1.66k| } 1252| 4.27k| else 1253| 4.27k| { 1254| 4.27k| stereo_center_parity = nNumBest ? BEST_PARITY : ------------------ | | 828| 211|#define BEST_PARITY 1 /* odd */ ------------------ | Branch (1254:40): [True: 211, False: 4.06k] ------------------ 1255| 4.27k| nNumWorse ? WORSE_PARITY : ------------------ | | 829| 209|#define WORSE_PARITY 2 ------------------ | Branch (1255:21): [True: 209, False: 3.85k] ------------------ 1256| 4.06k| nNumUnkn ? AB_PARITY_UNKN : ------------------ | | 221| 208|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (1256:21): [True: 208, False: 3.64k] ------------------ 1257| 3.85k| nNumUndf ? AB_PARITY_UNDF : AB_PARITY_NONE; ------------------ | | 222| 3.64k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ nNumUndf ? AB_PARITY_UNDF : AB_PARITY_NONE; ------------------ | | 218| 4.27k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (1257:21): [True: 3.64k, False: 0] ------------------ 1258| 4.27k| } 1259| 5.94k| } 1260| 2.17k| else 1261| 2.17k| { 1262| | /* djb-rwth: removing redundant code */ 1263| 2.17k| j1 = NextStereoParity2Test( &stereo_center_parity, &sb_parity_calc, 1264| 2.17k| nNumBest, nNumWorse, nNumUnkn, nNumUndf, nNumCalc, 1265| 2.17k| vABParityUnknown ); 1266| 2.17k| switch (j1) 1267| 2.17k| { 1268| 1.55k| case 0: ------------------ | Branch (1268:17): [True: 1.55k, False: 614] ------------------ 1269| 1.55k| break; /* obtained next parity to test */ 1270| 614| case 1: ------------------ | Branch (1270:17): [True: 614, False: 1.55k] ------------------ 1271| 614| goto next_canon_rank; 1272| 0| default: ------------------ | Branch (1272:17): [True: 0, False: 2.17k] ------------------ 1273| 0| return j1; /* program error */ 1274| 2.17k| } 1275| 2.17k| } 1276| | 1277| 7.50k| if (stereo_center_parity == AB_PARITY_NONE) ------------------ | | 218| 7.50k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (1277:13): [True: 0, False: 7.50k] ------------------ 1278| 0| { 1279| | /* error? */ 1280| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1281| 0| } 1282| | 1283| | /* check if the new requested parity is small enough */ 1284| 7.50k| if (!pCS->bStereoIsBetter) ------------------ | Branch (1284:13): [True: 6.02k, False: 1.47k] ------------------ 1285| 6.02k| { 1286| 6.02k| c = CompareLinCtStereoAtomToValues( nTotSuccess ? pCS->LinearCTStereoCarb + nNumMappedAtoms : &prevAtom, ------------------ | Branch (1286:49): [True: 818, False: 5.20k] ------------------ 1287| 6.02k| at_rank_canon1, (U_CHAR) stereo_center_parity ); 1288| 6.02k| if (c < 0) ------------------ | Branch (1288:17): [True: 1.81k, False: 4.21k] ------------------ 1289| 1.81k| { 1290| 1.81k| if (!nTotSuccess) ------------------ | Branch (1290:21): [True: 997, False: 818] ------------------ 1291| 997| { 1292| 997| pCS->LinearCTStereoCarb[nNumMappedAtoms] = prevAtom; 1293| 997| } 1294| 1.81k| CurTreeSetPos( cur_tree, tpos1 ); 1295| 1.81k| return nTotSuccess; 1296| 1.81k| } 1297| 6.02k| } 1298| | 1299| | /* djb-rwth: removing redundant code */ 1300| 5.68k| bStereoIsBetterWasSetHere = 0; 1301| | /* djb-rwth: removing redundant code */ 1302| 5.68k| CurTreeSetPos( cur_tree, tpos1 ); /* start over */ 1303| | 1304| | /* 1305| | if ( prev_stereo_center_parity != stereo_center_parity ) { 1306| | CurTreeSetPos( cur_tree, tpos1 ); 1307| | } 1308| | */ 1309| | /* nRankTo nAtomNumberTo */ 1310| 8.74k| for (j1 = 0; j1 <= iMax && at_rank1 == pRankStack2[0][at_to1 = pRankStack2[1][iMax - j1]]; j1++) ------------------ | Branch (1310:22): [True: 8.47k, False: 272] | Branch (1310:36): [True: 6.58k, False: 1.89k] ------------------ 1311| 6.58k| { 1312| 6.58k| int ret, ret1, ret2, parity1; 1313| 6.58k| nNumAtTo1Success = 0; 1314| | /* 1315| | if ( !(at[at_to1].stereo_atom_parity && !at[at_to1].stereo_bond_neighbor[0] && 1316| | pCS->bAtomUsedForStereo[at_to1] == STEREO_AT_MARK ) ) 1317| | */ 1318| 6.58k| if (!at[at_to1].stereo_atom_parity || at[at_to1].stereo_bond_neighbor[0] || ------------------ | Branch (1318:17): [True: 232, False: 6.34k] | Branch (1318:51): [True: 0, False: 6.34k] ------------------ 1319| 6.34k| pCS->bAtomUsedForStereo[at_to1] != STEREO_AT_MARK) /* simplify 12-17-2003 */ ------------------ | | 878| 6.34k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ | Branch (1319:19): [True: 0, False: 6.34k] ------------------ 1320| 232| { 1321| 232| continue; 1322| 232| } 1323| | /* Do not map on non-stereogenic atom constitutionally 1324| | * equivalent to a steregenic atom. Here 1325| | * at[at_to1] is not a sterereo center; | | 1326| | * bonds tautomerism is a usual cause. -P(+)-CH=P- 1327| | * For example, consider a fragment: | | 1328| | * The two atoms P may be constitutionally 1329| | * equivalent, P(+) may be seen as a stereocenter 1330| | * while another P has a double bond (Now such a P(V) IS a stereocenter). 1331| | */ 1332| | 1333| | /* check whether the stereocenter parity corresponds to the requested stereocenter parity */ 1334| 6.34k| if (PARITY_KNOWN( at[at_to1].stereo_atom_parity )) ------------------ | | 265| 6.34k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 6.34k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 12.6k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 6.34k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 6.34k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 6.34k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 6.34k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 6.34k, False: 0] | | | Branch (265:78): [True: 4.13k, False: 2.21k] | | ------------------ ------------------ 1335| 4.13k| { 1336| 4.13k| if (stereo_center_parity == sb_parity_calc) ------------------ | Branch (1336:21): [True: 381, False: 3.75k] ------------------ 1337| 381| { 1338| 381| continue; /* requested parity to be calculated, found known parity */ 1339| 381| } 1340| 3.75k| if (stereo_center_parity != PARITY_VAL( at[at_to1].stereo_atom_parity )) ------------------ | | 262| 3.75k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 3.75k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ | Branch (1340:21): [True: 64, False: 3.69k] ------------------ 1341| 64| { 1342| 64| continue; /* parity differs from the requested parity */ 1343| 64| } 1344| 3.75k| } 1345| 2.21k| else 1346| 2.21k| { 1347| 2.21k| if (PARITY_CALCULATE( at[at_to1].stereo_atom_parity )) ------------------ | | 267| 2.21k|#define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 224| 2.21k|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ | | ------------------ | | #define PARITY_CALCULATE(X) (AB_PARITY_CALC == PARITY_VAL(X)) | | ------------------ | | | | 262| 2.21k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 2.21k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | | Branch (267:37): [True: 2.21k, False: 0] | | ------------------ ------------------ 1348| 2.21k| { 1349| 2.21k| if (stereo_center_parity != sb_parity_calc) ------------------ | Branch (1349:25): [True: 0, False: 2.21k] ------------------ 1350| 0| { 1351| 0| continue; /* requested known parity, found patity to be calculated */ 1352| 0| } 1353| 2.21k| } 1354| 0| else 1355| 0| { 1356| 0| return CT_STEREOCOUNT_ERR; /* unknown parity type */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1357| 0| } 1358| 2.21k| } 1359| | 1360| 5.90k| bAllParitiesIdentical = ( ( at[at_to1].stereo_atom_parity & KNOWN_PARITIES_EQL ) && ------------------ | | 206| 5.90k|#define KNOWN_PARITIES_EQL 0x40 /* parity is same for all pairs of constit. equivalent atoms */ ------------------ | Branch (1360:39): [True: 1.57k, False: 4.33k] ------------------ 1361| 1.57k| PARITY_KNOWN( at[at_to1].stereo_atom_parity ) ); ------------------ | | 265| 1.57k|#define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 231| 1.57k|#define AB_MIN_KNOWN_PARITY 1 | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 3.14k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.57k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 262| 1.57k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | | | ------------------ | | | | | | 204| 1.57k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | | | ------------------ | | ------------------ | | #define PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= PARITY_VAL(X) && PARITY_VAL(X) <= AB_MAX_KNOWN_PARITY) | | ------------------ | | | | 230| 1.57k|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | ------------------ | | | Branch (265:38): [True: 1.57k, False: 0] | | | Branch (265:78): [True: 1.57k, False: 0] | | ------------------ ------------------ 1362| | 1363| 5.90k| if (!bAllParitiesIdentical && !nNumCalc && ------------------ | Branch (1363:17): [True: 4.33k, False: 1.57k] | Branch (1363:43): [True: 2.12k, False: 2.21k] ------------------ 1364| 2.12k| ( !nNumUndf + !nNumUnkn + !nNumBest + !nNumWorse ) == 3) ------------------ | Branch (1364:17): [True: 2.06k, False: 61] ------------------ 1365| 2.06k| { 1366| | /* only one kind of stereocenter parity is present; check whether all parities are really same */ 1367| 2.06k| bAllParitiesIdentical = All_SC_Same( at_rank_canon1, /* canonical number */ 1368| 2.06k| pRankStack1, pRankStack2, 1369| 2.06k| nAtomNumberCanonFrom, at ); 1370| 2.06k| if (bAllParitiesIdentical < 0) ------------------ | Branch (1370:21): [True: 0, False: 2.06k] ------------------ 1371| 0| { 1372| 0| return CT_STEREOCOUNT_ERR; ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1373| 0| } 1374| 2.06k| } 1375| 5.90k| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (1375:17): [True: 199, False: 5.70k] ------------------ 1376| 199| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 ) && ------------------ | Branch (1376:18): [True: 199, False: 0] ------------------ 1377| 199| 1 == CurTreeIsLastAtomEqu( cur_tree, at_to1, nSymmStereo )) ------------------ | Branch (1377:18): [True: 42, False: 157] ------------------ 1378| 42| { 1379| 42| continue; 1380| 42| } 1381| | 1382| | 1383| | /* initialize stack pointer nStackPtr[istk] for "hand-made" recursion */ 1384| | /* stacks are pRankStack1[], pRankStack2[], nNumMappedRanks[] */ 1385| 5.86k| istk = 0; 1386| 5.86k| nStackPtr[istk] = 0; 1387| 5.86k| nMappedRanks[istk] = nNumMappedRanksInput; 1388| 5.86k| bAddStack = 0; 1389| | /* if all equivalent atoms have same known parity, do not map any of them here */ 1390| 5.86k| if (!bAllParitiesIdentical) ------------------ | Branch (1390:17): [True: 2.47k, False: 3.38k] ------------------ 1391| 2.47k| { 1392| | /* map the central atom */ 1393| | /* this mapping is always possible */ 1394| 2.47k| ret1 = map_an_atom2( pCG, num_at_tg, num_max, at_from1, at_to1, 1395| 2.47k| nTempRank, nMappedRanks[istk], &nMappedRanks[istk + 1], pCS, 1396| 2.47k| NeighList, pRankStack1 + nStackPtr[istk], pRankStack2 + nStackPtr[istk], 1397| 2.47k| &bAddStack ); 1398| 2.47k| if (RETURNED_ERROR( ret1 )) ------------------ | | 44| 2.47k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.47k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.47k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.47k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.47k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.47k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.47k, False: 0] | | | Branch (44:53): [True: 0, False: 2.47k] | | ------------------ ------------------ 1399| 0| { 1400| 0| return ret1; /* error */ 1401| 0| } 1402| 2.47k| nStackPtr[istk + 1] = nStackPtr[istk] + bAddStack; 1403| 2.47k| istk++; 1404| 2.47k| } 1405| 3.38k| else 1406| 3.38k| { 1407| 3.38k| ClearPreviousMappings( pRankStack1 + 2 ); /* precaution */ 1408| 3.38k| } 1409| | 1410| | /********************************************************************************* 1411| | * 1412| | * Unknown Stereocenter Parity case: possibly need to map stereo center neighbors 1413| | */ 1414| 5.86k| if (stereo_center_parity == sb_parity_calc) ------------------ | Branch (1414:17): [True: 2.19k, False: 3.66k] ------------------ 1415| 2.19k| { 1416| | /* find out the parity */ 1417| 2.19k| parity1 = parity_of_mapped_atom2( pCG, at_from1, at_to1, at, &EN[istk], 1418| 2.19k| nCanonRankFrom, pRankStack1[nStackPtr[istk]], 1419| 2.19k| pRankStack2[nStackPtr[istk]] ); 1420| | /* if parity is well-defined then returned EN[istk].num_to=0 */ 1421| 2.19k| if (!parity1) ------------------ | Branch (1421:21): [True: 0, False: 2.19k] ------------------ 1422| 0| { 1423| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1424| 0| } 1425| 2.19k| if (!EN[istk].num_to && parity1 != sb_parity_calc) ------------------ | Branch (1425:21): [True: 1.50k, False: 694] | Branch (1425:41): [True: 536, False: 966] ------------------ 1426| 536| { 1427| 536| continue; /* looking for the parity value = sb_parity_calc */ 1428| 536| } 1429| 2.19k| } 1430| 3.66k| else 1431| 3.66k| { 1432| | /* Known parity */ 1433| 3.66k| parity1 = stereo_center_parity; 1434| 3.66k| EN[istk].num_to = 0; 1435| 3.66k| } 1436| | 1437| | /*********************************************************************** 1438| | * no need to map the neighbors: parity is known or has been calculated 1439| | */ 1440| 5.32k| if ((stereo_center_parity == sb_parity_calc && !EN[istk].num_to) || ------------------ | Branch (1440:18): [True: 1.66k, False: 3.66k] | Branch (1440:60): [True: 966, False: 694] ------------------ 1441| | /* now well-defined, but unknown in advance atom parity OR */ 1442| 4.35k| stereo_center_parity != sb_parity_calc) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1442:18): [True: 3.66k, False: 694] ------------------ 1443| | /* known in advance parity = stereo_center_parity */ 1444| 4.63k| { 1445| | /* do not need to map the neighbors */ 1446| 4.63k| c = CompareLinCtStereoAtomToValues( pCS->LinearCTStereoCarb + nNumMappedAtoms, 1447| 4.63k| at_rank_canon1, (U_CHAR) parity1 ); 1448| 4.63k| if (c < 0 && !pCS->bStereoIsBetter) ------------------ | Branch (1448:21): [True: 424, False: 4.20k] | Branch (1448:30): [True: 0, False: 424] ------------------ 1449| 0| { 1450| | /* reject */ 1451| 0| pCS->lNumRejectedCT++; 1452| 0| continue; /* Reject: not a minimal CT. Should not happen */ 1453| 0| } 1454| 4.63k| else 1455| 4.63k| { 1456| | /* accept */ 1457| 4.63k| if (bAddStack) ------------------ | Branch (1457:25): [True: 301, False: 4.33k] ------------------ 1458| 301| { 1459| 301| if (tpos1 == CurTreeGetPos( cur_tree ) || ------------------ | Branch (1459:29): [True: 261, False: 40] ------------------ 1460| 40| 0 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (1460:30): [True: 0, False: 40] ------------------ 1461| 261| { 1462| 261| CurTreeAddRank( cur_tree, at_rank_canon1 ); 1463| 261| } 1464| 301| CurTreeAddAtom( cur_tree, at_to1 ); 1465| 301| } 1466| | 1467| 4.63k| if (c > 0 && !pCS->bStereoIsBetter) ------------------ | Branch (1467:25): [True: 659, False: 3.97k] | Branch (1467:34): [True: 458, False: 201] ------------------ 1468| 458| { 1469| | /* stereo center entry is less than the previusly found */ 1470| 458| pCS->bStereoIsBetter = bStereoIsBetterWasSetHere = 1; 1471| 458| prevAtom2 = pCS->LinearCTStereoCarb[nNumMappedAtoms]; 1472| 458| } 1473| 4.63k| pCS->LinearCTStereoCarb[nNumMappedAtoms].parity = parity1; 1474| 4.63k| pCS->LinearCTStereoCarb[nNumMappedAtoms].at_num = at_rank_canon1; 1475| 4.63k| pCS->bRankUsedForStereo[at_from1] = 3; 1476| 4.63k|#if ( FIX_ChCh_STEREO_CANON_BUG == 1 ) 1477| 4.63k| if (!bAllParitiesIdentical) ------------------ | Branch (1477:25): [True: 1.24k, False: 3.38k] ------------------ 1478| 1.24k|#endif 1479| 1.24k| pCS->bAtomUsedForStereo[at_to1] -= STEREO_AT_MARK; ------------------ | | 878| 1.24k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ 1480| | 1481| | 1482| 4.63k| ret = map_stereo_atoms4( ic, pCG, 1483| 4.63k| at, num_atoms, num_at_tg, num_max, 1484| 4.63k| nCanonRankFrom, 1485| 4.63k| nAtomNumberCanonFrom, 1486| 4.63k| nCanonRankTo, 1487| 4.63k| nSymmRank, 1488| 4.63k| pRankStack1 + nStackPtr[istk], 1489| 4.63k| pRankStack2 + nStackPtr[istk], 1490| 4.63k| nTempRank, 1491| 4.63k| nMappedRanks[istk], 1492| 4.63k| nSymmStereo, 1493| 4.63k| NeighList, 1494| 4.63k| pCS, 1495| 4.63k| cur_tree, 1496| 4.63k| nNumMappedAtoms + 1, 1497| 4.63k| vABParityUnknown ); 1498| | 1499| 4.63k| pCS->bRankUsedForStereo[at_from1] = 0; 1500| 4.63k|#if ( FIX_ChCh_STEREO_CANON_BUG == 1 ) 1501| 4.63k| if (!bAllParitiesIdentical) ------------------ | Branch (1501:25): [True: 1.24k, False: 3.38k] ------------------ 1502| 1.24k|#endif 1503| 1.24k| pCS->bAtomUsedForStereo[at_to1] += STEREO_AT_MARK; ------------------ | | 878| 1.24k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ 1504| | 1505| 4.63k| if (ret == 4) ------------------ | Branch (1505:25): [True: 211, False: 4.42k] ------------------ 1506| 211| { 1507| 211| return ret; 1508| 211| } 1509| | 1510| 4.42k| if (RETURNED_ERROR( ret )) ------------------ | | 44| 4.42k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 4.42k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 4.42k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 4.42k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 4.42k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 4.42k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 4.42k, False: 0] | | | Branch (44:53): [True: 0, False: 4.42k] | | ------------------ ------------------ 1511| 0| { 1512| 0| return ret; /* program error */ /* djb-rwth: fixing coverity ID #499567 */ 1513| 0| } 1514| | 1515| 4.42k| if (ret > 0) ------------------ | Branch (1515:25): [True: 3.91k, False: 504] ------------------ 1516| 3.91k| { 1517| 3.91k| nTotSuccess |= 1; 1518| 3.91k| nNumAtTo1Success++; 1519| 3.91k| if (bStereoIsBetterWasSetHere || ( ret & 2 )) ------------------ | Branch (1519:29): [True: 438, False: 3.47k] | Branch (1519:58): [True: 540, False: 2.93k] ------------------ 1520| 978| { 1521| 978| CurTreeKeepLastAtomsOnly( cur_tree, tpos1, 1 ); /* start over */ 1522| 978| nTotSuccess |= 2; /* Obtained a smaller CT */ 1523| 978| } 1524| 3.91k| } 1525| 504| else 1526| 504| { 1527| 504| if (bStereoIsBetterWasSetHere) ------------------ | Branch (1527:29): [True: 0, False: 504] ------------------ 1528| 0| { 1529| 0| pCS->bStereoIsBetter = 0; 1530| 0| pCS->LinearCTStereoCarb[nNumMappedAtoms] = prevAtom2; 1531| 0| } 1532| | /* remove failed atom1 from the tree */ 1533| | 1534| 504| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (1534:29): [True: 14, False: 490] ------------------ 1535| 14| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (1535:30): [True: 14, False: 0] ------------------ 1536| 14| { 1537| 14| CurTreeRemoveIfLastAtom( cur_tree, at_to1 ); 1538| 14| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 1539| 14| } 1540| 504| } 1541| 4.42k| bStereoIsBetterWasSetHere = 0; 1542| 4.42k| } 1543| | 1544| | /* 1545| | if ( (at[at_to1].stereo_atom_parity & KNOWN_PARITIES_EQL ) && 1546| | ATOM_PARITY_KNOWN(stereo_center_parity) && !nSymmStereo ) { // ??? add && !nSymmStereo ??? 1547| | break; // do not repeat for the same kind of stereo atom with the parity known in advance 1548| | } 1549| | */ 1550| 4.42k| if (bAllParitiesIdentical) ------------------ | Branch (1550:21): [True: 3.21k, False: 1.20k] ------------------ 1551| 3.21k| { 1552| 3.21k| break; /* do not repeat for the same kind of stereo atom with the parity known in advance */ 1553| 3.21k| } 1554| 1.20k| continue; 1555| 4.42k| } 1556| | 1557| | /*************************************************** 1558| | * 1559| | * Need to map the neighbors 1560| | */ 1561| 694| if (stereo_center_parity != sb_parity_calc) ------------------ | Branch (1561:17): [True: 0, False: 694] ------------------ 1562| 0| { 1563| 0| return CT_STEREOCOUNT_ERR; /* program error */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1564| 0| } 1565| | /* -- has already been calculated -- 1566| | parity1 = parity_of_mapped_atom2( pCG, at_from1, at_to1, at, &EN[istk], 1567| | nCanonRankFrom, pRankStack1[nStackPtr[istk]], pRankStack2[nStackPtr[istk]] ); 1568| | */ 1569| 694| if (!parity1) ------------------ | Branch (1569:17): [True: 0, False: 694] ------------------ 1570| 0| { 1571| 0| return CT_STEREOCOUNT_ERR; /* 1/25/2002 */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1572| 0| } 1573| | 1574| 694| if (bAddStack) ------------------ | Branch (1574:17): [True: 405, False: 289] ------------------ 1575| 405| { 1576| 405| if (tpos1 == CurTreeGetPos( cur_tree ) || ------------------ | Branch (1576:21): [True: 288, False: 117] ------------------ 1577| 117| 0 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (1577:22): [True: 0, False: 117] ------------------ 1578| 288| { 1579| 288| CurTreeAddRank( cur_tree, at_rank_canon1 ); 1580| 288| } 1581| 405| CurTreeAddAtom( cur_tree, at_to1 ); 1582| 405| } 1583| | /****************************************************** 1584| | * Need to fix the neighbors to define the atom parity 1585| | ******************************************************/ 1586| | /* a recursion replaced with the hand-made stack */ 1587| 694| lvl = 0; /* the "recursion" depth level */ 1588| 694| nSP = &nStackPtr[istk]; 1589| 694| nMR = &nMappedRanks[istk]; 1590| 694| pEN = &EN[istk]; 1591| 694| bLastLvlFailed = 0; 1592| | 1593| | /* entering "recursion" depth level lvl */ 1594| 2.66k| next_lvl: 1595| 2.66k| if (pEN[lvl].num_to) ------------------ | Branch (1595:17): [True: 2.66k, False: 0] ------------------ 1596| 2.66k| { 1597| | /* Found tied neighbors. Try all transpositions of the tied neighbors. 1598| | * j is a number of the "to" tied neighbor in the pEN[lvl].to_at[*] to 1599| | * which the pEN[lvl].from_at "from" neighbor's canonical number is mapped 1600| | */ 1601| 2.66k| j[lvl] = 0; 1602| 6.00k| next_j: 1603| 6.00k| cr[lvl] = nCanonRankFrom[pEN[lvl].from_at]; 1604| 6.00k| at_to[lvl] = pEN[lvl].to_at[j[lvl]]; 1605| 6.00k| if (j[lvl] && tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (1605:21): [True: 3.34k, False: 2.66k] | Branch (1605:31): [True: 3.19k, False: 148] ------------------ 1606| 3.19k| 1 == CurTreeIsLastRank( cur_tree, cr[lvl] ) && ------------------ | Branch (1606:22): [True: 895, False: 2.29k] ------------------ 1607| 895| 1 == CurTreeIsLastAtomEqu( cur_tree, at_to[lvl], nSymmStereo )) ------------------ | Branch (1607:22): [True: 233, False: 662] ------------------ 1608| 233| { 1609| 233| lvl++; 1610| 233| bLastLvlFailed = 0; 1611| 233| goto backup; /* do not test stereo equivalent atoms except the first one */ 1612| 233| } 1613| | 1614| 5.76k| ret2 = map_an_atom2( pCG, num_at_tg, num_max, 1615| 5.76k| pEN[lvl].from_at, /* from */ 1616| 5.76k| pEN[lvl].to_at[j[lvl]], /* to */ 1617| 5.76k| nTempRank, nMR[lvl], &nMR[lvl + 1], pCS, 1618| 5.76k| NeighList, pRankStack1 + nSP[lvl], pRankStack2 + nSP[lvl], 1619| 5.76k| &bAddStack ); 1620| | 1621| 5.76k| if (RETURNED_ERROR( ret2 )) ------------------ | | 44| 5.76k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 5.76k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 5.76k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 5.76k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 5.76k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 5.76k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 5.76k, False: 0] | | | Branch (44:53): [True: 0, False: 5.76k] | | ------------------ ------------------ 1622| 0| { 1623| 0| return ret2; /* program error */ 1624| 0| } 1625| | 1626| | /* next recursion depth level */ 1627| 5.76k| if (bAddStack) ------------------ | Branch (1627:21): [True: 5.76k, False: 0] ------------------ 1628| 5.76k| { 1629| 5.76k| if (tpos1 == CurTreeGetPos( cur_tree ) || ------------------ | Branch (1629:25): [True: 437, False: 5.33k] ------------------ 1630| 5.33k| 0 == CurTreeIsLastRank( cur_tree, cr[lvl] )) ------------------ | Branch (1630:26): [True: 4.67k, False: 662] ------------------ 1631| 5.10k| { 1632| 5.10k| CurTreeAddRank( cur_tree, cr[lvl] ); 1633| 5.10k| } 1634| 5.76k| CurTreeAddAtom( cur_tree, at_to[lvl] ); 1635| 5.76k| } 1636| 5.76k| nSP[lvl + 1] = nSP[lvl] + bAddStack; 1637| 5.76k| lvl++; /* upon increment lvl = number of additionally mapped neighbors 1638| | * (entering next recursion level) */ 1639| | 1640| | /* check if the mapping has defined the parity */ 1641| 5.76k| parity1 = parity_of_mapped_atom2( pCG, at_from1, at_to1, at, &pEN[lvl], 1642| 5.76k| nCanonRankFrom, pRankStack1[nSP[lvl]], pRankStack2[nSP[lvl]] ); 1643| | 1644| 5.76k| if (!parity1) ------------------ | Branch (1644:21): [True: 0, False: 5.76k] ------------------ 1645| 0| { 1646| 0| return CT_STEREOCOUNT_ERR; /* 1/25/2002 */ /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1647| 0| } 1648| 5.76k| if (parity1 < 0) ------------------ | Branch (1648:21): [True: 1.96k, False: 3.80k] ------------------ 1649| 1.96k| { 1650| 1.96k| goto next_lvl; /* we need at least one more mapping to define the parity */ 1651| 1.96k| } 1652| | 1653| | /********************************************************** 1654| | * 1655| | * Check the parity 1656| | * 1657| | ********************************************************** 1658| | * make a decision whether to accept the current mapping */ 1659| | 1660| 3.80k| c = CompareLinCtStereoAtomToValues( pCS->LinearCTStereoCarb + nNumMappedAtoms, 1661| 3.80k| at_rank_canon1, (U_CHAR) parity1 ); 1662| 3.80k| if (sb_parity_calc != parity1 || ------------------ | Branch (1662:21): [True: 1.83k, False: 1.96k] ------------------ 1663| 1.96k| (c < 0 && !pCS->bStereoIsBetter)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1663:23): [True: 0, False: 1.96k] | Branch (1663:32): [True: 0, False: 0] ------------------ 1664| 1.83k| { 1665| 1.83k| pCS->lNumRejectedCT++; 1666| 1.83k| bLastLvlFailed = 1; 1667| 1.83k| } 1668| 1.96k| else 1669| | /* the parity has been defined (all neighbors have untied ranks) */ 1670| | /* if ( bAcceptAllParities || parity1 == BEST_PARITY ) */ 1671| 1.96k| { 1672| | /********************************************************************* 1673| | * 1674| | * Process the parity here. We are at the top of the recursion stack. 1675| | * 1676| | *********************************************************************/ 1677| | /* try to accept current neighbors mapping */ 1678| 1.96k| if (c > 0 && !pCS->bStereoIsBetter) ------------------ | Branch (1678:25): [True: 459, False: 1.50k] | Branch (1678:34): [True: 452, False: 7] ------------------ 1679| 452| { 1680| 452| pCS->bStereoIsBetter = bStereoIsBetterWasSetHere = 1; 1681| 452| prevAtom2 = pCS->LinearCTStereoCarb[nNumMappedAtoms]; 1682| 452| } 1683| 1.96k| pCS->LinearCTStereoCarb[nNumMappedAtoms].parity = parity1; 1684| 1.96k| pCS->LinearCTStereoCarb[nNumMappedAtoms].at_num = at_rank_canon1; 1685| 1.96k| pCS->bRankUsedForStereo[at_from1] = 3; 1686| 1.96k| pCS->bAtomUsedForStereo[at_to1] -= STEREO_AT_MARK; ------------------ | | 878| 1.96k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ 1687| | 1688| 1.96k| ret = map_stereo_atoms4( ic, pCG, at, num_atoms, num_at_tg, num_max, nCanonRankFrom, nAtomNumberCanonFrom, nCanonRankTo, 1689| 1.96k| nSymmRank, pRankStack1 + nSP[lvl], pRankStack2 + nSP[lvl], 1690| 1.96k| nTempRank, nMR[lvl], nSymmStereo, NeighList, 1691| 1.96k| pCS, cur_tree, nNumMappedAtoms + 1, 1692| 1.96k| vABParityUnknown ); 1693| | 1694| 1.96k| pCS->bRankUsedForStereo[at_from1] = 0; 1695| 1.96k| pCS->bAtomUsedForStereo[at_to1] += STEREO_AT_MARK; ------------------ | | 878| 1.96k|#define STEREO_AT_MARK 8 /* > MAX_NUM_STEREO_BONDS */ ------------------ 1696| 1.96k| if (ret == 4) ------------------ | Branch (1696:25): [True: 102, False: 1.86k] ------------------ 1697| 102| { 1698| 102| return ret; 1699| 102| } 1700| 1.86k| if (RETURNED_ERROR( ret )) ------------------ | | 44| 1.86k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 1.86k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 1.86k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 1.86k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 1.86k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 1.86k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 1.86k, False: 0] | | | Branch (44:53): [True: 0, False: 1.86k] | | ------------------ ------------------ 1701| 0| { 1702| 0| if (ret == CT_TIMEOUT_ERR) ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1702:29): [True: 0, False: 0] ------------------ 1703| 0| return ret; 1704| 0| else 1705| 0| return ret; /* program error */ 1706| 0| } 1707| 1.86k| if (ret > 0) ------------------ | Branch (1707:25): [True: 873, False: 993] ------------------ 1708| 873| { 1709| 873| nTotSuccess |= 1; 1710| 873| nNumAtTo1Success++; 1711| 873| if (bStereoIsBetterWasSetHere || ( ret & 2 )) ------------------ | Branch (1711:29): [True: 385, False: 488] | Branch (1711:58): [True: 256, False: 232] ------------------ 1712| 641| { 1713| 641| CurTreeKeepLastAtomsOnly( cur_tree, tpos1, 1 ); /* start over */ 1714| 641| nTotSuccess |= 2; /* Obtained a smaller CT */ 1715| 641| } 1716| 873| } 1717| 993| else 1718| 993| { 1719| 993| if (bStereoIsBetterWasSetHere) ------------------ | Branch (1719:29): [True: 0, False: 993] ------------------ 1720| 0| { 1721| 0| pCS->bStereoIsBetter = 0; 1722| 0| pCS->LinearCTStereoCarb[nNumMappedAtoms] = prevAtom2; 1723| 0| } 1724| 993| bLastLvlFailed = 1; 1725| 993| } 1726| 1.86k| bStereoIsBetterWasSetHere = 0; 1727| | 1728| | /* avoid redundant repetitions: */ 1729| | /* check if neighbors mappings have altered another stereo center parity */ 1730| 1.86k| if (!nSymmStereo && !might_change_other_atom_parity( at, num_atoms, at_to1, ------------------ | Branch (1730:25): [True: 0, False: 1.86k] | Branch (1730:41): [True: 0, False: 0] ------------------ 1731| 0| pRankStack2[nSP[lvl]] /* ranks after neigbors mapping */, 1732| 0| pRankStack2[nStackPtr[istk]] /* ranks before the mapping neighbors */ )) 1733| 0| { 1734| 0| goto done; 1735| 0| } 1736| 1.86k| } 1737| | /* Continue the cycle. Go to the previous "recursion" level */ 1738| 3.93k| backup: 1739| 6.45k| while (lvl-- > 0) ------------------ | Branch (1739:24): [True: 5.86k, False: 592] ------------------ 1740| 5.86k| { 1741| | 1742| 5.86k| j[lvl] ++; /* next neighbor at this level */ 1743| 5.86k| if (j[lvl] < pEN[lvl].num_to) ------------------ | Branch (1743:25): [True: 3.34k, False: 2.52k] ------------------ 1744| 3.34k| { 1745| 3.34k| if (bLastLvlFailed) ------------------ | Branch (1745:29): [True: 2.49k, False: 841] ------------------ 1746| 2.49k| { 1747| 2.49k| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (1747:33): [True: 2.49k, False: 0] ------------------ 1748| 2.49k| 1 == CurTreeIsLastRank( cur_tree, cr[lvl] )) ------------------ | Branch (1748:34): [True: 2.49k, False: 0] ------------------ 1749| 2.49k| { 1750| 2.49k| CurTreeRemoveIfLastAtom( cur_tree, at_to[lvl] ); 1751| 2.49k| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 1752| 2.49k| } 1753| 2.49k| bLastLvlFailed = 0; 1754| 2.49k| } 1755| | /* Done with this level. Go back one level */ 1756| 3.34k| goto next_j; 1757| 3.34k| } 1758| | /* remove failed atom from the tree */ 1759| 2.52k| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (1759:25): [True: 2.52k, False: 0] ------------------ 1760| 2.52k| 1 == CurTreeIsLastRank( cur_tree, cr[lvl] )) ------------------ | Branch (1760:26): [True: 2.52k, False: 0] ------------------ 1761| 2.52k| { 1762| 2.52k| CurTreeRemoveLastRank( cur_tree ); 1763| 2.52k| } 1764| 2.52k| } 1765| 592| goto done; 1766| 3.93k| } 1767| 0| else 1768| 0| { 1769| 0| cr[lvl] = 0; 1770| 0| } 1771| | 1772| 592|done:; /* at this point lvl=0. */ 1773| 592| if (!nNumAtTo1Success) ------------------ | Branch (1773:17): [True: 49, False: 543] ------------------ 1774| 49| { 1775| 49| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (1775:21): [True: 45, False: 4] ------------------ 1776| 45| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (1776:22): [True: 45, False: 0] ------------------ 1777| 45| { 1778| 45| CurTreeRemoveIfLastAtom( cur_tree, at_to1 ); 1779| 45| CurTreeRemoveLastRankIfNoAtoms( cur_tree ); 1780| 45| } 1781| 49| } 1782| 592| } /* end of stereo atom mapping cycle */ 1783| | 1784| 5.37k| if (tpos1 < CurTreeGetPos( cur_tree ) && ------------------ | Branch (1784:13): [True: 480, False: 4.89k] ------------------ 1785| 480| 1 == CurTreeIsLastRank( cur_tree, at_rank_canon1 )) ------------------ | Branch (1785:14): [True: 480, False: 0] ------------------ 1786| 480| { 1787| 480| CurTreeRemoveLastRank( cur_tree ); 1788| 480| } 1789| 4.89k| else 1790| 4.89k| { 1791| | /* CurTree consistency check (debug only) */ 1792| 4.89k| if (tpos1 != CurTreeGetPos( cur_tree )) ------------------ | Branch (1792:17): [True: 0, False: 4.89k] ------------------ 1793| 0| { 1794| 0| return CT_STEREOCOUNT_ERR; /* */ ------------------ | | 29| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1795| 0| } 1796| 4.89k| } 1797| | 1798| 5.37k| if (!nTotSuccess || stereo_center_parity == sb_parity_calc) ------------------ | Branch (1798:13): [True: 1.03k, False: 4.34k] | Branch (1798:29): [True: 1.14k, False: 3.20k] ------------------ 1799| 2.17k| { 1800| 2.17k| goto repeat_all; /* repeat with next parity if no success or with the same parity, now known */ 1801| 2.17k| } 1802| 5.37k| } 1803| | 1804| 2.29k| else 1805| 2.29k| { 1806| | 1807| | /**************************************************** 1808| | * 1809| | * All stereogenic atoms and bonds have been mapped 1810| | * 1811| | ****************************************************/ 1812| | 1813| 2.29k| if ((UserAction && USER_ACTION_QUIT == ( *UserAction )( )) || ------------------ | | 124| 0|#define USER_ACTION_QUIT 1 ------------------ | Branch (1813:14): [True: 0, False: 2.29k] | Branch (1813:28): [True: 0, False: 0] ------------------ 1814| 2.29k| (ConsoleQuit && ( *ConsoleQuit )( ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1814:15): [True: 0, False: 2.29k] | Branch (1814:30): [True: 0, False: 0] ------------------ 1815| 0| { 1816| 0| return CT_USER_QUIT_ERR; ------------------ | | 32| 0|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1817| 0| } 1818| | 1819| 2.29k| if (pCS->bStereoIsBetter || pCS->bFirstCT) ------------------ | Branch (1819:13): [True: 1.04k, False: 1.25k] | Branch (1819:37): [True: 971, False: 283] ------------------ 1820| 2.01k| { 1821| | /* All stereo atoms have been mapped. Current stereo name is better than all previous. 1822| | * Create new numbering for the new CT 1823| | * break all remaining "from" ties 1824| | */ 1825| 2.01k| int i1, ret; 1826| 2.01k| AT_RANK rc, n1, n2; 1827| | 1828| 2.01k| ret = BreakAllTies( pCG, num_at_tg, num_max, pRankStack1, 1829| 2.01k| NeighList, nTempRank, pCS ); 1830| | 1831| 2.01k| if (RETURNED_ERROR( ret )) ------------------ | | 44| 2.01k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.01k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.01k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.01k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.01k, False: 0] | | | Branch (44:53): [True: 0, False: 2.01k] | | ------------------ ------------------ 1832| 0| { 1833| 0| return ret; 1834| 0| } 1835| | 1836| | /* break all remaining "from" ties */ 1837| 2.01k| ret = BreakAllTies( pCG, num_at_tg, num_max, pRankStack2, 1838| 2.01k| NeighList, nTempRank, pCS ); 1839| | 1840| 2.01k| if (RETURNED_ERROR( ret )) ------------------ | | 44| 2.01k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.01k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.01k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.01k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.01k, False: 0] | | | Branch (44:53): [True: 0, False: 2.01k] | | ------------------ ------------------ 1841| 0| { 1842| 0| return ret; 1843| 0| } 1844| | /* move stack pointers to the "nAtomNumber[*]" after all ties are broken */ 1845| 2.01k| pRankStack1 += 2; 1846| 2.01k| pRankStack2 += 2; 1847| | /* Now final mapping ranks of "to" atom (*pRankStack2)[i] and "from" atom (*pRankStack1)[i] 1848| | * are equal and all ranks are different, that is, we have a full mapping 1849| | * Copy so far best canonical numbering from "from" to "to". 1850| | */ 1851| 2.01k| memset( pCS->nPrevAtomNumber, 0, num_at_tg * sizeof( pCS->nPrevAtomNumber[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1852| 13.9k| for (i1 = 0; i1 < num_at_tg; i1++) ------------------ | Branch (1852:26): [True: 11.9k, False: 2.01k] ------------------ 1853| 11.9k| { 1854| 11.9k| n1 = pRankStack1[1][i1]; 1855| 11.9k| rc = nCanonRankFrom[n1]; /* new canon. rank */ 1856| 11.9k| n2 = pRankStack2[1][i1]; /* orig. atom number */ 1857| 11.9k| nCanonRankTo[n2] = rc; /* assign new canon. number to the atom */ 1858| | /* use this array to find stereo-equivalent atoms */ 1859| 11.9k| pCS->nPrevAtomNumber[rc - 1] = n2; /* ord. number of the atom having canon. rank = rc */ 1860| 11.9k| nSymmStereo[i1] = i1; /* restart search for stereo equivalent atoms */ 1861| | /* check mapping correctness */ 1862| 11.9k| if (pRankStack1[0][n1] != pRankStack2[0][n2] || ------------------ | Branch (1862:21): [True: 0, False: 11.9k] ------------------ 1863| 11.9k| nSymmRank[n1] != nSymmRank[n2]) ------------------ | Branch (1863:22): [True: 0, False: 11.9k] ------------------ 1864| 0| { 1865| 0| return CT_STEREO_CANON_ERR; /* stereo mapping error */ ------------------ | | 36| 0|#define CT_STEREO_CANON_ERR (CT_ERR_FIRST-17) /*(-30017) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1866| 0| } 1867| 11.9k| } 1868| | /* statistics */ 1869| 2.01k| pCS->lNumTotCT++; 1870| 2.01k| pCS->lNumEqualCT = 1; 1871| 2.01k| pCS->lNumDecreasedCT++; 1872| 2.01k| pCS->bStereoIsBetter = 0; /* prepare to start over */ 1873| 2.01k| nTotSuccess = 1; 1874| 2.01k| pCS->bFirstCT = 0; 1875| | 1876| 2.01k|#if ( REMOVE_CALC_NONSTEREO == 1 ) /* { */ 1877| 2.01k| if (!( pCS->nMode & CMODE_REDNDNT_STEREO )) ------------------ | | 776| 2.01k|#define CMODE_REDNDNT_STEREO 0x000080 /* 6-11-2002: do not check for redundant stereo elements */ ------------------ | Branch (1877:17): [True: 2.01k, False: 0] ------------------ 1878| 2.01k| { 1879| 2.01k| i1 = RemoveCalculatedNonStereo( pCG, at, num_atoms, num_at_tg, 1880| 2.01k| pRankStack1, pRankStack2, nTempRank, NeighList, 1881| 2.01k| nSymmRank, nCanonRankTo, pCS->nPrevAtomNumber, pCS, 1882| 2.01k| vABParityUnknown ); 1883| 2.01k| if (RETURNED_ERROR( i1 )) ------------------ | | 44| 2.01k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.01k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.01k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.01k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.01k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.01k, False: 0] | | | Branch (44:53): [True: 0, False: 2.01k] | | ------------------ ------------------ 1884| 0| { 1885| 0| return i1; 1886| 0| } 1887| 2.01k| if (i1 < 0) ------------------ | Branch (1887:21): [True: 78, False: 1.93k] ------------------ 1888| 78| { 1889| |#if ( bRELEASE_VERSION == 0 ) 1890| | pCS->bExtract |= EXTR_REMOVE_PARITY_WARNING; 1891| |#endif 1892| 78| i1 = -( 1 + i1 ); 1893| 78| } 1894| 2.01k| if (i1 > 0) ------------------ | Branch (1894:21): [True: 171, False: 1.84k] ------------------ 1895| 171| { 1896| 171| return 4; /* total restart: due to newly found stereo equivalence */ 1897| | /* the length of the stereo CT has changed */ 1898| 171| } 1899| 2.01k| } 1900| 2.01k|#endif /* } REMOVE_CALC_NONSTEREO */ 1901| | 1902| | /* djb-rwth: removing redundant code */ 1903| 2.01k| } 1904| 283| else 1905| 283| { 1906| | /* current stereo name is same as previous. We do not need a full mapping. */ 1907| 283| if (nSymmStereo) ------------------ | Branch (1907:17): [True: 283, False: 0] ------------------ 1908| 283| { 1909| 283| int num_changes = 0; 1910| 283| AT_RANK r, n1, n2, r_max, cr; 1911| 283| r_max = (AT_RANK) num_at_tg; 1912| 1.95k| for (r = 1; r <= r_max; r++) ------------------ | Branch (1912:29): [True: 1.67k, False: 283] ------------------ 1913| 1.67k| { 1914| 1.67k| if (bUniqueAtNbrFromMappingRank( pRankStack1, r, &n1 )) ------------------ | Branch (1914:25): [True: 1.66k, False: 10] ------------------ 1915| 1.66k| { 1916| 1.66k| if (bUniqueAtNbrFromMappingRank( pRankStack2, r, &n2 )) ------------------ | Branch (1916:29): [True: 1.66k, False: 0] ------------------ 1917| 1.66k| { 1918| | /* atoms at[n1], at[n2] have identical untied mapping rank r */ 1919| 1.66k| cr = nCanonRankFrom[(int) n1] - 1; /* (new at[n2] canonical rank)-1 */ 1920| | /* pCS->nPrevAtomNumber[(int)cr] = */ 1921| | /* previous ordering number of an atom with the canon. rank = cr+1; */ 1922| | /* make this atom equivalent to atom at[n2]: */ 1923| 1.66k| num_changes += nJoin2Mcrs( nSymmStereo, pCS->nPrevAtomNumber[(int) cr], n2 ); 1924| 1.66k| } 1925| 0| else 1926| 0| { 1927| 0| return CT_MAPCOUNT_ERR; /* mapping ranks must be either both tied or untied. */ /* */ ------------------ | | 26| 0|#define CT_MAPCOUNT_ERR (CT_ERR_FIRST- 7) /*(-30007) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1928| 0| } 1929| 1.66k| } 1930| 1.67k| } 1931| 283| if (num_changes) ------------------ | Branch (1931:21): [True: 276, False: 7] ------------------ 1932| 276| { /* compress trees to stars */ 1933| 1.63k| for (r = r_max - 1; r; r--) ------------------ | Branch (1933:41): [True: 1.36k, False: 276] ------------------ 1934| 1.36k| { 1935| 1.36k| nGetMcr( nSymmStereo, r ); 1936| 1.36k| } 1937| 276| } 1938| 283| } 1939| | /* statistics */ 1940| 283| pCS->lNumEqualCT++; 1941| 283| pCS->lNumTotCT++; 1942| 283| nTotSuccess = 1; 1943| 283| } 1944| 2.12k| if (bInchiTimeIsOver( ic, pCS->ulTimeOutTime )) ------------------ | Branch (1944:13): [True: 0, False: 2.12k] ------------------ 1945| 0| { 1946| 0| return CT_TIMEOUT_ERR; ------------------ | | 27| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1947| 0| } 1948| 2.12k| } 1949| 5.32k| if (!nTotSuccess && nNumMappedAtoms < pCS->nLenLinearCTStereoCarb) ------------------ | Branch (1949:9): [True: 0, False: 5.32k] | Branch (1949:25): [True: 0, False: 0] ------------------ 1950| 0| { 1951| 0| pCS->LinearCTStereoCarb[nNumMappedAtoms] = prevAtom; 1952| 0| CurTreeSetPos( cur_tree, tpos1 ); 1953| 0| } 1954| | 1955| 5.32k| return nTotSuccess; /* return to the previous level of the recursion. */ 1956| 8.44k|} MarkRingSystemsInp: 26| 481k|{ 27| 481k| AT_NUMB *nStackAtom = NULL; 28| 481k| int nTopStackAtom = -1; 29| 481k| AT_NUMB *nRingStack = NULL; 30| 481k| int nTopRingStack = -1; /* was AT_NUMB */ 31| 481k| AT_NUMB *nDfsNumber = NULL; 32| 481k| AT_NUMB *nLowNumber = NULL; 33| 481k| S_CHAR *cNeighNumb = NULL; 34| 481k| AT_NUMB nDfs; 35| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 36| | AT_NUMB nRs, *nRsConnect = NULL; 37| | int k; 38| | AT_NUMB *tree = NULL; 39| | int nNumConnect, nMaxNumConnect, nLenConnect; 40| |#endif 41| 481k| AT_NUMB nNumAtInRingSystem; 42| 481k| int i, j, u, /*start,*/ nNumRingSystems, nNumStartChildren; 43| | 44| | /* allocate arrays */ 45| 481k| nStackAtom = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nStackAtom[0] ) ); ------------------ | | 1143| 481k|#define inchi_malloc malloc ------------------ 46| 481k| nRingStack = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nRingStack[0] ) ); ------------------ | | 1143| 481k|#define inchi_malloc malloc ------------------ 47| 481k| nDfsNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nDfsNumber[0] ) ); ------------------ | | 1143| 481k|#define inchi_malloc malloc ------------------ 48| 481k| nLowNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nLowNumber[0] ) ); ------------------ | | 1143| 481k|#define inchi_malloc malloc ------------------ 49| 481k| cNeighNumb = (S_CHAR *) inchi_malloc( num_atoms * sizeof( cNeighNumb[0] ) ); ------------------ | | 1143| 481k|#define inchi_malloc malloc ------------------ 50| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 51| | nRsConnect = (AT_NUMB *) inchi_calloc( 3 * num_atoms + 3, sizeof( nRsConnect[0] ) ); 52| |#endif 53| | /* check allocation */ 54| 481k| if (!nStackAtom || !nRingStack || !nDfsNumber || !nLowNumber || !cNeighNumb ------------------ | Branch (54:9): [True: 0, False: 481k] | Branch (54:24): [True: 0, False: 481k] | Branch (54:39): [True: 0, False: 481k] | Branch (54:54): [True: 0, False: 481k] | Branch (54:69): [True: 0, False: 481k] ------------------ 55| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 56| | || !nRsConnect 57| |#endif 58| 481k| ) 59| 0| { 60| 0| nNumRingSystems = CT_OUT_OF_RAM; /* program error */ /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 61| 0| goto exit_function; 62| 0| } 63| | 64| | /******************************************** 65| | * 66| | * Find Cut-vertices & Blocks 67| | * 68| | ********************************************/ 69| | 70| | /* initiation */ 71| | /*start = 0;*/ 72| 481k| nNumRingSystems = 0; 73| 481k| u = start; /* start atom */ 74| 481k| nDfs = 0; 75| 481k| nTopStackAtom = -1; 76| 481k| nTopRingStack = -1; 77| 481k| memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 78| 481k| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 79| | /* push the start atom on the stack */ 80| | /* djb-rwth: fixing oss-fuzz issue #66720 */ 81| 481k| if (u <= num_atoms - 1) ------------------ | Branch (81:9): [True: 481k, False: 0] ------------------ 82| 481k| { 83| 481k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 84| 481k| nStackAtom[++nTopStackAtom] = (AT_NUMB)u; 85| 481k| nRingStack[++nTopRingStack] = (AT_NUMB)u; 86| 481k| } 87| 0| else 88| 0| { 89| 0| nNumRingSystems = CT_OVERFLOW; /* program error */ /* */ ------------------ | | 19| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 90| 0| goto exit_function; 91| 0| } 92| | 93| 481k| nNumStartChildren = 0; 94| | 95| 481k| do 96| 946k| { 97| | 98| | /* advance */ 99| 1.99M| advance_block: 100| | 101| | /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) )*/ 102| | /* replaced due to missing sequence point */ 103| 1.99M| if (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valence > j) ------------------ | Branch (103:13): [True: 1.05M, False: 946k] ------------------ 104| 1.05M| { 105| 1.05M| cNeighNumb[i] ++; 106| 1.05M| u = (int) at[i].neighbor[j]; 107| 1.05M| if (!nDfsNumber[u]) ------------------ | Branch (107:17): [True: 464k, False: 587k] ------------------ 108| 464k| { 109| | /* tree edge, 1st visit -- advance */ 110| 464k| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 111| 464k| nRingStack[++nTopRingStack] = (AT_NUMB) u; 112| 464k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 113| 464k| nNumStartChildren += ( i == start ); 114| 464k| } 115| 587k| else 116| 587k| { 117| 587k| if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) ------------------ | Branch (117:21): [True: 41.7k, False: 545k] | Branch (117:39): [True: 81.1k, False: 464k] ------------------ 118| 122k| { 119| | /* may comment out ? */ 120| | /* back edge: u is not a predecessor of i */ 121| 122k| if (nDfsNumber[u] < nDfsNumber[i]) ------------------ | Branch (121:25): [True: 61.4k, False: 61.4k] ------------------ 122| 61.4k| { 123| | /* Back edge, 1st visit: u is an ancestor of i. Compare */ 124| 61.4k| if (nLowNumber[i] > nDfsNumber[u]) ------------------ | Branch (124:29): [True: 58.3k, False: 3.15k] ------------------ 125| 58.3k| { 126| 58.3k| nLowNumber[i] = nDfsNumber[u]; 127| 58.3k| } 128| 61.4k| } 129| 122k| } /* may comment out ? */ 130| 587k| } 131| 1.05M| goto advance_block; 132| 1.05M| } 133| 946k| else 134| 946k| { 135| 946k| cNeighNumb[i] = 0; 136| 946k| } 137| | 138| | /* back up */ 139| 946k| if (i != start) ------------------ | Branch (139:13): [True: 464k, False: 481k] ------------------ 140| 464k| { 141| 464k| u = (int) nStackAtom[nTopStackAtom - 1]; /* predecessor of i */ 142| 464k| if (nLowNumber[i] >= nDfsNumber[u]) ------------------ | Branch (142:17): [True: 374k, False: 90.1k] ------------------ 143| 374k| { 144| | /* output the block */ 145| 374k| nNumRingSystems++; 146| 374k| at[u].nBlockSystem = nNumRingSystems; 147| 374k| if (u != start || nNumStartChildren > 1) ------------------ | Branch (147:21): [True: 234k, False: 140k] | Branch (147:35): [True: 30.5k, False: 109k] ------------------ 148| 264k| { 149| 264k| at[u].bCutVertex += 1; 150| 264k| } 151| 464k| while (nTopRingStack >= 0) ------------------ | Branch (151:24): [True: 464k, False: 0] ------------------ 152| 464k| { 153| 464k| j = nRingStack[nTopRingStack--]; 154| 464k| at[j].nBlockSystem = nNumRingSystems; /* mark the atom */ 155| 464k| if (i == j) ------------------ | Branch (155:25): [True: 374k, False: 90.1k] ------------------ 156| 374k| { 157| 374k| break; 158| 374k| } 159| 464k| } 160| 374k| } 161| 90.1k| else 162| 90.1k| { 163| 90.1k| if (nLowNumber[u] > nLowNumber[i]) ------------------ | Branch (163:21): [True: 85.1k, False: 5.06k] ------------------ 164| 85.1k| { 165| | /* inherit */ 166| 85.1k| nLowNumber[u] = nLowNumber[i]; 167| 85.1k| } 168| 90.1k| } 169| 464k| } 170| 946k| } while (--nTopStackAtom >= 0); ------------------ | Branch (170:14): [True: 464k, False: 481k] ------------------ 171| | 172| | /**************************************************************************** 173| | * 174| | * Find Ring Systems 175| | * Including chain atoms X: A-X-B, where the bonds (of any kind) are bridges. 176| | * 177| | ****************************************************************************/ 178| | 179| | 180| | /* initiation */ 181| | /* start = 0;*/ 182| 481k| nNumRingSystems = 0; 183| 481k| u = start; /* start atom */ 184| 481k| nDfs = 0; 185| 481k| nTopStackAtom = -1; 186| 481k| nTopRingStack = -1; 187| 481k| memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 188| 481k| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 189| | /* push the start atom on the stack */ 190| 481k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 191| 481k| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 192| 481k| nRingStack[++nTopRingStack] = (AT_NUMB) u; 193| | 194| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 195| | nNumConnect = nLenConnect = nMaxNumConnect = 0; 196| |#endif 197| | 198| 481k| do 199| 946k| { 200| | /* advance */ 201| 1.99M| advance_ring: 202| | /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) )*/ 203| | /* replaced due to missing sequence point */ 204| 1.99M| if (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valence > j) ------------------ | Branch (204:13): [True: 1.05M, False: 946k] ------------------ 205| 1.05M| { 206| 1.05M| cNeighNumb[i] ++; 207| 1.05M| u = (int) at[i].neighbor[j]; 208| 1.05M| if (!nDfsNumber[u]) ------------------ | Branch (208:17): [True: 464k, False: 587k] ------------------ 209| 464k| { 210| | /* tree edge, 1st visit -- advance */ 211| 464k| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 212| 464k| nRingStack[++nTopRingStack] = (AT_NUMB) u; 213| 464k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 214| 464k| } 215| 587k| else 216| 587k| { 217| 587k| if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) ------------------ | Branch (217:21): [True: 41.7k, False: 545k] | Branch (217:39): [True: 81.1k, False: 464k] ------------------ 218| 122k| { 219| | /* back edge: u is not a predecessor of i */ 220| 122k| if (nDfsNumber[u] < nDfsNumber[i]) ------------------ | Branch (220:25): [True: 61.4k, False: 61.4k] ------------------ 221| 61.4k| { 222| | /* Back edge, 1st visit: u is ancestor of i. Compare */ 223| 61.4k| if (nLowNumber[i] > nDfsNumber[u]) ------------------ | Branch (223:29): [True: 58.3k, False: 3.15k] ------------------ 224| 58.3k| { 225| 58.3k| nLowNumber[i] = nDfsNumber[u]; 226| 58.3k| } 227| 61.4k| } 228| 122k| } 229| 587k| } 230| 1.05M| goto advance_ring; 231| 1.05M| } 232| 946k| else 233| 946k| { 234| 946k| cNeighNumb[i] = 0; 235| 946k| } 236| | 237| | /* back up */ 238| 946k| if (nDfsNumber[i] == nLowNumber[i]) ------------------ | Branch (238:13): [True: 804k, False: 141k] ------------------ 239| 804k| { 240| | /* found a ring system */ 241| 804k| nNumRingSystems++; 242| | /* unwind nRingStack[] down to i */ 243| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 244| | nNumConnect = 2; 245| | /* data structure: for each ring system nRsConnect[] contains: 246| | * 1) nNumConnect+1 = (number of already discovered neighboring "ring systems" + 1)+1 247| | * 2) nNumAtInRingSystem 248| | * 3) (nNumConnect-1) numbers (IDs) of neighboring ring systems. 249| | * BFS guarantees that each neighboring ring system is encountered only one time 250| | * Number of all neighboring ring systems = (nNumConnect-1)+1 = nNumConnect 251| | * (One additional ring system is where the BFS retracts from the vertex #i, 252| | * except when i=DFS root node. In the latter case there is/are only (nNumConnect-1) 253| | * neighboring ring system(s). 254| | */ 255| |#endif 256| | /* count atoms in a ring system */ 257| 946k| for (nNumAtInRingSystem = 0, j = nTopRingStack; 0 <= j; j--) ------------------ | Branch (257:61): [True: 946k, False: 0] ------------------ 258| 946k| { 259| 946k| nNumAtInRingSystem++; 260| 946k| if (i == (int) nRingStack[j]) ------------------ | Branch (260:21): [True: 804k, False: 141k] ------------------ 261| 804k| { 262| 804k| break; 263| 804k| } 264| 946k| } 265| 946k| while (nTopRingStack >= 0) ------------------ | Branch (265:20): [True: 946k, False: 0] ------------------ 266| 946k| { 267| 946k| j = (int) nRingStack[nTopRingStack--]; 268| 946k| at[j].nRingSystem = (AT_NUMB) nNumRingSystems; /* ring system id */ 269| 946k| at[j].nNumAtInRingSystem = nNumAtInRingSystem; 270| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 271| | for (k = 0; k < at[j].valence; k++) 272| | { 273| | if (( nRs = at[at[j].neighbor[k]].nRingSystem ) && (int) nRs != nNumRingSystems) 274| | { 275| | nRsConnect[nLenConnect + ( nNumConnect++ )] = nRs; /* adjacent ring system id */ 276| | } 277| | } 278| |#endif 279| 946k| if (i == j) ------------------ | Branch (279:21): [True: 804k, False: 141k] ------------------ 280| 804k| { 281| | /* reached atom on the top of nStackAtom[] stack */ 282| 804k| break; 283| 804k| } 284| 946k| } 285| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 286| | nRsConnect[nLenConnect] = nNumConnect; 287| | nRsConnect[nLenConnect + 1] = nNumAtInRingSystem; 288| | nLenConnect += nNumConnect; 289| | if (nMaxNumConnect < nNumConnect) 290| | { 291| | /* max number of neighboring ring systems */ 292| | nMaxNumConnect = nNumConnect; 293| | } 294| |#endif 295| 804k| } 296| 141k| else 297| 141k| { 298| 141k| if (nTopStackAtom > 0) ------------------ | Branch (298:17): [True: 141k, False: 0] ------------------ 299| 141k| { 300| 141k| j = (int) nStackAtom[nTopStackAtom - 1]; 301| | /* inherit nLowNumber */ 302| 141k| if (nLowNumber[j] > nLowNumber[i]) ------------------ | Branch (302:21): [True: 85.1k, False: 56.8k] ------------------ 303| 85.1k| { 304| 85.1k| nLowNumber[j] = nLowNumber[i]; 305| 85.1k| } 306| 141k| } 307| 141k| } 308| 946k| } while (--nTopStackAtom >= 0); ------------------ | Branch (308:14): [True: 464k, False: 481k] ------------------ 309| | 310| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) /* normally disabled */ 311| | nMaxNumConnect++; 312| | if (nNumRingSystems > 1) 313| | { 314| | int nCol = nMaxNumConnect + 1; 315| | int nNumInSyst = nMaxNumConnect; 316| | int nMaxNeigh = nMaxNumConnect - 1; 317| |#define T(a,b) tree[(a)*nCol+b] 318| | if (tree = (AT_NUMB *) inchi_calloc( nCol * ( nNumRingSystems + 1 ), sizeof( tree[0] ) )) 319| | { 320| | int len, neigh; 321| | /* reuse previous allocations */ 322| | AT_NUMB *nNumVisitedNeighbors = nStackAtom; 323| | AT_NUMB *nDistanceFromTerminal = nRingStack; 324| | AT_NUMB *nCurrActiveRingSystem = nDfsNumber; 325| | AT_NUMB *nNextActiveRingSystem = nLowNumber; 326| | int nNumCurrActiveRingSystems, nNumNextActiveRingSystems, pass; 327| | /* build a "condensation graph (actually, a tree)" in which 328| | * each vertex corresponds to a ring system T(row, col) = T(ring syst, neighbors) 329| | * Number of rows = column length = max. number of ring system neighbors + 2 330| | * Number of cols = row length = number of ring systems + 1 331| | * Neighboring ring systems are contiguously stored in a row 332| | * T(i,0) = number of neighbors, 1 <= i <= nNumRingSystems; 333| | * T(i,k) = number of a neighboring ring system, 1 <= k <= T(i,0) 334| | * T(i,nCol-1) = number of atoms in the system #i 335| | */ 336| | for (i = 1, j = 0; len = nRsConnect[j]; i++) 337| | { 338| | T( i, nNumInSyst ) = nRsConnect[j + 1]; 339| | for (k = 2; k < len; k++) 340| | { 341| | neigh = nRsConnect[j + k]; 342| | if (T( i, 0 ) < nMaxNeigh && T( neigh, 0 ) < nMaxNeigh) 343| | { 344| | T( i, 0 )++; 345| | T( neigh, 0 )++; 346| | T( i, T( i, 0 ) ) = neigh; 347| | T( neigh, T( neigh, 0 ) ) = i; 348| | } 349| | else 350| | { 351| | nNumRingSystems = CT_OVERFLOW; /* program error */ /* */ 352| | goto exit_function; 353| | } 354| | } 355| | j += len; 356| | } 357| | /* clear memory */ 358| | memset( nNumVisitedNeighbors, 0, nNumRingSystems * sizeof( nNumVisitedNeighbors[0] ) ); 359| | memset( nDistanceFromTerminal, 0, nNumRingSystems * sizeof( nDistanceFromTerminal[0] ) ); 360| | memset( nCurrActiveRingSystem, 0, nNumRingSystems * sizeof( nCurrActiveRingSystem[0] ) ); 361| | memset( nNextActiveRingSystem, 0, nNumRingSystems * sizeof( nNextActiveRingSystem[0] ) ); 362| | nNumNextActiveRingSystems = 0; 363| | for (i = 0; i < nNumRingSystems; i++) 364| | { 365| | if (1 == T( i + 1, 0 )) 366| | { 367| | nNextActiveRingSystem[i] = 1; /* number of traversed neighbors + 1 */ 368| | nDistanceFromTerminal[i] = 1; 369| | nNumNextActiveRingSystems++; 370| | } 371| | else 372| | { 373| | nNextActiveRingSystem[i] = 0; 374| | nDistanceFromTerminal[i] = 0; 375| | } 376| | nNumVisitedNeighbors[i] = 0; 377| | } 378| | 379| | /* nCurrActiveRingSystem[i] = a sum of: 380| | * 1) +1 if it is or was active 381| | * 2) +(number of neighbors from which it was reached) 382| | * 3) +1 if it was left and not active anymore 383| | */ 384| | pass = 0; 385| | do 386| | { 387| | nNumCurrActiveRingSystems = nNumNextActiveRingSystems; 388| | nNumNextActiveRingSystems = 0; 389| | memcpy( nCurrActiveRingSystem, nNextActiveRingSystem, 390| | nNumRingSystems * sizeof( nNextActiveRingSystem[0] ) ); 391| | for (i = 0; i < nNumRingSystems; i++) 392| | { 393| | if (T( i + 1, 0 ) == nCurrActiveRingSystem[i]) 394| | { 395| | /* on the previous pass currently active ring system i+1 bas been reached 396| | * from all neighbors except one; 397| | * the neighbors from which it was reached have 398| | * T(neigh,0)+1 == nCurrActiveRingSystem[i] 399| | * this ring system has not been left yet 400| | */ 401| | for (k = 1, len = T( i + 1, 0 ); k <= len; k++) 402| | { 403| | neigh = (int) T( i + 1, k ); 404| | if (T( neigh, 0 ) >= nCurrActiveRingSystem[neigh - 1]) 405| | { 406| | if (0 == pass) 407| | { 408| | nDistanceFromTerminal[i] = 1; 409| | } 410| | break; 411| | } 412| | } 413| | if (k <= len) 414| | { 415| | /* neigh was not reached from at least 2 neighbors 416| | * walk along -R- chain (T(neigh,0)==2) up to 417| | * 1) a terminal system, not including it or 418| | * 2) a branching point. 419| | * 420| | * pass = 0: started from terminal systems: 421| | * reach the branching point. 422| | * If chain system next to a terminal system has already been reached 423| | * then walk along it according to Note below 424| | * 425| | * pass > 0: started from branching points 426| | * 2a) If the branching point has not been reached from 2 or more neighbors, 427| | * then include it 428| | * 2b) If the branching point has not been reached from 1 neighbor only, 429| | * then do not include it: it will be a starting point later 430| | * Note: if a chain atom already has nDistanceFromTerminal[i] > 0, then 431| | * the last atom should be the one such that 432| | * its nDistanceFromTerminal[]+1>= nDistanceFromTerminal[] of the 433| | * next in the chain 434| | */ 435| | int bOk = 0; 436| | k = i + 1; /* starting point */ 437| | if (0 == pass && T( k, nNumInSyst ) > 1) 438| | { 439| | nNumNextActiveRingSystems++; /* request next pass */ 440| | continue; /* stop a the terminal ring system */ 441| | } 442| | while (2 == T( neigh, 0 )) 443| | { 444| | /* walk along a chain */ 445| | if (!nNextActiveRingSystem[neigh - 1]) 446| | { 447| | nNextActiveRingSystem[neigh - 1] = 1; /* make neighbor active */ 448| | } 449| | else 450| | if (nDistanceFromTerminal[k - 1] + 1 <= nDistanceFromTerminal[neigh - 1]) 451| | { 452| | /* walking along the chain; already have had a walk */ 453| | /* in the opposite direction at this pass */ 454| | } 455| | else 456| | { 457| | /* k is the last; neigh (it is a bridge -X-) has not been reached */ 458| | bOk = 1; 459| | break; 460| | } 461| | nNextActiveRingSystem[k - 1] ++; /* leave system k */ 462| | if (nNextActiveRingSystem[neigh - 1] < T( neigh, 0 )) 463| | { 464| | nNextActiveRingSystem[neigh - 1] ++; /* add one connection to neigh */ 465| | } 466| | nDistanceFromTerminal[neigh - 1] = nDistanceFromTerminal[k - 1] + 1; 467| | j = ( T( neigh, 1 ) == k ) ? 2 : 1; 468| | k = neigh; 469| | neigh = T( k, j ); /* next in the chain */ 470| | nNumNextActiveRingSystems++; 471| | if (T( k, nNumInSyst ) > 1) 472| | { 473| | bOk = 1; 474| | break; /* stop on a ring system */ 475| | } 476| | } 477| | /* neigh is a terminal or a bridge or a branching point */ 478| | if (2 > T( neigh, 0 )) 479| | { 480| | /* neighbor is a terminal atom */ 481| | if (1 < pass) 482| | { 483| | nNumRingSystems = CT_UNKNOWN_ERR; /* error (debug only) */ /* */ 484| | goto exit_function; 485| | } 486| | continue; 487| | } 488| | if (2 == T( neigh, 0 )) 489| | { 490| | /* neighbor is a bridge */ 491| | continue; 492| | } 493| | /* neighbor is a branching point */ 494| | if (T( neigh, 0 ) > nCurrActiveRingSystem[neigh - 1]) 495| | { 496| | /* move to the neigh (make neigh active): on previous pass it */ 497| | /* has not been reached from 2 or more neighbors */ 498| | if (!nNextActiveRingSystem[neigh - 1]) 499| | { 500| | nNextActiveRingSystem[neigh - 1] = 1; 501| | } 502| | if (nDistanceFromTerminal[neigh - 1] < nDistanceFromTerminal[k - 1] + 1) 503| | { 504| | nDistanceFromTerminal[neigh - 1] = nDistanceFromTerminal[k - 1] + 1; 505| | } 506| | nNextActiveRingSystem[k - 1] ++; /* leave system k */ 507| | if (nNextActiveRingSystem[neigh - 1] < T( neigh, 0 )) 508| | { 509| | nNextActiveRingSystem[neigh - 1] ++; /* add one connection to neigh */ 510| | } 511| | nNumNextActiveRingSystems++; 512| | } 513| | } 514| | } 515| | } 516| | pass++; 517| | } while (nNumNextActiveRingSystems); 518| | 519| | for (i = 0; i < num_atoms; i++) 520| | { 521| | at[i].nDistanceFromTerminal = nDistanceFromTerminal[(int) at[i].nRingSystem - 1]; 522| | } 523| | 524| | inchi_free( tree ); 525| | tree = NULL; 526| |#undef T 527| | } 528| | else 529| | { 530| | nNumRingSystems = CT_OUT_OF_RAM; /* error */ /* */ 531| | goto exit_function; 532| | } 533| | } 534| |#endif 535| | 536| 481k|exit_function: 537| | 538| 481k| if (nStackAtom) ------------------ | Branch (538:9): [True: 481k, False: 0] ------------------ 539| 481k| { 540| 481k| inchi_free( nStackAtom ); ------------------ | | 1152| 481k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 481k, False: 0] | | | Branch (1152:50): [Folded, False: 481k] | | ------------------ ------------------ 541| 481k| } 542| 481k| if (nRingStack) ------------------ | Branch (542:9): [True: 481k, False: 0] ------------------ 543| 481k| { 544| 481k| inchi_free( nRingStack ); ------------------ | | 1152| 481k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 481k, False: 0] | | | Branch (1152:50): [Folded, False: 481k] | | ------------------ ------------------ 545| 481k| } 546| 481k| if (nDfsNumber) ------------------ | Branch (546:9): [True: 481k, False: 0] ------------------ 547| 481k| { 548| 481k| inchi_free( nDfsNumber ); ------------------ | | 1152| 481k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 481k, False: 0] | | | Branch (1152:50): [Folded, False: 481k] | | ------------------ ------------------ 549| 481k| } 550| 481k| if (nLowNumber) ------------------ | Branch (550:9): [True: 481k, False: 0] ------------------ 551| 481k| { 552| 481k| inchi_free( nLowNumber ); ------------------ | | 1152| 481k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 481k, False: 0] | | | Branch (1152:50): [Folded, False: 481k] | | ------------------ ------------------ 553| 481k| } 554| 481k| if (cNeighNumb) ------------------ | Branch (554:9): [True: 481k, False: 0] ------------------ 555| 481k| { 556| 481k| inchi_free( cNeighNumb ); ------------------ | | 1152| 481k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 481k, False: 0] | | | Branch (1152:50): [Folded, False: 481k] | | ------------------ ------------------ 557| 481k| } 558| | 559| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 560| | if (nRsConnect) 561| | inchi_free( nRsConnect ); 562| | if (tree) 563| | inchi_free( tree ); 564| |#endif 565| | 566| 481k| return nNumRingSystems; 567| 481k|} set_common_options_by_parg: 139| 12.7k|{ 140| 12.7k| int got = 0; 141| | 142| | /* Input */ 143| 12.7k| if ( !inchi_stricmp(pArg, "INPAUX") ) ------------------ | Branch (143:10): [True: 0, False: 12.7k] ------------------ 144| 0| { 145| 0| if ( INPUT_NONE == ip->nInputType ) ------------------ | Branch (145:14): [True: 0, False: 0] ------------------ 146| 0| { 147| 0| ip->nInputType = INPUT_INCHI_PLAIN; 148| 0| } 149| 0| got = 1; 150| 0| } 151| 12.7k| else if ( !inchi_memicmp(pArg, "START:", 6) ) ------------------ | Branch (151:15): [True: 0, False: 12.7k] ------------------ 152| 0| { 153| 0| ip->first_struct_number = strtol(pArg + 6, NULL, 10); 154| 0| got = 1; 155| 0| } 156| 12.7k| else if ( !inchi_memicmp(pArg, "END:", 4) ) ------------------ | Branch (156:15): [True: 0, False: 12.7k] ------------------ 157| 0| { 158| 0| ip->last_struct_number = strtol(pArg + 4, NULL, 10); 159| 0| got = 1; 160| 0| } 161| 12.7k| else if ( !inchi_memicmp(pArg, "RECORD:", 7) ) ------------------ | Branch (161:15): [True: 0, False: 12.7k] ------------------ 162| 0| { 163| 0| long num = strtol(pArg + 7, NULL, 10); 164| | /* djb-rwth: removing redundant code */ 165| 0| ip->first_struct_number = num; 166| 0| ip->last_struct_number = num; 167| 0| got = 1; 168| 0| } 169| 12.7k| else if ( !inchi_stricmp(pArg, "NOLABELS") ) ------------------ | Branch (169:15): [True: 0, False: 12.7k] ------------------ 170| 0| { 171| 0| *pbNoStructLabels = 1; 172| 0| got = 1; 173| 0| } 174| 12.7k| else if ( !inchi_stricmp(pArg, "SAVEOPT") ) ------------------ | Branch (174:15): [True: 0, False: 12.7k] ------------------ 175| 0| { 176| 0| (*pbINChIOutputOptions) |= INCHI_OUT_SAVEOPT; ------------------ | | 146| 0|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ 177| 0| got = 1; 178| 0| } 179| | /* Generation */ 180| 12.7k| else if ( !inchi_stricmp(pArg, "AUXNONE") ) ------------------ | Branch (180:15): [True: 0, False: 12.7k] ------------------ 181| 0| { 182| | /* no aux. info */ 183| 0| (*pbINChIOutputOptions) |= INCHI_OUT_NO_AUX_INFO; /* no aux info */ ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 184| 0| (*pbINChIOutputOptions) &= ~INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 185| 0| got = 1; 186| 0| } 187| 12.7k| else if ( !inchi_stricmp(pArg, "MISMATCHISERROR") ) ------------------ | Branch (187:15): [True: 0, False: 12.7k] ------------------ 188| 0| { 189| | /* Consider InChI conversion "problem/mismatch" as error */ 190| 0| (*pbINChIOutputOptions2) |= INCHI_OUT_MISMATCH_AS_ERROR; ------------------ | | 150| 0|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ 191| 0| got = 1; 192| 0| } 193| 12.7k| else if ( !inchi_stricmp(pArg, "OUTERRINCHI") ) ------------------ | Branch (193:15): [True: 0, False: 12.7k] ------------------ 194| 0| { 195| | /* Signify InChI error generation on InChI strings output, not only report to log file */ 196| 0| (*pbINChIOutputOptions2) |= INCHI_OUT_INCHI_GEN_ERROR; ------------------ | | 149| 0|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ 197| 0| got = 1; 198| 0| } 199| | /* InChIKey/InChI hash */ 200| 12.7k| else if ( !inchi_stricmp(pArg, "Key") ) ------------------ | Branch (200:15): [True: 0, False: 12.7k] ------------------ 201| 0| { 202| 0| *pbHashKey = 1; 203| 0| got = 1; 204| 0| } 205| 12.7k| else if ( !inchi_stricmp(pArg, "XHash1") ) ------------------ | Branch (205:15): [True: 0, False: 12.7k] ------------------ 206| 0| { 207| 0| *pbHashXtra1 = 1; 208| 0| got = 1; 209| 0| } 210| 12.7k| else if ( !inchi_stricmp(pArg, "XHash2") ) ------------------ | Branch (210:15): [True: 0, False: 12.7k] ------------------ 211| 0| { 212| 0| *pbHashXtra2 = 1; 213| 0| got = 1; 214| 0| } 215| | /* (@nnuk :: NaumanUllahKhan) 216| | * Parameter option that deals with Molecular Inorganics (ON by default) 217| | */ 218| 12.7k| else if (!inchi_stricmp(pArg, "MolecularInorganics")) ------------------ | Branch (218:14): [True: 0, False: 12.7k] ------------------ 219| 0| { 220| 0| *pbMolecularInorganics = 1; 221| 0| *pbNPZz = 1; 222| 0| got = 1; 223| 0| } 224| | /* All modes (std and non-std InChI) structure perception options */ 225| | /* These options DO NOT TURN OFF Std flag */ 226| 12.7k| else if ( !inchi_stricmp(pArg, "SNON") ) ------------------ | Branch (226:15): [True: 0, False: 12.7k] ------------------ 227| 0| { 228| 0| (*pbVer1DefaultMode) &= ~REQ_MODE_STEREO; /* no stereo */ ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 229| 0| (*pnMode) &= ~(REQ_MODE_RACEMIC_STEREO | REQ_MODE_RELATIVE_STEREO | REQ_MODE_CHIR_FLG_STEREO); ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ (*pnMode) &= ~(REQ_MODE_RACEMIC_STEREO | REQ_MODE_RELATIVE_STEREO | REQ_MODE_CHIR_FLG_STEREO); ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ (*pnMode) &= ~(REQ_MODE_RACEMIC_STEREO | REQ_MODE_RELATIVE_STEREO | REQ_MODE_CHIR_FLG_STEREO); ------------------ | | 34| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 230| 0| got = 1; 231| 0| } 232| 12.7k| else if ( !inchi_stricmp(pArg, "NEWPSOFF") ) ------------------ | Branch (232:15): [True: 0, False: 12.7k] ------------------ 233| 0| { 234| 0| *pbPointedEdgeStereo = 0; 235| 0| got = 1; 236| 0| } 237| 12.7k| else if ( !inchi_stricmp(pArg, "DONOTADDH") ) ------------------ | Branch (237:15): [True: 0, False: 12.7k] ------------------ 238| 0| { 239| 0| *pbDoNotAddH = 1; 240| 0| got = 1; 241| 0| } 242| 12.7k| else if ( !inchi_stricmp(pArg, "LooseTSACheck") ) ------------------ | Branch (242:15): [True: 0, False: 12.7k] ------------------ 243| 0| { 244| 0| (*pbLooseTSACheck) = 1; 245| 0| got = 1; 246| 0| } 247| 12.7k| else if (!inchi_stricmp(pArg, "EnhancedStereochemistry")) ------------------ | Branch (247:14): [True: 0, False: 12.7k] ------------------ 248| 0| { 249| 0| *pbEnhancedStereochemistry = 1; 250| 0| got = 1; 251| 0| } 252| | 253| 12.7k|#ifndef USE_STDINCHI_API 254| | /* These options DO TURN OFF Std flag */ 255| 12.7k| else if ( !inchi_stricmp(pArg, "SREL") ) ------------------ | Branch (255:15): [True: 0, False: 12.7k] ------------------ 256| 0| { 257| 0| if ( (*pnMode) & REQ_MODE_RACEMIC_STEREO ) ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (257:14): [True: 0, False: 0] ------------------ 258| 0| { 259| 0| (*pnMode) ^= REQ_MODE_RACEMIC_STEREO; ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 260| 0| } 261| 0| if ( (*pnMode) & REQ_MODE_CHIR_FLG_STEREO ) ------------------ | | 34| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ | Branch (261:14): [True: 0, False: 0] ------------------ 262| 0| { 263| 0| (*pnMode) ^= REQ_MODE_CHIR_FLG_STEREO; ------------------ | | 34| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 264| 0| } 265| 0| (*pnMode) |= REQ_MODE_RELATIVE_STEREO; ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 266| 0| (*pnMode) |= REQ_MODE_STEREO; ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 267| 0| *pbStdFormat = 0; 268| 0| got = 1; 269| 0| } 270| 12.7k| else if ( !inchi_stricmp(pArg, "SRAC") ) ------------------ | Branch (270:15): [True: 0, False: 12.7k] ------------------ 271| 0| { 272| 0| if ( (*pnMode) & REQ_MODE_RELATIVE_STEREO ) ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (272:14): [True: 0, False: 0] ------------------ 273| 0| { 274| 0| (*pnMode) ^= REQ_MODE_RELATIVE_STEREO; ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 275| 0| } 276| 0| if ( (*pnMode) & REQ_MODE_CHIR_FLG_STEREO ) ------------------ | | 34| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ | Branch (276:14): [True: 0, False: 0] ------------------ 277| 0| { 278| 0| (*pnMode) ^= REQ_MODE_CHIR_FLG_STEREO; ------------------ | | 34| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 279| 0| } 280| 0| (*pnMode) |= REQ_MODE_RACEMIC_STEREO; ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 281| 0| (*pnMode) |= REQ_MODE_STEREO; ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 282| 0| *pbStdFormat = 0; 283| 0| got = 1; 284| 0| } 285| 12.7k| else if ( !inchi_stricmp(pArg, "SUCF") ) ------------------ | Branch (285:15): [True: 0, False: 12.7k] ------------------ 286| 0| { 287| 0| if ( (*pnMode) & REQ_MODE_RELATIVE_STEREO ) ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (287:14): [True: 0, False: 0] ------------------ 288| 0| { 289| 0| (*pnMode) ^= REQ_MODE_RELATIVE_STEREO; ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 290| 0| } 291| 0| if ( (*pnMode) & REQ_MODE_RACEMIC_STEREO ) ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (291:14): [True: 0, False: 0] ------------------ 292| 0| { 293| 0| (*pnMode) ^= REQ_MODE_RACEMIC_STEREO; ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 294| 0| } 295| 0| (*pnMode) |= REQ_MODE_CHIR_FLG_STEREO; /* stereo defined by the Chiral flag */ ------------------ | | 34| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 296| 0| (*pnMode) |= REQ_MODE_STEREO; ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 297| 0| *pbStdFormat = 0; 298| 0| got = 1; 299| 0| } 300| 12.7k| else if ( !inchi_stricmp(pArg, "ChiralFlagON") ) ------------------ | Branch (300:15): [True: 0, False: 12.7k] ------------------ 301| 0| { 302| | /* used only with /SUCF */ 303| | /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ 304| 0| (*pbForcedChiralFlag) &= ~FLAG_SET_INP_AT_NONCHIRAL; ------------------ | | 672| 0|#define FLAG_SET_INP_AT_NONCHIRAL 8 ------------------ 305| 0| (*pbForcedChiralFlag) |= FLAG_SET_INP_AT_CHIRAL; ------------------ | | 671| 0|#define FLAG_SET_INP_AT_CHIRAL 4 ------------------ 306| 0| got = 1; 307| 0| } 308| 12.7k| else if ( !inchi_stricmp(pArg, "ChiralFlagOFF") ) ------------------ | Branch (308:15): [True: 0, False: 12.7k] ------------------ 309| 0| { 310| | /* used only with /SUCF */ 311| | /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ 312| 0| (*pbForcedChiralFlag) &= ~FLAG_SET_INP_AT_CHIRAL; ------------------ | | 671| 0|#define FLAG_SET_INP_AT_CHIRAL 4 ------------------ 313| 0| (*pbForcedChiralFlag) |= FLAG_SET_INP_AT_NONCHIRAL; ------------------ | | 672| 0|#define FLAG_SET_INP_AT_NONCHIRAL 8 ------------------ 314| 0| got = 1; 315| 0| } 316| | 317| | /*--- Non-std InChI creation options ---*/ 318| | /* These options DO TURN OFF Std flag */ 319| 12.7k| else if ( !inchi_stricmp(pArg, "SUU") ) ------------------ | Branch (319:15): [True: 0, False: 12.7k] ------------------ 320| 0| { 321| | /* include omitted undef/unknown stereo */ 322| 0| (*pbVer1DefaultMode) &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU); ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ (*pbVer1DefaultMode) &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU); ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 323| 0| *pbStdFormat = 0; 324| 0| got = 1; 325| 0| } 326| | /* 327| | * (@nnuk) 328| | * Use the legacy salt and metal-bond handling. 329| | * This disables Molecular Inorganics and produces non-standard InChI. 330| | */ 331| 12.7k| else if (!inchi_stricmp(pArg, "LegacyMetalHandling")) ------------------ | Branch (331:14): [True: 0, False: 12.7k] ------------------ 332| 0| { 333| 0| *pbMolecularInorganics = 0; 334| 0| *pbNPZz = 1; 335| 0| *pbStdFormat = 0; 336| 0| got = 1; 337| 0| } 338| 12.7k| else if ( !inchi_stricmp(pArg, "SLUUD") ) ------------------ | Branch (338:15): [True: 0, False: 12.7k] ------------------ 339| 0| { 340| | /* make labels for unknown and undefined stereo different */ 341| 0| (*pbVer1DefaultMode) |= REQ_MODE_DIFF_UU_STEREO; ------------------ | | 40| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ 342| 0| *pbStdFormat = 0; 343| 0| got = 1; 344| 0| } 345| | /* FixedH */ 346| 12.7k| else if ( !inchi_stricmp(pArg, "FIXEDH") ) ------------------ | Branch (346:15): [True: 0, False: 12.7k] ------------------ 347| 0| { 348| 0| (*pbVer1DefaultMode) |= REQ_MODE_BASIC; /* tautomeric */ ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 349| 0| *pbStdFormat = 0; 350| 0| got = 1; 351| 0| } 352| | /* RecMet */ 353| 12.7k| else if ( !inchi_stricmp(pArg, "RECMET") ) ------------------ | Branch (353:15): [True: 0, False: 12.7k] ------------------ 354| 0| { 355| | /* reconnect metals */ 356| 0| *pbReconnectCoord = 1; 357| 0| *pbStdFormat = 0; 358| 0| got = 1; 359| 0| } 360| 12.7k|#if ( KETO_ENOL_TAUT == 1 ) 361| 12.7k| else if ( !inchi_stricmp(pArg, "KET") ) ------------------ | Branch (361:15): [True: 0, False: 12.7k] ------------------ 362| 0| { 363| 0| *pbKetoEnolTaut = 1; 364| 0| *pbStdFormat = 0; 365| 0| got = 1; 366| 0| } 367| 12.7k|#endif 368| 12.7k|#if ( TAUT_15_NON_RING == 1 ) 369| 12.7k| else if ( !inchi_stricmp(pArg, "15T") ) ------------------ | Branch (369:15): [True: 0, False: 12.7k] ------------------ 370| 0| { 371| 0| *pb15TautNonRing = 1; 372| 0| *pbStdFormat = 0; 373| 0| got = 1; 374| 0| } 375| 12.7k|#endif 376| | 377| 12.7k|#if ( TAUT_PT_22_00 == 1 ) 378| 12.7k| else if ( !inchi_stricmp(pArg, "PT_22_00") ) ------------------ | Branch (378:15): [True: 0, False: 12.7k] ------------------ 379| 0| { 380| 0| *pbPT_22_00_Taut = 1; 381| 0| *pbStdFormat = 0; 382| 0| } 383| 12.7k|#endif 384| | 385| 12.7k|#if ( TAUT_PT_16_00 == 1 ) 386| 12.7k| else if ( !inchi_stricmp(pArg, "PT_16_00") ) ------------------ | Branch (386:15): [True: 0, False: 12.7k] ------------------ 387| 0| { 388| 0| *pbPT_16_00_Taut = 1; 389| 0| *pbStdFormat = 0; 390| 0| } 391| 12.7k|#endif 392| | 393| 12.7k|#if ( TAUT_PT_06_00 == 1 ) 394| 12.7k| else if ( !inchi_stricmp(pArg, "PT_06_00") ) ------------------ | Branch (394:15): [True: 0, False: 12.7k] ------------------ 395| 0| { 396| 0| *pbPT_06_00_Taut = 1; 397| 0| *pbStdFormat = 0; 398| 0| } 399| 12.7k|#endif 400| | 401| 12.7k|#if ( TAUT_PT_39_00 == 1 ) 402| 12.7k| else if ( !inchi_stricmp(pArg, "PT_39_00") ) ------------------ | Branch (402:15): [True: 0, False: 12.7k] ------------------ 403| 0| { 404| 0| *pbPT_39_00_Taut = 1; 405| 0| *pbStdFormat = 0; 406| 0| } 407| 12.7k|#endif 408| | 409| 12.7k|#if ( TAUT_PT_13_00 == 1 ) 410| 12.7k| else if ( !inchi_stricmp(pArg, "PT_13_00") ) ------------------ | Branch (410:15): [True: 0, False: 12.7k] ------------------ 411| 0| { 412| 0| *pbPT_13_00_Taut = 1; 413| 0| *pbStdFormat = 0; 414| 0| } 415| 12.7k|#endif 416| | 417| 12.7k|#if ( TAUT_PT_18_00 == 1 ) 418| 12.7k| else if ( !inchi_stricmp(pArg, "PT_18_00") ) ------------------ | Branch (418:15): [True: 0, False: 12.7k] ------------------ 419| 0| { 420| 0| *pbPT_18_00_Taut = 1; 421| 0| *pbStdFormat = 0; 422| 0| } 423| 12.7k|#endif 424| | 425| 12.7k| else if ( !inchi_stricmp(pArg, "LargeMolecules") ) ------------------ | Branch (425:15): [True: 0, False: 12.7k] ------------------ 426| 0| { 427| 0| *pbLargeMolecules = 1; 428| 0| got = 1; 429| 0| } 430| 12.7k| else if ( !inchi_stricmp(pArg, "Polymers") ) ------------------ | Branch (430:15): [True: 0, False: 12.7k] ------------------ 431| 0| { 432| 0| *pbPolymers = POLYMERS_MODERN; ------------------ | | 1216| 0|#define POLYMERS_MODERN 1 /* v. 1.06+ way to treat polymers with Zz */ ------------------ 433| 0| got = 1; 434| 0| } 435| 12.7k| else if ( !inchi_stricmp(pArg, "Polymers105") ) ------------------ | Branch (435:15): [True: 0, False: 12.7k] ------------------ 436| 0| { 437| 0| *pbPolymers = POLYMERS_LEGACY; ------------------ | | 1217| 0|#define POLYMERS_LEGACY 2 /* v. 1.05 mode, no explicit Zz (internally they are here) */ ------------------ 438| 0| got = 1; 439| 0| } 440| 12.7k| else if ( !inchi_stricmp(pArg, "NPZz") ) ------------------ | Branch (440:15): [True: 0, False: 12.7k] ------------------ 441| 0| { 442| 0| *pbNPZz = 1; 443| 0| got = 1; 444| 0| } 445| 12.7k| else if ( !inchi_stricmp(pArg, "NoWarnings") ) ------------------ | Branch (445:15): [True: 0, False: 12.7k] ------------------ 446| 0| { 447| 0| *pbNoWarnings = 1; 448| 0| got = 1; 449| 0| } 450| 12.7k| else if ( !inchi_stricmp(pArg, "MergeHash") ) ------------------ | Branch (450:15): [True: 0, False: 12.7k] ------------------ 451| 0| { 452| 0| *pbMergeHash = 1; 453| 0| got = 1; 454| 0| } 455| 12.7k| else if ( !inchi_stricmp(pArg, "NoInChI") || !inchi_stricmp(pArg, "HideInChI") ) ------------------ | Branch (455:15): [True: 0, False: 12.7k] | Branch (455:50): [True: 0, False: 12.7k] ------------------ 456| 0| { 457| 0| *pbHideInChI = 1; 458| 0| got = 1; 459| 0| } 460| 12.7k| else if ( !inchi_stricmp(pArg, "FoldCRU") ) /* v. 1.06 */ ------------------ | Branch (460:15): [True: 0, False: 12.7k] ------------------ 461| 0| { 462| 0| *pbFoldPolymerSRU = 1; 463| 0| got = 1; 464| 0| } 465| 12.7k| else if ( !inchi_stricmp(pArg, "FoldSRU") ) /* v. 1.06 */ ------------------ | Branch (465:15): [True: 0, False: 12.7k] ------------------ 466| 0| { 467| 0| *pbFoldPolymerSRU = 1; 468| 0| got = 1; 469| 0| } 470| 12.7k| else if ( !inchi_memicmp(pArg, "FrameShift:", 11) ) ------------------ | Branch (470:15): [True: 0, False: 12.7k] ------------------ 471| 0| { 472| 0| int k; 473| 0| char wrd[256]; 474| 0| k = 0; 475| 0| mystrncpy(wrd, pArg + 11, 256); 476| 0| lrtrim(wrd, &k); 477| 0| if ( k ) ------------------ | Branch (477:14): [True: 0, False: 0] ------------------ 478| 0| { 479| 0| if ( !inchi_stricmp(wrd, "None") ) ------------------ | Branch (479:18): [True: 0, False: 0] ------------------ 480| 0| { 481| 0| *pbFrameShiftScheme = FSS_NONE; 482| 0| } 483| 0| else if ( !inchi_stricmp(wrd, "Cyclize") ) ------------------ | Branch (483:23): [True: 0, False: 0] ------------------ 484| 0| { 485| 0| *pbFrameShiftScheme = FSS_STARS_CYCLED; 486| 0| } 487| 0| else if ( !inchi_stricmp(wrd, "MoveStars") ) ------------------ | Branch (487:23): [True: 0, False: 0] ------------------ 488| 0| { 489| 0| *pbFrameShiftScheme = FSS_STARS_OPENED; 490| 0| } 491| 0| else if ( !inchi_stricmp(wrd, "MoveBrackets") ) ------------------ | Branch (491:23): [True: 0, False: 0] ------------------ 492| 0| { 493| 0| *pbFrameShiftScheme = FSS_STARS_ENDS_OPENED; 494| 0| } 495| 0| } 496| 0| else 497| 0| { 498| 0| *pbFrameShiftScheme = FSS_STARS_CYCLED; 499| 0| } 500| 0| got = 1; 501| 0| } 502| 12.7k| else if ( !inchi_stricmp(pArg, "NoFrameShift") ) ------------------ | Branch (502:15): [True: 0, False: 12.7k] ------------------ 503| 0| { 504| 0| *pbFrameShiftScheme = FSS_NONE; 505| 0| got = 1; 506| 0| } 507| 12.7k| else if ( !inchi_stricmp(pArg, "NoEdits") ) ------------------ | Branch (507:15): [True: 0, False: 12.7k] ------------------ 508| 0| { 509| 0| *pbFoldPolymerSRU = 0; 510| 0| *pbFrameShiftScheme = FSS_NONE; 511| 0| got = 1; 512| 0| } 513| 12.7k| else if ( !inchi_stricmp(pArg, "SATZZ") ) ------------------ | Branch (513:15): [True: 0, False: 12.7k] ------------------ 514| 0| { 515| 0| *pbStereoAtZz = 1; 516| 0| got = 1; 517| 0| } 518| | 519| | 520| 12.7k|#endif /* ifndef USE_STDINCHI_API */ 521| | 522| 12.7k| if ( !got && developer_options ) ------------------ | Branch (522:10): [True: 12.7k, False: 0] | Branch (522:18): [True: 0, False: 12.7k] ------------------ 523| 0| { 524| | 525| 0| if ( !inchi_stricmp(pArg, "PGO") ) ------------------ | Branch (525:14): [True: 0, False: 0] ------------------ 526| 0| { 527| | /* PGO : extract all good MOLfiles into the problem file */ 528| 0| ip->bSaveAllGoodStructsAsProblem = 1; 529| 0| got = 1; 530| 0| } 531| 0|#if ( ALLOW_SUBSTRUCTURE_FILTERING== 1 ) 532| 0| else if ( !inchi_stricmp(pArg, "FilterSS") ) ------------------ | Branch (532:19): [True: 0, False: 0] ------------------ 533| 0| { 534| 0| ip->bFilterSS = 1; 535| 0| got = 1; 536| 0| } 537| 0| else if ( !inchi_stricmp(pArg, "InvFilterSS") ) ------------------ | Branch (537:19): [True: 0, False: 0] ------------------ 538| 0| { 539| 0| ip->bFilterSS = -1; 540| 0| got = 1; 541| 0| } 542| 0|#endif 543| | /* Options below DO TURN OFF Std flag */ 544| 0| if ( !inchi_stricmp(pArg, "FNUDOFF") ) ------------------ | Branch (544:14): [True: 0, False: 0] ------------------ 545| 0| { 546| 0| ip->bFixNonUniformDraw = 0; 547| 0| *pbStdFormat = 0; 548| 0| got = 1; 549| 0| } 550| 0| else if ( !inchi_stricmp(pArg, "FixSp3bugOFF") ) ------------------ | Branch (550:19): [True: 0, False: 0] ------------------ 551| 0| { 552| 0| *pbFixSp3bug = 0; 553| 0| *pbStdFormat = 0; 554| 0| got = 1; 555| 0| } 556| 0| else if ( !inchi_stricmp(pArg, "FBOFF") ) ------------------ | Branch (556:19): [True: 0, False: 0] ------------------ 557| 0| { 558| 0| *pbFixSp3bug = 0; 559| 0| *pbStdFormat = 0; 560| 0| got = 1; 561| 0| } 562| 0| else if ( !inchi_stricmp(pArg, "FB2OFF") ) ------------------ | Branch (562:19): [True: 0, False: 0] ------------------ 563| 0| { 564| 0| *pbFixFB2 = 0; 565| 0| *pbStdFormat = 0; 566| 0| got = 1; 567| 0| } 568| 0| else if ( !inchi_stricmp(pArg, "SPXYZOFF") ) ------------------ | Branch (568:19): [True: 0, False: 0] ------------------ 569| 0| { 570| 0| *pbAddPhosphineStereo = 0; 571| 0| *pbStdFormat = 0; 572| 0| got = 1; 573| 0| } 574| 0| else if ( !inchi_stricmp(pArg, "SASXYZOFF") ) ------------------ | Branch (574:19): [True: 0, False: 0] ------------------ 575| 0| { 576| 0| *pbAddArsineStereo = 0; 577| 0| *pbStdFormat = 0; 578| 0| got = 1; 579| 0| } 580| 0| else if ( !inchi_stricmp(pArg, "Polymers105+") ) ------------------ | Branch (580:19): [True: 0, False: 0] ------------------ 581| 0| { 582| 0| *pbPolymers = POLYMERS_LEGACY_PLUS; ------------------ | | 1218| 0|#define POLYMERS_LEGACY_PLUS 3 /* v. 1.05 mode with an addition of that in all ------------------ 583| 0| *pbStdFormat = 0; 584| 0| got = 1; 585| 0| } 586| | 587| | 588| 0| } 589| | 590| 12.7k| return got; 591| 12.7k|} ReadCommandLineParms: 604| 12.7k|{ 605| |#if (BUILD_WITH_ENG_OPTIONS==1) 606| | const int developer_options = 1; 607| |#else 608| 12.7k| const int developer_options = 0; 609| 12.7k|#endif 610| 12.7k| const char* q; 611| 12.7k| const char* ext[MAX_NUM_PATHS + 1]; 612| 12.7k| const char* pArg; 613| 12.7k| char szNameSuffix[32], szOutputPath[512]; 614| | 615| 12.7k| unsigned long ul; 616| | 617| 12.7k| double t = 0; 618| | 619| 12.7k| int bVer1Options = 1; 620| 12.7k| int nMode = 0; 621| 12.7k| int nReleaseMode = nMode | (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO); ------------------ | | 15| 12.7k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ int nReleaseMode = nMode | (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO); ------------------ | | 16| 12.7k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ int nReleaseMode = nMode | (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO); ------------------ | | 17| 12.7k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ int nReleaseMode = nMode | (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO); ------------------ | | 19| 12.7k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 622| 12.7k| INCHI_MODE bVer1DefaultMode = VER103_DEFAULT_MODE; ------------------ | | 47| 12.7k|#define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 16| 12.7k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 17| 12.7k|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 19| 12.7k|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ | | 48| 12.7k| REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 32| 12.7k|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ | | ------------------ | | REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 30| 12.7k|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ | | ------------------ ------------------ 623| | 624| 12.7k| int bNameSuffix; 625| 12.7k| int bOutputPath; 626| 12.7k| int bMergeAllInputStructures; 627| 12.7k| int bForcedChiralFlag = 0; 628| | 629| 12.7k| int bDisconnectSalts = (DISCONNECT_SALTS == 1); ------------------ | | 525| 12.7k|#define DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont */ /* djb-rwth: default 1 */ ------------------ 630| 12.7k| int bDoNotAddH = 0; 631| 12.7k| int bRecognizedOption; 632| 12.7k| int bTgFlagVariableProtons = 1; 633| 12.7k| int bTgFlagHardAddRenProtons = 1; 634| 12.7k| int bReconnectCoord = (RECONNECT_METALS == 1); ------------------ | | 553| 12.7k|#define RECONNECT_METALS 0 /* 1=> by default add reconnected layer in case of coord. ------------------ 635| 12.7k| int bDisconnectCoord = (DISCONNECT_METALS == 1); ------------------ | | 552| 12.7k|#define DISCONNECT_METALS 1 /* make main layer disconnected */ /* djb-rwth: default 1 */ ------------------ 636| 12.7k| int bDisconnectCoordChkVal = (CHECK_METAL_VALENCE == 1); ------------------ | | 555| 12.7k|#define CHECK_METAL_VALENCE 0 /* 1=> disconnect only metals that have abnormal valence */ ------------------ 637| 12.7k| int bMovePositiveCharges = (MOVE_CHARGES == 1); ------------------ | | 535| 12.7k|#define MOVE_CHARGES 1 /* 1 => take moveable charges into account */ ------------------ 638| 12.7k| int bAcidTautomerism = (DISCONNECT_SALTS == 1) ? (TEST_REMOVE_S_ATOMS == 1 ? 2 : 1) : 0; ------------------ | | 525| 12.7k|#define DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont */ /* djb-rwth: default 1 */ ------------------ int bAcidTautomerism = (DISCONNECT_SALTS == 1) ? (TEST_REMOVE_S_ATOMS == 1 ? 2 : 1) : 0; ------------------ | | 526| 12.7k|#define TEST_REMOVE_S_ATOMS 1 /* 1=>default: after merging into one group test & ------------------ | Branch (638:28): [True: 12.7k, Folded] | Branch (638:55): [True: 12.7k, Folded] ------------------ 639| 12.7k| int bUnchargedAcidTaut = (CHARGED_SALTS_ONLY == 0); ------------------ | | 529| 12.7k|#define CHARGED_SALTS_ONLY 1 /* 1=>(default)do not test far salts tautomerism if ------------------ 640| 12.7k| int bMergeSaltTGroups = (DISCONNECT_SALTS == 1); ------------------ | | 525| 12.7k|#define DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont */ /* djb-rwth: default 1 */ ------------------ 641| 12.7k| int bEnhancedStereochemistry = 0; 642| 12.7k|#if ( MIN_SB_RING_SIZE > 0 ) 643| 12.7k| int nMinDbRinSize = MIN_SB_RING_SIZE, mdbr = 0; ------------------ | | 592| 12.7k|#define MIN_SB_RING_SIZE 8 /* do not assume stereo bonds in rings containing 3..MIN_SB_RING_SIZE-1 atoms */ ------------------ 644| 12.7k|#endif 645| 12.7k|#ifdef STEREO_WEDGE_ONLY 646| 12.7k| int bPointedEdgeStereo = STEREO_WEDGE_ONLY; /* NEWPS TG_FLAG_POINTED_EDGE_STEREO */ ------------------ | | 616| 12.7k|#define STEREO_WEDGE_ONLY 1 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends 1.12Beta */ ------------------ 647| 12.7k|#endif 648| |#if ( FIX_ADJ_RAD == 1 ) 649| | int bFixAdjacentRad = 0; 650| |#endif 651| 12.7k| int bAddPhosphineStereo = 1; 652| 12.7k| int bAddArsineStereo = 1; 653| 12.7k| int bFixSp3bug = 1; 654| 12.7k| int bFixFB2 = 1; 655| 12.7k| int bKetoEnolTaut = 0; 656| 12.7k| int b15TautNonRing = 0; 657| 12.7k| int bPT_22_00_Taut = 0; 658| 12.7k| int bPT_16_00_Taut = 0; 659| 12.7k| int bPT_06_00_Taut = 0; 660| 12.7k| int bPT_39_00_Taut = 0; 661| 12.7k| int bPT_13_00_Taut = 0; 662| 12.7k| int bPT_18_00_Taut = 0; 663| 12.7k| int bStdFormat = 1; 664| 12.7k| int bHashKey = 0; 665| 12.7k| int bHashXtra1 = 0; 666| 12.7k| int bHashXtra2 = 0; 667| 12.7k| int bLargeMolecules = 0; 668| 12.7k| int bPolymers = POLYMERS_NO; ------------------ | | 1215| 12.7k|#define POLYMERS_NO 0 /* ignore polymers */ ------------------ 669| |#ifdef TARGET_LIB_FOR_WINCHI 670| | int bFoldPolymerSRU = 0; 671| | int bFrameShiftScheme = FSS_STARS_CYCLED; 672| |#else 673| 12.7k| int bFoldPolymerSRU = 0; 674| 12.7k| int bFrameShiftScheme = FSS_STARS_CYCLED; 675| 12.7k|#endif 676| 12.7k| int bLooseTSACheck = 0; 677| 12.7k| int bStereoAtZz = 0; 678| 12.7k| int bNPZz = 1; 679| 12.7k| int bNoWarnings = 0; 680| 12.7k| int bMergeHash = 0; 681| 12.7k| int bHideInChI = 0; 682| 12.7k| int bMolecularInorganics = 1; /* @nnuk */ 683| 12.7k| int bOutputStyle = INCHI_OUT_PLAIN_TEXT; ------------------ | | 135| 12.7k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 684| 12.7k| int bDisplay = 0; 685| 12.7k| int bNoStructLabels = 0; 686| 12.7k| int bOutputMolfileOnly = 0; 687| 12.7k| int bOutputMolfileDT = 0; 688| 12.7k| int bOutputMolfileSplit = 0; 689| 12.7k| int bDisplayCompositeResults = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 690| 12.7k| int nFontSize = -9; /* djb-rwth: ignoring LLVM warning: variable used */ 691| 12.7k| int bINChIOutputOptions2 = 0; 692| |#ifdef TARGET_LIB_FOR_WINCHI 693| | int is_gui = 1; 694| | int bINChIOutputOptions = INCHI_OUT_EMBED_REC; /* embed reconnected & output full aux info */ 695| | int bCompareComponents = CMP_COMPONENTS; 696| |#else 697| 12.7k| int is_gui = 0; 698| 12.7k| int bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0); ------------------ | | 560| 12.7k|#define EMBED_REC_METALS_INCHI 1 /* 1=> (default) output Reconnected embedded in Disconnected INChI; ------------------ int bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0); ------------------ | | 132| 12.7k|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ | Branch (698:32): [True: 12.7k, Folded] ------------------ 699| 12.7k| int bCompareComponents = 0; 700| 12.7k|#endif 701| 12.7k|#if ( READ_INCHI_STRING == 1 ) 702| 12.7k| int bDisplayIfRestoreWarnings = 0; 703| 12.7k|#endif 704| |#if ( BUILD_WITH_AMI == 1 ) && ( OUTPUT_FILE_EXT == 1 ) 705| | int numOutNameExt; 706| | char szOutNameExt[3][128]; 707| |#endif 708| | 709| 12.7k| int i, k, c, got; 710| 12.7k| int timeout_set_warning = 0; 711| 12.7k| int timeout_set_error = 0; 712| | 713| 12.7k| ext[0] = ".mol"; 714| 12.7k| ext[1] = bVer1Options ? ".txt" : ".ich"; ------------------ | Branch (714:14): [True: 12.7k, False: 0] ------------------ 715| 12.7k| ext[2] = ".log"; 716| 12.7k| ext[3] = ".prb"; 717| 12.7k| ext[4] = ""; 718| | 719| | /* Init table of parameters */ 720| 12.7k| memset(ip, 0, sizeof(*ip)); /* djb-rwth: memset_s C11/Annex K variant? */ 721| | 722| | /* Default are StdInChI generation options */ 723| 12.7k| bVer1DefaultMode &= ~REQ_MODE_BASIC; /* "FIXEDH - OFF" */ ------------------ | | 15| 12.7k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 724| 12.7k| bReconnectCoord = 0; /* "RECMET - OFF" */ 725| 12.7k| bPointedEdgeStereo = 1; /* "NEWPS" */ 726| 12.7k| ip->bFixNonUniformDraw = 1; /* "FNUD" */ 727| | 728| |#ifndef COMPILE_ANSI_ONLY 729| | strcpy(ip->tdp.ReqShownFoundTxt[ilSHOWN], "Shown"); 730| | ip->dp.sdp.tdp = &ip->tdp; 731| | ip->dp.pdp = &ip->pdp; 732| |#endif 733| 12.7k| memset(szNameSuffix, 0, sizeof(szNameSuffix)); /* djb-rwth: memset_s C11/Annex K variant? */ 734| 12.7k| bNameSuffix = 0; 735| 12.7k| memset(szOutputPath, 0, sizeof(szOutputPath)); /* djb-rwth: memset_s C11/Annex K variant? */ 736| 12.7k| bOutputPath = 0; 737| |#if( OUTPUT_FILE_EXT == 1 ) 738| | memset(szOutNameExt, 0, sizeof(szOutNameExt)); /* djb-rwth: memset_s C11/Annex K variant? */ 739| | numOutNameExt = 0; 740| |#endif 741| 12.7k| bMergeAllInputStructures = 0; 742| 12.7k|#ifdef TARGET_API_LIB 743| 12.7k| ip->msec_MaxTime = 0; /* milliseconds, default in libinchi: unlimited */ 744| |#else 745| | ip->msec_MaxTime = 60000; /* milliseconds, default: 60 sec */ 746| |#endif 747| 12.7k| * ulDisplTime = 0; 748| | 749| 12.7k| if ( bReleaseVersion ) ------------------ | Branch (749:10): [True: 12.7k, False: 0] ------------------ 750| 12.7k| { 751| | /* normal */ 752| 12.7k| ip->bAbcNumbers = 0; 753| 12.7k| ip->bCtPredecessors = 0; 754| 12.7k| } 755| 0| else 756| 0| { 757| 0| nReleaseMode = 0; 758| 0| } 759| 12.7k| if ( bVer1Options ) ------------------ | Branch (759:10): [True: 12.7k, False: 0] ------------------ 760| 12.7k| { 761| 12.7k| bNameSuffix = 1; 762| 12.7k| szNameSuffix[0] = '\0'; 763| 12.7k| } 764| | 765| 12.7k|#if ( ALLOW_SUBSTRUCTURE_FILTERING== 1 ) 766| 12.7k| ip->bFilterSS = 0; 767| 12.7k|#endif 768| | 769| | 770| | 771| | /* Analyze command line switches */ 772| 25.4k| for ( i = 1; i < argc; i++ ) ------------------ | Branch (772:18): [True: 12.7k, False: 12.7k] ------------------ 773| 12.7k| { 774| | 775| 12.7k| if ( is_gui && INCHI_OPTION_PREFX == argv[i][0] && INCHI_OPTION_PREFX != argv[i][1] ) ------------------ | | 231| 0|#define INCHI_OPTION_PREFX '-' ------------------ if ( is_gui && INCHI_OPTION_PREFX == argv[i][0] && INCHI_OPTION_PREFX != argv[i][1] ) ------------------ | | 231| 0|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (775:14): [True: 0, False: 12.7k] | Branch (775:24): [True: 0, False: 0] | Branch (775:60): [True: 0, False: 0] ------------------ 776| 0| { 777| | /* Parsing TARGET_LIB_FOR_WINCHI GUI options (and v. 0.9xx Beta as well) */ 778| 0| pArg = argv[i] + 1; 779| 0| got = set_common_options_by_parg(pArg, developer_options, ip, &bVer1DefaultMode, &nMode, 780| 0| &bINChIOutputOptions, &bINChIOutputOptions2, 781| 0| &bStdFormat, &bHashKey, &bHashXtra1, &bHashXtra2, 782| 0| &bFixSp3bug, &bFixFB2, 783| 0| &bAddPhosphineStereo, &bAddArsineStereo, 784| 0| &bNoStructLabels, &bPointedEdgeStereo, 785| 0| &bDoNotAddH, &bForcedChiralFlag, &bReconnectCoord, 786| 0| &bKetoEnolTaut, 787| 0| &b15TautNonRing, 788| 0| &bPT_06_00_Taut, &bPT_13_00_Taut, &bPT_16_00_Taut, 789| 0| &bPT_18_00_Taut, &bPT_22_00_Taut, &bPT_39_00_Taut, 790| 0| &bLooseTSACheck, 791| 0| &bLargeMolecules, &bPolymers, 792| 0| &bFoldPolymerSRU, &bFrameShiftScheme, 793| 0| &bStereoAtZz, &bNPZz, 794| 0| &bNoWarnings, &bMergeHash, &bHideInChI, &bMolecularInorganics, &bEnhancedStereochemistry); 795| 0| if (got) ------------------ | Branch (795:17): [True: 0, False: 0] ------------------ 796| 0| { 797| 0| ; 798| 0| } 799| 0| else if ( INPUT_NONE == ip->nInputType && ------------------ | Branch (799:23): [True: 0, False: 0] ------------------ 800| 0| (!inchi_memicmp(pArg, "SDF", 3)) && ------------------ | Branch (800:17): [True: 0, False: 0] ------------------ 801| 0| (pArg[3] == ':') ) ------------------ | Branch (801:17): [True: 0, False: 0] ------------------ 802| 0| { 803| 0| k = 0; 804| 0| mystrncpy(ip->szSdfDataHeader, pArg + 4, MAX_SDF_HEADER + 1); ------------------ | | 17| 0|#define MAX_SDF_HEADER 64 /* max length of the SDFile data header */ ------------------ 805| 0| lrtrim(ip->szSdfDataHeader, &k); 806| 0| if ( k ) ------------------ | Branch (806:22): [True: 0, False: 0] ------------------ 807| 0| { 808| 0| ip->pSdfLabel = ip->szSdfDataHeader; 809| 0| ip->pSdfValue = szSdfDataValue; 810| 0| ip->nInputType = INPUT_SDFILE; 811| 0| } 812| 0| else 813| 0| { 814| 0| ip->pSdfLabel = NULL; 815| 0| ip->pSdfValue = NULL; 816| 0| ip->nInputType = INPUT_MOLFILE; 817| 0| } 818| 0| } 819| 0| else if ( INPUT_NONE == ip->nInputType && !inchi_stricmp(pArg, "MOL") ) ------------------ | Branch (819:23): [True: 0, False: 0] | Branch (819:55): [True: 0, False: 0] ------------------ 820| 0| { 821| 0| ip->nInputType = INPUT_MOLFILE; 822| 0| } 823| 0| else if ( INPUT_NONE == ip->nInputType && !inchi_stricmp(pArg, "SDF") ) ------------------ | Branch (823:23): [True: 0, False: 0] | Branch (823:55): [True: 0, False: 0] ------------------ 824| 0| { 825| 0| ip->nInputType = INPUT_MOLFILE; 826| 0| } 827| | /*--- Output options ---*/ 828| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) 829| | else if ( !inchi_stricmp(pArg, "Tabbed") || !inchi_stricmp(pArg, "Tab") ) 830| | { 831| | bOutputStyle |= INCHI_OUT_TABBED_OUTPUT; 832| | } 833| |#endif 834| | 835| | /* Removed condition 836| | #if ( defined(BUILD_WITH_ENG_OPTIONS) || defined(TARGET_LIB_FOR_WINCHI) ) 837| | which is always true, as we already are under condition 838| | 'if ( is_gui && ...)' and is_gui==1 means TARGET_LIB_FOR_WINCHI 839| | */ 840| | /* #if ( defined(BUILD_WITH_ENG_OPTIONS) || defined(TARGET_LIB_FOR_WINCHI) ) */ 841| 0| else if ( !inchi_stricmp(pArg, "SDFID") ) ------------------ | Branch (841:23): [True: 0, False: 0] ------------------ 842| 0| { 843| 0| ip->bGetSdfileId = 1; 844| 0| } 845| 0| else if ( !inchi_stricmp(pArg, "PLAIN") ) ------------------ | Branch (845:23): [True: 0, False: 0] ------------------ 846| 0| { 847| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT; ------------------ | | 135| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 848| 0| } 849| 0| else if ( !inchi_stricmp(pArg, "ANNPLAIN") ) ------------------ | Branch (849:23): [True: 0, False: 0] ------------------ 850| 0| { 851| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 136| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 852| 0| } 853| 0| else if ( !inchi_memicmp(pArg, "AUXINFO:", 8) && isdigit(UCINT pArg[8]) ) ------------------ | Branch (853:23): [True: 0, False: 0] | Branch (853:62): [True: 0, False: 0] ------------------ 854| 0| { 855| 0| k = strtol(pArg + 8, NULL, 10); 856| 0| if ( k == 0 ) ------------------ | Branch (856:22): [True: 0, False: 0] ------------------ 857| 0| { 858| 0| bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; /* no aux info */ ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 859| 0| bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 860| 0| } 861| 0| else if ( k == 1 ) ------------------ | Branch (861:27): [True: 0, False: 0] ------------------ 862| 0| { 863| 0| bINChIOutputOptions &= ~(INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO); /* include full aux info */ ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ bINChIOutputOptions &= ~(INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO); /* include full aux info */ ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 864| 0| } 865| 0| else if ( k == 2 ) ------------------ | Branch (865:27): [True: 0, False: 0] ------------------ 866| 0| { 867| 0| bINChIOutputOptions &= ~INCHI_OUT_NO_AUX_INFO; /* include short aux info */ ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 868| 0| bINChIOutputOptions |= INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 869| 0| } 870| 0| else 871| 0| { 872| 0| bINChIOutputOptions = k; /* override everything */ 873| 0| } 874| 0| } 875| 0| else if ( !inchi_stricmp(pArg, "MERGE") ) ------------------ | Branch (875:23): [True: 0, False: 0] ------------------ 876| 0| { 877| 0| bMergeAllInputStructures = 1; 878| 0| } 879| | 880| 0| else if ( !inchi_stricmp(pArg, "PGO") ) ------------------ | Branch (880:23): [True: 0, False: 0] ------------------ 881| 0| { 882| 0| ip->bSaveAllGoodStructsAsProblem = 1; 883| 0| } 884| 0| else if ( !inchi_stricmp(pArg, "DCR") ) ------------------ | Branch (884:23): [True: 0, False: 0] ------------------ 885| 0| { 886| 0| bDisplayCompositeResults = 1; 887| 0| } 888| | 889| 0| else if ( !inchi_stricmp(pArg, "DSB") ) ------------------ | Branch (889:23): [True: 0, False: 0] ------------------ 890| 0| { 891| 0| nMode |= REQ_MODE_NO_ALT_SBONDS; ------------------ | | 23| 0|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ 892| 0| } 893| 0| else if ( !inchi_stricmp(pArg, "NOHDR") ) ------------------ | Branch (893:23): [True: 0, False: 0] ------------------ 894| 0| { 895| 0| bNoStructLabels = 1; 896| 0| } 897| 0| else if ( !inchi_stricmp(pArg, "NoVarH") ) ------------------ | Branch (897:23): [True: 0, False: 0] ------------------ 898| 0| { 899| 0| bTgFlagVariableProtons = 0; 900| 0| } 901| | /*--- (hidden) Old structure-perception and InChI creation options ---*/ 902| | /*--- (engineering) Old structure-perception and InChI creation options ---*/ 903| 0| else if ( !inchi_stricmp(pArg, "NOUUSB") ) ------------------ | Branch (903:23): [True: 0, False: 0] ------------------ 904| 0| { 905| 0| nMode |= REQ_MODE_SB_IGN_ALL_UU; ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 906| 0| bStdFormat = 0; 907| 0| } 908| 0| else if ( !inchi_stricmp(pArg, "NOUUSC") ) ------------------ | Branch (908:23): [True: 0, False: 0] ------------------ 909| 0| { 910| 0| nMode |= REQ_MODE_SC_IGN_ALL_UU; ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 911| 0| bStdFormat = 0; 912| 0| } 913| |#if ( FIX_ADJ_RAD == 1 ) 914| | else if ( !inchi_stricmp(pArg, "FixRad") ) 915| | { 916| | bFixAdjacentRad = 1; 917| | bStdFormat = 0; 918| | } 919| |#endif 920| | 921| |#if ( RENUMBER_ATOMS_AND_RECALC_V106 == 1 ) 922| | else if ( !inchi_stricmp(pArg, "TestRenum") && developer_options ) 923| | { 924| | ip->bRenumber = 1; 925| | } 926| |#endif 927| | 928| 0|#if ( UNDERIVATIZE == 1 ) 929| 0| else if ( !inchi_stricmp(pArg, "DoDRV") ) ------------------ | Branch (929:23): [True: 0, False: 0] ------------------ 930| 0| { 931| 0| ip->bUnderivatize = 1; 932| 0| bStdFormat = 0; 933| 0| } 934| 0|#if( UNDERIVATIZE_REPORT == 1 ) 935| 0| else if ( !inchi_stricmp(pArg, "DoDrvReport") ) ------------------ | Branch (935:23): [True: 0, False: 0] ------------------ 936| 0| { 937| 0| ip->bUnderivatize = 3; 938| 0| bStdFormat = 0; 939| 0| } 940| 0|#endif 941| 0|#endif 942| 0|#if ( RING2CHAIN == 1 ) 943| 0| else if ( !inchi_stricmp(pArg, "DoR2C") ) ------------------ | Branch (943:23): [True: 0, False: 0] ------------------ 944| 0| { 945| 0| ip->bRing2Chain = 1; 946| 0| bStdFormat = 0; 947| 0| } 948| 0|#endif 949| 0|#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) 950| 0| else if ( !inchi_stricmp(pArg, "DoneOnly") ) ------------------ | Branch (950:23): [True: 0, False: 0] ------------------ 951| 0| { 952| 0| ip->bIgnoreUnchanged = 1; 953| 0| bStdFormat = 0; 954| 0| } 955| 0|#endif 956| 0| else if ( !inchi_stricmp(pArg, "NoADP") ) ------------------ | Branch (956:23): [True: 0, False: 0] ------------------ 957| 0| { 958| 0| bTgFlagHardAddRenProtons = 0; 959| 0| bStdFormat = 0; 960| 0| } 961| 0| else if ( !inchi_memicmp(pArg, "DISCONSALT:", 11) ) ------------------ | Branch (961:23): [True: 0, False: 0] ------------------ 962| 0| { 963| 0| bDisconnectSalts = (0 != strtol(pArg + 11, NULL, 10)); 964| 0| bStdFormat = 0; 965| 0| } 966| 0| else if ( !inchi_memicmp(pArg, "DISCONMETAL:", 12) ) ------------------ | Branch (966:23): [True: 0, False: 0] ------------------ 967| 0| { 968| 0| bDisconnectCoord = (0 != strtol(pArg + 12, NULL, 10)); 969| 0| bStdFormat = 0; 970| 0| } 971| 0| else if ( !inchi_memicmp(pArg, "RECONMETAL:", 11) ) ------------------ | Branch (971:23): [True: 0, False: 0] ------------------ 972| 0| { 973| 0| bReconnectCoord = (0 != strtol(pArg + 11, NULL, 10)); 974| 0| bStdFormat = 0; 975| 0| } 976| 0| else if ( !inchi_memicmp(pArg, "DISCONMETALCHKVAL:", 18) ) ------------------ | Branch (976:23): [True: 0, False: 0] ------------------ 977| 0| { 978| 0| bDisconnectCoordChkVal = (0 != strtol(pArg + 18, NULL, 10)); 979| 0| bStdFormat = 0; 980| 0| } 981| 0| else if ( !inchi_memicmp(pArg, "MOVEPOS:", 8) ) ------------------ | Branch (981:23): [True: 0, False: 0] ------------------ 982| 0| { 983| 0| bMovePositiveCharges = (0 != strtol(pArg + 8, NULL, 10)); 984| 0| bStdFormat = 0; 985| 0| } 986| 0| else if ( !inchi_memicmp(pArg, "MERGESALTTG:", 12) ) ------------------ | Branch (986:23): [True: 0, False: 0] ------------------ 987| 0| { 988| 0| bMergeSaltTGroups = (0 != strtol(pArg + 12, NULL, 10)); 989| 0| bStdFormat = 0; 990| 0| } 991| 0| else if ( !inchi_memicmp(pArg, "UNCHARGEDACIDS:", 15) ) ------------------ | Branch (991:23): [True: 0, False: 0] ------------------ 992| 0| { 993| 0| bUnchargedAcidTaut = (0 != strtol(pArg + 15, NULL, 16)); 994| 0| bStdFormat = 0; 995| 0| } 996| 0| else if ( !inchi_memicmp(pArg, "ACIDTAUT:", 9) ) ------------------ | Branch (996:23): [True: 0, False: 0] ------------------ 997| 0| { 998| 0| bAcidTautomerism = c = (int)strtol(pArg + 9, NULL, 10); 999| 0| if ( 0 <= c && c <= 2 ) bAcidTautomerism = c; ------------------ | Branch (999:22): [True: 0, False: 0] | Branch (999:32): [True: 0, False: 0] ------------------ 1000| | /*else bNotRecognized = 2*bReleaseVersion;*/ 1001| 0| bStdFormat = 0; 1002| 0| } 1003| | /*--- (hidden) Old output and other options ---*/ 1004| 0| else if ( !inchi_memicmp(pArg, "O:", 2) ) ------------------ | Branch (1004:23): [True: 0, False: 0] ------------------ 1005| 0| { 1006| 0| bNameSuffix = 1; 1007| 0| strncpy(szNameSuffix, pArg + 2, sizeof(szNameSuffix) - 1); 1008| 0| } 1009| 0| else if ( !inchi_memicmp(pArg, "OP:", 3) ) ------------------ | Branch (1009:23): [True: 0, False: 0] ------------------ 1010| 0| { 1011| 0| bOutputPath = 1; 1012| 0| strncpy(szOutputPath, pArg + 3, sizeof(szOutputPath) - 1); 1013| 0| } 1014| 0| else if ( !inchi_stricmp(pArg, "ALT") ) ------------------ | Branch (1014:23): [True: 0, False: 0] ------------------ 1015| 0| { 1016| 0| ip->bAbcNumbers = 1; 1017| 0| bStdFormat = 0; 1018| 0| } 1019| 0| else if ( !inchi_stricmp(pArg, "SCT") ) ------------------ | Branch (1019:23): [True: 0, False: 0] ------------------ 1020| 0| { 1021| 0| ip->bCtPredecessors = 1; 1022| 0| bStdFormat = 0; 1023| 0| } 1024| 0| else if ( !inchi_stricmp(pArg, "CMP") ) ------------------ | Branch (1024:23): [True: 0, False: 0] ------------------ 1025| 0| { 1026| 0| bCompareComponents = CMP_COMPONENTS; ------------------ | | 54| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ 1027| 0| } 1028| 0| else if ( !inchi_stricmp(pArg, "CMPNONISO") ) ------------------ | Branch (1028:23): [True: 0, False: 0] ------------------ 1029| 0| { 1030| 0| bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 54| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 55| 0|#define CMP_COMPONENTS_NONISO 0x0002 /* ignore isotopic */ ------------------ 1031| 0| } 1032| 0| else if ( !inchi_stricmp(pArg, "PW") ) ------------------ | Branch (1032:23): [True: 0, False: 0] ------------------ 1033| 0| { 1034| 0| ip->bSaveWarningStructsAsProblem = 1; 1035| 0| } 1036| | 1037| 0| else if ( !inchi_memicmp(pArg, "RSB:", 4) && developer_options ) ------------------ | Branch (1037:23): [True: 0, False: 0] | Branch (1037:58): [Folded, False: 0] ------------------ 1038| 0| { 1039| 0| mdbr = (int)strtol(pArg + 4, NULL, 10); 1040| 0| } 1041| 0| else if ( !inchi_memicmp(pArg, "DISCONSALT:", 11) && developer_options ) ------------------ | Branch (1041:23): [True: 0, False: 0] | Branch (1041:66): [Folded, False: 0] ------------------ 1042| 0| { 1043| 0| bDisconnectSalts = (0 != strtol(pArg + 11, NULL, 10)); 1044| 0| } 1045| 0| else if ( !inchi_memicmp(pArg, "DISCONMETAL:", 12) && developer_options ) ------------------ | Branch (1045:23): [True: 0, False: 0] | Branch (1045:67): [Folded, False: 0] ------------------ 1046| 0| { 1047| 0| bDisconnectCoord = (0 != strtol(pArg + 12, NULL, 10)); 1048| 0| } 1049| 0| else if ( !inchi_memicmp(pArg, "RECONMETAL:", 11) && developer_options ) ------------------ | Branch (1049:23): [True: 0, False: 0] | Branch (1049:66): [Folded, False: 0] ------------------ 1050| 0| { 1051| 0| bReconnectCoord = (0 != strtol(pArg + 11, NULL, 10)); 1052| 0| } 1053| 0| else if ( !inchi_memicmp(pArg, "DISCONMETALCHKVAL:", 18) && developer_options ) ------------------ | Branch (1053:23): [True: 0, False: 0] | Branch (1053:73): [Folded, False: 0] ------------------ 1054| 0| { 1055| 0| bDisconnectCoordChkVal = (0 != strtol(pArg + 18, NULL, 10)); 1056| 0| } 1057| 0| else if ( !inchi_memicmp(pArg, "MOVEPOS:", 8) && developer_options ) ------------------ | Branch (1057:23): [True: 0, False: 0] | Branch (1057:62): [Folded, False: 0] ------------------ 1058| 0| { 1059| 0| bMovePositiveCharges = (0 != strtol(pArg + 8, NULL, 10)); 1060| 0| } 1061| 0| else if ( !inchi_memicmp(pArg, "MERGESALTTG:", 12) && developer_options ) ------------------ | Branch (1061:23): [True: 0, False: 0] | Branch (1061:67): [Folded, False: 0] ------------------ 1062| 0| { 1063| 0| bMergeSaltTGroups = (0 != strtol(pArg + 12, NULL, 10)); 1064| 0| } 1065| 0| else if ( !inchi_memicmp(pArg, "UNCHARGEDACIDS:", 15) && developer_options ) ------------------ | Branch (1065:23): [True: 0, False: 0] | Branch (1065:70): [Folded, False: 0] ------------------ 1066| 0| { 1067| 0| bUnchargedAcidTaut = (0 != strtol(pArg + 15, NULL, 16));; 1068| 0| } 1069| 0| else if ( !inchi_memicmp(pArg, "ACIDTAUT:", 9) && developer_options ) ------------------ | Branch (1069:23): [True: 0, False: 0] | Branch (1069:63): [Folded, False: 0] ------------------ 1070| 0| { 1071| 0| bAcidTautomerism = c = (int)strtol(pArg + 9, NULL, 10); 1072| 0| if ( 0 <= c && c <= 2 ) ------------------ | Branch (1072:22): [True: 0, False: 0] | Branch (1072:32): [True: 0, False: 0] ------------------ 1073| 0| { 1074| 0| bAcidTautomerism = c; 1075| 0| } 1076| | /*else bNotRecognized = 2*bReleaseVersion;*/ 1077| 0| } 1078| | 1079| 0| else 1080| 0| { 1081| | /*for ( k = 0; c=pArg[k]; k ++ )*/ 1082| 0| k = 0; 1083| 0| c = pArg[k]; /* prohibit multiple option concatenations, strict syntax check 2008-11-05 DT */ 1084| 0| { 1085| 0| c = toupper(c); ------------------ | Branch (1085:25): [True: 0, False: 0] | Branch (1085:25): [True: 0, False: 0] | Branch (1085:25): [True: 0, Folded] ------------------ 1086| 0| switch ( c ) 1087| 0| { 1088| 0| case 'D': ------------------ | Branch (1088:21): [True: 0, False: 0] ------------------ 1089| 0| bDisplay |= 1; 1090| 0| if ( (pArg[k + 1] == 'C' || pArg[k + 1] == 'c') && !pArg[k + 2] ) ------------------ | Branch (1090:31): [True: 0, False: 0] | Branch (1090:53): [True: 0, False: 0] | Branch (1090:76): [True: 0, False: 0] ------------------ 1091| 0| { 1092| 0| bDisplay |= 1; 1093| 0| k++; 1094| 0| ip->bDisplayEachComponentINChI = 1; 1095| 0| } 1096| 0| else if ( !pArg[k + 1] ) ------------------ | Branch (1096:35): [True: 0, False: 0] ------------------ 1097| 0| { 1098| 0| bDisplay |= 1; 1099| 0| } 1100| 0| break; 1101| 0| case 'W': ------------------ | Branch (1101:21): [True: 0, False: 0] ------------------ 1102| 0| if ( pArg[k + 1] == 'D' ) ------------------ | Branch (1102:30): [True: 0, False: 0] ------------------ 1103| 0| { 1104| | /* restore Display Time functionality */ 1105| 0| c = 'D'; 1106| 0| k++; 1107| 0| } 1108| 0| t = strtod(pArg + k + 1, (char**)&q); /* cast deliberately discards 'const' qualifier */ 1109| 0| if ( (q > pArg + k + 1 && errno == ERANGE) || t < 0.0 || t * 1000.0 >(double)ULONG_MAX ) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1109:31): [True: 0, False: 0] | Branch (1109:51): [True: 0, False: 0] | Branch (1109:71): [True: 0, False: 0] | Branch (1109:82): [True: 0, False: 0] ------------------ 1110| 0| { 1111| 0| ul = 0; 1112| 0| } 1113| 0| else 1114| 0| { 1115| 0| ul = (unsigned long)(t * 1000.0); 1116| 0| } 1117| 0| if ( /*q > pArg+k &&*/ !*q ) ------------------ | Branch (1117:48): [True: 0, False: 0] ------------------ 1118| 0| { 1119| 0| k = q - pArg - 1; /* k will be incremented by the for() cycle */ 1120| 0| switch ( c ) ------------------ | Branch (1120:38): [True: 0, False: 0] ------------------ 1121| 0| { 1122| 0| case 'D': ------------------ | Branch (1122:29): [True: 0, False: 0] ------------------ 1123| 0| *ulDisplTime = ul; 1124| 0| break; 1125| 0| case 'W': ------------------ | Branch (1125:29): [True: 0, False: 0] ------------------ 1126| 0| ip->msec_MaxTime = ul; 1127| 0| break; 1128| 0| } 1129| 0| } 1130| 0| break; 1131| 0| case 'F': ------------------ | Branch (1131:21): [True: 0, False: 0] ------------------ 1132| 0| c = (int)strtol(pArg + k + 1, (char**)&q, 10); /* cast deliberately discards 'const' qualifier */ 1133| 0| if ( q > pArg + k && !*q ) ------------------ | Branch (1133:30): [True: 0, False: 0] | Branch (1133:46): [True: 0, False: 0] ------------------ 1134| 0| { 1135| 0| k = q - pArg - 1; 1136| 0| if ( abs(c) > 5 ) ------------------ | Branch (1136:34): [True: 0, False: 0] ------------------ 1137| 0| { 1138| 0| nFontSize = -c; /* font size 5 or less is too small */ 1139| 0| } 1140| 0| } 1141| 0| break; 1142| 0| default: ------------------ | Branch (1142:21): [True: 0, False: 0] ------------------ 1143| 0| if ( !pArg[k + 1] ) ------------------ | Branch (1143:30): [True: 0, False: 0] ------------------ 1144| 0| { 1145| 0| switch ( c ) 1146| 0| { 1147| 0| case 'B': ------------------ | Branch (1147:29): [True: 0, False: 0] ------------------ 1148| 0| nMode |= REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1149| 0| nReleaseMode = 0; 1150| | /*bNotRecognized = bReleaseVersion;*/ 1151| 0| bStdFormat = 0; 1152| 0| break; 1153| 0| case 'T': ------------------ | Branch (1153:29): [True: 0, False: 0] ------------------ 1154| 0| nMode |= REQ_MODE_TAUT; ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1155| 0| nReleaseMode = 0; 1156| | /*bNotRecognized = bReleaseVersion;*/ 1157| 0| break; 1158| 0| case 'I': ------------------ | Branch (1158:29): [True: 0, False: 0] ------------------ 1159| 0| nMode |= REQ_MODE_ISO; ------------------ | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1160| 0| nReleaseMode = 0; 1161| | /*bNotRecognized = bReleaseVersion;*/ 1162| 0| break; 1163| 0| case 'N': ------------------ | Branch (1163:29): [True: 0, False: 0] ------------------ 1164| 0| nMode |= REQ_MODE_NON_ISO; ------------------ | | 18| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1165| 0| nReleaseMode = 0; 1166| 0| bStdFormat = 0; 1167| | /*bNotRecognized = bReleaseVersion;*/ 1168| 0| break; 1169| 0| case 'S': ------------------ | Branch (1169:29): [True: 0, False: 0] ------------------ 1170| 0| nMode |= REQ_MODE_STEREO; ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 1171| 0| nReleaseMode = 0; 1172| | /*bNotRecognized = bReleaseVersion;*/ 1173| 0| break; 1174| 0| case 'E': ------------------ | Branch (1174:29): [True: 0, False: 0] ------------------ 1175| 0| if ( nReleaseMode & REQ_MODE_STEREO ) ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (1175:38): [True: 0, False: 0] ------------------ 1176| 0| { 1177| 0| nReleaseMode ^= REQ_MODE_STEREO; ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 1178| 0| bStdFormat = 0; 1179| 0| } 1180| 0| break; 1181| | 1182| 0|#ifndef TARGET_LIB_FOR_WINCHI 1183| 0| default: ------------------ | Branch (1183:29): [True: 0, False: 0] ------------------ 1184| 0| inchi_ios_eprint(log_file, "Unrecognized optionQ1: \"%c\".\n", c); 1185| | 1186| 0|#endif 1187| 0| } 1188| 0| } 1189| | 1190| | 1191| 0|#ifndef TARGET_LIB_FOR_WINCHI 1192| 0| else 1193| 0| { 1194| 0| inchi_ios_eprint(log_file, "Unrecognized optionQ2: \"%c\".\n", c); 1195| 0| } 1196| 0|#endif 1197| 0| } 1198| | /* 1199| | if ( bNotRecognized && bNotRecognized == bReleaseVersion ) { 1200| | inchi_ios_eprint(stderr, "Unrecognized option: \"%c\".\n", c); 1201| | bNotRecognized = 0; 1202| | } 1203| | */ 1204| 0| } 1205| 0| } 1206| | 1207| | /* 1208| | if ( bNotRecognized && bNotRecognized == 2*bReleaseVersion ) 1209| | { 1210| | inchi_ios_eprint(stderr, "Unrecognized option: \"%s\".\n", argv[i]); 1211| | bNotRecognized = 0; 1212| | } 1213| | */ 1214| | 1215| 0| } /* eof Parsing TARGET_LIB_FOR_WINCHI GUI options (and v. 0.9xx Beta as well) */ 1216| | 1217| 12.7k| else if ( (bVer1Options & 1) && INCHI_OPTION_PREFX == argv[i][0] && argv[i][1] ) ------------------ | | 231| 12.7k|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (1217:19): [True: 12.7k, False: 0] | Branch (1217:41): [True: 12.7k, False: 0] | Branch (1217:77): [True: 12.7k, False: 0] ------------------ 1218| 12.7k| { 1219| | /* Parsing stand-alone executable/libinchi options */ 1220| | 1221| 12.7k| pArg = argv[i] + 1; 1222| | 1223| 12.7k| bRecognizedOption = 2; 1224| 12.7k| bVer1Options += 2; 1225| | /* always on: REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO */ 1226| | 1227| 12.7k| got = set_common_options_by_parg(pArg, developer_options, ip, &bVer1DefaultMode, &nMode, 1228| 12.7k| &bINChIOutputOptions, &bINChIOutputOptions2, 1229| 12.7k| &bStdFormat, &bHashKey, &bHashXtra1, &bHashXtra2, 1230| 12.7k| &bFixSp3bug, &bFixFB2, 1231| 12.7k| &bAddPhosphineStereo, &bAddArsineStereo, 1232| 12.7k| &bNoStructLabels, &bPointedEdgeStereo, 1233| 12.7k| &bDoNotAddH, &bForcedChiralFlag, &bReconnectCoord, 1234| 12.7k| &bKetoEnolTaut, 1235| 12.7k| &b15TautNonRing, 1236| 12.7k| &bPT_06_00_Taut, &bPT_13_00_Taut, &bPT_16_00_Taut, 1237| 12.7k| &bPT_18_00_Taut, &bPT_22_00_Taut, &bPT_39_00_Taut, 1238| 12.7k| &bLooseTSACheck, 1239| 12.7k| &bLargeMolecules, &bPolymers, 1240| 12.7k| &bFoldPolymerSRU, &bFrameShiftScheme, 1241| 12.7k| &bStereoAtZz, &bNPZz, 1242| 12.7k| &bNoWarnings, &bMergeHash, &bHideInChI, &bMolecularInorganics, &bEnhancedStereochemistry); 1243| | 1244| 12.7k| if ( got ) ------------------ | Branch (1244:18): [True: 0, False: 12.7k] ------------------ 1245| 0| { 1246| 0| ; 1247| 0| } 1248| | /* Input */ 1249| 12.7k| else if ( !inchi_stricmp(pArg, "STDIO") ) ------------------ | Branch (1249:23): [True: 0, False: 12.7k] ------------------ 1250| 0| { 1251| 0| bNameSuffix = 0; 1252| 0| } 1253| 12.7k| else if ( /* INPUT_NONE == ip->nInputType &&*/ 1254| 12.7k| !inchi_memicmp(pArg, "SDF:", 4) ) ------------------ | Branch (1254:17): [True: 0, False: 12.7k] ------------------ 1255| 0| { 1256| | /* SDfile label */ 1257| 0| k = 0; 1258| 0| mystrncpy(ip->szSdfDataHeader, pArg + 4, MAX_SDF_HEADER + 1); ------------------ | | 17| 0|#define MAX_SDF_HEADER 64 /* max length of the SDFile data header */ ------------------ 1259| 0| lrtrim(ip->szSdfDataHeader, &k); 1260| 0| if ( k ) ------------------ | Branch (1260:22): [True: 0, False: 0] ------------------ 1261| 0| { 1262| 0| ip->pSdfLabel = ip->szSdfDataHeader; 1263| 0| ip->pSdfValue = szSdfDataValue; 1264| 0| if ( INPUT_NONE == ip->nInputType ) ------------------ | Branch (1264:26): [True: 0, False: 0] ------------------ 1265| 0| { 1266| 0| ip->nInputType = INPUT_SDFILE; 1267| 0| } 1268| 0| } 1269| 0| else 1270| 0| { 1271| 0| ip->pSdfLabel = NULL; 1272| 0| ip->pSdfValue = NULL; 1273| 0| if ( INPUT_NONE == ip->nInputType ) ------------------ | Branch (1273:26): [True: 0, False: 0] ------------------ 1274| 0| { 1275| 0| ip->nInputType = INPUT_MOLFILE; 1276| 0| } 1277| 0| } 1278| 0| } 1279| | 1280| 12.7k| else if ( !inchi_memicmp(pArg, "RSB:", 4) && developer_options ) ------------------ | Branch (1280:23): [True: 0, False: 12.7k] | Branch (1280:58): [Folded, False: 0] ------------------ 1281| 0| { 1282| 0| mdbr = (int)strtol(pArg + 4, NULL, 10); 1283| 0| } 1284| | 1285| | /* Output */ 1286| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) 1287| | else if ( !inchi_stricmp(pArg, "Tabbed") || !inchi_stricmp(pArg, "Tab") ) 1288| | { 1289| | bOutputStyle |= INCHI_OUT_TABBED_OUTPUT; 1290| | } 1291| |#endif 1292| 12.7k| else if ( !inchi_stricmp(pArg, "OUTPUTSDF") ) ------------------ | Branch (1292:23): [True: 0, False: 12.7k] ------------------ 1293| 0| { 1294| | /* output SDfile */ 1295| 0| bOutputMolfileOnly = 1; 1296| 0| } 1297| 12.7k| else if ( !inchi_stricmp(pArg, "SdfAtomsDT") ) ------------------ | Branch (1297:23): [True: 0, False: 12.7k] ------------------ 1298| 0| { 1299| | /* output isotopes H as D and T in SDfile */ 1300| 0| bOutputMolfileDT = 1; 1301| 0| } 1302| 12.7k| else if ( !inchi_stricmp(pArg, "D") ) ------------------ | Branch (1302:23): [True: 0, False: 12.7k] ------------------ 1303| 0| { 1304| | /* display the structures */ 1305| 0| bDisplay |= 1; 1306| 0| } 1307| 12.7k| else if ( !inchi_memicmp(pArg, "F", 1) && (c = (int)strtol(pArg + 1, (char**)&q, 10), q > pArg + 1) ) ------------------ | Branch (1307:23): [True: 0, False: 12.7k] | Branch (1307:55): [True: 0, False: 0] ------------------ 1308| 0| { 1309| 0| nFontSize = -c; /* struct. display font size */ 1310| 0| } 1311| 12.7k| else if ( !inchi_stricmp(pArg, "EQU") ) ------------------ | Branch (1311:23): [True: 0, False: 12.7k] ------------------ 1312| 0| { 1313| 0| bCompareComponents = CMP_COMPONENTS; ------------------ | | 54| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ 1314| 0| } 1315| |#if( OUTPUT_FILE_EXT == 1 ) 1316| | else if ( pArg[0] == '.' && numOutNameExt < (int)(sizeof(szOutNameExt) / sizeof(szOutNameExt[0])) ) 1317| | { 1318| | strncpy(szOutNameExt[numOutNameExt], pArg, sizeof(szOutNameExt[0]) - 1); 1319| | numOutNameExt++; 1320| | if ( ip->path[numOutNameExt] ) 1321| | { 1322| | ip->path[numOutNameExt] = ""; /*strcpy( ip->path[numOutNameExt], "");*/ 1323| | } 1324| | } 1325| |#endif 1326| | /* djb-rwth: avoiding Error 98 for empty .mol files -- GH issue #25, thanks to @wijnand1 */ 1327| 12.7k| else if ( !inchi_stricmp(pArg, "WarnOnEmptyStructure") ) ------------------ | Branch (1327:23): [True: 0, False: 12.7k] ------------------ 1328| 0| { 1329| 0| ip->bAllowEmptyStructure = 1; 1330| 0| } 1331| | 1332| | /* Generation options */ 1333| 12.7k| else if ( !inchi_memicmp(pArg, "W", 1) ) ------------------ | Branch (1333:23): [True: 0, False: 12.7k] ------------------ 1334| 0| { 1335| 0| long timeout_value; 1336| 0| const char c1 = *(pArg + 1); 1337| 0| if ( c1 && (c1 == 'M' || c1 == 'm') ) ------------------ | Branch (1337:22): [True: 0, False: 0] | Branch (1337:29): [True: 0, False: 0] | Branch (1337:42): [True: 0, False: 0] ------------------ 1338| 0| { 1339| | /* "WMnumber", milliseconds */ 1340| 0| timeout_value = strtol(pArg + 2, (char**)&q, 10); 1341| 0| if ( timeout_value && q > pArg + 2 && *q == '\0' ) ------------------ | Branch (1341:26): [True: 0, False: 0] | Branch (1341:43): [True: 0, False: 0] | Branch (1341:59): [True: 0, False: 0] ------------------ 1342| 0| { 1343| 0| if (errno == ERANGE || timeout_value < 0.0 || timeout_value>LONG_MAX) /* djb-rwth: addressing coverity ID #499550 -- the condition takes into account all possible overflows/errors */ ------------------ | Branch (1343:29): [True: 0, False: 0] | Branch (1343:48): [True: 0, False: 0] | Branch (1343:71): [True: 0, False: 0] ------------------ 1344| 0| { 1345| 0| timeout_value = 0; 1346| 0| timeout_set_warning = 1; 1347| 0| } 1348| 0| timeout_set_error = 0; 1349| 0| } 1350| 0| else 1351| 0| { 1352| 0| timeout_set_error = 1; 1353| 0| } 1354| 0| } 1355| 0| else 1356| 0| { 1357| | /* expect "Wnumber", seconds */ 1358| 0| t = strtod(pArg + 1, (char**)&q); 1359| 0| if ( t && q > pArg + 1 ) ------------------ | Branch (1359:26): [True: 0, False: 0] | Branch (1359:31): [True: 0, False: 0] ------------------ 1360| 0| { 1361| 0| if ( *q != '\0' ) ------------------ | Branch (1361:30): [True: 0, False: 0] ------------------ 1362| 0| { 1363| 0| timeout_set_warning = 1; 1364| 0| } 1365| 0| if ( errno == ERANGE || t < 0.0 || t * 1000.0 >(double)LONG_MAX ) ------------------ | Branch (1365:30): [True: 0, False: 0] | Branch (1365:49): [True: 0, False: 0] | Branch (1365:60): [True: 0, False: 0] ------------------ 1366| 0| { 1367| 0| timeout_value = 0; 1368| 0| timeout_set_warning = 1; 1369| 0| } 1370| 0| else 1371| 0| { 1372| 0| timeout_value = (long)(t * 1000.0); /* max. time per structure */ 1373| 0| } 1374| 0| timeout_set_error = 0; 1375| 0| } 1376| 0| else 1377| 0| { 1378| 0| timeout_set_error = 1; 1379| 0| } 1380| 0| } 1381| 0| if ( timeout_set_error == 0 ) ------------------ | Branch (1381:22): [True: 0, False: 0] ------------------ 1382| 0| { 1383| 0| ip->msec_MaxTime = timeout_value; 1384| 0| } 1385| 0| } 1386| | 1387| | /*--- Conversion modes ---*/ 1388| 12.7k|#if ( READ_INCHI_STRING == 1 ) 1389| | 1390| |/*#if (BUILD_WITH_ENG_OPTIONS==1)*/ 1391| 12.7k| else if ( !inchi_stricmp(pArg, "InChI2InChI") ) ------------------ | Branch (1391:23): [True: 6.37k, False: 6.37k] ------------------ 1392| 6.37k| { 1393| | /* Read InChI Identifiers and output InChI Identifiers */ 1394| 6.37k| ip->nInputType = INPUT_INCHI; 1395| 6.37k| ip->bReadInChIOptions |= READ_INCHI_OUTPUT_INCHI; ------------------ | | 988| 6.37k|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 1396| 6.37k| ip->bReadInChIOptions &= ~READ_INCHI_TO_STRUCTURE; ------------------ | | 991| 6.37k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 1397| 6.37k| } 1398| | /*#endif*/ 1399| | 1400| 6.37k| else if ( !inchi_stricmp(pArg, "InChI2Struct") ) ------------------ | Branch (1400:23): [True: 6.37k, False: 0] ------------------ 1401| 6.37k| { 1402| | /* Split InChI Identifiers into components */ 1403| 6.37k| ip->bReadInChIOptions |= READ_INCHI_TO_STRUCTURE; ------------------ | | 991| 6.37k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 1404| 6.37k| ip->bReadInChIOptions &= ~READ_INCHI_OUTPUT_INCHI; ------------------ | | 988| 6.37k|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 1405| 6.37k| ip->nInputType = INPUT_INCHI; 1406| 6.37k| } 1407| | 1408| 0| else if ( !inchi_stricmp(pArg, "KeepBalanceP") && developer_options ) ------------------ | Branch (1408:23): [True: 0, False: 0] | Branch (1408:63): [Folded, False: 0] ------------------ 1409| 0| { 1410| | /* When spliting InChI Identifiers into components: */ 1411| | /* If MobileH output then add p to each component; */ 1412| | /* Otherwise add one more component containing balance */ 1413| | /* of protons and exchangeable isotopic H */ 1414| 0| ip->bReadInChIOptions |= READ_INCHI_KEEP_BALANCE_P; ------------------ | | 990| 0|#define READ_INCHI_KEEP_BALANCE_P 0x00000004 ------------------ 1415| 0| bStdFormat = 0; 1416| 0| } 1417| 0|#endif 1418| | 1419| | /*--- (engineering) Undo bug/draw fixes options ---*/ 1420| | 1421| | /* (developer_options) Old structure-perception and InChI creation options */ 1422| |#if ( FIX_ADJ_RAD == 1 ) 1423| | else if ( !inchi_stricmp(pArg, "FixRad") && developer_options ) 1424| | { 1425| | bFixAdjacentRad = 1; 1426| | bStdFormat = 0; 1427| | } 1428| |#endif 1429| | 1430| | 1431| |#if ( RENUMBER_ATOMS_AND_RECALC_V106 == 1 ) 1432| | else if ( !inchi_stricmp(pArg, "TestRenum") && developer_options ) 1433| | { 1434| | ip->bRenumber = 1; 1435| | } 1436| |#endif 1437| | 1438| 0|#if ( UNDERIVATIZE == 1 ) 1439| 0| else if ( !inchi_stricmp(pArg, "DoDRV") && developer_options ) ------------------ | Branch (1439:23): [True: 0, False: 0] | Branch (1439:56): [Folded, False: 0] ------------------ 1440| 0| { 1441| 0| ip->bUnderivatize = 1; 1442| 0| bStdFormat = 0; 1443| 0| } 1444| 0|#if( UNDERIVATIZE_REPORT == 1 ) 1445| 0| else if ( !inchi_stricmp(pArg, "DoDrvReport") ) ------------------ | Branch (1445:23): [True: 0, False: 0] ------------------ 1446| 0| { 1447| 0| ip->bUnderivatize = 3; 1448| 0| bStdFormat = 0; 1449| 0| } 1450| 0|#endif 1451| 0|#endif 1452| 0|#if ( RING2CHAIN == 1 ) 1453| 0| else if ( !inchi_stricmp(pArg, "DoR2C") && developer_options ) ------------------ | Branch (1453:23): [True: 0, False: 0] | Branch (1453:56): [Folded, False: 0] ------------------ 1454| 0| { 1455| 0| ip->bRing2Chain = 1; 1456| 0| bStdFormat = 0; 1457| 0| } 1458| 0|#endif 1459| 0|#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) 1460| 0| else if ( !inchi_stricmp(pArg, "DoneOnly") && developer_options ) ------------------ | Branch (1460:23): [True: 0, False: 0] | Branch (1460:59): [Folded, False: 0] ------------------ 1461| 0| { 1462| 0| ip->bIgnoreUnchanged = 1; 1463| 0| bStdFormat = 0; 1464| 0| } 1465| 0|#endif 1466| 0| else if ( !inchi_memicmp(pArg, "MOVEPOS:", 8) && developer_options ) ------------------ | Branch (1466:23): [True: 0, False: 0] | Branch (1466:62): [Folded, False: 0] ------------------ 1467| 0| { 1468| 0| bMovePositiveCharges = (0 != strtol(pArg + 8, NULL, 10)); 1469| 0| bStdFormat = 0; 1470| 0| } 1471| | 1472| 0| else if ( !inchi_stricmp(pArg, "NoADP") && developer_options ) ------------------ | Branch (1472:23): [True: 0, False: 0] | Branch (1472:56): [Folded, False: 0] ------------------ 1473| 0| { 1474| 0| bTgFlagHardAddRenProtons = 0; 1475| 0| bStdFormat = 0; 1476| 0| } 1477| | /* Tautomer perception off */ 1478| 0| else if ( !inchi_stricmp(pArg, "EXACT") && developer_options ) ------------------ | Branch (1478:23): [True: 0, False: 0] | Branch (1478:56): [Folded, False: 0] ------------------ 1479| 0| { 1480| 0| bVer1DefaultMode |= REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1481| 0| bStdFormat = 0; 1482| 0| } 1483| 0| else if ( !inchi_stricmp(pArg, "ONLYRECSALT") && developer_options ) ------------------ | Branch (1483:23): [True: 0, False: 0] | Branch (1483:62): [Folded, False: 0] ------------------ 1484| 0| { 1485| | /* do not disconnect salts */ 1486| 0| bDisconnectSalts = 0; 1487| 0| bStdFormat = 0; 1488| 0| } 1489| 0| else if ( (!inchi_stricmp(pArg, "ONLYEXACT") || !inchi_stricmp(pArg, "ONLYFIXEDH")) && developer_options ) ------------------ | Branch (1489:24): [True: 0, False: 0] | Branch (1489:61): [True: 0, False: 0] | Branch (1489:100): [Folded, False: 0] ------------------ 1490| 0| { 1491| 0| bVer1DefaultMode |= REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1492| 0| bVer1DefaultMode &= ~REQ_MODE_TAUT; ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1493| 0| bStdFormat = 0; 1494| 0| } 1495| 0| else if ( !inchi_stricmp(pArg, "ONLYNONISO") && developer_options ) ------------------ | Branch (1495:23): [True: 0, False: 0] | Branch (1495:61): [Folded, False: 0] ------------------ 1496| 0| { 1497| 0| bVer1DefaultMode |= REQ_MODE_NON_ISO; ------------------ | | 18| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1498| 0| bVer1DefaultMode &= ~REQ_MODE_ISO; ------------------ | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1499| 0| bStdFormat = 0; 1500| 0| } 1501| 0| else if ( !inchi_stricmp(pArg, "TAUT") && developer_options ) ------------------ | Branch (1501:23): [True: 0, False: 0] | Branch (1501:55): [Folded, False: 0] ------------------ 1502| 0| { 1503| 0| bVer1DefaultMode &= ~REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1504| 0| bVer1DefaultMode |= REQ_MODE_TAUT; ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1505| 0| } 1506| 0| else if ( !inchi_stricmp(pArg, "ONLYRECMET") && developer_options ) ------------------ | Branch (1506:23): [True: 0, False: 0] | Branch (1506:61): [Folded, False: 0] ------------------ 1507| 0| { 1508| | /* do not disconnect metals */ 1509| 0| bDisconnectCoord = 0; 1510| 0| bStdFormat = 0; 1511| 0| } 1512| | 1513| | /*--- (hidden) Old output and other options ---*/ 1514| | 1515| 0| else if ( !inchi_stricmp(pArg, "SdfSplit") && developer_options ) ------------------ | Branch (1515:23): [True: 0, False: 0] | Branch (1515:59): [Folded, False: 0] ------------------ 1516| 0| { 1517| | /* Split single Molfiles into disconnected components */ 1518| 0| bOutputMolfileSplit = 1; 1519| 0| } 1520| 0| else if ( !inchi_stricmp(pArg, "DCR") && developer_options ) ------------------ | Branch (1520:23): [True: 0, False: 0] | Branch (1520:54): [Folded, False: 0] ------------------ 1521| 0| { 1522| 0| bDisplayCompositeResults = 1; 1523| 0| } 1524| 0| else if ( (!inchi_stricmp(pArg, "AUXFULL") || !inchi_stricmp(pArg, "AUXMAX")) && developer_options ) ------------------ | Branch (1524:24): [True: 0, False: 0] | Branch (1524:59): [True: 0, False: 0] | Branch (1524:94): [Folded, False: 0] ------------------ 1525| 0| { 1526| | /* full aux info */ 1527| 0| bINChIOutputOptions &= ~(INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO); /* include short aux info */ ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ bINChIOutputOptions &= ~(INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO); /* include short aux info */ ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1528| 0| } 1529| 0| else if ( !inchi_stricmp(pArg, "AUXMIN") && developer_options ) ------------------ | Branch (1529:23): [True: 0, False: 0] | Branch (1529:57): [Folded, False: 0] ------------------ 1530| 0| { 1531| | /* minimal aux info */ 1532| 0| bINChIOutputOptions &= ~INCHI_OUT_NO_AUX_INFO; /* include short aux info */ ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 1533| 0| bINChIOutputOptions |= INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1534| 0| } 1535| | 1536| 0|#if ( READ_INCHI_STRING == 1 ) 1537| 0| else if ( !inchi_stricmp(pArg, "DDSRC") && developer_options ) ------------------ | Branch (1537:23): [True: 0, False: 0] | Branch (1537:56): [Folded, False: 0] ------------------ 1538| 0| { 1539| 0| bDisplayIfRestoreWarnings = 1; /* InChI->Structure debugging: Display Debug Structure Restore Components */ 1540| 0| } 1541| 0|#endif 1542| | 1543| 0| else if ( !inchi_stricmp(pArg, "NoVarH") && developer_options ) ------------------ | Branch (1543:23): [True: 0, False: 0] | Branch (1543:57): [Folded, False: 0] ------------------ 1544| 0| { 1545| 0| bTgFlagVariableProtons = 0; 1546| 0| } 1547| 0| else if ( !inchi_stricmp(pArg, "FULL") && developer_options ) ------------------ | Branch (1547:23): [True: 0, False: 0] | Branch (1547:55): [Folded, False: 0] ------------------ 1548| 0| { 1549| 0| bVer1DefaultMode = VER103_DEFAULT_MODE; ------------------ | | 47| 0|#define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ | | 48| 0| REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ | | ------------------ | | REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ | | ------------------ ------------------ 1550| 0| nMode = 0; 1551| 0| bReconnectCoord = 1; /* full output */ 1552| 0| bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 560| 0|#define EMBED_REC_METALS_INCHI 1 /* 1=> (default) output Reconnected embedded in Disconnected INChI; ------------------ bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 132| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ | Branch (1552:40): [True: 0, Folded] ------------------ 1553| 0| ip->bCtPredecessors = 0; 1554| 0| ip->bAbcNumbers = 0; 1555| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 135| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 136| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1556| 0| } 1557| 0| else if ( !inchi_stricmp(pArg, "MIN") && developer_options ) ------------------ | Branch (1557:23): [True: 0, False: 0] | Branch (1557:54): [Folded, False: 0] ------------------ 1558| 0| { 1559| 0| bVer1DefaultMode = VER103_DEFAULT_MODE; ------------------ | | 47| 0|#define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ | | 48| 0| REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ | | ------------------ | | REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ | | ------------------ ------------------ 1560| 0| nMode = 0; 1561| 0| bReconnectCoord = 1; /* minimal output */ 1562| 0| bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_NO_AUX_INFO; /* minimal compressed output */ ------------------ | | 560| 0|#define EMBED_REC_METALS_INCHI 1 /* 1=> (default) output Reconnected embedded in Disconnected INChI; ------------------ bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_NO_AUX_INFO; /* minimal compressed output */ ------------------ | | 132| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ bINChIOutputOptions = ((EMBED_REC_METALS_INCHI == 1) ? INCHI_OUT_EMBED_REC : 0) | INCHI_OUT_NO_AUX_INFO; /* minimal compressed output */ ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1562:40): [True: 0, Folded] ------------------ 1563| 0| ip->bCtPredecessors = 1; 1564| 0| ip->bAbcNumbers = 1; 1565| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 135| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 136| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1566| 0| } 1567| 0| else if ( !inchi_stricmp(pArg, "COMPRESS") && developer_options ) ------------------ | Branch (1567:23): [True: 0, False: 0] | Branch (1567:59): [Folded, False: 0] ------------------ 1568| 0| { 1569| 0| ip->bAbcNumbers = 1; 1570| 0| ip->bCtPredecessors = 1; /* compressed output */ 1571| 0| } 1572| | 1573| 0|#if ( READ_INCHI_STRING == 1 ) 1574| 0| else if ( !inchi_stricmp(pArg, "InChI2InChI") ) /*&& developer_options)*/ ------------------ | Branch (1574:23): [True: 0, False: 0] ------------------ 1575| 0| { 1576| | /* Read InChI Identifiers and output InChI Identifiers */ 1577| 0| ip->nInputType = INPUT_INCHI; 1578| 0| ip->bReadInChIOptions |= READ_INCHI_OUTPUT_INCHI; ------------------ | | 988| 0|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 1579| 0| ip->bReadInChIOptions &= ~READ_INCHI_TO_STRUCTURE; ------------------ | | 991| 0|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 1580| 0| } 1581| | 1582| 0| else if ( !inchi_stricmp(pArg, "SplitInChI") && developer_options ) ------------------ | Branch (1582:23): [True: 0, False: 0] | Branch (1582:61): [Folded, False: 0] ------------------ 1583| 0| { 1584| | /* Split InChI Identifiers into components */ 1585| 0| ip->bReadInChIOptions |= READ_INCHI_SPLIT_OUTPUT; ------------------ | | 989| 0|#define READ_INCHI_SPLIT_OUTPUT 0x00000002 ------------------ 1586| 0| } 1587| 0|#endif 1588| | 1589| 0| else if ( !inchi_stricmp(pArg, "MOLFILENUMBER") && developer_options ) ------------------ | Branch (1589:23): [True: 0, False: 0] | Branch (1589:64): [Folded, False: 0] ------------------ 1590| 0| { 1591| 0| ip->bGetMolfileNumber |= 1; 1592| 0| } 1593| 0| else if ( !inchi_stricmp(pArg, "OutputPLAIN") && developer_options ) ------------------ | Branch (1593:23): [True: 0, False: 0] | Branch (1593:62): [Folded, False: 0] ------------------ 1594| 0| { 1595| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT; ------------------ | | 135| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1596| 0| } 1597| 0| else if ( !inchi_stricmp(pArg, "OutputANNPLAIN") && developer_options ) ------------------ | Branch (1597:23): [True: 0, False: 0] | Branch (1597:65): [Folded, False: 0] ------------------ 1598| 0| { 1599| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 136| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1600| 0| bOutputStyle |= INCHI_OUT_WINCHI_WINDOW; /* debug */ ------------------ | | 138| 0|#define INCHI_OUT_WINCHI_WINDOW 0x0200 /* output into wINChI text window */ ------------------ 1601| 0| } 1602| 0| else if ( (!inchi_stricmp(pArg, "ONLYEXACT") || !inchi_stricmp(pArg, "ONLYFIXEDH")) && developer_options ) ------------------ | Branch (1602:24): [True: 0, False: 0] | Branch (1602:61): [True: 0, False: 0] | Branch (1602:100): [Folded, False: 0] ------------------ 1603| 0| { 1604| 0| bVer1DefaultMode |= REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1605| 0| bVer1DefaultMode &= ~REQ_MODE_TAUT; ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1606| 0| } 1607| 0| else if ( !inchi_stricmp(pArg, "ONLYNONISO") && developer_options ) ------------------ | Branch (1607:23): [True: 0, False: 0] | Branch (1607:61): [Folded, False: 0] ------------------ 1608| 0| { 1609| 0| bVer1DefaultMode |= REQ_MODE_NON_ISO; ------------------ | | 18| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1610| 0| bVer1DefaultMode &= ~REQ_MODE_ISO; ------------------ | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1611| 0| } 1612| 0| else if ( !inchi_stricmp(pArg, "TAUT") && developer_options ) ------------------ | Branch (1612:23): [True: 0, False: 0] | Branch (1612:55): [Folded, False: 0] ------------------ 1613| 0| { 1614| 0| bVer1DefaultMode &= ~REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1615| 0| bVer1DefaultMode |= REQ_MODE_TAUT; ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1616| 0| } 1617| 0| else if ( !inchi_stricmp(pArg, "ONLYRECMET") && developer_options ) ------------------ | Branch (1617:23): [True: 0, False: 0] | Branch (1617:61): [Folded, False: 0] ------------------ 1618| 0| { /* do not disconnect metals */ 1619| 0| bDisconnectCoord = 0; 1620| 0| } 1621| 0| else if ( !inchi_stricmp(pArg, "ONLYRECSALT") && developer_options ) ------------------ | Branch (1621:23): [True: 0, False: 0] | Branch (1621:62): [Folded, False: 0] ------------------ 1622| 0| { /* do not disconnect salts */ 1623| 0| bDisconnectSalts = 0; 1624| 0| } 1625| 0| else if ( !inchi_memicmp(pArg, "MOVEPOS:", 8) && developer_options ) ------------------ | Branch (1625:23): [True: 0, False: 0] | Branch (1625:62): [Folded, False: 0] ------------------ 1626| 0| { /* added -- 2010-03-01 DT */ 1627| 0| bMovePositiveCharges = (0 != strtol(pArg + 8, NULL, 10)); 1628| 0| } 1629| 0| else if ( !inchi_memicmp(pArg, "RSB:", 4) && developer_options ) ------------------ | Branch (1629:23): [True: 0, False: 0] | Branch (1629:58): [Folded, False: 0] ------------------ 1630| 0| { 1631| 0| mdbr = (int)strtol(pArg + 4, NULL, 10); 1632| 0| } 1633| 0| else if ( !inchi_stricmp(pArg, "EQU") && developer_options ) ------------------ | Branch (1633:23): [True: 0, False: 0] | Branch (1633:54): [Folded, False: 0] ------------------ 1634| 0| { 1635| 0| bCompareComponents = CMP_COMPONENTS; ------------------ | | 54| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ 1636| 0| } 1637| 0| else if ( !inchi_stricmp(pArg, "EQUNONISO") && developer_options ) ------------------ | Branch (1637:23): [True: 0, False: 0] | Branch (1637:60): [Folded, False: 0] ------------------ 1638| 0| { 1639| 0| bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 54| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 55| 0|#define CMP_COMPONENTS_NONISO 0x0002 /* ignore isotopic */ ------------------ 1640| 0| } 1641| 0| else if ( !inchi_memicmp(pArg, "OP:", 3) && developer_options ) ------------------ | Branch (1641:23): [True: 0, False: 0] | Branch (1641:57): [Folded, False: 0] ------------------ 1642| 0| { 1643| 0| bOutputPath = 1; 1644| 0| strncpy(szOutputPath, pArg + 3, sizeof(szOutputPath) - 1); 1645| 0| } 1646| | /* eof developer_options */ 1647| | 1648| | /* Display unrecognized option */ 1649| 0| else 1650| 0| { 1651| 0| bRecognizedOption = 0; 1652| | 1653| 0|#ifndef TARGET_LIB_FOR_WINCHI 1654| 0| inchi_ios_eprint(log_file, "Unrecognized optionQ3: \"%s\".\n", pArg); 1655| 0|#endif 1656| 0| } 1657| 12.7k| bVer1Options |= bRecognizedOption; 1658| | 1659| 12.7k| } /* eof Parsing stand-alone executable/libinchi options */ 1660| | 1661| 0| else if ( ip->num_paths < MAX_NUM_PATHS ) ------------------ | | 58| 0|#define MAX_NUM_PATHS 4 ------------------ | Branch (1661:19): [True: 0, False: 0] ------------------ 1662| 0| { 1663| 0| char* sz; 1664| |#if( ALLOW_EMPTY_PATHS == 1 ) 1665| | if ( argv[i] ) 1666| |#else 1667| 0| if ( argv[i] && argv[i][0] ) ------------------ | Branch (1667:18): [True: 0, False: 0] | Branch (1667:29): [True: 0, False: 0] ------------------ 1668| 0|#endif 1669| 0| { 1670| 0| if ( (sz = (char*)inchi_malloc((strlen(argv[i]) + 1) * sizeof(sz[0]))) ) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ | Branch (1670:22): [True: 0, False: 0] ------------------ 1671| 0| { 1672| 0| strcpy(sz, argv[i]); 1673| 0| } 1674| | 1675| 0| ip->path[ip->num_paths++] = sz; 1676| 0| } 1677| 0| } 1678| 12.7k| } /* eof parsing argv loop */ 1679| | 1680| | 1681| | /* Print messages and set controil variables according to just parsed options */ 1682| | 1683| | /* Timeout option(s) */ 1684| 12.7k| if ( timeout_set_warning ) ------------------ | Branch (1684:10): [True: 0, False: 12.7k] ------------------ 1685| 0| { 1686| 0| inchi_ios_eprint(log_file, "Warning: timeout value may have been modified (truncated?) due to number formatting issues;\n"); 1687| 0| } 1688| 12.7k| if ( timeout_set_error ) ------------------ | Branch (1688:10): [True: 0, False: 12.7k] ------------------ 1689| 0| { 1690| 0| inchi_ios_eprint(log_file, "Warning: specified timeout value was ignored due to invalid number format, using the default;\n"); 1691| 0| } 1692| | 1693| | /* InChIKey option(s) */ 1694| 12.7k| if ( bHashKey != 0 ) ------------------ | Branch (1694:10): [True: 0, False: 12.7k] ------------------ 1695| 0| { 1696| | /* Suppress InChIKey calculation if: */ 1697| | /* compressed output OR Inchi2Struct OR Inchi2Inchi */ 1698| 0| if ( (ip->bAbcNumbers == 1) && (ip->bCtPredecessors == 1) ) ------------------ | Branch (1698:14): [True: 0, False: 0] | Branch (1698:40): [True: 0, False: 0] ------------------ 1699| 0| { 1700| 0| bHashKey = 0; 1701| 0|#ifndef TARGET_LIB_FOR_WINCHI 1702| 0| inchi_ios_eprint(log_file, "Terminating: generation of InChIKey is not available with 'Compress' option\n"); 1703| 0| return -1; 1704| 0|#endif 1705| 0| } 1706| 0| if ( ip->nInputType == INPUT_INCHI ) ------------------ | Branch (1706:14): [True: 0, False: 0] ------------------ 1707| 0| { 1708| 0| bHashKey = 0; 1709| 0|#ifndef TARGET_LIB_FOR_WINCHI 1710| 0| inchi_ios_eprint(log_file, "Terminating: generation of InChIKey is not available in InChI conversion mode\n"); 1711| 0| return -1; 1712| 0|#endif 1713| 0| } 1714| 0| else 1715| 0| { 1716| 0| if ( bOutputMolfileOnly == 1 ) ------------------ | Branch (1716:18): [True: 0, False: 0] ------------------ 1717| 0| { 1718| 0| bHashKey = 0; 1719| 0|#ifndef TARGET_LIB_FOR_WINCHI 1720| 0| inchi_ios_eprint(log_file, "Terminating: generation of InChIKey is not available with 'OutputSDF' option\n"); 1721| 0| return -1; 1722| 0|#endif 1723| 0| } 1724| 0| } 1725| 0| } 1726| | 1727| 12.7k| if ( bNameSuffix || bOutputPath ) ------------------ | Branch (1727:10): [True: 12.7k, False: 0] | Branch (1727:25): [True: 0, False: 0] ------------------ 1728| 12.7k| { 1729| 12.7k| const char szNUL[] = "NUL"; 1730| | /* fix for AMD processor: use const char[] instead of just "NUL" constant 2008-11-5 DT */ 1731| 12.7k| const char* p = NULL; 1732| 12.7k| char* p_prev = NULL; /* djb-rwth: avoiding use of memory after it is freed */ 1733| 12.7k| char* r = NULL; 1734| 12.7k| char* sz; 1735| 12.7k| int len; 1736| | /* find the 1st path */ 1737| 63.7k| for ( i = 0; i < MAX_NUM_PATHS; i++ ) ------------------ | | 58| 63.7k|#define MAX_NUM_PATHS 4 ------------------ | Branch (1737:22): [True: 50.9k, False: 12.7k] ------------------ 1738| 50.9k| { 1739| 50.9k| if ( !p && ip->path[i] && ip->path[i][0] ) ------------------ | Branch (1739:18): [True: 50.9k, False: 0] | Branch (1739:24): [True: 0, False: 50.9k] | Branch (1739:39): [True: 0, False: 0] ------------------ 1740| 0| { 1741| 0| p = ip->path[i]; 1742| 0| break; 1743| 0| } 1744| 50.9k| } 1745| | /* fix output path */ 1746| 12.7k| if ( bOutputPath && szOutputPath[0] && p ) ------------------ | Branch (1746:14): [True: 0, False: 12.7k] | Branch (1746:29): [True: 0, False: 0] | Branch (1746:48): [True: 0, False: 0] ------------------ 1747| 0| { 1748| | /* remove last slash */ 1749| 0| len = (int)strlen(szOutputPath); 1750| 0| if ( len > 0 && szOutputPath[len - 1] != INCHI_PATH_DELIM ) ------------------ | | 232| 0|#define INCHI_PATH_DELIM '/' ------------------ | Branch (1750:18): [True: 0, False: 0] | Branch (1750:29): [True: 0, False: 0] ------------------ 1751| 0| { 1752| 0| szOutputPath[len++] = INCHI_PATH_DELIM; ------------------ | | 232| 0|#define INCHI_PATH_DELIM '/' ------------------ 1753| 0| szOutputPath[len] = '\0'; 1754| 0| } 1755| 0| if ( len > 0 && (r = (char*)strrchr(p, INCHI_PATH_DELIM)) && r[1] ) ------------------ | | 232| 0|#define INCHI_PATH_DELIM '/' ------------------ | Branch (1755:18): [True: 0, False: 0] | Branch (1755:29): [True: 0, False: 0] | Branch (1755:74): [True: 0, False: 0] ------------------ 1756| 0| { 1757| 0| strcat(szOutputPath, r + 1); 1758| 0| p = szOutputPath; 1759| 0| } 1760| 0| } 1761| | /* djb-rwth: copying the value of p */ 1762| |#ifdef _WIN32 1763| | p_prev = _strdup(p); 1764| |#else 1765| 12.7k| p_prev = inchi__strdup(p); 1766| 12.7k|#endif 1767| | /* add missing paths */ 1768| | /* djb-rwth: this whole block had to be rewritten to avoid use of memory after it is freed */ 1769| 12.7k| for ( i = 0; p_prev && i < MAX_NUM_PATHS; i++ ) ------------------ | | 58| 0|#define MAX_NUM_PATHS 4 ------------------ | Branch (1769:22): [True: 0, False: 12.7k] | Branch (1769:32): [True: 0, False: 0] ------------------ 1770| 0| { 1771| | /* fix for AMD processor: changed order 2008-11-5 DT */ 1772| 0| if ( !ip->path[i] || !ip->path[i][0] ) ------------------ | Branch (1772:18): [True: 0, False: 0] | Branch (1772:34): [True: 0, False: 0] ------------------ 1773| 0| { 1774| |#if ( BUILD_WITH_AMI == 1 ) && ( OUTPUT_FILE_EXT == 1 ) 1775| | char* pLastExt = (i && numOutNameExt >= i) ? strrchr((char*)p_prev, '.') : 0; 1776| | char* pLastSlash = (i && numOutNameExt >= i) ? strrchr((char*)p_prev, INCHI_PATH_DELIM) : 0; 1777| | if ( pLastExt && pLastSlash && pLastSlash > pLastExt ) 1778| | pLastExt = NULL; 1779| |#else 1780| 0| char* pLastExt = NULL; 1781| 0|#endif 1782| 0| len = (int)strlen(p_prev) + strlen(szNameSuffix) + strlen(ext[i]); 1783| 0| if ((sz = (char*)inchi_malloc(((long long)len + 1) * sizeof(sz[0])))) /* djb-rwth: cast operators added; addressing and ignoring LLVM warnings */ ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ | Branch (1783:21): [True: 0, False: 0] ------------------ 1784| 0| { 1785| 0| strcpy(sz, p_prev); /* djb-rwth: fix for use of memory after being freed */ 1786| |#if ( BUILD_WITH_AMI == 1 ) && ( OUTPUT_FILE_EXT == 1 ) 1787| | if ( pLastExt ) 1788| | { 1789| | strcpy(sz + (pLastExt - p), szOutNameExt[i - 1]); 1790| | } 1791| |#endif 1792| 0| strcat(sz, szNameSuffix); 1793| 0| if ( !pLastExt ) ------------------ | Branch (1793:26): [True: 0, False: 0] ------------------ 1794| 0| strcat(sz, ext[i]); 1795| 0| ip->num_paths++; 1796| 0| if ( ip->path[i] ) ------------------ | Branch (1796:26): [True: 0, False: 0] ------------------ 1797| 0| { 1798| 0| inchi_free((char*)ip->path[i]); /* eliminate memory leak 2013-12-18 DCh */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1799| 0| } 1800| 0| ip->path[i] = sz; 1801| 0| } 1802| 0| } 1803| 0| else if ( !inchi_stricmp(ip->path[i], szNUL) ) ------------------ | Branch (1803:23): [True: 0, False: 0] ------------------ 1804| 0| { 1805| 0| inchi_free((char*)ip->path[i]); /* cast deliberately const qualifier */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1806| 0| ip->path[i] = NULL; 1807| 0| } 1808| 0| } 1809| 12.7k| free(p_prev); /* djb-rwth: freeing memory reserved for auxiliary variable */ 1810| 12.7k| } 1811| | 1812| | /* inchi2inchi and inchi2struct option(s) */ 1813| 12.7k|#if ( READ_INCHI_STRING == 1 ) 1814| 12.7k| if ( INPUT_INCHI == ip->nInputType ) ------------------ | Branch (1814:10): [True: 12.7k, False: 0] ------------------ 1815| 12.7k| { 1816| 12.7k| bCompareComponents = 0; 1817| | /*bDisplayCompositeResults = 0;*/ 1818| |#if ( I2S_MODIFY_OUTPUT == 1 ) 1819| | if ( !(ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE) ) 1820| |#endif 1821| 12.7k| { 1822| 12.7k| bOutputMolfileOnly = 0; 1823| 12.7k| bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; ------------------ | | 129| 12.7k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 1824| 12.7k| bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 130| 12.7k|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1825| 12.7k| bINChIOutputOptions &= ~INCHI_OUT_ONLY_AUX_INFO; ------------------ | | 131| 12.7k|#define INCHI_OUT_ONLY_AUX_INFO 0x0004 /* output only Aux Info */ ------------------ 1826| | /* bNoStructLabels = 1; */ 1827| 12.7k| } 1828| 12.7k| ip->bDisplayIfRestoreWarnings = bDisplayIfRestoreWarnings; 1829| 12.7k| if ( !(bINChIOutputOptions & ------------------ | Branch (1829:14): [True: 12.7k, False: 0] ------------------ 1830| 12.7k| (INCHI_OUT_SDFILE_ONLY | /* not in bINChIOutputOptions yet */ ------------------ | | 133| 12.7k|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ 1831| 12.7k| INCHI_OUT_PLAIN_TEXT | /* not in bINChIOutputOptions yet */ ------------------ | | 135| 12.7k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1832| 12.7k| INCHI_OUT_PLAIN_TEXT_COMMENTS /* not in bINChIOutputOptions yet */ ------------------ | | 136| 12.7k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1833| 12.7k| ) 1834| 12.7k| ) 1835| |#if ( I2S_MODIFY_OUTPUT == 1 ) 1836| | && !bOutputMolfileOnly 1837| | && !(bOutputStyle & (INCHI_OUT_PLAIN_TEXT)) 1838| |#endif 1839| 12.7k| ) 1840| 12.7k| { 1841| 12.7k| bINChIOutputOptions |= INCHI_OUT_PLAIN_TEXT; ------------------ | | 135| 12.7k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1842| 12.7k| } 1843| 12.7k| } 1844| 12.7k|#endif 1845| | 1846| 12.7k| if ( bVer1Options ) ------------------ | Branch (1846:10): [True: 12.7k, False: 0] ------------------ 1847| 12.7k| { 1848| 12.7k| nMode |= bVer1DefaultMode; 1849| 12.7k| } 1850| 0| else if ( bReleaseVersion ) ------------------ | Branch (1850:15): [True: 0, False: 0] ------------------ 1851| 0| { 1852| 0| nMode |= nReleaseMode; 1853| 0| } 1854| | 1855| 12.7k|#if ( defined(COMPILE_ANSI_ONLY) || defined(TARGET_LIB_FOR_WINCHI) ) 1856| 12.7k| if ( bCompareComponents && !(bDisplay & 1) ) ------------------ | Branch (1856:10): [True: 0, False: 12.7k] | Branch (1856:32): [True: 0, False: 0] ------------------ 1857| 0| { 1858| 0| bCompareComponents = 0; 1859| 0| } 1860| 12.7k|#endif 1861| | 1862| | /* Save original options */ 1863| | /* nOrigMode = nMode; */ 1864| |#ifndef COMPILE_ANSI_ONLY 1865| | ip->dp.sdp.nFontSize = nFontSize; 1866| | ip->dp.sdp.ulDisplTime = *ulDisplTime; 1867| | ip->bDisplay = bDisplay; 1868| |#ifdef TARGET_LIB_FOR_WINCHI 1869| | ip->bDisplayCompositeResults = bDisplay; 1870| |#else 1871| | ip->bDisplayCompositeResults = bDisplayCompositeResults; 1872| |#endif 1873| |#else 1874| 12.7k| ip->bDisplayEachComponentINChI = 0; 1875| 12.7k| bCompareComponents = 0; 1876| 12.7k|#endif 1877| | 1878| 12.7k| ip->bMergeAllInputStructures = bMergeAllInputStructures; 1879| 12.7k| ip->bDoNotAddH = bDoNotAddH; 1880| | 1881| | /* Set default options */ 1882| 12.7k| if ( !nMode || nMode == REQ_MODE_STEREO ) ------------------ | | 19| 12.7k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (1882:10): [True: 0, False: 12.7k] | Branch (1882:20): [True: 0, False: 12.7k] ------------------ 1883| 0| { 1884| | /* requested all output */ 1885| 0| nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO); ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO); ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO); ------------------ | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO); ------------------ | | 18| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO); ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 1886| 0| } 1887| 12.7k| else 1888| 12.7k| { 1889| 12.7k| if ( !(nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) ) ------------------ | | 15| 12.7k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ if ( !(nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) ) ------------------ | | 16| 12.7k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (1889:14): [True: 0, False: 12.7k] ------------------ 1890| 0| { 1891| 0| nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT); ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT); ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1892| 0| } 1893| 12.7k| if ( (nMode & REQ_MODE_STEREO) && !(nMode & (REQ_MODE_ISO | REQ_MODE_NON_ISO)) ) ------------------ | | 19| 12.7k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ if ( (nMode & REQ_MODE_STEREO) && !(nMode & (REQ_MODE_ISO | REQ_MODE_NON_ISO)) ) ------------------ | | 17| 12.7k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ if ( (nMode & REQ_MODE_STEREO) && !(nMode & (REQ_MODE_ISO | REQ_MODE_NON_ISO)) ) ------------------ | | 18| 12.7k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (1893:14): [True: 12.7k, False: 0] | Branch (1893:43): [True: 0, False: 12.7k] ------------------ 1894| 0| { 1895| 0| nMode |= (REQ_MODE_ISO | REQ_MODE_NON_ISO); ------------------ | | 17| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= (REQ_MODE_ISO | REQ_MODE_NON_ISO); ------------------ | | 18| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1896| 0| } 1897| 12.7k| } 1898| | /* if the user requested isotopic then unconditionally add non-isotopic output. */ 1899| 12.7k| if ( nMode & REQ_MODE_ISO ) ------------------ | | 17| 12.7k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (1899:10): [True: 12.7k, False: 0] ------------------ 1900| 12.7k| { 1901| 12.7k| nMode |= REQ_MODE_NON_ISO; ------------------ | | 18| 12.7k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1902| 12.7k| } 1903| | 1904| 12.7k|#if ( MIN_SB_RING_SIZE > 0 ) 1905| 12.7k| if ( mdbr ) ------------------ | Branch (1905:10): [True: 0, False: 12.7k] ------------------ 1906| 0| { 1907| 0| nMinDbRinSize = mdbr; 1908| 0| } 1909| 12.7k| nMode |= (nMinDbRinSize << REQ_MODE_MIN_SB_RING_SHFT) & REQ_MODE_MIN_SB_RING_MASK; ------------------ | | 44| 12.7k|#define REQ_MODE_MIN_SB_RING_SHFT 16 ------------------ nMode |= (nMinDbRinSize << REQ_MODE_MIN_SB_RING_SHFT) & REQ_MODE_MIN_SB_RING_MASK; ------------------ | | 43| 12.7k|#define REQ_MODE_MIN_SB_RING_MASK 0x0F0000 /* RSB */ ------------------ 1910| 12.7k|#endif 1911| | 1912| | /* Input file */ 1913| 12.7k| if ( ip->nInputType == INPUT_NONE && ip->num_paths > 0 ) ------------------ | Branch (1913:10): [True: 0, False: 12.7k] | Branch (1913:42): [True: 0, False: 0] ------------------ 1914| 0| { 1915| 0| ip->nInputType = INPUT_MOLFILE; /* default */ 1916| 0| } 1917| 12.7k| ip->nMode = nMode; 1918| | /* Compare components */ 1919| 12.7k| if ( (bCompareComponents & CMP_COMPONENTS) && (nMode & REQ_MODE_BASIC) ) ------------------ | | 54| 12.7k|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ if ( (bCompareComponents & CMP_COMPONENTS) && (nMode & REQ_MODE_BASIC) ) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (1919:10): [True: 0, False: 12.7k] | Branch (1919:51): [True: 0, False: 0] ------------------ 1920| 0| { 1921| 0| bCompareComponents |= CMP_COMPONENTS_NONTAUT; /* compare non-tautomeric */ ------------------ | | 56| 0|#define CMP_COMPONENTS_NONTAUT 0x0004 /* compare non-tautomeric */ ------------------ 1922| 0| } 1923| 12.7k| ip->bCompareComponents = bCompareComponents; 1924| | /* Output */ 1925| 12.7k| ip->bINChIOutputOptions = bINChIOutputOptions | (bOutputMolfileOnly ? INCHI_OUT_SDFILE_ONLY : 0); ------------------ | | 133| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (1925:54): [True: 0, False: 12.7k] ------------------ 1926| 12.7k| if ( bOutputMolfileOnly ) ------------------ | Branch (1926:10): [True: 0, False: 12.7k] ------------------ 1927| 0| { 1928| 0| bOutputStyle &= ~(INCHI_OUT_PLAIN_TEXT | ------------------ | | 135| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1929| 0| INCHI_OUT_PLAIN_TEXT_COMMENTS | ------------------ | | 136| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1930| 0| INCHI_OUT_TABBED_OUTPUT); ------------------ | | 139| 0|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 1931| 0|#if ( SDF_OUTPUT_DT == 1 ) 1932| 0| ip->bINChIOutputOptions |= bOutputMolfileDT ? INCHI_OUT_SDFILE_ATOMS_DT : 0; ------------------ | | 140| 0|#define INCHI_OUT_SDFILE_ATOMS_DT 0x0800 /* SDfile output H isotopes as D and T */ ------------------ | Branch (1932:36): [True: 0, False: 0] ------------------ 1933| 0| ip->bINChIOutputOptions |= bOutputMolfileSplit ? INCHI_OUT_SDFILE_SPLIT : 0; ------------------ | | 141| 0|#define INCHI_OUT_SDFILE_SPLIT 0x1000 /* Split SDfile into components */ ------------------ | Branch (1933:36): [True: 0, False: 0] ------------------ 1934| 0|#endif 1935| 0| } 1936| |#ifdef TARGET_LIB_FOR_WINCHI 1937| | if ( !(bDisplay & 1) ) 1938| | { 1939| | bOutputStyle &= ~(INCHI_OUT_PLAIN_TEXT_COMMENTS); /* do not ouput comments in wINChI text file results */ 1940| | } 1941| | else 1942| | { 1943| | bOutputStyle |= INCHI_OUT_WINCHI_WINDOW; 1944| | } 1945| |#endif 1946| 12.7k| ip->bINChIOutputOptions |= bOutputStyle; 1947| 12.7k| ip->bNoStructLabels = bNoStructLabels; 1948| | 1949| | /* Processing options */ 1950| 12.7k| if ( bForcedChiralFlag ) ------------------ | Branch (1950:10): [True: 0, False: 12.7k] ------------------ 1951| 0| { 1952| 0| ip->bChiralFlag = bForcedChiralFlag; 1953| 0| } 1954| | 1955| | /* Tautomeric/salts options */ 1956| 12.7k| ip->bTautFlags = 0; 1957| 12.7k| ip->bTautFlagsDone = 0; 1958| | 1959| | /* Find regular tautomerism */ 1960| 12.7k| ip->bTautFlags |= TG_FLAG_TEST_TAUT__ATOMS; ------------------ | | 918| 12.7k|#define TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */ ------------------ 1961| | 1962| | /* If possible, find long-range H/(-) taut. on =C-OH, >C=O */ 1963| 12.7k| ip->bTautFlags |= bAcidTautomerism ? TG_FLAG_TEST_TAUT__SALTS : 0; ------------------ | | 920| 12.7k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (1963:23): [True: 12.7k, False: 0] ------------------ 1964| | 1965| | /* Multi-attachment long-range H/(-) taut. on =C-OH, >C=O */ 1966| 12.7k| ip->bTautFlags |= (bAcidTautomerism > 1) ? TG_FLAG_TEST_TAUT2_SALTS : 0; ------------------ | | 922| 12.7k|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (1966:23): [True: 12.7k, False: 0] ------------------ 1967| | 1968| | /* (Debug) allow to find long-range H-only tautomerism on =C-OH, >C=O */ 1969| 12.7k| ip->bTautFlags |= (bUnchargedAcidTaut == 1) ? TG_FLAG_ALLOW_NO_NEGTV_O : 0; ------------------ | | 923| 0|#define TG_FLAG_ALLOW_NO_NEGTV_O 0x00000020 /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */ ------------------ | Branch (1969:23): [True: 0, False: 12.7k] ------------------ 1970| | 1971| | /* Merge =C-OH and >C=O containing t-groups and other =C-OH groups */ 1972| 12.7k| ip->bTautFlags |= bMergeSaltTGroups ? TG_FLAG_MERGE_TAUT_SALTS : 0; ------------------ | | 924| 12.7k|#define TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */ ------------------ | Branch (1972:23): [True: 12.7k, False: 0] ------------------ 1973| | 1974| | /* 1975| | * Legacy salt disconnection and metal-bond handling are disabled 1976| | * when Molecular Inorganics processing is enabled. 1977| | */ 1978| 12.7k| if (!bMolecularInorganics) ------------------ | Branch (1978:9): [True: 0, False: 12.7k] ------------------ 1979| 0| { 1980| 0| ip->bTautFlags |= bDisconnectSalts ? TG_FLAG_DISCONNECT_SALTS : 0; ------------------ | | 919| 0|#define TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */ ------------------ | Branch (1980:27): [True: 0, False: 0] ------------------ 1981| | 1982| 0| ip->bTautFlags |= bDisconnectCoord ? TG_FLAG_DISCONNECT_COORD : 0; ------------------ | | 931| 0|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (1982:27): [True: 0, False: 0] ------------------ 1983| 0| ip->bTautFlags |= (bDisconnectCoord && bReconnectCoord) ? TG_FLAG_RECONNECT_COORD : 0; ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1983:28): [True: 0, False: 0] | Branch (1983:48): [True: 0, False: 0] ------------------ 1984| 0| ip->bTautFlags |= bDisconnectCoordChkVal ? TG_FLAG_CHECK_VALENCE_COORD : 0; ------------------ | | 933| 0|#define TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */ ------------------ | Branch (1984:27): [True: 0, False: 0] ------------------ 1985| 0| } 1986| | 1987| | /* Allow long-range movement of N(+), P(+) charges */ 1988| 12.7k| ip->bTautFlags |= bMovePositiveCharges ? TG_FLAG_MOVE_POS_CHARGES : 0; ------------------ | | 921| 12.7k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (1988:23): [True: 12.7k, False: 0] ------------------ 1989| | 1990| 12.7k| ip->bTautFlags |= bTgFlagVariableProtons ? TG_FLAG_VARIABLE_PROTONS : 0; ------------------ | | 935| 12.7k|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (1990:23): [True: 12.7k, False: 0] ------------------ 1991| 12.7k| ip->bTautFlags |= bTgFlagHardAddRenProtons ? TG_FLAG_HARD_ADD_REM_PROTONS : 0; ------------------ | | 936| 12.7k|#define TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */ ------------------ | Branch (1991:23): [True: 12.7k, False: 0] ------------------ 1992| 12.7k| ip->bTautFlags |= bKetoEnolTaut ? TG_FLAG_KETO_ENOL_TAUT : 0; ------------------ | | 946| 0|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (1992:23): [True: 0, False: 12.7k] ------------------ 1993| 12.7k| ip->bTautFlags |= b15TautNonRing ? TG_FLAG_1_5_TAUT : 0; ------------------ | | 947| 0|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (1993:23): [True: 0, False: 12.7k] ------------------ 1994| | 1995| | /*^^^ IPl 2020-04-02 added to forcefully enable new tauto rules (in test_ixa, etc.) */ 1996| | /*^^^ IPl 2020-10-26 removed set to 1 1997| | bPT_22_00_Taut = 1; 1998| | bPT_16_00_Taut = 1; 1999| | bPT_06_00_Taut = 1; 2000| | bPT_39_00_Taut = 1; 2001| | */ 2002| | 2003| | /*^^^ IPl 2020-04-02 */ 2004| 12.7k| ip->bTautFlags |= bPT_22_00_Taut ? TG_FLAG_PT_22_00 : 0; ------------------ | | 953| 0|#define TG_FLAG_PT_22_00 0x00800000 ------------------ | Branch (2004:23): [True: 0, False: 12.7k] ------------------ 2005| 12.7k| ip->bTautFlags |= bPT_16_00_Taut ? TG_FLAG_PT_16_00 : 0; ------------------ | | 954| 0|#define TG_FLAG_PT_16_00 0x01000000 ------------------ | Branch (2005:23): [True: 0, False: 12.7k] ------------------ 2006| 12.7k| ip->bTautFlags |= bPT_06_00_Taut ? TG_FLAG_PT_06_00 : 0; ------------------ | | 955| 0|#define TG_FLAG_PT_06_00 0x02000000 ------------------ | Branch (2006:23): [True: 0, False: 12.7k] ------------------ 2007| 12.7k| ip->bTautFlags |= bPT_39_00_Taut ? TG_FLAG_PT_39_00 : 0; ------------------ | | 956| 0|#define TG_FLAG_PT_39_00 0x04000000 ------------------ | Branch (2007:23): [True: 0, False: 12.7k] ------------------ 2008| 12.7k| ip->bTautFlags |= bPT_13_00_Taut ? TG_FLAG_PT_13_00 : 0; ------------------ | | 957| 0|#define TG_FLAG_PT_13_00 0x08000000 ------------------ | Branch (2008:23): [True: 0, False: 12.7k] ------------------ 2009| 12.7k| ip->bTautFlags |= bPT_18_00_Taut ? TG_FLAG_PT_18_00 : 0; ------------------ | | 958| 0|#define TG_FLAG_PT_18_00 0x10000000 ------------------ | Branch (2009:23): [True: 0, False: 12.7k] ------------------ 2010| | 2011| 12.7k|#ifdef STEREO_WEDGE_ONLY 2012| 12.7k| ip->bTautFlags |= bPointedEdgeStereo ? TG_FLAG_POINTED_EDGE_STEREO : 0; ------------------ | | 937| 12.7k|#define TG_FLAG_POINTED_EDGE_STEREO 0x00002000 /* only pointed edge of stereo bond defines stereo */ ------------------ | Branch (2012:23): [True: 12.7k, False: 0] ------------------ 2013| 12.7k|#endif 2014| |#if ( FIX_ADJ_RAD == 1 ) 2015| | ip->bTautFlags |= bFixAdjacentRad ? TG_FLAG_FIX_ADJ_RADICALS : 0; 2016| |#endif 2017| 12.7k| ip->bTautFlags |= bAddPhosphineStereo ? TG_FLAG_PHOSPHINE_STEREO : 0; ------------------ | | 941| 12.7k|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ | Branch (2017:23): [True: 12.7k, False: 0] ------------------ 2018| 12.7k| ip->bTautFlags |= bAddArsineStereo ? TG_FLAG_ARSINE_STEREO : 0; ------------------ | | 942| 12.7k|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ | Branch (2018:23): [True: 12.7k, False: 0] ------------------ 2019| 12.7k| ip->bTautFlags |= bFixSp3bug ? TG_FLAG_FIX_SP3_BUG : 0; ------------------ | | 944| 12.7k|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ | Branch (2019:23): [True: 12.7k, False: 0] ------------------ 2020| | 2021| | /* Bug fixes */ 2022| 12.7k| if ( bFixFB2 ) ------------------ | Branch (2022:10): [True: 12.7k, False: 0] ------------------ 2023| 12.7k| { 2024| 12.7k|#if ( FIX_ISO_FIXEDH_BUG == 1 ) 2025| 12.7k| ip->bTautFlags |= TG_FLAG_FIX_ISO_FIXEDH_BUG; /* accomodate FIX_ISO_FIXEDH_BUG */ ------------------ | | 950| 12.7k|#define TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */ ------------------ 2026| 12.7k|#endif 2027| | 2028| 12.7k|#if ( FIX_TERM_H_CHRG_BUG == 1 ) 2029| 12.7k| ip->bTautFlags |= TG_FLAG_FIX_TERM_H_CHRG_BUG; /* accomodate FIX_TERM_H_CHRG_BUG */ ------------------ | | 951| 12.7k|#define TG_FLAG_FIX_TERM_H_CHRG_BUG 0x00400000 /* fix bug found after v.102b (moving H charge in 'remove_terminal_HDT') */ ------------------ 2030| 12.7k|#endif 2031| | 2032| 12.7k|#if ( FIX_TRANSPOSITION_CHARGE_BUG == 1 ) 2033| 12.7k| ip->bINChIOutputOptions |= INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG; ------------------ | | 143| 12.7k|#define INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG 0x2000 ------------------ 2034| 12.7k|#endif 2035| 12.7k| } 2036| | 2037| 12.7k| if ( !ip->nInputType ) ------------------ | Branch (2037:10): [True: 0, False: 12.7k] ------------------ 2038| 0| { 2039| 0| ip->nInputType = INPUT_MOLFILE; 2040| 0| } 2041| | 2042| | /* Check if /SNon requested turn OFF SUU/SLUUD */ 2043| 12.7k| if ( !(ip->nMode & REQ_MODE_STEREO) ) ------------------ | | 19| 12.7k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (2043:10): [True: 0, False: 12.7k] ------------------ 2044| 0| { 2045| 0| ip->nMode &= ~REQ_MODE_DIFF_UU_STEREO; ------------------ | | 40| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ 2046| 0| ip->nMode &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU); ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ ip->nMode &= ~(REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU); ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 2047| 0| } 2048| | 2049| | /* Standard InChI ? */ 2050| 12.7k| if ( bStdFormat ) ------------------ | Branch (2050:10): [True: 12.7k, False: 0] ------------------ 2051| 12.7k| { 2052| 12.7k| ip->bINChIOutputOptions |= INCHI_OUT_STDINCHI; ------------------ | | 145| 12.7k|#define INCHI_OUT_STDINCHI 0x4000 ------------------ 2053| 12.7k| } 2054| | 2055| | /* InChIKey ? */ 2056| 12.7k| if ( !bHashKey ) ------------------ | Branch (2056:10): [True: 12.7k, False: 0] ------------------ 2057| 12.7k| { 2058| 12.7k| ip->bCalcInChIHash = INCHIHASH_NONE; 2059| 12.7k| } 2060| 0| else 2061| 0| { 2062| 0| ip->bCalcInChIHash = INCHIHASH_KEY; 2063| 0| } 2064| | /* Extension(s) to hash (in non-std mode only) ? */ 2065| 12.7k| if ( !bHashKey ) ------------------ | Branch (2065:10): [True: 12.7k, False: 0] ------------------ 2066| 12.7k| { 2067| 12.7k| if ( (bHashXtra1 != 0) || (bHashXtra2 != 0) ) ------------------ | Branch (2067:14): [True: 0, False: 12.7k] | Branch (2067:35): [True: 0, False: 12.7k] ------------------ 2068| 0| { 2069| 0| inchi_ios_eprint(log_file, "Hash extension(s) not generated: InChIKey not requested"); 2070| 0| } 2071| 12.7k| } 2072| 0| else 2073| 0| { 2074| 0| if ( bHashXtra1 ) ------------------ | Branch (2074:14): [True: 0, False: 0] ------------------ 2075| 0| { 2076| 0| if ( bHashXtra2 ) ------------------ | Branch (2076:18): [True: 0, False: 0] ------------------ 2077| 0| { 2078| 0| ip->bCalcInChIHash = INCHIHASH_KEY_XTRA1_XTRA2; 2079| 0| } 2080| 0| else 2081| 0| { 2082| 0| ip->bCalcInChIHash = INCHIHASH_KEY_XTRA1; 2083| 0| } 2084| 0| } 2085| 0| else if ( bHashXtra2 ) ------------------ | Branch (2085:19): [True: 0, False: 0] ------------------ 2086| 0| { 2087| 0| ip->bCalcInChIHash = INCHIHASH_KEY_XTRA2; 2088| 0| } 2089| 0| } 2090| | 2091| 12.7k| ip->bLargeMolecules = bLargeMolecules; 2092| 12.7k| ip->bLooseTSACheck = bLooseTSACheck; 2093| | 2094| 12.7k| ip->bNPZz = bNPZz; 2095| 12.7k| ip->bStereoAtZz = bStereoAtZz; /*STEREO_AT_ZZ;*/ 2096| 12.7k| ip->bMolecularInorganics = bMolecularInorganics; /* @nnuk */ 2097| 12.7k| ip->bNoWarnings = bNoWarnings; 2098| 12.7k| ip->bMergeHash = bMergeHash; 2099| 12.7k| ip->bHideInChI = bHideInChI; 2100| | 2101| 12.7k| ip->bPolymers = bPolymers; 2102| 12.7k| ip->bFoldPolymerSRU = bFoldPolymerSRU; 2103| 12.7k| ip->bFrameShiftScheme = bFrameShiftScheme; 2104| | 2105| |#ifdef TARGET_LIB_FOR_WINCHI 2106| | ip->bLargeMolecules = 1; 2107| | /*ip->bPolymers = POLYMERS_MODERN; */ 2108| | /*ip->bNPZz = 1;*/ 2109| | /*ip->bFrameShiftScheme = FSS_NONE;*/ 2110| | /*ip->bFoldPolymerSRU = 1;*/ 2111| | 2112| |#if ( UNDERIVATIZE == 1 ) 2113| | ip->bUnderivatize = 1; 2114| | if ( ip->bUnderivatize ) 2115| | { 2116| | ip->bINChIOutputOptions &= ~INCHI_OUT_STDINCHI; 2117| | } 2118| |#endif 2119| | ip->bNoWarnings = 0; 2120| | ip->bMergeHash = 0; 2121| | ip->bHideInChI = 0; 2122| | 2123| |#endif 2124| | 2125| 12.7k| ip->bINChIOutputOptions2 = bINChIOutputOptions2; 2126| | 2127| 12.7k| ip->bEnhancedStereo = bEnhancedStereochemistry; 2128| | 2129| 12.7k| return 0; 2130| 12.7k|} PrintInputParms: 2138| 12.5k|{ 2139| | 2140| |#if (BUILD_WITH_ENG_OPTIONS==1) 2141| | const int developer_options = 1; 2142| |#else 2143| 12.5k| const int developer_options = 0; 2144| 12.5k|#endif 2145| |#ifdef TARGET_LIB_FOR_WINCHI 2146| | int bInChI2Struct = 0; /* winchi-1 can not convert InChI to structure */ 2147| |#else 2148| 12.5k| int bInChI2Struct = (ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE) && ip->nInputType == INPUT_INCHI; ------------------ | | 991| 12.5k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (2148:25): [True: 6.28k, False: 6.28k] | Branch (2148:78): [True: 6.28k, False: 0] ------------------ 2149| 12.5k|#endif 2150| | 2151| 12.5k| INCHI_MODE nMode = ip->nMode; 2152| 12.5k| int k; 2153| 12.5k| int bStdFormat = 1; 2154| 12.5k| int first = 1; 2155| | 2156| | 2157| 12.5k| if ( !(ip->bINChIOutputOptions & INCHI_OUT_STDINCHI) ) ------------------ | | 145| 12.5k|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (2157:10): [True: 0, False: 12.5k] ------------------ 2158| 0| { 2159| 0| bStdFormat = 0; 2160| 0| } 2161| | /* Some stereo */ 2162| 12.5k| if ( !(nMode & REQ_MODE_STEREO) ) ------------------ | | 19| 12.5k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (2162:10): [True: 0, False: 12.5k] ------------------ 2163| 0| { 2164| 0| inchi_ios_eprint(log_file, "Using specific structure perception features:\n"); 2165| 0| first = 0; 2166| 0| inchi_ios_eprint(log_file, " Stereo OFF\n"); 2167| 0| } 2168| 12.5k| else 2169| 12.5k| { 2170| 12.5k| if ( !(TG_FLAG_POINTED_EDGE_STEREO & ip->bTautFlags) ) ------------------ | | 937| 12.5k|#define TG_FLAG_POINTED_EDGE_STEREO 0x00002000 /* only pointed edge of stereo bond defines stereo */ ------------------ | Branch (2170:14): [True: 0, False: 12.5k] ------------------ 2171| 0| { 2172| 0| if ( first ) ------------------ | Branch (2172:18): [True: 0, False: 0] ------------------ 2173| 0| { 2174| 0| inchi_ios_eprint(log_file, "Using specific structure perception features:\n"); 2175| 0| first = 0; 2176| 0| } 2177| 0| inchi_ios_eprint(log_file, " Both ends of wedge point to stereocenters\n"); 2178| 0| } 2179| 12.5k| } 2180| 12.5k| if ( ip->bDoNotAddH ) ------------------ | Branch (2180:10): [True: 0, False: 12.5k] ------------------ 2181| 0| { 2182| 0| if ( first ) ------------------ | Branch (2182:14): [True: 0, False: 0] ------------------ 2183| 0| { 2184| 0| inchi_ios_eprint(log_file, "Using specific structure perception features:\n"); 2185| 0| } 2186| 0| inchi_ios_eprint(log_file, " Do not add H\n"); 2187| 0| } 2188| | 2189| | 2190| |#if ( RENUMBER_ATOMS_AND_RECALC_V106 == 1 ) 2191| | if ( ip->bRenumber == 1 ) 2192| | { 2193| | inchi_ios_eprint(log_file, "\nGenerate InChI upon random atom renumbering\n\n"); 2194| | } 2195| |#endif 2196| | 2197| 12.5k|#if ( UNDERIVATIZE == 1 ) 2198| 12.5k| if ( ip->bUnderivatize == 1 ) ------------------ | Branch (2198:10): [True: 0, False: 12.5k] ------------------ 2199| 0| { 2200| 0| inchi_ios_eprint(log_file, "\nConvert input structure to derivative precursor before InChI calculation\n\n"); 2201| 0| } 2202| 12.5k| else if ( ip->bUnderivatize == 3 ) ------------------ | Branch (2202:15): [True: 0, False: 12.5k] ------------------ 2203| 0| { 2204| 0| inchi_ios_eprint(log_file, "\nOutputs derivative information for the input structure\n\n"); 2205| 0| } 2206| 12.5k|#endif 2207| | 2208| | 2209| | 2210| | /* Generation/conversion indicator */ 2211| 12.5k| if ( bStdFormat ) ------------------ | Branch (2211:10): [True: 12.5k, False: 0] ------------------ 2212| 12.5k| { 2213| 12.5k| if ( !(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) && !bInChI2Struct ) ------------------ | | 133| 12.5k|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2213:14): [True: 12.5k, False: 0] | Branch (2213:68): [True: 6.28k, False: 6.28k] ------------------ 2214| 6.28k| { 2215| 6.28k| inchi_ios_eprint(log_file, "Generating standard InChI\n"); 2216| 6.28k| } 2217| | 2218| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) && !defined(TARGET_EXE_USING_API) ) 2219| | /* effective only in command line program InChI or stdInChI */ 2220| | else if ( bInChI2Struct ) 2221| | { 2222| | inchi_ios_eprint(log_file, "Converting InChI(s) to structure(s) in %s\n", 2223| | (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) ? 2224| | "MOL format" : "aux. info format"); 2225| | } 2226| |#endif 2227| 12.5k| } 2228| 0| else 2229| 0| { 2230| 0| inchi_ios_eprint(log_file, "Generating non-standard InChI with the options: \n"); 2231| 0| } 2232| | 2233| | /* SDfile output */ 2234| 12.5k| if ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) ------------------ | | 133| 12.5k|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2234:10): [True: 0, False: 12.5k] ------------------ 2235| 0| { 2236| 0| inchi_ios_eprint(log_file, 2237| 0| "Output SDfile only without stereochemical information and atom coordinates%s\n", 2238| 0| (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ATOMS_DT) ? ------------------ | | 140| 0|#define INCHI_OUT_SDFILE_ATOMS_DT 0x0800 /* SDfile output H isotopes as D and T */ ------------------ | Branch (2238:13): [True: 0, False: 0] ------------------ 2239| 0| "\n(write H isotopes as D, T)" : ""); 2240| 0| } 2241| | 2242| | /* Fixed/Mobile H */ 2243| 12.5k| if ( !bStdFormat ) ------------------ | Branch (2243:10): [True: 0, False: 12.5k] ------------------ 2244| 0| { 2245| 0| if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_BASIC | REQ_MODE_TAUT) ) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_BASIC | REQ_MODE_TAUT) ) ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_BASIC | REQ_MODE_TAUT) ) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_BASIC | REQ_MODE_TAUT) ) ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (2245:14): [True: 0, False: 0] ------------------ 2246| 0| { 2247| 0| inchi_ios_eprint(log_file, " Mobile H Perception OFF (include FixedH layer)\n"); 2248| 0| } 2249| 0| else if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_TAUT) ) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ else if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_TAUT) ) ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ else if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_TAUT) ) ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (2249:19): [True: 0, False: 0] ------------------ 2250| 0| { 2251| 0| inchi_ios_eprint(log_file, " Mobile H Perception ON (omit FixedH layer)\n"); 2252| 0| } 2253| 0| else if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_BASIC) ) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ else if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_BASIC) ) ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ else if ( (nMode & (REQ_MODE_BASIC | REQ_MODE_TAUT)) == (REQ_MODE_BASIC) ) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (2253:19): [True: 0, False: 0] ------------------ 2254| 0| { 2255| 0| inchi_ios_eprint(log_file, " Mobile H ignored\n"); 2256| 0| } 2257| 0| else 2258| 0| { 2259| 0| inchi_ios_eprint(log_file, " Undefined Mobile H mode\n"); 2260| 0| } 2261| | 2262| 0| if ( (ip->bTautFlags & TG_FLAG_VARIABLE_PROTONS) ) ------------------ | | 935| 0|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (2262:14): [True: 0, False: 0] ------------------ 2263| 0| { 2264| 0| if ( !(ip->bTautFlags & TG_FLAG_HARD_ADD_REM_PROTONS) ) ------------------ | | 936| 0|#define TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */ ------------------ | Branch (2264:18): [True: 0, False: 0] ------------------ 2265| 0| { 2266| 0| inchi_ios_eprint(log_file, " Disabled Aggressive (De)protonation\n"); 2267| 0| } 2268| 0| } 2269| | 2270| |#if ( FIND_RING_SYSTEMS != 1 ) 2271| | inchi_ios_eprint(log_file, " %s5-, 6-, 7-memb. ring taut. ignored\n", i ? "; " : ""); 2272| |#endif 2273| | 2274| | /* RecMet */ 2275| 0| if ( ip->bTautFlags & TG_FLAG_DISCONNECT_COORD ) ------------------ | | 931| 0|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (2275:14): [True: 0, False: 0] ------------------ 2276| 0| { 2277| 0| if ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD ) ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (2277:18): [True: 0, False: 0] ------------------ 2278| 0| { 2279| 0| inchi_ios_eprint(log_file, " Include bonds to metals\n"); 2280| 0| } 2281| 0| else 2282| 0| { 2283| 0| inchi_ios_eprint(log_file, " Do not reconnect metals (omit RecMet layer)\n"); 2284| 0| } 2285| 0| } 2286| 0| else 2287| 0| { 2288| 0| inchi_ios_eprint(log_file, " Do not disconnect metals\n"); 2289| 0| } 2290| | 2291| | /* Isotopic - always ON, output disabled. 09-17-2009*/ 2292| | /* 2293| | if ( nMode & REQ_MODE_ISO ) 2294| | inchi_ios_eprint( log_file, " Isotopic ON\n"); 2295| | else if ( nMode & REQ_MODE_NON_ISO ) 2296| | inchi_ios_eprint( log_file, " Isotopic OFF\n"); 2297| | */ 2298| | 2299| |#if ( FIX_ADJ_RAD == 1 ) 2300| | if ( ip->bTautFlags & TG_FLAG_FIX_ADJ_RADICALS ) 2301| | { 2302| | inchi_ios_eprint(log_file, "Fix Adjacent Radicals\n"); 2303| | } 2304| |#endif 2305| | 2306| | /* Stereo */ 2307| 0| if ( nMode & REQ_MODE_STEREO ) ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (2307:14): [True: 0, False: 0] ------------------ 2308| 0| { 2309| 0| inchi_ios_eprint(log_file, " %s%s%s%sStereo ON\n", 2310| 0| (nMode & REQ_MODE_NOEQ_STEREO) ? "Slow " : "", ------------------ | | 21| 0|#define REQ_MODE_NOEQ_STEREO 0x000040 /* SS */ ------------------ | Branch (2310:17): [True: 0, False: 0] ------------------ 2311| 0| (nMode & REQ_MODE_REDNDNT_STEREO) ? "Redund. " : "", ------------------ | | 22| 0|#define REQ_MODE_REDNDNT_STEREO 0x000080 /* RS */ ------------------ | Branch (2311:17): [True: 0, False: 0] ------------------ 2312| 0| (nMode & REQ_MODE_NO_ALT_SBONDS) ? "No AltBond " : "", ------------------ | | 23| 0|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ | Branch (2312:17): [True: 0, False: 0] ------------------ 2313| | 2314| 0| (nMode & REQ_MODE_RACEMIC_STEREO) ? "Racemic " : ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (2314:17): [True: 0, False: 0] ------------------ 2315| 0| (nMode & REQ_MODE_RELATIVE_STEREO) ? "Relative " : ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (2315:17): [True: 0, False: 0] ------------------ 2316| 0| (nMode & REQ_MODE_CHIR_FLG_STEREO) ? "Chiral Flag " : "Absolute "); ------------------ | | 34| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ | Branch (2316:17): [True: 0, False: 0] ------------------ 2317| | 2318| 0| if ( 0 == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ if ( 0 == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (2318:18): [True: 0, False: 0] ------------------ 2319| 0| { 2320| 0| inchi_ios_eprint(log_file, " Include undefined/unknown stereogenic centers and bonds\n"); 2321| 0| } 2322| 0| else if ( REQ_MODE_SC_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ else if ( REQ_MODE_SC_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ else if ( REQ_MODE_SC_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (2322:23): [True: 0, False: 0] ------------------ 2323| 0| { 2324| 0| inchi_ios_eprint(log_file, " Omit undefined/unknown stereogenic centers\n"); 2325| 0| } 2326| 0| else if ( REQ_MODE_SB_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ else if ( REQ_MODE_SB_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ else if ( REQ_MODE_SB_IGN_ALL_UU == (nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (2326:23): [True: 0, False: 0] ------------------ 2327| 0| { 2328| 0| inchi_ios_eprint(log_file, " Omit undefined/unknown stereogenic bonds\n"); 2329| 0| } 2330| 0| else 2331| 0| { 2332| | /*case REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU*/ 2333| 0| inchi_ios_eprint(log_file, " Omit undefined/unknown stereogenic centers and bonds\n"); 2334| 0| } 2335| 0| if ( 0 != (nMode & REQ_MODE_DIFF_UU_STEREO) ) ------------------ | | 40| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (2335:18): [True: 0, False: 0] ------------------ 2336| 0| { 2337| 0| inchi_ios_eprint(log_file, " Make labels for unknown and undefined stereo different\n"); 2338| 0| } 2339| | 2340| 0|#if ( defined(MIN_SB_RING_SIZE) && MIN_SB_RING_SIZE > 0 ) 2341| 0| k = (ip->nMode & REQ_MODE_MIN_SB_RING_MASK) >> REQ_MODE_MIN_SB_RING_SHFT; ------------------ | | 43| 0|#define REQ_MODE_MIN_SB_RING_MASK 0x0F0000 /* RSB */ ------------------ k = (ip->nMode & REQ_MODE_MIN_SB_RING_MASK) >> REQ_MODE_MIN_SB_RING_SHFT; ------------------ | | 44| 0|#define REQ_MODE_MIN_SB_RING_SHFT 16 ------------------ 2342| 0| if ( bRELEASE_VERSION != 1 || k != MIN_SB_RING_SIZE ) ------------------ | | 238| 0|#define bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */ ------------------ if ( bRELEASE_VERSION != 1 || k != MIN_SB_RING_SIZE ) ------------------ | | 592| 0|#define MIN_SB_RING_SIZE 8 /* do not assume stereo bonds in rings containing 3..MIN_SB_RING_SIZE-1 atoms */ ------------------ | Branch (2342:18): [Folded, False: 0] | Branch (2342:43): [True: 0, False: 0] ------------------ 2343| 0| { 2344| 0| if ( k >= 3 ) ------------------ | Branch (2344:22): [True: 0, False: 0] ------------------ 2345| 0| { 2346| 0| inchi_ios_eprint(log_file, " Min. stereobond ring size: %d\n", k); 2347| 0| } 2348| 0| else 2349| 0| { 2350| 0| inchi_ios_eprint(log_file, " Min. stereobond ring size: NONE\n"); 2351| 0| } 2352| 0| } 2353| 0|#endif 2354| 0| } /* Stereo */ 2355| 0| } /* !bStdFormat */ 2356| | 2357| 12.5k| if ( !bStdFormat ) ------------------ | Branch (2357:10): [True: 0, False: 12.5k] ------------------ 2358| 0| { 2359| 0| if ( TG_FLAG_KETO_ENOL_TAUT & ip->bTautFlags ) ------------------ | | 946| 0|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (2359:14): [True: 0, False: 0] ------------------ 2360| 0| { 2361| 0| inchi_ios_eprint(log_file, " Account for keto-enol tautomerism\n"); 2362| 0| } 2363| 0| else 2364| 0| { 2365| 0| inchi_ios_eprint(log_file, " Do not account for keto-enol tautomerism\n"); 2366| 0| } 2367| 0| if ( TG_FLAG_1_5_TAUT & ip->bTautFlags ) ------------------ | | 947| 0|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (2367:14): [True: 0, False: 0] ------------------ 2368| 0| { 2369| 0| inchi_ios_eprint(log_file, " Account for 1,5-tautomerism\n"); 2370| 0| } 2371| 0| else 2372| 0| { 2373| 0| inchi_ios_eprint(log_file, " Do not account for 1,5-tautomerism\n"); 2374| 0| } 2375| | 2376| 0| if ( TG_FLAG_PT_22_00 & ip->bTautFlags ) ------------------ | | 953| 0|#define TG_FLAG_PT_22_00 0x00800000 ------------------ | Branch (2376:14): [True: 0, False: 0] ------------------ 2377| 0| inchi_ios_eprint(log_file, " Account for PT_22_00 tautomerism\n"); 2378| 0| else 2379| 0| inchi_ios_eprint(log_file, " Do not account for PT_22_00 tautomerism\n"); 2380| 0| if ( TG_FLAG_PT_16_00 & ip->bTautFlags ) ------------------ | | 954| 0|#define TG_FLAG_PT_16_00 0x01000000 ------------------ | Branch (2380:14): [True: 0, False: 0] ------------------ 2381| 0| inchi_ios_eprint(log_file, " Account for PT_16_00 tautomerism\n"); 2382| 0| else 2383| 0| inchi_ios_eprint(log_file, " Do not account for PT_16_00 tautomerism\n"); 2384| 0| if ( TG_FLAG_PT_06_00 & ip->bTautFlags ) ------------------ | | 955| 0|#define TG_FLAG_PT_06_00 0x02000000 ------------------ | Branch (2384:14): [True: 0, False: 0] ------------------ 2385| 0| inchi_ios_eprint(log_file, " Account for PT_06_00 tautomerism\n"); 2386| 0| else 2387| 0| inchi_ios_eprint(log_file, " Do not account for PT_06_00 tautomerism\n"); 2388| 0| if ( TG_FLAG_PT_39_00 & ip->bTautFlags ) ------------------ | | 956| 0|#define TG_FLAG_PT_39_00 0x04000000 ------------------ | Branch (2388:14): [True: 0, False: 0] ------------------ 2389| 0| inchi_ios_eprint(log_file, " Account for PT_39_00 tautomerism\n"); 2390| 0| else 2391| 0| inchi_ios_eprint(log_file, " Do not account for PT_39_00 tautomerism\n"); 2392| 0| if ( TG_FLAG_PT_13_00 & ip->bTautFlags ) ------------------ | | 957| 0|#define TG_FLAG_PT_13_00 0x08000000 ------------------ | Branch (2392:14): [True: 0, False: 0] ------------------ 2393| 0| inchi_ios_eprint(log_file, " Account for PT_13_00 tautomerism\n"); 2394| 0| else 2395| 0| inchi_ios_eprint(log_file, " Do not account for PT_13_00 tautomerism\n"); 2396| 0| if ( TG_FLAG_PT_18_00 & ip->bTautFlags ) ------------------ | | 958| 0|#define TG_FLAG_PT_18_00 0x10000000 ------------------ | Branch (2396:14): [True: 0, False: 0] ------------------ 2397| 0| inchi_ios_eprint(log_file, " Account for PT_18_00 tautomerism\n"); 2398| 0| else 2399| 0| inchi_ios_eprint(log_file, " Do not account for PT_18_00 tautomerism\n"); 2400| | 2401| 0| if ( developer_options ) ------------------ | Branch (2401:14): [Folded, False: 0] ------------------ 2402| 0| { 2403| 0| if ( TG_FLAG_PHOSPHINE_STEREO & ip->bTautFlags ) ------------------ | | 941| 0|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ | Branch (2403:18): [True: 0, False: 0] ------------------ 2404| 0| { 2405| 0| inchi_ios_eprint(log_file, " Include phosphine stereochemistry\n"); 2406| 0| } 2407| 0| else 2408| 0| { 2409| 0| inchi_ios_eprint(log_file, " Do not include phosphine stereochemistry\n"); 2410| 0| } 2411| 0| if ( TG_FLAG_ARSINE_STEREO & ip->bTautFlags ) ------------------ | | 942| 0|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ | Branch (2411:18): [True: 0, False: 0] ------------------ 2412| 0| { 2413| 0| inchi_ios_eprint(log_file, " Include arsine stereochemistry\n"); 2414| 0| } 2415| 0| else 2416| 0| { 2417| 0| inchi_ios_eprint(log_file, " Do not include arsine stereochemistry\n"); 2418| 0| } 2419| 0| if ( !(TG_FLAG_FIX_SP3_BUG & ip->bTautFlags) ) ------------------ | | 944| 0|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ | Branch (2419:18): [True: 0, False: 0] ------------------ 2420| 0| { 2421| 0| inchi_ios_eprint(log_file, " Turned OFF fix of bug leading to missing or undefined sp3 parity\n"); 2422| 0| } 2423| 0| if ( !(TG_FLAG_FIX_ISO_FIXEDH_BUG & ip->bTautFlags) ) ------------------ | | 950| 0|#define TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */ ------------------ | Branch (2423:18): [True: 0, False: 0] ------------------ 2424| 0| { 2425| 0| inchi_ios_eprint(log_file, " Turned OFF bug-fixes found after v.1.02b release\n"); 2426| 0| } 2427| 0| if ( !(ip->bFixNonUniformDraw) ) ------------------ | Branch (2427:18): [True: 0, False: 0] ------------------ 2428| 0| { 2429| 0| inchi_ios_eprint(log_file, " Turned OFF fixes of non-uniform drawing issues\n"); 2430| 0| } 2431| 0| if ( !(TG_FLAG_MOVE_POS_CHARGES & ip->bTautFlags) ) ------------------ | | 921| 0|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (2431:18): [True: 0, False: 0] ------------------ 2432| 0| { 2433| 0| inchi_ios_eprint(log_file, " MovePos turned OFF\n"); 2434| 0| } 2435| 0| } 2436| | 2437| 0| } /* !bStdFormat */ 2438| | 2439| 12.5k| if ( ip->bCalcInChIHash != INCHIHASH_NONE ) ------------------ | Branch (2439:10): [True: 0, False: 12.5k] ------------------ 2440| 0| { 2441| 0| if ( bStdFormat ) ------------------ | Branch (2441:14): [True: 0, False: 0] ------------------ 2442| 0| { 2443| 0| inchi_ios_eprint(log_file, "Generating standard InChIKey\n"); 2444| 0| } 2445| 0| else 2446| 0| { 2447| 0| inchi_ios_eprint(log_file, "Generating InChIKey\n"); 2448| 0| } 2449| 0| if ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1 ) ------------------ | Branch (2449:14): [True: 0, False: 0] ------------------ 2450| 0| { 2451| 0| inchi_ios_eprint(log_file, "Generating hash extension (1st block)\n"); 2452| 0| } 2453| 0| else if ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA2 ) ------------------ | Branch (2453:19): [True: 0, False: 0] ------------------ 2454| 0| { 2455| 0| inchi_ios_eprint(log_file, "Generating hash extension (2nd block)\n"); 2456| 0| } 2457| 0| else if ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2 ) ------------------ | Branch (2457:19): [True: 0, False: 0] ------------------ 2458| 0| { 2459| 0| inchi_ios_eprint(log_file, "Generating hash extension (two blocks)\n"); 2460| 0| } 2461| 0| } 2462| | 2463| 12.5k| if ( ip->bINChIOutputOptions & INCHI_OUT_SAVEOPT ) ------------------ | | 146| 12.5k|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (2463:10): [True: 0, False: 12.5k] ------------------ 2464| 0| { 2465| 0| inchi_ios_eprint(log_file, "Saving InChI creation options"); 2466| 0| if ( bStdFormat ) ------------------ | Branch (2466:14): [True: 0, False: 0] ------------------ 2467| 0| { 2468| 0| inchi_ios_eprint(log_file, " suppressed for standard InChI"); 2469| | /* NB: actual suppression takes place on InChI serialization */ 2470| | /* (as on e.g. Inchi2Inchi conversion it may appear that we create non-std */ 2471| | /* InChI instead of standard one) */ 2472| 0| } 2473| 0| inchi_ios_eprint(log_file, "\n"); 2474| 0| } 2475| | 2476| 12.5k| if ( ip->bAllowEmptyStructure ) ------------------ | Branch (2476:10): [True: 0, False: 12.5k] ------------------ 2477| 0| { 2478| 0| inchi_ios_eprint(log_file, "Issue warning on empty structure\n"); 2479| 0| } 2480| | 2481| | /* Input */ 2482| 12.5k| if ( ip->nInputType ) ------------------ | Branch (2482:10): [True: 12.5k, False: 0] ------------------ 2483| 12.5k| { 2484| 12.5k| inchi_ios_eprint(log_file, "Input format: %s", 2485| 12.5k| ip->nInputType == INPUT_MOLFILE ? "MOLfile" : ------------------ | Branch (2485:13): [True: 0, False: 12.5k] ------------------ 2486| 12.5k| ip->nInputType == INPUT_SDFILE ? "SDfile" : ------------------ | Branch (2486:13): [True: 0, False: 12.5k] ------------------ 2487| 12.5k|#if ( READ_INCHI_STRING == 1 ) 2488| 12.5k| ip->nInputType == INPUT_INCHI ? "InChI (plain identifier)" : ------------------ | Branch (2488:13): [True: 12.5k, False: 0] ------------------ 2489| 12.5k|#endif 2490| 12.5k| ip->nInputType == INPUT_INCHI_PLAIN ? "InChI AuxInfo (plain)" : "Unknown"); ------------------ | Branch (2490:13): [True: 0, False: 0] ------------------ 2491| 12.5k| if ( (ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE) && ------------------ | Branch (2491:15): [True: 0, False: 12.5k] | Branch (2491:50): [True: 0, False: 12.5k] ------------------ 2492| 0| ip->bGetMolfileNumber ) ------------------ | Branch (2492:13): [True: 0, False: 0] ------------------ 2493| 0| { 2494| 0| inchi_ios_eprint(log_file, " (attempting to read Molfile number)"); 2495| 0| } 2496| 12.5k| inchi_ios_eprint(log_file, "\n"); 2497| 12.5k| } 2498| | 2499| 12.5k| if ( ip->szSdfDataHeader[0] && ip->nInputType != INPUT_SDFILE ) ------------------ | Branch (2499:10): [True: 0, False: 12.5k] | Branch (2499:36): [True: 0, False: 0] ------------------ 2500| 0| { 2501| 0| inchi_ios_eprint(log_file, " SDfile data header: \"%s\"\n", ip->szSdfDataHeader); 2502| 0| } 2503| | 2504| | /* Output */ 2505| 12.5k| inchi_ios_eprint(log_file, "Output format: %s%s\n", 2506| 12.5k| (ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT) ? "Plain text" : ------------------ | | 135| 12.5k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ | Branch (2506:9): [True: 12.5k, False: 0] ------------------ 2507| | 2508| 12.5k| ((ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) && bInChI2Struct) ? "SDfile only (without stereochemical info and atom coordinates)" : ------------------ | | 133| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2508:10): [True: 0, False: 0] | Branch (2508:63): [True: 0, False: 0] ------------------ 2509| 0| ((ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) && !bInChI2Struct) ? "SDfile only" : "Unknown", ------------------ | | 133| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2509:10): [True: 0, False: 0] | Branch (2509:63): [True: 0, False: 0] ------------------ 2510| | 2511| 12.5k| ((ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT) && ------------------ | | 135| 12.5k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ | Branch (2511:10): [True: 12.5k, False: 0] ------------------ 2512| 12.5k| (ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT)) ? ", tabbed" : ""); ------------------ | | 139| 12.5k|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ | Branch (2512:13): [True: 0, False: 12.5k] ------------------ 2513| | 2514| 12.5k|#if ( bRELEASE_VERSION == 1 ) 2515| 12.5k| if ( ip->bCtPredecessors || ip->bAbcNumbers ) ------------------ | Branch (2515:10): [True: 0, False: 12.5k] | Branch (2515:33): [True: 0, False: 12.5k] ------------------ 2516| 0| { 2517| 0| if ( ip->bCtPredecessors && ip->bAbcNumbers ) ------------------ | Branch (2517:14): [True: 0, False: 0] | Branch (2517:37): [True: 0, False: 0] ------------------ 2518| 0| { 2519| 0| inchi_ios_eprint(log_file, "Representation: Compressed\n"); 2520| 0| } 2521| 0| else 2522| 0| { 2523| 0| inchi_ios_eprint(log_file, "Connection table: %s, %s\n", 2524| 0| ip->bCtPredecessors ? "Predecessor_numbers(closures)" : "Canon_numbers(branching, ring closures)", ------------------ | Branch (2524:17): [True: 0, False: 0] ------------------ 2525| 0| ip->bAbcNumbers ? "Shorter alternative" : "Numerical"); ------------------ | Branch (2525:17): [True: 0, False: 0] ------------------ 2526| 0| } 2527| 0| } 2528| |#else 2529| | if ( (bRELEASE_VERSION != 1) || ip->bCtPredecessors || ip->bAbcNumbers ) 2530| | { 2531| | inchi_ios_eprint(log_file, "Connection table: %s, %s\n", 2532| | ip->bCtPredecessors ? "Predecessor_numbers(closures)" : "Canon_numbers(branching, ring closures)", 2533| | ip->bAbcNumbers ? "Shorter alternative" : "Numerical"); 2534| | } 2535| | else 2536| | { 2537| | inchi_ios_eprint(log_file, "Representation: Numerical"); 2538| | } 2539| |#endif 2540| | 2541| 12.5k| if ( ip->bNoWarnings ) ------------------ | Branch (2541:10): [True: 0, False: 12.5k] ------------------ 2542| 0| { 2543| 0| inchi_ios_eprint(log_file, "Warnings suppressed\n"); 2544| 0| } 2545| | 2546| 12.5k| if ( ip->bHideInChI ) ------------------ | Branch (2546:10): [True: 0, False: 12.5k] ------------------ 2547| 0| { 2548| 0| inchi_ios_eprint(log_file, "Printing InChI string itself suppressed\n"); 2549| 0| } 2550| 12.5k| if ( ip->bMergeHash ) ------------------ | Branch (2550:10): [True: 0, False: 12.5k] ------------------ 2551| 0| { 2552| 0| inchi_ios_eprint(log_file, "InChIKey combined with extra hash(es)\n"); 2553| 0| } 2554| | 2555| | 2556| | 2557| 12.5k| if ( !(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) ) ------------------ | | 133| 12.5k|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2557:10): [True: 12.5k, False: 0] ------------------ 2558| 12.5k| { 2559| 12.5k| if ( ip->bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO ) ------------------ | | 129| 12.5k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (2559:14): [True: 12.5k, False: 0] ------------------ 2560| 12.5k| { 2561| 12.5k| inchi_ios_eprint(log_file, "Aux. info suppressed\n"); 2562| 12.5k| } 2563| 0| else if ( ip->bINChIOutputOptions & INCHI_OUT_SHORT_AUX_INFO ) ------------------ | | 130| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ | Branch (2563:19): [True: 0, False: 0] ------------------ 2564| 0| { 2565| 0| inchi_ios_eprint(log_file, "Minimal Aux. info\n"); 2566| 0| } 2567| 0| else 2568| 0| { 2569| 0| inchi_ios_eprint(log_file, "Full Aux. info\n"); 2570| 0| } 2571| 12.5k| } 2572| 12.5k| if ( ip->first_struct_number > 1 ) ------------------ | Branch (2572:10): [True: 0, False: 12.5k] ------------------ 2573| 0| { 2574| 0| inchi_ios_eprint(log_file, "Skipping %ld structure%s\n", ip->first_struct_number - 1, ip->first_struct_number == 2 ? "" : "s"); ------------------ | Branch (2574:95): [True: 0, False: 0] ------------------ 2575| 0| } 2576| 12.5k| if ( ip->last_struct_number > 0 ) ------------------ | Branch (2576:10): [True: 0, False: 12.5k] ------------------ 2577| 0| { 2578| 0| inchi_ios_eprint(log_file, "Terminate after structure #%ld\n", ip->last_struct_number); 2579| 0| } 2580| 12.5k| if ( ip->bSaveWarningStructsAsProblem && ip->path[3] && ip->path[3][0] ) ------------------ | Branch (2580:10): [True: 0, False: 12.5k] | Branch (2580:46): [True: 0, False: 0] | Branch (2580:61): [True: 0, False: 0] ------------------ 2581| 0| { 2582| 0| inchi_ios_eprint(log_file, "Saving warning structures into the problem file\n"); 2583| 0| } 2584| 12.5k| if ( ip->bSaveAllGoodStructsAsProblem && ip->path[3] && ip->path[3][0] ) ------------------ | Branch (2584:10): [True: 0, False: 12.5k] | Branch (2584:46): [True: 0, False: 0] | Branch (2584:61): [True: 0, False: 0] ------------------ 2585| 0| { 2586| 0| inchi_ios_eprint(log_file, "Saving only all good structures into the problem file\n"); 2587| 0| } 2588| | 2589| 12.5k| if ( ip->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR ) ------------------ | | 149| 12.5k|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ | Branch (2589:10): [True: 0, False: 12.5k] ------------------ 2590| 0| { 2591| 0| inchi_ios_eprint(log_file, "Print empty InChI if generation fails\n"); 2592| 0| } 2593| 12.5k| if ( ip->bINChIOutputOptions2 & INCHI_OUT_MISMATCH_AS_ERROR ) ------------------ | | 150| 12.5k|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ | Branch (2593:10): [True: 0, False: 12.5k] ------------------ 2594| 0| { 2595| 0| inchi_ios_eprint(log_file, "Consider problem/mismatch on InChI conversion as error\n"); 2596| 0| } 2597| 12.5k| if ( ip->msec_MaxTime ) ------------------ | Branch (2597:10): [True: 0, False: 12.5k] ------------------ 2598| 0| { 2599| 0| inchi_ios_eprint(log_file, "Timeout per structure: %ld msec\n", ip->msec_MaxTime); 2600| | /* 2601| | unsigned long seconds = ip->msec_MaxTime / 1000; 2602| | unsigned long milliseconds = (ip->msec_MaxTime%1000); 2603| | inchi_ios_eprint( log_file, "Timeout per structure: %lu/*.%03lu sec\n", seconds, milliseconds); -- djb-rwth: ignoring LLVM warning 2604| | inchi_ios_eprint( log_file, "Timeout per structure: %lu sec\n", seconds ); 2605| | */ 2606| 0| } 2607| 12.5k| else 2608| 12.5k| { 2609| 12.5k| inchi_ios_eprint(log_file, "No timeout\n"); 2610| 12.5k| } 2611| | 2612| 12.5k| if ( ip->bLooseTSACheck ) ------------------ | Branch (2612:10): [True: 0, False: 12.5k] ------------------ 2613| 0| { 2614| 0| inchi_ios_eprint(log_file, "Relax criteria of ambiguous drawing for in-ring stereo centers\n"); 2615| 0| } 2616| | 2617| 12.5k| { 2618| 12.5k| int maxna = NORMALLY_ALLOWED_INP_MAX_ATOMS; ------------------ | | 16| 12.5k|#define NORMALLY_ALLOWED_INP_MAX_ATOMS 1024 ------------------ 2619| 12.5k| if ( ip->bLargeMolecules ) ------------------ | Branch (2619:14): [True: 0, False: 12.5k] ------------------ 2620| 0| { 2621| 0| inchi_ios_eprint(log_file, "Experimental mode: "); 2622| 0| maxna = MAX_ATOMS; ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ 2623| 0| } 2624| 12.5k| inchi_ios_eprint(log_file, "Up to %d atoms per structure\n", maxna); 2625| 12.5k| } 2626| | 2627| 12.5k| if ( ip->bPolymers != POLYMERS_NO ) ------------------ | | 1215| 12.5k|#define POLYMERS_NO 0 /* ignore polymers */ ------------------ | Branch (2627:10): [True: 0, False: 12.5k] ------------------ 2628| 0| { 2629| 0| inchi_ios_eprint(log_file, "Experimental mode: Treating polymers"); 2630| | 2631| 0| if ( ip->bPolymers == POLYMERS_MODERN ) ------------------ | | 1216| 0|#define POLYMERS_MODERN 1 /* v. 1.06+ way to treat polymers with Zz */ ------------------ | Branch (2631:14): [True: 0, False: 0] ------------------ 2632| 0| { 2633| 0| ; 2634| 0| } 2635| 0| else if ( ip->bPolymers == POLYMERS_LEGACY ) ------------------ | | 1217| 0|#define POLYMERS_LEGACY 2 /* v. 1.05 mode, no explicit Zz (internally they are here) */ ------------------ | Branch (2635:19): [True: 0, False: 0] ------------------ 2636| 0| { 2637| 0| inchi_ios_eprint(log_file, " (v. 1.05 legacy mode)"); 2638| 0| } 2639| 0| else if ( ip->bPolymers == POLYMERS_LEGACY_PLUS ) ------------------ | | 1218| 0|#define POLYMERS_LEGACY_PLUS 3 /* v. 1.05 mode with an addition of that in all ------------------ | Branch (2639:19): [True: 0, False: 0] ------------------ 2640| 0| { 2641| 0| inchi_ios_eprint(log_file, " (v. 1.05 legacy mode with senior link placed at start)"); 2642| 0| } 2643| 0| if ( ip->bFoldPolymerSRU ) ------------------ | Branch (2643:14): [True: 0, False: 0] ------------------ 2644| 0| { 2645| 0| inchi_ios_eprint(log_file, "; CRU folding enabled"); 2646| 0| } 2647| 0| } 2648| 12.5k| inchi_ios_eprint(log_file, "\n"); 2649| | 2650| 12.5k| if ( ip->bNPZz == 1 ) ------------------ | Branch (2650:10): [True: 12.5k, False: 0] ------------------ 2651| 12.5k| { 2652| 12.5k| inchi_ios_eprint(log_file, "Allowing non-polymer Zz pseudo atoms\n"); 2653| 12.5k| } 2654| 12.5k| if ( ip->bStereoAtZz == 1 ) ------------------ | Branch (2654:10): [True: 0, False: 12.5k] ------------------ 2655| 0| { 2656| 0| inchi_ios_eprint(log_file, "Allowing stereo at atoms connected to Zz\n"); 2657| 0| } 2658| | /* @nnuk */ 2659| 12.5k| if (ip->bMolecularInorganics == 1) ------------------ | Branch (2659:9): [True: 12.5k, False: 0] ------------------ 2660| 12.5k| { 2661| 12.5k| inchi_ios_eprint(log_file, "Molecular Inorganics mode enabled\n"); 2662| 12.5k| } 2663| | 2664| | /* Report debug modes */ 2665| |#if ( bRELEASE_VERSION != 1 ) 2666| | inchi_ios_eprint(log_file, "Release version = NO\n"); 2667| |#endif 2668| |#if ( TRACE_MEMORY_LEAKS == 1 && defined(_DEBUG) ) 2669| | inchi_ios_eprint(log_file, "Tracing memory leaks (SLOW)\n"); 2670| |#endif 2671| | 2672| |#if (BUILD_WITH_ENG_OPTIONS==1) 2673| | inchi_ios_eprint(log_file, "! Working in engineering mode\n"); 2674| |#endif 2675| 12.5k| inchi_ios_eprint(log_file, "\n"); 2676| | 2677| |#if ( bRELEASE_VERSION != 1 ) 2678| |#if ( FIND_RING_SYSTEMS == 1 ) 2679| | inchi_ios_eprint(log_file, "Find ring systems=Y\nTautomers:\n"); 2680| | inchi_ios_eprint(log_file, " 4-pyridinol=%s\n", TAUT_4PYRIDINOL_RINGS == 1 ? "Y" : "N"); 2681| | inchi_ios_eprint(log_file, " pyrazole=%s\n", TAUT_PYRAZOLE_RINGS == 1 ? "Y" : "N"); 2682| | inchi_ios_eprint(log_file, " tropolone=%s\n", TAUT_TROPOLONE_7 == 1 ? "Y" : "N"); 2683| | inchi_ios_eprint(log_file, " tropolone-5=%s\n", TAUT_TROPOLONE_5 == 1 ? "Y" : "N"); 2684| | inchi_ios_eprint(log_file, "Only chain attachments to tautomeric rings=%s\n", TAUT_RINGS_ATTACH_CHAIN == 1 ? "Y" : "N"); 2685| |#endif 2686| | 2687| | if ( ip->bGetSdfileId ) 2688| | { 2689| | inchi_ios_eprint(log_file, "Extracting SDfile IDs\n"); 2690| | } 2691| | inchi_ios_eprint(log_file, "\nDbg: MOVE_CHARGES=%d\n", 2692| | 0 != (ip->bTautFlags & TG_FLAG_MOVE_POS_CHARGES)); 2693| | inchi_ios_eprint(log_file, " REPLACE_ALT_WITH_TAUT=%d; NEUTRALIZE_ENDPOINTS=%d; BNS_PROTECT_FROM_TAUT=%d\n", 2694| | REPLACE_ALT_WITH_TAUT, NEUTRALIZE_ENDPOINTS, BNS_PROTECT_FROM_TAUT); 2695| | inchi_ios_eprint(log_file, " DISCONNECT_SALTS=%d; TEST_TAUT_SALTS=%d; TEST_TAUT2_SALTS=%d\n", 2696| | 0 != (ip->bTautFlags & TG_FLAG_DISCONNECT_SALTS), 2697| | 0 != (ip->bTautFlags & TG_FLAG_TEST_TAUT__SALTS), 2698| | 0 != (ip->bTautFlags & TG_FLAG_TEST_TAUT2_SALTS)); 2699| | inchi_ios_eprint(log_file, " CHARGED_ACID_TAUT_ONLY=%d MERGE_TAUT_SALTS=%d\n", 2700| | 0 == (ip->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O), 2701| | 0 != (ip->bTautFlags & TG_FLAG_MERGE_TAUT_SALTS)); 2702| | inchi_ios_eprint(log_file, " DISCONNECT_COORD=%d\n", 2703| | 0 != (ip->bTautFlags & TG_FLAG_DISCONNECT_COORD)); 2704| |#endif /* ( bRELEASE_VERSION != 1 ) */ 2705| | 2706| 12.5k| return 0; 2707| 12.5k|} EquString: 524| 3|{ 525| 3| int bFrom = EquVal & (iiSTEREO | iiSTEREO_INV | iiNUMB | iiEQU); ------------------ | | 55| 3|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ int bFrom = EquVal & (iiSTEREO | iiSTEREO_INV | iiNUMB | iiEQU); ------------------ | | 56| 3|#define iiSTEREO_INV 0x0002 /* inverted stereo (sp3) */ ------------------ int bFrom = EquVal & (iiSTEREO | iiSTEREO_INV | iiNUMB | iiEQU); ------------------ | | 57| 3|#define iiNUMB 0x0004 /* numbering or inverted stereo numbering */ ------------------ int bFrom = EquVal & (iiSTEREO | iiSTEREO_INV | iiNUMB | iiEQU); ------------------ | | 58| 3|#define iiEQU 0x0008 /* equivalence info */ ------------------ 526| 3| int bType = EquVal & (iitISO | iitNONTAUT); ------------------ | | 64| 3|#define iitISO 0x0010 /* Isotopic */ ------------------ int bType = EquVal & (iitISO | iitNONTAUT); ------------------ | | 65| 3|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ 527| 3| int bEq2 = EquVal & (iiEq2NONTAUT | iiEq2ISO | iiEq2INV); ------------------ | | 71| 3|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ int bEq2 = EquVal & (iiEq2NONTAUT | iiEq2ISO | iiEq2INV); ------------------ | | 72| 3|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ int bEq2 = EquVal & (iiEq2NONTAUT | iiEq2ISO | iiEq2INV); ------------------ | | 73| 3|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ 528| 3| const char *r = ""; 529| | 530| |#if (FIX_EMPTY_LAYER_BUG == 1) 531| | int bEmpty = EquVal & iiEmpty; 532| | if (bEmpty) 533| | { 534| | r = "e"; 535| | return r; 536| | } 537| |#endif 538| | 539| 3| switch (bFrom) 540| 3| { 541| | 542| 3| case iiSTEREO: /* ------------ Stereo --------------------*/ ------------------ | | 55| 3|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ | Branch (542:5): [True: 3, False: 0] ------------------ 543| 3| switch (bType) 544| 3| { 545| 3| case iitISO: /* iso main stereo =... */ ------------------ | | 64| 3|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (545:9): [True: 3, False: 0] ------------------ 546| 3| switch (bEq2) 547| 3| { 548| 3| case 0: ------------------ | Branch (548:13): [True: 3, False: 0] ------------------ 549| 3| r = "m"; /* iso main stereo = main stereo */ 550| 3| break; 551| 0| default: ------------------ | Branch (551:13): [True: 0, False: 3] ------------------ 552| 0| r = "??"; /* should not happen */ 553| 0| break; 554| 3| } 555| 3| break; 556| 3| case iitNONTAUT: /* non-taut stereo =... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (556:9): [True: 0, False: 3] ------------------ 557| 0| switch (bEq2) 558| 0| { 559| 0| case 0: ------------------ | Branch (559:13): [True: 0, False: 0] ------------------ 560| 0| r = "m"; /* non-taut stereo = main stereo */ 561| 0| break; 562| 0| default: ------------------ | Branch (562:13): [True: 0, False: 0] ------------------ 563| 0| r = "??"; /* should not happen */ 564| 0| break; 565| 0| } 566| 0| break; 567| 0| case (iitNONTAUT | iitISO): /* iso non-taut stereo = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ case (iitNONTAUT | iitISO): /* iso non-taut stereo = ... */ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (567:9): [True: 0, False: 3] ------------------ 568| 0| switch (bEq2) 569| 0| { 570| 0| case 0: ------------------ | Branch (570:13): [True: 0, False: 0] ------------------ 571| 0| r = "m"; /* iso non-taut stereo = main stereo */ 572| 0| break; 573| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (573:13): [True: 0, False: 0] ------------------ 574| 0| r = "M"; /* iso non-taut stereo = main iso stereo */ 575| 0| break; 576| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (576:13): [True: 0, False: 0] ------------------ 577| 0| r = "n"; /* iso non-taut stereo = non-taut stereo */ 578| 0| break; 579| 0| default: ------------------ | Branch (579:13): [True: 0, False: 0] ------------------ 580| 0| r = "??"; /* should not happen */ 581| 0| break; 582| 0| } 583| 0| break; 584| 0| default: ------------------ | Branch (584:9): [True: 0, False: 3] ------------------ 585| 0| r = "??"; /* should not happen */ 586| 0| break; 587| 3| } 588| 3| break; 589| | 590| 3| case iiSTEREO_INV: /*---------- Inverted Aux Stereo ------*/ ------------------ | | 56| 0|#define iiSTEREO_INV 0x0002 /* inverted stereo (sp3) */ ------------------ | Branch (590:5): [True: 0, False: 3] ------------------ 591| 0| if (bEq2 & iiEq2INV) ------------------ | | 73| 0|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ | Branch (591:13): [True: 0, False: 0] ------------------ 592| 0| { /* stereo = Inverted(another stereo) */ 593| 0| bEq2 &= ~iiEq2INV; ------------------ | | 73| 0|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ 594| 0| switch (bType) 595| 0| { 596| 0| case 0: /* main = ...*/ ------------------ | Branch (596:13): [True: 0, False: 0] ------------------ 597| 0| switch (bEq2) 598| 0| { 599| 0| case 0: ------------------ | Branch (599:17): [True: 0, False: 0] ------------------ 600| 0| r = "im"; /* main = Inv(main) */ 601| 0| break; 602| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (602:17): [True: 0, False: 0] ------------------ 603| 0| r = "iM"; /* main = Inv(main iso) */ 604| 0| break; 605| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (605:17): [True: 0, False: 0] ------------------ 606| 0| r = "in"; /* maim = Inv(non-taut) */ 607| 0| break; 608| 0| case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (608:17): [True: 0, False: 0] ------------------ 609| 0| r = "iN"; /* maim = Inv(non-taut iso ) */ 610| 0| break; 611| 0| default: ------------------ | Branch (611:17): [True: 0, False: 0] ------------------ 612| 0| r = "??"; /* should not happen */ 613| 0| break; 614| 0| } 615| 0| break; 616| 0| case iitISO: /* main iso = ...*/ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (616:13): [True: 0, False: 0] ------------------ 617| 0| switch (bEq2) 618| 0| { 619| 0| case 0: ------------------ | Branch (619:17): [True: 0, False: 0] ------------------ 620| 0| r = "im"; /* main iso = Inv(main) */ 621| 0| break; 622| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (622:17): [True: 0, False: 0] ------------------ 623| 0| r = "iM"; /* main iso = Inv(main iso) */ 624| 0| break; 625| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (625:17): [True: 0, False: 0] ------------------ 626| 0| r = "in"; /* maim iso = Inv(non-taut) */ 627| 0| break; 628| 0| case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (628:17): [True: 0, False: 0] ------------------ 629| 0| r = "iN"; /* maim = Inv(non-taut iso ) */ 630| 0| break; 631| 0| default: ------------------ | Branch (631:17): [True: 0, False: 0] ------------------ 632| 0| r = "??"; /* should not happen */ 633| 0| break; 634| 0| } 635| 0| break; 636| 0| case iitNONTAUT: /* non-taut = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (636:13): [True: 0, False: 0] ------------------ 637| 0| switch (bEq2) 638| 0| { 639| 0| case 0: ------------------ | Branch (639:17): [True: 0, False: 0] ------------------ 640| 0| r = "im"; /* non-taut = Inv(main) */ 641| 0| break; 642| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (642:17): [True: 0, False: 0] ------------------ 643| 0| r = "iM"; /* non-taut = Inv(main iso) */ 644| 0| break; 645| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (645:17): [True: 0, False: 0] ------------------ 646| 0| r = "in"; /* non-taut = Inv(non-taut) */ 647| 0| break; 648| 0| case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (648:17): [True: 0, False: 0] ------------------ 649| 0| r = "iN"; /* non-taut = Inv(non-taut iso ) */ 650| 0| break; 651| 0| default: ------------------ | Branch (651:17): [True: 0, False: 0] ------------------ 652| 0| r = "??"; /* should not happen */ 653| 0| break; 654| 0| } 655| 0| break; 656| 0| case (iitNONTAUT | iitISO): ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ case (iitNONTAUT | iitISO): ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (656:13): [True: 0, False: 0] ------------------ 657| 0| switch (bEq2) 658| 0| { 659| 0| case 0: ------------------ | Branch (659:17): [True: 0, False: 0] ------------------ 660| 0| r = "im"; /* non-taut iso = Inv(main) */ 661| 0| break; 662| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (662:17): [True: 0, False: 0] ------------------ 663| 0| r = "iM"; /* non-taut iso = Inv(main iso) */ 664| 0| break; 665| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (665:17): [True: 0, False: 0] ------------------ 666| 0| r = "in"; /* non-taut iso = Inv(non-taut) */ 667| 0| break; 668| 0| case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (668:17): [True: 0, False: 0] ------------------ 669| 0| r = "iN"; /* non-taut iso = Inv(non-taut iso ) */ 670| 0| break; 671| 0| default: ------------------ | Branch (671:17): [True: 0, False: 0] ------------------ 672| 0| r = "??"; /* should not happen */ 673| 0| } 674| 0| break; 675| 0| default: ------------------ | Branch (675:13): [True: 0, False: 0] ------------------ 676| 0| r = "??"; /* should not happen */ 677| 0| break; 678| 0| } 679| 0| } 680| 0| else 681| 0| { /* Inv stereo = another (non-inverted) stereo */ 682| | 683| 0| switch (bType) 684| 0| { 685| 0| case iitISO: /* main iso = ...*/ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (685:13): [True: 0, False: 0] ------------------ 686| 0| switch (bEq2) 687| 0| { 688| 0| case 0: ------------------ | Branch (688:17): [True: 0, False: 0] ------------------ 689| 0| r = "m"; /* main = (inverted aux) main */ 690| 0| break; 691| 0| default: ------------------ | Branch (691:17): [True: 0, False: 0] ------------------ 692| 0| r = "??"; /* should not happen */ 693| 0| break; 694| 0| } 695| 0| break; 696| 0| case iitNONTAUT: /* non-taut = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (696:13): [True: 0, False: 0] ------------------ 697| 0| switch (bEq2) 698| 0| { 699| 0| case 0: ------------------ | Branch (699:17): [True: 0, False: 0] ------------------ 700| 0| r = "m"; /* non-taut = (inverted aux) main */ 701| 0| break; 702| 0| default: ------------------ | Branch (702:17): [True: 0, False: 0] ------------------ 703| 0| r = "??"; /* should not happen */ 704| 0| break; 705| 0| } 706| 0| break; 707| 0| case (iitNONTAUT | iitISO): /* non-taut iso = ...*/ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ case (iitNONTAUT | iitISO): /* non-taut iso = ...*/ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (707:13): [True: 0, False: 0] ------------------ 708| 0| switch (bEq2) 709| 0| { 710| 0| case 0: ------------------ | Branch (710:17): [True: 0, False: 0] ------------------ 711| 0| r = "m"; /* non-taut iso = (inverted aux) main */ 712| 0| break; 713| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (713:17): [True: 0, False: 0] ------------------ 714| 0| r = "M"; /* non-taut iso = (inverted aux) main iso */ 715| 0| break; 716| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (716:17): [True: 0, False: 0] ------------------ 717| 0| r = "n"; /* non-taut iso = (inverted aux) non-taut */ 718| 0| break; 719| 0| default: ------------------ | Branch (719:17): [True: 0, False: 0] ------------------ 720| 0| r = "??"; /* should not happen */ 721| 0| break; 722| 0| } 723| 0| break; 724| 0| default: ------------------ | Branch (724:13): [True: 0, False: 0] ------------------ 725| 0| r = "??"; /* should not happen */ 726| 0| break; 727| 0| } 728| 0| } 729| 0| break; 730| | 731| 0| case (iiNUMB | iiSTEREO_INV): /*------------- Inv Stereo Numbering ------------*/ ------------------ | | 57| 0|#define iiNUMB 0x0004 /* numbering or inverted stereo numbering */ ------------------ case (iiNUMB | iiSTEREO_INV): /*------------- Inv Stereo Numbering ------------*/ ------------------ | | 56| 0|#define iiSTEREO_INV 0x0002 /* inverted stereo (sp3) */ ------------------ | Branch (731:5): [True: 0, False: 3] ------------------ 732| 0| switch (bType) 733| 0| { 734| 0| case 0: /* inv stereo numb main = ...*/ ------------------ | Branch (734:9): [True: 0, False: 0] ------------------ 735| 0| switch (bEq2) 736| 0| { 737| 0| case 0: ------------------ | Branch (737:13): [True: 0, False: 0] ------------------ 738| 0| r = "m"; /* inv stereo numb main = main numb */ 739| 0| break; 740| 0| default: ------------------ | Branch (740:13): [True: 0, False: 0] ------------------ 741| 0| r = "??"; /* should not happen */ 742| 0| break; 743| 0| } 744| 0| break; 745| 0| case iitISO: /* inv stereo iso numb main = ...*/ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (745:9): [True: 0, False: 0] ------------------ 746| 0| switch (bEq2) 747| 0| { 748| 0| case 0: ------------------ | Branch (748:13): [True: 0, False: 0] ------------------ 749| 0| r = "m"; /* inv stereo iso numb main = main numb */ 750| 0| break; 751| 0| case iiEq2INV: ------------------ | | 73| 0|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ | Branch (751:13): [True: 0, False: 0] ------------------ 752| 0| r = "im"; /* inv stereo iso numb main = InvStereo(main) numb */ 753| 0| break; 754| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (754:13): [True: 0, False: 0] ------------------ 755| 0| r = "M"; /* inv stereo iso numb main = isotopic main numb */ 756| 0| break; 757| 0| default: ------------------ | Branch (757:13): [True: 0, False: 0] ------------------ 758| 0| r = "??"; /* should not happen */ 759| 0| break; 760| 0| } 761| 0| break; 762| 0| case iitNONTAUT: /* inv stereo numb non-taut = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (762:9): [True: 0, False: 0] ------------------ 763| 0| switch (bEq2) 764| 0| { 765| 0| case 0: ------------------ | Branch (765:13): [True: 0, False: 0] ------------------ 766| 0| r = "m"; /* inv stereo numb non-taut = main numb */ 767| 0| break; 768| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (768:13): [True: 0, False: 0] ------------------ 769| 0| r = "n"; /* inv stereo numb non-taut = non-taut numb */ 770| 0| break; 771| 0| case iiEq2INV: ------------------ | | 73| 0|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ | Branch (771:13): [True: 0, False: 0] ------------------ 772| 0| r = "im"; /* inv stereo numb non-taut = InvStereo(main) numb */ 773| 0| break; 774| 0| default: ------------------ | Branch (774:13): [True: 0, False: 0] ------------------ 775| 0| r = "??"; /* should not happen */ 776| 0| break; 777| 0| } 778| 0| break; 779| 0| case (iitNONTAUT | iitISO): /* inv stereo numb non-taut iso = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ case (iitNONTAUT | iitISO): /* inv stereo numb non-taut iso = ... */ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (779:9): [True: 0, False: 0] ------------------ 780| 0| switch (bEq2) 781| 0| { 782| 0| case 0: ------------------ | Branch (782:13): [True: 0, False: 0] ------------------ 783| 0| r = "m"; /* inv stereo numb non-taut iso = main numb */ 784| 0| break; 785| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (785:13): [True: 0, False: 0] ------------------ 786| 0| r = "M"; /* inv stereo numb non-taut iso = main numb iso */ 787| 0| break; 788| 0| case (iiEq2ISO | iiEq2INV): ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ case (iiEq2ISO | iiEq2INV): ------------------ | | 73| 0|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ | Branch (788:13): [True: 0, False: 0] ------------------ 789| 0| r = "iM"; /* inv stereo numb non-taut iso = InvStereo(main iso) numb */ 790| 0| break; 791| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (791:13): [True: 0, False: 0] ------------------ 792| 0| r = "n"; /* inv stereo numb non-taut iso = non-taut numb */ 793| 0| break; 794| 0| case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ case (iiEq2NONTAUT | iiEq2ISO): ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (794:13): [True: 0, False: 0] ------------------ 795| 0| r = "N"; /* inv stereo numb non-taut iso = non-taut iso numb */ 796| 0| break; 797| 0| case iiEq2INV: ------------------ | | 73| 0|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ | Branch (797:13): [True: 0, False: 0] ------------------ 798| 0| r = "im"; /* inv stereo numb non-taut iso = InvStereo(main) numb */ 799| 0| break; 800| 0| case (iiEq2NONTAUT | iiEq2INV): ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ case (iiEq2NONTAUT | iiEq2INV): ------------------ | | 73| 0|#define iiEq2INV 0x0100 /* equal to inverted (stereo sp3) or to numbering of inverted stereo */ ------------------ | Branch (800:13): [True: 0, False: 0] ------------------ 801| 0| r = "in"; /* inv stereo numb non-taut iso = InvStereo(non-taut) numb ) */ 802| 0| break; 803| 0| default: ------------------ | Branch (803:13): [True: 0, False: 0] ------------------ 804| 0| r = "??"; /* should not happen */ 805| 0| break; 806| 0| } 807| 0| break; 808| 0| default: ------------------ | Branch (808:9): [True: 0, False: 0] ------------------ 809| 0| r = "??"; /* should not happen */ 810| 0| break; 811| 0| } 812| 0| break; 813| | 814| 0| case iiNUMB: /*------------- Canonical Numbering ------------*/ ------------------ | | 57| 0|#define iiNUMB 0x0004 /* numbering or inverted stereo numbering */ ------------------ | Branch (814:5): [True: 0, False: 3] ------------------ 815| 0| switch (bType) 816| 0| { 817| 0| case 0: /* numb main = ...*/ ------------------ | Branch (817:9): [True: 0, False: 0] ------------------ 818| 0| r = "??"; /* should not happen */ 819| 0| break; 820| 0| case iitISO: /* iso numb main = ...*/ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (820:9): [True: 0, False: 0] ------------------ 821| 0| switch (bEq2) 822| 0| { 823| 0| case 0: ------------------ | Branch (823:13): [True: 0, False: 0] ------------------ 824| 0| r = "m"; /* iso numb main = main numb */ 825| 0| break; 826| 0| default: ------------------ | Branch (826:13): [True: 0, False: 0] ------------------ 827| 0| r = "??"; /* should not happen */ 828| 0| } 829| 0| break; 830| 0| case iitNONTAUT: /* numb non-taut = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (830:9): [True: 0, False: 0] ------------------ 831| 0| switch (bEq2) 832| 0| { 833| 0| case 0: ------------------ | Branch (833:13): [True: 0, False: 0] ------------------ 834| 0| r = "m"; /* numb non-taut = main numb */ 835| 0| break; 836| 0| default: ------------------ | Branch (836:13): [True: 0, False: 0] ------------------ 837| 0| r = "??"; /* should not happen */ 838| 0| } 839| 0| break; 840| 0| case (iitNONTAUT | iitISO): /* numb non-taut iso = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ case (iitNONTAUT | iitISO): /* numb non-taut iso = ... */ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (840:9): [True: 0, False: 0] ------------------ 841| 0| switch (bEq2) 842| 0| { 843| 0| case 0: ------------------ | Branch (843:13): [True: 0, False: 0] ------------------ 844| 0| r = "m"; /* numb non-taut iso = main numb */ 845| 0| break; 846| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (846:13): [True: 0, False: 0] ------------------ 847| 0| r = "M"; /* numb non-taut iso = main numb iso */ 848| 0| break; 849| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (849:13): [True: 0, False: 0] ------------------ 850| 0| r = "n"; /* numb non-taut iso = non-taut numb */ 851| 0| break; 852| 0| default: ------------------ | Branch (852:13): [True: 0, False: 0] ------------------ 853| 0| r = "??"; /* should not happen */ 854| 0| break; 855| 0| } 856| 0| break; 857| 0| default: ------------------ | Branch (857:9): [True: 0, False: 0] ------------------ 858| 0| r = "??"; /* should not happen */ 859| 0| break; 860| 0| } 861| 0| break; 862| | 863| 0| case iiEQU: /*------------- Atom Equivalence ------------*/ ------------------ | | 58| 0|#define iiEQU 0x0008 /* equivalence info */ ------------------ | Branch (863:5): [True: 0, False: 3] ------------------ 864| 0| switch (bType) 865| 0| { 866| 0| case 0: /* equivalence main = ...*/ ------------------ | Branch (866:9): [True: 0, False: 0] ------------------ 867| 0| r = "??"; /* should not happen */ 868| 0| break; 869| 0| case iitISO: /* equivalence main iso = ...*/ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (869:9): [True: 0, False: 0] ------------------ 870| 0| switch (bEq2) 871| 0| { 872| 0| case 0: ------------------ | Branch (872:13): [True: 0, False: 0] ------------------ 873| 0| r = "m"; /* equivalence main = main equ */ 874| 0| break; 875| 0| default: ------------------ | Branch (875:13): [True: 0, False: 0] ------------------ 876| 0| r = "??"; /* should not happen */ 877| 0| break; 878| 0| } 879| 0| break; 880| 0| case iitNONTAUT: /* equivalence non-taut = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (880:9): [True: 0, False: 0] ------------------ 881| 0| switch (bEq2) 882| 0| { 883| 0| case 0: ------------------ | Branch (883:13): [True: 0, False: 0] ------------------ 884| 0| r = "m"; /* equivalence non-taut = main equ */ 885| 0| break; 886| 0| default: ------------------ | Branch (886:13): [True: 0, False: 0] ------------------ 887| 0| r = "??"; /* should not happen */ 888| 0| break; 889| 0| } 890| 0| break; 891| 0| case (iitNONTAUT | iitISO): /* equivalence non-taut iso = ... */ ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ case (iitNONTAUT | iitISO): /* equivalence non-taut iso = ... */ ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (891:9): [True: 0, False: 0] ------------------ 892| 0| switch (bEq2) 893| 0| { 894| 0| case 0: ------------------ | Branch (894:13): [True: 0, False: 0] ------------------ 895| 0| r = "m"; /* equivalence non-taut iso = main equ */ 896| 0| break; 897| 0| case iiEq2ISO: ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (897:13): [True: 0, False: 0] ------------------ 898| 0| r = "M"; /* equivalence non-taut iso = main iso equ */ 899| 0| break; 900| 0| case iiEq2NONTAUT: ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (900:13): [True: 0, False: 0] ------------------ 901| 0| r = "n"; /* equivalence non-taut iso = non-taut equ */ 902| 0| break; 903| 0| default: ------------------ | Branch (903:13): [True: 0, False: 0] ------------------ 904| 0| r = "??"; /* should not happen */ 905| 0| break; 906| 0| } 907| 0| break; 908| 0| default: ------------------ | Branch (908:9): [True: 0, False: 0] ------------------ 909| 0| r = "??"; /* should not happen */ 910| 0| break; 911| 0| } 912| 0| break; 913| 0| default: ------------------ | Branch (913:5): [True: 0, False: 3] ------------------ 914| 0| r = "??"; /* should not happen */ 915| 0| break; 916| 3| } 917| 3| return r; 918| 3|} OutputINChI2: 943| 5.02k|{ 944| 5.02k| int bINChIOutputOptions0 = bINChIOutputOptions & ~(INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS); ------------------ | | 135| 5.02k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ int bINChIOutputOptions0 = bINChIOutputOptions & ~(INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS); ------------------ | | 136| 5.02k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 945| 5.02k| int bINChIOutputOptionsCur; 946| 5.02k| int bCurOption, ret, i; 947| | 948| 5.02k| ret = 0; 949| | 950| 20.1k| for (i = 0; i < 3; i++) ------------------ | Branch (950:17): [True: 15.0k, False: 5.02k] ------------------ 951| 15.0k| { 952| 15.0k| switch (i) 953| 15.0k| { 954| 5.02k| case 1: ------------------ | Branch (954:9): [True: 5.02k, False: 10.0k] ------------------ 955| 5.02k| bCurOption = INCHI_OUT_PLAIN_TEXT; ------------------ | | 135| 5.02k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 956| 5.02k| break; 957| 5.02k| case 2: ------------------ | Branch (957:9): [True: 5.02k, False: 10.0k] ------------------ 958| 5.02k| bCurOption = INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 136| 5.02k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 959| 5.02k| break; 960| 5.02k| default: ------------------ | Branch (960:9): [True: 5.02k, False: 10.0k] ------------------ 961| 5.02k| continue; 962| 15.0k| } 963| 10.0k| if (bINChIOutputOptions & bCurOption) ------------------ | Branch (963:13): [True: 5.02k, False: 5.02k] ------------------ 964| 5.02k| { 965| 5.02k| bINChIOutputOptionsCur = bINChIOutputOptions0 | bCurOption; 966| 5.02k| if (i != 1) ------------------ | Branch (966:17): [True: 0, False: 5.02k] ------------------ 967| 0| { 968| 0| bINChIOutputOptionsCur &= ~INCHI_OUT_TABBED_OUTPUT; ------------------ | | 139| 0|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 969| 0| } 970| 5.02k| ret |= OutputINChI1(pCG, 971| 5.02k| strbuf, 972| 5.02k| pINChISortTautAndNonTaut2, 973| 5.02k| INCHI_basic_or_INCHI_reconnected, 974| 5.02k| orig_inp_data, 975| 5.02k| pOrigStruct, 976| 5.02k| ip, 977| 5.02k| bDisconnectedCoord, 978| 5.02k| bOutputType, 979| 5.02k| bINChIOutputOptionsCur, 980| 5.02k| num_components2, 981| 5.02k| num_non_taut2, 982| 5.02k| num_taut2, 983| 5.02k| output_file, 984| 5.02k| log_file, 985| 5.02k| num_input_struct, 986| 5.02k| pSortPrintINChIFlags, 987| 5.02k| save_opt_bits); 988| 5.02k| } 989| 10.0k| } 990| | 991| 5.02k| return ret; 992| 5.02k|} OutputINChI1: 1035| 5.02k|{ 1036| 5.02k| INCHI_OUT_CTL io; 1037| | /* 1038| | bINChIOutputOptions bits: 1039| | INCHI_OUT_NO_AUX_INFO 0x0001 do not output Aux Info 1040| | INCHI_OUT_SHORT_AUX_INFO 0x0002 output short version of Aux Info 1041| | INCHI_OUT_ONLY_AUX_INFO 0x0004 output only Aux Info 1042| | INCHI_OUT_EMBED_REC 0x0008 embed reconnected INChI into disconnected INChI 1043| | 1044| | bOutputType = 1045| | TAUT_YES => tautomeric only (if no tautomeric components then no output; 1046| | TAUT_NON => only non-tautomeric output (if no non-taut present then no output; 1047| | TAUT_BOTH => tautomeric and non-tautomeric 1048| | */ 1049| 5.02k| int i, j, ii, jj, /*ii2, jj2,*/ bEmbeddedOutputCalled = 0; 1050| 5.02k| int bTautIsoHNum, bTautIsoAt, bHasIsotopicAtoms[TAUT_NUM]; 1051| 5.02k| int bStereoSp2[TAUT_NUM], bStereoSp3[TAUT_NUM]; 1052| 5.02k| int bIsotopicStereoSp2[TAUT_NUM], bIsotopicStereoSp3[TAUT_NUM]; 1053| 5.02k| int bStereoAbsInverted[TAUT_NUM], bIsotopicStereoAbsInverted[TAUT_NUM]; 1054| 5.02k| int bStereoAbs[TAUT_NUM], bIsotopicStereoAbs[TAUT_NUM]; 1055| 5.02k| int bTautomericAcid, bHardAddRemProton; 1056| 5.02k| int bRequestedRacemicStereo = 0, bRequestedRelativeStereo = 0; 1057| 5.02k| int npass = 0; /* djb-rwth: removing redundant variables */ 1058| 5.02k| int is_molecular_inorganic = 0; 1059| | 1060| 5.02k| INCHI_SORT *is, *is2; 1061| 5.02k| INChI *pINChI /*, *pINChI2*/; 1062| 5.02k| INChI_Aux *pINChI_Aux = NULL; 1063| | 1064| 5.02k| int ret = 0; /* 0 failed, 1 success */ 1065| 5.02k| int intermediate_result = 0; 1066| 5.02k| int then_goto_repeat = 0; 1067| | /* djb-rwth: removing redundant variables */ 1068| 5.02k| int bHasIsoH; 1069| | /* djb-rwth: removing redundant variables */ 1070| 5.02k| int bTautAndNonTaut, bTautIsNonTaut; 1071| 5.02k| int nAtomsAllComp1, nAtomsAllComp2; /* v. 1.05 Total atoms in all components */ 1072| | 1073| 5.02k| int bPlainText = 0 != (bINChIOutputOptions & (INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS)); ------------------ | | 135| 5.02k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ int bPlainText = 0 != (bINChIOutputOptions & (INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS)); ------------------ | | 136| 5.02k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1074| 5.02k| int bPlainTextCommnts = 0 != (bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT_COMMENTS); ------------------ | | 136| 5.02k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1075| | 1076| 5.02k| char *pLF, *pTAB; 1077| |#ifdef TARGET_LIB_FOR_WINCHI 1078| | int silent = 1; 1079| |#endif 1080| | 1081| 5.02k| int bFixTranspChargeBug = 0; 1082| 5.02k|#if (FIX_TRANSPOSITION_CHARGE_BUG == 1) /* 2008-01-02 */ 1083| 5.02k| if (INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG & bINChIOutputOptions) ------------------ | | 143| 5.02k|#define INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG 0x2000 ------------------ | Branch (1083:9): [True: 5.02k, False: 0] ------------------ 1084| 5.02k| bFixTranspChargeBug = 1; 1085| 5.02k|#endif 1086| | 1087| 5.02k| io.bAbcNumbers = ip->bAbcNumbers; 1088| | 1089| 5.02k| io.ATOM_MODE = ((io.bAbcNumbers ? CT_MODE_ABC_NUMBERS : 0) | CT_MODE_ATOM_COUNTS | CT_MODE_NO_ORPHANS ------------------ | | 26| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ io.ATOM_MODE = ((io.bAbcNumbers ? CT_MODE_ABC_NUMBERS : 0) | CT_MODE_ATOM_COUNTS | CT_MODE_NO_ORPHANS ------------------ | | 27| 5.02k|#define CT_MODE_ATOM_COUNTS 4 ------------------ io.ATOM_MODE = ((io.bAbcNumbers ? CT_MODE_ABC_NUMBERS : 0) | CT_MODE_ATOM_COUNTS | CT_MODE_NO_ORPHANS ------------------ | | 25| 5.02k|#define CT_MODE_NO_ORPHANS 1 /* no orphans, that CT should have only atoms with neighbors */ ------------------ | Branch (1089:22): [True: 0, False: 5.02k] ------------------ 1090| 5.02k|#if (EQL_H_NUM_TOGETHER == 1) 1091| 5.02k| | CT_MODE_EQL_H_TOGETHER ------------------ | | 29| 5.02k|#define CT_MODE_EQL_H_TOGETHER 16 ------------------ 1092| 5.02k|#endif 1093| 5.02k|#if (ABC_CT_NUM_CLOSURES == 1) 1094| 5.02k| | (io.bAbcNumbers && ip->bCtPredecessors ? CT_MODE_ABC_NUM_CLOSURES : 0) ------------------ | | 30| 0|#define CT_MODE_ABC_NUM_CLOSURES 32 /* in CT_MODE_ABC_NUMBERS output AB1AC2AB instead of AB-AC-A-B */ ------------------ | Branch (1094:24): [True: 0, False: 5.02k] | Branch (1094:42): [True: 0, False: 0] ------------------ 1095| 5.02k|#endif 1096| 5.02k| | (ip->bCtPredecessors ? CT_MODE_PREDECESSORS : 0)); ------------------ | | 28| 0|#define CT_MODE_PREDECESSORS 8 ------------------ | Branch (1096:24): [True: 0, False: 5.02k] ------------------ 1097| | 1098| 5.02k| io.TAUT_MODE = (io.bAbcNumbers ? CT_MODE_ABC_NUMBERS : 0); ------------------ | | 26| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (1098:21): [True: 0, False: 5.02k] ------------------ 1099| 5.02k| io.pSortPrintINChIFlags = pSortPrintINChIFlags; 1100| 5.02k| io.num_components = num_components2[INCHI_basic_or_INCHI_reconnected]; 1101| 5.02k| io.pINChISortTautAndNonTaut = pINChISortTautAndNonTaut2[INCHI_basic_or_INCHI_reconnected]; 1102| 5.02k| io.pINChISort = io.pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1103| 5.02k| io.pINChISort2 = io.pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1104| 5.02k| io.bAlways = 0; 1105| 5.02k| io.bUseMulipliers = 1; 1106| 5.02k| io.bOmitRepetitions = 1; 1107| 5.02k| io.bPlainTextTags = 2; /* 0 => no plain tags, 1=> plain text tags, 2=>plaintext tags without consecutive // */ 1108| 5.02k| io.bOutputType = bOutputType; /* remains constant */ 1109| 5.02k| io.bOutType = bOutputType; /* will change! */ 1110| 5.02k| io.bOverflow = 0; 1111| 5.02k| io.bSecondNonTautPass = 0; 1112| 5.02k| io.bNonTautIsoIdentifierNotEmpty = 0; 1113| 5.02k| io.bNonTautNonIsoIdentifierNotEmpty = 0; 1114| 5.02k| io.bNonTautIsIdenticalToTaut = 1; 1115| 5.02k| io.bFhTag = 0; 1116| 5.02k| io.nTag = bPlainTextCommnts ? 3 : bPlainText ? 2 ------------------ | Branch (1116:15): [True: 0, False: 5.02k] | Branch (1116:39): [True: 5.02k, False: 0] ------------------ 1117| 5.02k| : 0; /* tag type */ 1118| | 1119| 5.02k| if (NULL == orig_inp_data) ------------------ | Branch (1119:9): [True: 5.02k, False: 0] ------------------ 1120| 5.02k| { 1121| | /*intermediate_result = 1; 1122| | goto exit_function;*/ 1123| 5.02k| io.n_zy = 0; 1124| 5.02k| io.n_pzz = 0; 1125| 5.02k| io.n_pzz = 0; 1126| 5.02k| } 1127| 0| else 1128| 0| { 1129| 0| io.n_zy = orig_inp_data->n_zy; 1130| 0| io.n_pzz = 0; 1131| 0| if (orig_inp_data->polymer) ------------------ | Branch (1131:13): [True: 0, False: 0] ------------------ 1132| 0| { 1133| 0| io.n_pzz = orig_inp_data->polymer->n_pzz; 1134| 0| } 1135| 0| } 1136| | 1137| | /* 1138| | * @nnuk 1139| | * The Molecular Inorganics subversion designator is structure-specific. 1140| | * For structure input it is determined from the Molecular Inorganics 1141| | * element classification when Molecular Inorganics processing is enabled. 1142| | * For InChI-derived input, the subversion designator is preserved from 1143| | * the input version prefix. 1144| | */ 1145| 5.02k| if (ip->bMolecularInorganics) ------------------ | Branch (1145:9): [True: 5.02k, False: 0] ------------------ 1146| 5.02k| { 1147| 5.02k|#if ( READ_INCHI_STRING == 1 ) 1148| 5.02k| if (ip->bReadInChIOptions & (READ_INCHI_OUTPUT_INCHI | READ_INCHI_TO_STRUCTURE)) ------------------ | | 988| 5.02k|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ if (ip->bReadInChIOptions & (READ_INCHI_OUTPUT_INCHI | READ_INCHI_TO_STRUCTURE)) ------------------ | | 991| 5.02k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (1148:13): [True: 5.02k, False: 0] ------------------ 1149| 5.02k| { 1150| 5.02k| if (ip->bReadInChIOptions & READ_INCHI_INPUT_MI) ------------------ | | 993| 5.02k|#define READ_INCHI_INPUT_MI 0x00000020 ------------------ | Branch (1150:17): [True: 0, False: 5.02k] ------------------ 1151| 0| { 1152| 0| is_molecular_inorganic = 1; 1153| 0| } 1154| 5.02k| } 1155| 0| else 1156| 0|#endif 1157| 0| if (orig_inp_data && orig_inp_data->at) ------------------ | Branch (1157:13): [True: 0, False: 0] | Branch (1157:30): [True: 0, False: 0] ------------------ 1158| 0| { 1159| 0| for (i = 0; i < orig_inp_data->num_inp_atoms; i++) ------------------ | Branch (1159:25): [True: 0, False: 0] ------------------ 1160| 0| { 1161| 0| if (getElTypeforMolecularInorganics(orig_inp_data->at[i].el_number) != 0) ------------------ | Branch (1161:21): [True: 0, False: 0] ------------------ 1162| 0| { 1163| 0| is_molecular_inorganic = 1; 1164| 0| break; 1165| 0| } 1166| 0| } 1167| 0| } 1168| 5.02k| } 1169| | 1170| 5.02k| io.bPolymers = ip->bPolymers; 1171| | 1172| | /* djb-rwth: removing redundant code */ 1173| | 1174| |#ifdef TARGET_LIB_FOR_WINCHI 1175| | /* @@@ From now on we will go with silent output; it ends on @@@ below */ 1176| | silent = 1; 1177| |#endif 1178| | 1179| | /* Analyze layers, make adjustments and fixes, etc. */ 1180| | 1181| 5.02k| set_line_separators(bINChIOutputOptions, &pLF, &pTAB); 1182| 5.02k| memset(io.sDifSegs, DIFV_BOTH_EMPTY, sizeof(io.sDifSegs)); /* djb-rwth: memset_s C11/Annex K variant? */ 1183| 5.02k| if (!strbuf || !(strbuf->pStr) || strbuf->nAllocatedLength <= 0) ------------------ | Branch (1183:9): [True: 0, False: 5.02k] | Branch (1183:20): [True: 0, False: 5.02k] | Branch (1183:39): [True: 0, False: 5.02k] ------------------ 1184| 0| { 1185| 0| inchi_ios_eprint(log_file, "Cannot allocate output buffer. No output for structure #%d.%s%s%s%s\n", 1186| 0| num_input_struct, SDF_LBL_VAL(ip->pSdfLabel, ip->pSdfValue)); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ 1187| 0| return ret; 1188| 0| } 1189| | 1190| | /* -- commented out to allow empty InChI -- 1191| | if (!io.num_components ) return 0; 1192| | */ 1193| | 1194| 15.0k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 15.0k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1194:17): [True: 10.0k, False: 5.02k] ------------------ 1195| 10.0k| { 1196| 10.0k| bHasIsotopicAtoms[i] = 1197| 10.0k| io.num_comp[i] = 1198| 10.0k| bStereoSp2[i] = 1199| 10.0k| bStereoSp3[i] = 1200| 10.0k| bIsotopicStereoSp2[i] = 1201| 10.0k| bIsotopicStereoSp3[i] = 1202| 10.0k| io.bIsotopicOrigNumb[i] = 1203| 10.0k| bStereoAbs[i] = 1204| 10.0k| bIsotopicStereoAbs[i] = 1205| 10.0k| bStereoAbsInverted[i] = 1206| 10.0k| bIsotopicStereoAbsInverted[i] = 1207| 10.0k| io.bRacemicStereo[i] = 1208| 10.0k| io.bRelativeStereo[i] = 1209| 10.0k| io.bIsotopicRacemicStereo[i] = 1210| 10.0k| io.bIsotopicRelativeStereo[i] = 1211| 10.0k| io.bAtomEqu[i] = 1212| 10.0k| io.bTautEqu[i] = 1213| 10.0k| io.bIsotopicAtomEqu[i] = 1214| 10.0k| io.bIsotopicTautEqu[i] = 1215| 10.0k| io.bInvStereo[i] = 1216| 10.0k| io.bInvIsotopicStereo[i] = 1217| 10.0k| io.bInvStereoOrigNumb[i] = 1218| 10.0k| io.bInvIsotopicStereoOrigNumb[i] = 1219| 10.0k| io.bIgn_UU_Sp3[i] = 1220| 10.0k| io.bIgn_UU_Sp2[i] = 1221| 10.0k| io.bIgn_UU_Sp3_Iso[i] = 1222| 10.0k| io.bIgn_UU_Sp2_Iso[i] = 1223| 10.0k| io.bChargesRadVal[i] = 1224| 10.0k| io.bOrigCoord[i] = 0; 1225| 10.0k| } 1226| | 1227| | /* Find if it is isotopic */ 1228| 5.02k| io.bIsotopic = 1229| 5.02k| io.bTautomeric = 1230| 5.02k| io.bNonTautomeric = 1231| 5.02k| bTautomericAcid = 1232| 5.02k| bHardAddRemProton = 1233| 5.02k| bTautIsoHNum = 1234| 5.02k| bTautIsoAt = 1235| 5.02k| bTautAndNonTaut = 1236| 5.02k| bTautIsNonTaut = 0; 1237| | 1238| | /* 1239| | x = bStereo, bStereoSp2, bStereoSp3, bStereoAbsInverted, 1240| | bIsotopicStereo, bIsotopicStereoSp2, bIsotopicStereoSp3, bIsotopicStereoAbsInverted 1241| | 1242| | OUT_N1: x[TAUT_NON] refers to non-tautomeric only 1243| | OUT_T1: x[TAUT_YES] refers to tautomeric if exists otherwise non-tautomeric 1244| | OUT_NT: x[TAUT_NON] refers to non-taut representations of tautomeric 1245| | OUT_TN: x[TAUT_YES] refers to tautomeric if exists otherwise non-tautomeric 1246| | x[TAUT_NON] refers to non-taut representations of tautomeric 1247| | */ 1248| | 1249| 5.02k| memset(io.num_iso_H, 0, sizeof(io.num_iso_H)); /* djb-rwth: memset_s C11/Annex K variant? */ 1250| 5.02k| io.nNumRemovedProtons = 0; 1251| | /* djb-rwth: removing redundant code */ 1252| 5.02k| bHasIsoH = 0; 1253| 5.02k| io.bTautomericOutputAllowed = (io.bOutType == OUT_T1 || io.bOutType == OUT_TN); ------------------ | | 581| 10.0k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ io.bTautomericOutputAllowed = (io.bOutType == OUT_T1 || io.bOutType == OUT_TN); ------------------ | | 583| 5.02k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1253:36): [True: 0, False: 5.02k] | Branch (1253:61): [True: 5.02k, False: 0] ------------------ 1254| 5.02k| io.pINChISort = io.pINChISortTautAndNonTaut[io.bTautomericOutputAllowed ? TAUT_YES : TAUT_NON]; ------------------ | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ io.pINChISort = io.pINChISortTautAndNonTaut[io.bTautomericOutputAllowed ? TAUT_YES : TAUT_NON]; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1254:49): [True: 5.02k, False: 0] ------------------ 1255| 5.02k| is = io.pINChISort; 1256| | /* djb-rwth: removing redundant variables/code */ 1257| | 1258| 102k| for (i = 0, is2 = io.pINChISortTautAndNonTaut[TAUT_NON]; i < io.num_components; i++, is++, is2 ? is2++ : NULL) ------------------ | | 574| 5.02k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1258:62): [True: 97.5k, False: 5.02k] | Branch (1258:96): [True: 97.5k, False: 0] ------------------ 1259| 97.5k| { 1260| | 1261| 97.5k| CompINChILayers(is, is2, io.sDifSegs, bFixTranspChargeBug); 1262| | 1263| 97.5k| io.bNonTautIsIdenticalToTaut = io.bNonTautIsIdenticalToTaut && !CompINChITautVsNonTaut(is, is2, 1); ------------------ | Branch (1263:40): [True: 97.5k, False: 0] | Branch (1263:72): [True: 97.5k, False: 0] ------------------ 1264| | 1265| 97.5k| if (is && (pINChI_Aux = is->pINChI_Aux[TAUT_YES])) ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1265:13): [True: 97.5k, False: 0] | Branch (1265:19): [True: 97.5k, False: 0] ------------------ 1266| 97.5k| { 1267| 390k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 25| 390k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1267:25): [True: 292k, False: 97.5k] ------------------ 1268| 292k| { 1269| 292k| bHasIsoH += abs(pINChI_Aux->nNumRemovedIsotopicH[j]); 1270| 292k| io.num_iso_H[j] += pINChI_Aux->nNumRemovedIsotopicH[j]; 1271| 292k| } 1272| 97.5k| io.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1273| | /* djb-rwth: removing redundant code */ 1274| 97.5k| } 1275| | 1276| 97.5k| if (io.bTautomericOutputAllowed && is) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (1276:13): [True: 97.5k, False: 0] | Branch (1276:44): [True: 97.5k, False: 0] ------------------ 1277| 97.5k| { 1278| | /* Check for removed isotopic H */ 1279| 195k| for (j = TAUT_YES; j < TAUT_NUM; j++) ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ for (j = TAUT_YES; j < TAUT_NUM; j++) ------------------ | | 573| 195k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1279:32): [True: 97.5k, False: 97.5k] ------------------ 1280| 97.5k| { 1281| 97.5k| switch (io.bOutType) 1282| 97.5k| { 1283| 0| case OUT_N1: /* x[TAUT_NON]: non-tautomeric only -- never happens */ ------------------ | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ ------------------ | Branch (1283:17): [True: 0, False: 97.5k] ------------------ 1284| 0| jj = GET_II(io.bOutType, is); ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 0] | | | Branch (46:36): [True: 0, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ 1285| 0| if (jj != j) ------------------ | Branch (1285:25): [True: 0, False: 0] ------------------ 1286| 0| continue; 1287| | /* djb-rwth: removing redundant code */ 1288| 0| break; 1289| 0| case OUT_T1: /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric */ ------------------ | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ | Branch (1289:17): [True: 0, False: 97.5k] ------------------ 1290| 0| jj = GET_II(io.bOutType, is); ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 0] | | | Branch (46:36): [True: 0, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ 1291| 0| if (jj != j) ------------------ | Branch (1291:25): [True: 0, False: 0] ------------------ 1292| 0| continue; 1293| | /* djb-rwth: removing redundant code */ 1294| 0| break; 1295| 0| case OUT_NT: /* x[TAUT_NON]: only non-taut representations of tautomeric -- never happens */ ------------------ | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ ------------------ | Branch (1295:17): [True: 0, False: 97.5k] ------------------ 1296| 0| jj = GET_II(io.bOutType, is); ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 0] | | | Branch (46:36): [True: 0, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ 1297| 0| if (jj != j) ------------------ | Branch (1297:25): [True: 0, False: 0] ------------------ 1298| 0| continue; 1299| | /* djb-rwth: removing redundant code */ 1300| 0| break; 1301| | /* main path of control flow */ 1302| 97.5k| case OUT_TN: /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric; ------------------ | | 583| 97.5k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1302:17): [True: 97.5k, False: 0] ------------------ 1303| | * x[TAUT_NON]: non-taut only if tautomeric is present */ 1304| 97.5k| jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 45| 97.5k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 97.5k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 97.5k] | | ------------------ | | 46| 97.5k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 195k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 97.5k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 97.5k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 97.5k, False: 0] | | | | | Branch (35:43): [True: 97.5k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 97.5k, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 97.5k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [Folded, False: 0] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, Folded] | | ------------------ ------------------ | Branch (1304:26): [True: 97.5k, False: 0] | Branch (1304:65): [True: 0, False: 0] ------------------ 1305| 0| : -1; 1306| 97.5k| if (jj == TAUT_YES) ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1306:25): [True: 97.5k, False: 0] ------------------ 1307| 97.5k| { 1308| | /* Fix12 */ 1309| 97.5k| if (is->pINChI[jj]->lenTautomer > 0) ------------------ | Branch (1309:29): [True: 1.24k, False: 96.2k] ------------------ 1310| 1.24k| { 1311| 1.24k| bTautAndNonTaut += (!is->pINChI[jj]->bDeleted && HAS_N(is)); ------------------ | | 37| 1.23k|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 574| 1.23k|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (37:20): [True: 0, False: 1.23k] | | | Branch (37:43): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1311:49): [True: 1.23k, False: 6] ------------------ 1312| 1.24k| } 1313| 96.2k| else 1314| 96.2k| { 1315| 96.2k| bTautIsNonTaut++; 1316| 96.2k| } 1317| 97.5k| } 1318| 97.5k| if (jj < 0) ------------------ | Branch (1318:25): [True: 0, False: 97.5k] ------------------ 1319| 0| continue; 1320| | /* djb-rwth: removing redundant code */ 1321| 97.5k| break; 1322| 97.5k| default: ------------------ | Branch (1322:17): [True: 0, False: 97.5k] ------------------ 1323| 0| continue; 1324| 97.5k| } 1325| 97.5k| if (jj != j) ------------------ | Branch (1325:21): [True: 0, False: 97.5k] ------------------ 1326| 0| continue; 1327| 97.5k| if ((pINChI = is->pINChI[jj]) && pINChI->nNumberOfAtoms > 0 && (pINChI_Aux = is->pINChI_Aux[jj])) ------------------ | Branch (1327:21): [True: 97.5k, False: 0] | Branch (1327:50): [True: 97.5k, False: 0] | Branch (1327:80): [True: 97.5k, False: 0] ------------------ 1328| 97.5k| { 1329| 97.5k| bTautIsoHNum += (pINChI_Aux->nNumRemovedIsotopicH[0] + 1330| 97.5k| pINChI_Aux->nNumRemovedIsotopicH[1] + 1331| 97.5k| pINChI_Aux->nNumRemovedIsotopicH[2]); 1332| 97.5k| bTautIsoAt += (pINChI->nNumberOfIsotopicAtoms > 0 || pINChI->nNumberOfIsotopicTGroups > 0); ------------------ | Branch (1332:36): [True: 628, False: 96.8k] | Branch (1332:74): [True: 0, False: 96.8k] ------------------ 1333| 97.5k| } 1334| 97.5k| } 1335| 97.5k| } 1336| 97.5k| } 1337| | 1338| 5.02k| io.sDifSegs[DIFL_M][DIFS_p_PROTONS] = io.nNumRemovedProtons ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1338:43): [True: 147, False: 4.88k] ------------------ 1339| 5.02k| io.sDifSegs[DIFL_MI][DIFS_h_H_ATOMS] = bHasIsoH ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1339:44): [True: 74, False: 4.95k] ------------------ 1340| | 1341| 5.02k| MarkUnusedAndEmptyLayers(io.sDifSegs); 1342| | 1343| 5.02k| io.bNonTautIsIdenticalToTaut = io.bNonTautIsIdenticalToTaut && !bTautIsoHNum; ------------------ | Branch (1343:36): [True: 5.02k, False: 0] | Branch (1343:68): [True: 4.95k, False: 73] ------------------ 1344| 5.02k| nAtomsAllComp1 = nAtomsAllComp2 = 0; 1345| | 1346| 102k| for (i = 0, is = io.pINChISort; i < io.num_components; i++, is++) ------------------ | Branch (1346:37): [True: 97.5k, False: 5.02k] ------------------ 1347| 97.5k| { 1348| 97.5k| int bCurIso, bCurHasIsoStereo /* Fix14 */, bCurTaut /*, bCurTaut2*/; /* djb-rwth: removing redundant variables */ 1349| 97.5k| int bCompExists, bCurIsoHPos, bCurIsoHStereo; 1350| 97.5k| int bCurStereoSp2, bCurIsoStereoSp2, bCurStereoSp3, bCurIsoStereoSp3, bCurIsoStereoSp3Inv; 1351| 97.5k| int bCurRacemic, bCurRelative, bCurIsoRacemic, bCurIsoRelative; 1352| 97.5k| bCompExists = 0; 1353| | 1354| 292k| for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 573| 292k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1354:28): [True: 195k, False: 97.5k] ------------------ 1355| 195k| { 1356| 195k| switch (io.bOutType) 1357| 195k| { 1358| 0| case OUT_N1: ------------------ | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ ------------------ | Branch (1358:13): [True: 0, False: 195k] ------------------ 1359| | /* x[TAUT_NON]: non-tautomeric only */ 1360| 0| jj = GET_II(io.bOutType, is); ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 0] | | | Branch (46:36): [True: 0, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ 1361| 0| if (jj != j) ------------------ | Branch (1361:21): [True: 0, False: 0] ------------------ 1362| 0| continue; 1363| 0| ii = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1364| 0| break; 1365| 0| case OUT_T1: ------------------ | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ | Branch (1365:13): [True: 0, False: 195k] ------------------ 1366| | /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric */ 1367| 0| jj = GET_II(io.bOutType, is); ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 0] | | | Branch (46:36): [True: 0, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ 1368| 0| if (jj != j) ------------------ | Branch (1368:21): [True: 0, False: 0] ------------------ 1369| 0| continue; 1370| 0| ii = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1371| 0| break; 1372| 0| case OUT_NT: ------------------ | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ ------------------ | Branch (1372:13): [True: 0, False: 195k] ------------------ 1373| | /* x[TAUT_NON]: only non-taut representations of tautomeric */ 1374| 0| jj = GET_II(io.bOutType, is); ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 0] | | | Branch (46:36): [True: 0, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ 1375| 0| if (jj != j) ------------------ | Branch (1375:21): [True: 0, False: 0] ------------------ 1376| 0| continue; 1377| 0| ii = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1378| 0| break; 1379| | /* main control flow comes here: requested both mobile and fixed H results */ 1380| 195k| case OUT_TN: ------------------ | | 583| 195k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1380:13): [True: 195k, False: 0] ------------------ 1381| | /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric; */ 1382| | /* x[TAUT_NON]: non-taut only if tautomeric is present */ 1383| 195k| jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 575| 195k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 45| 97.5k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 97.5k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 97.5k] | | ------------------ | | 46| 97.5k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 195k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 97.5k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 97.5k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 97.5k, False: 0] | | | | | Branch (35:43): [True: 97.5k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 97.5k, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 97.5k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ jj = (j == TAUT_YES) ? GET_II(OUT_T1, is) : (j == TAUT_NON) ? GET_II(OUT_NT, is) ------------------ | | 45| 97.5k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 97.5k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 97.5k] | | ------------------ | | 46| 97.5k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 195k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 97.5k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [Folded, False: 0] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 97.5k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 97.5k|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 97.5k] | | ------------------ | | 48| 97.5k| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 97.5k|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 195k|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 97.5k, False: 0] | | | | | Branch (40:43): [True: 97.5k, False: 0] | | | | | Branch (40:82): [True: 1.24k, False: 96.2k] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 1.24k|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 1.24k|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 1.24k] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 97.5k, Folded] | | ------------------ ------------------ | Branch (1383:22): [True: 97.5k, False: 97.5k] | Branch (1383:61): [True: 97.5k, False: 0] ------------------ 1384| 97.5k| : -1; 1385| 195k| if (jj < 0) ------------------ | Branch (1385:21): [True: 97.5k, False: 97.5k] ------------------ 1386| 97.5k| { 1387| | /* Fix12 */ 1388| 97.5k| if (bTautAndNonTaut && bTautIsNonTaut && ------------------ | Branch (1388:25): [True: 0, False: 97.5k] | Branch (1388:44): [True: 0, False: 0] ------------------ 1389| 0| j == TAUT_NON && 0 <= (jj = GET_II(OUT_T1, is)) && ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ j == TAUT_NON && 0 <= (jj = GET_II(OUT_T1, is)) && ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ | Branch (1389:25): [True: 0, False: 0] | Branch (1389:42): [True: 0, False: 0] ------------------ 1390| 0| !is->pINChI[jj]->bDeleted && !is->pINChI[jj]->lenTautomer) ------------------ | Branch (1390:25): [True: 0, False: 0] | Branch (1390:54): [True: 0, False: 0] ------------------ 1391| 0| { 1392| 0| ; /* the requested non-tautomeric component is in tautomeric position */ 1393| | /* (is->pINChI[TAUT_YES]); */ 1394| | /* process it also as non-tautomeric if Fixed-H layer was requested */ 1395| 0| } 1396| 97.5k| else 1397| 97.5k| { 1398| 97.5k| continue; 1399| 97.5k| } 1400| 97.5k| } 1401| | 1402| 97.5k| ii = j; /* ii is what we wanted; jj is what we found (0 = TAUT_NON: fixed_H, 1 = TAUT_YES: mobile_H) */ 1403| | 1404| | /* -- not used 2004-09-16 --- 1405| | if ( is2 ) { 1406| | jj2 = ( j == TAUT_YES )? GET_II(OUT_T1,is2) : ( j == TAUT_NON )? GET_II(OUT_NT,is2) : -1; 1407| | if ( jj2 >= 0 ) { 1408| | ii2 = j; 1409| | } else { 1410| | ii2 = -1; 1411| | } 1412| | } else { 1413| | jj2 = ii2 = -1; 1414| | } 1415| | -----------------------------*/ 1416| 97.5k| break; 1417| | 1418| 0| default: ------------------ | Branch (1418:13): [True: 0, False: 195k] ------------------ 1419| 0| continue; 1420| 195k| } 1421| | 1422| 97.5k| if ((pINChI = is->pINChI[jj]) && pINChI->nNumberOfAtoms > 0) ------------------ | Branch (1422:17): [True: 97.5k, False: 0] | Branch (1422:46): [True: 97.5k, False: 0] ------------------ 1423| 97.5k| { 1424| | /*pINChI_Aux = is->pINChI_Aux[jj];*/ 1425| 97.5k| bCompExists++; 1426| | 1427| 97.5k| if (j == TAUT_NON) ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1427:21): [True: 0, False: 97.5k] ------------------ 1428| 0| nAtomsAllComp1 += pINChI->nNumberOfAtoms; 1429| 97.5k| else if (j == TAUT_YES) ------------------ | | 575| 97.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1429:26): [True: 97.5k, False: 0] ------------------ 1430| 97.5k| nAtomsAllComp2 += pINChI->nNumberOfAtoms; 1431| | 1432| 97.5k| bCurTaut = (pINChI->lenTautomer > 0); 1433| 97.5k| bCurIso = (pINChI->nNumberOfIsotopicAtoms > 0 || pINChI->nNumberOfIsotopicTGroups > 0); ------------------ | Branch (1433:28): [True: 628, False: 96.8k] | Branch (1433:66): [True: 0, False: 96.8k] ------------------ 1434| 97.5k| bCurIsoHPos = ((pINChI->nPossibleLocationsOfIsotopicH && pINChI->nPossibleLocationsOfIsotopicH[0] > 1) || pINChI->lenTautomer > 1); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1434:33): [True: 0, False: 97.5k] | Branch (1434:74): [True: 0, False: 0] | Branch (1434:123): [True: 1.23k, False: 96.2k] ------------------ 1435| | /* present isotopic H + their possible positions AND/OR isotopic atoms */ 1436| 97.5k| bCurIsoHStereo = (bCurIsoHPos && (bTautIsoHNum || bTautIsoAt)) || bCurIso; /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1436:35): [True: 1.23k, False: 96.2k] | Branch (1436:51): [True: 2, False: 1.23k] | Branch (1436:67): [True: 0, False: 1.23k] | Branch (1436:83): [True: 628, False: 96.8k] ------------------ 1437| 97.5k| if (jj == j && pINChI->bDeleted) ------------------ | Branch (1437:21): [True: 97.5k, False: 0] | Branch (1437:32): [True: 6, False: 97.5k] ------------------ 1438| 6| { 1439| 6| io.num_comp[j]--; 1440| 6| if (bCurTaut) ------------------ | Branch (1440:25): [True: 6, False: 0] ------------------ 1441| 6| { 1442| 6| io.bTautomeric |= 1; /* tautomeric representation is present */ 1443| 6| io.bNonTautomeric |= HAS_N(is); ------------------ | | 37| 6|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 574| 6|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (37:20): [True: 0, False: 6] | | | Branch (37:43): [True: 0, False: 0] | | ------------------ ------------------ 1444| 6| } 1445| 6| io.bIsotopic |= bCurIso; 1446| 6| continue; /* deleted H(+) in tautomeric representation */ 1447| 6| } 1448| | 1449| 97.5k| bCurStereoSp2 = pINChI->Stereo && (pINChI->Stereo->nNumberOfStereoBonds > 0); ------------------ | Branch (1449:33): [True: 10.0k, False: 87.4k] | Branch (1449:51): [True: 411, False: 9.59k] ------------------ 1450| | 1451| 97.5k| bCurHasIsoStereo = 1452| 97.5k| bCurStereoSp3 = pINChI->Stereo && (pINChI->Stereo->nNumberOfStereoCenters > 0); ------------------ | Branch (1452:37): [True: 10.0k, False: 87.4k] | Branch (1452:55): [True: 382, False: 9.62k] ------------------ 1453| | 1454| 97.5k| bCurIsoStereoSp2 = bCurIsoHStereo && pINChI->StereoIsotopic && (pINChI->StereoIsotopic->nNumberOfStereoBonds > 0); ------------------ | Branch (1454:36): [True: 630, False: 96.8k] | Branch (1454:54): [True: 146, False: 484] | Branch (1454:80): [True: 55, False: 91] ------------------ 1455| 97.5k| bCurIsoStereoSp3 = bCurIsoHStereo && pINChI->StereoIsotopic && (pINChI->StereoIsotopic->nNumberOfStereoCenters > 0); ------------------ | Branch (1455:36): [True: 630, False: 96.8k] | Branch (1455:54): [True: 146, False: 484] | Branch (1455:80): [True: 74, False: 72] ------------------ 1456| 97.5k| bCurIsoStereoSp3Inv = bCurIsoStereoSp3 && pINChI->StereoIsotopic->nCompInv2Abs; /* inversion changes sp3 stereo */ ------------------ | Branch (1456:39): [True: 74, False: 97.4k] | Branch (1456:59): [True: 6, False: 68] ------------------ 1457| 97.5k| bRequestedRacemicStereo |= (0 != (pINChI->nFlags & INCHI_FLAG_RAC_STEREO)); ------------------ | | 122| 97.5k|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 1458| 97.5k| bRequestedRelativeStereo |= (0 != (pINChI->nFlags & INCHI_FLAG_REL_STEREO)); ------------------ | | 121| 97.5k|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ 1459| | 1460| | /* Check whether isotopic stereo is same as non-isotopic; if same than do not output isotopic stereo */ 1461| 97.5k| if (bCurStereoSp2 && bCurIsoStereoSp2) ------------------ | Branch (1461:21): [True: 411, False: 97.0k] | Branch (1461:38): [True: 37, False: 374] ------------------ 1462| 37| { 1463| 37| bCurIsoStereoSp2 = !Eql_INChI_Stereo(pINChI->Stereo, EQL_SP2, pINChI->StereoIsotopic, EQL_SP2, 0); ------------------ | | 477| 37|#define EQL_SP2 8 ------------------ bCurIsoStereoSp2 = !Eql_INChI_Stereo(pINChI->Stereo, EQL_SP2, pINChI->StereoIsotopic, EQL_SP2, 0); ------------------ | | 477| 37|#define EQL_SP2 8 ------------------ 1464| 37| } 1465| 97.5k| if (bCurStereoSp3 && bCurIsoStereoSp3) ------------------ | Branch (1465:21): [True: 382, False: 97.1k] | Branch (1465:38): [True: 37, False: 345] ------------------ 1466| 37| { 1467| | /* bCurIsoStereoSp3=0 means (iso stereo sp3) = (non-iso stereo sp3) or (iso stereo sp3) = Inv(non-iso stereo sp3) */ 1468| 37| bCurIsoStereoSp3 = !Eql_INChI_Stereo(pINChI->Stereo, EQL_SP3, pINChI->StereoIsotopic, EQL_SP3, ------------------ | | 475| 37|#define EQL_SP3 2 ------------------ bCurIsoStereoSp3 = !Eql_INChI_Stereo(pINChI->Stereo, EQL_SP3, pINChI->StereoIsotopic, EQL_SP3, ------------------ | | 475| 37|#define EQL_SP3 2 ------------------ 1469| 37| (pINChI->nFlags & INCHI_FLAG_RAC_STEREO) || (pINChI->nFlags & INCHI_FLAG_REL_STEREO)); ------------------ | | 122| 37|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ (pINChI->nFlags & INCHI_FLAG_RAC_STEREO) || (pINChI->nFlags & INCHI_FLAG_REL_STEREO)); ------------------ | | 121| 36|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ | Branch (1469:58): [True: 1, False: 36] | Branch (1469:102): [True: 4, False: 32] ------------------ 1470| 37| if (!bCurIsoStereoSp3) ------------------ | Branch (1470:25): [True: 37, False: 0] ------------------ 1471| 37| { 1472| | /* Inversion changes iso sp3 differently from non-iso sp3 Fix11 */ 1473| 37| bCurIsoStereoSp3Inv &= (pINChI->StereoIsotopic->nCompInv2Abs != pINChI->Stereo->nCompInv2Abs); 1474| 37| } 1475| 37| } 1476| | 1477| 97.5k| bCurRelative = bRequestedRelativeStereo && bCurStereoSp3; ------------------ | Branch (1477:32): [True: 69, False: 97.4k] | Branch (1477:60): [True: 22, False: 47] ------------------ 1478| |#if (REL_RAC_STEREO_IGN_1_SC == 1) 1479| | bCurRelative = bCurRelative && 1480| | (pINChI->Stereo->nNumberOfStereoCenters > 1) && 1481| | (pINChI->Stereo->nCompInv2Abs != 0) && 1482| |#endif 1483| | 1484| 97.5k| bCurIsoRelative = bRequestedRelativeStereo && (bCurIsoStereoSp3 || bCurIsoStereoSp3Inv); ------------------ | Branch (1484:50): [True: 69, False: 97.4k] | Branch (1484:79): [True: 0, False: 69] | Branch (1484:99): [True: 3, False: 66] ------------------ 1485| |#if (REL_RAC_STEREO_IGN_1_SC == 1) 1486| | bCurIsoRelative = bCurIsoRelative && 1487| | (pINChI->StereoIsotopic->nNumberOfStereoCenters > 1) && 1488| | (pINChI->StereoIsotopic->nCompInv2Abs != 0) && 1489| |#endif 1490| | 1491| 97.5k| bCurRacemic = bRequestedRacemicStereo && bCurStereoSp3; ------------------ | Branch (1491:49): [True: 61, False: 97.4k] | Branch (1491:76): [True: 16, False: 45] ------------------ 1492| |#if (REL_RAC_STEREO_IGN_1_SC == 1) 1493| | bCurRacemic = bCurRacemic && 1494| | (pINChI->Stereo->nCompInv2Abs != 0) && 1495| | (pINChI->Stereo->nNumberOfStereoCenters > 0) 1496| | ? pINChI->Stereo->nNumberOfStereoCenters 1497| | : 0; 1498| |#endif 1499| | 1500| 97.5k| bCurIsoRacemic = bRequestedRacemicStereo && (bCurIsoStereoSp3 || bCurIsoStereoSp3Inv); ------------------ | Branch (1500:34): [True: 61, False: 97.4k] | Branch (1500:62): [True: 0, False: 61] | Branch (1500:82): [True: 1, False: 60] ------------------ 1501| |#if (REL_RAC_STEREO_IGN_1_SC == 1) 1502| | bCurIsoRacemic = bCurIsoRacemic & 1503| | (pINChI->StereoIsotopic->nCompInv2Abs != 0) && 1504| | (pINChI->StereoIsotopic->nNumberOfStereoCenters > 0) 1505| | ? pINChI->StereoIsotopic->nNumberOfStereoCenters 1506| | : 0; 1507| |#endif 1508| 97.5k| if (bRequestedRelativeStereo) ------------------ | Branch (1508:21): [True: 69, False: 97.4k] ------------------ 1509| 69| { 1510| 69| bCurStereoSp3 = bCurRelative || (bCurStereoSp3 && (pINChI->Stereo->nNumberOfStereoCenters > 1)); /* Fix11 */ /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1510:37): [True: 22, False: 47] | Branch (1510:54): [True: 0, False: 47] | Branch (1510:71): [True: 0, False: 0] ------------------ 1511| 69| bCurIsoStereoSp3 = bCurIsoRelative ? bCurIsoStereoSp3 : 0; ------------------ | Branch (1511:40): [True: 3, False: 66] ------------------ 1512| 69| } 1513| 97.4k| else 1514| 97.4k| { 1515| 97.4k| if (bRequestedRacemicStereo) ------------------ | Branch (1515:25): [True: 61, False: 97.3k] ------------------ 1516| 61| { 1517| 61| bCurStereoSp3 = bCurRacemic > 1 || (bCurStereoSp3 && (pINChI->Stereo->nNumberOfStereoCenters > 1)); /* Fix11 */ /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1517:41): [True: 0, False: 61] | Branch (1517:61): [True: 16, False: 45] | Branch (1517:78): [True: 0, False: 16] ------------------ 1518| 61| bCurIsoStereoSp3 = bCurIsoRacemic > 1 ? bCurIsoStereoSp3 : 0; ------------------ | Branch (1518:44): [True: 0, False: 61] ------------------ 1519| 61| } 1520| 97.4k| } 1521| | /* djb-rwth: removing redundant code */ 1522| | 1523| 97.5k| io.bIsotopic |= bCurIso; 1524| 97.5k| bHasIsotopicAtoms[ii] |= bCurIso; 1525| 97.5k| bStereoSp2[ii] |= bCurStereoSp2; 1526| 97.5k| bStereoSp3[ii] |= bCurStereoSp3; 1527| 97.5k| io.bIgn_UU_Sp3[ii] |= !bCurStereoSp3 && (pINChI->nFlags & INCHI_FLAG_SC_IGN_ALL_UU); ------------------ | | 123| 97.1k|#define INCHI_FLAG_SC_IGN_ALL_UU 0x0008 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1527:39): [True: 97.1k, False: 366] | Branch (1527:57): [True: 0, False: 97.1k] ------------------ 1528| 97.5k| io.bIgn_UU_Sp2[ii] |= !bCurStereoSp2 && (pINChI->nFlags & INCHI_FLAG_SB_IGN_ALL_UU); ------------------ | | 124| 97.0k|#define INCHI_FLAG_SB_IGN_ALL_UU 0x0010 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1528:39): [True: 97.0k, False: 411] | Branch (1528:57): [True: 0, False: 97.0k] ------------------ 1529| 97.5k| bIsotopicStereoSp2[ii] |= bCurIsoStereoSp2; 1530| 97.5k| bIsotopicStereoSp3[ii] |= bCurIsoStereoSp3; 1531| 97.5k| io.bIgn_UU_Sp3_Iso[ii] |= !bCurIsoStereoSp3 && (pINChI->nFlags & INCHI_FLAG_SC_IGN_ALL_ISO_UU); ------------------ | | 125| 97.4k|#define INCHI_FLAG_SC_IGN_ALL_ISO_UU 0x0020 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1531:43): [True: 97.4k, False: 37] | Branch (1531:64): [True: 0, False: 97.4k] ------------------ 1532| 97.5k| io.bIgn_UU_Sp2_Iso[ii] |= !bCurIsoStereoSp2 && (pINChI->nFlags & INCHI_FLAG_SB_IGN_ALL_ISO_UU); ------------------ | | 126| 97.4k|#define INCHI_FLAG_SB_IGN_ALL_ISO_UU 0x0040 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1532:43): [True: 97.4k, False: 19] | Branch (1532:64): [True: 0, False: 97.4k] ------------------ 1533| 97.5k| bStereoAbs[ii] |= bCurStereoSp3 && (pINChI->Stereo->nCompInv2Abs != 0); ------------------ | Branch (1533:35): [True: 366, False: 97.1k] | Branch (1533:52): [True: 12, False: 354] ------------------ 1534| | 1535| 97.5k| bStereoAbsInverted[ii] |= bCurStereoSp3 && (pINChI->Stereo->nCompInv2Abs < 0); ------------------ | Branch (1535:43): [True: 366, False: 97.1k] | Branch (1535:60): [True: 0, False: 366] ------------------ 1536| | 1537| | /* Fix08: missing isotopic inverted flag if isotopic = inverted non-isotopic */ 1538| 97.5k| bIsotopicStereoAbsInverted[ii] |= (bCurIsoStereoSp3 && (pINChI->StereoIsotopic->nCompInv2Abs < 0)) || ------------------ | Branch (1538:52): [True: 37, False: 97.4k] | Branch (1538:72): [True: 0, False: 37] ------------------ 1539| 97.5k| (!bCurIsoStereoSp3 && pINChI->StereoIsotopic && pINChI->Stereo && ------------------ | Branch (1539:52): [True: 97.4k, False: 37] | Branch (1539:73): [True: 283, False: 97.1k] | Branch (1539:99): [True: 133, False: 150] ------------------ 1540| 133| pINChI->StereoIsotopic->nCompInv2Abs && ------------------ | Branch (1540:52): [True: 19, False: 114] ------------------ 1541| 19| pINChI->StereoIsotopic->nCompInv2Abs != pINChI->Stereo->nCompInv2Abs); /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1541:52): [True: 19, False: 0] ------------------ 1542| | 1543| | /* Fix 11: missing /s1 if only isotopic stereo is inverted */ 1544| 97.5k| bIsotopicStereoAbs[ii] |= (bCurIsoStereoSp3 && (pINChI->StereoIsotopic->nCompInv2Abs != 0)) || ------------------ | Branch (1544:44): [True: 37, False: 97.4k] | Branch (1544:64): [True: 0, False: 37] ------------------ 1545| 97.5k| (!bCurIsoStereoSp3 && pINChI->StereoIsotopic && pINChI->Stereo && ------------------ | Branch (1545:44): [True: 97.4k, False: 37] | Branch (1545:65): [True: 283, False: 97.1k] | Branch (1545:91): [True: 133, False: 150] ------------------ 1546| 133| pINChI->StereoIsotopic->nCompInv2Abs && ------------------ | Branch (1546:44): [True: 19, False: 114] ------------------ 1547| 19| pINChI->StereoIsotopic->nCompInv2Abs != pINChI->Stereo->nCompInv2Abs); /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1547:44): [True: 19, False: 0] ------------------ 1548| | 1549| 97.5k| io.bRelativeStereo[ii] |= bCurRelative; 1550| 97.5k| io.bIsotopicRelativeStereo[ii] |= bCurIsoRelative; 1551| 97.5k| io.bRacemicStereo[ii] |= bCurRacemic; 1552| 97.5k| io.bIsotopicRacemicStereo[ii] |= bCurIsoRacemic; 1553| | 1554| 97.5k| bTautomericAcid |= (0 != (pINChI->nFlags & INCHI_FLAG_ACID_TAUT)); ------------------ | | 120| 97.5k|#define INCHI_FLAG_ACID_TAUT 0x0001 /* tautomerism of dissociated acid invoked */ ------------------ 1555| 97.5k| bHardAddRemProton |= (0 != (pINChI->nFlags & INCHI_FLAG_HARD_ADD_REM_PROTON)); ------------------ | | 127| 97.5k|#define INCHI_FLAG_HARD_ADD_REM_PROTON 0x0080 /* in normalization a proton has been added or removed along alt path */ ------------------ 1556| 97.5k| if (bCurTaut) ------------------ | Branch (1556:21): [True: 1.23k, False: 96.2k] ------------------ 1557| 1.23k| { 1558| 1.23k| io.bTautomeric |= 1; /* tautomeric representation is present */ 1559| | /* does tautomeric structure have also a non-tautomeric repesentation? */ 1560| 1.23k| io.bNonTautomeric |= HAS_N(is); ------------------ | | 37| 1.23k|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 574| 1.23k|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (37:20): [True: 0, False: 1.23k] | | | Branch (37:43): [True: 0, False: 0] | | ------------------ ------------------ 1561| 1.23k| } 1562| | 1563| | /* Auxiliary info */ 1564| 97.5k| if (!(bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO) && (pINChI_Aux = is->pINChI_Aux[jj])) ------------------ | | 129| 97.5k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1564:21): [True: 0, False: 97.5k] | Branch (1564:71): [True: 0, False: 0] ------------------ 1565| 0| { 1566| | /* detect presence of constitutional equivalence onfo */ 1567| 0| int bCurEqu, bCurTautEqu = 0, bCurIsoEqu = 0, bCurIsoTautEqu = 0; /* Fix15-disabled */ 1568| 0| io.bAtomEqu[ii] |= (bCurEqu = bHasEquString(pINChI_Aux->nConstitEquNumbers, 1569| 0| pINChI_Aux->nNumberOfAtoms)); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1570| 0| if (bCurTaut) ------------------ | Branch (1570:25): [True: 0, False: 0] ------------------ 1571| 0| { 1572| 0| io.bTautEqu[ii] |= (bCurTautEqu = bHasEquString(pINChI_Aux->nConstitEquTGroupNumbers, 1573| 0| pINChI_Aux->nNumberOfTGroups)); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1574| 0| } 1575| 0| if (bCurIso) ------------------ | Branch (1575:25): [True: 0, False: 0] ------------------ 1576| 0| { 1577| 0| io.bIsotopicAtomEqu[ii] |= (bCurIsoEqu = bHasEquString(pINChI_Aux->nConstitEquIsotopicNumbers, 1578| 0| pINChI_Aux->nNumberOfAtoms)) /*|| bCurEqu*/; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1579| 0| if (bCurTaut) ------------------ | Branch (1579:29): [True: 0, False: 0] ------------------ 1580| 0| { 1581| 0| io.bIsotopicTautEqu[ii] |= (bCurIsoTautEqu = bHasEquString(pINChI_Aux->nConstitEquIsotopicTGroupNumbers, 1582| 0| pINChI_Aux->nNumberOfTGroups)) /*|| bCurTautEqu*/; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1583| 0| } 1584| | /* non-zero if isotopic numbering for inverted isotopic stereo is different */ 1585| 0| io.bIsotopicOrigNumb[ii] |= bCurHasIsoStereo && /* Fix14 */ ------------------ | Branch (1585:53): [True: 0, False: 0] ------------------ 1586| 0| pINChI_Aux->nOrigAtNosInCanonOrdInv && ------------------ | Branch (1586:53): [True: 0, False: 0] ------------------ 1587| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrd && ------------------ | Branch (1587:53): [True: 0, False: 0] ------------------ 1588| 0| (0 != memcmp(pINChI_Aux->nOrigAtNosInCanonOrdInv, ------------------ | Branch (1588:53): [True: 0, False: 0] ------------------ 1589| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrd, 1590| 0| sizeof(pINChI_Aux->nOrigAtNosInCanonOrdInv[0]) * pINChI_Aux->nNumberOfAtoms)); 1591| 0| } 1592| | /* Inverted stereo */ 1593| 0| if (bCurStereoSp3 && pINChI->Stereo->nCompInv2Abs) ------------------ | Branch (1593:25): [True: 0, False: 0] | Branch (1593:42): [True: 0, False: 0] ------------------ 1594| 0| { 1595| 0| io.bInvStereo[ii] |= 1; 1596| 0| io.bInvStereoOrigNumb[ii] |= pINChI_Aux->nOrigAtNosInCanonOrd && ------------------ | Branch (1596:54): [True: 0, False: 0] ------------------ 1597| 0| pINChI_Aux->nOrigAtNosInCanonOrdInv && ------------------ | Branch (1597:54): [True: 0, False: 0] ------------------ 1598| 0| (0 != memcmp(pINChI_Aux->nOrigAtNosInCanonOrd, ------------------ | Branch (1598:54): [True: 0, False: 0] ------------------ 1599| 0| pINChI_Aux->nOrigAtNosInCanonOrdInv, 1600| 0| sizeof(pINChI_Aux->nOrigAtNosInCanonOrd[0]) * pINChI_Aux->nNumberOfAtoms)); 1601| 0| } 1602| | 1603| | /* Inverted isotopic stereo */ 1604| 0| if (bCurIsoStereoSp3 && pINChI->StereoIsotopic->nCompInv2Abs) ------------------ | Branch (1604:25): [True: 0, False: 0] | Branch (1604:45): [True: 0, False: 0] ------------------ 1605| 0| { 1606| 0| io.bInvIsotopicStereo[ii] |= 1; 1607| | 1608| 0| io.bInvIsotopicStereoOrigNumb[ii] |= pINChI_Aux->nIsotopicOrigAtNosInCanonOrd && ------------------ | Branch (1608:62): [True: 0, False: 0] ------------------ 1609| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv && ------------------ | Branch (1609:62): [True: 0, False: 0] ------------------ 1610| 0| (0 != memcmp(pINChI_Aux->nIsotopicOrigAtNosInCanonOrd, ------------------ | Branch (1610:62): [True: 0, False: 0] ------------------ 1611| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv, 1612| 0| sizeof(pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0]) * pINChI_Aux->nNumberOfAtoms)); 1613| 0| } 1614| | 1615| 0| if (pINChI_Aux->OrigInfo && bHasOrigInfo(pINChI_Aux->OrigInfo, pINChI_Aux->nNumberOfAtoms)) ------------------ | Branch (1615:25): [True: 0, False: 0] | Branch (1615:49): [True: 0, False: 0] ------------------ 1616| 0| { 1617| 0| io.bChargesRadVal[ii] |= 1; 1618| 0| } 1619| 0| } 1620| | 1621| 97.5k| if (ip->bEnhancedStereo) ------------------ | Branch (1621:21): [True: 0, False: 97.5k] ------------------ 1622| 0| { 1623| 0| set_EnhancedStereo_t_m_layers(orig_inp_data, pINChI, pINChI_Aux); 1624| 0| } 1625| 97.5k| } 1626| 97.5k| } 1627| 97.5k| if (bCompExists) ------------------ | Branch (1627:13): [True: 97.5k, False: 0] ------------------ 1628| 97.5k| { 1629| 292k| for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 573| 292k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1629:32): [True: 195k, False: 97.5k] ------------------ 1630| 195k| { 1631| 195k| io.num_comp[j]++; 1632| 195k| } 1633| 97.5k| } 1634| 97.5k| } 1635| 5.02k| if (io.bTautomeric /*&& bTautomericAcid*/) /* "&& bTautomericAcid" commented out 2004-06-02 */ ------------------ | Branch (1635:9): [True: 1.16k, False: 3.85k] ------------------ 1636| 1.16k| { 1637| 1.16k| io.bTautomeric += bTautomericAcid; /* long-range tautomerism */ 1638| 1.16k| io.bTautomeric += (bHardAddRemProton ? 4 : 0); ------------------ | Branch (1638:28): [True: 0, False: 1.16k] ------------------ 1639| 1.16k| } 1640| 5.02k| if (bRequestedRacemicStereo || bRequestedRelativeStereo) ------------------ | Branch (1640:9): [True: 20, False: 5.00k] | Branch (1640:36): [True: 24, False: 4.98k] ------------------ 1641| 44| { 1642| | /* do not output inverted stereo info */ 1643| 132| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 132|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1643:21): [True: 88, False: 44] ------------------ 1644| 88| { 1645| | /* Fix11 */ 1646| 88| bStereoAbsInverted[i] = 1647| 88| bStereoAbs[i] = 1648| 88| io.bInvStereo[i] = 1649| 88| io.bInvStereoOrigNumb[i] = 0; 1650| | /* io.bIsotopicRelativeStereo[i]=0 may happen because iso stereo is same or inverted non-iso stereo */ 1651| 88| bIsotopicStereoAbsInverted[i] = 1652| 88| bIsotopicStereoAbs[i] = 1653| 88| io.bInvIsotopicStereo[i] = 1654| 88| io.bInvIsotopicStereoOrigNumb[i] = 0; 1655| 88| } 1656| 44| } 1657| | 1658| 5.02k| io.iCurTautMode = io.bOutType == OUT_N1 ? TAUT_NON : /* only non-taut */ ------------------ | | 580| 5.02k|#define OUT_N1 0 /* non-tautomeric only */ ------------------ io.iCurTautMode = io.bOutType == OUT_N1 ? TAUT_NON : /* only non-taut */ ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1658:23): [True: 0, False: 5.02k] ------------------ 1659| | 1660| 5.02k| io.bOutType == OUT_T1 ? TAUT_YES ------------------ | | 581| 5.02k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ io.bOutType == OUT_T1 ? TAUT_YES ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1660:27): [True: 0, False: 5.02k] ------------------ 1661| 5.02k| : /* tautomeric if present, otherwise non-tautomeric */ 1662| 5.02k| io.bOutType == OUT_NT ? TAUT_NON ------------------ | | 582| 5.02k|#define OUT_NT 2 /* only non-taut representations of tautomeric */ ------------------ io.bOutType == OUT_NT ? TAUT_NON ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1662:27): [True: 0, False: 5.02k] ------------------ 1663| 5.02k| : /* only non-taut representations of tautomeric */ 1664| 5.02k| io.bOutType == OUT_TN ? TAUT_YES ------------------ | | 583| 5.02k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ io.bOutType == OUT_TN ? TAUT_YES ------------------ | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1664:27): [True: 5.02k, False: 0] ------------------ 1665| 5.02k| : /* tautomeric if present otherwise non-tautomeric; */ 1666| 5.02k| -1; /* separately output non-taut representations of tautomeric if present */ 1667| | 1668| 5.02k| if (io.iCurTautMode < 0) ------------------ | Branch (1668:9): [True: 0, False: 5.02k] ------------------ 1669| 0| { 1670| 0| return 0; /* error */ 1671| 0| } 1672| | 1673| | /* Now print out */ 1674| | 1675| 5.02k| io.bOverflow = 0; 1676| 5.02k| io.num_components = io.num_comp[io.iCurTautMode]; 1677| | /* djb-rwth: removing redundant code */ 1678| | 1679| 5.02k| if (bINChIOutputOptions & INCHI_OUT_ONLY_AUX_INFO) ------------------ | | 131| 5.02k|#define INCHI_OUT_ONLY_AUX_INFO 0x0004 /* output only Aux Info */ ------------------ | Branch (1679:9): [True: 0, False: 5.02k] ------------------ 1680| 0| { 1681| 0| goto output_aux_info; 1682| 0| } 1683| | 1684| 5.02k| io.nCurINChISegment = DIFL_M; 1685| | 1686| | /* InChI output: version prefix */ 1687| 5.02k| if (INCHI_basic_or_INCHI_reconnected == INCHI_BAS || !(bINChIOutputOptions & INCHI_OUT_EMBED_REC)) ------------------ | | 570| 10.0k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (INCHI_basic_or_INCHI_reconnected == INCHI_BAS || !(bINChIOutputOptions & INCHI_OUT_EMBED_REC)) ------------------ | | 132| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ | Branch (1687:9): [True: 5.02k, False: 0] | Branch (1687:58): [True: 0, False: 0] ------------------ 1688| 5.02k| { 1689| 5.02k| int is_beta = 0; 1690| 5.02k| int nAtomsAllComp = inchi_max(nAtomsAllComp1, nAtomsAllComp2); ------------------ | | 138| 5.02k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 5.02k] | | ------------------ ------------------ 1691| | 1692| 5.02k|#if ( READ_INCHI_STRING == 1 ) 1693| 5.02k| if (ip->bReadInChIOptions & (READ_INCHI_OUTPUT_INCHI | READ_INCHI_TO_STRUCTURE)) ------------------ | | 988| 5.02k|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ if (ip->bReadInChIOptions & (READ_INCHI_OUTPUT_INCHI | READ_INCHI_TO_STRUCTURE)) ------------------ | | 991| 5.02k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (1693:13): [True: 5.02k, False: 0] ------------------ 1694| 5.02k| { 1695| 5.02k| if (ip->bReadInChIOptions & READ_INCHI_INPUT_BETA) ------------------ | | 992| 5.02k|#define READ_INCHI_INPUT_BETA 0x00000010 ------------------ | Branch (1695:17): [True: 3, False: 5.02k] ------------------ 1696| 3| { 1697| 3| is_beta = 1; 1698| 3| } 1699| 5.02k| } 1700| 0| else 1701| 0|#endif 1702| 0| if (is_molecular_inorganic) ------------------ | Branch (1702:13): [True: 0, False: 0] ------------------ 1703| 0| { 1704| | /* 1705| | * Molecular Inorganics is a Beta feature in this release. 1706| | */ 1707| 0| is_beta = 1; 1708| 0| } 1709| | 1710| 5.02k| if (nAtomsAllComp > NORMALLY_ALLOWED_INP_MAX_ATOMS) ------------------ | | 16| 5.02k|#define NORMALLY_ALLOWED_INP_MAX_ATOMS 1024 ------------------ | Branch (1710:13): [True: 123, False: 4.90k] ------------------ 1711| 123| { 1712| | /* v. 1.05 for LargeMolecules */ 1713| 123| is_beta = 1; 1714| 123| } 1715| 5.02k| if (pOrigStruct && pOrigStruct->polymer) ------------------ | Branch (1715:13): [True: 0, False: 5.02k] | Branch (1715:28): [True: 0, False: 0] ------------------ 1716| 0| { 1717| | /* v. 1.05 for Polymers */ 1718| 0| is_beta = 1; 1719| 0| } 1720| | /* specifically put 'B' for empty structure InChI */ 1721| | /* if "Polymers" or "LargeMolecules" requested */ 1722| 5.02k| else if (!pOrigStruct && (ip->bLargeMolecules || ip->bPolymers)) ------------------ | Branch (1722:18): [True: 5.02k, False: 0] | Branch (1722:35): [True: 0, False: 5.02k] | Branch (1722:58): [True: 0, False: 5.02k] ------------------ 1723| 0| { 1724| 0| is_beta = 1; 1725| 0| } 1726| 5.02k| else if (pOrigStruct && pOrigStruct->n_zy) ------------------ | Branch (1726:18): [True: 0, False: 5.02k] | Branch (1726:33): [True: 0, False: 0] ------------------ 1727| 0| { 1728| 0| is_beta = 1; 1729| 0| } 1730| 5.02k| else if (ip->bEnhancedStereo) ------------------ | Branch (1730:18): [True: 0, False: 5.02k] ------------------ 1731| 0| { 1732| 0| is_beta = 1; 1733| 0| } 1734| | 1735| 5.02k| OutputINCHI_VersionAndKind(out_file, strbuf, bINChIOutputOptions, is_beta, is_molecular_inorganic, pLF, pTAB); 1736| 5.02k| } 1737| | 1738| | /* InChI output: atoms */ 1739| 5.02k| intermediate_result = OutputINCHI_MainLayerFormula(pCG, out_file, strbuf, 1740| 5.02k| num_components2, 1741| 5.02k| &INCHI_basic_or_INCHI_reconnected, 1742| 5.02k| &io, pLF, pTAB); 1743| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1743:9): [True: 0, False: 5.02k] ------------------ 1744| 0| goto exit_function; 1745| | 1746| | /* InChI output: connection table */ 1747| 5.02k| intermediate_result = OutputINCHI_MainLayerConnections(pCG, out_file, strbuf, num_components2, 1748| 5.02k| &INCHI_basic_or_INCHI_reconnected, 1749| 5.02k| &io, pLF, pTAB); 1750| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1750:9): [True: 0, False: 5.02k] ------------------ 1751| 0| goto exit_function; 1752| | 1753| | /* InChI output: hydrogens (with tautomeric info) */ 1754| 5.02k| intermediate_result = OutputINCHI_MainLayerHydrogens(pCG, out_file, strbuf, num_components2, 1755| 5.02k| &INCHI_basic_or_INCHI_reconnected, 1756| 5.02k| &io, pLF, pTAB); 1757| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1757:9): [True: 0, False: 5.02k] ------------------ 1758| 0| goto exit_function; 1759| | 1760| 5.02k| io.bFhTag = 0; 1761| 5.02k| npass = 0; 1762| | 1763| 5.02k|repeat_INChI_output: 1764| | 1765| | /* InChI output: charge and removed protons */ 1766| 5.02k| intermediate_result = OutputINCHI_ChargeAndRemovedAddedProtonsLayers(pCG, out_file, strbuf, 1767| 5.02k| &io, pLF, pTAB); 1768| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1768:9): [True: 0, False: 5.02k] ------------------ 1769| 0| goto exit_function; 1770| | 1771| | /* InChI output: polymer layer */ 1772| 5.02k| if (npass == 0) ------------------ | Branch (1772:9): [True: 5.02k, False: 0] ------------------ 1773| 5.02k| { 1774| 5.02k| intermediate_result = OutputINCHI_PolymerLayer(pCG, out_file, strbuf, 1775| 5.02k| &INCHI_basic_or_INCHI_reconnected, 1776| 5.02k| orig_inp_data, pOrigStruct, 1777| 5.02k| &io, pLF, pTAB); 1778| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1778:13): [True: 0, False: 5.02k] ------------------ 1779| 0| goto exit_function; 1780| 5.02k| } 1781| | 1782| | /* InChI output: stereo (non-isotopic) */ 1783| 5.02k| if (ip->bEnhancedStereo) { ------------------ | Branch (1783:9): [True: 0, False: 5.02k] ------------------ 1784| 0| intermediate_result = OutputINCHI_StereoLayer_EnhancedStereo( pCG, out_file, strbuf, &io, orig_inp_data, pLF, pTAB ); 1785| 5.02k| } else { 1786| 5.02k| intermediate_result = OutputINCHI_StereoLayer( pCG, out_file, strbuf, &io, pLF, pTAB ); 1787| 5.02k| } 1788| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1788:9): [True: 0, False: 5.02k] ------------------ 1789| 0| goto exit_function; 1790| | 1791| | /* Switch from M to MI or from F to FI */ 1792| 5.02k| io.nCurINChISegment++; 1793| | 1794| | /* InChI output: isotopic */ 1795| 5.02k| intermediate_result = OutputINCHI_IsotopicLayer(pCG, out_file, strbuf, 1796| 5.02k| &INCHI_basic_or_INCHI_reconnected, 1797| 5.02k| &io, pLF, pTAB); 1798| | 1799| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1799:9): [True: 0, False: 5.02k] ------------------ 1800| 0| { 1801| 0| goto exit_function; 1802| 0| } 1803| | 1804| | /* 1805| | At this point the INChI part of the output has been done. 1806| | If this INChI is tautomeric and non-tautomeric results exist, 1807| | then we need to output non-tautomeric data: 1808| | fixed H 1809| | stereo 1810| | isotopic 1811| | isotopic stereo 1812| | */ 1813| | 1814| | /* InChI output: FixedH and sublayers */ 1815| 5.02k| intermediate_result = OutputINCHI_FixedHLayerWithSublayers(pCG, out_file, strbuf, 1816| 5.02k| &INCHI_basic_or_INCHI_reconnected, 1817| 5.02k| &io, pLF, pTAB, 1818| 5.02k| &then_goto_repeat); 1819| 5.02k| if (intermediate_result != 0) ------------------ | Branch (1819:9): [True: 0, False: 5.02k] ------------------ 1820| 0| { 1821| 0| goto exit_function; 1822| 0| } 1823| 5.02k| if (then_goto_repeat) ------------------ | Branch (1823:9): [True: 0, False: 5.02k] ------------------ 1824| 0| { 1825| 0| npass++; 1826| 0| goto repeat_INChI_output; 1827| 0| } 1828| | 1829| | /* 1830| | InChI output: reconnected structure 1831| | */ 1832| | 1833| 5.02k| bEmbeddedOutputCalled = 0; 1834| 5.02k| if (bDisconnectedCoord && INCHI_basic_or_INCHI_reconnected == INCHI_BAS && ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1834:9): [True: 0, False: 5.02k] | Branch (1834:31): [True: 0, False: 0] ------------------ 1835| 0| (bINChIOutputOptions & INCHI_OUT_EMBED_REC) && num_components2[INCHI_REC]) ------------------ | | 132| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ (bINChIOutputOptions & INCHI_OUT_EMBED_REC) && num_components2[INCHI_REC]) ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1835:9): [True: 0, False: 0] | Branch (1835:56): [True: 0, False: 0] ------------------ 1836| 0| { 1837| 0| int nRet; 1838| 0| bEmbeddedOutputCalled = 1; 1839| | 1840| | /* output blank line before /R: in case of bPlainTextCommnts=1 */ 1841| 0| inchi_ios_print_nodisplay(out_file, "%s", pLF); 1842| | /* end of disconnected INChI output */ 1843| | 1844| 0| nRet = OutputINChI1(pCG, 1845| 0| strbuf, 1846| 0| pINChISortTautAndNonTaut2, 1847| 0| INCHI_REC, ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1848| 0| orig_inp_data, 1849| 0| pOrigStruct, 1850| 0| ip, 1851| 0| 0 /*bDisconnectedCoord*/, 1852| 0| bOutputType, 1853| 0| bINChIOutputOptions | INCHI_OUT_NO_AUX_INFO, ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 1854| 0| num_components2, 1855| 0| num_non_taut2, 1856| 0| num_taut2, 1857| 0| out_file, 1858| 0| log_file, 1859| 0| num_input_struct, 1860| 0| pSortPrintINChIFlags, 1861| 0| save_opt_bits); 1862| | 1863| 0| if (!nRet) ------------------ | Branch (1863:13): [True: 0, False: 0] ------------------ 1864| 0| { 1865| 0| goto exit_function; /* error */ 1866| 0| } 1867| 0| } 1868| | 1869| | /* InChI output: save InChI creation options if requested */ 1870| 5.02k| if (!bEmbeddedOutputCalled && ------------------ | Branch (1870:9): [True: 5.02k, False: 0] ------------------ 1871| 5.02k| (bINChIOutputOptions & INCHI_OUT_SAVEOPT) && ------------------ | | 146| 5.02k|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (1871:9): [True: 0, False: 5.02k] ------------------ 1872| 0| (0 == (bINChIOutputOptions & INCHI_OUT_STDINCHI)) /* not std-InChI output */ ------------------ | | 145| 0|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (1872:9): [True: 0, False: 0] ------------------ 1873| 5.02k| ) 1874| 0| { 1875| 0| char let1, let2; 1876| 0| GetSaveOptLetters(save_opt_bits, &let1, &let2); 1877| 0| inchi_ios_print_nodisplay(out_file, "\\%c%c", let1, let2); 1878| 0| } 1879| 5.02k| if (!bEmbeddedOutputCalled && !bPlainTextCommnts) ------------------ | Branch (1879:9): [True: 5.02k, False: 0] | Branch (1879:35): [True: 5.02k, False: 0] ------------------ 1880| 5.02k| { /* plain text comment earlier ended with LF */ 1881| 5.02k| inchi_ios_print_nodisplay(out_file, "%s%s", 1882| 5.02k| (!num_components2[0] && !num_components2[1]) ? "//" : "", /* empty InChI=// */ ------------------ | Branch (1882:36): [True: 0, False: 5.02k] | Branch (1882:59): [True: 0, False: 0] ------------------ 1883| 5.02k| (bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO) ? "\n" : pTAB); ------------------ | | 129| 5.02k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1883:35): [True: 5.02k, False: 0] ------------------ 1884| | /* end of INChI= output */ 1885| 5.02k| } 1886| | 1887| 5.02k| inchi_strbuf_reset(strbuf); 1888| | 1889| |#ifdef TARGET_LIB_FOR_WINCHI 1890| | /* @@@ Here we end up with silent output: display previously hidden output */ 1891| | if (inchi_ios_flush_not_displayed(out_file) != -1) 1892| | silent = 0; 1893| |#endif 1894| | 1895| 5.02k|output_aux_info: 1896| | 1897| | /* Output Aux Info */ 1898| | 1899| 5.02k| io.bFhTag = 0; 1900| 5.02k| if ((bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO) == 0) ------------------ | | 129| 5.02k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1900:9): [True: 0, False: 5.02k] ------------------ 1901| 0| { 1902| | 1903| 0| io.num_components = io.num_comp[io.iCurTautMode]; 1904| | 1905| | /* AuxInfo: header and normalization type */ 1906| 0| intermediate_result = OutputAUXINFO_HeaderAndNormalization_type(pCG, out_file, strbuf, 1907| 0| bINChIOutputOptions, 1908| 0| &INCHI_basic_or_INCHI_reconnected, 1909| 0| num_components2, 1910| 0| &io, pLF, pTAB); 1911| 0| if (intermediate_result != 0) ------------------ | Branch (1911:13): [True: 0, False: 0] ------------------ 1912| 0| goto exit_function; 1913| | 1914| 0| repeat_INChI_Aux_output: 1915| | 1916| | /* AuxInfo: original atom numbers and symmetry numbers (constit. equivalence /E: ) */ 1917| 0| intermediate_result = OutputAUXINFO_OriginalNumbersAndEquivalenceClasses(pCG, out_file, strbuf, 1918| 0| num_components2, 1919| 0| &io, pLF, pTAB); 1920| 0| if (intermediate_result != 0) ------------------ | Branch (1920:13): [True: 0, False: 0] ------------------ 1921| 0| goto exit_function; 1922| | 1923| | /* AuxInfo: tautomeric groups equivalence */ 1924| 0| intermediate_result = OutputAUXINFO_TautomericGroupsEquivalence(pCG, out_file, strbuf, &io); 1925| 0| if (intermediate_result != 0) ------------------ | Branch (1925:13): [True: 0, False: 0] ------------------ 1926| 0| goto exit_function; 1927| | 1928| | /* AuxInfo: stereo data */ 1929| 0| intermediate_result = OutputAUXINFO_Stereo(pCG, out_file, strbuf, &io, pLF, pTAB); 1930| 0| if (intermediate_result != 0) ------------------ | Branch (1930:13): [True: 0, False: 0] ------------------ 1931| 0| goto exit_function; 1932| | 1933| 0| repeat_INChI_Aux_Iso_output: 1934| | /* AuxInfo: isotopic info */ 1935| 0| intermediate_result = OutputAUXINFO_IsotopicInfo(pCG, out_file, strbuf, 1936| 0| &INCHI_basic_or_INCHI_reconnected, 1937| 0| &io, pLF, pTAB); 1938| 0| if (intermediate_result != 0) ------------------ | Branch (1938:13): [True: 0, False: 0] ------------------ 1939| 0| { 1940| 0| goto exit_function; 1941| 0| } 1942| | 1943| | /* 1944| | At this point the INChI_Aux part of the output has been completed. 1945| | If this INChI is tautomeric and non-tautomeric results exist, 1946| | then we need to output non-tautomeric auxilialy data 1947| | (same as above excluding tautomeric information). 1948| | Currently, this is enabled for xml output only 1949| | */ 1950| | 1951| 0| if (io.bOutType == OUT_TN && io.bTautomeric && io.bNonTautomeric && ------------------ | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1951:13): [True: 0, False: 0] | Branch (1951:38): [True: 0, False: 0] | Branch (1951:56): [True: 0, False: 0] ------------------ 1952| | /* Check whether the Fixed-H layer is empty */ 1953| 0| (*pSortPrintINChIFlags & ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC)) && ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (*pSortPrintINChIFlags & ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC)) && ------------------ | | 662| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ (*pSortPrintINChIFlags & ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC)) && ------------------ | | 663| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ | Branch (1953:13): [True: 0, False: 0] | Branch (1953:39): [True: 0, False: 0] ------------------ 1954| 0| (*pSortPrintINChIFlags & ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC))) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (*pSortPrintINChIFlags & ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC))) ------------------ | | 664| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */ ------------------ (*pSortPrintINChIFlags & ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC))) ------------------ | | 665| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */ ------------------ | Branch (1954:13): [True: 0, False: 0] | Branch (1954:39): [True: 0, False: 0] ------------------ 1955| 0| { 1956| 0| io.bNonTautomeric = 0; /* bNonTautIdentifierNotEmpty == 0 => no fixed H info 02-10-2995 */ 1957| 0| } 1958| | 1959| 0| if (io.bOutType == OUT_TN && io.bTautomeric && io.bNonTautomeric) ------------------ | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1959:13): [True: 0, False: 0] | Branch (1959:38): [True: 0, False: 0] | Branch (1959:56): [True: 0, False: 0] ------------------ 1960| 0| { 1961| | /* add the second (non-tautomeric) output */ 1962| 0| io.bOutType = OUT_NONTAUT; ------------------ | | 920| 0|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ 1963| 0| io.iCurTautMode = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1964| 0| io.pINChISort = io.pINChISortTautAndNonTaut[TAUT_NON]; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1965| 0| io.bSecondNonTautPass = 1; 1966| 0| io.num_components = io.num_comp[io.iCurTautMode]; 1967| 0| io.bFhTag = AL_FIXH; 1968| 0| inchi_strbuf_reset(strbuf); /*pStr[io.tot_len=0] = '\0';*/ 1969| | 1970| | /* if InChI Fixed-H isotopic is empty then do not output corresponding AuxInfo */ 1971| 0| if (!(*pSortPrintINChIFlags & ------------------ | Branch (1971:17): [True: 0, False: 0] ------------------ 1972| 0| ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC))) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC))) ------------------ | | 662| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ ((INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC))) ------------------ | | 663| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ | Branch (1972:20): [True: 0, False: 0] ------------------ 1973| 0| { 1974| 0| npass++; 1975| 0| goto repeat_INChI_Aux_output; 1976| 0| } 1977| 0| else 1978| 0| { 1979| 0| npass++; 1980| 0| goto repeat_INChI_Aux_Iso_output; 1981| 0| } 1982| 0| } 1983| 0| else 1984| 0| { 1985| 0| if (io.bOutType == OUT_NONTAUT && io.bOutputType == OUT_TN && io.bTautomeric && io.bNonTautomeric) ------------------ | | 920| 0|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ if (io.bOutType == OUT_NONTAUT && io.bOutputType == OUT_TN && io.bTautomeric && io.bNonTautomeric) ------------------ | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1985:17): [True: 0, False: 0] | Branch (1985:47): [True: 0, False: 0] | Branch (1985:75): [True: 0, False: 0] | Branch (1985:93): [True: 0, False: 0] ------------------ 1986| 0| { 1987| | /* the second (non-taut) output has been done; restore variables */ 1988| 0| io.bOutType = OUT_TN; ------------------ | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ 1989| 0| io.iCurTautMode = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1990| 0| io.pINChISort = io.pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1991| 0| io.bSecondNonTautPass = 0; 1992| | /* set correct num components for the reversibility info 02-10-2005 */ 1993| 0| io.num_components = io.num_comp[io.iCurTautMode]; 1994| 0| io.bFhTag = 0; 1995| 0| } 1996| 0| } 1997| | 1998| | /* Charges, radicals, unusual valences */ 1999| 0| intermediate_result = OutputAUXINFO_ChargesRadicalsAndUnusualValences(pCG, out_file, strbuf, &io, pLF, pTAB); 2000| 0| if (intermediate_result != 0) ------------------ | Branch (2000:13): [True: 0, False: 0] ------------------ 2001| 0| { 2002| 0| goto exit_function; 2003| 0| } 2004| | 2005| | /* Output the original input structure -- quick fix */ 2006| 0| intermediate_result = OutputAUXINFO_ReversibilityInfo(pCG, out_file, strbuf, pOrigStruct, &io, pLF, pTAB); 2007| 0| if (intermediate_result != 0) ------------------ | Branch (2007:13): [True: 0, False: 0] ------------------ 2008| 0| { 2009| 0| goto exit_function; 2010| 0| } 2011| | 2012| | /* Output polymeric Aux Info */ 2013| 0| intermediate_result = OutputAUXINFO_PolymerInfo(pCG, out_file, strbuf, pOrigStruct, &io, pLF, pTAB); 2014| 0| if (intermediate_result != 0) ------------------ | Branch (2014:13): [True: 0, False: 0] ------------------ 2015| 0| { 2016| 0| goto exit_function; 2017| 0| } 2018| | 2019| | /* 2020| | Output INChI_Aux of the reconnected structure 2021| | */ 2022| | 2023| 0| bEmbeddedOutputCalled = 0; 2024| 0| if (bDisconnectedCoord && INCHI_basic_or_INCHI_reconnected == INCHI_BAS && (bINChIOutputOptions & INCHI_OUT_EMBED_REC) && ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (bDisconnectedCoord && INCHI_basic_or_INCHI_reconnected == INCHI_BAS && (bINChIOutputOptions & INCHI_OUT_EMBED_REC) && ------------------ | | 132| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ | Branch (2024:13): [True: 0, False: 0] | Branch (2024:35): [True: 0, False: 0] | Branch (2024:84): [True: 0, False: 0] ------------------ 2025| 0| num_components2[INCHI_REC] && !(bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO)) ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ num_components2[INCHI_REC] && !(bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO)) ------------------ | | 129| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (2025:13): [True: 0, False: 0] | Branch (2025:43): [True: 0, False: 0] ------------------ 2026| 0| { 2027| 0| int nRet; 2028| 0| bEmbeddedOutputCalled = 1; 2029| 0| inchi_ios_print(out_file, "%s", pLF); 2030| | 2031| 0| nRet = OutputINChI1(pCG, 2032| 0| strbuf, 2033| 0| pINChISortTautAndNonTaut2, 2034| 0| INCHI_REC, ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 2035| 0| NULL, 2036| 0| NULL, 2037| 0| ip, 2038| 0| 0 /*bDisconnectedCoord*/, 2039| 0| bOutputType, 2040| 0| INCHI_OUT_ONLY_AUX_INFO | bINChIOutputOptions, ------------------ | | 131| 0|#define INCHI_OUT_ONLY_AUX_INFO 0x0004 /* output only Aux Info */ ------------------ 2041| 0| num_components2, 2042| 0| num_non_taut2, 2043| 0| num_taut2, 2044| 0| out_file, 2045| 0| log_file, 2046| 0| num_input_struct, 2047| 0| pSortPrintINChIFlags, 2048| 0| save_opt_bits); 2049| | 2050| 0| if (!nRet) ------------------ | Branch (2050:17): [True: 0, False: 0] ------------------ 2051| 0| { 2052| 0| goto exit_function; /* error */ 2053| 0| } 2054| 0| } 2055| | 2056| | /* Close INChI_Aux */ 2057| 0| if (!bEmbeddedOutputCalled && !bPlainTextCommnts) ------------------ | Branch (2057:13): [True: 0, False: 0] | Branch (2057:39): [True: 0, False: 0] ------------------ 2058| 0| { 2059| 0| inchi_ios_print(out_file, "%s\n", (!num_components2[0] && !num_components2[1]) ? "//" : ""); ------------------ | Branch (2059:48): [True: 0, False: 0] | Branch (2059:71): [True: 0, False: 0] ------------------ 2060| | /* plain text comment earlier ended with LF */ 2061| 0| } 2062| | 2063| | /* in wINChI window, separate AuxInfo: from InChIKey: with blank line */ 2064| 0| inchi_ios_print(out_file, "%s", 2065| 0| (bINChIOutputOptions & INCHI_OUT_WINCHI_WINDOW) ? "\n" : ""); ------------------ | | 138| 0|#define INCHI_OUT_WINCHI_WINDOW 0x0200 /* output into wINChI text window */ ------------------ | Branch (2065:25): [True: 0, False: 0] ------------------ 2066| 0| } /* end of output AuxInfo */ 2067| | 2068| 5.02k| ret = 1; 2069| | 2070| 5.02k|exit_function: 2071| | 2072| |#ifdef TARGET_LIB_FOR_WINCHI 2073| | /* @@@ If for any error we get here silent, display previously hidden output */ 2074| | if (silent) 2075| | { 2076| | /* 2077| | if ( !inchi_ios_flush_not_displayed( out_file ) != -1 ) 2078| | silent = 0; 2079| | */ 2080| | silent = 0; 2081| | } 2082| |#endif 2083| | 2084| 5.02k| if (io.bOverflow) ------------------ | Branch (2084:9): [True: 0, False: 5.02k] ------------------ 2085| 0| { 2086| 0| inchi_ios_print(out_file, "\nFATAL ERROR: Output buffer overflow\n"); 2087| 0| } 2088| | 2089| 5.02k| if (intermediate_result) ------------------ | Branch (2089:9): [True: 0, False: 5.02k] ------------------ 2090| 0| { 2091| 0| ret = 0; 2092| 0| inchi_ios_eprint(log_file, "InChI serialization error for structure #%d.%s%s%s%s\n", 2093| 0| num_input_struct, SDF_LBL_VAL(ip->pSdfLabel, ip->pSdfValue)); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ 2094| 0| } 2095| | 2096| 5.02k| return ret; 2097| 5.02k|} /* OutputINChI1 */ szGetTag: 2106| 15.2k|{ 2107| 15.2k| int i, j, bit, num, len; 2108| 15.2k| const int MAX_TAG_NUM = tag_flag ? (int)IL_MAX_ORD : (int)AL_MAX_ORD; /* djb-rwth: fixing GHI #160 */ ------------------ | Branch (2108:29): [True: 15.2k, False: 0] ------------------ 2109| 15.2k| if (0 < nTag && nTag < 3) ------------------ | Branch (2109:9): [True: 15.2k, False: 0] | Branch (2109:21): [True: 15.2k, False: 0] ------------------ 2110| 15.2k| { 2111| | /* no plain text comments: pick up the last tag */ 2112| 305k| for (i = 0, j = -1, bit = 1; i < MAX_TAG_NUM; i++, bit <<= 1) ------------------ | Branch (2112:38): [True: 289k, False: 15.2k] ------------------ 2113| 289k| { 2114| 289k| if (bTag & bit) ------------------ | Branch (2114:17): [True: 17.0k, False: 272k] ------------------ 2115| 17.0k| { 2116| 17.0k| j = i; 2117| 17.0k| } 2118| 289k| } 2119| 15.2k| if (j >= 0) ------------------ | Branch (2119:13): [True: 15.2k, False: 0] ------------------ 2120| 15.2k| { 2121| |#if USE_BCF 2122| | int stl1, stl2, dstsz; 2123| | stl1 = strlen(Tag[j].szXmlLabel) + 1; 2124| | stl2 = strlen(Tag[j].szPlainLabel) + 1; 2125| | dstsz = max_3(stl1, stl2, 5); 2126| | strcpy_s(szTag, dstsz, nTag == 1 ? Tag[j].szXmlLabel : nTag == 2 ? Tag[j].szPlainLabel 2127| | : "???"); /* djb-rwth: function replaced with its safe C11 variant */ 2128| |#else 2129| 15.2k| strcpy(szTag, nTag == 1 ? Tag[j].szXmlLabel : nTag == 2 ? Tag[j].szPlainLabel : "???"); /* djb-rwth: addressing coverity ID #499488 -- when nTag == 2, the "???" is avoided, which is correct */ ------------------ | Branch (2129:27): [True: 0, False: 15.2k] | Branch (2129:59): [True: 15.2k, False: 0] ------------------ 2130| 15.2k|#endif 2131| 15.2k| if (nTag != 2) ------------------ | Branch (2131:17): [True: 0, False: 15.2k] ------------------ 2132| 0| { 2133| 0| *bAlways = Tag[j].bAlwaysOutput; 2134| 0| } 2135| 15.2k| return szTag; 2136| 15.2k| } 2137| 15.2k| } 2138| 0| else if (nTag == 3) ------------------ | Branch (2138:14): [True: 0, False: 0] ------------------ 2139| 0| { 2140| | /* plain text with comments */ 2141| 0| szTag[0] = '{'; 2142| 0| szTag[1] = '\0'; 2143| 0| for (i = 0, j = -1, bit = 1, num = 0; i < MAX_TAG_NUM; i++, bit <<= 1) ------------------ | Branch (2143:47): [True: 0, False: 0] ------------------ 2144| 0| { 2145| 0| if (bTag & bit) ------------------ | Branch (2145:17): [True: 0, False: 0] ------------------ 2146| 0| { 2147| 0| j = i; 2148| 0| if (num++) ------------------ | Branch (2148:21): [True: 0, False: 0] ------------------ 2149| 0| { 2150| 0| strcat(szTag, ":"); 2151| 0| } 2152| 0| strcat(szTag, Tag[i].szPlainComment); 2153| 0| } 2154| 0| } 2155| 0| if (num) ------------------ | Branch (2155:13): [True: 0, False: 0] ------------------ 2156| 0| { 2157| 0| strcat(szTag, "}"); 2158| 0| num = (int)strlen(Tag[j].szPlainLabel); 2159| 0| len = (int)strlen(szTag); 2160| 0| if (len) ------------------ | Branch (2160:17): [True: 0, False: 0] ------------------ 2161| 0| { 2162| 0| memmove(szTag + num, szTag, (long long)len + 1); /* djb-rwth: cast operator added */ 2163| 0| memcpy(szTag, Tag[j].szPlainLabel, num); 2164| 0| } 2165| 0| else 2166| 0| { 2167| 0| strcpy(szTag, Tag[j].szPlainLabel); 2168| 0| } 2169| 0| *bAlways = Tag[j].bAlwaysOutput; 2170| 0| } 2171| 0| else 2172| 0| { 2173| 0| strcpy(szTag, "???"); 2174| 0| } 2175| 0| return szTag; 2176| 0| } 2177| | 2178| 0| strcpy(szTag, "???"); 2179| 0| return szTag; 2180| 15.2k|} OrigStruct_FillOut: 2942| 70.4k|{ 2943| 70.4k| char szBuf[ORIG_STR_BUFLEN]; 2944| 70.4k| int i, len, len_coord, len_atoms, len_bonds; 2945| | 2946| 70.4k| pOrigStruct->polymer = NULL; 2947| 70.4k| pOrigStruct->v3000 = NULL; 2948| | 2949| 70.4k| pOrigStruct->n_zy = orig_inp_data->n_zy; 2950| | /* Coordinates */ 2951| 70.4k| len_coord = i = 0; 2952| | 2953| 70.4k| if (orig_inp_data->szCoord) ------------------ | Branch (2953:9): [True: 0, False: 70.4k] ------------------ 2954| 0| { 2955| | 2956| 0| while ((len = WriteOrigCoord(orig_inp_data->num_inp_atoms, ------------------ | Branch (2956:16): [True: 0, False: 0] ------------------ 2957| 0| orig_inp_data->szCoord, &i, szBuf, sizeof(szBuf)))) /* djb-rwth: addressing LLVM warning */ 2958| 0| { 2959| 0| len_coord += len; 2960| 0| } 2961| 0| pOrigStruct->szCoord = (char *)inchi_malloc(((long long)len_coord + 1) * sizeof(pOrigStruct->szCoord[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 2962| 0| i = 0; 2963| 0| if (pOrigStruct->szCoord && ------------------ | Branch (2963:13): [True: 0, False: 0] ------------------ 2964| 0| len_coord == WriteOrigCoord(orig_inp_data->num_inp_atoms, ------------------ | Branch (2964:13): [True: 0, False: 0] ------------------ 2965| 0| orig_inp_data->szCoord, &i, pOrigStruct->szCoord, len_coord + 1) && 2966| 0| i == orig_inp_data->num_inp_atoms) ------------------ | Branch (2966:13): [True: 0, False: 0] ------------------ 2967| 0| { 2968| | /* success */ 2969| 0| if (orig_inp_data->szCoord) ------------------ | Branch (2969:17): [True: 0, False: 0] ------------------ 2970| 0| { 2971| 0| inchi_free(orig_inp_data->szCoord); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2972| 0| orig_inp_data->szCoord = NULL; 2973| 0| } 2974| 0| } 2975| 0| else 2976| 0| { 2977| 0| return -1; 2978| 0| } 2979| 0| } 2980| | 2981| | /* Atoms */ 2982| 70.4k| len_atoms = i = 0; 2983| 141k| while ((len = WriteOrigAtoms(pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (2983:12): [True: 70.6k, False: 70.4k] ------------------ 2984| 141k| orig_inp_data->at, &i, szBuf, sizeof(szBuf), sd))) /* djb-rwth: addressing LLVM warning */ 2985| 70.6k| { 2986| 70.6k| len_atoms += len; 2987| 70.6k| if (!orig_inp_data->num_inp_atoms) ------------------ | Branch (2987:13): [True: 0, False: 70.6k] ------------------ 2988| 0| break; 2989| 70.6k| } 2990| 70.4k| pOrigStruct->szAtoms = (char *)inchi_malloc(((long long)len_atoms + 1) * sizeof(pOrigStruct->szAtoms[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 70.4k|#define inchi_malloc malloc ------------------ 2991| 70.4k| i = 0; 2992| 70.4k| if (pOrigStruct->szAtoms && ------------------ | Branch (2992:9): [True: 70.4k, False: 0] ------------------ 2993| 70.4k| len_atoms == WriteOrigAtoms(pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (2993:9): [True: 70.4k, False: 0] ------------------ 2994| 70.4k| orig_inp_data->at, &i, pOrigStruct->szAtoms, len_atoms + 1, sd) && 2995| 70.4k| i == orig_inp_data->num_inp_atoms) ------------------ | Branch (2995:9): [True: 70.4k, False: 0] ------------------ 2996| 70.4k| { 2997| 70.4k| ; /* success */ 2998| 70.4k| } 2999| 0| else 3000| 0| { 3001| 0| return -1; 3002| 0| } 3003| | 3004| | /* Bonds */ 3005| 70.4k| len_bonds = 0; 3006| 70.4k| i = 1; 3007| 83.8k| while ((len = WriteOrigBonds(pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (3007:12): [True: 13.3k, False: 70.4k] ------------------ 3008| 83.8k|#if (FIX_CURE53_ISSUE_OOB_ALREADY_HAVE_THIS_MESSAGE == 1) 3009| 83.8k| orig_inp_data->at, &i, szBuf, sizeof(szBuf), sd))) /* djb-rwth: addressing LLVM warning */ 3010| |#else 3011| | orig_inp_data->at, &i, szBuf, sizeof(szBuf), NULL))) 3012| |#endif 3013| 13.3k| { 3014| 13.3k| len_bonds += len; 3015| 13.3k| if (!orig_inp_data->num_inp_atoms) ------------------ | Branch (3015:13): [True: 0, False: 13.3k] ------------------ 3016| 0| { 3017| 0| break; 3018| 0| } 3019| 13.3k| } 3020| | 3021| 70.4k| pOrigStruct->szBonds = (char *)inchi_malloc(((long long)len_bonds + 2) * sizeof(pOrigStruct->szBonds[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 70.4k|#define inchi_malloc malloc ------------------ 3022| 70.4k| i = 1; 3023| | 3024| 70.4k| if (pOrigStruct->szBonds && ------------------ | Branch (3024:9): [True: 70.4k, False: 0] ------------------ 3025| 70.4k| len_bonds == WriteOrigBonds(pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (3025:9): [True: 70.4k, False: 0] ------------------ 3026| 70.4k| orig_inp_data->at, &i, pOrigStruct->szBonds, len_bonds + 2, sd) && 3027| 70.4k| i == orig_inp_data->num_inp_atoms) ------------------ | Branch (3027:9): [True: 70.4k, False: 0] ------------------ 3028| 70.4k| { 3029| 70.4k| ; /* success */ 3030| 70.4k| } 3031| 0| else 3032| 0| { 3033| 0| return -1; 3034| 0| } 3035| 70.4k| pOrigStruct->num_atoms = orig_inp_data->num_inp_atoms; 3036| | 3037| | /* Extensions of v. 1.05 */ 3038| 70.4k| if (orig_inp_data->polymer != NULL && orig_inp_data->polymer->n > 0 && orig_inp_data->valid_polymer) ------------------ | Branch (3038:9): [True: 0, False: 70.4k] | Branch (3038:43): [True: 0, False: 0] | Branch (3038:76): [True: 0, False: 0] ------------------ 3039| 0| { 3040| 0| pOrigStruct->polymer = orig_inp_data->polymer; 3041| | /* pointer copy, do not free after use! */ 3042| 0| } 3043| 70.4k| if (orig_inp_data->v3000 != NULL) ------------------ | Branch (3043:9): [True: 0, False: 70.4k] ------------------ 3044| 0| { 3045| 0| pOrigStruct->v3000 = orig_inp_data->v3000; 3046| | /* pointer copy, do not free after use! */ 3047| 0| } 3048| | 3049| 70.4k| return 0; 3050| 70.4k|} OrigStruct_Free: 3054| 70.4k|{ 3055| 70.4k| if (pOrigStruct) ------------------ | Branch (3055:9): [True: 70.4k, False: 0] ------------------ 3056| 70.4k| { 3057| 70.4k| if (pOrigStruct->szAtoms) ------------------ | Branch (3057:13): [True: 70.4k, False: 0] ------------------ 3058| 70.4k| { 3059| 70.4k| inchi_free(pOrigStruct->szAtoms); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 3060| 70.4k| } 3061| 70.4k| if (pOrigStruct->szBonds) ------------------ | Branch (3061:13): [True: 70.4k, False: 0] ------------------ 3062| 70.4k| { 3063| 70.4k| inchi_free(pOrigStruct->szBonds); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 3064| 70.4k| } 3065| 70.4k| if (pOrigStruct->szCoord) ------------------ | Branch (3065:13): [True: 0, False: 70.4k] ------------------ 3066| 0| { 3067| 0| inchi_free(pOrigStruct->szCoord); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3068| 0| } 3069| | 3070| | /* For 3071| | 3072| | OAD_Polymer *polymer; 3073| | OAD_V3000 *v3000; 3074| | 3075| | we used shallow (pointer) copy of analogs from orig_inp_data, so do not free these here */ 3076| | 3077| | /*memset( pOrigStruct, 0, sizeof(*pOrigStruct) );*/ 3078| 70.4k| pOrigStruct->szAtoms = NULL; 3079| 70.4k| pOrigStruct->szBonds = NULL; 3080| | pOrigStruct->szCoord = NULL; 3081| 70.4k| } 3082| 70.4k|} set_line_separators: 3113| 5.02k|{ 3114| 5.02k| int bPlainTextCommnts = 0 != (bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT_COMMENTS); ------------------ | | 136| 5.02k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 3115| | 3116| 5.02k| *pLF = (char *)(bPlainTextCommnts ? "\n" : "\0"); ------------------ | Branch (3116:21): [True: 0, False: 5.02k] ------------------ 3117| | 3118| |#if (!defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI)) 3119| | { 3120| | int bPlainText = 0 != (bINChIOutputOptions & (INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS)); 3121| | int bPlainTabbedOutput = 0 != (bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT) && 3122| | bPlainText && !bPlainTextCommnts; 3123| | 3124| | *pTAB = bPlainTabbedOutput ? (char*)"\t" : (char*)"\n"; 3125| | } 3126| |#else 3127| 5.02k| *pTAB = "\n"; 3128| 5.02k|#endif 3129| | 3130| 5.02k| return; 3131| 5.02k|} ichiprt1.c:WriteOrigAtoms: 2425| 211k|{ 2426| 211k| int j, k, n, len, len0, cur_len, val, bonds_val, mw, parity, num_trans, is_ok, b_self; 2427| 211k| static const char szIsoH[] = "hdt"; 2428| 211k| char szCurAtom[32]; 2429| 211k| AT_NUMB nNeighOrder[MAXVAL], neigh; 2430| | 2431| 211k| cur_len = 0; 2432| 211k| if (0 == *i) ------------------ | Branch (2432:9): [True: 140k, False: 70.6k] ------------------ 2433| 140k| { 2434| 140k| cur_len = sprintf(szBuf, "%d%s", num_inp_atoms, 2435| 140k| (sd->bChiralFlag & FLAG_INP_AT_CHIRAL) ? "c" : (sd->bChiralFlag & FLAG_INP_AT_NONCHIRAL) ? "n" ------------------ | | 669| 140k|#define FLAG_INP_AT_CHIRAL 1 ------------------ (sd->bChiralFlag & FLAG_INP_AT_CHIRAL) ? "c" : (sd->bChiralFlag & FLAG_INP_AT_NONCHIRAL) ? "n" ------------------ | | 670| 140k|#define FLAG_INP_AT_NONCHIRAL 2 ------------------ | Branch (2435:27): [True: 0, False: 140k] | Branch (2435:74): [True: 0, False: 140k] ------------------ 2436| 140k| : ""); 2437| 140k| } 2438| 529k| for (j = *i; j < num_inp_atoms;) ------------------ | Branch (2438:18): [True: 318k, False: 211k] ------------------ 2439| 318k| { 2440| | /* tetrahedral parity treatment */ 2441| 318k| parity = 0; 2442| 318k| num_trans = 0; 2443| 318k| if (at[j].p_parity) ------------------ | Branch (2443:13): [True: 502, False: 318k] ------------------ 2444| 502| { 2445| | /* verify neighbors */ 2446| 502| is_ok = 1; 2447| 502| b_self = 0; 2448| 2.51k| for (n = 0, k = 0; n < MAX_NUM_STEREO_ATOM_NEIGH; n++) ------------------ | | 877| 2.51k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2448:32): [True: 2.00k, False: 502] ------------------ 2449| 2.00k| { 2450| 2.00k| neigh = at[j].p_orig_at_num[n] - 1; 2451| 2.00k| if (is_in_the_list(at[j].neighbor, neigh, at[j].valence) && ------------------ | Branch (2451:21): [True: 1.83k, False: 176] ------------------ 2452| 1.83k| at[neigh].orig_at_number == at[j].p_orig_at_num[n]) ------------------ | Branch (2452:21): [True: 1.83k, False: 0] ------------------ 2453| 1.83k| { 2454| | /* real neighbor */ 2455| 1.83k| nNeighOrder[k++] = at[j].p_orig_at_num[n]; 2456| 1.83k| } 2457| 176| else 2458| 176| { 2459| 176| if ((int)neigh == j && at[neigh].orig_at_number == at[j].p_orig_at_num[n]) ------------------ | Branch (2459:25): [True: 176, False: 0] | Branch (2459:44): [True: 176, False: 0] ------------------ 2460| 176| { 2461| | /* central atom is a neighbor */ 2462| 176| num_trans = n; /* move this neighbor to 0 position permutation parity */ 2463| 176| b_self++; 2464| 176| } 2465| 0| else 2466| 0| { 2467| 0| is_ok = 0; 2468| 0| break; 2469| 0| } 2470| 176| } 2471| 2.00k| } 2472| 502| if (is_ok && b_self <= 1 && b_self + k == MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 502|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2472:17): [True: 502, False: 0] | Branch (2472:26): [True: 502, False: 0] | Branch (2472:41): [True: 502, False: 0] ------------------ 2473| 502| { 2474| 502| num_trans += insertions_sort(pCG, nNeighOrder, k, sizeof(nNeighOrder[0]), comp_AT_RANK); 2475| 502| if (ATOM_PARITY_WELL_DEF(at[j].p_parity)) ------------------ | | 259| 502|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 502|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 502|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 502, False: 0] | | | Branch (259:75): [True: 426, False: 76] | | ------------------ ------------------ 2476| 426| { 2477| 426| parity = 2 - (num_trans + at[j].p_parity) % 2; 2478| 426| } 2479| 76| else 2480| 76| { 2481| 76| if (ATOM_PARITY_ILL_DEF(at[j].p_parity)) ------------------ | | 257| 76|#define ATOM_PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 239| 76|#define AB_MIN_ILL_DEFINED_PARITY 3 | | ------------------ | | #define ATOM_PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 240| 76|#define AB_MAX_ILL_DEFINED_PARITY 4 | | ------------------ | | | Branch (257:38): [True: 76, False: 0] | | | Branch (257:74): [True: 76, False: 0] | | ------------------ ------------------ 2482| 76| { 2483| 76| parity = at[j].p_parity; 2484| 76| } 2485| 0| else 2486| 0| { 2487| 0| ; /* invalid atom parity */ 2488| 0| } 2489| 76| } 2490| 502| } 2491| 0| else 2492| 0| { 2493| 0| ; /* add error message here */ 2494| 0| } 2495| 502| } 2496| | 2497| 318k| len = len0 = (int)strlen(at[j].elname); 2498| | 2499| 318k| memcpy(szCurAtom, at[j].elname, len); 2500| 318k| bonds_val = nBondsValenceInpAt(at + j, NULL, NULL); 2501| | 2502| 318k| if ((val = needed_unusual_el_valence(at[j].el_number, at[j].charge, at[j].radical, ------------------ | Branch (2502:13): [True: 65.7k, False: 252k] ------------------ 2503| 318k| at[j].chem_bonds_valence, bonds_val, at[j].num_H, at[j].valence)) || 2504| 252k| at[j].charge || at[j].radical || at[j].iso_atw_diff || NUM_ISO_H(at, j) || parity) ------------------ | | 55| 455k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ | | | Branch (55:26): [True: 8, False: 136k] | | ------------------ ------------------ | Branch (2504:13): [True: 109k, False: 142k] | Branch (2504:29): [True: 6.20k, False: 136k] | Branch (2504:46): [True: 220, False: 136k] | Branch (2504:88): [True: 354, False: 136k] ------------------ 2505| 182k| { 2506| | /* valence */ 2507| 182k| if (val) ------------------ | Branch (2507:17): [True: 65.7k, False: 116k] ------------------ 2508| 65.7k| { 2509| 65.7k| len += sprintf(szCurAtom + len, "%d", val > 0 ? val : 0); ------------------ | Branch (2509:55): [True: 15.8k, False: 49.9k] ------------------ 2510| 65.7k| } 2511| | /* charge */ 2512| 182k| if ((val = at[j].charge)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2512:17): [True: 111k, False: 71.0k] ------------------ 2513| 111k| { 2514| 111k| szCurAtom[len++] = val > 0 ? '+' : '-'; ------------------ | Branch (2514:36): [True: 90.4k, False: 20.9k] ------------------ 2515| 111k| if ((val = abs(val)) > 1) ------------------ | Branch (2515:21): [True: 2.02k, False: 109k] ------------------ 2516| 2.02k| { 2517| 2.02k| len += sprintf(szCurAtom + len, "%d", val); 2518| 2.02k| } 2519| 111k| } 2520| | /* radical */ 2521| 182k| if ((val = at[j].radical)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2521:17): [True: 9.84k, False: 172k] ------------------ 2522| 9.84k| { 2523| 9.84k| len += sprintf(szCurAtom + len, ".%d", val); 2524| 9.84k| } 2525| | /* isotopic shift */ 2526| 182k| if ((val = at[j].iso_atw_diff)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2526:17): [True: 1.46k, False: 180k] ------------------ 2527| 1.46k| { 2528| 1.46k| mw = get_atomic_mass_from_elnum(at[j].el_number); 2529| 1.46k| if (val == 1) ------------------ | Branch (2529:21): [True: 1.11k, False: 348] ------------------ 2530| 1.11k| val = mw; 2531| 348| else if (val > 0) ------------------ | Branch (2531:26): [True: 286, False: 62] ------------------ 2532| 286| val = mw + val - 1; 2533| 62| else 2534| 62| val = mw + val; 2535| | 2536| 1.46k| len += sprintf(szCurAtom + len, "%si%d", len == len0 ? "." : "", val); ------------------ | Branch (2536:58): [True: 220, False: 1.24k] ------------------ 2537| 1.46k| } 2538| | /* parity */ 2539| 182k| if (parity) ------------------ | Branch (2539:17): [True: 502, False: 181k] ------------------ 2540| 502| { 2541| 502| len += sprintf(szCurAtom + len, "%s%s", len == len0 ? "." : "", ------------------ | Branch (2541:57): [True: 354, False: 148] ------------------ 2542| 502| parity == AB_PARITY_ODD ? "o" : parity == AB_PARITY_EVEN ? "e" ------------------ | | 219| 502|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ parity == AB_PARITY_ODD ? "o" : parity == AB_PARITY_EVEN ? "e" ------------------ | | 220| 278|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (2542:32): [True: 224, False: 278] | Branch (2542:64): [True: 202, False: 76] ------------------ 2543| 278| : parity == AB_PARITY_UNKN ? "u" ------------------ | | 221| 76|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2543:62): [True: 32, False: 44] ------------------ 2544| 76| : parity == AB_PARITY_UNDF ? "?" ------------------ | | 222| 44|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2544:62): [True: 44, False: 0] ------------------ 2545| 44| : ""); 2546| 502| } 2547| | /* implicit isotopic H */ 2548| 182k| if (NUM_ISO_H(at, j)) ------------------ | | 55| 182k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ | | | Branch (55:26): [True: 218, False: 182k] | | ------------------ ------------------ 2549| 218| { 2550| 872| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 25| 872|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (2550:29): [True: 654, False: 218] ------------------ 2551| 654| { 2552| 654| if ((val = at[j].num_iso_H[k])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2552:25): [True: 258, False: 396] ------------------ 2553| 258| { 2554| 258| len += sprintf(szCurAtom + len, "%s%c", len == len0 ? "." : "", szIsoH[k]); ------------------ | Branch (2554:65): [True: 8, False: 250] ------------------ 2555| 258| if (val > 1) ------------------ | Branch (2555:29): [True: 48, False: 210] ------------------ 2556| 48| { 2557| 48| len += sprintf(szCurAtom + len, "%d", val); 2558| 48| } 2559| 258| } 2560| 654| } 2561| 218| } 2562| 182k| } 2563| | 2564| 318k| if (len + cur_len < buf_len) ------------------ | Branch (2564:13): [True: 318k, False: 194] ------------------ 2565| 318k| { 2566| 318k| memcpy(szBuf + cur_len, szCurAtom, len); 2567| 318k| cur_len += len; 2568| 318k| j++; 2569| 318k| } 2570| 194| else 2571| 194| { 2572| 194| break; 2573| 194| } 2574| 318k| szBuf[cur_len] = '\0'; 2575| 318k| *i = j; 2576| 318k| } 2577| | 2578| 211k| return cur_len; 2579| 211k|} ichiprt1.c:WriteOrigBonds: 2623| 154k|{ 2624| 154k| int j, k, k2, kk, len, cur_len, j2 = 0, bond_stereo, bond_char, bond_parity, bond_parityNM, num_trans; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2625| 154k| char szCurBonds[7 * MAXVAL + 2]; /* num_neigh*(1 byte bond type + 2 bytes for bond parity up to 4 digits per neighbor number) + at the end one ';' */ 2626| 154k| AT_RANK nNeighOrder[MAXVAL]; 2627| 154k| int chain_len, pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; 2628| 154k| int chain_len2, pnxt_atom2, pinxt2cur2, pinxt_sb_parity_ord2, m1, m2; 2629| 154k| int pcur_atom, picur2nxt, picur_sb_parity_ord; 2630| | 2631| 154k| cur_len = 0; 2632| 331k| for (j = *i; j < num_inp_atoms;) ------------------ | Branch (2632:18): [True: 177k, False: 154k] ------------------ 2633| 177k| { 2634| 177k| len = 0; 2635| 177k| if (at[j].valence >= 1) /* djb-rwth: changing condition to avoid garbage values */ ------------------ | Branch (2635:13): [True: 107k, False: 69.9k] ------------------ 2636| 107k| { 2637| 311k| for (k = 0; k < at[j].valence; k++) ------------------ | Branch (2637:25): [True: 203k, False: 107k] ------------------ 2638| 203k| { 2639| 203k| nNeighOrder[k] = k; 2640| 203k| } 2641| 107k| pCG->m_pn_RankForSort = at[j].neighbor; 2642| 107k| num_trans = insertions_sort(pCG, nNeighOrder, at[j].valence, sizeof(nNeighOrder[0]), CompRank); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2643| 107k| } 2644| 69.9k| else 2645| 69.9k| { 2646| 69.9k| num_trans = 0; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2647| 69.9k| nNeighOrder[0] = 0; 2648| 69.9k| } 2649| 381k| for (kk = 0; kk < at[j].valence; kk++) ------------------ | Branch (2649:22): [True: 203k, False: 177k] ------------------ 2650| 203k| { 2651| 203k| k = nNeighOrder[kk]; 2652| 203k| j2 = at[j].neighbor[k]; 2653| 203k| bond_parity = 0; 2654| 203k| bond_parityNM = 0; 2655| 203k| if (j2 < j) ------------------ | Branch (2655:17): [True: 124k, False: 79.4k] ------------------ 2656| 124k| { 2657| 124k| bond_stereo = at[j].bond_stereo[k]; 2658| 124k| switch (at[j].bond_type[k]) 2659| 124k| { 2660| 84.6k| case BOND_TYPE_SINGLE: ------------------ | | 32| 84.6k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2660:17): [True: 84.6k, False: 39.4k] ------------------ 2661| 84.6k| switch (bond_stereo) 2662| 84.6k| { 2663| 0| case STEREO_SNGL_UP: ------------------ | | 37| 0|#define STEREO_SNGL_UP 1 ------------------ | Branch (2663:21): [True: 0, False: 84.6k] ------------------ 2664| 0| bond_char = 'p'; 2665| 0| break; 2666| 0| case -STEREO_SNGL_UP: ------------------ | | 37| 0|#define STEREO_SNGL_UP 1 ------------------ | Branch (2666:21): [True: 0, False: 84.6k] ------------------ 2667| 0| bond_char = 'P'; 2668| 0| break; 2669| 0| case STEREO_SNGL_DOWN: ------------------ | | 39| 0|#define STEREO_SNGL_DOWN 6 ------------------ | Branch (2669:21): [True: 0, False: 84.6k] ------------------ 2670| 0| bond_char = 'n'; 2671| 0| break; 2672| 0| case -STEREO_SNGL_DOWN: ------------------ | | 39| 0|#define STEREO_SNGL_DOWN 6 ------------------ | Branch (2672:21): [True: 0, False: 84.6k] ------------------ 2673| 0| bond_char = 'N'; 2674| 0| break; 2675| 0|#if (FIX_EITHER_STEREO_IN_AUX_INFO == 1) 2676| 0| case STEREO_SNGL_EITHER: ------------------ | | 38| 0|#define STEREO_SNGL_EITHER 4 ------------------ | Branch (2676:21): [True: 0, False: 84.6k] ------------------ 2677| 0| bond_char = 'v'; 2678| 0| break; 2679| 0| case -STEREO_SNGL_EITHER: ------------------ | | 38| 0|#define STEREO_SNGL_EITHER 4 ------------------ | Branch (2679:21): [True: 0, False: 84.6k] ------------------ 2680| 0| bond_char = 'V'; 2681| 0| break; 2682| |#else 2683| | case STEREO_SNGL_EITHER: 2684| | case -STEREO_SNGL_EITHER: 2685| | bond_char = 'v'; 2686| | break; 2687| |#endif 2688| 84.6k| default: ------------------ | Branch (2688:21): [True: 84.6k, False: 0] ------------------ 2689| 84.6k| bond_char = 's'; 2690| 84.6k| break; 2691| 84.6k| } 2692| 84.6k| break; 2693| 84.6k| case BOND_TYPE_DOUBLE: ------------------ | | 33| 26.6k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2693:17): [True: 26.6k, False: 97.3k] ------------------ 2694| 26.6k| switch (bond_stereo) 2695| 26.6k| { 2696| 74| case STEREO_DBLE_EITHER: ------------------ | | 40| 74|#define STEREO_DBLE_EITHER 3 ------------------ | Branch (2696:21): [True: 74, False: 26.6k] ------------------ 2697| 74| case -STEREO_DBLE_EITHER: ------------------ | | 40| 74|#define STEREO_DBLE_EITHER 3 ------------------ | Branch (2697:21): [True: 0, False: 26.6k] ------------------ 2698| 74| bond_char = 'w'; 2699| 74| break; 2700| 26.6k| default: ------------------ | Branch (2700:21): [True: 26.6k, False: 74] ------------------ 2701| 26.6k| bond_char = 'd'; 2702| 26.6k| break; 2703| 26.6k| } 2704| 26.6k| break; 2705| 26.6k| case BOND_TYPE_TRIPLE: ------------------ | | 34| 12.7k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (2705:17): [True: 12.7k, False: 111k] ------------------ 2706| 12.7k| bond_char = 't'; 2707| 12.7k| break; 2708| 0| case BOND_TYPE_ALTERN: ------------------ | | 35| 0|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (2708:17): [True: 0, False: 124k] ------------------ 2709| 0| bond_char = 'a'; 2710| 0| break; 2711| 0| default: ------------------ | Branch (2711:17): [True: 0, False: 124k] ------------------ 2712| 0| bond_char = 's'; 2713| 0| break; 2714| 124k| } 2715| | /* check for allene/cumulene */ 2716| 124k| k2 = (int)(is_in_the_list(at[j2].neighbor, (AT_NUMB)j, at[j2].valence) - at[j2].neighbor); 2717| 124k| chain_len = chain_len2 = 0; 2718| 124k| if (at[j].sb_parity[0]) ------------------ | Branch (2718:21): [True: 1.09k, False: 122k] ------------------ 2719| 1.09k| { 2720| 1.54k| for (m1 = 0; m1 < MAX_NUM_STEREO_BONDS && at[j].sb_parity[m1]; m1++) ------------------ | | 873| 3.09k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2720:34): [True: 1.54k, False: 0] | Branch (2720:63): [True: 1.21k, False: 330] ------------------ 2721| 1.21k| { 2722| 1.21k| if (k == at[j].sb_ord[m1]) ------------------ | Branch (2722:29): [True: 766, False: 450] ------------------ 2723| 766| { 2724| 766| chain_len = get_opposite_sb_atom(at, j, k, 2725| 766| &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord); 2726| 766| break; 2727| 766| } 2728| 1.21k| } 2729| 1.09k| } 2730| 124k| if (at[j2].sb_parity[0]) ------------------ | Branch (2730:21): [True: 1.77k, False: 122k] ------------------ 2731| 1.77k| { 2732| 2.97k| for (m2 = 0; m2 < MAX_NUM_STEREO_BONDS && at[j2].sb_parity[m2]; m2++) ------------------ | | 873| 5.95k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2732:34): [True: 2.97k, False: 0] | Branch (2732:63): [True: 1.94k, False: 1.02k] ------------------ 2733| 1.94k| { 2734| 1.94k| if (k2 == at[j2].sb_ord[m2]) ------------------ | Branch (2734:29): [True: 742, False: 1.20k] ------------------ 2735| 742| { 2736| 742| chain_len2 = get_opposite_sb_atom(at, j2, k2, 2737| 742| &pnxt_atom2, &pinxt2cur2, &pinxt_sb_parity_ord2); 2738| 742| break; 2739| 742| } 2740| 1.94k| } 2741| 1.77k| } 2742| 124k| if ((chain_len == 1 && chain_len2 == 1) || /* regular stereobond */ ------------------ | Branch (2742:22): [True: 734, False: 123k] | Branch (2742:40): [True: 734, False: 0] ------------------ 2743| 123k| (chain_len > 1 && j > pnxt_atom)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2743:22): [True: 20, False: 123k] | Branch (2743:39): [True: 10, False: 10] ------------------ 2744| 744| { 2745| | /* j is a cumulene endpoint */ 2746| 744| int m; 2747| 744| pcur_atom = j; /* pcur_atom > pnxt_atom */ 2748| 744| picur2nxt = k; 2749| 744| picur_sb_parity_ord = -1; 2750| 834| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[pcur_atom].sb_parity[m]; m++) ------------------ | | 873| 1.66k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2750:33): [True: 834, False: 0] | Branch (2750:61): [True: 834, False: 0] ------------------ 2751| 834| { 2752| 834| if (at[pcur_atom].sb_ord[m] == k) ------------------ | Branch (2752:29): [True: 744, False: 90] ------------------ 2753| 744| { 2754| 744| picur_sb_parity_ord = m; 2755| 744| break; 2756| 744| } 2757| 834| } 2758| | /* djb-rwth: removing redundant code */ 2759| 744| } 2760| 123k| else 2761| 123k| { 2762| 123k| if (chain_len2 > 1 && j2 > pnxt_atom2) ------------------ | Branch (2762:25): [True: 4, False: 123k] | Branch (2762:43): [True: 2, False: 2] ------------------ 2763| 2| { /* j2 is a cumulene endpoint */ 2764| 2| int m; 2765| 2| pcur_atom = j2; 2766| 2| picur2nxt = k2; 2767| 2| pnxt_atom = pnxt_atom2; 2768| 2| pinxt2cur = pinxt2cur2; 2769| 2| pinxt_sb_parity_ord = pinxt_sb_parity_ord2; 2770| 2| picur_sb_parity_ord = -1; 2771| 4| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[pcur_atom].sb_parity[m]; m++) ------------------ | | 873| 8|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2771:37): [True: 4, False: 0] | Branch (2771:65): [True: 2, False: 2] ------------------ 2772| 2| { 2773| 2| if (at[pcur_atom].sb_ord[m] == k2) ------------------ | Branch (2773:33): [True: 2, False: 0] ------------------ 2774| 2| picur_sb_parity_ord = m; 2775| 2| } 2776| 2| chain_len = chain_len2; 2777| | /* djb-rwth: removing redundant code */ 2778| 2| } 2779| 123k| else 2780| 123k| { 2781| 123k| chain_len = 0; /* djb-rwth: removing redundant code */ 2782| 123k| } 2783| 123k| } 2784| | /*len += sprintf( szCurBonds + len, "%c%d", bond_char, val+1);*/ 2785| 124k| if (chain_len) ------------------ | Branch (2785:21): [True: 746, False: 123k] ------------------ 2786| 746| { 2787| | /* both atoms belong to a stereo bond */ 2788| 746| int kc; 2789| 746| int p1 = 0, p2, p1NM = 0, p2NM, neigh, neigh1, neigh2, bHasMetal, bWellDef; /* djb-rwth: initialising p1 and p1NM */ 2790| 746| int bNeighSwitched1, bNeighSwitched2; 2791| | 2792| | /* djb-rwth: avoiding buffer overrun as picur_sb_parity_ord == -1 is possible */ 2793| 746| if (picur_sb_parity_ord >= 0) ------------------ | Branch (2793:25): [True: 746, False: 0] ------------------ 2794| 746| { 2795| 746| p1 = SB_PARITY_1(at[pcur_atom].sb_parity[picur_sb_parity_ord]); ------------------ | | 65| 746|#define SB_PARITY_1(X) (X & SB_PARITY_MASK) /**< refers to connected structure */ | | ------------------ | | | | 64| 746|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2796| 746| p1NM = SB_PARITY_2(at[pcur_atom].sb_parity[picur_sb_parity_ord]); ------------------ | | 66| 746|#define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /**< refers to connected structure */ | | ------------------ | | | | 63| 746|#define SB_PARITY_SHFT 3 /**< number of right shift bits to get disconnected metal parity */ | | ------------------ | | #define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /**< refers to connected structure */ | | ------------------ | | | | 64| 746|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2797| 746| } 2798| | 2799| 746| p2 = SB_PARITY_1(at[pnxt_atom].sb_parity[pinxt_sb_parity_ord]); ------------------ | | 65| 746|#define SB_PARITY_1(X) (X & SB_PARITY_MASK) /**< refers to connected structure */ | | ------------------ | | | | 64| 746|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2800| 746| p2NM = SB_PARITY_2(at[pnxt_atom].sb_parity[pinxt_sb_parity_ord]); ------------------ | | 66| 746|#define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /**< refers to connected structure */ | | ------------------ | | | | 63| 746|#define SB_PARITY_SHFT 3 /**< number of right shift bits to get disconnected metal parity */ | | ------------------ | | #define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /**< refers to connected structure */ | | ------------------ | | | | 64| 746|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2801| | 2802| 746| bWellDef = ATOM_PARITY_WELL_DEF(p1) && ATOM_PARITY_WELL_DEF(p2); ------------------ | | 259| 1.49k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 746|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 746|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 746, False: 0] | | | Branch (259:75): [True: 504, False: 242] | | ------------------ ------------------ bWellDef = ATOM_PARITY_WELL_DEF(p1) && ATOM_PARITY_WELL_DEF(p2); ------------------ | | 259| 1.25k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 504|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 504|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 504, False: 0] | | | Branch (259:75): [True: 504, False: 0] | | ------------------ ------------------ 2803| 746| bHasMetal = ATOM_PARITY_WELL_DEF(p1NM) && ATOM_PARITY_WELL_DEF(p2NM); ------------------ | | 259| 1.49k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 746|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 746] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ bHasMetal = ATOM_PARITY_WELL_DEF(p1NM) && ATOM_PARITY_WELL_DEF(p2NM); ------------------ | | 259| 746|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 2804| | 2805| 746| bNeighSwitched1 = bNeighSwitched2 = 0; 2806| | 2807| 746| if (bWellDef || bHasMetal) ------------------ | Branch (2807:25): [True: 504, False: 242] | Branch (2807:37): [True: 0, False: 242] ------------------ 2808| 504| { 2809| | 2810| 504| neigh1 = num_inp_atoms; 2811| 1.63k| for (kc = 0; kc < at[pcur_atom].valence; kc++) ------------------ | Branch (2811:38): [True: 1.13k, False: 504] ------------------ 2812| 1.13k| { 2813| 1.13k| if (kc == picur2nxt) ------------------ | Branch (2813:33): [True: 504, False: 630] ------------------ 2814| 504| continue; 2815| 630| neigh = at[pcur_atom].neighbor[kc]; 2816| 630| if (bHasMetal && is_el_a_metal(at[neigh].el_number)) ------------------ | Branch (2816:33): [True: 0, False: 630] | Branch (2816:46): [True: 0, False: 0] ------------------ 2817| 0| continue; 2818| 630| if (neigh < neigh1) ------------------ | Branch (2818:33): [True: 510, False: 120] ------------------ 2819| 510| neigh1 = neigh; 2820| 630| } 2821| 504| if (neigh1 < num_inp_atoms) ------------------ | Branch (2821:29): [True: 504, False: 0] ------------------ 2822| 504| { 2823| 504| bNeighSwitched1 = (neigh1 != at[pcur_atom].neighbor[(int)at[pcur_atom].sn_ord[picur_sb_parity_ord]]); 2824| 504| } 2825| 0| else 2826| 0| { 2827| 0| AddErrorMessage(sd->pStrErrStruct, "Cannot find 0D stereobond neighbor"); 2828| | /* 2829| | sd->nStructReadError = 99; 2830| | sd->nErrorType = _IS_ERROR; 2831| | */ 2832| 0| } 2833| | 2834| 504| neigh2 = num_inp_atoms; 2835| 1.62k| for (kc = 0; kc < at[pnxt_atom].valence; kc++) ------------------ | Branch (2835:38): [True: 1.12k, False: 504] ------------------ 2836| 1.12k| { 2837| 1.12k| if (kc == pinxt2cur) ------------------ | Branch (2837:33): [True: 504, False: 620] ------------------ 2838| 504| continue; 2839| 620| neigh = at[pnxt_atom].neighbor[kc]; 2840| 620| if (bHasMetal && is_el_a_metal(at[neigh].el_number)) ------------------ | Branch (2840:33): [True: 0, False: 620] | Branch (2840:46): [True: 0, False: 0] ------------------ 2841| 0| continue; 2842| 620| if (neigh < neigh2) ------------------ | Branch (2842:33): [True: 516, False: 104] ------------------ 2843| 516| neigh2 = neigh; 2844| 620| } 2845| 504| if (neigh2 < num_inp_atoms) ------------------ | Branch (2845:29): [True: 504, False: 0] ------------------ 2846| 504| { 2847| 504| bNeighSwitched2 = (neigh2 != at[pnxt_atom].neighbor[(int)at[pnxt_atom].sn_ord[pinxt_sb_parity_ord]]); 2848| 504| } 2849| 0| else 2850| 0| { 2851| 0| AddErrorMessage(sd->pStrErrStruct, "Cannot find 0D stereobond neighbor"); 2852| | /* 2853| | sd->nStructReadError = 99; 2854| | sd->nErrorType = _IS_ERROR; 2855| | */ 2856| 0| } 2857| | 2858| 504| if (neigh1 < num_inp_atoms && neigh2 < num_inp_atoms) ------------------ | Branch (2858:29): [True: 504, False: 0] | Branch (2858:55): [True: 504, False: 0] ------------------ 2859| 504| { 2860| 504| if (ATOM_PARITY_WELL_DEF(p1) && ATOM_PARITY_WELL_DEF(p2)) ------------------ | | 259| 1.00k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 504|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 504|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 504, False: 0] | | | Branch (259:75): [True: 504, False: 0] | | ------------------ ------------------ if (ATOM_PARITY_WELL_DEF(p1) && ATOM_PARITY_WELL_DEF(p2)) ------------------ | | 259| 504|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 504|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 504|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 504, False: 0] | | | Branch (259:75): [True: 504, False: 0] | | ------------------ ------------------ 2861| 504| { 2862| 504| bond_parity = 2 - (p1 + p2 + bNeighSwitched1 + bNeighSwitched2) % 2; 2863| 504| } 2864| 0| else 2865| 0| { 2866| 0| bond_parity = inchi_min(p1, p2); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2867| 0| } 2868| | 2869| 504| if (bHasMetal) ------------------ | Branch (2869:33): [True: 0, False: 504] ------------------ 2870| 0| { 2871| 0| bond_parityNM = 2 - (p1NM + p2NM + bNeighSwitched1 + bNeighSwitched2) % 2; 2872| 0| } 2873| 504| else 2874| 504| { 2875| 504| if (p1NM && p2NM) ------------------ | Branch (2875:37): [True: 0, False: 504] | Branch (2875:45): [True: 0, False: 0] ------------------ 2876| 0| { 2877| 0| bond_parityNM = inchi_min(p1NM, p2NM); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2878| 0| } 2879| 504| } 2880| 504| } 2881| 504| } 2882| 242| else 2883| 242| { 2884| 242| if (p1 && p2) ------------------ | Branch (2884:29): [True: 242, False: 0] | Branch (2884:35): [True: 242, False: 0] ------------------ 2885| 242| { 2886| 242| bond_parity = inchi_min(p1, p2); ------------------ | | 139| 242|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 242] | | ------------------ ------------------ 2887| 242| } 2888| 242| if (p1NM && p2NM) ------------------ | Branch (2888:29): [True: 0, False: 242] | Branch (2888:37): [True: 0, False: 0] ------------------ 2889| 0| { 2890| 0| bond_parityNM = inchi_min(p1NM, p2NM); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2891| 0| } 2892| 242| if (bond_parityNM && !bond_parity) ------------------ | Branch (2892:29): [True: 0, False: 242] | Branch (2892:46): [True: 0, False: 0] ------------------ 2893| 0| { 2894| 0| bond_parity = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2895| 0| } 2896| 242| } 2897| 746| } 2898| | 2899| 124k| len += sprintf(szCurBonds + len, "%c%s%s%d", 2900| 124k| bond_char, 2901| | 2902| 124k| (bond_parity == AB_PARITY_ODD) ? "-" : (bond_parity == AB_PARITY_EVEN) ? "+" ------------------ | | 219| 124k|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ (bond_parity == AB_PARITY_ODD) ? "-" : (bond_parity == AB_PARITY_EVEN) ? "+" ------------------ | | 220| 123k|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (2902:32): [True: 304, False: 123k] | Branch (2902:71): [True: 200, False: 123k] ------------------ 2903| 123k| : (bond_parity == AB_PARITY_UNKN) ? "u" ------------------ | | 221| 123k|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2903:69): [True: 88, False: 123k] ------------------ 2904| 123k| : (bond_parity == AB_PARITY_UNDF) ? "?" ------------------ | | 222| 123k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2904:69): [True: 154, False: 123k] ------------------ 2905| 123k| : "", 2906| | 2907| 124k| (bond_parityNM == AB_PARITY_ODD) ? "-" : (bond_parityNM == AB_PARITY_EVEN) ? "+" ------------------ | | 219| 124k|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ (bond_parityNM == AB_PARITY_ODD) ? "-" : (bond_parityNM == AB_PARITY_EVEN) ? "+" ------------------ | | 220| 124k|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (2907:32): [True: 0, False: 124k] | Branch (2907:73): [True: 0, False: 124k] ------------------ 2908| 124k| : (bond_parityNM == AB_PARITY_UNKN) ? "u" ------------------ | | 221| 124k|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2908:71): [True: 0, False: 124k] ------------------ 2909| 124k| : (bond_parityNM == AB_PARITY_UNDF) ? "?" ------------------ | | 222| 124k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2909:71): [True: 0, False: 124k] ------------------ 2910| 124k| : "", 2911| | 2912| 124k| j2 + 1); 2913| 124k| } 2914| 203k| } 2915| 177k| if (len + cur_len + 2 < buf_len) ------------------ | Branch (2915:13): [True: 177k, False: 93] ------------------ 2916| 177k| { 2917| 177k| memcpy(szBuf + cur_len, szCurBonds, len); 2918| 177k| cur_len += len; 2919| 177k| szBuf[cur_len++] = ';'; 2920| 177k| j++; 2921| 177k| } 2922| 93| else 2923| 93| { 2924| 93| break; 2925| 93| } 2926| 177k| } 2927| 154k| szBuf[cur_len] = '\0'; 2928| 154k| *i = num_inp_atoms > 0 ? j : 0; ------------------ | Branch (2928:10): [True: 154k, False: 0] ------------------ 2929| | 2930| 154k| return cur_len; 2931| 154k|} ichiprt1.c:OutputINCHI_VersionAndKind: 3143| 5.02k|{ 3144| 5.02k| inchi_ios_print_nodisplay(out_file, "%s%s=%s", pLF, INCHI_NAME, pLF); ------------------ | | 224| 5.02k|#define INCHI_NAME "InChI" ------------------ 3145| | 3146| 5.02k| inchi_strbuf_reset(strbuf); 3147| 5.02k| inchi_strbuf_printf(strbuf, "%s", x_curr_ver); 3148| | 3149| | /* 3150| | * (@nnuk) 3151| | * The calculation class designator is: 3152| | * S = Standard 3153| | * B = Beta 3154| | * N = non-standard 3155| | * 3156| | * Molecular Inorganics adds the subversion designator 'B'. 3157| | * 3158| | * Non-standard takes precedence over Beta because use of a non-standard 3159| | * option makes the resulting InChI non-standard irrespective of any 3160| | * experimental feature that would otherwise require the Beta designator. 3161| | */ 3162| 5.02k| if (!(bINChIOutputOptions & INCHI_OUT_STDINCHI)) ------------------ | | 145| 5.02k|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (3162:9): [True: 5.00k, False: 22] ------------------ 3163| 5.00k| { 3164| 5.00k| inchi_strbuf_printf(strbuf, "N"); 3165| 5.00k| } 3166| 22| else if (is_beta) ------------------ | Branch (3166:14): [True: 5, False: 17] ------------------ 3167| 5| { 3168| 5| inchi_strbuf_printf(strbuf, "B"); 3169| 5| } 3170| 17| else 3171| 17| { 3172| 17| inchi_strbuf_printf(strbuf, "S"); 3173| 17| } 3174| | 3175| 5.02k| if (is_molecular_inorganic) ------------------ | Branch (3175:9): [True: 0, False: 5.02k] ------------------ 3176| 0| { 3177| 0| inchi_strbuf_printf(strbuf, "B"); 3178| 0| } 3179| | 3180| 5.02k| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3181| | 3182| 5.02k| return 0; 3183| 5.02k|} ichiprt1.c:OutputINCHI_MainLayerFormula: 3197| 5.02k|{ 3198| | 3199| | /* constitution ( dot-disconnected Hill formulas: ) */ 3200| | 3201| 5.02k| if (num_components2[0] || num_components2[1]) ------------------ | Branch (3201:9): [True: 5.02k, False: 0] | Branch (3201:31): [True: 0, False: 0] ------------------ 3202| 5.02k| { 3203| 5.02k| szGetTag(IdentLbl, io->nTag, io->bTag1 = *INCHI_basic_or_INCHI_reconnected == INCHI_REC ? IL_REC_ : IL_FML_, io->szTag1, &io->bAlways, 1); ------------------ | | 571| 5.02k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (3203:50): [True: 0, False: 5.02k] ------------------ 3204| 5.02k| inchi_strbuf_reset(strbuf); 3205| 5.02k| io->tot_len = str_HillFormula(io->pINChISort, strbuf, &io->bOverflow, io->bOutType, 3206| 5.02k| io->num_components, io->bUseMulipliers); 3207| | 3208| 5.02k| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -1, 1)) ------------------ | Branch (3208:13): [True: 0, False: 5.02k] ------------------ 3209| 0| { 3210| 0| return 1; 3211| 0| } 3212| 5.02k| if (io->n_pzz > 0 && io->n_zy > 0) ------------------ | Branch (3212:13): [True: 0, False: 5.02k] | Branch (3212:30): [True: 0, False: 0] ------------------ 3213| 0| { 3214| 0| int retm = MergeZzInHillFormula(strbuf); 3215| 0| if (0 != retm) ------------------ | Branch (3215:17): [True: 0, False: 0] ------------------ 3216| 0| { 3217| 0| return -1; 3218| 0| } 3219| 0| } 3220| 5.02k| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3221| 5.02k| } 3222| | 3223| 5.02k| LOG_NO_ARGS("\n#################### (L3318:ichiprt1.c) ##########################\n"); 3224| 5.02k| LOG_MULT_ARGS("This is the Chemical formula : %s\n", strbuf->pStr); 3225| 5.02k| LOG_NO_ARGS("####################################################################\n"); 3226| | 3227| 5.02k| return 0; 3228| 5.02k|} ichiprt1.c:str_LineEnd: 2199| 13.0k|{ 2200| | /* djb-rwth: removing redundant variables */ 2201| 13.0k| int tag_len; 2202| | 2203| | /* check buffer overflow */ 2204| 13.0k| if (*bOverflow) ------------------ | Branch (2204:9): [True: 0, False: 13.0k] ------------------ 2205| 0| { 2206| 0| return 1; 2207| 0| } 2208| | 2209| 13.0k| if (ind < 0) ------------------ | Branch (2209:9): [True: 13.0k, False: 0] ------------------ 2210| 13.0k| { 2211| | /* Plain text */ 2212| | /* insert plain text tag if: 2213| | (a) pStr has non-zero length, or 2214| | (b) ind < -1 2215| | */ 2216| 13.0k| if (buf->pStr[0] || ind < -1) ------------------ | Branch (2216:13): [True: 12.5k, False: 480] | Branch (2216:29): [True: 94, False: 386] ------------------ 2217| 12.6k| { 2218| 12.6k| tag_len = bPlainTextTags ? (int)strlen(tag) : 0; ------------------ | Branch (2218:23): [True: 12.6k, False: 0] ------------------ 2219| 12.6k| if (tag_len > 0) ------------------ | Branch (2219:17): [True: 12.6k, False: 0] ------------------ 2220| 12.6k| { 2221| 12.6k| int n_added = tag_len + 2 + 2; 2222| 12.6k| inchi_strbuf_update(buf, n_added); 2223| | 2224| 12.6k| memmove(buf->pStr + tag_len, buf->pStr, (long long)buf->nUsedLength + 1); /* djb-rwth: cast operator added */ 2225| | /* NB: trailing 0 is also memmoved */ 2226| 12.6k| memcpy(buf->pStr, tag, tag_len); 2227| | 2228| | /* to be sure... */ 2229| 12.6k| buf->nUsedLength = strlen(buf->pStr); 2230| 12.6k| } 2231| 12.6k| } 2232| 13.0k| } 2233| | 2234| 13.0k| return 0; 2235| 13.0k|} ichiprt1.c:OutputINCHI_MainLayerConnections: 3239| 5.02k|{ 3240| | /* connections ( semicolon/dot-disconnected connection tables ) */ 3241| | 3242| 5.02k| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_CONN, io->szTag1, &io->bAlways, 1); 3243| 5.02k| inchi_strbuf_reset(strbuf); 3244| 5.02k| io->tot_len = 0; 3245| 5.02k| io->tot_len2 = str_Connections(pCG, io->pINChISort, strbuf, &io->bOverflow, io->bOutType, 3246| 5.02k| io->ATOM_MODE, io->num_components, io->bUseMulipliers); 3247| | 3248| | /* current version does not output empty (";;;;") connectivity */ 3249| | 3250| 5.02k| if (io->tot_len != io->tot_len2) ------------------ | Branch (3250:9): [True: 4.24k, False: 780] ------------------ 3251| 4.24k| { /* 2004-06-30: never output empty connection table */ 3252| 4.24k| io->tot_len = io->tot_len2; 3253| 4.24k| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -2, io->bPlainTextTags)) ------------------ | Branch (3253:13): [True: 0, False: 4.24k] ------------------ 3254| 0| { 3255| 0| return 1; /* pStr overfow */ 3256| 0| } 3257| 4.24k| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3258| 4.24k| } 3259| | 3260| 5.02k| LOG_NO_ARGS("\n##################### (L3357:ichiprt1.c) #########################\n"); 3261| 5.02k| LOG_MULT_ARGS("This is the Connection Layer : %s\n", strbuf->pStr); 3262| 5.02k| LOG_NO_ARGS("####################################################################\n"); 3263| | 3264| 5.02k| return 0; 3265| 5.02k|} ichiprt1.c:OutputINCHI_MainLayerHydrogens: 3276| 5.02k|{ 3277| | 3278| | /* hydrogen atoms (do not output empty) */ 3279| | 3280| 5.02k| if (INCHI_SEGM_FILL == INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_h_H_ATOMS])) ------------------ | Branch (3280:9): [True: 1.86k, False: 3.16k] ------------------ 3281| 1.86k| { 3282| 1.86k| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_ALLH, io->szTag1, &io->bAlways, 1); 3283| 1.86k| inchi_strbuf_reset(strbuf); 3284| 1.86k| io->tot_len = 0; 3285| 1.86k| io->tot_len2 = str_H_atoms(io->pINChISort, strbuf, &io->bOverflow, io->bOutType, 3286| 1.86k| io->ATOM_MODE, io->TAUT_MODE, 3287| 1.86k| io->num_components, io->bUseMulipliers); 3288| 1.86k| if (io->tot_len != io->tot_len2) ------------------ | Branch (3288:13): [True: 1.86k, False: 0] ------------------ 3289| 1.86k| { /* 2004-06-21: never output empty */ 3290| 1.86k| io->tot_len = io->tot_len2; 3291| 1.86k| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -2, 1)) ------------------ | Branch (3291:17): [True: 0, False: 1.86k] ------------------ 3292| 0| { 3293| 0| return 1; 3294| 0| } 3295| 1.86k| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3296| 1.86k| } 3297| 1.86k| } 3298| | 3299| 5.02k| LOG_NO_ARGS("\n###################### (L3396:ichiprt1.c) ########################\n"); 3300| 5.02k| LOG_MULT_ARGS("This is the Hydrogen Layer : %s\n", strbuf->pStr); 3301| 5.02k| LOG_NO_ARGS("####################################################################\n"); 3302| | 3303| 5.02k| return 0; 3304| 5.02k|} ichiprt1.c:OutputINCHI_ChargeAndRemovedAddedProtonsLayers: 3315| 5.02k|{ 3316| | 3317| | /* charge */ 3318| | 3319| 5.02k| io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_q_CHARGE]); 3320| 5.02k| if (io->nSegmAction) ------------------ | Branch (3320:9): [True: 243, False: 4.78k] ------------------ 3321| 243| { 3322| 243| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_CHRG | io->bFhTag, io->szTag1, &io->bAlways, 1); 3323| 243| inchi_strbuf_reset(strbuf); 3324| 243| io->tot_len = 0; 3325| 243| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3325:13): [True: 243, False: 0] ------------------ 3326| 243| { 3327| 243| io->tot_len = str_Charge2(io->pINChISort, io->pINChISort2, 3328| 243| strbuf, &io->bOverflow, io->bOutType, io->num_components, 3329| 243| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers); 3330| 243| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3331| 243| } 3332| 243| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3332:13): [True: 0, False: 243] ------------------ 3333| 0| { 3334| 0| return 1; 3335| 0| } 3336| 243| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3337| 243| } 3338| | 3339| | /* removed protons */ 3340| | 3341| 5.02k| if (io->iCurTautMode == TAUT_YES && !io->bSecondNonTautPass) ------------------ | | 575| 10.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3341:9): [True: 5.02k, False: 0] | Branch (3341:41): [True: 5.02k, False: 0] ------------------ 3342| 5.02k| { 3343| | 3344| 5.02k| io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_p_PROTONS]); 3345| 5.02k| if (io->nSegmAction) ------------------ | Branch (3345:13): [True: 147, False: 4.88k] ------------------ 3346| 147| { 3347| 147| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_PROT | io->bFhTag, io->szTag1, &io->bAlways, 1); 3348| 147| inchi_strbuf_reset(strbuf); 3349| 147| io->tot_len = 0; 3350| 147| inchi_strbuf_printf(strbuf, "%+d", io->nNumRemovedProtons); 3351| 147| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3351:17): [True: 0, False: 147] ------------------ 3352| 0| { 3353| 0| return 1; 3354| 0| } 3355| 147| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3356| 147| } 3357| 4.88k| else 3358| 4.88k| { 3359| 4.88k| if (io->bPlainTextTags == 1) ------------------ | Branch (3359:17): [True: 0, False: 4.88k] ------------------ 3360| 0| inchi_ios_print_nodisplay(out_file, "/"); 3361| 4.88k| } 3362| 5.02k| } 3363| | 3364| 5.02k| return 0; 3365| 5.02k|} ichiprt1.c:OutputINCHI_StereoLayer: 3384| 5.02k|{ 3385| | 3386| 5.02k| if (INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS] ) || ------------------ | Branch (3386:9): [True: 410, False: 4.61k] ------------------ 3387| 4.61k| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ) || ------------------ | Branch (3387:9): [True: 357, False: 4.26k] ------------------ 3388| 4.26k| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV] ) || ------------------ | Branch (3388:9): [True: 0, False: 4.26k] ------------------ 3389| 4.26k| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE] )) ------------------ | Branch (3389:9): [True: 0, False: 4.26k] ------------------ 3390| 767| { 3391| | 3392| | /* stereo */ 3393| | 3394| 767| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_STER | io->bFhTag, io->szTag1, &io->bAlways, 1); 3395| | 3396| | /* sp2 */ 3397| | 3398| 767| if ((io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS] ))) ------------------ | Branch (3398:13): [True: 410, False: 357] ------------------ 3399| 410| { 3400| 410| szGetTag(IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_DBND, io->szTag2, &io->bAlways, 1); 3401| 410| inchi_strbuf_reset(strbuf); 3402| 410| io->tot_len = 0; 3403| 410| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3403:17): [True: 410, False: 0] ------------------ 3404| 410| { 3405| 410| io->tot_len = str_Sp2( io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3406| 410| io->bOutType, io->TAUT_MODE, io->num_components, 3407| 410| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3408| | 3409| 410| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3410| 410| } 3411| | 3412| 410| if (str_LineEnd(io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3412:17): [True: 0, False: 410] ------------------ 3413| 0| { 3414| 0| return 1; 3415| 0| } 3416| 410| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3417| 410| } 3418| 357| else 3419| 357| { 3420| 357| if (io->bPlainTextTags == 1) ------------------ | Branch (3420:17): [True: 0, False: 357] ------------------ 3421| 0| { 3422| 0| inchi_ios_print_nodisplay(out_file, "/"); /* sp2 */ 3423| 0| } 3424| 357| } 3425| | 3426| | /* sp3 */ 3427| | 3428| | /* t-layer */ 3429| 767| if ((io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3429:13): [True: 357, False: 410] ------------------ 3430| 357| { 3431| 357| io->bRelRac = io->bRelativeStereo[io->iCurTautMode] || io->bRacemicStereo[io->iCurTautMode]; ------------------ | Branch (3431:27): [True: 16, False: 341] | Branch (3431:68): [True: 10, False: 331] ------------------ 3432| 357| szGetTag(IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_SP3S, io->szTag2, &io->bAlways, 1); 3433| 357| inchi_strbuf_reset(strbuf); 3434| 357| io->tot_len = 0; 3435| 357| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3435:17): [True: 357, False: 0] ------------------ 3436| 357| { 3437| 357| io->tot_len = str_Sp3( io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3438| 357| io->bOutType, io->TAUT_MODE, io->num_components, io->bRelRac, 3439| 357| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3440| | 3441| 357| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3442| 357| } 3443| | 3444| 357| if (str_LineEnd(io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3444:17): [True: 0, False: 357] ------------------ 3445| 0| { 3446| 0| return 2; 3447| 0| } 3448| 357| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3449| 357| } 3450| 410| else 3451| 410| { 3452| 410| if (io->bPlainTextTags == 1) ------------------ | Branch (3452:17): [True: 0, False: 410] ------------------ 3453| 0| { 3454| 0| inchi_ios_print_nodisplay( out_file, "/" ); /* sp3 */ 3455| 0| } 3456| 410| } 3457| | 3458| | /* m-layer */ 3459| 767| if ((io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV] ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3459:13): [True: 2, False: 765] ------------------ 3460| 2| { 3461| 2| szGetTag(IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_INVS, io->szTag2, &io->bAlways, 1); 3462| 2| inchi_strbuf_reset(strbuf); 3463| 2| io->tot_len = 0; 3464| 2| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3464:17): [True: 2, False: 0] ------------------ 3465| 2| { 3466| 2| io->tot_len = str_StereoAbsInv( io->pINChISort, strbuf, 3467| 2| &io->bOverflow, io->bOutType, io->num_components ); 3468| 2| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3469| 2| } 3470| | 3471| 2| if (str_LineEnd(io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3471:17): [True: 0, False: 2] ------------------ 3472| 0| { 3473| 0| return 3; 3474| 0| } 3475| 2| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3476| 2| } 3477| 765| else 3478| 765| { 3479| 765| if (io->bPlainTextTags == 1) ------------------ | Branch (3479:17): [True: 0, False: 765] ------------------ 3480| 0| { 3481| 0| inchi_ios_print_nodisplay(out_file, "/"); /* stereo-abs-inv */ 3482| 0| } 3483| 765| } 3484| | 3485| | /* stereo type */ 3486| | 3487| | /* s-layer */ 3488| 767| if ((io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE] ))) ------------------ | Branch (3488:13): [True: 11, False: 756] ------------------ 3489| 11| { 3490| 11| const char *p_stereo = io->bRelativeStereo[io->iCurTautMode] ? x_rel : io->bRacemicStereo[io->iCurTautMode] ? x_rac ------------------ | Branch (3490:36): [True: 7, False: 4] | Branch (3490:84): [True: 2, False: 2] ------------------ 3491| 4| : x_abs; 3492| 11| szGetTag(IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_TYPS, io->szTag2, &io->bAlways, 1); 3493| 11| inchi_strbuf_reset(strbuf); 3494| 11| io->tot_len = 0; 3495| 11| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3495:17): [True: 11, False: 0] ------------------ 3496| 11| { 3497| 11| (io->tot_len) += MakeDelim(p_stereo, strbuf, &io->bOverflow); 3498| 11| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3499| 11| } 3500| 11| if (str_LineEnd(io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3500:17): [True: 0, False: 11] ------------------ 3501| 0| { 3502| 0| return 1; 3503| 0| } 3504| 11| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3505| 11| } 3506| 767| if (io->bPlainTextTags == 1) ------------------ | Branch (3506:13): [True: 0, False: 767] ------------------ 3507| 0| { 3508| 0| inchi_ios_print_nodisplay(out_file, "/"); /* no abs, inv or racemic stereo */ 3509| 0| } 3510| 767| } 3511| 4.26k| else 3512| 4.26k| { 3513| 4.26k| if (io->bPlainTextTags == 1) ------------------ | Branch (3513:13): [True: 0, False: 4.26k] ------------------ 3514| 0| { 3515| 0| inchi_ios_print_nodisplay( out_file, "////" ); /* sp2, sp3, abs-inv, stereo.type */ 3516| 0| } 3517| 4.26k| } 3518| | 3519| 5.02k| return 0; 3520| 5.02k|} ichiprt1.c:OutputINCHI_IsotopicLayer: 3707| 5.02k|{ 3708| | 3709| 5.02k| if (INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_i_IATOMS])) ------------------ | Branch (3709:9): [True: 545, False: 4.48k] ------------------ 3710| 545| { 3711| | /* isotopic #1: composition -- atoms -- do not output in xml if empty */ 3712| 545| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_ISOT | io->bFhTag, io->szTag1, &io->bAlways, 1); 3713| | /* isotopic atoms without mobile H. 3714| | * Fixed 2004-06-15: always output if not bXml. Note: 3715| | * Previous condition if( bHasIsotopicAtoms[io->iCurTautMode] || bIsotopic && !bXml) 3716| | * did not optput /i in case of only mobile isotopic H 3717| | */ 3718| 545| if ((io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_i_IATOMS]))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3718:13): [True: 545, False: 0] ------------------ 3719| 545| { 3720| 545| szGetTag(IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_ATMS, io->szTag2, &io->bAlways, 1); 3721| 545| inchi_strbuf_reset(strbuf); 3722| 545| io->tot_len = 0; 3723| | /*if ( bHasIsotopicAtoms[io->iCurTautMode] )*/ 3724| 545| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3724:17): [True: 451, False: 94] ------------------ 3725| 451| { 3726| 451| io->tot_len2 = str_IsoAtoms(io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3727| 451| io->bOutType, io->TAUT_MODE, io->num_components, io->bAbcNumbers, 3728| 451| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers); 3729| 451| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3730| 451| } 3731| 94| else 3732| 94| { 3733| 94| io->tot_len2 = io->tot_len; 3734| 94| } 3735| | 3736| 545| io->tot_len = io->tot_len2; 3737| 545| if (str_LineEnd(io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3737:17): [True: 0, False: 545] ------------------ 3738| 0| { 3739| 0| return 1; 3740| 0| } 3741| 545| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3742| 545| } 3743| | 3744| | /* isotopic #1a: composition -- exchangeable isotopic H (mobile H only) */ 3745| | /*if ( !io->bSecondNonTautPass && bHasIsoH )*/ 3746| 545| if ((io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_h_H_ATOMS]))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3746:13): [True: 74, False: 471] ------------------ 3747| 74| { 3748| 74| szGetTag(IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_XCGA, io->szTag2, &io->bAlways, 1); 3749| 74| inchi_strbuf_reset(strbuf); 3750| 74| io->tot_len = 0; 3751| 74| (io->tot_len) += MakeIsoHString(io->num_iso_H, strbuf, io->TAUT_MODE, &io->bOverflow); 3752| 74| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3753| 74| if (str_LineEnd(io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3753:17): [True: 0, False: 74] ------------------ 3754| 0| { 3755| 0| return 2; 3756| 0| } 3757| 74| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3758| 74| } 3759| | 3760| | /*************************************************** 3761| | * 3762| | * Isotopic stereo 3763| | * 3764| | ***************************************************/ 3765| | 3766| | /*if ( bIsotopicStereo[io->iCurTautMode] )*/ 3767| 545| if (INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS]) || ------------------ | Branch (3767:13): [True: 40, False: 505] ------------------ 3768| 505| INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS]) || ------------------ | Branch (3768:13): [True: 65, False: 440] ------------------ 3769| 440| INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV]) || ------------------ | Branch (3769:13): [True: 2, False: 438] ------------------ 3770| 438| INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE])) ------------------ | Branch (3770:13): [True: 7, False: 431] ------------------ 3771| 114| { 3772| | /* stereo */ 3773| 114| szGetTag(IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_STER, io->szTag2, &io->bAlways, 1); 3774| | 3775| | /************************ 3776| | isotopic #2: sp2 3777| | ************************/ 3778| | /*if ( bIsotopicStereoSp2[io->iCurTautMode] )*/ 3779| 114| if ((io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS]))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3779:17): [True: 40, False: 74] ------------------ 3780| 40| { 3781| 40| szGetTag(IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_DBND, io->szTag3, &io->bAlways, 1); 3782| 40| inchi_strbuf_reset(strbuf); 3783| 40| io->tot_len = 0; 3784| 40| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3784:21): [True: 40, False: 0] ------------------ 3785| 40| { 3786| 40| io->tot_len = str_IsoSp2(io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3787| 40| io->bOutType, io->TAUT_MODE, io->num_components, 3788| 40| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers); 3789| 40| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3790| 40| } 3791| 40| if (str_LineEnd(io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3791:21): [True: 0, False: 40] ------------------ 3792| 0| { 3793| 0| return 3; 3794| 0| } 3795| 40| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3796| 40| } 3797| 74| else 3798| 74| { 3799| 74| if (io->bPlainTextTags == 1) ------------------ | Branch (3799:21): [True: 0, False: 74] ------------------ 3800| 0| inchi_ios_print_nodisplay(out_file, "/"); /* iso sp2 */ 3801| 74| } 3802| | 3803| | /************************ 3804| | isotopic #3: sp3 3805| | ************************/ 3806| | /*if ( bIsotopicStereoSp3[io->iCurTautMode] )*/ 3807| 114| if ((io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS]))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3807:17): [True: 65, False: 49] ------------------ 3808| 65| { 3809| 65| io->bRelRac = io->bIsotopicRelativeStereo[io->iCurTautMode] || io->bIsotopicRacemicStereo[io->iCurTautMode]; ------------------ | Branch (3809:31): [True: 0, False: 65] | Branch (3809:80): [True: 0, False: 65] ------------------ 3810| | 3811| 65| szGetTag(IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_SP3S, io->szTag3, &io->bAlways, 1); 3812| 65| inchi_strbuf_reset(strbuf); 3813| 65| io->tot_len = 0; 3814| 65| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3814:21): [True: 65, False: 0] ------------------ 3815| 65| { 3816| 65| io->tot_len = str_IsoSp3(io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3817| 65| io->bOutType, io->TAUT_MODE, io->num_components, io->bRelRac, 3818| 65| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers); 3819| 65| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3820| 65| } 3821| 65| if (str_LineEnd(io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3821:21): [True: 0, False: 65] ------------------ 3822| 0| { 3823| 0| return 5; 3824| 0| } 3825| 65| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3826| 65| } 3827| 49| else 3828| 49| { 3829| 49| if (io->bPlainTextTags == 1) ------------------ | Branch (3829:21): [True: 0, False: 49] ------------------ 3830| 0| { 3831| 0| inchi_ios_print_nodisplay(out_file, "/"); /* iso-sp3 */ 3832| 0| } 3833| 49| } 3834| | 3835| | /* isotopic #4: abs inverted */ 3836| 114| if ((io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV]))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3836:17): [True: 2, False: 112] ------------------ 3837| 2| { 3838| 2| szGetTag(IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_INVS, io->szTag3, &io->bAlways, 1); 3839| 2| inchi_strbuf_reset(strbuf); 3840| 2| io->tot_len = 0; 3841| 2| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3841:21): [True: 2, False: 0] ------------------ 3842| 2| { 3843| 2| io->tot_len = str_IsoStereoAbsInv(io->pINChISort, strbuf, 3844| 2| &io->bOverflow, io->bOutType, io->num_components); 3845| 2| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3846| 2| } 3847| 2| if (str_LineEnd(io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3847:21): [True: 0, False: 2] ------------------ 3848| 0| { 3849| 0| return 5; 3850| 0| } 3851| 2| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3852| 2| } 3853| 112| else 3854| 112| { 3855| 112| if (io->bPlainTextTags == 1) ------------------ | Branch (3855:21): [True: 0, False: 112] ------------------ 3856| 0| { 3857| 0| inchi_ios_print_nodisplay(out_file, "/"); 3858| 0| } 3859| 112| } 3860| | 3861| | /* isotopic #5: stereo type. Do not output if it has already been output in non-iso */ 3862| 114| if ((io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE]))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3862:17): [True: 19, False: 95] ------------------ 3863| 19| { 3864| 19| const char *p_stereo = io->bIsotopicRelativeStereo[io->iCurTautMode] ? x_rel : io->bIsotopicRacemicStereo[io->iCurTautMode] ? x_rac ------------------ | Branch (3864:40): [True: 3, False: 16] | Branch (3864:96): [True: 1, False: 15] ------------------ 3865| 16| : x_abs; 3866| 19| szGetTag(IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_TYPS, io->szTag3, &io->bAlways, 1); 3867| 19| inchi_strbuf_reset(strbuf); 3868| 19| io->tot_len = 0; 3869| 19| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3869:21): [True: 19, False: 0] ------------------ 3870| 19| { 3871| 19| io->tot_len += MakeDelim(p_stereo, strbuf, &io->bOverflow); 3872| 19| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3873| 19| } 3874| 19| if (str_LineEnd(io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (3874:21): [True: 0, False: 19] ------------------ 3875| 0| { 3876| 0| return 6; 3877| 0| } 3878| 19| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3879| 19| } 3880| 114| if (io->bPlainTextTags == 1) ------------------ | Branch (3880:17): [True: 0, False: 114] ------------------ 3881| 0| { 3882| 0| inchi_ios_print_nodisplay(out_file, "/"); /* no abs, inv or racemic stereo */ 3883| 0| } 3884| 114| } 3885| 431| else 3886| 431| { 3887| | /* no isotopic stereo */ 3888| 431| if (io->bPlainTextTags == 1) ------------------ | Branch (3888:17): [True: 0, False: 431] ------------------ 3889| 0| { 3890| 0| inchi_ios_print_nodisplay(out_file, "////"); /* sp3, sp2, abs-inv, stereo.type */ 3891| 0| } 3892| 431| } 3893| 545| } 3894| 4.48k| else 3895| 4.48k| { 3896| 4.48k| if (io->bPlainTextTags == 1) ------------------ | Branch (3896:13): [True: 0, False: 4.48k] ------------------ 3897| 0| { 3898| 0| inchi_ios_print_nodisplay(out_file, "///"); /* isotopic composition, sp2, sp3 */ 3899| 0| } 3900| 4.48k| if (io->bPlainTextTags == 1) ------------------ | Branch (3900:13): [True: 0, False: 4.48k] ------------------ 3901| 0| { 3902| 0| inchi_ios_print_nodisplay(out_file, "//"); /* inv or racemic stereo */ 3903| 0| } 3904| 4.48k| } 3905| | 3906| 5.02k|#if (CANON_FIXH_TRANS == 1) 3907| 5.02k| if (io->bOutType == OUT_NONTAUT && io->bOutputType == OUT_TN && io->bSecondNonTautPass && ------------------ | | 920| 5.02k|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 585| 10.0k|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ if (io->bOutType == OUT_NONTAUT && io->bOutputType == OUT_TN && io->bSecondNonTautPass && ------------------ | | 583| 5.02k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (3907:9): [True: 0, False: 5.02k] | Branch (3907:40): [True: 0, False: 0] | Branch (3907:69): [True: 0, False: 0] ------------------ 3908| 0| INCHI_SEGM_FILL == INChI_SegmentAction(io->sDifSegs[DIFL_F][DIFS_o_TRANSP])) ------------------ | Branch (3908:9): [True: 0, False: 0] ------------------ 3909| 0| { 3910| | /* find and print non-tautomeric components transposition, if non-trivial */ 3911| 0| AT_NUMB *nTrans_n, *nTrans_s; 3912| | 3913| 0| if (0 < bin_AuxTautTrans(io->pINChISort, io->pINChISort2, &nTrans_n, &nTrans_s, io->bOutType, io->num_components)) ------------------ | Branch (3913:13): [True: 0, False: 0] ------------------ 3914| 0| { 3915| | /* a non-trivial transposition does exist; output start tag */ 3916| 0| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_TRNS | io->bFhTag, io->szTag1, &io->bAlways, 1); 3917| 0| inchi_strbuf_reset(strbuf); 3918| 0| io->tot_len = 0; 3919| | /* print the transposition, cycle after cycle */ 3920| 0| io->tot_len = str_AuxTautTrans(pCG, nTrans_n, nTrans_s, strbuf, 3921| 0| &io->bOverflow, io->TAUT_MODE, io->num_components); 3922| 0| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3923| 0| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -1, io->bPlainTextTags)) ------------------ | Branch (3923:17): [True: 0, False: 0] ------------------ 3924| 0| { 3925| 0| return 7; 3926| 0| } 3927| 0| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 3928| | /* detected transposition */ 3929| 0| (*io->pSortPrintINChIFlags) |= 3930| 0| (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_TRANSPOS_BAS : FLAG_SORT_PRINT_TRANSPOS_REC; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_TRANSPOS_BAS : FLAG_SORT_PRINT_TRANSPOS_REC; ------------------ | | 660| 0|#define FLAG_SORT_PRINT_TRANSPOS_BAS 1 /* transposition in the main InChI layer */ ------------------ (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_TRANSPOS_BAS : FLAG_SORT_PRINT_TRANSPOS_REC; ------------------ | | 661| 0|#define FLAG_SORT_PRINT_TRANSPOS_REC 2 /* transposition in the reconnected InChI layer */ ------------------ | Branch (3930:17): [True: 0, False: 0] ------------------ 3931| 0| } 3932| 0| else 3933| 0| { 3934| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3934:17): [True: 0, False: 0] ------------------ 3935| 0| { 3936| 0| inchi_ios_print_nodisplay(out_file, "/"); 3937| 0| } 3938| 0| } 3939| 0| } 3940| 5.02k|#endif 3941| | 3942| 5.02k| return 0; 3943| 5.02k|} ichiprt1.c:OutputINCHI_FixedHLayerWithSublayers: 3956| 5.02k|{ 3957| | 3958| 5.02k| *then_goto_repeat = 0; 3959| | 3960| 5.02k| if (io->bOutType == OUT_TN && ------------------ | | 583| 10.0k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (3960:9): [True: 5.02k, False: 0] ------------------ 3961| 5.02k| !(io->bSecondNonTautPass) && ------------------ | Branch (3961:9): [True: 5.02k, False: 0] ------------------ 3962| 5.02k| io->bNonTautIsIdenticalToTaut && ------------------ | Branch (3962:9): [True: 4.95k, False: 73] ------------------ 3963| 4.95k| io->bTautomeric && ------------------ | Branch (3963:9): [True: 1.16k, False: 3.79k] ------------------ 3964| 1.16k| io->bNonTautomeric) ------------------ | Branch (3964:9): [True: 0, False: 1.16k] ------------------ 3965| 0| { 3966| | /* Fixed-H layer is empty in the Identifier */ 3967| 0| (*io->pSortPrintINChIFlags) |= 3968| 0| (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 662| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 663| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ | Branch (3968:13): [True: 0, False: 0] ------------------ 3969| 0| (*io->pSortPrintINChIFlags) |= 3970| 0| (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 664| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */ ------------------ (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 665| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */ ------------------ | Branch (3970:13): [True: 0, False: 0] ------------------ 3971| 0| } 3972| | 3973| 5.02k| if (io->bOutType == OUT_TN && ------------------ | | 583| 10.0k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (3973:9): [True: 5.02k, False: 0] ------------------ 3974| 5.02k| !io->bNonTautIsIdenticalToTaut && /* added 2004-10-04 Fix16 */ ------------------ | Branch (3974:9): [True: 73, False: 4.95k] ------------------ 3975| |#ifdef OLD_ITEM_DISCOVERY 3976| | io->bTautomeric && 3977| | io->bNonTautomeric && 3978| |#endif 3979| 73| INChI_SegmentAction(io->sDifSegs[DIFL_F][DIFS_f_FORMULA]) ------------------ | Branch (3979:9): [True: 0, False: 73] ------------------ 3980| | /* special case: removed isolated H(+): */ 3981| | /* || io->iCurTautMode == TAUT_YES && num_comp[TAUT_YES] < num_comp[TAUT_NON] && 3982| | 0 < num_comp[TAUT_NON]*/ 3983| 5.02k| ) 3984| | 3985| 0| { 3986| | /* add the second (non-tautomeric) output */ 3987| 0| io->bOutType = OUT_NONTAUT; /* pick up only non-tautomeric representation of tautomeric */ ------------------ | | 920| 0|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ 3988| 0| io->iCurTautMode = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3989| 0| io->pINChISort = io->pINChISortTautAndNonTaut[TAUT_NON]; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3990| 0| io->bSecondNonTautPass = 1; 3991| 0| io->nCurINChISegment = DIFL_F; 3992| 0| io->num_components = io->num_comp[io->iCurTautMode]; /* number of components could change due to removal of isolated H(+) from tautomeric */ 3993| 0| io->bFhTag = IL_FIXH; 3994| 0| szGetTag(IdentLbl, io->nTag, io->bTag1 = io->bFhTag, io->szTag1, &io->bAlways, 1); 3995| | /***** constitution non-taut: dot-disconnected Hill formulas: -- only if different */ 3996| 0| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_FMLF | io->bFhTag, io->szTag1, &io->bAlways, 1); 3997| 0| inchi_strbuf_reset(strbuf); 3998| 0| io->tot_len = 0; 3999| 0| io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_f_FORMULA]); 4000| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (4000:13): [True: 0, False: 0] ------------------ 4001| 0| { 4002| 0| io->tot_len2 = str_HillFormula2(io->pINChISort, io->pINChISort2, 4003| 0| strbuf, &io->bOverflow, io->bOutType, 4004| 0| io->num_components, io->bUseMulipliers); 4005| 0| if (io->n_pzz > 0 && io->n_zy > 0) ------------------ | Branch (4005:17): [True: 0, False: 0] | Branch (4005:34): [True: 0, False: 0] ------------------ 4006| 0| { 4007| 0| MergeZzInHillFormula(strbuf); 4008| 0| } 4009| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 4010| 0| } 4011| 0| else 4012| 0| { 4013| 0| io->tot_len2 = io->tot_len; 4014| 0| } 4015| 0| io->tot_len = io->tot_len2; 4016| 0| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (4016:13): [True: 0, False: 0] ------------------ 4017| 0| { 4018| 0| return 1; 4019| 0| } 4020| 0| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 4021| | 4022| 0| io->nSegmAction = INChI_SegmentAction(io->sDifSegs[io->nCurINChISegment][DIFS_h_H_ATOMS]); 4023| | 4024| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (4024:13): [True: 0, False: 0] ------------------ 4025| 0| { 4026| 0| szGetTag(IdentLbl, io->nTag, io->bTag1 = IL_HFIX | io->bFhTag, io->szTag1, &io->bAlways, 1); 4027| 0| inchi_strbuf_reset(strbuf); 4028| 0| io->tot_len = 0; /* open H-fixed */ 4029| | /* output the second non-tautomeric item: fixed H -- do not output in xml if empty */ 4030| 0| io->tot_len2 = str_FixedH_atoms(io->pINChISort, strbuf, 4031| 0| &io->bOverflow, io->bOutType, io->ATOM_MODE, 4032| 0| io->num_components, io->bUseMulipliers); 4033| 0| io->tot_len = io->tot_len2; 4034| 0| if (str_LineEnd(io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags)) ------------------ | Branch (4034:17): [True: 0, False: 0] ------------------ 4035| 0| { 4036| 0| return 2; 4037| 0| } 4038| 0| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 4039| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 4040| 0| } 4041| 0| *then_goto_repeat = 1; 4042| 0| return 0; 4043| 0| } 4044| | 4045| 5.02k| else 4046| 5.02k| { 4047| 5.02k| if (io->bOutType == OUT_NONTAUT && io->bOutputType == OUT_TN && io->bSecondNonTautPass /* && io->bTautomeric && io->bNonTautomeric*/) ------------------ | | 920| 5.02k|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 585| 10.0k|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ if (io->bOutType == OUT_NONTAUT && io->bOutputType == OUT_TN && io->bSecondNonTautPass /* && io->bTautomeric && io->bNonTautomeric*/) ------------------ | | 583| 5.02k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (4047:13): [True: 0, False: 5.02k] | Branch (4047:44): [True: 0, False: 0] | Branch (4047:73): [True: 0, False: 0] ------------------ 4048| 0| { 4049| | /* the second (non-taut) output has been done; restore variables */ 4050| 0| io->bOutType = OUT_TN; ------------------ | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ 4051| 0| io->iCurTautMode = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4052| 0| io->pINChISort = io->pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4053| 0| io->bSecondNonTautPass = 0; 4054| 0| io->num_components = io->num_comp[io->iCurTautMode]; 4055| 0| if (!io->bNonTautNonIsoIdentifierNotEmpty) ------------------ | Branch (4055:17): [True: 0, False: 0] ------------------ 4056| 0| { 4057| | /* Fixed-H layer is empty in the Identifier */ 4058| 0| (*io->pSortPrintINChIFlags) |= (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (*io->pSortPrintINChIFlags) |= (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 662| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ (*io->pSortPrintINChIFlags) |= (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 663| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ | Branch (4058:48): [True: 0, False: 0] ------------------ 4059| 0| } 4060| 0| if (!io->bNonTautIsoIdentifierNotEmpty) ------------------ | Branch (4060:17): [True: 0, False: 0] ------------------ 4061| 0| { 4062| | /* Fixed-H layer is empty in the Identifier */ 4063| 0| (*io->pSortPrintINChIFlags) |= (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (*io->pSortPrintINChIFlags) |= (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 664| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */ ------------------ (*io->pSortPrintINChIFlags) |= (*INCHI_basic_or_INCHI_reconnected == INCHI_BAS) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 665| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */ ------------------ | Branch (4063:48): [True: 0, False: 0] ------------------ 4064| 0| } 4065| 0| io->bFhTag = 0; 4066| 0| } 4067| 5.02k| } 4068| | 4069| 5.02k| return 0; 4070| 5.02k|} ichiprt1.c:OutputINCHI_PolymerLayer: 4084| 5.02k|{ 4085| 5.02k| int i, err = 0; 4086| 5.02k| int nunits2 = 0; 4087| 5.02k| int n_used_stars = 0; 4088| 5.02k| int *cano_nums = NULL, *compnt_nums = NULL, *unum = NULL, *old_stars = NULL; 4089| 5.02k| OAD_PolymerUnit *u = NULL; 4090| 5.02k| OAD_PolymerUnit **units2 = NULL; 4091| 5.02k| OAD_Polymer *p = NULL; 4092| 5.02k| OAD_AtProps *aprops = NULL; 4093| 5.02k| int nat, num_inp_bonds; 4094| 5.02k| inp_ATOM *at = NULL; 4095| 5.02k| int is_inchi2inchi = 0; 4096| | 4097| 5.02k| if (!orig_inp_data) ------------------ | Branch (4097:9): [True: 5.02k, False: 0] ------------------ 4098| 5.02k| { 4099| 5.02k| goto exit_function; 4100| 5.02k| } 4101| | 4102| 0| at = orig_inp_data->at; 4103| 0| nat = orig_inp_data->num_inp_atoms; 4104| 0| num_inp_bonds = orig_inp_data->num_inp_bonds; 4105| | 4106| | 4107| 0| if (pOrigStruct && !pOrigStruct->polymer) ------------------ | Branch (4107:9): [True: 0, False: 0] | Branch (4107:24): [True: 0, False: 0] ------------------ 4108| 0| { 4109| 0| return 0; 4110| 0| } 4111| | 4112| 0| if (pOrigStruct) ------------------ | Branch (4112:9): [True: 0, False: 0] ------------------ 4113| 0| { 4114| 0| p = pOrigStruct->polymer; 4115| 0| is_inchi2inchi = !pOrigStruct->szAtoms && !pOrigStruct->szBonds && !pOrigStruct->szCoord; ------------------ | Branch (4115:26): [True: 0, False: 0] | Branch (4115:51): [True: 0, False: 0] | Branch (4115:76): [True: 0, False: 0] ------------------ 4116| | 4117| 0| if (is_inchi2inchi) ------------------ | Branch (4117:13): [True: 0, False: 0] ------------------ 4118| 0| { 4119| 0| err = NOT_YET_I2I_FOR_POLYMERS; ------------------ | | 470| 0|#define NOT_YET_I2I_FOR_POLYMERS 40 ------------------ 4120| 0| goto exit_function; 4121| 0| } 4122| | 4123| | /*OAD_Polymer_DebugTrace( p );*/ 4124| | 4125| | /* Get canonical numbers and numbers-of-components for each original atom */ 4126| 0| cano_nums = (int *)inchi_calloc((long long)pOrigStruct->num_atoms + 1, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 4127| 0| if (!cano_nums) ------------------ | Branch (4127:13): [True: 0, False: 0] ------------------ 4128| 0| { 4129| 0| err = 1; 4130| 0| goto exit_function; 4131| 0| } 4132| 0| compnt_nums = (int *)inchi_calloc((long long)pOrigStruct->num_atoms + 1, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 4133| 0| if (!compnt_nums) ------------------ | Branch (4133:13): [True: 0, False: 0] ------------------ 4134| 0| { 4135| 0| err = 2; 4136| 0| goto exit_function; 4137| 0| } 4138| 0| err = InternallyGetCanoNumsAndComponentNums(pCG, 4139| 0| strbuf, 4140| 0| io, 4141| 0| pOrigStruct->num_atoms, 4142| 0| cano_nums, 4143| 0| compnt_nums); 4144| 0| if (err != 0) ------------------ | Branch (4144:13): [True: 0, False: 0] ------------------ 4145| 0| { 4146| 0| err = 3; 4147| 0| goto exit_function; 4148| 0| } 4149| | 4150| | /* Set atom properties for sorting */ 4151| 0| aprops = (OAD_AtProps *)inchi_calloc((long long)nat + 1, sizeof(OAD_AtProps)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 4152| | /* nat + 1: add extra element for possibe 1-based indexing */ 4153| 0| if (!aprops) ------------------ | Branch (4153:13): [True: 0, False: 0] ------------------ 4154| 0| { 4155| | /* djb-rwth: avoiding memory leak */ 4156| 0| if (cano_nums) ------------------ | Branch (4156:17): [True: 0, False: 0] ------------------ 4157| 0| { 4158| 0| inchi_free(cano_nums); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4159| 0| } 4160| 0| if (compnt_nums) ------------------ | Branch (4160:17): [True: 0, False: 0] ------------------ 4161| 0| { 4162| 0| inchi_free(compnt_nums); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4163| 0| } 4164| 0| if (aprops) ------------------ | Branch (4164:17): [True: 0, False: 0] ------------------ 4165| 0| { 4166| 0| inchi_free(aprops); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4167| 0| } 4168| 0| return 0; 4169| 0| } 4170| | 4171| | /* Note that aprops[] is in orig_atoms domain (0-based) and */ 4172| | /* u (from units) are in cano_nums domain (1-based) */ 4173| | /* Supply non-NULL cano_nums to adjust the domains (base will be adjusted at place) */ 4174| 0| OAD_Polymer_SetAtProps(p, at, nat, &num_inp_bonds, aprops, cano_nums); 4175| | 4176| | /* Make a working copy of polymer units data: units2 is a copy */ 4177| | /* of original polymer units (p->units) with atomic numbers changed */ 4178| | /* to curr canonical ones; atoms in alists sorted; atoms in blists */ 4179| | /* and blists themselves sorted */ 4180| 0| units2 = (OAD_PolymerUnit **)inchi_calloc(p->n, sizeof(OAD_PolymerUnit *)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 4181| | 4182| 0| if (NULL == units2) ------------------ | Branch (4182:13): [True: 0, False: 0] ------------------ 4183| 0| { 4184| 0| err = 3; 4185| 0| goto exit_function; 4186| 0| } 4187| 0| memset(units2, 0, sizeof(*units2)); /* djb-rwth: memset_s C11/Annex K variant? */ 4188| | 4189| 0| old_stars = (int *)inchi_calloc(pOrigStruct->polymer->n_pzz, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 4190| 0| if (NULL == old_stars) ------------------ | Branch (4190:13): [True: 0, False: 0] ------------------ 4191| 0| { 4192| 0| err = 3; 4193| 0| goto exit_function; 4194| 0| } 4195| 0| for (i = 0; i < pOrigStruct->polymer->n_pzz; i++) ------------------ | Branch (4195:21): [True: 0, False: 0] ------------------ 4196| 0| { 4197| 0| old_stars[i] = pOrigStruct->polymer->pzz[i]; 4198| 0| } 4199| | 4200| 0| for (i = 0; i < p->n; i++) ------------------ | Branch (4200:21): [True: 0, False: 0] ------------------ 4201| 0| { 4202| 0| units2[i] = OAD_PolymerUnit_CreateCopy(p->units[i]); 4203| 0| if (NULL == units2[i]) /* djb-rwth: unresolved issue -- revision required? -- units2 properly allocated, and loop index well defined */ ------------------ | Branch (4203:17): [True: 0, False: 0] ------------------ 4204| 0| { 4205| 0| err = 4; 4206| 0| goto exit_function; 4207| 0| } 4208| 0| nunits2 = i + 1; 4209| 0| } 4210| | 4211| | /* unum contains numbers of units (0..p->n) as they go */ 4212| | /* when sorted by alist's in lexicographic order */ 4213| 0| unum = (int *)inchi_calloc(p->n, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 4214| 0| if (NULL == unum) ------------------ | Branch (4214:13): [True: 0, False: 0] ------------------ 4215| 0| { 4216| 0| err = 4; 4217| 0| goto exit_function; 4218| 0| } 4219| | 4220| 0| err = OAD_Polymer_PrepareWorkingSet(p, cano_nums, compnt_nums, units2, unum); 4221| | 4222| 0| if (err != 0) ------------------ | Branch (4222:13): [True: 0, False: 0] ------------------ 4223| 0| { 4224| 0| err = 5; 4225| 0| goto exit_function; 4226| 0| } 4227| | 4228| | /* Prepare polymer substring */ 4229| | 4230| | /* Mark layer beginning */ 4231| 0| inchi_strbuf_printf(strbuf, "%s", "/z"); 4232| | 4233| | /* Print polymer units data */ 4234| 0| n_used_stars = 0; 4235| 0| for (i = 0; i < p->n; i++) ------------------ | Branch (4235:21): [True: 0, False: 0] ------------------ 4236| 0| { 4237| | /* For each unit u ... */ 4238| 0| u = units2[unum[i]]; 4239| | /* djb-rwth: addressing coverity ID #499574 -- all NULL checks already done above */ 4240| 0| err = OutputINCHI_PolymerLayer_SingleUnit(u, 4241| 0| io->bPolymers, 4242| 0| pOrigStruct->polymer->n_pzz, 4243| 0| &n_used_stars, aprops, 4244| 0| cano_nums, 4245| 0| orig_inp_data, 4246| 0| pOrigStruct, strbuf); 4247| 0| if (err) ------------------ | Branch (4247:17): [True: 0, False: 0] ------------------ 4248| 0| { 4249| 0| goto exit_function; 4250| 0| } 4251| 0| if (i < p->n - 1) ------------------ | Branch (4251:17): [True: 0, False: 0] ------------------ 4252| 0| { 4253| 0| inchi_strbuf_printf(strbuf, ";"); 4254| 0| } 4255| 0| } 4256| 0| inchi_ios_print_nodisplay(out_file, "%s%s", strbuf->pStr, pLF); 4257| | 4258| 0| LOG_NO_ARGS("\n******************* (L4184:ichiprt1.c) ********************\n"); 4259| 0| LOG_MULT_ARGS("Polymer Layer start: %s\n", strbuf->pStr); 4260| 0| LOG_NO_ARGS("\n***********************************************************\n"); 4261| | 4262| 5.02k| exit_function: 4263| 5.02k| if (cano_nums) ------------------ | Branch (4263:13): [True: 0, False: 5.02k] ------------------ 4264| 0| { 4265| 0| inchi_free(cano_nums); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4266| 0| } 4267| 5.02k| if (compnt_nums) ------------------ | Branch (4267:13): [True: 0, False: 5.02k] ------------------ 4268| 0| { 4269| 0| inchi_free(compnt_nums); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4270| 0| } 4271| 5.02k| if (aprops) ------------------ | Branch (4271:13): [True: 0, False: 5.02k] ------------------ 4272| 0| { 4273| 0| inchi_free(aprops); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4274| 0| } 4275| 5.02k| if (unum) ------------------ | Branch (4275:13): [True: 0, False: 5.02k] ------------------ 4276| 0| { 4277| 0| inchi_free(unum); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4278| 0| } 4279| 5.02k| if (units2) ------------------ | Branch (4279:13): [True: 0, False: 5.02k] ------------------ 4280| 0| { 4281| 0| for (i = 0; i < nunits2; i++) ------------------ | Branch (4281:25): [True: 0, False: 0] ------------------ 4282| 0| { 4283| 0| OAD_PolymerUnit_Free(units2[i]); 4284| 0| } 4285| 0| inchi_free(units2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4286| 0| } 4287| 5.02k| if (old_stars) ------------------ | Branch (4287:13): [True: 0, False: 5.02k] ------------------ 4288| 0| { 4289| 0| for (i = 0; i < pOrigStruct->polymer->n_pzz; i++) ------------------ | Branch (4289:25): [True: 0, False: 0] ------------------ 4290| 0| pOrigStruct->polymer->pzz[i] = old_stars[i]; 4291| 0| inchi_free(old_stars); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4292| 0| } 4293| 5.02k| } 4294| 5.02k| return err; 4295| 0|} Eql_INChI_Stereo: 24| 370|{ 25| 370| int inv1 = 0, inv2 = 0, len; 26| | 27| 370| if (!s1) ------------------ | Branch (27:9): [True: 0, False: 370] ------------------ 28| 0| { 29| 0| return 0; 30| 0| } 31| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 32| |#else 33| 370| bRelRac = 0; 34| 370|#endif 35| | 36| 370| if (EQL_SP2 == eql1) ------------------ | | 477| 370|#define EQL_SP2 8 ------------------ | Branch (36:9): [True: 121, False: 249] ------------------ 37| 121| { 38| 121| if (( len = s1->nNumberOfStereoBonds ) > 0 && s1->b_parity && s1->nBondAtom1 && s1->nBondAtom2) ------------------ | Branch (38:13): [True: 121, False: 0] | Branch (38:55): [True: 121, False: 0] | Branch (38:71): [True: 121, False: 0] | Branch (38:89): [True: 121, False: 0] ------------------ 39| 121| { 40| 121| if (!s2) ------------------ | Branch (40:17): [True: 38, False: 83] ------------------ 41| 38| { 42| 38| if (EQL_EXISTS == eql2) ------------------ | | 474| 38|#define EQL_EXISTS 1 ------------------ | Branch (42:21): [True: 0, False: 38] ------------------ 43| 0| { 44| | /* find whether double bond stereo exists*/ 45| 0| return 1; 46| 0| } 47| 38| return 0; 48| 38| } 49| 83| if (EQL_SP2 == eql2 && ------------------ | | 477| 83|#define EQL_SP2 8 ------------------ | Branch (49:17): [True: 83, False: 0] ------------------ 50| 83| len == s2->nNumberOfStereoBonds && s2->b_parity && s2->nBondAtom1 && s2->nBondAtom2 && ------------------ | Branch (50:18): [True: 81, False: 2] | Branch (50:53): [True: 81, False: 0] | Branch (50:69): [True: 81, False: 0] | Branch (50:87): [True: 81, False: 0] ------------------ 51| 81| !memcmp( s1->nBondAtom1, s2->nBondAtom1, len * sizeof( s1->nBondAtom1[0] ) ) && ------------------ | Branch (51:18): [True: 78, False: 3] ------------------ 52| 78| !memcmp( s1->nBondAtom2, s2->nBondAtom2, len * sizeof( s1->nBondAtom2[0] ) ) && ------------------ | Branch (52:18): [True: 78, False: 0] ------------------ 53| 78| !memcmp( s1->b_parity, s2->b_parity, len * sizeof( s1->b_parity[0] ) )) ------------------ | Branch (53:18): [True: 78, False: 0] ------------------ 54| 78| { 55| 78| return 1; 56| 78| } 57| 83| } 58| 5| return 0; 59| 121| } 60| | 61| 249| else 62| 249| { 63| 249| if (( eql1 == EQL_SP3 || ( inv1 = ( eql1 == EQL_SP3_INV ) ) ) && ------------------ | | 475| 498|#define EQL_SP3 2 ------------------ if (( eql1 == EQL_SP3 || ( inv1 = ( eql1 == EQL_SP3_INV ) ) ) && ------------------ | | 476| 0|#define EQL_SP3_INV 4 ------------------ | Branch (63:15): [True: 249, False: 0] | Branch (63:34): [True: 0, False: 0] ------------------ 64| 249| ( len = s1->nNumberOfStereoCenters ) > ( bRelRac ? 1 : 0 )) /* djb-rwth: addressing coverity ID #499484 -- bRelRac does not have to be 0 */ ------------------ | Branch (64:13): [True: 234, False: 15] | Branch (64:54): [True: 0, False: 249] ------------------ 65| 234| { 66| | 67| 234| S_CHAR *t_parity1, *t_parity2; 68| 234| AT_NUMB *nNumber1, *nNumber2; 69| 234| if (inv1) ------------------ | Branch (69:17): [True: 0, False: 234] ------------------ 70| 0| { 71| 0| if (s1->nCompInv2Abs) ------------------ | Branch (71:21): [True: 0, False: 0] ------------------ 72| 0| { 73| 0| t_parity1 = s1->t_parityInv; 74| 0| nNumber1 = s1->nNumberInv; 75| 0| } 76| 0| else 77| 0| { 78| 0| return 0; 79| 0| } 80| 0| } 81| 234| else 82| 234| { 83| 234| t_parity1 = s1->t_parity; 84| 234| nNumber1 = s1->nNumber; 85| 234| } 86| 234| if (t_parity1 && nNumber1) ------------------ | Branch (86:17): [True: 234, False: 0] | Branch (86:30): [True: 234, False: 0] ------------------ 87| 234| { 88| 234| if (!s2) ------------------ | Branch (88:21): [True: 53, False: 181] ------------------ 89| 53| { 90| 53| if (EQL_EXISTS == eql2 && ( !inv1 || s1->nCompInv2Abs )) ------------------ | | 474| 53|#define EQL_EXISTS 1 ------------------ | Branch (90:25): [True: 0, False: 53] | Branch (90:49): [True: 0, False: 0] | Branch (90:58): [True: 0, False: 0] ------------------ 91| 0| { 92| | /* the 1st sp3 (inverted if requested) stereo exists*/ 93| 0| return 1; 94| 0| } 95| 53| return 0; /* both sp3 do not exist */ 96| 53| } 97| 181| if (( eql2 == EQL_SP3 || ( inv2 = ( eql2 == EQL_SP3_INV ) ) ) && ------------------ | | 475| 362|#define EQL_SP3 2 ------------------ if (( eql2 == EQL_SP3 || ( inv2 = ( eql2 == EQL_SP3_INV ) ) ) && ------------------ | | 476| 0|#define EQL_SP3_INV 4 ------------------ | Branch (97:23): [True: 181, False: 0] | Branch (97:42): [True: 0, False: 0] ------------------ 98| 181| len == s2->nNumberOfStereoCenters) ------------------ | Branch (98:21): [True: 146, False: 35] ------------------ 99| 146| { 100| 146| if (inv2) ------------------ | Branch (100:25): [True: 0, False: 146] ------------------ 101| 0| { 102| 0| if (s2->nCompInv2Abs && s1->nCompInv2Abs) ------------------ | Branch (102:29): [True: 0, False: 0] | Branch (102:49): [True: 0, False: 0] ------------------ 103| 0| { 104| 0| t_parity2 = s2->t_parityInv; 105| 0| nNumber2 = s2->nNumberInv; 106| 0| } 107| 0| else 108| 0| { 109| | /* if one sp3 is inverted then another should have non-trivial inverted stereo */ 110| 0| return 0; 111| 0| } 112| 0| } 113| 146| else 114| 146| { 115| 146| if (inv1 && !s2->nCompInv2Abs) ------------------ | Branch (115:29): [True: 0, False: 146] | Branch (115:37): [True: 0, False: 0] ------------------ 116| 0| { 117| | /* if one sp3 is inverted then another should have non-trivial inverted stereo */ 118| 0| return 0; 119| 0| } 120| 146| t_parity2 = s2->t_parity; 121| 146| nNumber2 = s2->nNumber; 122| 146| } 123| 146| if (t_parity2 && nNumber2) ------------------ | Branch (123:25): [True: 146, False: 0] | Branch (123:38): [True: 146, False: 0] ------------------ 124| 146| { 125| 146| if (inv1 ^ inv2) ------------------ | Branch (125:29): [True: 0, False: 146] ------------------ 126| 0| { 127| 0| int i, num_inv; 128| 0| for (i = 0, num_inv = 0; i < len; i++) ------------------ | Branch (128:54): [True: 0, False: 0] ------------------ 129| 0| { 130| 0| if (nNumber1[i] != nNumber2[i]) ------------------ | Branch (130:37): [True: 0, False: 0] ------------------ 131| 0| break; 132| 0| if (ATOM_PARITY_WELL_DEF( t_parity1[i] ) && ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 133| 0| ATOM_PARITY_WELL_DEF( t_parity2[i] )) ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 134| 0| { 135| 0| if (3 == t_parity1[i] + t_parity2[i]) ------------------ | Branch (135:41): [True: 0, False: 0] ------------------ 136| 0| { 137| 0| num_inv++; 138| 0| } 139| 0| else 140| 0| { 141| 0| break; 142| 0| } 143| 0| } 144| 0| else 145| 0| if (t_parity1[i] != t_parity2[i]) ------------------ | Branch (145:41): [True: 0, False: 0] ------------------ 146| 0| { 147| 0| break; 148| 0| } 149| 0| } 150| 0| return ( len == i && num_inv > 0 ); ------------------ | Branch (150:38): [True: 0, False: 0] | Branch (150:50): [True: 0, False: 0] ------------------ 151| 0| } 152| 146| else 153| 146| { 154| 146| return !memcmp( t_parity1, t_parity2, len * sizeof( t_parity1[0] ) ) && ------------------ | Branch (154:36): [True: 112, False: 34] ------------------ 155| 112| !memcmp( nNumber1, nNumber2, len * sizeof( nNumber1[0] ) ); ------------------ | Branch (155:33): [True: 91, False: 21] ------------------ 156| 146| } 157| 146| } 158| 146| } 159| 181| } 160| 234| } 161| 249| } 162| | 163| 50| return 0; 164| 370|} Eql_INChI_Isotopic: 169| 628|{ 170| 628| int eq = i1 ------------------ | Branch (170:14): [True: 177, False: 451] ------------------ 171| 177| && i2 ------------------ | Branch (171:16): [True: 177, False: 0] ------------------ 172| 177| && !i1->bDeleted ------------------ | Branch (172:16): [True: 177, False: 0] ------------------ 173| 177| && !i2->bDeleted ------------------ | Branch (173:16): [True: 177, False: 0] ------------------ 174| 177| && ( i1->nNumberOfIsotopicAtoms > 0 || i1->nNumberOfIsotopicTGroups > 0 ) ------------------ | Branch (174:18): [True: 177, False: 0] | Branch (174:52): [True: 0, False: 0] ------------------ 175| 177| && i1->nNumberOfIsotopicAtoms == i2->nNumberOfIsotopicAtoms ------------------ | Branch (175:16): [True: 177, False: 0] ------------------ 176| 177| && i1->nNumberOfIsotopicTGroups == i2->nNumberOfIsotopicTGroups ------------------ | Branch (176:16): [True: 177, False: 0] ------------------ 177| 177| && ( !i1->nNumberOfIsotopicAtoms || ------------------ | Branch (177:18): [True: 0, False: 177] ------------------ 178| 177| (i1->IsotopicAtom && i2->IsotopicAtom && ------------------ | Branch (178:18): [True: 177, False: 0] | Branch (178:38): [True: 177, False: 0] ------------------ 179| 177| !memcmp( i1->IsotopicAtom, i2->IsotopicAtom, ------------------ | Branch (179:17): [True: 175, False: 2] ------------------ 180| 177| i1->nNumberOfIsotopicAtoms * sizeof( i1->IsotopicAtom[0] ) )) ) 181| 175| && ( !i1->nNumberOfIsotopicTGroups || ------------------ | Branch (181:18): [True: 175, False: 0] ------------------ 182| 0| (i1->IsotopicTGroup && i2->IsotopicTGroup && ------------------ | Branch (182:18): [True: 0, False: 0] | Branch (182:40): [True: 0, False: 0] ------------------ 183| 0| !memcmp( i1->IsotopicTGroup, i2->IsotopicTGroup, ------------------ | Branch (183:17): [True: 0, False: 0] ------------------ 184| 0| i1->nNumberOfIsotopicTGroups * sizeof( i1->IsotopicAtom[0] )) ) 185| 175| ); /* djb-rwth: addressing LLVM warnings */ 186| | 187| 628| return eq; 188| 628|} MakeMult: 401| 13.3k|{ 402| 13.3k| char szValue[2048]; 403| 13.3k| int len = 0, len_delim, n; 404| | 405| 13.3k| if (mult == 1 || *bOverflow) ------------------ | Branch (405:9): [True: 10.6k, False: 2.74k] | Branch (405:22): [True: 0, False: 2.74k] ------------------ 406| 10.6k| { 407| 10.6k| return 0; 408| 10.6k| } 409| 2.74k| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 2.74k|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (409:9): [True: 0, False: 2.74k] ------------------ 410| 0| { 411| 0| len += MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, mult ); 412| 0| } 413| 2.74k| else 414| 2.74k| { 415| 2.74k| len += MakeDecNumber( szValue, ( int )sizeof( szValue ), NULL, mult ); 416| 2.74k| } 417| 2.74k| len_delim = (int) strlen( szTailingDelim ); 418| | 419| 2.74k| if (len + len_delim < ( int )sizeof( szValue )) ------------------ | Branch (419:9): [True: 2.74k, False: 0] ------------------ 420| 2.74k| { 421| 2.74k| strcpy(szValue + len, szTailingDelim); 422| 2.74k| n = inchi_strbuf_printf( buf, "%s", szValue ); 423| 2.74k| if (-1 == n) *bOverflow |= 1; ------------------ | Branch (423:13): [True: 0, False: 2.74k] ------------------ 424| 2.74k| return n; 425| | /* 426| | len += len_delim; 427| | if ( len < nLen_szLinearCT ) 428| | { 429| | strcpy( szLinearCT, szValue ); 430| | return len; 431| | }*/ 432| 2.74k| } 433| | 434| 0| *bOverflow |= 1; 435| | 436| 0| return 0; 437| 2.74k|} MakeDelim: 500| 98.5k|{ 501| 98.5k| int n; 502| 98.5k| if (!szTailingDelim || !*szTailingDelim || *bOverflow) ------------------ | Branch (502:9): [True: 0, False: 98.5k] | Branch (502:28): [True: 0, False: 98.5k] | Branch (502:48): [True: 0, False: 98.5k] ------------------ 503| 0| { 504| 0| return 0; 505| 0| } 506| | 507| 98.5k| n = inchi_strbuf_printf( buf, szTailingDelim ); 508| 98.5k| if (-1 == n) ------------------ | Branch (508:9): [True: 0, False: 98.5k] ------------------ 509| 0| { 510| 0| *bOverflow |= 1; 511| 0| } 512| | 513| 98.5k| return n; 514| | /* 515| | len_delim = (int) strlen(szTailingDelim); 516| | if ( len_delim < nLen_szLinearCT ) { 517| | strcpy( szLinearCT, szTailingDelim ); 518| | return len_delim; 519| | } 520| | *bOverflow |= 1; 521| | return 0; 522| | */ 523| 98.5k|} MakeEqStr: 531| 3|{ 532| 3| int n = 0, n0; 533| 3| char szValue[2048]; 534| | 535| 3| if (!szTailingDelim || !*szTailingDelim || *bOverflow) ------------------ | Branch (535:9): [True: 0, False: 3] | Branch (535:28): [True: 0, False: 3] | Branch (535:48): [True: 0, False: 3] ------------------ 536| 0| { 537| 0| return 0; 538| 0| } 539| | 540| 3| n0 = buf->nUsedLength; 541| | 542| 3| if (mult != 1) ------------------ | Branch (542:9): [True: 0, False: 3] ------------------ 543| 0| { 544| 0| n = MakeDecNumber( szValue, ( int )sizeof( szValue ), NULL, mult ); 545| 0| if (-1 == n) ------------------ | Branch (545:13): [True: 0, False: 0] ------------------ 546| 0| { 547| 0| *bOverflow |= 1; 548| 0| return -1; 549| 0| } 550| 0| } 551| 3| if (n > 0) ------------------ | Branch (551:9): [True: 0, False: 3] ------------------ 552| 0| { 553| 0| n = inchi_strbuf_printf( buf, "%-s", szValue ); 554| 0| if (-1 == n) *bOverflow |= 1; ------------------ | Branch (554:13): [True: 0, False: 0] ------------------ 555| 0| } 556| 3| n = inchi_strbuf_printf( buf, "%-s", szTailingDelim ); 557| 3| if (-1 == n) ------------------ | Branch (557:9): [True: 0, False: 3] ------------------ 558| 0| { 559| 0| *bOverflow |= 1; 560| 0| } 561| | 562| 3| return ( buf->nUsedLength - n0 ); 563| 3|} MakeCtStringNew: 581| 4.30k|{ 582| | /* produce output string; */ 583| 4.30k| int nUsedLength0 = 0, nLen = 0, len, i, bOvfl = *bOverflow; 584| 4.30k| char szValue[2048]; 585| 4.30k| int nValue, nDelim, num_H; 586| 4.30k| AT_NUMB *nDfsOrderCT = NULL; 587| 4.30k| int bNoNum_H = ( NULL == nNum_H ); 588| 4.30k| int nNumRingClosures; 589| 4.30k| int bAbcNumbers = ( 0 != ( nCtMode & CT_MODE_ABC_NUMBERS ) ); ------------------ | | 26| 4.30k|#define CT_MODE_ABC_NUMBERS 2 ------------------ 590| 4.30k| int bPredecessors = ( 0 != ( nCtMode & CT_MODE_PREDECESSORS ) ); ------------------ | | 28| 4.30k|#define CT_MODE_PREDECESSORS 8 ------------------ 591| 4.30k| int bCountRingClosures = bAbcNumbers && bPredecessors && ( nCtMode & CT_MODE_ABC_NUM_CLOSURES ); ------------------ | | 30| 0|#define CT_MODE_ABC_NUM_CLOSURES 32 /* in CT_MODE_ABC_NUMBERS output AB1AC2AB instead of AB-AC-A-B */ ------------------ | Branch (591:35): [True: 0, False: 4.30k] | Branch (591:50): [True: 0, False: 0] | Branch (591:67): [True: 0, False: 0] ------------------ 592| | 593| 4.30k| if (nLenCT <= 1) ------------------ | Branch (593:9): [True: 0, False: 4.30k] ------------------ 594| 0| { 595| 0| return 0; /* no atoms or a single atom: no connection table */ 596| 0| } 597| | 598| 4.30k| nUsedLength0 = strbuf->nUsedLength; 599| | 600| | /* make array containing connection string data */ 601| 4.30k| if (!( nDfsOrderCT = GetDfsOrder4CT( pCG, LinearCT, nLenCT, ------------------ | Branch (601:9): [True: 0, False: 4.30k] ------------------ 602| 4.30k| nNum_H, num_atoms, nCtMode ) )) 603| 0| { 604| 0| ( *bOverflow )++; 605| 0| return 0; 606| 0| } 607| | 608| | /* add connection table string */ 609| 4.30k| if (!bOvfl && bAddDelim) ------------------ | Branch (609:9): [True: 4.30k, False: 0] | Branch (609:19): [True: 0, False: 4.30k] ------------------ 610| 0| { 611| 0| inchi_strbuf_printf( strbuf, "," ); 612| 0| } 613| | 614| 4.30k| if (!bOvfl) ------------------ | Branch (614:9): [True: 4.30k, False: 0] ------------------ 615| 4.30k| { 616| 4.30k| nNumRingClosures = 0; 617| 34.9k| for (i = 0; nDfsOrderCT[i]/* && nLen < nLen_szLinearCT*/; i += 3) ------------------ | Branch (617:21): [True: 30.5k, False: 4.30k] ------------------ 618| 30.5k| { 619| 30.5k| nValue = ( nDfsOrderCT[i] > MAX_ATOMS ) ? 0 : nDfsOrderCT[i]; ------------------ | | 15| 30.5k|#define MAX_ATOMS 32766 ------------------ | Branch (619:22): [True: 0, False: 30.5k] ------------------ 620| 30.5k| num_H = nDfsOrderCT[i + 1] ? nDfsOrderCT[i + 1] - 16 : 0; ------------------ | Branch (620:21): [True: 0, False: 30.5k] ------------------ 621| 30.5k| nDelim = nDfsOrderCT[i + 2]; 622| 30.5k| len = 0; 623| | /* delimiter */ 624| 30.5k| if (bPredecessors) ------------------ | Branch (624:17): [True: 0, False: 30.5k] ------------------ 625| 0| { 626| 0| if (bCountRingClosures) ------------------ | Branch (626:21): [True: 0, False: 0] ------------------ 627| 0| { 628| 0| if (nDelim == '-' && i > 3 && bNoNum_H) ------------------ | Branch (628:25): [True: 0, False: 0] | Branch (628:42): [True: 0, False: 0] | Branch (628:51): [True: 0, False: 0] ------------------ 629| 0| { 630| 0| if (!nNumRingClosures) ------------------ | Branch (630:29): [True: 0, False: 0] ------------------ 631| 0| { 632| 0| int j; 633| 0| for (j = i; nDfsOrderCT[j] && '-' == nDfsOrderCT[j + 2]; j += 3) ------------------ | Branch (633:41): [True: 0, False: 0] | Branch (633:59): [True: 0, False: 0] ------------------ 634| 0| { 635| 0| nNumRingClosures++; 636| 0| } 637| 0| if (nNumRingClosures) ------------------ | Branch (637:33): [True: 0, False: 0] ------------------ 638| 0| { 639| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nNumRingClosures ); 640| 0| } 641| 0| nNumRingClosures--; 642| 0| } 643| 0| else 644| 0| { 645| 0| nNumRingClosures--; 646| 0| } 647| 0| } 648| 0| else 649| 0| { 650| 0| nNumRingClosures = 0; 651| 0| } 652| 0| } 653| 0| else if (nDelim && !( bAbcNumbers && nDelim == ',' )) ------------------ | Branch (653:26): [True: 0, False: 0] | Branch (653:39): [True: 0, False: 0] | Branch (653:54): [True: 0, False: 0] ------------------ 654| 0| { 655| 0| if (nNum_H || i > 3) ------------------ | Branch (655:25): [True: 0, False: 0] | Branch (655:35): [True: 0, False: 0] ------------------ 656| 0| { 657| 0| szValue[len++] = nDelim; 658| 0| } 659| 0| } 660| 0| } 661| 30.5k| else 662| 30.5k| { 663| 30.5k| if (nDelim && !( bAbcNumbers && nDelim == '-' )) ------------------ | Branch (663:21): [True: 26.2k, False: 4.30k] | Branch (663:34): [True: 0, False: 26.2k] | Branch (663:49): [True: 0, False: 0] ------------------ 664| 26.2k| { 665| 26.2k| szValue[len++] = nDelim; 666| 26.2k| } 667| 30.5k| } 668| 30.5k| if (bAbcNumbers) ------------------ | Branch (668:17): [True: 0, False: 30.5k] ------------------ 669| 0| { 670| 0| if (nValue || i) ------------------ | Branch (670:21): [True: 0, False: 0] | Branch (670:31): [True: 0, False: 0] ------------------ 671| 0| { 672| | /* the 1st value may be zero in case of presdecessor list */ 673| 0| len += MakeAbcNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nValue ); 674| 0| } 675| 0| if (num_H) ------------------ | Branch (675:21): [True: 0, False: 0] ------------------ 676| 0| { 677| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, num_H ); 678| 0| } 679| 0| } 680| 30.5k| else 681| 30.5k| { 682| 30.5k| if (nValue || i) ------------------ | Branch (682:21): [True: 30.5k, False: 0] | Branch (682:31): [True: 0, False: 0] ------------------ 683| 30.5k| { 684| | /* the 1st value may be zero in case of presdecessor list */ 685| 30.5k| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nValue ); 686| 30.5k| } 687| 30.5k| if (num_H) ------------------ | Branch (687:21): [True: 0, False: 30.5k] ------------------ 688| 0| { 689| 0| szValue[len] = 'H'; 690| 0| len++; 691| 0| if (num_H > 1) ------------------ | Branch (691:25): [True: 0, False: 0] ------------------ 692| 0| { 693| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, num_H ); 694| 0| } 695| 0| } 696| 30.5k| } 697| | 698| 30.5k| if (len > 0) ------------------ | Branch (698:17): [True: 30.5k, False: 0] ------------------ 699| 30.5k| { 700| 30.5k| inchi_strbuf_printf( strbuf, "%s", szValue ); 701| 30.5k| } 702| 30.5k| } 703| 4.30k| } 704| | 705| 4.30k| *bOverflow |= bOvfl; 706| 4.30k| if (nDfsOrderCT) ------------------ | Branch (706:9): [True: 4.30k, False: 0] ------------------ 707| 4.30k| { 708| 4.30k| inchi_free( nDfsOrderCT ); ------------------ | | 1152| 4.30k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 4.30k, False: 0] | | | Branch (1152:50): [Folded, False: 4.30k] | | ------------------ ------------------ 709| 4.30k| } 710| | 711| 4.30k| nLen = strbuf->nUsedLength - nUsedLength0; 712| | 713| 4.30k| return nLen; 714| 4.30k|} MakeHString: 816| 1.86k|{ 817| 1.86k|#define INIT_MIN_NUM_H (-4) 818| 1.86k|#define INIT_MAX_NUM_H 16 819| 1.86k|#define INIT_LEN_NUM_H (INIT_MAX_NUM_H - INIT_MIN_NUM_H + 1) 820| | 821| | /* produce output string; */ 822| 1.86k| int nUsedLength0 = 0, nLen = 0, len, i, iFirst, nVal, bOvfl = *bOverflow; 823| 1.86k| char szValue[2048]; 824| 1.86k| const char *pH; 825| 1.86k| int bNext = 0; 826| | 827| 1.86k| nUsedLength0 = strbuf->nUsedLength; 828| | 829| | /* add connection table string */ 830| 1.86k| if (!( nCtMode & CT_MODE_ABC_NUMBERS ) && !bOvfl && bAddDelim) ------------------ | | 26| 1.86k|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (830:9): [True: 1.86k, False: 0] | Branch (830:47): [True: 1.86k, False: 0] | Branch (830:57): [True: 0, False: 1.86k] ------------------ 831| 0| { 832| 0| inchi_strbuf_printf( strbuf, "," ); 833| | /*if ( nLen_szLinearCT > 1 ) { 834| | strcpy( szLinearCT, "," ); 835| | nLen ++; 836| | } else { 837| | bOvfl = 1; 838| | }*/ 839| 0| } 840| 1.86k| if (!bOvfl && 0 < nLenCT && LinearCT) ------------------ | Branch (840:9): [True: 1.86k, False: 0] | Branch (840:19): [True: 1.86k, False: 0] | Branch (840:33): [True: 1.86k, False: 0] ------------------ 841| 1.86k| { 842| 1.86k| if (nCtMode & CT_MODE_EQL_H_TOGETHER) ------------------ | | 29| 1.86k|#define CT_MODE_EQL_H_TOGETHER 16 ------------------ | Branch (842:13): [True: 1.86k, False: 0] ------------------ 843| 1.86k| { 844| 1.86k| int curMinH = INIT_MIN_NUM_H; ------------------ | | 817| 1.86k|#define INIT_MIN_NUM_H (-4) ------------------ 845| 1.86k| int curMaxH = INIT_MAX_NUM_H; ------------------ | | 818| 1.86k|#define INIT_MAX_NUM_H 16 ------------------ 846| 1.86k| int curLenH = INIT_LEN_NUM_H; ------------------ | | 819| 1.86k|#define INIT_LEN_NUM_H (INIT_MAX_NUM_H - INIT_MIN_NUM_H + 1) | | ------------------ | | | | 818| 1.86k|#define INIT_MAX_NUM_H 16 | | ------------------ | | #define INIT_LEN_NUM_H (INIT_MAX_NUM_H - INIT_MIN_NUM_H + 1) | | ------------------ | | | | 817| 1.86k|#define INIT_MIN_NUM_H (-4) | | ------------------ ------------------ 847| 1.86k| int nInitNumH[INIT_LEN_NUM_H]; 848| 1.86k| int *nNumH = nInitNumH; 849| 1.86k| int numAt, curNumH; 850| 1.86k| int j, bOutOfRange, tot_num_no_H; 851| | /* count atoms H */ 852| 1.86k| do 853| 1.87k| { 854| 1.87k| bOutOfRange = 0; 855| 1.87k| tot_num_no_H = 0; /* number of atoms that have no H */ 856| 1.87k| memset( nNumH, 0, curLenH * sizeof( nNumH[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 857| 295k| for (i = 0; i < nLenCT; i++) ------------------ | Branch (857:29): [True: 293k, False: 1.87k] ------------------ 858| 293k| { 859| 293k| curNumH = LinearCT[i]; 860| 293k| if (curNumH < curMinH) ------------------ | Branch (860:25): [True: 7, False: 293k] ------------------ 861| 7| { 862| 7| curMinH = curNumH; 863| 7| bOutOfRange++; 864| 7| } 865| 293k| else 866| 293k| { 867| 293k| if (curNumH > curMaxH) ------------------ | Branch (867:29): [True: 8, False: 293k] ------------------ 868| 8| { 869| 8| curMaxH = curNumH; 870| 8| bOutOfRange++; 871| 8| } 872| 293k| else 873| 293k| if (!bOutOfRange) ------------------ | Branch (873:33): [True: 286k, False: 6.65k] ------------------ 874| 286k| { 875| 286k| nNumH[curNumH - curMinH] ++; 876| 286k| } 877| 293k| } 878| 293k| tot_num_no_H += !curNumH; 879| 293k| } 880| 1.87k| if (tot_num_no_H == nLenCT) ------------------ | Branch (880:21): [True: 1.14k, False: 737] ------------------ 881| 1.14k| { 882| 1.14k| return nLen; /* empty string */ 883| 1.14k| } 884| 737| if (bOutOfRange) ------------------ | Branch (884:21): [True: 11, False: 726] ------------------ 885| 11| { 886| | /* for debug only */ 887| 11| if (nNumH != nInitNumH) ------------------ | Branch (887:25): [True: 0, False: 11] ------------------ 888| 0| { 889| 0| *bOverflow |= 1; 890| 0| inchi_free( nNumH ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 891| 0| return nLen; 892| 0| } 893| | /* end debug */ 894| 11| curLenH = curMaxH - curMinH + 1; 895| 11| nNumH = (int*) inchi_malloc( curLenH * sizeof( nNumH[0] ) ); ------------------ | | 1143| 11|#define inchi_malloc malloc ------------------ 896| 11| if (!nNumH) ------------------ | Branch (896:25): [True: 0, False: 11] ------------------ 897| 0| { 898| 0| *bOverflow |= 1; 899| 0| return nLen; 900| 0| } 901| 11| } 902| 737| } 903| 1.86k| while (bOutOfRange); /* the loop may be executed 1 or 2 times only */ ------------------ | Branch (903:20): [True: 11, False: 726] ------------------ 904| | 905| 16.8k| for (curNumH = curMinH; curNumH <= curMaxH; curNumH++) ------------------ | Branch (905:37): [True: 16.1k, False: 726] ------------------ 906| 16.1k| { 907| 16.1k| numAt = nNumH[curNumH - curMinH]; /* number of atoms that have curNumH atoms H */ 908| 16.1k| if (!numAt || !curNumH) ------------------ | Branch (908:21): [True: 14.6k, False: 1.45k] | Branch (908:31): [True: 722, False: 734] ------------------ 909| 15.4k| { 910| 15.4k| continue; /* no atom has this number of H or number of H = 0 */ 911| 15.4k| } 912| 734| j = 0; 913| 3.47k| while (j < nLenCT && numAt) ------------------ | Branch (913:24): [True: 3.41k, False: 55] | Branch (913:38): [True: 2.73k, False: 679] ------------------ 914| 2.73k| { 915| 2.73k| if (curNumH == LinearCT[j]) ------------------ | Branch (915:25): [True: 797, False: 1.94k] ------------------ 916| 797| { 917| 797| iFirst = ++j; 918| 797| numAt--; 919| 2.65k| for (; j < nLenCT && curNumH == LinearCT[j] && numAt; j++) ------------------ | Branch (919:32): [True: 2.60k, False: 55] | Branch (919:46): [True: 1.85k, False: 742] | Branch (919:72): [True: 1.85k, False: 0] ------------------ 920| 1.85k| { 921| 1.85k| numAt--; 922| 1.85k| } 923| 797| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 797|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (923:29): [True: 0, False: 797] ------------------ 924| 0| { 925| 0| len = MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, iFirst ); 926| 0| } 927| 797| else 928| 797| { 929| 797| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), bNext ? ITEM_DELIMETER : NULL, iFirst ); ------------------ | | 17| 71|#define ITEM_DELIMETER "," ------------------ | Branch (929:85): [True: 71, False: 726] ------------------ 930| 797| bNext++; /* add a delimiter (comma) before all except the first */ 931| 797| } 932| 797| if (iFirst < j) ------------------ | Branch (932:29): [True: 127, False: 670] ------------------ 933| 127| { 934| | /* output last canonical number */ 935| 127| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 127|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (935:33): [True: 0, False: 127] ------------------ 936| 0| { 937| 0| len += MakeAbcNumber( szValue + len, ( int )sizeof( szValue ), NULL, j ); 938| 0| } 939| 127| else 940| 127| { 941| 127| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, "-", j ); 942| 127| } 943| 127| } 944| 797| if (!numAt || ( nCtMode & CT_MODE_ABC_NUMBERS )) ------------------ | | 26| 63|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (944:29): [True: 734, False: 63] | Branch (944:39): [True: 0, False: 63] ------------------ 945| 734| { 946| | /* add number of H */ 947| | /* output number of H */ 948| 734| nVal = curNumH; 949| 734| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 734|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (949:33): [True: 0, False: 734] ------------------ 950| 0| { 951| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nVal ); 952| 0| } 953| 734| else 954| 734| { 955| 734| pH = nVal > 0 ? "H" : "h"; ------------------ | Branch (955:38): [True: 727, False: 7] ------------------ 956| 734| nVal = abs( nVal ); 957| 734| if (nVal > 1) ------------------ | Branch (957:37): [True: 141, False: 593] ------------------ 958| 141| { 959| 141| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, pH, nVal ); 960| 141| } 961| 593| else 962| 593| { 963| 593| strcpy(szValue + len, pH); 964| 593| len++; 965| 593| } 966| 734| } 967| 734| } 968| | /* add to the output */ 969| 797| if (len > 0) ------------------ | Branch (969:29): [True: 797, False: 0] ------------------ 970| 797| { 971| 797| inchi_strbuf_printf( strbuf, "%-s", szValue ); 972| 797| bNext++; 973| 797| } 974| | /* 975| | if ( 0 <= len && nLen+len < nLen_szLinearCT ) { 976| | if ( len ) { 977| | strcpy( szLinearCT+nLen, szValue ); 978| | nLen += len; 979| | bNext ++; 980| | } 981| | } else { 982| | bOvfl = 1; 983| | break; 984| | }*/ 985| 797| } 986| 1.94k| else 987| 1.94k| { 988| 1.94k| j++; 989| 1.94k| } 990| 2.73k| } 991| 734| } 992| 726| if (nNumH != nInitNumH) ------------------ | Branch (992:17): [True: 11, False: 715] ------------------ 993| 11| { 994| 11| inchi_free( nNumH ); ------------------ | | 1152| 11|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 11, False: 0] | | | Branch (1152:50): [Folded, False: 11] | | ------------------ ------------------ 995| 11| } 996| 726| } 997| 0| else 998| 0| { 999| 0| iFirst = 0; 1000| 0| for (i = iFirst + 1; i <= nLenCT/* && nLen < nLen_szLinearCT*/; i++) ------------------ | Branch (1000:34): [True: 0, False: 0] ------------------ 1001| 0| { 1002| 0| if (i < nLenCT && LinearCT[i] == LinearCT[iFirst]) ------------------ | Branch (1002:21): [True: 0, False: 0] | Branch (1002:35): [True: 0, False: 0] ------------------ 1003| 0| { 1004| 0| continue; 1005| 0| } 1006| | /* output identical values located at i = iFirst..i-1 */ 1007| 0| if (LinearCT[iFirst]) ------------------ | Branch (1007:21): [True: 0, False: 0] ------------------ 1008| 0| { /* output only non-zero values */ 1009| | /* first canonical number */ 1010| 0| nVal = LinearCT[iFirst]; 1011| 0| iFirst++; 1012| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (1012:25): [True: 0, False: 0] ------------------ 1013| 0| { 1014| 0| len = MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, iFirst ); 1015| 0| } 1016| 0| else 1017| 0| { 1018| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), bNext ? ITEM_DELIMETER : NULL, iFirst ); ------------------ | | 17| 0|#define ITEM_DELIMETER "," ------------------ | Branch (1018:81): [True: 0, False: 0] ------------------ 1019| 0| } 1020| 0| if (iFirst < i) ------------------ | Branch (1020:25): [True: 0, False: 0] ------------------ 1021| 0| { 1022| | /* output last canonical number */ 1023| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (1023:29): [True: 0, False: 0] ------------------ 1024| 0| { 1025| 0| len += MakeAbcNumber( szValue + len, ( int )sizeof( szValue ), NULL, i ); 1026| 0| } 1027| 0| else 1028| 0| { 1029| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, "-", i ); 1030| 0| } 1031| 0| } 1032| | /* output number of H */ 1033| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (1033:25): [True: 0, False: 0] ------------------ 1034| 0| { 1035| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nVal ); 1036| 0| } 1037| 0| else 1038| 0| { 1039| 0| pH = nVal > 0 ? "H" : "h"; ------------------ | Branch (1039:30): [True: 0, False: 0] ------------------ 1040| 0| nVal = abs( nVal ); 1041| 0| if (nVal > 1) ------------------ | Branch (1041:29): [True: 0, False: 0] ------------------ 1042| 0| { 1043| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, pH, nVal ); 1044| 0| } 1045| 0| else 1046| 0| { 1047| 0| strcpy(szValue + len, pH); /* djb-rwth: GCC 14 false positive */ 1048| 0| len++; 1049| 0| } 1050| 0| } 1051| 0| if (0 <= len/* && nLen+len < nLen_szLinearCT*/) ------------------ | Branch (1051:25): [True: 0, False: 0] ------------------ 1052| 0| { 1053| 0| if (len) ------------------ | Branch (1053:29): [True: 0, False: 0] ------------------ 1054| 0| { 1055| 0| inchi_strbuf_printf( strbuf, "%-s", szValue ); 1056| | /*strcpy( szLinearCT+nLen, szValue ); 1057| | nLen += len;*/ 1058| 0| bNext++; 1059| 0| } 1060| 0| } 1061| 0| else 1062| 0| { 1063| 0| bOvfl = 1; 1064| 0| break; 1065| 0| } 1066| 0| } 1067| 0| iFirst = i; 1068| 0| } 1069| 0| } 1070| 1.86k| } 1071| 726| *bOverflow |= bOvfl; 1072| | 1073| 726| nLen = strbuf->nUsedLength - nUsedLength0; 1074| 726| return nLen; 1075| | 1076| 1.86k|#undef INIT_MIN_NUM_H 1077| 1.86k|#undef INIT_MAX_NUM_H 1078| 1.86k|#undef INIT_LEN_NUM_H 1079| 1.86k|} MakeTautString: 1138| 1.86k|{ 1139| | /* produce output string; */ 1140| 1.86k| int nUsedLength0 = 0, nLen = 0, len, i, bOvfl = *bOverflow; 1141| 1.86k| char szValue[2048]; 1142| 1.86k| const char *p; 1143| 1.86k| int nValue, nGroupLen, iGroupOutputCount, bCompressed; 1144| | /* make tautomer string */ 1145| 1.86k| if (!nLenCT || !LinearCT || !*LinearCT) ------------------ | Branch (1145:9): [True: 704, False: 1.16k] | Branch (1145:20): [True: 0, False: 1.16k] | Branch (1145:33): [True: 0, False: 1.16k] ------------------ 1146| 704| { 1147| 704| return nLen; 1148| 704| } 1149| | 1150| 1.16k| nUsedLength0 = strbuf->nUsedLength; 1151| | 1152| 1.16k| bCompressed = ( nCtMode & CT_MODE_ABC_NUMBERS ); ------------------ | | 26| 1.16k|#define CT_MODE_ABC_NUMBERS 2 ------------------ 1153| 1.16k| if (!bCompressed && !bOvfl && bAddDelim) ------------------ | Branch (1153:9): [True: 1.16k, False: 0] | Branch (1153:25): [True: 1.16k, False: 0] | Branch (1153:35): [True: 22, False: 1.14k] ------------------ 1154| 22| { 1155| 22| inchi_strbuf_printf( strbuf, "%s", COMMA_EXTRA_SPACE ); ------------------ | | 19| 22|#define COMMA_EXTRA_SPACE "," ------------------ 1156| | /*if ( nLen_szLinearCT > 1+LEN_EXTRA_SPACE ) { 1157| | strcpy( szLinearCT, COMMA_EXTRA_SPACE); 1158| | nLen += 1+LEN_EXTRA_SPACE; 1159| | } else { 1160| | bOvfl = 1; 1161| | }*/ 1162| 22| } 1163| 1.16k| LinearCT++; /* bypass number of tautomeric groups */ 1164| 1.16k| nLenCT--; 1165| | 1166| 1.16k| if (!bOvfl) ------------------ | Branch (1166:9): [True: 1.16k, False: 0] ------------------ 1167| 1.16k| { 1168| 24.5k| for (i = nGroupLen = iGroupOutputCount = 0; i < nLenCT/* && nLen < nLen_szLinearCT*/; i++) ------------------ | Branch (1168:53): [True: 23.3k, False: 1.16k] ------------------ 1169| 23.3k| { 1170| 23.3k| nValue = (int) LinearCT[i]; 1171| 23.3k| if (nGroupLen == iGroupOutputCount) ------------------ | Branch (1171:17): [True: 2.15k, False: 21.2k] ------------------ 1172| 2.15k| { 1173| 2.15k| nGroupLen = nValue; 1174| 2.15k| iGroupOutputCount = 0; 1175| | /* group delimiter (uncompressed) */ 1176| 2.15k| if (!bCompressed) ------------------ | Branch (1176:21): [True: 2.15k, False: 0] ------------------ 1177| 2.15k| { 1178| 2.15k| if (!i) ------------------ | Branch (1178:25): [True: 1.16k, False: 996] ------------------ 1179| 1.16k| { 1180| 1.16k| strcpy( szValue, "(" ); 1181| 1.16k| len = 1; 1182| 1.16k| } 1183| 996| else 1184| 996| { 1185| 996| strcpy( szValue, ")(" ); 1186| 996| len = 2; 1187| 996| } 1188| 2.15k| } 1189| 0| else 1190| 0| { 1191| 0| len = 0; 1192| 0| } 1193| 2.15k| } 1194| 21.2k| else 1195| 21.2k| { 1196| 21.2k| if (bCompressed && iGroupOutputCount >= INCHI_T_NUM_MOVABLE) ------------------ | | 749| 0|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (1196:21): [True: 0, False: 21.2k] | Branch (1196:36): [True: 0, False: 0] ------------------ 1197| 0| { 1198| | /* compressed canon number in Abc */ 1199| 0| len = MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, nValue ); 1200| 0| iGroupOutputCount++; 1201| 0| } 1202| 21.2k| else 1203| 21.2k| { 1204| | /* always output number of hydrogen atoms as a decimal */ 1205| | /* output leading space if: */ 1206| | /* (a) this is the first output value in compressed mode (i==1 && bCompressed) */ 1207| | /* (b) this is not the first output value in non-compressed mode ( iGroupOutputCount && !bCompressed) */ 1208| 21.2k| if (bCompressed) ------------------ | Branch (1208:25): [True: 0, False: 21.2k] ------------------ 1209| 0| { 1210| 0| p = NULL; 1211| 0| len = 0; 1212| 0| switch (iGroupOutputCount) ------------------ | Branch (1212:33): [True: 0, False: 0] ------------------ 1213| 0| { 1214| 0| case 0: ------------------ | Branch (1214:29): [True: 0, False: 0] ------------------ 1215| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), ( i == 1 ) ? ITEM_DELIMETER : NULL, nValue ); ------------------ | | 17| 0|#define ITEM_DELIMETER "," ------------------ | Branch (1215:89): [True: 0, False: 0] ------------------ 1216| 0| break; 1217| 0| case 1: ------------------ | Branch (1217:29): [True: 0, False: 0] ------------------ 1218| 0| p = "-"; 1219| 0| break; 1220| 0| case 2: ------------------ | Branch (1220:29): [True: 0, False: 0] ------------------ 1221| 0| p = "+"; 1222| 0| break; 1223| 0| } 1224| 0| if (p) ------------------ | Branch (1224:29): [True: 0, False: 0] ------------------ 1225| 0| { 1226| 0| switch (nValue) 1227| 0| { 1228| 0| case 0: ------------------ | Branch (1228:33): [True: 0, False: 0] ------------------ 1229| 0| len = 0; 1230| 0| break; 1231| 0| case 1: ------------------ | Branch (1231:33): [True: 0, False: 0] ------------------ 1232| 0| strcpy(szValue, p); 1233| 0| len = (int) strlen( szValue ); 1234| 0| break; 1235| 0| default: ------------------ | Branch (1235:33): [True: 0, False: 0] ------------------ 1236| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), p, nValue ); 1237| 0| break; 1238| 0| } 1239| 0| } 1240| 0| } 1241| 21.2k| else 1242| 21.2k| { 1243| 21.2k| if (iGroupOutputCount >= INCHI_T_NUM_MOVABLE) ------------------ | | 749| 21.2k|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (1243:29): [True: 16.8k, False: 4.31k] ------------------ 1244| 16.8k| { 1245| | /* canonical number of the atom in the tautomeric group */ 1246| 16.8k| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), ITEM_DELIMETER, nValue ); ------------------ | | 17| 16.8k|#define ITEM_DELIMETER "," ------------------ 1247| 16.8k| } 1248| 4.31k| else 1249| 4.31k| { 1250| 4.31k| p = NULL; 1251| 4.31k| len = 0; 1252| 4.31k| if (nValue) ------------------ | Branch (1252:33): [True: 675, False: 3.64k] ------------------ 1253| 675| { 1254| 675| switch (iGroupOutputCount) ------------------ | Branch (1254:41): [True: 675, False: 0] ------------------ 1255| 675| { 1256| 200| case 0: ------------------ | Branch (1256:37): [True: 200, False: 475] ------------------ 1257| 200| p = "H"; 1258| 200| break; 1259| 475| case 1: ------------------ | Branch (1259:37): [True: 475, False: 200] ------------------ 1260| 475| p = "-"; 1261| 475| break; 1262| 0| case 2: ------------------ | Branch (1262:37): [True: 0, False: 675] ------------------ 1263| 0| p = "+"; 1264| 0| break; 1265| 675| } 1266| 675| if (p) ------------------ | Branch (1266:37): [True: 675, False: 0] ------------------ 1267| 675| { 1268| | /* number of hydrogens */ 1269| 675| if (nValue == 1) ------------------ | Branch (1269:41): [True: 366, False: 309] ------------------ 1270| 366| { 1271| 366| strcpy(szValue, p); 1272| 366| len = (int) strlen( szValue ); 1273| 366| } 1274| 309| else 1275| 309| { 1276| 309| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), p, nValue ); 1277| 309| } 1278| 675| } 1279| 675| } 1280| 4.31k| } 1281| 21.2k| } 1282| 21.2k| iGroupOutputCount++; 1283| 21.2k| } 1284| 21.2k| } 1285| | 1286| 23.3k| if (len > 0) ------------------ | Branch (1286:17): [True: 19.7k, False: 3.64k] ------------------ 1287| 19.7k| { 1288| 19.7k| inchi_strbuf_printf( strbuf, "%s", szValue ); 1289| 19.7k| } 1290| | /*if ( 0 <= len && nLen+len < nLen_szLinearCT ) { 1291| | if ( len ) { 1292| | strcpy( szLinearCT+nLen, szValue ); 1293| | nLen += len; 1294| | } 1295| | } else { 1296| | bOvfl = 1; 1297| | break; 1298| | }*/ 1299| 23.3k| } 1300| | 1301| 1.16k| if (!bOvfl && !bCompressed && i) ------------------ | Branch (1301:13): [True: 1.16k, False: 0] | Branch (1301:23): [True: 1.16k, False: 0] | Branch (1301:39): [True: 1.16k, False: 0] ------------------ 1302| 1.16k| { 1303| 1.16k| inchi_strbuf_printf( strbuf, ")" ); 1304| | /*if ( nLen + 1 < nLen_szLinearCT ) { 1305| | strcpy( szLinearCT+nLen, ")" ); 1306| | nLen ++; 1307| | } else { 1308| | bOvfl = 1; 1309| | }*/ 1310| 1.16k| } 1311| 1.16k| } 1312| 1.16k| *bOverflow |= bOvfl; 1313| | 1314| 1.16k| nLen = strbuf->nUsedLength - nUsedLength0; 1315| | 1316| 1.16k| return nLen; 1317| 1.16k|} MakeIsoAtomString: 1671| 453|{ 1672| | /* produce output string; */ 1673| 453| int nUsedLength0 = 0, nLen = 0, len, tot_len, ret, i, j, bOvfl = *bOverflow; 1674| 453| char szValue[2048]; 1675| 453| char *p; 1676| 453| int nValue; 1677| 453| int bAbcNumbers = ( nCtMode & CT_MODE_ABC_NUMBERS ); ------------------ | | 26| 453|#define CT_MODE_ABC_NUMBERS 2 ------------------ 1678| 453| static const char letter[] = "itdh"; 1679| 453| static const char *h[] = { "T", "D", "H" }; 1680| 453| static const char *sign[] = { "-", "+" }; 1681| | 1682| 453| nUsedLength0 = strbuf->nUsedLength; 1683| | 1684| 453| if (!bOvfl) ------------------ | Branch (1684:9): [True: 453, False: 0] ------------------ 1685| 453| { 1686| 2.59k| for (i = 0; i < nNumberOfIsotopicAtoms/* && nLen < nLen_szLinearCT*/; i++) ------------------ | Branch (1686:21): [True: 2.14k, False: 453] ------------------ 1687| 2.14k| { 1688| 2.14k| p = szValue; 1689| 2.14k| tot_len = 0; 1690| 12.8k| for (j = 0; j < 5; j++) ------------------ | Branch (1690:25): [True: 10.7k, False: 2.14k] ------------------ 1691| 10.7k| { 1692| 10.7k| len = 0; 1693| 10.7k| switch (j) ------------------ | Branch (1693:25): [True: 10.7k, False: 0] ------------------ 1694| 10.7k| { 1695| 2.14k| case 0: ------------------ | Branch (1695:21): [True: 2.14k, False: 8.57k] ------------------ 1696| 2.14k| nValue = (int) IsotopicAtom[i].nAtomNumber; 1697| 2.14k| break; 1698| 2.14k| case 1: ------------------ | Branch (1698:21): [True: 2.14k, False: 8.57k] ------------------ 1699| 2.14k| nValue = (int) IsotopicAtom[i].nIsoDifference; 1700| 2.14k| break; 1701| 2.14k| case 2: ------------------ | Branch (1701:21): [True: 2.14k, False: 8.57k] ------------------ 1702| 2.14k| nValue = (int) IsotopicAtom[i].nNum_T; 1703| 2.14k| break; 1704| 2.14k| case 3: ------------------ | Branch (1704:21): [True: 2.14k, False: 8.57k] ------------------ 1705| 2.14k| nValue = (int) IsotopicAtom[i].nNum_D; 1706| 2.14k| break; 1707| 2.14k| case 4: ------------------ | Branch (1707:21): [True: 2.14k, False: 8.57k] ------------------ 1708| 2.14k| nValue = (int) IsotopicAtom[i].nNum_H; 1709| 2.14k| break; 1710| 10.7k| } 1711| 10.7k| if (!j) ------------------ | Branch (1711:21): [True: 2.14k, False: 8.57k] ------------------ 1712| 2.14k| { 1713| | /* atom canonical number */ 1714| 2.14k| len = ( bAbcNumbers ? MakeAbcNumber : MakeDecNumber ) ------------------ | Branch (1714:29): [True: 0, False: 2.14k] ------------------ 1715| 2.14k| ( p, ( int )sizeof( szValue ) - tot_len, 1716| 2.14k| bAbcNumbers ? NULL : ( i ? ITEM_DELIMETER : EXTRA_SPACE ), nValue ------------------ | | 17| 1.69k|#define ITEM_DELIMETER "," ------------------ bAbcNumbers ? NULL : ( i ? ITEM_DELIMETER : EXTRA_SPACE ), nValue ------------------ | | 18| 453|#define EXTRA_SPACE "" ------------------ | Branch (1716:27): [True: 0, False: 2.14k] | Branch (1716:50): [True: 1.69k, False: 453] ------------------ 1717| 2.14k| ); 1718| 2.14k| } 1719| 8.57k| else 1720| 8.57k| { 1721| 8.57k| if (bAbcNumbers) ------------------ | Branch (1721:25): [True: 0, False: 8.57k] ------------------ 1722| 0| { 1723| | /* Abc output */ 1724| 0| switch (j) ------------------ | Branch (1724:33): [True: 0, False: 0] ------------------ 1725| 0| { 1726| 0| case 1: /* nIsoDifference */ ------------------ | Branch (1726:29): [True: 0, False: 0] ------------------ 1727| 0| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, NULL, nValue ); 1728| 0| break; 1729| 0| case 2: /* nNum_T */ ------------------ | Branch (1729:29): [True: 0, False: 0] ------------------ 1730| 0| case 3: /* nNum_D */ ------------------ | Branch (1730:29): [True: 0, False: 0] ------------------ 1731| 0| case 4: /* nNum_H */ ------------------ | Branch (1731:29): [True: 0, False: 0] ------------------ 1732| 0| if (nValue) ------------------ | Branch (1732:37): [True: 0, False: 0] ------------------ 1733| 0| { 1734| 0| if (( int )sizeof( szValue ) - tot_len > 1) ------------------ | Branch (1734:41): [True: 0, False: 0] ------------------ 1735| 0| { 1736| 0| p[len++] = letter[j - 1]; 1737| 0| if (1 == nValue) ------------------ | Branch (1737:45): [True: 0, False: 0] ------------------ 1738| 0| { 1739| 0| p[len] = '\0'; 1740| 0| } 1741| 0| else 1742| 0| { 1743| 0| ret = MakeDecNumber( p + len, ( int )sizeof( szValue ) - tot_len - len, NULL, nValue ); 1744| 0| len = ( ret >= 0 ) ? len + ret : ret; ------------------ | Branch (1744:51): [True: 0, False: 0] ------------------ 1745| 0| } 1746| 0| } 1747| 0| else 1748| 0| { 1749| 0| len = -1; /* overflow */ 1750| 0| } 1751| 0| } 1752| 0| } 1753| 0| } 1754| 8.57k| else 1755| 8.57k| { 1756| 8.57k| if (nValue) ------------------ | Branch (1756:29): [True: 2.39k, False: 6.17k] ------------------ 1757| 2.39k| { 1758| 2.39k| if (j == 1) ------------------ | Branch (1758:33): [True: 564, False: 1.83k] ------------------ 1759| 564| { 1760| | /* Decimal output */ 1761| | /* signed isotopic mass difference */ 1762| 564| int subtract = ( nValue > 0 ); 1763| | /* (n = mass difference) > 0 corresponds to nValue = n+1 */ 1764| | /* subtract 1 from it so that mass difference for 35Cl or 12C is zero */ 1765| 564| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, sign[nValue >= 0], abs( nValue - subtract ) ); 1766| 564| } 1767| 1.83k| else 1768| 1.83k| { 1769| | /* hydrogen isotope */ 1770| 1.83k| if (nValue != 1) ------------------ | Branch (1770:37): [True: 572, False: 1.26k] ------------------ 1771| 572| { 1772| 572| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, h[j - 2], nValue ); 1773| 572| } 1774| 1.26k| else 1775| 1.26k| { 1776| 1.26k| if (( int )sizeof( szValue ) - tot_len > 1) ------------------ | Branch (1776:41): [True: 1.26k, False: 0] ------------------ 1777| 1.26k| { 1778| 1.26k| strcpy(p, h[j - 2]); 1779| 1.26k| len = 1; 1780| 1.26k| } 1781| 0| else 1782| 0| { 1783| 0| len = -1; /* overflow */ 1784| 0| } 1785| 1.26k| } 1786| 1.83k| } 1787| 2.39k| } 1788| 6.17k| else 1789| 6.17k| { 1790| 6.17k| continue; /* do not write zeroes */ 1791| 6.17k| } 1792| 8.57k| } 1793| 8.57k| } 1794| 4.54k| if (len < 0) ------------------ | Branch (1794:21): [True: 0, False: 4.54k] ------------------ 1795| 0| { 1796| 0| bOvfl = 1; 1797| 0| break; 1798| 0| } 1799| 4.54k| tot_len += len; 1800| 4.54k| p += len; 1801| 4.54k| } 1802| 2.14k| inchi_strbuf_printf( strbuf, "%s", szValue ); 1803| | /*if ( nLen+tot_len < nLen_szLinearCT ) 1804| | { 1805| | memcpy( szLinearCT+nLen, szValue, tot_len+1 ); 1806| | nLen += tot_len; 1807| | } 1808| | else 1809| | { 1810| | bOvfl = 1; 1811| | break; 1812| | }*/ 1813| 2.14k| } 1814| 453| } 1815| 453| *bOverflow |= bOvfl; 1816| | 1817| 453| nLen = strbuf->nUsedLength - nUsedLength0; 1818| | 1819| 453| return nLen; 1820| 453|} MakeIsoHString: 1949| 74|{ 1950| | /* produce output string; */ 1951| 74| int nUsedLength0 = 0, nLen = 0, len, tot_len, j, bOvfl = *bOverflow; 1952| | /* djb-rwth: removing redundant variables */ 1953| 74| char szValue[2048]; 1954| 74| char *p; 1955| 74| int nValue; 1956| 74| int bAbcNumbers = ( nCtMode & CT_MODE_ABC_NUMBERS ); ------------------ | | 26| 74|#define CT_MODE_ABC_NUMBERS 2 ------------------ 1957| 74| static const char letter[] = "tdh"; 1958| 74| static const char *h[] = { "T", "D", "H" }; 1959| | 1960| 74| nUsedLength0 = strbuf->nUsedLength; 1961| | 1962| | /* add connection table string */ 1963| | /* djb-rwth: removing redundant code */ 1964| 74| if (!bOvfl) ------------------ | Branch (1964:9): [True: 74, False: 0] ------------------ 1965| 74| { 1966| 74| p = szValue; 1967| 74| tot_len = 0; 1968| 296| for (j = 1; j < 4; j++) ------------------ | Branch (1968:21): [True: 222, False: 74] ------------------ 1969| 222| { 1970| 222| nValue = num_iso_H[NUM_H_ISOTOPES - j];/* j: 1=>T, 2=>D, 3=>1H */ ------------------ | | 25| 222|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ 1971| 222| if (nValue) ------------------ | Branch (1971:17): [True: 96, False: 126] ------------------ 1972| 96| { 1973| 96| if (bAbcNumbers) ------------------ | Branch (1973:21): [True: 0, False: 96] ------------------ 1974| 0| { 1975| 0| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, NULL, nValue ); 1976| 0| if (len > 0) ------------------ | Branch (1976:25): [True: 0, False: 0] ------------------ 1977| 0| { 1978| | /* make sure overflow has not happened */ 1979| 0| if (( int )sizeof( szValue ) - tot_len - len > 1) ------------------ | Branch (1979:29): [True: 0, False: 0] ------------------ 1980| 0| { 1981| 0| p[len++] = letter[j - 1]; 1982| 0| p[len] = '\0'; 1983| 0| } 1984| 0| else 1985| 0| { 1986| 0| len = -1; /* overflow */ 1987| 0| } 1988| 0| } 1989| 0| } 1990| 96| else 1991| 96| { 1992| | /* hydrogen isotope */ 1993| 96| if (nValue != 1) ------------------ | Branch (1993:25): [True: 44, False: 52] ------------------ 1994| 44| { 1995| 44| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, h[j - 1], nValue ); 1996| 44| } 1997| 52| else 1998| 52| { 1999| 52| if (( int )sizeof( szValue ) - tot_len > 1) ------------------ | Branch (1999:29): [True: 52, False: 0] ------------------ 2000| 52| { 2001| 52| strcpy(p, h[j - 1]); 2002| 52| len = 1; 2003| 52| } 2004| 0| else 2005| 0| { 2006| 0| len = -1; /* overflow */ 2007| 0| } 2008| 52| } 2009| 96| } 2010| 96| } 2011| 126| else 2012| 126| { 2013| 126| continue; /* do not write zeroes */ 2014| 126| } 2015| 96| if (len < 0) ------------------ | Branch (2015:17): [True: 0, False: 96] ------------------ 2016| 0| { 2017| 0| bOvfl = 1; 2018| 0| break; 2019| 0| } 2020| 96| p += len; 2021| 96| tot_len += len; 2022| 96| } 2023| 74| inchi_strbuf_printf( strbuf, "%s", szValue ); 2024| | /*if ( nLen+tot_len < nLen_szLinearCT ) { 2025| | memcpy( szLinearCT+nLen, szValue, tot_len+1 ); 2026| | nLen += tot_len; 2027| | } else { 2028| | bOvfl = 1; 2029| | }*/ 2030| 74| } 2031| 74| *bOverflow |= bOvfl; 2032| | 2033| 74| nLen = strbuf->nUsedLength - nUsedLength0; 2034| | 2035| 74| return nLen; 2036| 74|} MakeStereoString: 2048| 907|{ 2049| | /* produce output string; */ 2050| 907| int nUsedLength0 = 0, nLen = 0, len, tot_len, i, j, bOvfl = *bOverflow; 2051| 907| char szValue[2048]; 2052| 907| char *p; 2053| 907| int nValue; 2054| 907| static const char parity_char[] = "!-+u?"; 2055| | 2056| 907| nUsedLength0 = strbuf->nUsedLength; 2057| 907| bAddDelim = 0; 2058| | 2059| 907| if (!bOvfl) ------------------ | Branch (2059:9): [True: 907, False: 0] ------------------ 2060| 907| { 2061| 2.26k| for (i = 0; i < nLenCT/* && nLen < nLen_szLinearCT*/; i++) ------------------ | Branch (2061:21): [True: 1.35k, False: 907] ------------------ 2062| 1.35k| { 2063| 1.35k| p = szValue; 2064| 1.35k| tot_len = 0; 2065| 5.43k| for (j = 0; j < 3; j++) ------------------ | Branch (2065:25): [True: 4.07k, False: 1.35k] ------------------ 2066| 4.07k| { 2067| 4.07k| if (j == 0 && at1) ------------------ | Branch (2067:21): [True: 1.35k, False: 2.71k] | Branch (2067:31): [True: 1.35k, False: 0] ------------------ 2068| 1.35k| { 2069| 1.35k| nValue = (int) at1[i]; 2070| 1.35k| } 2071| 2.71k| else 2072| 2.71k| { 2073| 2.71k| if (j == 1 && at2) ------------------ | Branch (2073:25): [True: 1.35k, False: 1.35k] | Branch (2073:35): [True: 670, False: 688] ------------------ 2074| 670| { 2075| 670| nValue = (int) at2[i]; 2076| 670| } 2077| 2.04k| else 2078| 2.04k| { 2079| 2.04k| if (j == 2 && parity) ------------------ | Branch (2079:29): [True: 1.35k, False: 688] | Branch (2079:39): [True: 1.35k, False: 0] ------------------ 2080| 1.35k| { 2081| 1.35k| nValue = (int) parity[i]; 2082| 1.35k| } 2083| 688| else 2084| 688| { 2085| 688| continue; 2086| 688| } 2087| 2.04k| } 2088| 2.71k| } 2089| 3.38k| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 26| 3.38k|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (2089:21): [True: 0, False: 3.38k] ------------------ 2090| 0| { 2091| 0| len = ( j == 2 ? MakeDecNumber : MakeAbcNumber )( p, ( int )sizeof( szValue ) - tot_len, NULL, nValue ); ------------------ | Branch (2091:29): [True: 0, False: 0] ------------------ 2092| 0| } 2093| 3.38k| else 2094| 3.38k| { 2095| 3.38k| if (j < 2) ------------------ | Branch (2095:25): [True: 2.02k, False: 1.35k] ------------------ 2096| 2.02k| { 2097| 2.02k| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, tot_len ? "-" : ( i || bAddDelim ) ? ITEM_DELIMETER : NULL, nValue ); ------------------ | | 17| 451|#define ITEM_DELIMETER "," ------------------ | Branch (2097:85): [True: 670, False: 1.35k] | Branch (2097:103): [True: 451, False: 907] | Branch (2097:108): [True: 0, False: 907] ------------------ 2098| 2.02k| } 2099| 1.35k| else 2100| 1.35k| { 2101| 1.35k| if (tot_len + 1 < ( int )sizeof( szValue )) ------------------ | Branch (2101:29): [True: 1.35k, False: 0] ------------------ 2102| 1.35k| { 2103| 1.35k| *p++ = ( 0 <= nValue && nValue <= 4 ) ? parity_char[nValue] : parity_char[0]; ------------------ | Branch (2103:38): [True: 1.35k, False: 0] | Branch (2103:53): [True: 1.35k, False: 0] ------------------ 2104| 1.35k| *p = '\0'; 2105| 1.35k| len = 1; 2106| 1.35k| } 2107| 0| else 2108| 0| { 2109| 0| len = -1; /* Overflow */ 2110| 0| } 2111| 1.35k| } 2112| 3.38k| } 2113| 3.38k| if (len < 0) ------------------ | Branch (2113:21): [True: 0, False: 3.38k] ------------------ 2114| 0| { 2115| 0| bOvfl = 1; 2116| 0| break; 2117| 0| } 2118| 3.38k| p += len; 2119| 3.38k| tot_len += len; 2120| 3.38k| } 2121| | 2122| 1.35k| inchi_strbuf_printf( strbuf, "%s", szValue ); 2123| | /* 2124| | if ( nLen+tot_len < nLen_szLinearCT ) { 2125| | memcpy( szLinearCT+nLen, szValue, tot_len+1 ); 2126| | nLen += tot_len; 2127| | } else { 2128| | bOvfl = 1; 2129| | break; 2130| | }*/ 2131| 1.35k| } 2132| 907| } 2133| 907| *bOverflow |= bOvfl; 2134| | 2135| 907| nLen = strbuf->nUsedLength - nUsedLength0; 2136| | 2137| 907| return nLen; 2138| 907|} inchi_strtol: 2553| 372k|{ 2554| 372k| if (base == ALPHA_BASE) { ------------------ | | 170| 372k|#define ALPHA_BASE 27 ------------------ | Branch (2554:9): [True: 0, False: 372k] ------------------ 2555| 0| return abctol(str, (char **)p); /* cast deliberately discards const qualifier */ 2556| 0| } 2557| 372k| else { 2558| 372k| return strtol(str, (char **)p, base); /* cast deliberately discards const qualifier */ 2559| 372k| } 2560| 372k|} MakeDecNumber: 2589| 56.9k|{ 2590| 56.9k|#define DECIMAL_BASE 10 2591| 56.9k|#define DECIMAL_MINUS '-' 2592| 56.9k|#define DECIMAL_ZERO_VAL '0' 2593| 56.9k|#define DECIMAL_ONE '1' 2594| 56.9k|#define DECIMAL_ZERO '0' 2595| | 2596| 56.9k| char *p = szString; 2597| 56.9k| char *q; 2598| 56.9k| int nChar; 2599| | 2600| 56.9k| if (nStringLen < 2) ------------------ | Branch (2600:9): [True: 0, False: 56.9k] ------------------ 2601| 0| { 2602| 0| return -1; 2603| 0| } 2604| 78.4k| while (szLeadingDelim && *szLeadingDelim && --nStringLen) ------------------ | Branch (2604:12): [True: 43.5k, False: 34.9k] | Branch (2604:30): [True: 21.5k, False: 21.9k] | Branch (2604:49): [True: 21.5k, False: 0] ------------------ 2605| 21.5k| { 2606| 21.5k| *p++ = *szLeadingDelim++; /* djb-rwth: GCC 14 false positive */ 2607| 21.5k| } 2608| 56.9k| if (nStringLen < 2) ------------------ | Branch (2608:9): [True: 0, False: 56.9k] ------------------ 2609| 0| { 2610| 0| return -1; 2611| 0| } 2612| 56.9k| if (!nValue) ------------------ | Branch (2612:9): [True: 39, False: 56.9k] ------------------ 2613| 39| { 2614| 39| *p++ = DECIMAL_ZERO_VAL; /* zero value (cannot use 0) */ ------------------ | | 2592| 39|#define DECIMAL_ZERO_VAL '0' ------------------ 2615| 39| *p = '\0'; 2616| 39| return (int) ( p - szString ); 2617| 39| } 2618| 56.9k| if (nValue < 0) ------------------ | Branch (2618:9): [True: 136, False: 56.7k] ------------------ 2619| 136| { 2620| 136| *p++ = DECIMAL_MINUS; ------------------ | | 2591| 136|#define DECIMAL_MINUS '-' ------------------ 2621| 136| nStringLen--; 2622| 136| nValue = -nValue; 2623| 136| } 2624| 121k| for (q = p; nValue && --nStringLen; nValue /= DECIMAL_BASE) ------------------ | | 2590| 64.6k|#define DECIMAL_BASE 10 ------------------ | Branch (2624:17): [True: 64.6k, False: 56.9k] | Branch (2624:27): [True: 64.6k, False: 0] ------------------ 2625| 64.6k| { 2626| 64.6k| if ((nChar = nValue % DECIMAL_BASE)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 2590| 64.6k|#define DECIMAL_BASE 10 ------------------ | Branch (2626:13): [True: 63.7k, False: 859] ------------------ 2627| 63.7k| { 2628| 63.7k| nChar = DECIMAL_ONE + nChar - 1; ------------------ | | 2593| 63.7k|#define DECIMAL_ONE '1' ------------------ 2629| 63.7k| } 2630| 859| else 2631| 859| { 2632| 859| nChar = DECIMAL_ZERO; ------------------ | | 2594| 859|#define DECIMAL_ZERO '0' ------------------ 2633| 859| } 2634| 64.6k| *q++ = nChar; 2635| 64.6k| } 2636| 56.9k| if (nStringLen <= 0) ------------------ | Branch (2636:9): [True: 0, False: 56.9k] ------------------ 2637| 0| { 2638| 0| return -1; 2639| 0| } 2640| 56.9k| *q = '\0'; 2641| 56.9k| mystrrev( p ); 2642| | 2643| 56.9k| return (int) ( q - szString ); 2644| | 2645| 56.9k|#undef DECIMAL_BASE 2646| 56.9k|#undef DECIMAL_MINUS 2647| 56.9k|#undef DECIMAL_ZERO_VAL 2648| 56.9k|#undef DECIMAL_ONE 2649| 56.9k|#undef DECIMAL_ZERO 2650| 56.9k|} str_HillFormula: 31| 5.02k|{ 32| 5.02k| int i, ii, nUsedLength0; 33| 5.02k| INCHI_SORT *is, *is0; 34| 5.02k| INChI *pINChI, *pINChI_Prev; 35| 5.02k| int mult, eq2prev, bNext; 36| | 37| 5.02k| nUsedLength0 = strbuf->nUsedLength; 38| | 39| 5.02k| if (!( is0 = pINChISort )) ------------------ | Branch (39:9): [True: 0, False: 5.02k] ------------------ 40| 0| { 41| 0| return nUsedLength0; 42| 0| } 43| 5.02k| i = 0; 44| 5.02k| pINChI_Prev = ( 0 <= ( ii = GET_II( bOutType, is0 ) ) ) ? is0->pINChI[ii] : NULL; ------------------ | | 45| 5.02k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 5.02k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 5.02k] | | ------------------ | | 46| 5.02k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 10.0k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 10.0k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 5.02k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 5.02k, False: 0] | | | | | Branch (35:43): [True: 5.02k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 5.02k] | | | Branch (46:36): [True: 5.02k, False: 0] | | ------------------ | | 47| 5.02k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (44:19): [True: 5.02k, False: 0] ------------------ 45| 5.02k| mult = 0; 46| 5.02k| bNext = 0; 47| | 48| | /* For each connected component */ 49| 102k| for (i++; i <= num_components; i++) ------------------ | Branch (49:15): [True: 97.5k, False: 5.02k] ------------------ 50| 97.5k| { 51| | 52| 97.5k| pINChI = ( i < num_components && ------------------ | Branch (52:20): [True: 92.4k, False: 5.02k] ------------------ 53| 92.4k| ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ------------------ | | 45| 92.4k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 92.4k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 92.4k] | | ------------------ | | 46| 92.4k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 184k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 184k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 92.4k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 92.4k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 92.4k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 92.4k, False: 0] | | | | | Branch (35:43): [True: 92.4k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 92.4k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 92.4k] | | | Branch (46:36): [True: 92.4k, False: 0] | | ------------------ | | 47| 92.4k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (53:13): [True: 92.4k, False: 0] ------------------ 54| 97.5k| ? is->pINChI[ii] 55| 97.5k| : NULL; 56| | 57| 97.5k| eq2prev = bUseMulipliers && ------------------ | Branch (57:19): [True: 97.5k, False: 0] ------------------ 58| 97.5k| pINChI && ------------------ | Branch (58:13): [True: 92.4k, False: 5.02k] ------------------ 59| 92.4k| pINChI_Prev && ------------------ | Branch (59:13): [True: 92.4k, False: 0] ------------------ 60| 92.4k| pINChI->szHillFormula && ------------------ | Branch (60:13): [True: 57.6k, False: 34.8k] ------------------ 61| 57.6k| pINChI_Prev->szHillFormula && ------------------ | Branch (61:13): [True: 57.5k, False: 37] ------------------ 62| 57.5k| pINChI->szHillFormula[0] && ------------------ | Branch (62:13): [True: 57.5k, False: 0] ------------------ 63| 57.5k| !strcmp( pINChI_Prev->szHillFormula, pINChI->szHillFormula ); ------------------ | Branch (63:13): [True: 56.5k, False: 1.00k] ------------------ 64| | 65| 97.5k| if (eq2prev) ------------------ | Branch (65:13): [True: 56.5k, False: 40.9k] ------------------ 66| 56.5k| { 67| 56.5k| mult++; /* mult = (number of non-empty equal items)-1 */ 68| 56.5k| continue; 69| 56.5k| } 70| 40.9k| else 71| 40.9k| { 72| 40.9k| int ok; 73| 40.9k| if (bNext++) ------------------ | Branch (73:17): [True: 35.8k, False: 5.02k] ------------------ 74| 35.8k| { 75| 35.8k| MakeDelim( ".", strbuf, bOverflow ); 76| 35.8k| } 77| | 78| 40.9k| ok = pINChI_Prev && ------------------ | Branch (78:18): [True: 40.9k, False: 0] ------------------ 79| 40.9k| pINChI_Prev->szHillFormula && ------------------ | Branch (79:17): [True: 5.62k, False: 35.2k] ------------------ 80| 5.62k| pINChI_Prev->szHillFormula[0]; ------------------ | Branch (80:17): [True: 5.62k, False: 0] ------------------ 81| | 82| 40.9k| if (ok) ------------------ | Branch (82:17): [True: 5.62k, False: 35.2k] ------------------ 83| 5.62k| { 84| 5.62k| MakeMult( mult + 1, "", strbuf, 0, bOverflow ); 85| 5.62k| MakeHillFormulaString( pINChI_Prev->szHillFormula, 86| 5.62k| strbuf, 87| 5.62k| bOverflow ); 88| 5.62k| } 89| 40.9k| } 90| 40.9k| pINChI_Prev = pINChI; 91| 40.9k| mult = 0; /* we do not know whether the item is empty */ 92| 40.9k| } 93| | 94| 5.02k| return ( strbuf->nUsedLength - nUsedLength0 ); 95| 5.02k|} str_Connections: 197| 5.02k|{ 198| 5.02k| int i, ii, nUsedLength0; 199| 5.02k| INCHI_SORT *is, *is0; 200| 5.02k| INChI *pINChI, *pINChI_Prev; 201| 5.02k| int mult, eq2prev, bNext, nNumEmpty; 202| | 203| 5.02k| nUsedLength0 = strbuf->nUsedLength; 204| 5.02k| if (!( is0 = pINChISort )) ------------------ | Branch (204:9): [True: 0, False: 5.02k] ------------------ 205| 0| { 206| 0| return nUsedLength0; 207| 0| } 208| 5.02k| i = 0; 209| 5.02k| pINChI_Prev = ( 0 <= ( ii = GET_II( bOutType, is0 ) ) ) ? is0->pINChI[ii] : NULL; ------------------ | | 45| 5.02k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 5.02k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 5.02k] | | ------------------ | | 46| 5.02k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 10.0k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 10.0k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 5.02k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 5.02k, False: 0] | | | | | Branch (35:43): [True: 5.02k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 5.02k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 5.02k] | | | Branch (46:36): [True: 5.02k, False: 0] | | ------------------ | | 47| 5.02k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (209:19): [True: 5.02k, False: 0] ------------------ 210| 5.02k| is = NULL; 211| 5.02k| mult = 0; 212| 5.02k| bNext = 0; 213| 5.02k| nNumEmpty = 0; 214| | 215| | /* For each connected component... */ 216| 102k| for (i++; i <= num_components; i++) ------------------ | Branch (216:15): [True: 97.5k, False: 5.02k] ------------------ 217| 97.5k| { 218| 97.5k| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 92.4k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 92.4k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 92.4k] | | ------------------ | | 46| 92.4k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 184k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 184k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 92.4k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 92.4k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 92.4k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 92.4k, False: 0] | | | | | Branch (35:43): [True: 92.4k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 92.4k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 92.4k] | | | Branch (46:36): [True: 92.4k, False: 0] | | ------------------ | | 47| 92.4k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (218:20): [True: 92.4k, False: 5.02k] | Branch (218:42): [True: 92.4k, False: 0] ------------------ 219| 97.5k| eq2prev = bUseMulipliers && ------------------ | Branch (219:19): [True: 97.5k, False: 0] ------------------ 220| 97.5k| pINChI && pINChI_Prev && pINChI->lenConnTable > 1 && ------------------ | Branch (220:13): [True: 92.4k, False: 5.02k] | Branch (220:23): [True: 92.4k, False: 0] | Branch (220:38): [True: 30.0k, False: 62.4k] ------------------ 221| 30.0k| pINChI_Prev->lenConnTable == pINChI->lenConnTable && ------------------ | Branch (221:13): [True: 29.9k, False: 36] ------------------ 222| 29.9k| !memcmp( pINChI_Prev->nConnTable, pINChI->nConnTable, ------------------ | Branch (222:13): [True: 29.9k, False: 23] ------------------ 223| 29.9k| pINChI_Prev->lenConnTable * sizeof( pINChI->nConnTable[0] ) ); 224| 97.5k| if (eq2prev) ------------------ | Branch (224:13): [True: 29.9k, False: 67.5k] ------------------ 225| 29.9k| { 226| 29.9k| mult++; /* mult = (number of non-empty equal items)-1 */ 227| 29.9k| continue; 228| 29.9k| } 229| 67.5k| else 230| 67.5k| { 231| 67.5k| if (pINChI_Prev) ------------------ | Branch (231:17): [True: 67.5k, False: 0] ------------------ 232| 67.5k| { 233| 67.5k| if (bNext++) ------------------ | Branch (233:21): [True: 62.5k, False: 5.02k] ------------------ 234| 62.5k| { 235| 62.5k| MakeDelim( sCompDelim, strbuf, bOverflow ); 236| 62.5k| } 237| 67.5k| if (pINChI_Prev && pINChI_Prev->lenConnTable > 1) ------------------ | Branch (237:21): [True: 67.5k, False: 0] | Branch (237:36): [True: 4.30k, False: 63.2k] ------------------ 238| 4.30k| { 239| 4.30k| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 240| 4.30k| MakeCtStringNew( pCG, pINChI_Prev->nConnTable, 241| 4.30k| pINChI_Prev->lenConnTable, 242| 4.30k| 0, NULL, 243| 4.30k| pINChI_Prev->nNumberOfAtoms, 244| 4.30k| strbuf, ATOM_MODE, bOverflow ); 245| 4.30k| } 246| 63.2k| else 247| 63.2k| { 248| 63.2k| nNumEmpty++; 249| 63.2k| } 250| 67.5k| } 251| 67.5k| } 252| 67.5k| pINChI_Prev = pINChI; 253| 67.5k| mult = 0; /* we do not know whether the item is empty */ 254| 67.5k| } 255| 5.02k| if (nNumEmpty == num_components && strbuf->nUsedLength > nUsedLength0) ------------------ | Branch (255:9): [True: 780, False: 4.24k] | Branch (255:40): [True: 317, False: 463] ------------------ 256| 317| { 257| 317| strbuf->nUsedLength = nUsedLength0; 258| 317| strbuf->pStr[strbuf->nUsedLength] = '\0'; 259| 317| } 260| | /* 261| | if ( nNumEmpty == num_components && tot_len > tot_len_inp ) { 262| | tot_len = tot_len_inp; 263| | strbuf->pStr[tot_len] = '\0'; 264| | } 265| | */ 266| | 267| 5.02k| return ( strbuf->nUsedLength - nUsedLength0 ); 268| 5.02k|} str_H_atoms: 282| 1.86k|{ 283| 1.86k| int i, j, ii, len_H, nUsedLength0; 284| 1.86k| INCHI_SORT *is, *is0; 285| 1.86k| INChI *pINChI, *pINChI_Prev; 286| 1.86k| int mult, eq2prev, bNext, bNotEmpty, nNumEmpty; 287| | 288| 1.86k| nNumEmpty = 0; 289| 1.86k| is0 = pINChISort; 290| 1.86k| is = NULL; 291| 1.86k| i = 0; 292| 1.86k| pINChI_Prev = ( 0 <= ( ii = GET_II( bOutType, is0 ) ) ) ? is0->pINChI[ii] : NULL; ------------------ | | 45| 1.86k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 1.86k|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 1.86k] | | ------------------ | | 46| 1.86k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 3.73k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 3.73k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 1.86k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 1.86k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 1.86k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 1.86k, False: 0] | | | | | Branch (35:43): [True: 1.86k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 1.86k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 1.86k] | | | Branch (46:36): [True: 1.86k, False: 0] | | ------------------ | | 47| 1.86k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (292:19): [True: 1.86k, False: 0] ------------------ 293| 1.86k| mult = 0; 294| 1.86k| bNext = 0; 295| 1.86k| nUsedLength0 = strbuf->nUsedLength; 296| | 297| | /* For each connected component... */ 298| 3.81k| for (i++; i <= num_components; i++) ------------------ | Branch (298:15): [True: 1.94k, False: 1.86k] ------------------ 299| 1.94k| { 300| | 301| 1.94k| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 79|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 79|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 79] | | ------------------ | | 46| 79| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 158|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 158|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 79|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 79|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 79|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 79, False: 0] | | | | | Branch (35:43): [True: 79, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 79|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 79] | | | Branch (46:36): [True: 79, False: 0] | | ------------------ | | 47| 79| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (301:20): [True: 79, False: 1.86k] | Branch (301:42): [True: 79, False: 0] ------------------ 302| | /*========== compare to previous ============*/ 303| 1.94k| eq2prev = bUseMulipliers && ------------------ | Branch (303:19): [True: 1.94k, False: 0] ------------------ 304| 1.94k| pINChI && pINChI_Prev && ( pINChI->nNumberOfAtoms > 0 || pINChI->lenTautomer > 1 ) && ------------------ | Branch (304:13): [True: 79, False: 1.86k] | Branch (304:23): [True: 79, False: 0] | Branch (304:40): [True: 79, False: 0] | Branch (304:70): [True: 0, False: 0] ------------------ 305| 79| pINChI_Prev->nNumberOfAtoms == pINChI->nNumberOfAtoms && ------------------ | Branch (305:13): [True: 78, False: 1] ------------------ 306| 78| ( !pINChI_Prev->nNumberOfAtoms || !memcmp( pINChI_Prev->nNum_H, pINChI->nNum_H, ------------------ | Branch (306:15): [True: 0, False: 78] | Branch (306:47): [True: 78, False: 0] ------------------ 307| 78| pINChI_Prev->nNumberOfAtoms * sizeof( pINChI->nNum_H[0] ) ) ) && 308| 78| !CompareTautNonIsoPartOfINChI( pINChI_Prev, pINChI ); ------------------ | Branch (308:13): [True: 78, False: 0] ------------------ 309| | 310| 1.94k| if (eq2prev && pINChI_Prev->lenTautomer <= 1) ------------------ | Branch (310:13): [True: 78, False: 1.86k] | Branch (310:24): [True: 1, False: 77] ------------------ 311| 1| { 312| | /* make sure it is not empty */ 313| 1| eq2prev = 0; 314| 12| for (j = 0; j < pINChI_Prev->nNumberOfAtoms; j++) ------------------ | Branch (314:25): [True: 11, False: 1] ------------------ 315| 11| { 316| 11| if (pINChI_Prev->nNum_H[j]) ------------------ | Branch (316:21): [True: 0, False: 11] ------------------ 317| 0| { 318| 0| eq2prev = 1; 319| 0| break; 320| 0| } 321| 11| } 322| 1| } 323| 1.94k| if (eq2prev) ------------------ | Branch (323:13): [True: 77, False: 1.86k] ------------------ 324| 77| { 325| 77| mult++; /* mult = (number of non-empty equal items)-1 */ 326| 77| continue; 327| 77| } 328| 1.86k| else 329| 1.86k| { 330| 1.86k| if (pINChI_Prev) ------------------ | Branch (330:17): [True: 1.86k, False: 0] ------------------ 331| 1.86k| { 332| | /* delimiter */ 333| 1.86k| if (bNext++) ------------------ | Branch (333:21): [True: 2, False: 1.86k] ------------------ 334| 2| { 335| 2| MakeDelim( sCompDelim, strbuf, bOverflow ); 336| 2| } 337| | /* verify non-empty */ 338| 1.86k| bNotEmpty = 0; 339| 1.86k| if (pINChI_Prev) ------------------ | Branch (339:21): [True: 1.86k, False: 0] ------------------ 340| 1.86k| { 341| 1.86k| bNotEmpty = ( pINChI_Prev->lenTautomer > 1 ); 342| 1.86k| if (!bNotEmpty) ------------------ | Branch (342:25): [True: 706, False: 1.16k] ------------------ 343| 706| { 344| 2.47k| for (j = 0; j < pINChI_Prev->nNumberOfAtoms; j++) ------------------ | Branch (344:37): [True: 2.47k, False: 2] ------------------ 345| 2.47k| { 346| 2.47k| if (pINChI_Prev->nNum_H[j]) ------------------ | Branch (346:33): [True: 704, False: 1.76k] ------------------ 347| 704| { 348| 704| bNotEmpty = 1; 349| 704| break; 350| 704| } 351| 2.47k| } 352| 706| } 353| 1.86k| } 354| 1.86k| if (bNotEmpty) ------------------ | Branch (354:21): [True: 1.86k, False: 2] ------------------ 355| 1.86k| { 356| 1.86k| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 357| | /* H-atoms */ 358| 1.86k| len_H = MakeHString( 0, pINChI_Prev->nNum_H, pINChI_Prev->nNumberOfAtoms, 359| 1.86k| strbuf, ATOM_MODE, bOverflow ); 360| | /* tautomeric groups */ 361| 1.86k| MakeTautString( pINChI_Prev->nTautomer, pINChI_Prev->lenTautomer, ( 0 != len_H ), 362| 1.86k| strbuf, TAUT_MODE, bOverflow ); 363| 1.86k| } 364| 2| else 365| 2| { 366| 2| nNumEmpty++; 367| 2| } 368| 1.86k| } 369| 1.86k| } 370| 1.86k| pINChI_Prev = pINChI; 371| 1.86k| mult = 0; /* we do not know whether the item is empty */ 372| 1.86k| } 373| 1.86k| if (nNumEmpty == num_components && strbuf->nUsedLength > nUsedLength0) ------------------ | Branch (373:9): [True: 0, False: 1.86k] | Branch (373:40): [True: 0, False: 0] ------------------ 374| 0| { 375| 0| strbuf->nUsedLength = nUsedLength0; 376| 0| strbuf->pStr[nUsedLength0] = '\0'; 377| 0| } 378| | /* 379| | if ( nNumEmpty == num_components && tot_len > tot_len_inp ) { 380| | tot_len = tot_len_inp; 381| | strbuf->pStr[tot_len] = '\0'; 382| | } 383| | */ 384| | 385| 1.86k| return ( strbuf->nUsedLength - nUsedLength0 ); 386| 1.86k|} str_Charge2: 401| 243|{ 402| 243| int i, ii, ii2, nUsedLength0; 403| 243| INCHI_SORT *is, *is2, *is0, *is20; 404| 243| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 405| 243| int nTotalCharge, nTotalCharge_Prev, nTotalCharge_Taut; /* djb-rwth: removing redundant variables */ 406| 243| int mult, eq2prev, eq2taut, eq2tautPrev, bNext; 407| 243| const char *pPrevEquStr, *pCurrEquStr; 408| 243| int multPrevEquStr; 409| 243| pINChI_Taut = NULL; 410| 243| pINChI_Prev = NULL; 411| 243| pINChI_Taut_Prev = NULL; 412| 243| mult = 0; 413| 243| bNext = 0; 414| 243| is = NULL; 415| 243| is2 = NULL; 416| 243| is0 = pINChISort; 417| 243| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (417:12): [True: 0, False: 243] ------------------ 418| | /* djb-rwth: removing redundant code */ 419| 243| eq2tautPrev = 1; /* pINChI_Prev (previous pINChI) does not exist */ 420| 243| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 421| 243| multPrevEquStr = 0; 422| 243| nUsedLength0 = strbuf->nUsedLength; 423| | 424| | /* For each connected component... */ 425| 740| for (i = 0; i <= num_components; i++) ------------------ | Branch (425:17): [True: 497, False: 243] ------------------ 426| 497| { 427| | 428| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 429| 497| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 254|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 254|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 254] | | ------------------ | | 46| 254| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 508|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 508|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 254|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 254|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 254|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 254, False: 0] | | | | | Branch (35:43): [True: 254, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 254|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 254] | | | Branch (46:36): [True: 254, False: 0] | | ------------------ | | 47| 254| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (429:20): [True: 254, False: 243] | Branch (429:42): [True: 254, False: 0] ------------------ 430| | /*================ compare sp3 to previous =====================*/ 431| 497| if (bSecondNonTautPass) ------------------ | Branch (431:13): [True: 0, False: 497] ------------------ 432| 0| { 433| | /* component that was output on the 1st pass */ 434| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ | Branch (434:29): [True: 0, False: 0] | Branch (434:51): [True: 0, False: 0] ------------------ 435| 0| } 436| | /*========= if bSecondNonTautPass then compare non-iso non-taut stereo to non-iso taut ========*/ 437| 497| eq2taut = 0; 438| 497| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (438:13): [True: 497, False: 0] | Branch (438:25): [True: 0, False: 497] | Branch (438:47): [True: 0, False: 0] ------------------ 439| 0| { 440| 0| eq2taut = pINChI && pINChI_Taut && !pINChI_Taut->bDeleted && ------------------ | Branch (440:23): [True: 0, False: 0] | Branch (440:33): [True: 0, False: 0] | Branch (440:48): [True: 0, False: 0] ------------------ 441| 0| ( nTotalCharge = pINChI->nTotalCharge ) && ( nTotalCharge_Taut = pINChI_Taut->nTotalCharge ) && ------------------ | Branch (441:17): [True: 0, False: 0] | Branch (441:60): [True: 0, False: 0] ------------------ 442| 0| nTotalCharge == nTotalCharge_Taut; ------------------ | Branch (442:17): [True: 0, False: 0] ------------------ 443| 0| eq2taut = eq2taut ? ( iiEQU | iitNONTAUT ) : 0; ------------------ | | 58| 0|#define iiEQU 0x0008 /* equivalence info */ ------------------ eq2taut = eq2taut ? ( iiEQU | iitNONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (443:23): [True: 0, False: 0] ------------------ 444| 0| } 445| 497| if (eq2taut) ------------------ | Branch (445:13): [True: 0, False: 497] ------------------ 446| 0| { 447| | /* we may be here only in case of the second (non-taut) pass */ 448| | /* current non-taut stereo has been found to be same as tautomeric */ 449| 0| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (449:17): [True: 0, False: 0] | Branch (449:32): [True: 0, False: 0] ------------------ 450| 0| { 451| | /* previous component exists; output it */ 452| 0| if (bNext++) ------------------ | Branch (452:21): [True: 0, False: 0] ------------------ 453| 0| { 454| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 455| 0| } 456| 0| if ((nTotalCharge_Prev = pINChI_Prev->nTotalCharge)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (456:21): [True: 0, False: 0] ------------------ 457| 0| { 458| 0| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 459| 0| inchi_strbuf_printf( strbuf, "%+d", nTotalCharge_Prev ); 460| 0| } 461| 0| } 462| 0| else 463| 0| { 464| 0| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms && !pINChI_Taut_Prev->bDeleted) ------------------ | Branch (464:21): [True: 0, False: 0] | Branch (464:41): [True: 0, False: 0] | Branch (464:77): [True: 0, False: 0] ------------------ 465| 0| { 466| | /* previous non-taut component exists only in taut list */ 467| 0| if (bNext++) ------------------ | Branch (467:25): [True: 0, False: 0] ------------------ 468| 0| { 469| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 470| 0| } 471| 0| } 472| 0| } 473| | /* we have found pINChI->nTotalCharge same as in pINChI_Taut */ 474| | /* output this (current) equivalence as '*', that is, same as tautomeric */ 475| | /* that was printed on the 1st pass. */ 476| | 477| 0| pCurrEquStr = EquString( eq2taut ); 478| 0| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (478:17): [True: 0, False: 0] | Branch (478:35): [True: 0, False: 0] ------------------ 479| 0| { 480| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (480:21): [True: 0, False: 0] | Branch (480:36): [True: 0, False: 0] ------------------ 481| 0| { 482| 0| multPrevEquStr++; 483| 0| } 484| 0| else 485| 0| { 486| | /* new EqStr is different; output it */ 487| 0| if (bNext++) ------------------ | Branch (487:25): [True: 0, False: 0] ------------------ 488| 0| { 489| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 490| 0| } 491| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 492| 0| pPrevEquStr = pCurrEquStr; 493| 0| multPrevEquStr = 1; 494| 0| } 495| 0| } 496| 0| else 497| 0| { 498| 0| pPrevEquStr = pCurrEquStr; 499| 0| multPrevEquStr = 1; 500| 0| } 501| | 502| 0| pINChI_Prev = NULL; /* pINChI_Prev sp2 does not exist since */ 503| 0| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 504| 0| mult = 0; 505| 0| eq2tautPrev = 1; /* pINChI_Prev sp2 does not exist */ 506| 0| } 507| 497| else 508| 497| { 509| 497| if (eq2tautPrev) ------------------ | Branch (509:17): [True: 243, False: 254] ------------------ 510| 243| { 511| | /* at this point pINChI_Prev does not exist; however, pINChI */ 512| | /*might have been discovered and it is different from pINChI_Taut */ 513| 243| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (513:21): [True: 0, False: 243] | Branch (513:39): [True: 0, False: 0] ------------------ 514| 0| { 515| | /* new EqStr is different; output it */ 516| 0| if (bNext++) ------------------ | Branch (516:25): [True: 0, False: 0] ------------------ 517| 0| { 518| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 519| 0| } 520| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 521| 0| pPrevEquStr = NULL; 522| 0| multPrevEquStr = 0; 523| 0| } 524| 243| eq2tautPrev = 0; 525| 243| pINChI_Prev = pINChI; 526| 243| pINChI_Taut_Prev = pINChI_Taut; 527| 243| mult = 0; 528| 243| } 529| 254| else 530| 254| { 531| | /* check whether pINChI and pINChI_Prev have non-zero identical stereo sp3 */ 532| | /*================ compare sp3 to previous =====================*/ 533| 254| eq2prev = bUseMulipliers && ------------------ | Branch (533:27): [True: 254, False: 0] ------------------ 534| 254| pINChI && pINChI_Prev && ------------------ | Branch (534:21): [True: 11, False: 243] | Branch (534:31): [True: 11, False: 0] ------------------ 535| 11| ( nTotalCharge = pINChI->nTotalCharge ) && ( nTotalCharge_Prev = pINChI_Prev->nTotalCharge ) && ------------------ | Branch (535:21): [True: 11, False: 0] | Branch (535:64): [True: 10, False: 1] ------------------ 536| 10| nTotalCharge == nTotalCharge_Prev; ------------------ | Branch (536:21): [True: 7, False: 3] ------------------ 537| 254| if (eq2prev) ------------------ | Branch (537:21): [True: 7, False: 247] ------------------ 538| 7| { 539| 7| mult++; /* mult = (number of non-empty equal items)-1 */ 540| 7| continue; 541| 7| } 542| 247| else 543| 247| { 544| 247| if (bNext++) ------------------ | Branch (544:25): [True: 4, False: 243] ------------------ 545| 4| { 546| 4| MakeDelim( sCompDelim, strbuf, bOverflow ); 547| 4| } 548| 247| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (548:25): [True: 247, False: 0] | Branch (548:40): [True: 247, False: 0] ------------------ 549| 247| { 550| 247| if ((nTotalCharge_Prev = pINChI_Prev->nTotalCharge)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (550:29): [True: 246, False: 1] ------------------ 551| 246| { 552| | /* pINChI_Prev exists and has charge info */ 553| 246| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 554| 246| inchi_strbuf_printf( strbuf, "%+d", nTotalCharge_Prev ); 555| 246| } 556| | /* else charge is not present in pINChI_Prev */ 557| 247| } 558| 0| else 559| 0| { 560| | /* djb-rwth: removing redundant code */ 561| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 562| | if (!(bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms && !pINChI_Taut_Prev->bDeleted)) 563| | { 564| | int stop = 1; /* */ 565| | } 566| |#endif 567| 0| } 568| 247| } 569| 247| pINChI_Prev = pINChI; 570| 247| pINChI_Taut_Prev = pINChI_Taut; 571| 247| mult = 0; /* we do not know whether the item is empty */ 572| 247| } 573| 497| } 574| 497| } 575| | 576| 243| return ( strbuf->nUsedLength - nUsedLength0 ); 577| 243|} str_Sp2: 711| 410|{ 712| 410| int i, ii, ii2, nUsedLength0; 713| 410| INCHI_SORT *is, *is2, *is0, *is20; 714| 410| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 715| 410| INChI_Stereo *Stereo, *Stereo_Prev, *Stereo_Taut, *Stereo_Taut_Prev; 716| 410| int mult, eq2prev, eq2taut, eq2tautPrev, bNext; 717| 410| const char *pPrevEquStr, *pCurrEquStr; 718| 410| int multPrevEquStr; 719| | 720| 410| pINChI_Taut = NULL; 721| 410| pINChI_Prev = NULL; 722| 410| pINChI_Taut_Prev = NULL; 723| 410| mult = 0; 724| 410| bNext = 0; 725| 410| is = NULL; 726| 410| is2 = NULL; 727| 410| is0 = pINChISort; 728| 410| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (728:12): [True: 0, False: 410] ------------------ 729| | /* djb-rwth: removing redundant code */ 730| 410| eq2tautPrev = 1; /* pINChI_Prev (previous pINChI) does not exist */ 731| 410| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 732| 410| multPrevEquStr = 0; 733| 410| nUsedLength0 = strbuf->nUsedLength; 734| | 735| | /* For each connected component ... */ 736| 1.23k| for (i = 0; i <= num_components; i++) ------------------ | Branch (736:17): [True: 821, False: 410] ------------------ 737| 821| { 738| | 739| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 740| 821| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 411|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 411|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 411] | | ------------------ | | 46| 411| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 822|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 822|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 411|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 411|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 411|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 411, False: 0] | | | | | Branch (35:43): [True: 411, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 411|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 411] | | | Branch (46:36): [True: 411, False: 0] | | ------------------ | | 47| 411| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (740:20): [True: 411, False: 410] | Branch (740:42): [True: 411, False: 0] ------------------ 741| | /*================ compare sp2 to previous =====================*/ 742| 821| if (bSecondNonTautPass) ------------------ | Branch (742:13): [True: 0, False: 821] ------------------ 743| 0| { 744| | /* component that was output on the 1st pass */ 745| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ | Branch (745:29): [True: 0, False: 0] | Branch (745:51): [True: 0, False: 0] ------------------ 746| 0| } 747| | /*========= if bSecondNonTautPass then compare non-iso non-taut stereo to non-iso taut ========*/ 748| 821| eq2taut = 0; 749| |#if ( FIX_EMPTY_LAYER_BUG == 1 ) 750| | if (!eq2taut && bSecondNonTautPass && bOmitRepetitions && pINChI && pINChI_Taut) 751| | { 752| | Stereo = pINChI->Stereo; 753| | Stereo_Taut = pINChI_Taut->Stereo; 754| | eq2taut = Stereo && Stereo_Taut && 755| | Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); 756| | eq2taut = eq2taut ? ( iiSTEREO | iitNONTAUT ) : 0; 757| | 758| | if (!eq2taut && 759| | !Eql_INChI_Stereo( Stereo, EQL_SP2, NULL, EQL_EXISTS, 0 ) && 760| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP2, NULL, EQL_EXISTS, 0 )) 761| | { 762| | eq2taut = iiEmpty; /* the current is empty while the preceding (taut) is not */ 763| | } 764| | } 765| |#else 766| 821| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (766:13): [True: 821, False: 0] | Branch (766:25): [True: 0, False: 821] | Branch (766:47): [True: 0, False: 0] ------------------ 767| 0| { 768| 0| eq2taut = pINChI && pINChI_Taut && ------------------ | Branch (768:23): [True: 0, False: 0] | Branch (768:33): [True: 0, False: 0] ------------------ 769| 0| ( Stereo = pINChI->Stereo ) && ( Stereo_Taut = pINChI_Taut->Stereo ) && ------------------ | Branch (769:17): [True: 0, False: 0] | Branch (769:48): [True: 0, False: 0] ------------------ 770| 0| Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (770:17): [True: 0, False: 0] ------------------ 771| 0| eq2taut = eq2taut ? ( iiSTEREO | iitNONTAUT ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitNONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (771:23): [True: 0, False: 0] ------------------ 772| 0| } 773| 821|#endif 774| 821| if (eq2taut) ------------------ | Branch (774:13): [True: 0, False: 821] ------------------ 775| 0| { 776| | /* we may be here only in case of the second (non-taut) pass */ 777| | /* current non-taut stereo has been found to be same as tautomeric */ 778| 0| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (778:17): [True: 0, False: 0] | Branch (778:32): [True: 0, False: 0] ------------------ 779| 0| { 780| | /* previous component exists; output it */ 781| 0| if (bNext++) ------------------ | Branch (781:21): [True: 0, False: 0] ------------------ 782| 0| { 783| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 784| 0| } 785| 0| if (( Stereo_Prev = pINChI_Prev->Stereo ) && Stereo_Prev->nNumberOfStereoBonds > 0) ------------------ | Branch (785:21): [True: 0, False: 0] | Branch (785:62): [True: 0, False: 0] ------------------ 786| 0| { 787| 0| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 788| | 789| 0| MakeStereoString( Stereo_Prev->nBondAtom1, Stereo_Prev->nBondAtom2, 790| 0| Stereo_Prev->b_parity, 791| 0| 0, Stereo_Prev->nNumberOfStereoBonds, 792| 0| strbuf, TAUT_MODE, bOverflow ); 793| 0| } 794| 0| } 795| 0| else 796| 0| { 797| 0| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (797:21): [True: 0, False: 0] | Branch (797:41): [True: 0, False: 0] ------------------ 798| 0| { 799| | /* previous non-taut component exists only in taut list */ 800| 0| if (bNext++) ------------------ | Branch (800:25): [True: 0, False: 0] ------------------ 801| 0| { 802| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 803| 0| } 804| 0| } 805| 0| } 806| | /* we have found pINChI->Stereo sp2 same as in pINChI_Taut */ 807| | /* output this (current) equivalence as '*', that is, same as tautomeric */ 808| | /* that was printed on the 1st pass. */ 809| 0| pCurrEquStr = EquString( eq2taut ); 810| 0| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (810:17): [True: 0, False: 0] | Branch (810:35): [True: 0, False: 0] ------------------ 811| 0| { 812| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (812:21): [True: 0, False: 0] | Branch (812:36): [True: 0, False: 0] ------------------ 813| 0| { 814| 0| multPrevEquStr++; 815| 0| } 816| 0| else 817| 0| { 818| | /* new EqStr is different; output the previous one */ 819| 0| if (bNext++) ------------------ | Branch (819:25): [True: 0, False: 0] ------------------ 820| 0| { 821| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 822| 0| } 823| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 824| 0| pPrevEquStr = pCurrEquStr; 825| 0| multPrevEquStr = 1; 826| 0| } 827| 0| } 828| 0| else 829| 0| { 830| 0| pPrevEquStr = pCurrEquStr; 831| 0| multPrevEquStr = 1; 832| 0| } 833| 0| pINChI_Prev = NULL; /* pINChI_Prev sp2 does not exist since */ 834| 0| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 835| 0| mult = 0; 836| 0| eq2tautPrev = 1; /* pINChI_Prev sp2 does not exist */ 837| 0| } 838| 821| else 839| 821| { 840| 821| if (eq2tautPrev) ------------------ | Branch (840:17): [True: 410, False: 411] ------------------ 841| 410| { 842| | /* at this point pINChI_Prev does not exist; however, pINChI */ 843| | /*might have been discovered and it is different from pINChI_Taut */ 844| 410| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (844:21): [True: 0, False: 410] | Branch (844:39): [True: 0, False: 0] ------------------ 845| 0| { 846| | /* new EqStr is different; output it */ 847| 0| if (bNext++) ------------------ | Branch (847:25): [True: 0, False: 0] ------------------ 848| 0| { 849| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 850| 0| } 851| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 852| 0| pPrevEquStr = NULL; 853| 0| multPrevEquStr = 0; 854| 0| } 855| 410| eq2tautPrev = 0; 856| 410| pINChI_Prev = pINChI; 857| 410| pINChI_Taut_Prev = pINChI_Taut; 858| 410| mult = 0; 859| 410| } 860| 411| else 861| 411| { 862| | /* check whether pINChI and pINChI_Prev have non-zero identical stereo sp2 */ 863| 411| eq2prev = bUseMulipliers && ------------------ | Branch (863:27): [True: 411, False: 0] ------------------ 864| 411| pINChI && pINChI_Prev && ------------------ | Branch (864:21): [True: 1, False: 410] | Branch (864:31): [True: 1, False: 0] ------------------ 865| 1| ( Stereo = pINChI->Stereo ) && ( Stereo_Prev = pINChI_Prev->Stereo ) && ------------------ | Branch (865:21): [True: 1, False: 0] | Branch (865:52): [True: 1, False: 0] ------------------ 866| 1| Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Prev, EQL_SP2, 0 ); ------------------ | | 477| 1|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Prev, EQL_SP2, 0 ); ------------------ | | 477| 1|#define EQL_SP2 8 ------------------ | Branch (866:21): [True: 1, False: 0] ------------------ 867| 411| if (eq2prev) ------------------ | Branch (867:21): [True: 1, False: 410] ------------------ 868| 1| { 869| 1| mult++; /* mult = (number of non-empty equal items)-1 */ 870| 1| continue; 871| 1| } 872| 410| else 873| 410| { 874| | /* pINChI sp2 info is either different or trivial. Output pINChI_Prev anyway */ 875| 410| if (bNext++) ------------------ | Branch (875:25): [True: 0, False: 410] ------------------ 876| 0| { 877| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 878| 0| } 879| 410| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (879:25): [True: 410, False: 0] | Branch (879:40): [True: 410, False: 0] ------------------ 880| 410| { 881| 410| if (( Stereo_Prev = pINChI_Prev->Stereo ) && Stereo_Prev->nNumberOfStereoBonds > 0) ------------------ | Branch (881:29): [True: 410, False: 0] | Branch (881:70): [True: 410, False: 0] ------------------ 882| 410| { 883| | /* pINChI_Prev exists and has sp2 info */ 884| 410| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 885| | 886| 410| MakeStereoString( Stereo_Prev->nBondAtom1, Stereo_Prev->nBondAtom2, 887| 410| Stereo_Prev->b_parity, 888| 410| 0, Stereo_Prev->nNumberOfStereoBonds, 889| 410| strbuf, TAUT_MODE, bOverflow ); 890| 410| } 891| | /* else sp2 info is not present in pINChI_Prev */ 892| 410| } 893| 0| else 894| 0| { 895| 0| if (bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (895:29): [True: 0, False: 0] | Branch (895:51): [True: 0, False: 0] | Branch (895:71): [True: 0, False: 0] ------------------ 896| 0| { 897| 0| if (( Stereo_Taut_Prev = pINChI_Taut_Prev->Stereo ) && Stereo_Taut_Prev->nNumberOfStereoBonds > 0) ------------------ | Branch (897:33): [True: 0, False: 0] | Branch (897:84): [True: 0, False: 0] ------------------ 898| 0| { 899| | /* since pINChI_Prev does not exist, pINChI_Taut_Prev is non-tautomeric */ 900| | /* and it has non-trivial sp2 info */ 901| | /* 902| | tot_len += MakeDelim( sIdenticalValues, strbuf, bOverflow); 903| | */ 904| 0| ;/* pINChI_Taut_Prev sp2 info was output in the main stereo section */ 905| 0| } 906| 0| else 907| 0| { 908| 0| ; /* pINChI_Taut_Prev exists and has not sp2 info */ 909| 0| } 910| 0| } 911| 0| } 912| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 913| | else 914| | { 915| | int stop = 1; /* */ 916| | } 917| |#endif 918| 410| } 919| 410| pINChI_Prev = pINChI; 920| 410| pINChI_Taut_Prev = pINChI_Taut; 921| 410| mult = 0; /* we do not know whether the item is empty */ 922| 410| } 923| 821| } 924| 821| } /* end of for each connected component ... */ 925| | 926| 410| return ( strbuf->nUsedLength - nUsedLength0 ); 927| 410|} str_Sp3: 956| 357|{ 957| 357| int i, ii, ii2, nUsedLength0; 958| 357| INCHI_SORT *is, *is2, *is0, *is20; 959| 357| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 960| 357| INChI_Stereo *Stereo, *Stereo_Prev, *Stereo_Taut, *Stereo_Taut_Prev; 961| 357| int mult, eq2prev, eq2taut, eq2tautPrev, bNext; 962| 357| const char *pPrevEquStr, *pCurrEquStr; 963| 357| int multPrevEquStr; 964| 357| pINChI_Taut = NULL; 965| 357| pINChI_Prev = NULL; 966| 357| pINChI_Taut_Prev = NULL; 967| 357| mult = 0; 968| 357| bNext = 0; 969| 357| is = NULL; 970| 357| is2 = NULL; 971| 357| is0 = pINChISort; 972| 357| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (972:12): [True: 0, False: 357] ------------------ 973| | /* djb-rwth: removing redundant code */ 974| 357| eq2tautPrev = 1; /* pINChI_Prev (previous pINChI) does not exist */ 975| 357| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 976| 357| multPrevEquStr = 0; 977| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 978| |#else 979| 357| bRelRac = 0; 980| 357|#endif 981| 357| nUsedLength0 = strbuf->nUsedLength; 982| | 983| | /* For each connected component... */ 984| 1.10k| for (i = 0; i <= num_components; i++) ------------------ | Branch (984:17): [True: 745, False: 357] ------------------ 985| 745| { 986| | 987| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 988| 745| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 388|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 388|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 388] | | ------------------ | | 46| 388| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 776|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 776|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 388|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 388|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 388|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 388, False: 0] | | | | | Branch (35:43): [True: 388, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 388|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 388] | | | Branch (46:36): [True: 388, False: 0] | | ------------------ | | 47| 388| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (988:20): [True: 388, False: 357] | Branch (988:42): [True: 388, False: 0] ------------------ 989| | /*================ compare sp3 to previous =====================*/ 990| 745| if (bSecondNonTautPass) ------------------ | Branch (990:13): [True: 0, False: 745] ------------------ 991| 0| { 992| | /* component that was output on the 1st pass */ 993| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ | Branch (993:29): [True: 0, False: 0] | Branch (993:51): [True: 0, False: 0] ------------------ 994| 0| } 995| | /*========= if bSecondNonTautPass then compare non-iso non-taut stereo to non-iso taut ========*/ 996| 745| eq2taut = 0; 997| |#if ( FIX_EMPTY_LAYER_BUG == 1 ) 998| | if (!eq2taut && bSecondNonTautPass && bOmitRepetitions && pINChI && pINChI_Taut) 999| | { 1000| | Stereo = pINChI->Stereo; 1001| | Stereo_Taut = pINChI_Taut->Stereo; 1002| | eq2taut = Stereo && Stereo_Taut && 1003| | Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); 1004| | eq2taut = eq2taut ? ( iiSTEREO | iitNONTAUT ) : 0; 1005| | if (!eq2taut && 1006| | !Eql_INChI_Stereo( Stereo, EQL_SP3, NULL, EQL_EXISTS, 0 ) && 1007| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP3, NULL, EQL_EXISTS, 0 )) 1008| | { 1009| | eq2taut = iiEmpty; /* the current is empty while the preceding (taut) is not */ 1010| | } 1011| | } 1012| |#else 1013| 745| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1013:13): [True: 745, False: 0] | Branch (1013:25): [True: 0, False: 745] | Branch (1013:47): [True: 0, False: 0] ------------------ 1014| 0| { 1015| 0| eq2taut = pINChI && pINChI_Taut && ------------------ | Branch (1015:23): [True: 0, False: 0] | Branch (1015:33): [True: 0, False: 0] ------------------ 1016| 0| ( Stereo = pINChI->Stereo ) && ( Stereo_Taut = pINChI_Taut->Stereo ) && ------------------ | Branch (1016:17): [True: 0, False: 0] | Branch (1016:48): [True: 0, False: 0] ------------------ 1017| 0| Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ | Branch (1017:17): [True: 0, False: 0] ------------------ 1018| 0| eq2taut = eq2taut ? ( iiSTEREO | iitNONTAUT ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitNONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (1018:23): [True: 0, False: 0] ------------------ 1019| 0| } 1020| 745|#endif 1021| 745| if (eq2taut) ------------------ | Branch (1021:13): [True: 0, False: 745] ------------------ 1022| 0| { 1023| | /* we may be here only in case of the second (non-taut) pass */ 1024| | /* current non-taut stereo has been found to be same as tautomeric */ 1025| 0| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1025:17): [True: 0, False: 0] | Branch (1025:32): [True: 0, False: 0] ------------------ 1026| 0| { 1027| | /* previous component exists; output it */ 1028| 0| if (bNext++) ------------------ | Branch (1028:21): [True: 0, False: 0] ------------------ 1029| 0| { 1030| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1031| 0| } 1032| 0| if (( Stereo_Prev = pINChI_Prev->Stereo ) && Stereo_Prev->nNumberOfStereoCenters > 0) ------------------ | Branch (1032:21): [True: 0, False: 0] | Branch (1032:62): [True: 0, False: 0] ------------------ 1033| 0| { 1034| | /* non-empty item */ 1035| 0| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1036| 0| MakeStereoString( Stereo_Prev->nNumber, NULL, 1037| 0| Stereo_Prev->t_parity,0, 1038| 0| Stereo_Prev->nNumberOfStereoCenters, 1039| 0| strbuf, TAUT_MODE, bOverflow ); 1040| 0| } 1041| 0| } 1042| 0| else 1043| 0| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1043:21): [True: 0, False: 0] | Branch (1043:41): [True: 0, False: 0] ------------------ 1044| 0| { 1045| | /* previous non-taut component exists only in taut list */ 1046| 0| if (bNext++) ------------------ | Branch (1046:25): [True: 0, False: 0] ------------------ 1047| 0| { 1048| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1049| 0| } 1050| 0| } 1051| | /* we have found pINChI->Stereo sp3 same as in pINChI_Taut */ 1052| | /* output this (current) equivalence as '*', that is, same as tautomeric */ 1053| | /* that was printed on the 1st pass. */ 1054| | 1055| 0| pCurrEquStr = EquString( eq2taut ); 1056| 0| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1056:17): [True: 0, False: 0] | Branch (1056:35): [True: 0, False: 0] ------------------ 1057| 0| { 1058| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (1058:21): [True: 0, False: 0] | Branch (1058:36): [True: 0, False: 0] ------------------ 1059| 0| { 1060| 0| multPrevEquStr++; 1061| 0| } 1062| 0| else 1063| 0| { 1064| | /* new EqStr is different; output it */ 1065| 0| if (bNext++) ------------------ | Branch (1065:25): [True: 0, False: 0] ------------------ 1066| 0| { 1067| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1068| 0| } 1069| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1070| 0| pPrevEquStr = pCurrEquStr; 1071| 0| multPrevEquStr = 1; 1072| 0| } 1073| 0| } 1074| 0| else 1075| 0| { 1076| 0| pPrevEquStr = pCurrEquStr; 1077| 0| multPrevEquStr = 1; 1078| 0| } 1079| | 1080| 0| pINChI_Prev = NULL; /* pINChI_Prev sp2 does not exist since */ 1081| 0| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 1082| 0| mult = 0; 1083| 0| eq2tautPrev = 1; /* pINChI_Prev sp2 does not exist */ 1084| 0| } 1085| 745| else 1086| 745| { 1087| 745| if (eq2tautPrev) ------------------ | Branch (1087:17): [True: 357, False: 388] ------------------ 1088| 357| { 1089| | /* at this point pINChI_Prev does not exist; however, pINChI */ 1090| | /*might have been discovered and it is different from pINChI_Taut */ 1091| 357| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1091:21): [True: 0, False: 357] | Branch (1091:39): [True: 0, False: 0] ------------------ 1092| 0| { 1093| | /* new EqStr is different; output it */ 1094| 0| if (bNext++) ------------------ | Branch (1094:25): [True: 0, False: 0] ------------------ 1095| 0| { 1096| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1097| 0| } 1098| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1099| 0| pPrevEquStr = NULL; 1100| 0| multPrevEquStr = 0; 1101| 0| } 1102| 357| eq2tautPrev = 0; 1103| 357| pINChI_Prev = pINChI; 1104| 357| pINChI_Taut_Prev = pINChI_Taut; 1105| 357| mult = 0; 1106| 357| } 1107| 388| else 1108| 388| { 1109| | /* check whether pINChI and pINChI_Prev have non-zero identical stereo sp3 */ 1110| | /*================ compare sp3 to previous =====================*/ 1111| 388| eq2prev = bUseMulipliers && ------------------ | Branch (1111:27): [True: 388, False: 0] ------------------ 1112| 388| pINChI && pINChI_Prev && ------------------ | Branch (1112:21): [True: 31, False: 357] | Branch (1112:31): [True: 31, False: 0] ------------------ 1113| 31| ( Stereo = pINChI->Stereo ) && ( Stereo_Prev = pINChI_Prev->Stereo ) && ------------------ | Branch (1113:21): [True: 31, False: 0] | Branch (1113:52): [True: 31, False: 0] ------------------ 1114| 31| Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Prev, EQL_SP3, bRelRac ); ------------------ | | 475| 31|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Prev, EQL_SP3, bRelRac ); ------------------ | | 475| 31|#define EQL_SP3 2 ------------------ | Branch (1114:21): [True: 1, False: 30] ------------------ 1115| 388| if (eq2prev) ------------------ | Branch (1115:21): [True: 1, False: 387] ------------------ 1116| 1| { 1117| 1| mult++; /* mult = (number of non-empty equal items)-1 */ 1118| 1| continue; 1119| 1| } 1120| 387| else 1121| 387| { 1122| 387| if (bNext++) ------------------ | Branch (1122:25): [True: 30, False: 357] ------------------ 1123| 30| { 1124| 30| MakeDelim( sCompDelim, strbuf, bOverflow ); 1125| 30| } 1126| 387| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1126:25): [True: 387, False: 0] | Branch (1126:40): [True: 387, False: 0] ------------------ 1127| 387| { 1128| 387| if (( Stereo_Prev = pINChI_Prev->Stereo ) && Stereo_Prev->nNumberOfStereoCenters > bRelRac) ------------------ | Branch (1128:29): [True: 387, False: 0] | Branch (1128:70): [True: 381, False: 6] ------------------ 1129| 381| { 1130| | /* pINChI_Prev exists and has sp3 info */ 1131| 381| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1132| | 1133| 381| MakeStereoString( Stereo_Prev->nNumber, NULL, Stereo_Prev->t_parity, 1134| 381| 0, Stereo_Prev->nNumberOfStereoCenters, 1135| 381| strbuf, TAUT_MODE, bOverflow ); 1136| 381| } 1137| | /* else sp3 info is not present in pINChI_Prev */ 1138| 387| } 1139| 0| else 1140| 0| { 1141| 0| if (bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1141:29): [True: 0, False: 0] | Branch (1141:51): [True: 0, False: 0] | Branch (1141:71): [True: 0, False: 0] ------------------ 1142| 0| { 1143| 0| if (( Stereo_Taut_Prev = pINChI_Taut_Prev->Stereo ) && Stereo_Taut_Prev->nNumberOfStereoCenters > bRelRac) ------------------ | Branch (1143:33): [True: 0, False: 0] | Branch (1143:84): [True: 0, False: 0] ------------------ 1144| 0| { 1145| | /* since pINChI_Prev does not exist, pINChI_Taut_Prev is non-tautomeric */ 1146| | /* and it has non-trivial sp3 info. This info has already been printed in the main section */ 1147| | /* 1148| | tot_len += MakeDelim( sIdenticalValues, strbuf, bOverflow); 1149| | */ 1150| 0| ; /* pINChI_Taut_Prev sp3 info was output in the main stereo section */ 1151| 0| } 1152| 0| else 1153| 0| { 1154| 0| ; /* pINChI_Taut_Prev exists and has not sp3 info */ 1155| 0| } 1156| 0| } 1157| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 1158| | else 1159| | { 1160| | int stop = 1; /* */ 1161| | } 1162| |#endif 1163| 0| } 1164| 387| } 1165| 387| pINChI_Prev = pINChI; 1166| 387| pINChI_Taut_Prev = pINChI_Taut; 1167| 387| mult = 0; /* we do not know whether the item is empty */ 1168| 387| } 1169| 745| } 1170| 745| } 1171| | 1172| 357| return ( strbuf->nUsedLength - nUsedLength0 ); 1173| 357|} str_StereoAbsInv: 1189| 2|{ 1190| 2| int i, j, ii, nUsedLength0; 1191| 2| INCHI_SORT *is, *is0; 1192| 2| INChI_Stereo *Stereo; 1193| 2| INChI *pINChI; 1194| | 1195| 2| is = NULL; 1196| 2| is0 = pINChISort; 1197| 2| nUsedLength0 = strbuf->nUsedLength; 1198| | 1199| | /* For each connected component... */ 1200| 5| for (i = 0; !*bOverflow && i < num_components; i++) ------------------ | Branch (1200:17): [True: 5, False: 0] | Branch (1200:32): [True: 3, False: 2] ------------------ 1201| 3| { 1202| | 1203| 3| is = is0 + i; 1204| 3| pINChI = ( 0 <= ( ii = GET_II( bOutType, is ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 3|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 3|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 3] | | ------------------ | | 46| 3| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 6|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 6|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 3|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 3, False: 0] | | | | | Branch (35:43): [True: 3, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 3] | | | Branch (46:36): [True: 3, False: 0] | | ------------------ | | 47| 3| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1204:18): [True: 3, False: 0] ------------------ 1205| 3| if (pINChI && ( Stereo = pINChI->Stereo ) && ( j = Stereo->nCompInv2Abs )) ------------------ | Branch (1205:13): [True: 3, False: 0] | Branch (1205:23): [True: 3, False: 0] | Branch (1205:54): [True: 3, False: 0] ------------------ 1206| 3| { 1207| 3| MakeDelim( j < 0 ? "1" : "0", strbuf, bOverflow ); ------------------ | Branch (1207:24): [True: 0, False: 3] ------------------ 1208| 3| } 1209| 0| else 1210| 0| { 1211| 0| MakeDelim( ".", strbuf, bOverflow ); 1212| 0| } 1213| 3| } 1214| | 1215| 2| return ( strbuf->nUsedLength - nUsedLength0 ); 1216| 2|} str_IsoAtoms: 1233| 451|{ 1234| 451| int i, ii, ii2, nUsedLength0; 1235| 451| INCHI_SORT *is, *is2, *is0, *is20; 1236| 451| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 1237| 451| int mult, eq2prev, eq2taut, eq2tautPrev, bNext; 1238| 451| const char *pPrevEquStr, *pCurrEquStr; 1239| 451| int multPrevEquStr; 1240| 451| pINChI_Taut = NULL; 1241| 451| pINChI_Prev = NULL; 1242| 451| pINChI_Taut_Prev = NULL; 1243| 451| mult = 0; 1244| 451| bNext = 0; 1245| 451| is = NULL; 1246| 451| is2 = NULL; 1247| 451| is0 = pINChISort; 1248| 451| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (1248:12): [True: 0, False: 451] ------------------ 1249| | /* djb-rwth: removing redundant code */ 1250| 451| eq2tautPrev = 1; /* pINChI_Prev (previous pINChI) does not exist */ 1251| 451| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 1252| 451| multPrevEquStr = 0; 1253| 451| nUsedLength0 = strbuf->nUsedLength; 1254| | 1255| | /* For each connected component... */ 1256| 1.53k| for (i = 0; i <= num_components; i++) ------------------ | Branch (1256:17): [True: 1.07k, False: 451] ------------------ 1257| 1.07k| { 1258| | 1259| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 1260| 1.07k| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 628|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 628|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 628] | | ------------------ | | 46| 628| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 1.25k|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 1.25k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 628|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 628|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 628|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 628, False: 0] | | | | | Branch (35:43): [True: 628, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 628|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 628] | | | Branch (46:36): [True: 628, False: 0] | | ------------------ | | 47| 628| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1260:20): [True: 628, False: 451] | Branch (1260:42): [True: 628, False: 0] ------------------ 1261| | /*================ compare isotopic info to previous component =====================*/ 1262| 1.07k| if (bSecondNonTautPass) ------------------ | Branch (1262:13): [True: 0, False: 1.07k] ------------------ 1263| 0| { 1264| | /* component that was output on the 1st pass */ 1265| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ | Branch (1265:29): [True: 0, False: 0] | Branch (1265:51): [True: 0, False: 0] ------------------ 1266| 0| } 1267| | /*========= if bSecondNonTautPass then compare iso non-taut to taut non-iso ========*/ 1268| 1.07k| eq2taut = 0; 1269| 1.07k| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1269:13): [True: 1.07k, False: 0] | Branch (1269:25): [True: 0, False: 1.07k] | Branch (1269:47): [True: 0, False: 0] ------------------ 1270| 0| { 1271| 0| eq2taut = Eql_INChI_Isotopic( pINChI, pINChI_Taut ); 1272| 0| eq2taut = eq2taut ? ( iiNUMB | iitNONTAUT ) : 0; ------------------ | | 57| 0|#define iiNUMB 0x0004 /* numbering or inverted stereo numbering */ ------------------ eq2taut = eq2taut ? ( iiNUMB | iitNONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (1272:23): [True: 0, False: 0] ------------------ 1273| 0| } 1274| 1.07k| if (eq2taut) ------------------ | Branch (1274:13): [True: 0, False: 1.07k] ------------------ 1275| 0| { 1276| | /* we may be here only in case of the second (non-taut) pass */ 1277| | /* current non-taut isotopic info has been found to be same as current tautomeric */ 1278| 0| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1278:17): [True: 0, False: 0] | Branch (1278:32): [True: 0, False: 0] ------------------ 1279| 0| { 1280| | /* previous component exists; output it */ 1281| 0| if (bNext++) ------------------ | Branch (1281:21): [True: 0, False: 0] ------------------ 1282| 0| { 1283| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1284| 0| } 1285| 0| if (pINChI_Prev && ( pINChI_Prev->nNumberOfIsotopicAtoms > 0 || ------------------ | Branch (1285:21): [True: 0, False: 0] | Branch (1285:38): [True: 0, False: 0] ------------------ 1286| 0| pINChI_Prev->nNumberOfIsotopicTGroups > 0 )) ------------------ | Branch (1286:21): [True: 0, False: 0] ------------------ 1287| 0| { 1288| | /* non-empty item */ 1289| 0| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1290| | /* Isotopic atoms */ 1291| 0| if (pINChI_Prev->nNumberOfIsotopicAtoms > 0/* && nStrLen-tot_len > 2*/ && !*bOverflow) ------------------ | Branch (1291:25): [True: 0, False: 0] | Branch (1291:95): [True: 0, False: 0] ------------------ 1292| 0| { /* dereferenced bOverflow 2004-06-07 */ 1293| 0| MakeIsoAtomString( pINChI_Prev->IsotopicAtom, 1294| 0| pINChI_Prev->nNumberOfIsotopicAtoms, 1295| 0| strbuf, 1296| 0| TAUT_MODE, bOverflow ); 1297| 0| } 1298| | /* Isotopic tautomeric groups */ 1299| 0| if (pINChI_Prev->nNumberOfIsotopicTGroups > 0 && ------------------ | Branch (1299:25): [True: 0, False: 0] ------------------ 1300| | /*nStrLen-tot_len > 3 && */ 1301| 0| !*bOverflow) ------------------ | Branch (1301:25): [True: 0, False: 0] ------------------ 1302| 0| { 1303| 0| MakeDelim( bAbcNumbers ? ITEM_DELIMETER : "(", strbuf, bOverflow ); ------------------ | | 17| 0|#define ITEM_DELIMETER "," ------------------ | Branch (1303:36): [True: 0, False: 0] ------------------ 1304| 0| MakeIsoTautString( pINChI_Prev->IsotopicTGroup, pINChI_Prev->nNumberOfIsotopicTGroups, 1305| 0| strbuf, TAUT_MODE, bOverflow ); 1306| 0| if (!bAbcNumbers) ------------------ | Branch (1306:29): [True: 0, False: 0] ------------------ 1307| 0| { 1308| 0| MakeDelim( ")", strbuf, bOverflow ); 1309| 0| } 1310| 0| } 1311| 0| } 1312| 0| } 1313| 0| else 1314| 0| { 1315| 0| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1315:21): [True: 0, False: 0] | Branch (1315:41): [True: 0, False: 0] ------------------ 1316| 0| { 1317| | /* previous non-taut component exists only in taut list */ 1318| 0| if (bNext++) ------------------ | Branch (1318:25): [True: 0, False: 0] ------------------ 1319| 0| { 1320| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1321| 0| } 1322| 0| } 1323| 0| } 1324| | /* we have found pINChI isotopic info to be same as in pINChI_Taut */ 1325| | /* output this (current) equivalence as '*', that is, same as tautomeric */ 1326| | /* that was printed on the 1st pass. */ 1327| 0| pCurrEquStr = EquString( eq2taut ); 1328| 0| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1328:17): [True: 0, False: 0] | Branch (1328:35): [True: 0, False: 0] ------------------ 1329| 0| { 1330| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (1330:21): [True: 0, False: 0] | Branch (1330:36): [True: 0, False: 0] ------------------ 1331| 0| { 1332| 0| multPrevEquStr++; 1333| 0| } 1334| 0| else 1335| 0| { 1336| | /* new EqStr is different; output it */ 1337| 0| if (bNext++) ------------------ | Branch (1337:25): [True: 0, False: 0] ------------------ 1338| 0| { 1339| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1340| 0| } 1341| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1342| 0| pPrevEquStr = pCurrEquStr; 1343| 0| multPrevEquStr = 1; 1344| 0| } 1345| 0| } 1346| 0| else 1347| 0| { 1348| 0| pPrevEquStr = pCurrEquStr; 1349| 0| multPrevEquStr = 1; 1350| 0| } 1351| 0| pINChI_Prev = NULL; /* pINChI_Prev isotopic info does not exist since */ 1352| 0| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 1353| 0| mult = 0; 1354| 0| eq2tautPrev = 1; /* pINChI_Prev isotopic info does not exist */ 1355| 0| } 1356| 1.07k| else 1357| 1.07k| if (eq2tautPrev) ------------------ | Branch (1357:17): [True: 451, False: 628] ------------------ 1358| 451| { 1359| | /* at this point pINChI_Prev does not exist; however, pINChI */ 1360| | /* might have been discovered and it is different from pINChI_Taut */ 1361| 451| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1361:21): [True: 0, False: 451] | Branch (1361:39): [True: 0, False: 0] ------------------ 1362| 0| { 1363| | /* new EqStr is different; output it */ 1364| 0| if (bNext++) ------------------ | Branch (1364:25): [True: 0, False: 0] ------------------ 1365| 0| { 1366| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1367| 0| } 1368| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1369| 0| pPrevEquStr = NULL; 1370| 0| multPrevEquStr = 0; 1371| 0| } 1372| 451| eq2tautPrev = 0; 1373| 451| pINChI_Prev = pINChI; 1374| 451| pINChI_Taut_Prev = pINChI_Taut; 1375| 451| mult = 0; 1376| 451| } 1377| 628| else 1378| 628| { 1379| | /*================ compare iso composition to previous =====================*/ 1380| | /* check whether pINChI and pINChI_Prev have non-zero identical isotopic info */ 1381| 628| eq2prev = bUseMulipliers && Eql_INChI_Isotopic( pINChI, pINChI_Prev ); ------------------ | Branch (1381:27): [True: 628, False: 0] | Branch (1381:45): [True: 175, False: 453] ------------------ 1382| 628| if (eq2prev) ------------------ | Branch (1382:21): [True: 175, False: 453] ------------------ 1383| 175| { 1384| 175| mult++; /* mult = (number of non-empty equal items)-1 */ 1385| 175| continue; 1386| 175| } 1387| 453| else 1388| 453| { 1389| | /* pINChI isotopic info is either different or empty. Output pINChI_Prev anyway */ 1390| 453| if (bNext++) ------------------ | Branch (1390:25): [True: 2, False: 451] ------------------ 1391| 2| { 1392| 2| MakeDelim( sCompDelim, strbuf, bOverflow ); 1393| 2| } 1394| 453| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1394:25): [True: 453, False: 0] | Branch (1394:40): [True: 453, False: 0] ------------------ 1395| 453| { 1396| 453| if (( pINChI_Prev->nNumberOfIsotopicAtoms > 0 || ------------------ | Branch (1396:31): [True: 453, False: 0] ------------------ 1397| 0| pINChI_Prev->nNumberOfIsotopicTGroups > 0 )) ------------------ | Branch (1397:31): [True: 0, False: 0] ------------------ 1398| 453| { 1399| | /* pINChI_Prev exists and has isotopic info */ 1400| 453| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1401| | /* Isotopic atoms */ 1402| 453| if (pINChI_Prev->nNumberOfIsotopicAtoms > 0 && ------------------ | Branch (1402:33): [True: 453, False: 0] ------------------ 1403| | /*nStrLen-tot_len > 2 && */ 1404| 453| !*bOverflow) ------------------ | Branch (1404:33): [True: 453, False: 0] ------------------ 1405| 453| { 1406| 453| MakeIsoAtomString( pINChI_Prev->IsotopicAtom, 1407| 453| pINChI_Prev->nNumberOfIsotopicAtoms, 1408| 453| strbuf, TAUT_MODE, bOverflow ); 1409| 453| } 1410| | /* Isotopic tautomeric groups */ 1411| 453| if (pINChI_Prev->nNumberOfIsotopicTGroups > 0 && ------------------ | Branch (1411:33): [True: 0, False: 453] ------------------ 1412| | /*nStrLen-tot_len > 3 && */ 1413| 0| !*bOverflow) ------------------ | Branch (1413:33): [True: 0, False: 0] ------------------ 1414| 0| { 1415| 0| MakeDelim( bAbcNumbers ? ITEM_DELIMETER : "(", strbuf, bOverflow ); ------------------ | | 17| 0|#define ITEM_DELIMETER "," ------------------ | Branch (1415:44): [True: 0, False: 0] ------------------ 1416| 0| MakeIsoTautString( pINChI_Prev->IsotopicTGroup, pINChI_Prev->nNumberOfIsotopicTGroups, 1417| 0| strbuf, TAUT_MODE, bOverflow ); 1418| 0| if (!bAbcNumbers) ------------------ | Branch (1418:37): [True: 0, False: 0] ------------------ 1419| 0| { 1420| 0| MakeDelim( ")", strbuf, bOverflow ); 1421| 0| } 1422| 0| } 1423| 453| } 1424| | /* else isotopic info is not present in pINChI_Prev */ 1425| 453| } 1426| 0| else 1427| 0| { 1428| 0| if (bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1428:29): [True: 0, False: 0] | Branch (1428:51): [True: 0, False: 0] | Branch (1428:71): [True: 0, False: 0] ------------------ 1429| 0| { 1430| 0| if (( pINChI_Taut_Prev->nNumberOfIsotopicAtoms > 0 || ------------------ | Branch (1430:35): [True: 0, False: 0] ------------------ 1431| 0| pINChI_Taut_Prev->nNumberOfIsotopicTGroups > 0 )) ------------------ | Branch (1431:35): [True: 0, False: 0] ------------------ 1432| 0| { 1433| | /* since pINChI_Prev does not exist, pINChI_Taut_Prev is non-tautomeric */ 1434| | /* and it has non-trivial isotopic info */ 1435| | /* 1436| | tot_len += MakeDelim( sIdenticalValues, strbuf, bOverflow); 1437| | */ 1438| 0| ;/* pINChI_Taut_Prev isotopic info was output in the main isotopic section */ 1439| 0| } 1440| 0| else 1441| 0| { 1442| 0| ; /* pINChI_Taut_Prev exists and has not isotopic info */ 1443| 0| } 1444| 0| } 1445| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 1446| | else 1447| | { 1448| | int stop = 1; /* */ 1449| | } 1450| |#endif 1451| 0| } 1452| 453| } 1453| | /* Fix17: moved here 2004-10-08 */ 1454| 453| pINChI_Prev = pINChI; 1455| 453| pINChI_Taut_Prev = pINChI_Taut; 1456| 453| mult = 0; /* we do not know whether the item is empty */ 1457| 453| } 1458| | /* Fix17: moved from here 2004-10-08 1459| | pINChI_Prev = pINChI; 1460| | pINChI_Taut_Prev = pINChI_Taut; 1461| | mult = 0; 1462| | */ 1463| 1.07k| } 1464| | 1465| 451| return ( strbuf->nUsedLength - nUsedLength0 ); 1466| 451|} str_IsoSp2: 1482| 40|{ 1483| 40| int i, ii, ii2, nUsedLength0; 1484| 40| INCHI_SORT *is, *is2, *is0, *is20; 1485| 40| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 1486| 40| INChI_Stereo *Stereo, *Stereo_Prev, *Stereo_Taut, *Stereo_Taut_Prev; 1487| 40| int mult, eq2prev, eq2taut, eq2tautPrev = 1, bNext; /* djb-rwth: initialisation required to avoid garbage values */ 1488| 40| const char *pPrevEquStr, *pCurrEquStr; 1489| 40| int multPrevEquStr; 1490| 40| pINChI_Taut = NULL; 1491| 40| pINChI_Prev = NULL; 1492| 40| pINChI_Taut_Prev = NULL; 1493| 40| mult = 0; 1494| 40| bNext = 0; 1495| 40| is = NULL; 1496| 40| is2 = NULL; 1497| 40| is0 = pINChISort; 1498| 40| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (1498:12): [True: 0, False: 40] ------------------ 1499| | /* djb-rwth: removing redundant code */ 1500| 40| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 1501| 40| multPrevEquStr = 0; 1502| 40| nUsedLength0 = strbuf->nUsedLength; 1503| | 1504| | /* For each connected component... */ 1505| 120| for (i = 0; i <= num_components; i++) ------------------ | Branch (1505:17): [True: 80, False: 40] ------------------ 1506| 80| { 1507| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 1508| 80| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 40|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 40|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 40] | | ------------------ | | 46| 40| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 80|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 80|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 40|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 40|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 40|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 40, False: 0] | | | | | Branch (35:43): [True: 40, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 40|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 40] | | | Branch (46:36): [True: 40, False: 0] | | ------------------ | | 47| 40| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1508:20): [True: 40, False: 40] | Branch (1508:42): [True: 40, False: 0] ------------------ 1509| | /*================ compare sp2 to previous =====================*/ 1510| 80| if (bSecondNonTautPass) ------------------ | Branch (1510:13): [True: 0, False: 80] ------------------ 1511| 0| { 1512| | /* component that was output on the 1st pass */ 1513| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ | Branch (1513:29): [True: 0, False: 0] | Branch (1513:51): [True: 0, False: 0] ------------------ 1514| 0| } 1515| 80| eq2taut = 0; 1516| | /*========= if bSecondNonTautPass then compare iso non-taut stereo to other stereo ========*/ 1517| 80| if (bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1517:13): [True: 0, False: 80] | Branch (1517:35): [True: 0, False: 0] ------------------ 1518| 0| { 1519| | /* compare non-tautomeric isotopic to: 1520| | * a) non-tautomeric non-isotopic 1521| | * b) tautomeric non-isotopic 1522| | * c) tautomeric isotopic 1523| | */ 1524| | /* a) compare non-tautomeric isotopic to non-tautomeric non-isotopic */ 1525| 0| if (!eq2taut) ------------------ | Branch (1525:17): [True: 0, False: 0] ------------------ 1526| 0| { 1527| 0| eq2taut = pINChI && ------------------ | Branch (1527:27): [True: 0, False: 0] ------------------ 1528| | /* non-taut isotopic */ /* non-taut non-isotopic */ 1529| 0| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI->Stereo ) && ------------------ | Branch (1529:21): [True: 0, False: 0] | Branch (1529:60): [True: 0, False: 0] ------------------ 1530| 0| Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (1530:21): [True: 0, False: 0] ------------------ 1531| | /* stereo isotopic non-taut = non-taut (stereo) */ 1532| 0| eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (1532:27): [True: 0, False: 0] ------------------ 1533| 0| } 1534| | /* b) compare non-tautomeric isotopic to tautomeric non-isotopic */ 1535| 0| if (!eq2taut) ------------------ | Branch (1535:17): [True: 0, False: 0] ------------------ 1536| 0| { 1537| 0| eq2taut = pINChI && pINChI_Taut && ------------------ | Branch (1537:27): [True: 0, False: 0] | Branch (1537:37): [True: 0, False: 0] ------------------ 1538| | /* non-taut isotopic */ /* taut non-isotopic */ 1539| 0| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI_Taut->Stereo ) && ------------------ | Branch (1539:21): [True: 0, False: 0] | Branch (1539:60): [True: 0, False: 0] ------------------ 1540| 0| Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (1540:21): [True: 0, False: 0] ------------------ 1541| | /* stereo isotopic non-taut = taut (stereo) */ 1542| 0| eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT ) : 0; ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (1542:27): [True: 0, False: 0] ------------------ 1543| 0| } 1544| | /* c) compare non-tautomeric isotopic to tautomeric isotopic */ 1545| 0| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1545:17): [True: 0, False: 0] | Branch (1545:29): [True: 0, False: 0] | Branch (1545:51): [True: 0, False: 0] ------------------ 1546| 0| { 1547| 0| eq2taut = pINChI && pINChI_Taut && ------------------ | Branch (1547:27): [True: 0, False: 0] | Branch (1547:37): [True: 0, False: 0] ------------------ 1548| 0| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI_Taut->StereoIsotopic ) && ------------------ | Branch (1548:21): [True: 0, False: 0] | Branch (1548:60): [True: 0, False: 0] ------------------ 1549| 0| Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (1549:21): [True: 0, False: 0] ------------------ 1550| | /* stereo isotopic non-taut = isotopic taut (stereo) */ 1551| 0| eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (1551:27): [True: 0, False: 0] ------------------ 1552| 0| } 1553| |#if ( FIX_EMPTY_LAYER_BUG == 1 ) 1554| | if (!eq2taut && pINChI && !( ( Stereo = pINChI->StereoIsotopic ) && 1555| | Eql_INChI_Stereo( Stereo, EQL_SP2, NULL, EQL_EXISTS, 0 ) )) 1556| | { 1557| | /* component has no stereo; check whether it has stereo in the preceding layers */ 1558| | if (pINChI_Taut && ( Stereo_Taut = pINChI_Taut->Stereo ) && /* F is not empty */ 1559| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP2, NULL, EQL_EXISTS, 0 ) || 1560| | !( pINChI_Taut && ( Stereo_Taut = pINChI_Taut->Stereo ) && /* M is empty and ... */ 1561| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP2, NULL, EQL_EXISTS, 0 ) ) && 1562| | ( pINChI_Taut && ( Stereo_Taut = pINChI_Taut->StereoIsotopic ) && /* ... MI is not empty */ 1563| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP2, NULL, EQL_EXISTS, 0 ) )) 1564| | { 1565| | 1566| | eq2taut = iiEmpty; /* the component has stereo in the preceding layer */ 1567| | } 1568| | } 1569| |#endif 1570| 0| } 1571| 80| else 1572| 80| { 1573| | /*========= if not bSecondNonTautPass then compare iso taut stereo to non-iso taut ========*/ 1574| 80| if (!bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1574:17): [True: 80, False: 0] | Branch (1574:40): [True: 80, False: 0] ------------------ 1575| 80| { 1576| | /* compare tautomeric isotopic to tautomeric non-isotopic */ 1577| 80| if (!eq2taut) ------------------ | Branch (1577:21): [True: 80, False: 0] ------------------ 1578| 80| { 1579| 80| eq2taut = pINChI && ------------------ | Branch (1579:31): [True: 40, False: 40] ------------------ 1580| | /* taut isotopic */ /* taut non-isotopic */ 1581| 40| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI->Stereo ) && ------------------ | Branch (1581:25): [True: 40, False: 0] | Branch (1581:64): [True: 2, False: 38] ------------------ 1582| 2| Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 2|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Taut, EQL_SP2, 0 ); ------------------ | | 477| 2|#define EQL_SP2 8 ------------------ | Branch (1582:25): [True: 0, False: 2] ------------------ 1583| | /* stereo isotopic taut = taut (stereo) */ 1584| 80| eq2taut = eq2taut ? ( iiSTEREO | iitISO ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO ) : 0; ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (1584:31): [True: 0, False: 80] ------------------ 1585| |#if ( FIX_EMPTY_LAYER_BUG == 1 ) 1586| | if (!eq2taut && pINChI && !( ( Stereo = pINChI->StereoIsotopic ) && 1587| | Eql_INChI_Stereo( Stereo, EQL_SP2, NULL, EQL_EXISTS, 0 ) )) 1588| | { 1589| | /* component has no MI stereo; check whether it has stereo in the preceding layer M */ 1590| | if (( Stereo_Taut = pINChI->Stereo ) && 1591| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP2, NULL, EQL_EXISTS, 0 )) 1592| | { 1593| | eq2taut = iiEmpty; /* the component has stereo in the preceding layer */ 1594| | } 1595| | } 1596| |#endif 1597| 80| } 1598| 80| } 1599| 80| } 1600| 80| if (eq2taut) ------------------ | Branch (1600:13): [True: 0, False: 80] ------------------ 1601| 0| { 1602| | /* we may be here only in case of the current layer found equal in another layer the same component */ 1603| 0| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1603:17): [True: 0, False: 0] | Branch (1603:32): [True: 0, False: 0] ------------------ 1604| 0| { 1605| | /* previous component exists; output it before output the current component */ 1606| 0| if (bNext++) ------------------ | Branch (1606:21): [True: 0, False: 0] ------------------ 1607| 0| { 1608| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1609| 0| } 1610| 0| if (( Stereo_Prev = pINChI_Prev->StereoIsotopic ) && Stereo_Prev->nNumberOfStereoBonds > 0) ------------------ | Branch (1610:21): [True: 0, False: 0] | Branch (1610:70): [True: 0, False: 0] ------------------ 1611| 0| { 1612| 0| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1613| | 1614| 0| MakeStereoString( Stereo_Prev->nBondAtom1, Stereo_Prev->nBondAtom2, 1615| 0| Stereo_Prev->b_parity, 1616| 0| 0, Stereo_Prev->nNumberOfStereoBonds, 1617| 0| strbuf, TAUT_MODE, bOverflow ); 1618| 0| } 1619| 0| } 1620| 0| else 1621| 0| { 1622| 0| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1622:21): [True: 0, False: 0] | Branch (1622:41): [True: 0, False: 0] ------------------ 1623| 0| { 1624| | /* previous non-taut component exists only in taut list */ 1625| 0| if (bNext++) ------------------ | Branch (1625:25): [True: 0, False: 0] ------------------ 1626| 0| { 1627| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1628| 0| } 1629| | /* do not output stereo of non-tautomeric in non-taut layer: it has been output in the main layer */ 1630| 0| } 1631| 0| } 1632| | /* we have found another (previously printed) layer of the current component equal to this layer */ 1633| | /* output this (current) equivalence mark = EquString(eq2taut) */ 1634| 0| pCurrEquStr = EquString( eq2taut ); 1635| 0| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1635:17): [True: 0, False: 0] | Branch (1635:35): [True: 0, False: 0] ------------------ 1636| 0| { 1637| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (1637:21): [True: 0, False: 0] | Branch (1637:36): [True: 0, False: 0] ------------------ 1638| 0| { 1639| 0| multPrevEquStr++; 1640| 0| } 1641| 0| else 1642| 0| { 1643| | /* new EqStr is different; output it */ 1644| 0| if (bNext++) ------------------ | Branch (1644:25): [True: 0, False: 0] ------------------ 1645| 0| { 1646| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1647| 0| } 1648| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1649| 0| pPrevEquStr = pCurrEquStr; 1650| 0| multPrevEquStr = 1; 1651| 0| } 1652| 0| } 1653| 0| else 1654| 0| { 1655| 0| pPrevEquStr = pCurrEquStr; 1656| 0| multPrevEquStr = 1; 1657| 0| } 1658| 0| pINChI_Prev = NULL; /* pINChI_Prev sp2 does not exist since */ 1659| 0| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 1660| 0| mult = 0; 1661| 0| eq2tautPrev = 1; /* pINChI_Prev and pINChI_Taut_Prev have already been */ 1662| 0| } 1663| 80| else 1664| 80| { 1665| 80| if (eq2tautPrev) ------------------ | Branch (1665:17): [True: 40, False: 40] ------------------ 1666| 40| { 1667| | /* at this point pINChI_Prev does not exist; however, pINChI */ 1668| | /*might have been discovered and it is different from pINChI_Taut */ 1669| 40| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1669:21): [True: 0, False: 40] | Branch (1669:39): [True: 0, False: 0] ------------------ 1670| 0| { 1671| | /* new EqStr is different; output it */ 1672| 0| if (bNext++) ------------------ | Branch (1672:25): [True: 0, False: 0] ------------------ 1673| 0| { 1674| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1675| 0| } 1676| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1677| 0| pPrevEquStr = NULL; 1678| 0| multPrevEquStr = 0; 1679| 0| } 1680| 40| eq2tautPrev = 0; 1681| 40| pINChI_Prev = pINChI; 1682| 40| pINChI_Taut_Prev = pINChI_Taut; 1683| 40| mult = 0; 1684| 40| } 1685| 40| else 1686| 40| { 1687| | /* current layer is different from previously printed layers of the current component */ 1688| | /* compare the current layer to this layer of the previous component: */ 1689| | /* check whether pINChI and pINChI_Prev have non-zero identical stereo sp2 */ 1690| | /*================ compare iso sp2 to previous =====================*/ 1691| 40| eq2prev = bUseMulipliers && ------------------ | Branch (1691:27): [True: 40, False: 0] ------------------ 1692| 40| pINChI && pINChI_Prev && ------------------ | Branch (1692:21): [True: 0, False: 40] | Branch (1692:31): [True: 0, False: 0] ------------------ 1693| 0| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Prev = pINChI_Prev->StereoIsotopic ) && ------------------ | Branch (1693:21): [True: 0, False: 0] | Branch (1693:60): [True: 0, False: 0] ------------------ 1694| 0| Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Prev, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP2, Stereo_Prev, EQL_SP2, 0 ); ------------------ | | 477| 0|#define EQL_SP2 8 ------------------ | Branch (1694:21): [True: 0, False: 0] ------------------ 1695| 40| if (eq2prev) ------------------ | Branch (1695:21): [True: 0, False: 40] ------------------ 1696| 0| { 1697| 0| mult++; /* mult = (number of non-empty equal items)-1 */ 1698| 0| continue; 1699| 0| } 1700| 40| else 1701| 40| { 1702| | /* the current layer is different from this layer of the previous component */ 1703| | /* therefore print the current layer */ 1704| 40| if (bNext++) ------------------ | Branch (1704:25): [True: 0, False: 40] ------------------ 1705| 0| { 1706| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1707| 0| } 1708| 40| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1708:25): [True: 40, False: 0] | Branch (1708:40): [True: 40, False: 0] ------------------ 1709| 40| { 1710| 40| if (( Stereo_Prev = pINChI_Prev->StereoIsotopic ) && Stereo_Prev->nNumberOfStereoBonds > 0) ------------------ | Branch (1710:29): [True: 40, False: 0] | Branch (1710:78): [True: 40, False: 0] ------------------ 1711| 40| { 1712| 40| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1713| | 1714| 40| MakeStereoString( Stereo_Prev->nBondAtom1, Stereo_Prev->nBondAtom2, 1715| 40| Stereo_Prev->b_parity, 1716| 40| 0, Stereo_Prev->nNumberOfStereoBonds, 1717| 40| strbuf, TAUT_MODE, bOverflow ); 1718| 40| } 1719| | /* else sp2 info is not present in pINChI_Prev */ 1720| 40| } 1721| 0| else 1722| 0| {/* do not print pINChI_Prev because it either do not exist of have already been printed */ 1723| 0| if (bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1723:29): [True: 0, False: 0] | Branch (1723:51): [True: 0, False: 0] | Branch (1723:71): [True: 0, False: 0] ------------------ 1724| 0| { 1725| 0| if (( Stereo_Taut_Prev = pINChI_Taut_Prev->StereoIsotopic ) && Stereo_Taut_Prev->nNumberOfStereoBonds > 0) ------------------ | Branch (1725:33): [True: 0, False: 0] | Branch (1725:92): [True: 0, False: 0] ------------------ 1726| 0| { 1727| | /* since pINChI_Prev does not exist, pINChI_Taut_Prev is non-tautomeric */ 1728| | /* and it has non-trivial sp2 info */ 1729| | /* 1730| | tot_len += MakeDelim( sIdenticalValues, strbuf, bOverflow); 1731| | */ 1732| 0| ;/* pINChI_Taut_Prev sp3 info was output in the main stereo section */ 1733| 0| } 1734| 0| else 1735| 0| { 1736| 0| ; /* pINChI_Taut_Prev exists and has not sp2 info */ 1737| 0| } 1738| 0| } 1739| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 1740| | else 1741| | { 1742| | int stop = 1; /* */ 1743| | } 1744| |#endif 1745| 0| } 1746| 40| } 1747| 40| pINChI_Prev = pINChI; 1748| 40| pINChI_Taut_Prev = pINChI_Taut; 1749| 40| mult = 0; /* we do not know whether the item is empty */ 1750| 40| } 1751| 80| } 1752| 80| } 1753| | 1754| 40| return ( strbuf->nUsedLength - nUsedLength0 ); 1755| 40|} str_IsoSp3: 1772| 65|{ 1773| 65| int i, ii, ii2, nUsedLength0; 1774| 65| INCHI_SORT *is, *is2, *is0, *is20; 1775| 65| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 1776| 65| INChI_Stereo *Stereo, *Stereo_Prev, *Stereo_Taut, *Stereo_Taut_Prev; 1777| 65| int mult, eq2prev, eq2taut, eq2tautPrev, bNext; 1778| 65| const char *pPrevEquStr, *pCurrEquStr; 1779| 65| int multPrevEquStr; 1780| 65| pINChI_Taut = NULL; 1781| 65| pINChI_Prev = NULL; 1782| 65| pINChI_Taut_Prev = NULL; 1783| 65| mult = 0; 1784| 65| bNext = 0; 1785| 65| is = NULL; 1786| 65| is2 = NULL; 1787| 65| is0 = pINChISort; 1788| 65| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (1788:12): [True: 0, False: 65] ------------------ 1789| | /* djb-rwth: removing redundant code */ 1790| 65| eq2tautPrev = 1; /* pINChI_Prev (previous pINChI) does not exist */ 1791| 65| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 1792| 65| multPrevEquStr = 0; 1793| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1794| |#else 1795| 65| bRelRac = 0; 1796| 65|#endif 1797| 65| nUsedLength0 = strbuf->nUsedLength; 1798| | 1799| | /* For each connected component... */ 1800| 219| for (i = 0; i <= num_components; i++) ------------------ | Branch (1800:17): [True: 154, False: 65] ------------------ 1801| 154| { 1802| | 1803| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 1804| 154| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 45| 89|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 89|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 89] | | ------------------ | | 46| 89| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 178|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 178|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 89|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 89|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 89|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 89, False: 0] | | | | | Branch (35:43): [True: 89, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 89|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 89] | | | Branch (46:36): [True: 89, False: 0] | | ------------------ | | 47| 89| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1804:20): [True: 89, False: 65] | Branch (1804:42): [True: 89, False: 0] ------------------ 1805| | /*================ compare sp2 to previous =====================*/ 1806| 154| if (bSecondNonTautPass) ------------------ | Branch (1806:13): [True: 0, False: 154] ------------------ 1807| 0| { 1808| | /* component that was output on the 1st pass */ 1809| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 45| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [Folded, False: 0] | | ------------------ | | 46| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 0, False: 0] | | | | | Branch (35:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, Folded] | | | Branch (46:36): [Folded, False: 0] | | ------------------ | | 47| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [Folded, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [Folded, False: 0] | | ------------------ ------------------ | Branch (1809:29): [True: 0, False: 0] | Branch (1809:51): [True: 0, False: 0] ------------------ 1810| 0| } 1811| 154| eq2taut = 0; 1812| | /*========= if bSecondNonTautPass then compare iso non-taut stereo to other stereo ========*/ 1813| 154| if (bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1813:13): [True: 0, False: 154] | Branch (1813:35): [True: 0, False: 0] ------------------ 1814| 0| { 1815| | /* compare non-tautomeric isotopic to: 1816| | * a) non-tautomeric non-isotopic 1817| | * b) tautomeric non-isotopic 1818| | * c) tautomeric isotopic 1819| | */ 1820| | /* a) compare non-tautomeric isotopic to non-tautomeric non-isotopic */ 1821| 0| if (!eq2taut) ------------------ | Branch (1821:17): [True: 0, False: 0] ------------------ 1822| 0| { 1823| 0| eq2taut = pINChI && /* non-taut isotopic */ /* non-taut non-isotopic */ ------------------ | Branch (1823:27): [True: 0, False: 0] ------------------ 1824| 0| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI->Stereo ) && ------------------ | Branch (1824:21): [True: 0, False: 0] | Branch (1824:60): [True: 0, False: 0] ------------------ 1825| 0| Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ | Branch (1825:21): [True: 0, False: 0] ------------------ 1826| | /* stereo isotopic non-taut = non-taut (stereo) */ 1827| 0| eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2NONTAUT ) : 0; ------------------ | | 71| 0|#define iiEq2NONTAUT 0x0040 /* non-tautomeric */ ------------------ | Branch (1827:27): [True: 0, False: 0] ------------------ 1828| 0| } 1829| | /* b) compare non-tautomeric isotopic to tautomeric non-isotopic */ 1830| 0| if (!eq2taut) ------------------ | Branch (1830:17): [True: 0, False: 0] ------------------ 1831| 0| { 1832| 0| eq2taut = pINChI && pINChI_Taut && ------------------ | Branch (1832:27): [True: 0, False: 0] | Branch (1832:37): [True: 0, False: 0] ------------------ 1833| | /* non-taut isotopic */ /* taut non-isotopic */ 1834| 0| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI_Taut->Stereo ) && ------------------ | Branch (1834:21): [True: 0, False: 0] | Branch (1834:60): [True: 0, False: 0] ------------------ 1835| 0| Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ | Branch (1835:21): [True: 0, False: 0] ------------------ 1836| | /* stereo isotopic non-taut = taut (stereo) */ 1837| 0| eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT ) : 0; ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (1837:27): [True: 0, False: 0] ------------------ 1838| 0| } 1839| | /* c) compare non-tautomeric isotopic to tautomeric isotopic */ 1840| 0| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1840:17): [True: 0, False: 0] | Branch (1840:29): [True: 0, False: 0] | Branch (1840:51): [True: 0, False: 0] ------------------ 1841| 0| { 1842| 0| eq2taut = pINChI && pINChI_Taut && ------------------ | Branch (1842:27): [True: 0, False: 0] | Branch (1842:37): [True: 0, False: 0] ------------------ 1843| 0| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI_Taut->StereoIsotopic ) && ------------------ | Branch (1843:21): [True: 0, False: 0] | Branch (1843:60): [True: 0, False: 0] ------------------ 1844| 0| Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 0|#define EQL_SP3 2 ------------------ | Branch (1844:21): [True: 0, False: 0] ------------------ 1845| | /* stereo isotopic non-taut = isotopic taut (stereo) */ 1846| 0| eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 55| 0|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 64| 0|#define iitISO 0x0010 /* Isotopic */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 65| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO | iitNONTAUT | iiEq2ISO ) : 0; ------------------ | | 72| 0|#define iiEq2ISO 0x0080 /* isotopic */ ------------------ | Branch (1846:27): [True: 0, False: 0] ------------------ 1847| 0| } 1848| |#if ( FIX_EMPTY_LAYER_BUG == 1 ) 1849| | if (!eq2taut && pINChI && !( ( Stereo = pINChI->StereoIsotopic ) && 1850| | Eql_INChI_Stereo( Stereo, EQL_SP3, NULL, EQL_EXISTS, 0 ) )) 1851| | { 1852| | /* component has no stereo; check whether it has stereo in the preceding layers */ 1853| | if (pINChI_Taut && ( Stereo_Taut = pINChI_Taut->Stereo ) && /* F is not empty */ 1854| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP3, NULL, EQL_EXISTS, 0 ) || 1855| | !( pINChI_Taut && ( Stereo_Taut = pINChI_Taut->Stereo ) && /* M is empty and ... */ 1856| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP3, NULL, EQL_EXISTS, 0 ) ) && 1857| | ( pINChI_Taut && ( Stereo_Taut = pINChI_Taut->StereoIsotopic ) && /* ... MI is not empty */ 1858| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP3, NULL, EQL_EXISTS, 0 ) )) 1859| | { 1860| | 1861| | eq2taut = iiEmpty; /* the component has stereo in the preceding layer */ 1862| | } 1863| | } 1864| |#endif 1865| 0| } 1866| 154| else 1867| 154| { 1868| | /*========= if not bSecondNonTautPass then compare iso taut stereo to non-iso taut ========*/ 1869| 154| if (!bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1869:17): [True: 154, False: 0] | Branch (1869:40): [True: 154, False: 0] ------------------ 1870| 154| { 1871| | /* compare tautomeric isotopic to tautomeric non-isotopic */ 1872| 154| if (!eq2taut) ------------------ | Branch (1872:21): [True: 154, False: 0] ------------------ 1873| 154| { 1874| 154| eq2taut = pINChI && ------------------ | Branch (1874:31): [True: 89, False: 65] ------------------ 1875| | /* taut isotopic */ /* taut non-isotopic */ 1876| 89| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Taut = pINChI->Stereo ) && ------------------ | Branch (1876:25): [True: 89, False: 0] | Branch (1876:64): [True: 34, False: 55] ------------------ 1877| 34| Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 34|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Taut, EQL_SP3, bRelRac ); ------------------ | | 475| 34|#define EQL_SP3 2 ------------------ | Branch (1877:25): [True: 3, False: 31] ------------------ 1878| | /* stereo isotopic taut = taut (stereo) */ 1879| 154| eq2taut = eq2taut ? ( iiSTEREO | iitISO ) : 0; ------------------ | | 55| 3|#define iiSTEREO 0x0001 /* stereo (sp2 or sp3) */ ------------------ eq2taut = eq2taut ? ( iiSTEREO | iitISO ) : 0; ------------------ | | 64| 3|#define iitISO 0x0010 /* Isotopic */ ------------------ | Branch (1879:31): [True: 3, False: 151] ------------------ 1880| |#if ( FIX_EMPTY_LAYER_BUG == 1 ) 1881| | if (!eq2taut && pINChI && !( ( Stereo = pINChI->StereoIsotopic ) && 1882| | Eql_INChI_Stereo( Stereo, EQL_SP3, NULL, EQL_EXISTS, 0 ) )) 1883| | { 1884| | /* component has no MI stereo; check whether it has stereo in the preceding layer M */ 1885| | if (( Stereo_Taut = pINChI->Stereo ) && 1886| | Eql_INChI_Stereo( Stereo_Taut, EQL_SP3, NULL, EQL_EXISTS, 0 )) 1887| | { 1888| | eq2taut = iiEmpty; /* the component has stereo in the preceding layer */ 1889| | } 1890| | } 1891| |#endif 1892| 154| } 1893| 154| } 1894| 154| } 1895| 154| if (eq2taut) ------------------ | Branch (1895:13): [True: 3, False: 151] ------------------ 1896| 3| { 1897| | /* we may be here only in case of the current layer found equal in another layer the same component */ 1898| 3| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1898:17): [True: 1, False: 2] | Branch (1898:32): [True: 1, False: 0] ------------------ 1899| 1| { 1900| | /* previous component exists; output it before output the current component */ 1901| 1| if (bNext++) ------------------ | Branch (1901:21): [True: 0, False: 1] ------------------ 1902| 0| { 1903| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1904| 0| } 1905| 1| if (( Stereo_Prev = pINChI_Prev->StereoIsotopic ) && Stereo_Prev->nNumberOfStereoCenters > bRelRac) ------------------ | Branch (1905:21): [True: 1, False: 0] | Branch (1905:70): [True: 1, False: 0] ------------------ 1906| 1| { 1907| 1| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1908| | 1909| 1| MakeStereoString( Stereo_Prev->nNumber, NULL, Stereo_Prev->t_parity, 1910| 1| 0, Stereo_Prev->nNumberOfStereoCenters, 1911| 1| strbuf, TAUT_MODE, bOverflow ); 1912| 1| } 1913| 1| } 1914| 2| else 1915| 2| { 1916| 2| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1916:21): [True: 0, False: 2] | Branch (1916:41): [True: 0, False: 0] ------------------ 1917| 0| { 1918| | /* previous non-taut component exists only in taut list */ 1919| 0| if (bNext++) ------------------ | Branch (1919:25): [True: 0, False: 0] ------------------ 1920| 0| { 1921| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1922| 0| } 1923| | /* do not output stereo of non-tautomeric in non-taut layer: it has been output in the main layer */ 1924| 0| } 1925| 2| } 1926| | /* we have found another (previously printed) layer of the current component equal to this layer */ 1927| | /* output this (current) equivalence mark = EquString(eq2taut) */ 1928| 3| pCurrEquStr = EquString( eq2taut ); 1929| 3| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1929:17): [True: 0, False: 3] | Branch (1929:35): [True: 0, False: 0] ------------------ 1930| 0| { 1931| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (1931:21): [True: 0, False: 0] | Branch (1931:36): [True: 0, False: 0] ------------------ 1932| 0| { 1933| 0| multPrevEquStr++; 1934| 0| } 1935| 0| else 1936| 0| { 1937| | /* new EqStr is different; output it */ 1938| 0| if (bNext++) ------------------ | Branch (1938:25): [True: 0, False: 0] ------------------ 1939| 0| { 1940| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1941| 0| } 1942| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1943| 0| pPrevEquStr = pCurrEquStr; 1944| 0| multPrevEquStr = 1; 1945| 0| } 1946| 0| } 1947| 3| else 1948| 3| { 1949| 3| pPrevEquStr = pCurrEquStr; 1950| 3| multPrevEquStr = 1; 1951| 3| } 1952| 3| pINChI_Prev = NULL; /* pINChI_Prev sp2 does not exist since */ 1953| 3| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 1954| 3| mult = 0; 1955| 3| eq2tautPrev = 1; /* pINChI_Prev and pINChI_Taut_Prev have already been output */ 1956| 3| } 1957| 151| else 1958| 151| { 1959| 151| if (eq2tautPrev) ------------------ | Branch (1959:17): [True: 66, False: 85] ------------------ 1960| 66| { 1961| | /* at this point pINChI_Prev does not exist; however, pINChI */ 1962| | /*might have been discovered and it is different from pINChI_Taut */ 1963| 66| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1963:21): [True: 3, False: 63] | Branch (1963:39): [True: 3, False: 0] ------------------ 1964| 3| { 1965| | /* new EqStr is different; output it */ 1966| 3| if (bNext++) ------------------ | Branch (1966:25): [True: 1, False: 2] ------------------ 1967| 1| { 1968| 1| MakeDelim( sCompDelim, strbuf, bOverflow ); 1969| 1| } 1970| 3| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1971| 3| pPrevEquStr = NULL; 1972| 3| multPrevEquStr = 0; 1973| 3| } 1974| 66| eq2tautPrev = 0; 1975| 66| pINChI_Prev = pINChI; 1976| 66| pINChI_Taut_Prev = pINChI_Taut; 1977| 66| mult = 0; 1978| 66| } 1979| 85| else 1980| 85| { 1981| | /* current layer is different from previously printed layers of the current component */ 1982| | /* compare the current layer to this layer of the previous component: */ 1983| | /* check whether pINChI and pINChI_Prev have non-zero identical stereo sp2 */ 1984| | /*================ compare iso sp3 to previous =====================*/ 1985| 85| eq2prev = bUseMulipliers && pINChI && pINChI_Prev && ------------------ | Branch (1985:27): [True: 85, False: 0] | Branch (1985:45): [True: 21, False: 64] | Branch (1985:55): [True: 21, False: 0] ------------------ 1986| 21| ( Stereo = pINChI->StereoIsotopic ) && ( Stereo_Prev = pINChI_Prev->StereoIsotopic ) && ------------------ | Branch (1986:21): [True: 21, False: 0] | Branch (1986:60): [True: 21, False: 0] ------------------ 1987| 21| Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Prev, EQL_SP3, bRelRac ); ------------------ | | 475| 21|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( Stereo, EQL_SP3, Stereo_Prev, EQL_SP3, bRelRac ); ------------------ | | 475| 21|#define EQL_SP3 2 ------------------ | Branch (1987:21): [True: 3, False: 18] ------------------ 1988| 85| if (eq2prev) ------------------ | Branch (1988:21): [True: 3, False: 82] ------------------ 1989| 3| { 1990| 3| mult++; /* mult = (number of non-empty equal items)-1 */ 1991| 3| continue; 1992| 3| } 1993| 82| else 1994| 82| { 1995| 82| if (bNext++) ------------------ | Branch (1995:25): [True: 20, False: 62] ------------------ 1996| 20| { 1997| 20| MakeDelim( sCompDelim, strbuf, bOverflow ); 1998| 20| } 1999| 82| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1999:25): [True: 82, False: 0] | Branch (1999:40): [True: 82, False: 0] ------------------ 2000| 82| { 2001| 82| if (( Stereo_Prev = pINChI_Prev->StereoIsotopic ) && Stereo_Prev->nNumberOfStereoCenters > bRelRac) ------------------ | Branch (2001:29): [True: 82, False: 0] | Branch (2001:78): [True: 75, False: 7] ------------------ 2002| 75| { 2003| 75| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 2004| | 2005| 75| MakeStereoString( Stereo_Prev->nNumber, NULL, Stereo_Prev->t_parity, 2006| 75| 0, Stereo_Prev->nNumberOfStereoCenters, 2007| 75| strbuf, TAUT_MODE, bOverflow ); 2008| 75| } 2009| | /* else sp3 info is not present in pINChI_Prev */ 2010| 82| } 2011| 0| else 2012| | /* do not print pINChI_Prev because it either do not exist of have already been printed */ 2013| 0| if (bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (2013:29): [True: 0, False: 0] | Branch (2013:51): [True: 0, False: 0] | Branch (2013:71): [True: 0, False: 0] ------------------ 2014| 0| { 2015| 0| if (( Stereo_Taut_Prev = pINChI_Taut_Prev->StereoIsotopic ) && Stereo_Taut_Prev->nNumberOfStereoCenters > bRelRac) ------------------ | Branch (2015:33): [True: 0, False: 0] | Branch (2015:92): [True: 0, False: 0] ------------------ 2016| 0| { 2017| | /* since pINChI_Prev does not exist, pINChI_Taut_Prev is non-tautomeric */ 2018| | /* and it has non-trivial sp2 info */ 2019| | /* 2020| | tot_len += MakeDelim( sIdenticalValues, strbuf, bOverflow); 2021| | */ 2022| 0| ;/* pINChI_Taut_Prev sp3 info was output in the main stereo section */ 2023| 0| } 2024| 0| else 2025| 0| { 2026| 0| ; /* pINChI_Taut_Prev exists and has not sp3 info */ 2027| 0| } 2028| 0| } 2029| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2030| | else 2031| | { 2032| | int stop = 1; /* */ 2033| | } 2034| |#endif 2035| 82| } 2036| 82| pINChI_Prev = pINChI; 2037| 82| pINChI_Taut_Prev = pINChI_Taut; 2038| 82| mult = 0; /* we do not know whether the item is empty */ 2039| 82| } 2040| 151| } 2041| 154| } 2042| | 2043| 65| return ( strbuf->nUsedLength - nUsedLength0 ); 2044| 65|} str_IsoStereoAbsInv: 2056| 2|{ 2057| 2| int i, j, ii, nUsedLength0; 2058| 2| INCHI_SORT *is, *is0; 2059| 2| INChI_Stereo *Stereo; 2060| 2| INChI *pINChI; 2061| | 2062| 2| is = NULL; 2063| 2| is0 = pINChISort; 2064| 2| nUsedLength0 = strbuf->nUsedLength; 2065| | 2066| | /* For each connected component... */ 2067| 4| for (i = 0; !*bOverflow && i < num_components; i++) ------------------ | Branch (2067:17): [True: 4, False: 0] | Branch (2067:32): [True: 2, False: 2] ------------------ 2068| 2| { 2069| 2| is = is0 + i; 2070| 2| pINChI = ( 0 <= ( ii = GET_II( bOutType, is ) ) ) ------------------ | | 45| 2|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 2|#define OUT_N1 0 /* non-tautomeric only */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (45:22): [True: 0, False: 2] | | ------------------ | | 46| 2| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 581| 4|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 583| 4|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 35| 2|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 2|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 575| 2|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (35:20): [True: 2, False: 0] | | | | | Branch (35:43): [True: 2, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 575| 2|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 37| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (37:20): [True: 0, False: 0] | | | | | Branch (37:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (46:23): [True: 0, False: 2] | | | Branch (46:36): [True: 2, False: 0] | | ------------------ | | 47| 2| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 585| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 42| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (42:20): [True: 0, False: 0] | | | | | Branch (42:43): [True: 0, False: 0] | | | | | Branch (42:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (47:22): [True: 0, False: 0] | | ------------------ | | 48| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 582| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 40| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (40:20): [True: 0, False: 0] | | | | | Branch (40:43): [True: 0, False: 0] | | | | | Branch (40:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 44| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (44:20): [True: 0, False: 0] | | | | | Branch (44:43): [True: 0, False: 0] | | | | | Branch (44:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (48:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2070:18): [True: 2, False: 0] ------------------ 2071| 2| ? is->pINChI[ii] 2072| 2| : NULL; 2073| 2| if (pINChI && ------------------ | Branch (2073:13): [True: 2, False: 0] ------------------ 2074| 2| ( Stereo = pINChI->StereoIsotopic ) && ------------------ | Branch (2074:13): [True: 2, False: 0] ------------------ 2075| 2| ( j = Stereo->nCompInv2Abs )) ------------------ | Branch (2075:13): [True: 2, False: 0] ------------------ 2076| 2| { 2077| 2| MakeDelim( j < 0 ? "1" : "0", strbuf, bOverflow ); ------------------ | Branch (2077:24): [True: 0, False: 2] ------------------ 2078| 2| } 2079| 0| else 2080| 0| { 2081| 0| MakeDelim( ".", strbuf, bOverflow ); 2082| 0| } 2083| 2| } 2084| | 2085| 2| return ( strbuf->nUsedLength - nUsedLength0 ); 2086| 2|} bIsCenterPointStrict: 181| 95.4k|{ 182| 95.4k| if (atom[iat].valence == atom[iat].chem_bonds_valence) ------------------ | Branch (182:9): [True: 24.9k, False: 70.4k] ------------------ 183| 24.9k| { 184| 24.9k| int endpoint_valence = get_endpoint_valence( atom[iat].el_number ); 185| 24.9k| if (endpoint_valence && ( (endpoint_valence > atom[iat].valence && /* added a check for negative charge or H 3-31-03 */ ------------------ | Branch (185:13): [True: 17.5k, False: 7.48k] | Branch (185:36): [True: 12.2k, False: 5.27k] ------------------ 186| 12.2k| ( atom[iat].num_H || atom[iat].charge == -1 )) || ------------------ | Branch (186:15): [True: 6.81k, False: 5.42k] | Branch (186:34): [True: 3.13k, False: 2.28k] ------------------ 187| 7.56k| (!atom[iat].charge && atom[iat].c_point) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (187:14): [True: 6.85k, False: 709] | Branch (187:35): [True: 440, False: 6.41k] ------------------ 188| 10.3k| { 189| 10.3k| return 1; /* may appear to be tautomeric or chargable 190| | (this increases chem_bonds_valence), should be explored */ 191| 10.3k| } 192| 14.6k| return 0; 193| 24.9k| } 194| 70.4k| if (atom[iat].valence + 1 == atom[iat].chem_bonds_valence && ------------------ | Branch (194:9): [True: 62.2k, False: 8.25k] ------------------ 195| 62.2k| is_centerpoint_elem_strict( atom[iat].el_number )) ------------------ | Branch (195:9): [True: 57.2k, False: 4.92k] ------------------ 196| 57.2k| { 197| 57.2k| return 1; 198| 57.2k| } 199| | 200| 13.1k| return 0; 201| 70.4k|} nGet14TautIn5MembAltRing: 266| 376|{ 267| 376| int nRet; 268| | 269| 376| *pnNumEndPoint = 0; 270| 376| *pnNumBondPos = 0; 271| | 272| 376| if (nMaxLenDfsPath <= 5) ------------------ | Branch (272:9): [True: 0, False: 376] ------------------ 273| 0| { 274| 0| return -1; /* path is too short */ 275| 0| } 276| | 277| 376| nRet = DFS_FindTautInARing( pCG, atom, nStartAtom, nStartAtomNeighbor, 278| 376| nStartAtomNeighborEndpoint, nStartAtomNeighborNeighborEndpoint, 5, 279| 376| nDfsPathPos, DfsPath, Check7MembTautRing, bIsCenterPointStrict, 280| 376| EndPoint, nMaxNumEndPoint, BondPos, nMaxNumBondPos, 281| 376| pnNumEndPoint, pnNumBondPos, pBNS, pBD, num_atoms ); 282| | 283| 376| return nRet; 284| 376|} nGet12TautIn5MembAltRing: 303| 2.40k|{ 304| 2.40k| int nRet; 305| | 306| 2.40k| *pnNumEndPoint = 0; 307| 2.40k| *pnNumBondPos = 0; 308| | 309| 2.40k| if (nMaxLenDfsPath <= 5) ------------------ | Branch (309:9): [True: 0, False: 2.40k] ------------------ 310| 0| { 311| 0| return -1; /* path is too short */ 312| 0| } 313| | 314| 2.40k| nRet = DFS_FindTautInARing( pCG, atom, nStartAtom, nStartAtomNeighbor, 315| 2.40k| -1, -1, 5, 316| 2.40k| nDfsPathPos, DfsPath, Check5MembTautRing, 317| 2.40k| bIsCenterPointStrict, EndPoint, nMaxNumEndPoint, 318| 2.40k| BondPos, nMaxNumBondPos, pnNumEndPoint, 319| 2.40k| pnNumBondPos, pBNS, pBD, num_atoms ); 320| | 321| 2.40k| return nRet; 322| 2.40k|} nGet15TautIn6MembAltRing: 341| 6.09k|{ 342| 6.09k| int nRet; 343| | 344| 6.09k| *pnNumEndPoint = 0; 345| 6.09k| *pnNumBondPos = 0; 346| | 347| 6.09k| if (nMaxLenDfsPath <= 7) ------------------ | Branch (347:9): [True: 0, False: 6.09k] ------------------ 348| 0| { 349| 0| return -1; /* path is too short */ 350| 0| } 351| | 352| 6.09k| nRet = DFS_FindTautInARing( pCG, atom, nStartAtom, 353| 6.09k| -1/*nStartAtomNeighbor*/, 354| 6.09k| -1/*nStartAtomNeighbor2*/, 355| 6.09k| -1/*nStartAtomNeighborNeighbor*/, 356| 6.09k| 6 /* nCycleLen*/, 357| 6.09k| nDfsPathPos, DfsPath, 358| 6.09k| Check6MembTautRing, bIsCenterPointStrict, 359| 6.09k| EndPoint, nMaxNumEndPoint, 360| 6.09k| BondPos, nMaxNumBondPos, 361| 6.09k| pnNumEndPoint, pnNumBondPos, 362| 6.09k| pBNS, pBD, num_atoms ); 363| | 364| 6.09k| return nRet; 365| 6.09k|} DFS_FindTautInARing: 443| 8.88k|{ 444| | /* Depth First Search */ 445| | /* Ignore all atoms not belonging to the current ring system (=biconnected component) */ 446| 8.88k| AT_RANK nMinLenDfsPath; 447| 8.88k| int j, cur_at, nxt_at, prv_at; 448| 8.88k| int nLenDfsPath, nNumFound, ret; 449| | /* djb-rwth: removing redundant variables */ 450| 8.88k| int nDoNotTouchAtom1 = -1, nDoNotTouchAtom2 = -1; 451| | 452| 8.88k| nLenDfsPath = 0; 453| 8.88k| nNumFound = 0; 454| | 455| 8.88k| nCycleLen--; 456| | 457| 8.88k| DfsPath[nLenDfsPath].at_no = cur_at = nStartAtom; 458| 8.88k| DfsPath[nLenDfsPath].bond_type = 0; 459| 8.88k| DfsPath[nLenDfsPath].bond_pos = -1; 460| 8.88k| nDfsPathPos[cur_at] = nLenDfsPath + 1; /* mark */ 461| | /* djb-rwth: removing redundant code */ 462| 8.88k| nMinLenDfsPath = 0; 463| 8.88k| if (nStartAtomNeighbor2 >= 0) ------------------ | Branch (463:9): [True: 376, False: 8.50k] ------------------ 464| 376| { 465| 376| nDoNotTouchAtom1 = (int) atom[cur_at].neighbor[nStartAtomNeighbor2]; 466| 376| } 467| | 468| | /* add the first neighbor to the 2nd tree position if required */ 469| 8.88k| if (nStartAtomNeighbor >= 0) ------------------ | Branch (469:9): [True: 2.78k, False: 6.09k] ------------------ 470| 2.78k| { 471| 2.78k| j = nStartAtomNeighbor; 472| 2.78k| prv_at = cur_at; 473| 2.78k| cur_at = atom[prv_at].neighbor[j]; 474| 2.78k| DfsPath[nLenDfsPath].bond_type = ( atom[prv_at].bond_type[j] & ~BOND_MARK_ALL ); ------------------ | | 191| 2.78k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 475| |#if ( FIX_BOND23_IN_TAUT == 1 ) 476| | DfsPath[nLenDfsPath].bond_type = ACTUAL_ORDER( pBNS, prv_at, j, DfsPath[nLenDfsPath].bond_type ); 477| |#endif 478| 2.78k| DfsPath[nLenDfsPath].bond_pos = j; 479| | 480| 2.78k| nLenDfsPath++; 481| | 482| 2.78k| DfsPath[nLenDfsPath].at_no = cur_at; 483| 2.78k| DfsPath[nLenDfsPath].bond_type = 0; 484| 2.78k| DfsPath[nLenDfsPath].bond_pos = -1; 485| 2.78k| nDfsPathPos[cur_at] = nLenDfsPath + 1; 486| 2.78k| nMinLenDfsPath++; 487| 2.78k| if (nStartAtomNeighborNeighbor >= 0) ------------------ | Branch (487:13): [True: 376, False: 2.40k] ------------------ 488| 376| { 489| 376| nDoNotTouchAtom2 = (int) atom[cur_at].neighbor[nStartAtomNeighborNeighbor]; 490| 376| } 491| 2.78k| } 492| | 493| | /* MAIN DFS CYCLE: may find one and the same t-group 2 times; saves only one instance */ 494| | /* traverse *all* paths starting at atom[nStartAtom]; max. path length = (nCycleLen+1) */ 495| 176k| while (nLenDfsPath >= nMinLenDfsPath) ------------------ | Branch (495:12): [True: 168k, False: 8.88k] ------------------ 496| 168k| { 497| 168k| j = ++DfsPath[nLenDfsPath].bond_pos; 498| 168k| if (j < atom[cur_at = (int) DfsPath[nLenDfsPath].at_no].valence) ------------------ | Branch (498:13): [True: 113k, False: 54.4k] ------------------ 499| 113k| { 500| 113k| DfsPath[nLenDfsPath].bond_type = ( atom[cur_at].bond_type[j] & ~BOND_MARK_ALL ); ------------------ | | 191| 113k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 501| |#if ( FIX_BOND23_IN_TAUT == 1 ) 502| | DfsPath[nLenDfsPath].bond_type = ACTUAL_ORDER( pBNS, cur_at, j, DfsPath[nLenDfsPath].bond_type ); 503| |#endif 504| 113k| nxt_at = (int) atom[cur_at].neighbor[j]; 505| 113k| if (nxt_at == nDoNotTouchAtom1 || ------------------ | Branch (505:17): [True: 0, False: 113k] ------------------ 506| 113k| nxt_at == nDoNotTouchAtom2) ------------------ | Branch (506:17): [True: 376, False: 113k] ------------------ 507| 376| { 508| 376| ; /* ignore */ 509| 376| } 510| 113k| else 511| 113k| { 512| 113k| if (nDfsPathPos[nxt_at]) ------------------ | Branch (512:21): [True: 51.9k, False: 61.3k] ------------------ 513| 51.9k| { 514| | /* found a ring closure or a step backwards */ 515| 51.9k| if (1 == nDfsPathPos[nxt_at] && nLenDfsPath == nCycleLen) ------------------ | Branch (515:25): [True: 15.2k, False: 36.6k] | Branch (515:53): [True: 2.35k, False: 12.8k] ------------------ 516| 2.35k| { 517| | /* we have found the cycle; check it */ 518| 2.35k| ret = ( *CheckDfsRing )( pCG, 519| 2.35k| atom, 520| 2.35k| DfsPath, nLenDfsPath, 521| 2.35k| nStartAtomNeighbor, 522| 2.35k| nStartAtomNeighbor2, 523| 2.35k| nStartAtomNeighborNeighbor, 524| 2.35k| EndPoint, nMaxNumEndPoint, 525| 2.35k| BondPos, nMaxNumBondPos, 526| 2.35k| pnNumEndPoint, pnNumBondPos, 527| 2.35k| pBNS, pBD, num_atoms ); 528| 2.35k| if (ret < 0) ------------------ | Branch (528:29): [True: 0, False: 2.35k] ------------------ 529| 0| { 530| 0| nNumFound = ret; 531| 0| goto clear_path; 532| 0| } 533| 2.35k| nNumFound += ret; 534| 2.35k| } 535| 51.9k| } 536| 61.3k| else 537| 61.3k| { 538| 61.3k| if (!( *CheckCenterPoint )( atom, nxt_at )) ------------------ | Branch (538:25): [True: 11.4k, False: 49.8k] ------------------ 539| 11.4k| { 540| 11.4k| ; /* cannot advance to a non-centerpoint; ignore */ 541| 11.4k| } 542| 49.8k| else 543| 49.8k| { 544| 49.8k| if (nLenDfsPath < nCycleLen) ------------------ | Branch (544:29): [True: 45.6k, False: 4.27k] ------------------ 545| 45.6k| { 546| | /* advance */ 547| 45.6k| nLenDfsPath++; 548| 45.6k| cur_at = nxt_at; 549| 45.6k| DfsPath[nLenDfsPath].at_no = cur_at; 550| 45.6k| DfsPath[nLenDfsPath].bond_type = 0; 551| 45.6k| DfsPath[nLenDfsPath].bond_pos = -1; 552| 45.6k| nDfsPathPos[cur_at] = nLenDfsPath + 1; /* mark */ 553| 45.6k| } 554| 49.8k| } 555| 61.3k| } 556| 113k| } 557| 113k| } 558| 54.4k| else 559| 54.4k| { 560| | /* retract */ 561| 54.4k| nDfsPathPos[(int) DfsPath[nLenDfsPath].at_no] = 0; 562| 54.4k| nLenDfsPath--; 563| 54.4k| } 564| 168k| } 565| | 566| 8.88k|clear_path: 567| 11.6k| while (0 <= nLenDfsPath) ------------------ | Branch (567:12): [True: 2.78k, False: 8.88k] ------------------ 568| 2.78k| { 569| 2.78k| nDfsPathPos[(int) DfsPath[nLenDfsPath].at_no] = 0; 570| 2.78k| nLenDfsPath--; 571| 2.78k| } 572| | 573| 8.88k| return nNumFound; 574| 8.88k|} are_alt_bonds: 744| 1.06k|{ 745| 1.06k| U_CHAR next_bond; 746| 1.06k| int i, bAnyBond, bTautBondPresent = BOND_ALTERN; ------------------ | | 180| 1.06k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 1.06k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ 747| 1.06k| if (len < 2 || bonds[0] == BOND_TRIPLE || bonds[0] == BOND_ALT_13) ------------------ | | 179| 1.06k|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 2.13k|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ if (len < 2 || bonds[0] == BOND_TRIPLE || bonds[0] == BOND_ALT_13) ------------------ | | 183| 1.06k|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (747:9): [True: 0, False: 1.06k] | Branch (747:20): [True: 0, False: 1.06k] | Branch (747:47): [True: 0, False: 1.06k] ------------------ 748| 0| { 749| 0| return 0; 750| 0| } 751| 1.06k| next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; /* djb-rwth: removing redundant code; ignoring LLVM warning: possible presence of global variables */ ------------------ | | 177| 1.06k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 1.06k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; /* djb-rwth: removing redundant code; ignoring LLVM warning: possible presence of global variables */ ------------------ | | 178| 60|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 60|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; /* djb-rwth: removing redundant code; ignoring LLVM warning: possible presence of global variables */ ------------------ | | 178| 1.00k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 1.00k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; /* djb-rwth: removing redundant code; ignoring LLVM warning: possible presence of global variables */ ------------------ | | 177| 47|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 47|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (751:17): [True: 60, False: 1.00k] | Branch (751:57): [True: 47, False: 960] ------------------ 752| 1.06k| if (bonds[0] == BOND_TAUTOM) ------------------ | | 185| 1.06k|#define BOND_TAUTOM 8 ------------------ | Branch (752:9): [True: 889, False: 178] ------------------ 753| 889| { 754| 889| bTautBondPresent = BOND_TAUTOM; ------------------ | | 185| 889|#define BOND_TAUTOM 8 ------------------ 755| 889| next_bond = 0; 756| 889| } 757| 178| else 758| 178| { 759| 178| next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; ------------------ | | 177| 178|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 178|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; ------------------ | | 178| 60|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 60|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; ------------------ | | 178| 118|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 118|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ next_bond = bonds[0] == BOND_SINGLE ? BOND_DOUBLE : bonds[0] == BOND_DOUBLE ? BOND_SINGLE : 0; ------------------ | | 177| 47|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 47|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (759:21): [True: 60, False: 118] | Branch (759:61): [True: 47, False: 71] ------------------ 760| 178| } 761| | 762| 5.25k| for (i = 1; i < len; i++) ------------------ | Branch (762:17): [True: 4.26k, False: 994] ------------------ 763| 4.26k| { 764| 4.26k| if (bonds[i] == BOND_TAUTOM) ------------------ | | 185| 4.26k|#define BOND_TAUTOM 8 ------------------ | Branch (764:13): [True: 3.55k, False: 701] ------------------ 765| 3.55k| { 766| 3.55k| bTautBondPresent = BOND_TAUTOM; ------------------ | | 185| 3.55k|#define BOND_TAUTOM 8 ------------------ 767| 3.55k| bAnyBond = 1; 768| 3.55k| } 769| 701| else 770| 701| { 771| 701| bAnyBond = ( bonds[i] == BOND_ALTERN || bonds[i] == BOND_ALT12NS ); ------------------ | | 180| 701|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 1.40k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAnyBond = ( bonds[i] == BOND_ALTERN || bonds[i] == BOND_ALT12NS ); ------------------ | | 186| 586|#define BOND_ALT12NS 9 ------------------ | Branch (771:26): [True: 115, False: 586] | Branch (771:53): [True: 108, False: 478] ------------------ 772| 701| } 773| 4.26k| if (next_bond) ------------------ | Branch (773:13): [True: 526, False: 3.73k] ------------------ 774| 526| { 775| 526| if (bonds[i] == next_bond || bAnyBond) ------------------ | Branch (775:17): [True: 324, False: 202] | Branch (775:42): [True: 153, False: 49] ------------------ 776| 477| { 777| 477| next_bond = ( next_bond == BOND_SINGLE ) ? BOND_DOUBLE : BOND_SINGLE; ------------------ | | 177| 477|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 477|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ next_bond = ( next_bond == BOND_SINGLE ) ? BOND_DOUBLE : BOND_SINGLE; ------------------ | | 178| 235|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 235|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ next_bond = ( next_bond == BOND_SINGLE ) ? BOND_DOUBLE : BOND_SINGLE; ------------------ | | 177| 242|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 719|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (777:29): [True: 235, False: 242] ------------------ 778| 477| continue; 779| 477| } 780| 49| return 0; 781| 526| } 782| 3.73k| else 783| 3.73k| { 784| 3.73k| if (bonds[i] == BOND_SINGLE) ------------------ | | 177| 3.73k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 3.73k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (784:17): [True: 76, False: 3.65k] ------------------ 785| 76| { 786| 76| next_bond = BOND_DOUBLE; ------------------ | | 178| 76|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 76|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 787| 76| continue; 788| 76| } 789| 3.65k| else 790| 3.65k| { 791| 3.65k| if (bonds[i] == BOND_DOUBLE) ------------------ | | 178| 3.65k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 3.65k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (791:21): [True: 5, False: 3.65k] ------------------ 792| 5| { 793| 5| next_bond = BOND_SINGLE; ------------------ | | 177| 5|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 5|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ 794| 5| continue; 795| 5| } 796| 3.65k| else 797| 3.65k| { 798| 3.65k| if (!bAnyBond) ------------------ | Branch (798:25): [True: 24, False: 3.62k] ------------------ 799| 24| { 800| 24| return 0; 801| 24| } 802| 3.65k| } 803| 3.65k| } 804| 3.73k| } 805| 4.26k| } 806| 994| return !next_bond ? bTautBondPresent : ( next_bond == BOND_SINGLE ) ------------------ | | 177| 139|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 139|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (806:12): [True: 855, False: 139] | Branch (806:44): [True: 59, False: 80] ------------------ 807| 139| ? BOND_DOUBLE : BOND_SINGLE; /* bond to the end atom */ ------------------ | | 178| 59|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 59|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ ? BOND_DOUBLE : BOND_SINGLE; /* bond to the end atom */ ------------------ | | 177| 80|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 80|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ 808| 1.06k|} AddBondsPos: 817| 603|{ 818| 603| int i, j, k, cur_at, nxt_at; 819| | /* add opposite direction bonds to BondPosTmp */ 820| 980| for (j = 0; j < nNumBondPosTmp; j += 2) ------------------ | Branch (820:17): [True: 377, False: 603] ------------------ 821| 377| { 822| 377| cur_at = BondPosTmp[j].nAtomNumber; 823| 377| nxt_at = atom[cur_at].neighbor[(int) BondPosTmp[j].neighbor_index]; 824| 537| for (k = 0; k < atom[nxt_at].valence; k++) ------------------ | Branch (824:21): [True: 537, False: 0] ------------------ 825| 537| { 826| 537| if (cur_at == atom[nxt_at].neighbor[k]) ------------------ | Branch (826:17): [True: 377, False: 160] ------------------ 827| 377| { 828| 377| BondPosTmp[j + 1].nAtomNumber = nxt_at; 829| 377| BondPosTmp[j + 1].neighbor_index = k; 830| 377| break; 831| 377| } 832| 537| } 833| 377| } 834| | /* add new tautomeric bonds */ 835| 980| for (j = 0; j < nNumBondPosTmp; j += 2) ------------------ | Branch (835:17): [True: 377, False: 603] ------------------ 836| 377| { 837| 1.18k| for (i = 0; i < nNumBondPos; i++) ------------------ | Branch (837:21): [True: 849, False: 331] ------------------ 838| 849| { 839| 849| if ((BondPos[i].nAtomNumber == BondPosTmp[j].nAtomNumber && ------------------ | Branch (839:18): [True: 69, False: 780] ------------------ 840| 69| BondPos[i].neighbor_index == BondPosTmp[j].neighbor_index) || ------------------ | Branch (840:17): [True: 6, False: 63] ------------------ 841| 843| (BondPos[i].nAtomNumber == BondPosTmp[j + 1].nAtomNumber && ------------------ | Branch (841:18): [True: 65, False: 778] ------------------ 842| 65| BondPos[i].neighbor_index == BondPosTmp[j + 1].neighbor_index)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (842:17): [True: 40, False: 25] ------------------ 843| 46| { 844| 46| break; /* bond has already been added */ 845| 46| } 846| 849| } 847| 377| if (i == nNumBondPos) ------------------ | Branch (847:13): [True: 331, False: 46] ------------------ 848| 331| { 849| 331| if (i > nMaxNumBondPos) ------------------ | Branch (849:17): [True: 0, False: 331] ------------------ 850| 0| { 851| 0| return -1; /* overflow */ 852| 0| } 853| 331| BondPos[nNumBondPos++] = BondPosTmp[j]; 854| 331| } 855| 377| } 856| | 857| 603| return nNumBondPos; 858| 603|} AddEndPoints: 867| 603|{ 868| 603| int i, j; 869| | /* add new endpoints */ 870| 1.80k| for (j = 0; j < nNumNewEndPoint; j++) ------------------ | Branch (870:17): [True: 1.20k, False: 603] ------------------ 871| 1.20k| { 872| 1.80k| for (i = 0; i < nNumEndPoint; i++) ------------------ | Branch (872:21): [True: 685, False: 1.12k] ------------------ 873| 685| { 874| 685| if (EndPoint[i].nAtomNumber == EndPointTmp[j].nAtomNumber) ------------------ | Branch (874:17): [True: 82, False: 603] ------------------ 875| 82| { 876| 82| break; 877| 82| } 878| 685| } 879| 1.20k| if (i == nNumEndPoint) ------------------ | Branch (879:13): [True: 1.12k, False: 82] ------------------ 880| 1.12k| { 881| 1.12k| if (i > nMaxNumEndPoint) ------------------ | Branch (881:17): [True: 0, False: 1.12k] ------------------ 882| 0| { 883| 0| return -1; /* overflow */ 884| 0| } 885| 1.12k| EndPoint[nNumEndPoint++] = EndPointTmp[j]; 886| 1.12k| } 887| 1.20k| } 888| | 889| 603| return nNumEndPoint; 890| 603|} Check7MembTautRing: 932| 290|{ 933| 290|#define PATH_LEN 8 934| | 935| 290| int i, j, k, /*m,*/ nNumEndPoint, nNumEndPointTmp, nNumBondPos, nNumBondPosTmp; 936| 290| int endpoint, /*nMobile, nMobile1, nMobile2,*/ o1_at, o2_at; 937| 290| int ret; 938| 290| U_CHAR path_bonds[PATH_LEN + 1], bond_type; 939| 290| T_ENDPOINT EndPointTmp[2]; 940| 290| T_BONDPOS BondPosTmp[2 * PATH_LEN]; 941| 290| ENDPOINT_INFO eif1, eif2; 942| 290| int nErr = 0; 943| | 944| | 945| 290| if (nLenDfsPath + 2 > PATH_LEN) ------------------ | | 933| 290|#define PATH_LEN 8 ------------------ | Branch (945:9): [True: 0, False: 290] ------------------ 946| 0| { 947| 0| return -1; /* too long path */ 948| 0| } 949| 290| if (nLenDfsPath != 6 && nLenDfsPath != 4) ------------------ | Branch (949:9): [True: 290, False: 0] | Branch (949:29): [True: 0, False: 290] ------------------ 950| 0| { 951| 0| return -1; /* wrong call */ 952| 0| } 953| | 954| 290| nNumBondPos = *pnNumBondPos; 955| 290| nNumEndPoint = *pnNumEndPoint; 956| 290| nNumBondPosTmp = 0; 957| 290| nNumEndPointTmp = 0; 958| 290| ret = 0; 959| | 960| 290| o1_at = atom[(int) DfsPath[1].at_no].neighbor[nStartAtomNeighborNeighbor]; 961| 290| o2_at = atom[(int) DfsPath[0].at_no].neighbor[nStartAtomNeighbor2]; 962| | /* 963| | nMobile1 = (atom[o1_at].charge == -1) + atom[o1_at].num_H; 964| | nMobile2 = (atom[o2_at].charge == -1) + atom[o2_at].num_H; 965| | */ 966| 290| if (!nGetEndpointInfo( atom, o1_at, &eif1 ) || ------------------ | Branch (966:9): [True: 0, False: 290] ------------------ 967| 290| !nGetEndpointInfo( atom, o2_at, &eif2 )) ------------------ | Branch (967:9): [True: 0, False: 290] ------------------ 968| 0| { 969| 0| return 0; 970| 0| } 971| | 972| | /* save endpoints */ 973| 870| for (j = 0; j < 2; j++) ------------------ | Branch (973:17): [True: 580, False: 290] ------------------ 974| 580| { 975| 580| endpoint = j ? o2_at : o1_at; ------------------ | Branch (975:20): [True: 290, False: 290] ------------------ 976| 580| if (!atom[endpoint].endpoint) ------------------ | Branch (976:13): [True: 83, False: 497] ------------------ 977| 83| { 978| 83| AddAtom2num( EndPointTmp[nNumEndPointTmp].num, atom, endpoint, 2 ); /* fill out */ 979| 83| AddAtom2DA( EndPointTmp[nNumEndPointTmp].num_DA, atom, endpoint, 2 ); 980| | /* 981| | nMobile = j? nMobile2 : nMobile1; 982| | } else { 983| | nMobile = 0; 984| | } 985| | if ( nMobile ) { 986| | EndPointTmp[nNumEndPointTmp].num[1] = (atom[endpoint].charge == -1); 987| | EndPointTmp[nNumEndPointTmp].num[0] = nMobile; 988| | for ( m = 0; m < T_NUM_ISOTOPIC; m ++ ) { 989| | EndPointTmp[nNumEndPointTmp].num[T_NUM_NO_ISOTOPIC+m] = atom[endpoint].num_iso_H[NUM_H_ISOTOPES-m-1]; 990| | } 991| | */ 992| 83| } 993| 497| else 994| 497| { 995| 497| memset( EndPointTmp + nNumEndPointTmp, 0, sizeof( EndPointTmp[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 996| 497| } 997| 580| EndPointTmp[nNumEndPointTmp].nAtomNumber = endpoint; 998| 580| EndPointTmp[nNumEndPointTmp].nGroupNumber = atom[endpoint].endpoint; 999| 580| EndPointTmp[nNumEndPointTmp].nEquNumber = 0; 1000| 580| nNumEndPointTmp++; 1001| 580| } 1002| | 1003| | /* extract bonds */ 1004| 290| k = (int) DfsPath[1].at_no; 1005| 290| bond_type = ( atom[k].bond_type[nStartAtomNeighborNeighbor] & ~BOND_MARK_ALL ); ------------------ | | 191| 290|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 1006| |#if ( FIX_BOND23_IN_TAUT == 1 ) 1007| | bond_type = ACTUAL_ORDER( pBNS, k, nStartAtomNeighborNeighbor, bond_type ); 1008| |#endif 1009| 290| path_bonds[0] = bond_type; 1010| 290| if (REPLACE_THE_BOND( bond_type )) ------------------ | | 173| 290|#define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 177| 290|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | | | ------------------ | | | | | | 32| 580|#define BOND_TYPE_SINGLE 1 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 178| 272|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | | | ------------------ | | | | | | 33| 562|#define BOND_TYPE_DOUBLE 2 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 180| 254|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | | | ------------------ | | | | | | 35| 544|#define BOND_TYPE_ALTERN 4 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 186| 247|#define BOND_ALT12NS 9 | | ------------------ | | | Branch (173:31): [True: 18, False: 272] | | | Branch (173:53): [True: 18, False: 254] | | | Branch (173:75): [True: 7, False: 247] | | | Branch (173:97): [True: 6, False: 241] | | ------------------ ------------------ 1011| 49| { 1012| 49| BondPosTmp[nNumBondPosTmp].nAtomNumber = k; 1013| 49| BondPosTmp[nNumBondPosTmp].neighbor_index = nStartAtomNeighborNeighbor; 1014| 49| nNumBondPosTmp += 2; 1015| 49| } 1016| 1.45k| for (i = 1; i <= nLenDfsPath; i++) ------------------ | Branch (1016:17): [True: 1.16k, False: 290] ------------------ 1017| 1.16k| { 1018| 1.16k| bond_type = DfsPath[i].bond_type; 1019| 1.16k| path_bonds[i] = bond_type; 1020| 1.16k| if (REPLACE_THE_BOND( bond_type )) ------------------ | | 173| 1.16k|#define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 177| 1.16k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | | | ------------------ | | | | | | 32| 2.32k|#define BOND_TYPE_SINGLE 1 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 178| 1.06k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | | | ------------------ | | | | | | 33| 2.22k|#define BOND_TYPE_DOUBLE 2 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 180| 1.00k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | | | ------------------ | | | | | | 35| 2.16k|#define BOND_TYPE_ALTERN 4 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 186| 979|#define BOND_ALT12NS 9 | | ------------------ | | | Branch (173:31): [True: 96, False: 1.06k] | | | Branch (173:53): [True: 57, False: 1.00k] | | | Branch (173:75): [True: 28, False: 979] | | | Branch (173:97): [True: 25, False: 954] | | ------------------ ------------------ 1021| 206| { 1022| 206| BondPosTmp[nNumBondPosTmp].nAtomNumber = DfsPath[i].at_no; 1023| 206| BondPosTmp[nNumBondPosTmp].neighbor_index = DfsPath[i].bond_pos; 1024| 206| nNumBondPosTmp += 2; 1025| 206| } 1026| 1.16k| } 1027| 290| bond_type = ( atom[(int) DfsPath[0].at_no].bond_type[nStartAtomNeighbor2] & ~BOND_MARK_ALL ); ------------------ | | 191| 290|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 1028| |#if ( FIX_BOND23_IN_TAUT == 1 ) 1029| | bond_type = ACTUAL_ORDER( pBNS, (int) DfsPath[0].at_no, nStartAtomNeighbor2, bond_type ); 1030| |#endif 1031| 290| path_bonds[i++] = bond_type; 1032| 290| if (REPLACE_THE_BOND( bond_type )) ------------------ | | 173| 290|#define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 177| 290|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | | | ------------------ | | | | | | 32| 580|#define BOND_TYPE_SINGLE 1 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 178| 267|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | | | ------------------ | | | | | | 33| 557|#define BOND_TYPE_DOUBLE 2 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 180| 255|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | | | ------------------ | | | | | | 35| 545|#define BOND_TYPE_ALTERN 4 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 186| 248|#define BOND_ALT12NS 9 | | ------------------ | | | Branch (173:31): [True: 23, False: 267] | | | Branch (173:53): [True: 12, False: 255] | | | Branch (173:75): [True: 7, False: 248] | | | Branch (173:97): [True: 6, False: 242] | | ------------------ ------------------ 1033| 48| { 1034| 48| BondPosTmp[nNumBondPosTmp].nAtomNumber = DfsPath[0].at_no; 1035| 48| BondPosTmp[nNumBondPosTmp].neighbor_index = nStartAtomNeighbor2; 1036| 48| nNumBondPosTmp += 2; 1037| 48| } 1038| | 1039| 290| if (!are_alt_bonds( path_bonds, i )) ------------------ | Branch (1039:9): [True: 14, False: 276] ------------------ 1040| 14| { 1041| 14| return 0; 1042| 14| } 1043| | 1044| | /* path_bonds is from at_n1 to at_n2 */ 1045| 276| if (!( j = are_alt_bonds( path_bonds, i ) )) ------------------ | Branch (1045:9): [True: 0, False: 276] ------------------ 1046| 0| { 1047| 0| return 0; 1048| 0| } 1049| | /* j is a bond type of the last bond to o2_at, the first bond from o1_at is 2-j if j=1 or 2 */ 1050| | 1051| | /* single bond at o2_at: it should have a mobile atom, o1_at should not */ 1052| 276| if ((j == BOND_SINGLE && ( (!atom[o2_at].endpoint && !eif2.cDonor) || (!atom[o1_at].endpoint && !eif1.cAcceptor) )) || ------------------ | | 177| 276|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 552|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1052:10): [True: 22, False: 254] | Branch (1052:33): [True: 18, False: 4] | Branch (1052:58): [True: 0, False: 18] | Branch (1052:76): [True: 20, False: 2] | Branch (1052:101): [True: 0, False: 20] ------------------ 1053| | /* double bond at o2_at: it should not have a mobile atom, o1_at should */ 1054| 276| (j == BOND_DOUBLE && ( (!atom[o2_at].endpoint && !eif2.cAcceptor) || (!atom[o1_at].endpoint && !eif1.cDonor) ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 178| 276|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 552|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1054:10): [True: 16, False: 260] | Branch (1054:33): [True: 14, False: 2] | Branch (1054:58): [True: 0, False: 14] | Branch (1054:79): [True: 13, False: 3] | Branch (1054:104): [True: 0, False: 13] ------------------ 1055| 0| { 1056| 0| return 0; /* bond pattern does not fit */ 1057| 0| } 1058| | 1059| 276| nNumBondPos = AddBondsPos( atom, BondPosTmp, nNumBondPosTmp, BondPos, nMaxNumBondPos, nNumBondPos ); 1060| 276| nNumEndPoint = AddEndPoints( EndPointTmp, nNumEndPointTmp, EndPoint, nMaxNumEndPoint, nNumEndPoint ); 1061| | 1062| 276| if (nNumBondPos >= 0 && nNumEndPoint >= 0) ------------------ | Branch (1062:9): [True: 276, False: 0] | Branch (1062:29): [True: 276, False: 0] ------------------ 1063| 276| { 1064| 276| if ((ret = ( nNumBondPos > *pnNumBondPos ) || ( nNumEndPoint > *pnNumEndPoint ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1064:13): [True: 276, False: 0] | Branch (1064:20): [True: 44, False: 232] | Branch (1064:55): [True: 232, False: 0] ------------------ 1065| 276| { 1066| 276| *pnNumBondPos = nNumBondPos; 1067| 276| *pnNumEndPoint = nNumEndPoint; 1068| 276| } 1069| 276| } 1070| | 1071| 276| if (ret) ------------------ | Branch (1071:9): [True: 276, False: 0] ------------------ 1072| 276| { 1073| | /* finally check whether the bonds allow moving the hydrogens */ 1074| 276| if (( atom[o1_at].endpoint != atom[o2_at].endpoint || !atom[o1_at].endpoint )) ------------------ | Branch (1074:15): [True: 10, False: 266] | Branch (1074:63): [True: 28, False: 238] ------------------ 1075| 38| { 1076| | 1077| 38| nErr = bExistsAnyAltPath( pCG, pBNS, pBD, atom, num_atoms, o1_at, o2_at, ALT_PATH_MODE_TAUTOM ); ------------------ | | 310| 38|#define ALT_PATH_MODE_TAUTOM 1 ------------------ 1078| | 1079| 38| if (nErr <= 0) ------------------ | Branch (1079:17): [True: 0, False: 38] ------------------ 1080| 0| { 1081| 0| return nErr; 1082| 0| } 1083| 38| } 1084| 276| } 1085| | 1086| 276| return ret; 1087| | 1088| | 1089| 276|#undef PATH_LEN 1090| 276|} Check6MembTautRing: 1123| 1.79k|{ 1124| 1.79k|#define PATH_LEN 4 1125| 1.79k| int i, j, k, /*m,*/ nNumBondPos, nNumEndPoint, ept, eptn; 1126| 1.79k| int nNumEndPointTmp, nNumBondPosTmp, o_at = 0, ret; 1127| | /* int num_taut_endpoints, num_H; */ 1128| 1.79k| int middle_pos; 1129| 1.79k| int nMobile, endpoint, endpoint_valence, chem_bonds_valence; 1130| 1.79k| int nMobile1, endpoint_valence1; /* o_at */ 1131| 1.79k| int nMobile2, endpoint_valence2; /* n_at */ 1132| 1.79k| int nxt_at; 1133| 1.79k| int n_at; 1134| 1.79k| U_CHAR path_bonds[2][PATH_LEN + 1], bond_type; 1135| 1.79k| T_ENDPOINT EndPointTmp[2]; 1136| 1.79k| T_BONDPOS BondPosTmp[4 * PATH_LEN]; 1137| 1.79k| ENDPOINT_INFO eif1, eif2; 1138| | 1139| 1.79k| if (nStartAtomNeighbor >= 0 || nStartAtomNeighbor2 >= 0 || nStartAtomNeighborNeighbor >= 0) ------------------ | Branch (1139:9): [True: 0, False: 1.79k] | Branch (1139:36): [True: 0, False: 1.79k] | Branch (1139:64): [True: 0, False: 1.79k] ------------------ 1140| 0| { 1141| 0| return -1; /* wrong call */ 1142| 0| } 1143| 1.79k| if (nLenDfsPath != 5) ------------------ | Branch (1143:9): [True: 0, False: 1.79k] ------------------ 1144| 0| { 1145| 0| return -1; /* wrong call */ 1146| 0| } 1147| | 1148| 1.79k| nNumBondPos = *pnNumBondPos; 1149| 1.79k| nNumEndPoint = *pnNumEndPoint; 1150| | /* djb-rwth: removing redundant code */ 1151| 1.79k| nNumEndPointTmp = 0; 1152| 1.79k| ret = 0; 1153| 5.37k| for (ept = 0; ept < 2; ept++) /* djb-rwth: initialisation needed for num array */ ------------------ | Branch (1153:19): [True: 3.58k, False: 1.79k] ------------------ 1154| 21.5k| for (eptn = 0; eptn < T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC; eptn++) ------------------ | | 69| 21.5k|#define T_NUM_NO_ISOTOPIC 2 ------------------ for (eptn = 0; eptn < T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC; eptn++) ------------------ | | 70| 21.5k|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 25| 21.5k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (1154:24): [True: 17.9k, False: 3.58k] ------------------ 1155| 17.9k| EndPointTmp[ept].num[eptn] = 0; 1156| | 1157| 1.79k| n_at = (int) DfsPath[0].at_no; /* -N= or -NH- atom */ 1158| 1.79k| nxt_at = DfsPath[middle_pos = ( nLenDfsPath + 1 ) / 2].at_no; /* must have tautomeric neighbor -OH or =O or -NH2 or =NH */ 1159| | 1160| 1.79k| if (atom[nxt_at].valence != 3 ------------------ | Branch (1160:9): [True: 1.57k, False: 216] ------------------ 1161| 216|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 1162| 216| || !atom[nxt_at].bCutVertex ------------------ | Branch (1162:12): [True: 34, False: 182] ------------------ 1163| 1.79k|#endif 1164| 1.79k| ) 1165| 1.61k| { 1166| 1.61k| return 0; 1167| 1.61k| } 1168| | 1169| 440| for (i = 0; i < atom[nxt_at].valence; i++) ------------------ | Branch (1169:17): [True: 440, False: 0] ------------------ 1170| 440| { 1171| 440| o_at = atom[nxt_at].neighbor[i]; 1172| 440| if (o_at != DfsPath[middle_pos - 1].at_no && o_at != DfsPath[middle_pos + 1].at_no) ------------------ | Branch (1172:13): [True: 311, False: 129] | Branch (1172:54): [True: 182, False: 129] ------------------ 1173| 182| { 1174| 182| break; /* >=O or />-OH has been found */ 1175| 182| } 1176| 440| } 1177| 182| if (i == atom[nxt_at].valence) ------------------ | Branch (1177:9): [True: 0, False: 182] ------------------ 1178| 0| { 1179| 0| return 0; /* no neighboring atom >=O or />-OH */ 1180| 0| } 1181| 182| bond_type = ( atom[nxt_at].bond_type[i] & ~BOND_MARK_ALL ); ------------------ | | 191| 182|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 1182| |#if ( FIX_BOND23_IN_TAUT == 1 ) 1183| | bond_type = ACTUAL_ORDER( pBNS, nxt_at, i, bond_type ); 1184| |#endif 1185| 182| if (bond_type != BOND_SINGLE && ------------------ | | 177| 182|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 364|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1185:9): [True: 152, False: 30] ------------------ 1186| 152| bond_type != BOND_DOUBLE && ------------------ | | 178| 152|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 334|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1186:9): [True: 122, False: 30] ------------------ 1187| 122| bond_type != BOND_TAUTOM && ------------------ | | 185| 304|#define BOND_TAUTOM 8 ------------------ | Branch (1187:9): [True: 28, False: 94] ------------------ 1188| 28| bond_type != BOND_ALT12NS && ------------------ | | 186| 210|#define BOND_ALT12NS 9 ------------------ | Branch (1188:9): [True: 10, False: 18] ------------------ 1189| 10| bond_type != BOND_ALTERN) ------------------ | | 180| 10|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 10|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (1189:9): [True: 0, False: 10] ------------------ 1190| 0| { 1191| 0| return 0; 1192| 0| } 1193| | 1194| | /* check whether the two atoms already belong to one tautomeric group */ 1195| |#if ( TAUT_IGNORE_EQL_ENDPOINTS == 1 ) 1196| | if (atom[n_at].endpoint && atom[n_at].endpoint == atom[o_at].endpoint) 1197| | { 1198| | return 0; 1199| | } 1200| |#endif 1201| | /* check =O valence; must be 2 for O, S, Se or 3 for N */ 1202| 182| if (!( endpoint_valence1 = nGetEndpointInfo( atom, o_at, &eif1 ) )) ------------------ | Branch (1202:9): [True: 30, False: 152] ------------------ 1203| 30| { 1204| 30| return 0; /* n_at has been checked in MarkTautomerGroups(...) */ 1205| 30| } 1206| | /* 1207| | if ( 2 != endpoint_valence1 ) 1208| | return 0; // accept only O, S, Se 1209| | */ 1210| | /* check hydrogens/endpoints */ 1211| 152| nMobile1 = atom[o_at].num_H + ( atom[o_at].charge == -1 ); 1212| 152| if (bond_type == BOND_SINGLE && !eif1.cDonor && !atom[o_at].endpoint) ------------------ | | 177| 152|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 304|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1212:9): [True: 22, False: 130] | Branch (1212:37): [True: 6, False: 16] | Branch (1212:53): [True: 6, False: 0] ------------------ 1213| 6| { 1214| 6| return 0; 1215| 6| } 1216| | /* not needed since nGetEndpointInfo returned non-zero 1217| | if ( nMobile1 + atom[o_at].chem_bonds_valence != endpoint_valence1 ) 1218| | return 0; 1219| | */ 1220| | 1221| 146| if (!( endpoint_valence2 = nGetEndpointInfo( atom, n_at, &eif2 ) )) ------------------ | Branch (1221:9): [True: 0, False: 146] ------------------ 1222| 0| { 1223| 0| return 0; /* should not happen here */ 1224| 0| } 1225| 146| nMobile2 = atom[n_at].num_H + ( atom[n_at].charge == -1 ); 1226| | 1227| 146| nMobile = 0; 1228| | 1229| | /* can mobile group move from o_at to n_at? */ 1230| 146| nMobile += ( atom[o_at].endpoint || eif1.cDonor ) && /* from o_at */ ------------------ | Branch (1230:18): [True: 102, False: 44] | Branch (1230:41): [True: 20, False: 24] ------------------ 1231| 122| bond_type != BOND_DOUBLE && ------------------ | | 178| 122|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 268|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1231:9): [True: 122, False: 0] ------------------ 1232| 122| ( atom[n_at].endpoint || /* to n_at */ ------------------ | Branch (1232:11): [True: 98, False: 24] ------------------ 1233| 24| eif2.cNeutralBondsValence > atom[n_at].valence ); ------------------ | Branch (1233:13): [True: 8, False: 16] ------------------ 1234| | /* can mobile group move from n_at to o_at? */ 1235| 146| nMobile += ( atom[n_at].endpoint || eif2.cDonor ) && /* from n_at */ ------------------ | Branch (1235:18): [True: 106, False: 40] | Branch (1235:41): [True: 26, False: 14] ------------------ 1236| 132| ( atom[o_at].endpoint || /* to o_at */ ------------------ | Branch (1236:11): [True: 102, False: 30] ------------------ 1237| 30| eif1.cNeutralBondsValence > atom[o_at].valence ) && ------------------ | Branch (1237:13): [True: 18, False: 12] ------------------ 1238| 120| bond_type != BOND_SINGLE; ------------------ | | 177| 120|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 266|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1238:9): [True: 120, False: 0] ------------------ 1239| | 1240| | 1241| 146| if (!nMobile) ------------------ | Branch (1241:9): [True: 10, False: 136] ------------------ 1242| 10| { 1243| 10| return 0; 1244| 10| } 1245| | 1246| | /* 1247| | num_H = atom[n_at].num_H + atom[o_at].num_H; 1248| | num_taut_endpoints = (0!=atom[n_at].endpoint) + (0!=atom[o_at].endpoint); // if O, N already are endpoints 1249| | if ( num_H != 1 && num_taut_endpoints != 2 && !(num_H==2 && num_taut_endpoints >= 1) ) { 1250| | return 0; 1251| | } 1252| | */ 1253| | /* extract -OH bond */ 1254| 136| nNumBondPosTmp = 0; 1255| | 1256| 136| path_bonds[0][0] = path_bonds[1][0] = bond_type; 1257| 136| if (REPLACE_THE_BOND( bond_type )) ------------------ | | 173| 136|#define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 177| 136|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | | | ------------------ | | | | | | 32| 272|#define BOND_TYPE_SINGLE 1 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 178| 124|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | | | ------------------ | | | | | | 33| 260|#define BOND_TYPE_DOUBLE 2 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 180| 116|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | | | ------------------ | | | | | | 35| 252|#define BOND_TYPE_ALTERN 4 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 186| 106|#define BOND_ALT12NS 9 | | ------------------ | | | Branch (173:31): [True: 12, False: 124] | | | Branch (173:53): [True: 8, False: 116] | | | Branch (173:75): [True: 10, False: 106] | | | Branch (173:97): [True: 12, False: 94] | | ------------------ ------------------ 1258| 42| { 1259| 42| BondPosTmp[nNumBondPosTmp].nAtomNumber = nxt_at; /* accumulate bonds to be */ 1260| 42| BondPosTmp[nNumBondPosTmp].neighbor_index = i; /* marked as tautomeric */ 1261| 42| nNumBondPosTmp += 2; /* leave room for the same bond in the opposite direction */ 1262| 42| } 1263| | 1264| | /* extract other bonds */ 1265| | /* path_bonds[] contents: 1266| | 1267| | 1268| | O OH OH 1269| | || | | 1270| | / \ // \ / \\ 1271| | || || <--> | || <--> || | 1272| | \ / \\ / \ // 1273| | NH N N 1274| | 1275| | path[0]: O=NH-=- OH-N... OH.N... 1276| | path[1] O=NH-=- OH-N... OH.N... 1277| | bonds are all bonds all bonds 1278| | single and are either are either 1279| | double alt or taut alt or taut 1280| | */ 1281| 544| for (j = 0; j < middle_pos; j++) ------------------ | Branch (1281:17): [True: 408, False: 136] ------------------ 1282| 408| { 1283| 1.22k| for (i = 0; i < 2; i++) ------------------ | Branch (1283:21): [True: 816, False: 408] ------------------ 1284| 816| { 1285| | /* k = i? j : middle_pos-1-j; */ 1286| 816| k = i ? middle_pos + j : middle_pos - 1 - j; ------------------ | Branch (1286:17): [True: 408, False: 408] ------------------ 1287| | /* i=0: from O neighbor i=0: down to N, i=1: up to N */ 1288| 816| bond_type = DfsPath[k].bond_type; 1289| | 1290| 816| path_bonds[i][j + 1] = bond_type; 1291| 816| if (REPLACE_THE_BOND( bond_type )) ------------------ | | 173| 816|#define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 177| 816|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | | | ------------------ | | | | | | 32| 1.63k|#define BOND_TYPE_SINGLE 1 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 178| 672|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | | | ------------------ | | | | | | 33| 1.48k|#define BOND_TYPE_DOUBLE 2 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 180| 642|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | | | ------------------ | | | | | | 35| 1.45k|#define BOND_TYPE_ALTERN 4 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 186| 584|#define BOND_ALT12NS 9 | | ------------------ | | | Branch (173:31): [True: 144, False: 672] | | | Branch (173:53): [True: 30, False: 642] | | | Branch (173:75): [True: 58, False: 584] | | | Branch (173:97): [True: 44, False: 540] | | ------------------ ------------------ 1292| 276| { 1293| 276| BondPosTmp[nNumBondPosTmp].nAtomNumber = DfsPath[k].at_no; /* accumulate bonds to be */ 1294| 276| BondPosTmp[nNumBondPosTmp].neighbor_index = DfsPath[k].bond_pos; /* marked as tautomeric */ 1295| 276| nNumBondPosTmp += 2; /* leave room for the same bond in the opposite direction */ 1296| 276| } 1297| 816| } 1298| 408| } 1299| | 1300| 136| if (!are_alt_bonds( path_bonds[0], middle_pos + 1 ) || !are_alt_bonds( path_bonds[1], middle_pos + 1 )) ------------------ | Branch (1300:9): [True: 27, False: 109] | Branch (1300:60): [True: 23, False: 86] ------------------ 1301| 50| { 1302| 50| return 0; 1303| 50| } 1304| | 1305| | /* finally check whether the bonds allow moving the hydrogens */ 1306| 86| if (( atom[o_at].endpoint != atom[n_at].endpoint || !atom[o_at].endpoint )) ------------------ | Branch (1306:11): [True: 10, False: 76] | Branch (1306:57): [True: 8, False: 68] ------------------ 1307| 18| { 1308| 18| int nErr; 1309| 18| nErr = bExistsAnyAltPath( pCG, pBNS, pBD, atom, num_atoms, n_at, o_at, ALT_PATH_MODE_TAUTOM ); ------------------ | | 310| 18|#define ALT_PATH_MODE_TAUTOM 1 ------------------ 1310| 18| if (nErr <= 0) ------------------ | Branch (1310:13): [True: 4, False: 14] ------------------ 1311| 4| { 1312| 4| return nErr; 1313| 4| } 1314| 18| } 1315| | 1316| | /* save endpoints */ 1317| 246| for (j = 0; j < 2; j++) ------------------ | Branch (1317:17): [True: 164, False: 82] ------------------ 1318| 164| { 1319| 164| endpoint = j ? n_at : /* =N- 2 */ ------------------ | Branch (1319:20): [True: 82, False: 82] ------------------ 1320| 164| o_at; /* -OH 1 */ 1321| 164| if (!atom[endpoint].endpoint) ------------------ | Branch (1321:13): [True: 22, False: 142] ------------------ 1322| 22| { /* not a known endpoint */ 1323| 22| endpoint_valence = j ? endpoint_valence2 : endpoint_valence1; ------------------ | Branch (1323:32): [True: 10, False: 12] ------------------ 1324| 22| chem_bonds_valence = j ? eif2.cNeutralBondsValence : eif1.cNeutralBondsValence; ------------------ | Branch (1324:34): [True: 10, False: 12] ------------------ 1325| | /* endpoint_valence = get_endpoint_valence( atom[endpoint].el_number ); */ 1326| 22| nMobile = j ? nMobile2 : nMobile1; ------------------ | Branch (1326:23): [True: 10, False: 12] ------------------ 1327| | /* nMobile = (atom[endpoint].charge == -1) + atom[endpoint].num_H; */ 1328| | /* if ( nMobile + atom[endpoint].chem_bonds_valence != endpoint_valence ) -- fixed 02-06-2003*/ 1329| 22| if (nMobile + chem_bonds_valence != endpoint_valence) ------------------ | Branch (1329:17): [True: 0, False: 22] ------------------ 1330| 0| return 0; /* abnormal endpoint valence; ignore. */ 1331| 22| AddAtom2num( EndPointTmp[nNumEndPointTmp].num, atom, endpoint, 2 ); /* fill out */ 1332| 22| AddAtom2DA( EndPointTmp[nNumEndPointTmp].num_DA, atom, endpoint, 2 ); 1333| | /* 1334| | EndPointTmp[nNumEndPointTmp].num[1] = (atom[endpoint].charge == -1); 1335| | EndPointTmp[nNumEndPointTmp].num[0] = nMobile; 1336| | for ( m = 0; m < T_NUM_ISOTOPIC; m ++ ) { 1337| | EndPointTmp[nNumEndPointTmp].num[T_NUM_NO_ISOTOPIC+m] = atom[endpoint].num_iso_H[NUM_H_ISOTOPES-m-1]; 1338| | } 1339| | */ 1340| 22| } 1341| 142| else 1342| 142| { /* already an endpoint */ /* **now it is wrong:** no mobile atom/charge at this endpoint */ 1343| 142| memset( EndPointTmp + nNumEndPointTmp, 0, sizeof( EndPointTmp[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1344| 142| } 1345| 164| EndPointTmp[nNumEndPointTmp].nAtomNumber = endpoint; 1346| 164| EndPointTmp[nNumEndPointTmp].nGroupNumber = atom[endpoint].endpoint; 1347| 164| EndPointTmp[nNumEndPointTmp].nEquNumber = 0; 1348| | 1349| 164| nNumEndPointTmp++; 1350| 164| } 1351| | /* add collected tautomeric bonds and endpoints to the input/output data */ 1352| 82| nNumBondPos = AddBondsPos( atom, BondPosTmp, nNumBondPosTmp, BondPos, nMaxNumBondPos, nNumBondPos ); 1353| 82| nNumEndPoint = AddEndPoints( EndPointTmp, nNumEndPointTmp, EndPoint, nMaxNumEndPoint, nNumEndPoint ); 1354| | 1355| 82| if (nNumBondPos >= 0 && nNumEndPoint >= 0) ------------------ | Branch (1355:9): [True: 82, False: 0] | Branch (1355:29): [True: 82, False: 0] ------------------ 1356| 82| { 1357| 82| if ((ret = ( nNumBondPos > *pnNumBondPos ) || ( nNumEndPoint > *pnNumEndPoint ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1357:13): [True: 41, False: 41] | Branch (1357:20): [True: 11, False: 71] | Branch (1357:55): [True: 30, False: 41] ------------------ 1358| 41| { 1359| 41| *pnNumBondPos = nNumBondPos; 1360| 41| *pnNumEndPoint = nNumEndPoint; 1361| 41| } 1362| 82| } 1363| | 1364| 82| return ret; 1365| 82|#undef PATH_LEN 1366| 82|} Check5MembTautRing: 1647| 271|{ 1648| 271|#define PATH_LEN 4 1649| 271| int i, j, /*m,*/ nMobile, nMobile1, nMobile2, ept, eptn; 1650| 271| int num_taut_endpoints, nNumBondPos, nNumBondPosTmp, nNumEndPoint, nNumEndPointTmp, ret; 1651| 271| int endpoint; 1652| 271| int n1_at = (int) DfsPath[0].at_no; 1653| 271| int n2_at = (int) DfsPath[1].at_no; 1654| 271| U_CHAR path_bonds[PATH_LEN + 1], bond_type; 1655| 271| T_ENDPOINT EndPointTmp[2]; 1656| 271| T_BONDPOS BondPosTmp[2 * PATH_LEN]; 1657| 271| ENDPOINT_INFO eif1, eif2; 1658| | 1659| | /* the two root atoms (atom[n1_at] and atom[n2_at]) cannot belong */ 1660| | /* to one and the same tautomeric group: it has been verified in MarkTautomerGroups() */ 1661| | 1662| | /* check hydrogens/endpoints */ 1663| 271| if (nLenDfsPath != 4) ------------------ | Branch (1663:9): [True: 0, False: 271] ------------------ 1664| 0| { 1665| 0| return 0; /* program error */ 1666| 0| } 1667| 271| if (nStartAtomNeighbor2 >= 0 || nStartAtomNeighborNeighbor >= 0) ------------------ | Branch (1667:9): [True: 0, False: 271] | Branch (1667:37): [True: 0, False: 271] ------------------ 1668| 0| { 1669| 0| return 0; /* program error: wrong call */ 1670| 0| } 1671| | 1672| 271| nNumBondPos = *pnNumBondPos; 1673| 271| nNumEndPoint = *pnNumEndPoint; 1674| 271| nNumEndPointTmp = 0; 1675| | /* djb-rwth: removing redundant code */ 1676| 271| ret = 0; 1677| 813| for (ept = 0; ept < 2; ept++) /* djb-rwth: initialisation needed for num array */ ------------------ | Branch (1677:19): [True: 542, False: 271] ------------------ 1678| 3.25k| for (eptn = 0; eptn < T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC; eptn++) ------------------ | | 69| 3.25k|#define T_NUM_NO_ISOTOPIC 2 ------------------ for (eptn = 0; eptn < T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC; eptn++) ------------------ | | 70| 3.25k|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 25| 3.25k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (1678:24): [True: 2.71k, False: 542] ------------------ 1679| 2.71k| EndPointTmp[ept].num[eptn] = 0; 1680| | 1681| 271| if (!nGetEndpointInfo( atom, n1_at, &eif1 ) || ------------------ | Branch (1681:9): [True: 0, False: 271] ------------------ 1682| 271| !nGetEndpointInfo( atom, n2_at, &eif2 )) ------------------ | Branch (1682:9): [True: 0, False: 271] ------------------ 1683| 0| { 1684| 0| return 0; 1685| 0| } 1686| | 1687| 271| nMobile1 = atom[n1_at].num_H + ( atom[n1_at].charge == -1 ); 1688| 271| nMobile2 = atom[n2_at].num_H + ( atom[n2_at].charge == -1 ); 1689| 271| nMobile = nMobile1 + nMobile2; 1690| 271| num_taut_endpoints = ( 0 != atom[n1_at].endpoint ) + ( 0 != atom[n2_at].endpoint ); /* if both N atoms already are endpoints */ 1691| | /* 1692| | if ( !(nMobile == 1 || num_taut_endpoints == 2) && !(nMobile>1 && num_taut_endpoints >= 1) ) { 1693| | return 0; 1694| | } 1695| | */ 1696| 271| if (num_taut_endpoints == 0 && nMobile != 1) ------------------ | Branch (1696:9): [True: 14, False: 257] | Branch (1696:36): [True: 0, False: 14] ------------------ 1697| 0| { 1698| 0| return 0; 1699| 0| } 1700| | 1701| | /* finally check whether the bonds allow moving the hydrogens */ 1702| 271| if (( atom[n1_at].endpoint != atom[n2_at].endpoint || !atom[n1_at].endpoint )) ------------------ | Branch (1702:11): [True: 33, False: 238] | Branch (1702:59): [True: 14, False: 224] ------------------ 1703| 47| { 1704| 47| int nErr; 1705| 47| nErr = bExistsAnyAltPath( pCG, pBNS, pBD, atom, num_atoms, n1_at, n2_at, ALT_PATH_MODE_TAUTOM ); ------------------ | | 310| 47|#define ALT_PATH_MODE_TAUTOM 1 ------------------ 1706| 47| if (nErr <= 0) ------------------ | Branch (1706:13): [True: 15, False: 32] ------------------ 1707| 15| { 1708| 15| return nErr; 1709| 15| } 1710| 47| } 1711| | 1712| | /* save endpoints */ 1713| 768| for (j = 0; j < 2; j++) ------------------ | Branch (1713:17): [True: 512, False: 256] ------------------ 1714| 512| { 1715| 512| endpoint = j ? n1_at : n2_at; ------------------ | Branch (1715:20): [True: 256, False: 256] ------------------ 1716| 512| if (!atom[endpoint].endpoint) ------------------ | Branch (1716:13): [True: 40, False: 472] ------------------ 1717| 40| { 1718| | /* not a known endpoint */ 1719| | /* 1720| | nMobile = (atom[endpoint].charge == -1) + atom[endpoint].num_H; 1721| | } else { 1722| | nMobile = 0; 1723| | } 1724| | if ( nMobile ) { 1725| | */ 1726| 40| AddAtom2num( EndPointTmp[nNumEndPointTmp].num, atom, endpoint, 2 ); /* fill out */ 1727| 40| AddAtom2DA( EndPointTmp[nNumEndPointTmp].num_DA, atom, endpoint, 2 ); 1728| | /* 1729| | EndPointTmp[nNumEndPointTmp].num[1] = (atom[endpoint].charge == -1); 1730| | EndPointTmp[nNumEndPointTmp].num[0] = nMobile; 1731| | for ( m = 0; m < T_NUM_ISOTOPIC; m ++ ) { 1732| | EndPointTmp[nNumEndPointTmp].num[T_NUM_NO_ISOTOPIC+m] = atom[endpoint].num_iso_H[NUM_H_ISOTOPES-m-1]; 1733| | } 1734| | */ 1735| 40| } 1736| 472| else 1737| 472| { 1738| 472| memset( EndPointTmp + nNumEndPointTmp, 0, sizeof( EndPointTmp[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1739| 472| } 1740| 512| EndPointTmp[nNumEndPointTmp].nAtomNumber = endpoint; 1741| 512| EndPointTmp[nNumEndPointTmp].nGroupNumber = atom[endpoint].endpoint; 1742| 512| EndPointTmp[nNumEndPointTmp].nEquNumber = 0; 1743| | 1744| 512| nNumEndPointTmp++; 1745| 512| } 1746| | 1747| | /* extract bonds */ 1748| 256| nNumBondPosTmp = 0; 1749| 1.28k| for (i = 1; i <= nLenDfsPath; i++) ------------------ | Branch (1749:17): [True: 1.02k, False: 256] ------------------ 1750| 1.02k| { 1751| 1.02k| bond_type = DfsPath[i].bond_type; 1752| 1.02k| path_bonds[i - 1] = bond_type; 1753| 1.02k| if (REPLACE_THE_BOND( bond_type )) ------------------ | | 173| 1.02k|#define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 177| 1.02k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | | | ------------------ | | | | | | 32| 2.04k|#define BOND_TYPE_SINGLE 1 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 178| 997|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | | | ------------------ | | | | | | 33| 2.02k|#define BOND_TYPE_DOUBLE 2 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 180| 991|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | | | ------------------ | | | | | | 35| 2.01k|#define BOND_TYPE_ALTERN 4 | | | | ------------------ | | ------------------ | | #define REPLACE_THE_BOND(X) ( (X) == BOND_SINGLE || (X) == BOND_DOUBLE || (X) == BOND_ALTERN || (X) == BOND_ALT12NS ) | | ------------------ | | | | 186| 978|#define BOND_ALT12NS 9 | | ------------------ | | | Branch (173:31): [True: 27, False: 997] | | | Branch (173:53): [True: 6, False: 991] | | | Branch (173:75): [True: 13, False: 978] | | | Branch (173:97): [True: 23, False: 955] | | ------------------ ------------------ 1754| 69| { 1755| 69| BondPosTmp[nNumBondPosTmp].nAtomNumber = DfsPath[i].at_no; 1756| 69| BondPosTmp[nNumBondPosTmp].neighbor_index = DfsPath[i].bond_pos; 1757| 69| nNumBondPosTmp += 2; 1758| 69| } 1759| 1.02k| } 1760| | /* path_bonds is from at_n2 to at_n1 */ 1761| 256| if (!( i = are_alt_bonds( path_bonds, nLenDfsPath ) )) ------------------ | Branch (1761:9): [True: 9, False: 247] ------------------ 1762| 9| { 1763| 9| return 0; 1764| 9| } 1765| | /* i is a bond type of the last bond to at_n1, the first bond from at_n2 is 2-i if i=1 or 2 */ 1766| | 1767| | /* single bond at n1_at: it should have a mobile atom, n2_at should not */ 1768| 247| if ((i == BOND_SINGLE && ( (!atom[n1_at].endpoint && !eif1.cDonor) || (!atom[n2_at].endpoint && !eif2.cAcceptor) )) || ------------------ | | 177| 247|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 494|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1768:10): [True: 9, False: 238] | Branch (1768:33): [True: 6, False: 3] | Branch (1768:58): [True: 0, False: 6] | Branch (1768:76): [True: 6, False: 3] | Branch (1768:101): [True: 0, False: 6] ------------------ 1769| | /* double bond at n1_at: it should not have a mobile atom, n2_at should */ 1770| 247| (i == BOND_DOUBLE && ( (!atom[n1_at].endpoint && !eif1.cAcceptor) || (!atom[n2_at].endpoint && !eif2.cDonor) ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 178| 247|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 494|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1770:10): [True: 10, False: 237] | Branch (1770:33): [True: 5, False: 5] | Branch (1770:58): [True: 0, False: 5] | Branch (1770:79): [True: 6, False: 4] | Branch (1770:104): [True: 2, False: 4] ------------------ 1771| 2| { 1772| 2| return 0; /* bond pattern does not fit */ 1773| 2| } 1774| | 1775| 245| nNumBondPos = AddBondsPos( atom, BondPosTmp, nNumBondPosTmp, BondPos, nMaxNumBondPos, nNumBondPos ); 1776| 245| nNumEndPoint = AddEndPoints( EndPointTmp, nNumEndPointTmp, EndPoint, nMaxNumEndPoint, nNumEndPoint ); 1777| | 1778| 245| if (nNumBondPos >= 0 && nNumEndPoint >= 0) ------------------ | Branch (1778:9): [True: 245, False: 0] | Branch (1778:29): [True: 245, False: 0] ------------------ 1779| 245| { 1780| 245| if ((ret = ( nNumBondPos > *pnNumBondPos ) || ( nNumEndPoint > *pnNumEndPoint ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1780:13): [True: 245, False: 0] | Branch (1780:20): [True: 21, False: 224] | Branch (1780:55): [True: 224, False: 0] ------------------ 1781| 245| { 1782| 245| *pnNumBondPos = nNumBondPos; 1783| 245| *pnNumEndPoint = nNumEndPoint; 1784| 245| } 1785| 245| } 1786| 245| return ret; 1787| | 1788| 247|#undef PATH_LEN 1789| 247|} ReadWriteInChI: 603| 12.5k|{ 604| 12.5k| InpInChI OneInput; 605| 12.5k| char* strHdr = NULL; 606| 12.5k| char* szCurHdr = NULL; 607| 12.5k| int num_components[INCHI_NUM]; 608| 12.5k| int bReqNonTaut = (0 != ((ip_inp->nMode & REQ_MODE_BASIC) && ------------------ | | 15| 12.5k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (608:30): [True: 0, False: 12.5k] ------------------ 609| 0| (ip_inp->nMode & REQ_MODE_TAUT))); ------------------ | | 16| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (609:9): [True: 0, False: 0] ------------------ 610| | /* 611| | int bReqRecmet = (0 != ((ip->bTautFlags & TG_FLAG_RECONNECT_COORD) && 612| | (ip->bTautFlags & TG_FLAG_DISCONNECT_COORD))); 613| | */ 614| 12.5k| int bReqStereo = (0 != (ip_inp->nMode & REQ_MODE_STEREO)); ------------------ | | 19| 12.5k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 615| 12.5k| int bHasSomeReconnected = 0, bHasSomeFixedH = 0, bHasMetal = 0; 616| 12.5k| int nModeFlagsStereo = 0, bTautFlags = 0; /* InChI creation flags modifications derived from current InChI */ 617| 12.5k| MODE_PIXH nModeProtonIsoExchgH[INCHI_NUM]; 618| | 619| 12.5k| NORM_CANON_FLAGS ncFlags; 620| 12.5k| NORM_CANON_FLAGS* pncFlags = &ncFlags; 621| 12.5k| INPUT_PARMS ip_cur, * ip; 622| 12.5k| STRUCT_DATA sd_cur, * sd; 623| | 624| 12.5k| int pState; /* djb-rwth: removing redundant variables */ 625| 12.5k| int bReqProtonsForEachComponent = 0; 626| 12.5k| int bReqSplitOutputInChI = 0; 627| 12.5k| SEGM_LINE Line; 628| 12.5k| SEGM_LINE* pLine = &Line; 629| 12.5k| long ulProcessingTime = 0; 630| 12.5k| inchiTime ulTStart; 631| 12.5k| long num_processed = 0, num_errors = 0; 632| 12.5k| int bPlainTabbedOutput; /* djb-rwth: ignoring LLVM warning: variable used */ 633| 12.5k| const char* pTAB; /* djb-rwth: ignoring LLVM warning: variable used */ 634| | 635| 12.5k| long num_inp = 0; 636| | 637| 12.5k| int read_inchi_ok = 0; 638| 12.5k| int end_of_data_reached = 0; 639| 12.5k| int treat_save_opt = 0; 640| 12.5k| int input_is_stdinchi = 0; 641| 12.5k| int input_has_save_opt = 0; 642| 12.5k| unsigned char input_save_opt_bits = 0; 643| 12.5k| unsigned char save_opt_bits = 0; 644| | 645| 12.5k| const int bInChI2Structure = 0 != (ip_inp->bReadInChIOptions & READ_INCHI_TO_STRUCTURE); ------------------ | | 991| 12.5k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 646| 12.5k| const int bInChI2InChI = 0 != (ip_inp->bReadInChIOptions & READ_INCHI_OUTPUT_INCHI); ------------------ | | 988| 12.5k|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 647| 12.5k| const int bReadCoord = bInChI2Structure; 648| | 649| 12.5k| int nMessageLen = MAX_MSG_LEN; ------------------ | | 423| 12.5k|#define MAX_MSG_LEN 512 ------------------ 650| 12.5k| char szMessage[MAX_MSG_LEN]; 651| 12.5k| int nInitLenMessage; 652| 12.5k| int invalid_opt = 0; 653| 12.5k| int j, nErr, iINChI; 654| | 655| 12.5k| int treat_mismatch_as_error = ip_inp->bINChIOutputOptions2 & INCHI_OUT_MISMATCH_AS_ERROR; ------------------ | | 150| 12.5k|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ 656| 12.5k| int output_error_inchi = ip_inp->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR; ------------------ | | 149| 12.5k|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ 657| | 658| 12.5k| int ret = 0; 659| 12.5k| int nReadStatus = RI_ERR_EOL; ------------------ | | 18| 12.5k|#define RI_ERR_EOL (-4) ------------------ 660| | 661| 12.5k| INCHI_IOSTREAM* pRealOut = pOut; 662| | /* temporary output buffer pTmpOut may be used */ 663| | /* locally instead of legal pOut to capture */ 664| | /* InChI string which may then be recognised */ 665| | /* as erratic (whence should not be finally */ 666| | /* printed) */ 667| 12.5k| INCHI_IOSTREAM tmpoutputstr; 668| 12.5k| INCHI_IOSTREAM* pTmpOut = &tmpoutputstr; 669| 12.5k| if (bInChI2Structure) ------------------ | Branch (669:9): [True: 6.28k, False: 6.28k] ------------------ 670| 6.28k| { 671| 6.28k| inchi_ios_init(pTmpOut, INCHI_IOS_TYPE_STRING, NULL); ------------------ | | 1016| 6.28k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 672| 6.28k| if (pTmpOut->s.pStr) ------------------ | Branch (672:13): [True: 0, False: 6.28k] ------------------ 673| 0| pRealOut = pTmpOut; 674| 6.28k| } 675| | 676| |#ifdef GHI100_FIX 677| |#if ((SPRINTF_FLAG != 1) && (SPRINTF_FLAG != 2)) 678| | setlocale(LC_ALL, "en-US"); /* djb-rwth: setting all locales to "en-US" */ 679| |#endif 680| |#endif 681| | 682| 12.5k| memset(szMessage, 0, sizeof(szMessage)); /* djb-rwth: memset_s C11/Annex K variant? */ 683| 12.5k| memset(&OneInput, 0, sizeof(OneInput)); /* djb-rwth: memset_s C11/Annex K variant? */ 684| 12.5k| memset(pLine, 0, sizeof(pLine[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 685| 12.5k| if (szMsg) ------------------ | Branch (685:9): [True: 12.5k, False: 0] ------------------ 686| 12.5k| szMsg[0] = '\0'; 687| | 688| 12.5k| OneInput.polymer = NULL; /* v. 1.05 added */ 689| 12.5k| OneInput.v3000 = NULL; 690| | 691| | 692| | /* Read input, InChI by InChI*/ 693| 12.5k| while (nReadStatus != RI_ERR_EOF) ------------------ | | 19| 12.5k|#define RI_ERR_EOF (0) ------------------ | Branch (693:12): [True: 12.5k, False: 0] ------------------ 694| 12.5k| { 695| 37.6k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 37.6k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (695:26): [True: 25.1k, False: 12.5k] ------------------ 696| 25.1k| { 697| 75.3k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 75.3k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (697:25): [True: 50.2k, False: 25.1k] ------------------ 698| 50.2k| { 699| 50.2k| if (OneInput.nNumProtons[iINChI][j].pNumProtons) ------------------ | Branch (699:21): [True: 0, False: 50.2k] ------------------ 700| 0| { 701| 0| inchi_free(OneInput.nNumProtons[iINChI][j].pNumProtons); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 702| 0| OneInput.nNumProtons[iINChI][j].pNumProtons = NULL; 703| 0| } 704| 50.2k| } 705| 25.1k| } 706| | 707| 12.5k| memset(&OneInput, 0, sizeof(OneInput)); /* djb-rwth: memset_s C11/Annex K variant? */ 708| 12.5k| memset(pncFlags, 0, sizeof(*pncFlags)); /* djb-rwth: memset_s C11/Annex K variant? */ 709| | /* djb-rwth: removing redundant code */ 710| 12.5k| ip_cur = *ip_inp; 711| 12.5k| ip = &ip_cur; 712| 12.5k| sd_cur = *sd_inp; 713| 12.5k| sd = &sd_cur; 714| | 715| 12.5k| bReqSplitOutputInChI = 716| 12.5k| 0 != (ip->bReadInChIOptions & READ_INCHI_SPLIT_OUTPUT); ------------------ | | 989| 12.5k|#define READ_INCHI_SPLIT_OUTPUT 0x00000002 ------------------ 717| 12.5k| bReqProtonsForEachComponent = 718| 12.5k| bReqSplitOutputInChI && ------------------ | Branch (718:13): [True: 0, False: 12.5k] ------------------ 719| 0| 0 != (READ_INCHI_KEEP_BALANCE_P & ip->bReadInChIOptions); ------------------ | | 990| 0|#define READ_INCHI_KEEP_BALANCE_P 0x00000004 ------------------ | Branch (719:13): [True: 0, False: 0] ------------------ 720| 12.5k| bPlainTabbedOutput = 721| 12.5k| 0 != (ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT); ------------------ | | 139| 12.5k|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 722| | 723| 12.5k| pTAB = 724| 12.5k|#if ( defined(TARGET_API_LIB) || defined(TARGET_LIB_FOR_WINCHI) ) 725| 12.5k| "\n"; 726| |#else 727| | bPlainTabbedOutput ? "\t" : "\n"; 728| |#endif 729| | 730| | 731| 12.5k| if (bInChI2Structure) ------------------ | Branch (731:13): [True: 6.28k, False: 6.28k] ------------------ 732| 6.28k| { 733| 6.28k| bReqStereo = 1; 734| 6.28k| bReqSplitOutputInChI = 1; 735| 6.28k| bReqProtonsForEachComponent = bReqNonTaut; 736| 6.28k| ip->bTautFlags |= (TG_FLAG_DISCONNECT_COORD | TG_FLAG_RECONNECT_COORD); ------------------ | | 931| 6.28k|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ ip->bTautFlags |= (TG_FLAG_DISCONNECT_COORD | TG_FLAG_RECONNECT_COORD); ------------------ | | 932| 6.28k|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ 737| 6.28k| ip->nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_ISO); ------------------ | | 15| 6.28k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ ip->nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_ISO); ------------------ | | 16| 6.28k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ ip->nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_ISO); ------------------ | | 19| 6.28k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ ip->nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_ISO); ------------------ | | 20| 6.28k|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ ip->nMode |= (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_ISO); ------------------ | | 17| 6.28k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 738| | /* bReqRecmet = 1; */ 739| 6.28k|#if ( bRELEASE_VERSION == 1 ) 740| 6.28k| bReqNonTaut = 1; /* bReqNonTaut=0 ignores Fixed-H layer in input InChI, for testing only */ 741| 6.28k|#endif 742| | /* polymer stuff added */ 743| 6.28k| if (pInp->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1016| 6.28k|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (743:17): [True: 6.28k, False: 0] ------------------ 744| 6.28k| { 745| 6.28k| int res; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 746| | 747| 6.28k| if (ip_inp->lMolfileNumber) ------------------ | Branch (747:21): [True: 0, False: 6.28k] ------------------ 748| | /* get here from inchi-1 main emulation mode */ 749| 0| num_inp = ip_inp->lMolfileNumber - 1; 750| | 751| 6.28k| res = DetectAndExposePolymerInternals(pInp); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 752| | /* proceed silently for now, errs mist be uncovered further on conversion */ 753| 6.28k| } 754| 6.28k| } 755| | 756| 12.5k| InchiTimeGet(&ulTStart); 757| | 758| | /* Read InChI string */ 759| 12.5k| nReadStatus = InChILine2Data(pInp, pLine, &strHdr, &pState, &nErr, 760| 12.5k| OneInput.pInpInChI, OneInput.nNumComponents, 761| 12.5k| OneInput.nNumProtons, OneInput.s, 762| 12.5k| bReadCoord, bInChI2Structure, ip_inp->nMode, 763| 12.5k| &input_is_stdinchi, &input_has_save_opt, 764| 12.5k| &input_save_opt_bits, 765| 12.5k| &OneInput.polymer, &OneInput.v3000); 766| | 767| 12.5k| ulProcessingTime += InchiTimeElapsed(ic, &ulTStart); 768| | 769| |#if 0 770| | if (!bInChI2Structure && OneInput.polymer) 771| | { 772| | /* inchi2inchi for polymers: for now skip */ 773| | pState == IST_MOBILE_H_POLYMER; 774| | nReadStatus = -2; 775| | } 776| |#endif 777| | 778| | 779| 12.5k| end_of_data_reached = nReadStatus == RI_ERR_EOL || nReadStatus == RI_ERR_EOF; ------------------ | | 18| 25.1k|#define RI_ERR_EOL (-4) ------------------ end_of_data_reached = nReadStatus == RI_ERR_EOL || nReadStatus == RI_ERR_EOF; ------------------ | | 19| 24.0k|#define RI_ERR_EOF (0) ------------------ | Branch (779:31): [True: 1.03k, False: 11.5k] | Branch (779:60): [True: 9.31k, False: 2.21k] ------------------ 780| | 781| 12.5k| if (!bInChI2Structure) ------------------ | Branch (781:13): [True: 6.28k, False: 6.28k] ------------------ 782| 6.28k| { 783| | /* i2i, disable polymer related */ 784| 6.28k| if (OneInput.polymer) ------------------ | Branch (784:17): [True: 416, False: 5.86k] ------------------ 785| 416| { 786| 416| pState = IST_MOBILE_H_POLYMER; 787| 416| nErr = RI_ERR_PROGR; ------------------ | | 17| 416|#define RI_ERR_PROGR (-3) ------------------ 788| 416| } 789| 6.28k| } 790| | 791| 12.5k| read_inchi_ok = end_of_data_reached && !nErr; ------------------ | Branch (791:25): [True: 10.3k, False: 2.21k] | Branch (791:48): [True: 10.2k, False: 104] ------------------ 792| | 793| | /* then uncommented... commented out 2020-07-10 (potentially dangerous change, needs testing (TODO: i2s for InChI=1// )*/ 794| 12.5k| read_inchi_ok = read_inchi_ok && ------------------ | Branch (794:25): [True: 10.2k, False: 2.31k] ------------------ 795| 10.2k| (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 570| 10.2k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 575| 10.2k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 570| 10.2k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 574| 10.2k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (795:13): [True: 10.2k, False: 31] ------------------ 796| | 797| |#if ALLOW_EMPTY_INCHI_AS_INPUT!=1 798| | /* no empty InChI allowed */ 799| | read_inchi_ok = read_inchi_ok && 800| | (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + 801| | OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); 802| |#endif 803| |#ifdef TARGET_EXE_STANDALONE 804| | /* inchi-1: we currently disable conversion of polymeric InChI (inchi2struct) 805| | to anything but SDF (would it be necessary in the future?) */ 806| | if (OneInput.polymer && 807| | bInChI2Structure && 808| | !(ip_inp->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)) 809| | { 810| | read_inchi_ok = 0; 811| | nErr = RI_ERR_PROGR; 812| | } 813| |#endif 814| | 815| 12.5k| if (!read_inchi_ok) ------------------ | Branch (815:13): [True: 2.34k, False: 10.2k] ------------------ 816| 2.34k| { 817| 2.34k| TreatErrorsInReadInChIString(nReadStatus, nErr, pState, ip_inp, pRealOut, pLog, 818| 2.34k| &num_inp, &num_errors, &num_processed, 819| 2.34k| &strHdr, &szCurHdr, &OneInput); 820| 2.34k| if (nReadStatus == RI_ERR_SYNTAX || nReadStatus == RI_ERR_PROGR) ------------------ | | 16| 4.69k|#define RI_ERR_SYNTAX (-2) ------------------ if (nReadStatus == RI_ERR_SYNTAX || nReadStatus == RI_ERR_PROGR) ------------------ | | 17| 184|#define RI_ERR_PROGR (-3) ------------------ | Branch (820:17): [True: 2.16k, False: 184] | Branch (820:49): [True: 18, False: 166] ------------------ 821| 2.18k| { 822| 2.18k| ret = nReadStatus; 823| 2.18k| } 824| 2.34k| } 825| 10.2k| else 826| 10.2k| { 827| | /* InChI has been successfully read */ 828| 10.2k| ret = 0; 829| 10.2k| num_inp++; 830| 10.2k| ip->lMolfileNumber = num_inp; 831| 10.2k| bHasSomeReconnected = 0; 832| 10.2k| bHasSomeFixedH = 0; 833| | 834| 10.2k| if (pRealOut == pTmpOut) ------------------ | Branch (834:17): [True: 0, False: 10.2k] ------------------ 835| 0| { 836| 0| inchi_ios_reset(pRealOut); 837| | /*inchi_ios_close( pRealOut ); 838| | inchi_ios_init( pRealOut, INCHI_IOS_TYPE_STRING, NULL );*/ 839| 0| } 840| | /* inchi_ios_print( pRealOut, ""); */ 841| | 842| | /* Does not allow conversion of a non-standard input to Standard output. */ 843| 10.2k| if (ip_inp->bINChIOutputOptions & INCHI_OUT_STDINCHI) ------------------ | | 145| 10.2k|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (843:17): [True: 10.2k, False: 0] ------------------ 844| 10.2k| { 845| 10.2k| if ((input_is_stdinchi & INCHI_INPUT_CLASS_MASK) == ------------------ | | 75| 10.2k|#define INCHI_INPUT_CLASS_MASK 0x03 ------------------ | Branch (845:21): [True: 10.1k, False: 41] ------------------ 846| 10.2k| INCHI_INPUT_CLASS_NONSTANDARD) ------------------ | | 76| 10.2k|#define INCHI_INPUT_CLASS_NONSTANDARD 0x00 ------------------ 847| 10.1k| { 848| | /* Input InChI is non-standard. */ 849| 10.1k| ip->bINChIOutputOptions &= ~INCHI_OUT_STDINCHI; ------------------ | | 145| 10.1k|#define INCHI_OUT_STDINCHI 0x4000 ------------------ 850| | /* 851| | if (szCurHdr && szCurHdr[0]) 852| | inchi_ios_eprint( pLog, "Warning: forced conversion to non-standard InChI for non-std input, %s\n", szCurHdr ); 853| | else 854| | inchi_ios_eprint( pLog, "Warning: forced conversion to non-standard InChI for non-std input, Structure %ld\n", num_inp ); 855| | */ 856| 10.1k| } 857| 10.2k| } 858| | 859| | /* 860| | * Preserve the input calculation-class designator and subversion 861| | * designator when an InChI is converted or restored to a structure. 862| | */ 863| 10.2k| if (bInChI2InChI || bInChI2Structure) ------------------ | Branch (863:17): [True: 5.02k, False: 5.18k] | Branch (863:33): [True: 5.18k, False: 0] ------------------ 864| 10.2k| { 865| 10.2k| ip->bReadInChIOptions &= ~(READ_INCHI_INPUT_BETA | READ_INCHI_INPUT_MI); ------------------ | | 992| 10.2k|#define READ_INCHI_INPUT_BETA 0x00000010 ------------------ ip->bReadInChIOptions &= ~(READ_INCHI_INPUT_BETA | READ_INCHI_INPUT_MI); ------------------ | | 993| 10.2k|#define READ_INCHI_INPUT_MI 0x00000020 ------------------ 866| | 867| 10.2k| if ((input_is_stdinchi & INCHI_INPUT_CLASS_MASK) == INCHI_INPUT_CLASS_BETA) ------------------ | | 75| 10.2k|#define INCHI_INPUT_CLASS_MASK 0x03 ------------------ if ((input_is_stdinchi & INCHI_INPUT_CLASS_MASK) == INCHI_INPUT_CLASS_BETA) ------------------ | | 78| 10.2k|#define INCHI_INPUT_CLASS_BETA 0x02 ------------------ | Branch (867:21): [True: 5, False: 10.2k] ------------------ 868| 5| { 869| 5| ip->bReadInChIOptions |= READ_INCHI_INPUT_BETA; ------------------ | | 992| 5|#define READ_INCHI_INPUT_BETA 0x00000010 ------------------ 870| 5| } 871| | 872| 10.2k| if (input_is_stdinchi & INCHI_INPUT_MI_MARKER) ------------------ | | 79| 10.2k|#define INCHI_INPUT_MI_MARKER 0x04 ------------------ | Branch (872:21): [True: 0, False: 10.2k] ------------------ 873| 0| { 874| 0| ip->bReadInChIOptions |= READ_INCHI_INPUT_MI; ------------------ | | 993| 0|#define READ_INCHI_INPUT_MI 0x00000020 ------------------ 875| 0| } 876| 10.2k| } 877| | 878| 10.2k| treat_save_opt = ip->bINChIOutputOptions & INCHI_OUT_SAVEOPT; ------------------ | | 146| 10.2k|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ 879| | 880| 10.2k| if (treat_save_opt) ------------------ | Branch (880:17): [True: 0, False: 10.2k] ------------------ 881| 0| { 882| 0| PrepareSaveOptBits(ip, pLog, num_inp, szCurHdr, 883| 0| input_has_save_opt, 884| 0| input_save_opt_bits, 885| 0| &save_opt_bits); 886| 0| } 887| | 888| |#ifndef TARGET_API_LIB 889| | /* 890| | inchi_ios_eprint(stderr, "%ld: %s\r", num_inp, strHdr? strHdr : ""); 891| | inchi_ios_eprint(pLog, "%ld: %s\n", num_inp, strHdr? strHdr : ""); 892| | */ 893| | 894| | if (!ip->bNoStructLabels && 895| | !(bInChI2Structure && (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)) 896| | ) 897| | { 898| | /* Added 2nd item: Do not output this extra line into the output SDfile. 2008-11-17 DCh */ 899| | if (strHdr && strstr(strHdr, "Structure:")) 900| | { 901| | inchi_ios_print(pRealOut, "%s%s", strHdr, pTAB); /* output header */ 902| |#if ( FIX_DALKE_BUGS == 1 ) 903| |#else 904| | sprintf(szMessage, "%s (%ld)", strHdr ? strHdr : "", num_inp); 905| |#endif 906| | } 907| | else 908| | { 909| | if (bInChI2Structure) inchi_ios_print(pRealOut, "Structure: %ld. (%s)%s", 910| | num_inp, strHdr ? strHdr : "No struct name", 911| | pTAB); /* output header */ 912| |#if ( FIX_DALKE_BUGS == 1 ) 913| |#else 914| | sprintf(szMessage, "Structure: %ld. (%s)%s", num_inp, strHdr ? strHdr : "No struct name", pTAB); 915| |#endif 916| | } 917| | if (strHdr && strHdr[0]) 918| | { 919| | strncpy(ip->szSdfDataHeader, strHdr, sizeof(ip->szSdfDataHeader)); 920| | ip->szSdfDataHeader[sizeof(ip->szSdfDataHeader) - 1] = '\0'; 921| | ip->pSdfLabel = NULL; 922| | ip->pSdfValue = ip->szSdfDataHeader; 923| | } 924| | else 925| | { 926| | ip->pSdfValue = NULL; 927| | ip->szSdfDataHeader[0] = '\0'; 928| | } 929| | } 930| | 931| |#if ( FIX_DALKE_BUGS == 1 ) 932| | sprintf(szMessage, "%ld: %.400s", num_inp, strHdr ? strHdr : ""); 933| |#else 934| | sprintf(szMessage, "%ld: %s", num_inp, strHdr ? strHdr : ""); 935| |#endif 936| |#endif 937| | 938| 10.2k| nInitLenMessage = (int)strlen(szMessage); 939| 10.2k| if (strHdr) ------------------ | Branch (939:17): [True: 0, False: 10.2k] ------------------ 940| 0| { 941| 0| szCurHdr = strHdr; 942| 0| strHdr = NULL; 943| 0| } 944| 10.2k| if (szCurHdr && ip && ip->first_struct_number > 0) ------------------ | Branch (944:17): [True: 0, False: 10.2k] | Branch (944:29): [True: 0, False: 0] | Branch (944:35): [True: 0, False: 0] ------------------ 945| 0| { 946| | /* Check whether the structure should be skipped */ 947| 0| static const char szStruct[] = "Structure:"; 948| 0| char* pStrNum = strstr(szCurHdr, szStruct); 949| 0| long cur_struct_number; 950| 0| if (pStrNum) ------------------ | Branch (950:21): [True: 0, False: 0] ------------------ 951| 0| { 952| 0| pStrNum += sizeof(szStruct) - 1; /* -1 takes care of the string terminal zero */ 953| 0| cur_struct_number = inchi_strtol(pStrNum, NULL, 10); 954| 0| if (cur_struct_number) ------------------ | Branch (954:25): [True: 0, False: 0] ------------------ 955| 0| { 956| 0| OneInput.num_inp = cur_struct_number; 957| 0| } 958| | /* Process request to bypass first several InChIs */ 959| 0| if (cur_struct_number > 0 && cur_struct_number < ip->first_struct_number) ------------------ | Branch (959:25): [True: 0, False: 0] | Branch (959:50): [True: 0, False: 0] ------------------ 960| 0| { 961| | 962| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_EXE_STANDALONE) ) 963| | inchi_fprintf(stderr, "Skipping %s\r", szMessage); 964| |#endif 965| 0| FreeInpInChI(&OneInput); 966| 0| if (szCurHdr) ------------------ | Branch (966:29): [True: 0, False: 0] ------------------ 967| 0| { 968| 0| inchi_free(szCurHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 969| 0| szCurHdr = NULL; 970| 0| } 971| 0| INCHI_HEAPCHK 972| 0| continue; 973| 0| } 974| 0| } 975| 0| } 976| | 977| 10.2k| num_processed++; 978| | 979| | /* In case of splitting InChI into separate components */ 980| | /* decide whether to keep /p in each component or */ 981| | /* output /p and /i/h as a separate component */ 982| | /* Note: if InChI is not to be splitted DO NOT create */ 983| | /* a separate component for /p, /i/h: it would be a bug*/ 984| | 985| 10.2k| InchiTimeGet(&ulTStart); 986| | 987| | INCHI_HEAPCHK 988| | 989| 10.2k| ret = SetProtonsAndXchgIsoH(bInChI2Structure, bReqSplitOutputInChI, 990| 10.2k| bReqProtonsForEachComponent, bReqNonTaut, bReqStereo, 991| 10.2k| num_components, nModeProtonIsoExchgH, &OneInput); 992| 10.2k| INCHI_HEAPCHK 993| | 994| 10.2k| if (ret < 0) ------------------ | Branch (994:21): [True: 0, False: 10.2k] ------------------ 995| 0| { 996| 0| num_errors++; 997| 0| goto exit_error; 998| 0| } 999| | 1000| 10.2k| sd->num_components[INCHI_BAS] = num_components[INCHI_BAS]; ------------------ | | 570| 10.2k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->num_components[INCHI_BAS] = num_components[INCHI_BAS]; ------------------ | | 570| 10.2k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1001| 10.2k| sd->num_components[INCHI_REC] = num_components[INCHI_REC]; ------------------ | | 571| 10.2k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->num_components[INCHI_REC] = num_components[INCHI_REC]; ------------------ | | 571| 10.2k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1002| | 1003| | /* Do we have reconnected InChI ? */ 1004| 10.2k| if ((OneInput.nNumComponents[INCHI_REC][TAUT_YES] || ------------------ | | 571| 10.2k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if ((OneInput.nNumComponents[INCHI_REC][TAUT_YES] || ------------------ | | 575| 10.2k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1004:18): [True: 50, False: 10.1k] ------------------ 1005| 10.1k| OneInput.nNumComponents[INCHI_REC][TAUT_NON]) && ------------------ | | 571| 10.1k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ OneInput.nNumComponents[INCHI_REC][TAUT_NON]) && ------------------ | | 574| 10.1k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1005:17): [True: 0, False: 10.1k] ------------------ 1006| 50| (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) && ------------------ | | 932| 50|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1006:17): [True: 25, False: 25] ------------------ 1007| 25| (ip->bTautFlags & TG_FLAG_DISCONNECT_COORD) ------------------ | | 931| 25|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (1007:17): [True: 25, False: 0] ------------------ 1008| 10.2k| ) 1009| 25| { 1010| | /* needed for InChI string output to include reconnected InChI */ 1011| 25| sd->bTautFlagsDone[0] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 975| 25|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 1012| 25| bHasSomeReconnected = 1; 1013| 25| } 1014| | 1015| | /* Do we have fixed H InChI ? */ 1016| 10.2k| if (bReqNonTaut && ------------------ | Branch (1016:17): [True: 5.18k, False: 5.02k] ------------------ 1017| | /*OneInput.nNumComponents[bHasSomeReconnected?INCHI_REC:INCHI_BAS][TAUT_NON]*/ 1018| 5.18k| (OneInput.nNumComponents[INCHI_REC][TAUT_NON] || ------------------ | | 571| 5.18k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ (OneInput.nNumComponents[INCHI_REC][TAUT_NON] || ------------------ | | 574| 5.18k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1018:18): [True: 19, False: 5.17k] ------------------ 1019| 5.17k| OneInput.nNumComponents[INCHI_BAS][TAUT_NON])) ------------------ | | 570| 5.17k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ OneInput.nNumComponents[INCHI_BAS][TAUT_NON])) ------------------ | | 574| 5.17k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1019:21): [True: 1.25k, False: 3.91k] ------------------ 1020| 1.27k| { 1021| 1.27k| bHasSomeFixedH = 1; 1022| 1.27k| } 1023| | 1024| 10.2k| ulProcessingTime += InchiTimeElapsed(ic, &ulTStart); 1025| | 1026| 10.2k| invalid_opt = (!bInChI2Structure && !bInChI2InChI) || ------------------ | Branch (1026:28): [True: 5.02k, False: 5.18k] | Branch (1026:49): [True: 0, False: 5.02k] ------------------ 1027| 10.2k| (bInChI2Structure && bInChI2InChI); ------------------ | Branch (1027:18): [True: 5.18k, False: 5.02k] | Branch (1027:38): [True: 0, False: 5.18k] ------------------ 1028| | 1029| 10.2k| if (invalid_opt) ------------------ | Branch (1029:17): [True: 0, False: 10.2k] ------------------ 1030| 0| { 1031| 0| inchi_ios_eprint(pLog, "\nWrong command line options: expected Inch2Struct or Inchi2Inchi\n", num_inp); 1032| 0| break; 1033| 0| } 1034| | 1035| | /* InChI --> Structure */ 1036| 10.2k| if (bInChI2Structure) ------------------ | Branch (1036:17): [True: 5.18k, False: 5.02k] ------------------ 1037| 5.18k| { 1038| 5.18k| char* result_string; 1039| | 1040| 5.18k| if (OneInput.polymer && OneInput.polymer->n) ------------------ | Branch (1040:21): [True: 175, False: 5.01k] | Branch (1040:41): [True: 175, False: 0] ------------------ 1041| 175| { 1042| 175| OneInput.valid_polymer = 1; 1043| 175| } 1044| | 1045| 5.18k| ret = ConvertInChI2Struct(ip_inp, ip, &OneInput, 1046| 5.18k| at, num_at, 1047| 5.18k| polymer, v3000, 1048| 5.18k| pRealOut, pLog, 1049| 5.18k| sd, num_components, nModeProtonIsoExchgH, 1050| 5.18k| &szCurHdr, szMsg, nMsgLen, szMessage, 1051| 5.18k| nInitLenMessage, nMessageLen, 1052| 5.18k| input_is_stdinchi, bHasSomeReconnected, 1053| 5.18k| bHasSomeFixedH, bHasMetal, 1054| 5.18k| nModeFlagsStereo, bTautFlags, bReqNonTaut, 1055| 5.18k| WarningFlags, num_inp, &num_errors, 1056| 5.18k| save_opt_bits, &ulTStart, &ulProcessingTime, 1057| 5.18k| ic, pCG); 1058| | 1059| 5.18k| result_string = pRealOut->s.pStr; 1060| 5.18k| if (ret == 0) /* no problems */ ------------------ | Branch (1060:21): [True: 1.75k, False: 3.43k] ------------------ 1061| 1.75k| { 1062| 1.75k| ; 1063| 1.75k| } 1064| 3.43k| else if (ret > 0) ------------------ | Branch (1064:26): [True: 0, False: 3.43k] ------------------ 1065| 0| { 1066| | /* error */ 1067| 0| if (output_error_inchi) ------------------ | Branch (1067:25): [True: 0, False: 0] ------------------ 1068| 0| { 1069| | /* emit error string */ 1070| 0| inchi_ios_eprint(pRealOut, "InChI creation Error!\n"); 1071| 0| } 1072| 0| } 1073| 3.43k| else if (ret < 0) ------------------ | Branch (1073:26): [True: 3.43k, False: 0] ------------------ 1074| 3.43k| { 1075| | /* error or a mismatch possibly treated as error */ 1076| 3.43k| if (ret != RI_ERR_MISMATCH) ------------------ | | 21| 3.43k|#define RI_ERR_MISMATCH (-9) ------------------ | Branch (1076:25): [True: 3.43k, False: 0] ------------------ 1077| 3.43k| { 1078| 3.43k| goto exit_error; 1079| 3.43k| } 1080| 0| else 1081| 0| { 1082| 0| if (!treat_mismatch_as_error) ------------------ | Branch (1082:29): [True: 0, False: 0] ------------------ 1083| 0| { 1084| | /* ignore mismatch, print InChI as usual */ 1085| 0| if (result_string) ------------------ | Branch (1085:33): [True: 0, False: 0] ------------------ 1086| 0| { 1087| 0| inchi_ios_eprint(pRealOut, "%-s\n", result_string); 1088| 0| } 1089| 0| } 1090| 0| else 1091| 0| { 1092| | /* concider mismatch an error */ 1093| 0| if (!output_error_inchi) ------------------ | Branch (1093:33): [True: 0, False: 0] ------------------ 1094| 0| { 1095| 0| ; /* print nothing for now*/ 1096| 0| } 1097| 0| else 1098| 0| { 1099| | /* emit err string instead of InChI */ 1100| 0| if (result_string) ------------------ | Branch (1100:37): [True: 0, False: 0] ------------------ 1101| 0| { 1102| | /* try to preserve header if any */ 1103| 0| char* pi = strstr(result_string, "InChI="); 1104| 0| if (pi) ------------------ | Branch (1104:41): [True: 0, False: 0] ------------------ 1105| 0| { 1106| 0| int np = pi - result_string; 1107| 0| if (np) ------------------ | Branch (1107:45): [True: 0, False: 0] ------------------ 1108| 0| result_string[np - 1] = '\0'; 1109| 0| inchi_ios_eprint(pRealOut, "%-s\n", result_string); 1110| 0| } 1111| 0| } 1112| 0| inchi_ios_eprint(pRealOut, "InChICreationError!\n"); /* emit err string */ 1113| 0| } 1114| 0| } 1115| 0| FreeInpInChI(&OneInput); 1116| 0| if (strHdr) ------------------ | Branch (1116:29): [True: 0, False: 0] ------------------ 1117| 0| { 1118| 0| inchi_free(strHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1119| 0| strHdr = NULL; 1120| 0| } 1121| 0| if (szCurHdr) ------------------ | Branch (1121:29): [True: 0, False: 0] ------------------ 1122| 0| { 1123| 0| inchi_free(szCurHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1124| 0| szCurHdr = NULL; 1125| 0| } 1126| 0| INCHI_HEAPCHK 1127| 0| continue; 1128| 0| } 1129| 3.43k| } 1130| 5.18k| } /* ( bInChI2Structure ) */ 1131| | 1132| | 1133| | /* InChI --> InChI */ 1134| 5.02k| else if (bInChI2InChI) ------------------ | Branch (1134:22): [True: 5.02k, False: 0] ------------------ 1135| 5.02k| { 1136| 5.02k| ret = ConvertInChI2InChI(ip, &OneInput, pRealOut, pLog, sd, 1137| 5.02k| num_components, nModeProtonIsoExchgH, 1138| 5.02k| &szCurHdr, num_inp, &num_errors, 1139| 5.02k| save_opt_bits, &ulTStart, 1140| 5.02k| &ulProcessingTime, ic, pCG); 1141| 5.02k| } 1142| | 1143| 6.78k| if (nReadStatus == RI_ERR_EOF) ------------------ | | 19| 6.78k|#define RI_ERR_EOF (0) ------------------ | Branch (1143:17): [True: 6.08k, False: 700] ------------------ 1144| |#if ( FIX_ONE_LINE_INCHI_INPUT_CONVERSION_ISSUE==1 && defined(TARGET_EXE_STANDALONE) && !defined(TARGET_API_LIB) ) 1145| | { 1146| | inchi_ios_flush(pRealOut); 1147| | inchi_ios_flush2(pLog, stderr); 1148| | break; 1149| | } 1150| |#else 1151| 6.08k| break; 1152| 6.78k|#endif 1153| 6.78k| } /* InChI has been successfully read */ 1154| | 1155| | 1156| |#ifdef TARGET_EXE_STANDALONE 1157| |#ifndef TARGET_API_LIB 1158| | inchi_ios_flush(pRealOut); 1159| | inchi_ios_flush2(pLog, stderr); 1160| |#endif 1161| |#endif 1162| 3.04k|#ifdef TARGET_API_LIB 1163| 3.04k| break; /* exit after the 1st structure */ 1164| 12.5k|#endif 1165| 12.5k| } /* while */ 1166| | 1167| 12.5k|exit_error: 1168| 12.5k| FreeInpInChI(&OneInput); 1169| 12.5k| if (strHdr) ------------------ | Branch (1169:9): [True: 0, False: 12.5k] ------------------ 1170| 0| { 1171| 0| inchi_free(strHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1172| 0| strHdr = NULL; 1173| 0| } 1174| 12.5k| if (pLine->str) ------------------ | Branch (1174:9): [True: 12.5k, False: 0] ------------------ 1175| 12.5k| { 1176| 12.5k| inchi_free(pLine->str); ------------------ | | 1152| 12.5k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 12.5k, False: 0] | | | Branch (1152:50): [Folded, False: 12.5k] | | ------------------ ------------------ 1177| 12.5k| } 1178| 12.5k| if (szCurHdr) ------------------ | Branch (1178:9): [True: 0, False: 12.5k] ------------------ 1179| 0| { 1180| 0| inchi_free(szCurHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1181| 0| szCurHdr = NULL; 1182| 0| } 1183| | 1184| | INCHI_HEAPCHK 1185| | 1186| 12.5k| if (sd_inp) ------------------ | Branch (1186:13): [True: 12.5k, False: 0] ------------------ 1187| 12.5k| { 1188| 12.5k| sd_inp->ulStructTime = ulProcessingTime; 1189| 12.5k| sd_inp->fPtrStart = num_processed; 1190| 12.5k| sd_inp->fPtrEnd = num_errors; 1191| 12.5k| } 1192| 12.5k| if (pRealOut == pTmpOut) ------------------ | Branch (1192:9): [True: 0, False: 12.5k] ------------------ 1193| 0| { 1194| 0| inchi_ios_close(pTmpOut); 1195| 0| } 1196| | 1197| 12.5k| return ret; 1198| 12.5k|} GetNumNeighborsFromInchi: 1636| 229|{ 1637| 229| int i, j, n_vertex, n_neigh, nNumNeigh, bTautAtom, nNumH, nTotNumNeigh, num_atoms; 1638| 229| AT_NUMB taut_at_number; 1639| 229| nAtNumber -= 1; 1640| 229| nNumNeigh = 0; /* number of bonds */ 1641| 229| bTautAtom = 0; /* 1 if atom belongs to a Mobile-H group */ 1642| 229| nNumH = 0; /* number of terminal neighbors H */ 1643| 229| num_atoms = 0; /* djb-rwth: initialisation with pInChI below */ 1644| | 1645| 229| if (pInChI) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (1645:9): [True: 229, False: 0] ------------------ 1646| 229| { 1647| 229| num_atoms = pInChI->nNumberOfAtoms; 1648| | /* from RestoreAtomConnectionsSetStereo() */ 1649| | /* Connection table structure: 1650| | Vert(1) [, Neigh(11), Neigh(12),...], Vert(2) [, Neigh(2,1), Neigh(2,2),...] ... 1651| | where Neigh(i,1) < Neigh(i,2) <... < Vert(i); 1652| | Vert(i) < Vert(i+1) 1653| | */ 1654| 2.64k| for (i = 1, n_vertex = pInChI->nConnTable[0] - 1; i < pInChI->lenConnTable; i++) ------------------ | Branch (1654:59): [True: 2.41k, False: 229] ------------------ 1655| 2.41k| { 1656| 2.41k| if ((n_neigh = pInChI->nConnTable[i] - 1) < n_vertex) ------------------ | Branch (1656:17): [True: 1.52k, False: 882] ------------------ 1657| 1.52k| { 1658| | /* vertex - neighbor connection */ 1659| 1.52k| nNumNeigh += (nAtNumber == n_vertex || nAtNumber == n_neigh); ------------------ | Branch (1659:31): [True: 244, False: 1.28k] | Branch (1659:56): [True: 415, False: 870] ------------------ 1660| 1.52k| } 1661| 882| else 1662| 882| {/* n_neigh is the next vertex */ 1663| 882| if ((n_vertex = n_neigh) >= num_atoms) ------------------ | Branch (1663:21): [True: 0, False: 882] ------------------ 1664| 0| { 1665| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1666| 0| } 1667| 882| } 1668| 2.41k| } 1669| 229| } 1670| | 1671| | 1672| | /* is atom tautomeric, from GetTgroupInfoFromInChI() */ 1673| 229| if (pInChI && pInChI->lenTautomer > 1 && pInChI->nTautomer && pInChI->nTautomer[0] > 0) ------------------ | Branch (1673:9): [True: 229, False: 0] | Branch (1673:19): [True: 13, False: 216] | Branch (1673:46): [True: 13, False: 0] | Branch (1673:67): [True: 13, False: 0] ------------------ 1674| 13| { 1675| 13| int itg, len_tg; 1676| 13| int tot_len_tg = pInChI->lenTautomer - T_GROUP_HDR_LEN * pInChI->nTautomer[0] - 1; /* number of endpoints */ ------------------ | | 72| 13|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 13|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 1677| 13| j = 1; /* index in pInChI->nTautomer[] */ 1678| 13| i = 0; /* index in ti->nEndpointAtomNumber[] */ 1679| 47| for (itg = 0; itg < pInChI->nTautomer[0]; itg++) ------------------ | Branch (1679:23): [True: 34, False: 13] ------------------ 1680| 34| { 1681| 34| len_tg = pInChI->nTautomer[j]; /* t-group length not including pInChI->nTautomer[j] */ 1682| 34| j += T_GROUP_HDR_LEN; /* skip t-group header */ ------------------ | | 72| 34|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 34|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 1683| 34| len_tg -= T_GROUP_HDR_LEN - 1; ------------------ | | 72| 34|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 34|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 1684| 71| for (; 0 < len_tg--; j++, i++) ------------------ | Branch (1684:20): [True: 37, False: 34] ------------------ 1685| 37| { 1686| 37| taut_at_number = pInChI->nTautomer[j] - 1; /* Mobile-H group atom number */ 1687| 37| bTautAtom += (taut_at_number == nAtNumber); 1688| 37| } 1689| 34| } 1690| 13| if (i != tot_len_tg) ------------------ | Branch (1690:13): [True: 0, False: 13] ------------------ 1691| 0| { 1692| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1693| 0| } 1694| 13| } 1695| | /* count hydrogen neighbors */ 1696| 229| if (pInChI && pInChI->nNum_H) /* djb-rwth: condition added for fixing a NULL pointer dereference */ ------------------ | Branch (1696:9): [True: 229, False: 0] | Branch (1696:19): [True: 229, False: 0] ------------------ 1697| 229| { 1698| 229| nNumH = pInChI->nNum_H[nAtNumber]; 1699| 229| } 1700| | /* conclusion: if not tautomeric then return positive number, otherwise add 1000 */ 1701| 229| nTotNumNeigh = nNumNeigh + nNumH; 1702| 229| if (bTautAtom) ------------------ | Branch (1702:9): [True: 5, False: 224] ------------------ 1703| 5| { 1704| 5| nTotNumNeigh += 1000; 1705| 5| } 1706| 229| return nTotNumNeigh; 1707| | 1708| 229|} CountStereoTypes: 1719| 180k|{ 1720| 180k| INChI_Stereo* Stereo; 1721| 180k| int i, ret; 1722| 180k| AT_NUMB nAtNumber; 1723| 180k| U_CHAR el_number; 1724| | 1725| 180k| if (!pInChI->nNumberOfAtoms || pInChI->bDeleted) ------------------ | Branch (1725:9): [True: 30.3k, False: 150k] | Branch (1725:36): [True: 3.92k, False: 146k] ------------------ 1726| 34.2k| { 1727| 34.2k| return 0; /* no InChI */ 1728| 34.2k| } 1729| 146k| Stereo = (pInChI->StereoIsotopic && ------------------ | Branch (1729:15): [True: 616, False: 146k] ------------------ 1730| 616| (pInChI->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1730:9): [True: 252, False: 364] ------------------ 1731| 616| pInChI->StereoIsotopic->nNumberOfStereoCenters)) ? pInChI->StereoIsotopic : 1732| 146k| (pInChI->Stereo && ------------------ | Branch (1732:10): [True: 12.2k, False: 134k] ------------------ 1733| 12.2k| (pInChI->Stereo->nNumberOfStereoBonds + ------------------ | Branch (1733:13): [True: 874, False: 11.3k] ------------------ 1734| 146k| pInChI->Stereo->nNumberOfStereoCenters)) ? pInChI->Stereo : NULL; 1735| 146k| if (!Stereo) ------------------ | Branch (1735:9): [True: 145k, False: 1.12k] ------------------ 1736| 145k| { 1737| 145k| return 1; /* No Stereo */ 1738| 145k| } 1739| | 1740| | /* count SB and cumulenes */ 1741| 1.92k| for (i = 0; i < Stereo->nNumberOfStereoBonds; i++) ------------------ | Branch (1741:17): [True: 794, False: 1.12k] ------------------ 1742| 794| { 1743| 794| if (ATOM_PARITY_WELL_DEF(Stereo->b_parity[i])) ------------------ | | 259| 794|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 794|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 794|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 794, False: 0] | | | Branch (259:75): [True: 551, False: 243] | | ------------------ ------------------ 1744| 551| { 1745| 551| (*num_known_SB)++; 1746| 551| } 1747| 243| else 1748| 243| { 1749| 243| (*num_unk_und_SB)++; 1750| 243| } 1751| 794| } 1752| | /* count SC and allenes */ 1753| 1.96k| for (i = 0; i < Stereo->nNumberOfStereoCenters; i++) ------------------ | Branch (1753:17): [True: 840, False: 1.12k] ------------------ 1754| 840| { 1755| 840| if (!(nAtNumber = Stereo->nNumber[i]) || nAtNumber > pInChI->nNumberOfAtoms) ------------------ | Branch (1755:13): [True: 0, False: 840] | Branch (1755:50): [True: 0, False: 840] ------------------ 1756| 0| { 1757| 0| return RI_ERR_PROGR; /* wrong data, should never happen */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1758| 0| } 1759| 840| if (ATOM_PARITY_WELL_DEF(Stereo->t_parity[i])) ------------------ | | 259| 840|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 840|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 840|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 840, False: 0] | | | Branch (259:75): [True: 683, False: 157] | | ------------------ ------------------ 1760| 683| { 1761| 683| (*num_known_SC)++; 1762| 683| } 1763| 157| else 1764| 157| { 1765| 157| (*num_unk_und_SC)++; 1766| 157| } 1767| 840| el_number = pInChI->nAtom[nAtNumber - 1]; 1768| 840| if (el_number != EL_NUMBER_P && el_number != EL_NUMBER_AS) ------------------ | | 18| 1.68k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ if (el_number != EL_NUMBER_P && el_number != EL_NUMBER_AS) ------------------ | | 22| 618|#define EL_NUMBER_AS ((U_CHAR)33) ------------------ | Branch (1768:13): [True: 618, False: 222] | Branch (1768:41): [True: 611, False: 7] ------------------ 1769| 611| { 1770| 611| continue; 1771| 611| } 1772| 229| ret = GetNumNeighborsFromInchi(pInChI, nAtNumber); 1773| 229| if (ret < 0) ------------------ | Branch (1773:13): [True: 0, False: 229] ------------------ 1774| 0| { 1775| 0| return ret; 1776| 0| } 1777| 229| if (3 == ret) ------------------ | Branch (1777:13): [True: 118, False: 111] ------------------ 1778| 118| { 1779| 118| *num_SC_PIII += (EL_NUMBER_P == el_number); ------------------ | | 18| 118|#define EL_NUMBER_P ((U_CHAR)15) ------------------ 1780| 118| *num_SC_AsIII += (EL_NUMBER_AS == el_number); ------------------ | | 22| 118|#define EL_NUMBER_AS ((U_CHAR)33) ------------------ 1781| 118| } 1782| 229| } 1783| | 1784| 1.12k| return 2; /* Has Stereo */ 1785| 1.12k|} bInpInchiComponentExists: 1793| 34.1k|{ 1794| 34.1k| if ((INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 570| 34.1k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ((INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 571| 32|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1794:10): [True: 32, False: 34.0k] | Branch (1794:33): [True: 0, False: 32] ------------------ 1795| 34.1k| (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 574| 34.1k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 34.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1795:10): [True: 34.1k, False: 12] | Branch (1795:34): [True: 0, False: 34.1k] | Branch (1795:59): [True: 0, False: 34.1k] ------------------ 1796| 0| { 1797| 0| return 0; 1798| 0| } 1799| | 1800| 34.1k| return (k < pOneInput->nNumComponents[iInChI][bMobileH] && ------------------ | Branch (1800:13): [True: 34.1k, False: 0] ------------------ 1801| 34.1k| pOneInput->pInpInChI[iInChI][bMobileH] && ------------------ | Branch (1801:9): [True: 34.1k, False: 0] ------------------ 1802| 34.1k| pOneInput->pInpInChI[iInChI][bMobileH][k].nNumberOfAtoms > 0 && ------------------ | Branch (1802:9): [True: 34.1k, False: 2] ------------------ 1803| 34.1k| !pOneInput->pInpInChI[iInChI][bMobileH][k].bDeleted); ------------------ | Branch (1803:9): [True: 32.6k, False: 1.51k] ------------------ 1804| 34.1k|} bInpInchiComponentDeleted: 1812| 3|{ 1813| 3| if ((INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 570| 3|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ((INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 571| 3|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1813:10): [True: 3, False: 0] | Branch (1813:33): [True: 0, False: 3] ------------------ 1814| 3| (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 574| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1814:10): [True: 3, False: 0] | Branch (1814:34): [True: 0, False: 3] | Branch (1814:59): [True: 0, False: 3] ------------------ 1815| 0| { 1816| 0| return 0; 1817| 0| } 1818| | 1819| 3| return (k < pOneInput->nNumComponents[iInChI][bMobileH] && ------------------ | Branch (1819:13): [True: 3, False: 0] ------------------ 1820| 3| pOneInput->pInpInChI[iInChI][bMobileH] && ------------------ | Branch (1820:9): [True: 3, False: 0] ------------------ 1821| 3| pOneInput->pInpInChI[iInChI][bMobileH][k].nNumberOfAtoms > 0 && ------------------ | Branch (1821:9): [True: 3, False: 0] ------------------ 1822| 3| pOneInput->pInpInChI[iInChI][bMobileH][k].bDeleted); ------------------ | Branch (1822:9): [True: 3, False: 0] ------------------ 1823| 3|} bRevInchiComponentExists: 1831| 142k|{ 1832| 142k| if (!pStruct || /*!pStruct->at2 ||*/ !pStruct->num_atoms || ------------------ | Branch (1832:9): [True: 0, False: 142k] | Branch (1832:42): [True: 0, False: 142k] ------------------ 1833| 142k| (INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 570| 142k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 571| 71.6k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1833:10): [True: 71.6k, False: 70.4k] | Branch (1833:33): [True: 0, False: 71.6k] ------------------ 1834| 142k| (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 574| 142k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 142k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1834:10): [True: 142k, False: 7] | Branch (1834:34): [True: 0, False: 142k] | Branch (1834:59): [True: 0, False: 142k] ------------------ 1835| 0| { 1836| 0| return 0; 1837| 0| } 1838| | 1839| 142k| return (k < pStruct->RevInChI.num_components[iInChI] && ------------------ | Branch (1839:13): [True: 70.4k, False: 71.6k] ------------------ 1840| 70.4k| pStruct->RevInChI.pINChI[iInChI] && ------------------ | Branch (1840:9): [True: 70.4k, False: 0] ------------------ 1841| 70.4k| pStruct->RevInChI.pINChI[iInChI][k][bMobileH] && ------------------ | Branch (1841:9): [True: 70.4k, False: 0] ------------------ 1842| 70.4k| pStruct->RevInChI.pINChI[iInChI][k][bMobileH]->nNumberOfAtoms > 0 && ------------------ | Branch (1842:9): [True: 70.4k, False: 7] ------------------ 1843| 70.4k| !pStruct->RevInChI.pINChI[iInChI][k][bMobileH]->bDeleted); ------------------ | Branch (1843:9): [True: 70.2k, False: 156] ------------------ 1844| 142k|} bRevInchiComponentDeleted: 1852| 1|{ 1853| 1| if (!pStruct || /*!pStruct->at2 ||*/ !pStruct->num_atoms || ------------------ | Branch (1853:9): [True: 0, False: 1] | Branch (1853:42): [True: 0, False: 1] ------------------ 1854| 1| (INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 570| 1|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (INCHI_BAS != iInChI && iInChI != INCHI_REC) || ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1854:10): [True: 0, False: 1] | Branch (1854:33): [True: 0, False: 0] ------------------ 1855| 1| (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 574| 1|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ (TAUT_NON != bMobileH && TAUT_YES != bMobileH) || k < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1855:10): [True: 1, False: 0] | Branch (1855:34): [True: 0, False: 1] | Branch (1855:59): [True: 0, False: 1] ------------------ 1856| 0| { 1857| 0| return 0; 1858| 0| } 1859| | 1860| 1| return (k < pStruct->RevInChI.num_components[iInChI] && ------------------ | Branch (1860:13): [True: 1, False: 0] ------------------ 1861| 1| pStruct->RevInChI.pINChI[iInChI] && ------------------ | Branch (1861:9): [True: 1, False: 0] ------------------ 1862| 1| pStruct->RevInChI.pINChI[iInChI][k][bMobileH] && ------------------ | Branch (1862:9): [True: 1, False: 0] ------------------ 1863| 1| pStruct->RevInChI.pINChI[iInChI][k][bMobileH]->nNumberOfAtoms > 0 && ------------------ | Branch (1863:9): [True: 1, False: 0] ------------------ 1864| 1| pStruct->RevInChI.pINChI[iInChI][k][bMobileH]->bDeleted); ------------------ | Branch (1864:9): [True: 1, False: 0] ------------------ 1865| 1|} DetectInpInchiCreationOptions: 1875| 5.18k|{ 1876| 5.18k| int ret = 0, bHasStereo; 1877| 5.18k| int nModeFlagsValue = 0, bTautFlagsValue; /* stereo flags */ 1878| 5.18k| int iInChI, iMobileH, bIso, k, max_components, num_components; 1879| 5.18k| INChI* pInChI; 1880| 5.18k| int num_known_SB /*Stereo Bonds & Cumulenes >C==C==C==C< */; 1881| 5.18k| int num_known_SC /* Stereo Centers & Allenes >C=C=C< */; 1882| 5.18k| int num_unk_und_SB, num_unk_und_SC; 1883| 5.18k| int num_SC_PIII, num_SC_AsIII; /* has Phosphine or Arsine stereo center(s) */ 1884| | 1885| 5.18k| *bHasReconnected = *bHasFixedH = *nModeFlagsStereo = *bTautFlagsStereo = 0; 1886| 5.18k| nModeFlagsValue = bTautFlagsValue = bHasStereo = 0; 1887| 5.18k| num_known_SB = num_known_SC = num_unk_und_SB = num_unk_und_SC = num_SC_PIII = num_SC_AsIII = 0; 1888| 5.18k| *bHasMetal = 0; 1889| | 1890| 15.5k| for (iInChI = 0; iInChI < INCHI_NUM; iInChI++) ------------------ | | 569| 15.5k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1890:22): [True: 10.3k, False: 5.18k] ------------------ 1891| 10.3k| { 1892| 31.1k| for (iMobileH = 0; iMobileH < TAUT_NUM; iMobileH++) ------------------ | | 573| 31.1k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1892:28): [True: 20.7k, False: 10.3k] ------------------ 1893| 20.7k| { 1894| 61.9k| for (bIso = 1; !nModeFlagsValue && 0 <= bIso; bIso--) ------------------ | Branch (1894:28): [True: 61.7k, False: 204] | Branch (1894:48): [True: 41.2k, False: 20.5k] ------------------ 1895| 41.2k| { 1896| 41.2k| switch (pOneInput->s[iInChI][iMobileH][bIso]) ------------------ | Branch (1896:25): [True: 63, False: 41.1k] ------------------ 1897| 41.2k| { 1898| 7| case 1: /* SABS */ ------------------ | Branch (1898:17): [True: 7, False: 41.1k] ------------------ 1899| 7| nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; ------------------ | | 19| 7|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; ------------------ | | 20| 7|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 1900| 7| break; 1901| 39| case 2: ------------------ | Branch (1901:17): [True: 39, False: 41.1k] ------------------ 1902| 39| nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RELATIVE_STEREO; ------------------ | | 19| 39|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RELATIVE_STEREO; ------------------ | | 20| 39|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RELATIVE_STEREO; ------------------ | | 26| 39|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 1903| 39| break; 1904| 17| case 3: ------------------ | Branch (1904:17): [True: 17, False: 41.1k] ------------------ 1905| 17| nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RACEMIC_STEREO; ------------------ | | 19| 17|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RACEMIC_STEREO; ------------------ | | 20| 17|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RACEMIC_STEREO; ------------------ | | 28| 17|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 1906| 41.2k| } 1907| 41.2k| } 1908| | 1909| 20.7k| max_components = pOneInput->pInpInChI[iInChI][iMobileH] ? ------------------ | Branch (1909:30): [True: 6.50k, False: 14.2k] ------------------ 1910| 14.2k| pOneInput->nNumComponents[iInChI][iMobileH] : 0; 1911| | 1912| 201k| for (k = num_components = 0; k < max_components; k++) ------------------ | Branch (1912:42): [True: 180k, False: 20.7k] ------------------ 1913| 180k| { 1914| 180k| pInChI = pOneInput->pInpInChI[iInChI][iMobileH] + k; 1915| 180k| ret = CountStereoTypes(pInChI, 1916| 180k| &num_known_SB, &num_known_SC, 1917| 180k| &num_unk_und_SB, &num_unk_und_SC, 1918| 180k| &num_SC_PIII, &num_SC_AsIII); 1919| 180k| if (ret < 0) ------------------ | Branch (1919:21): [True: 0, False: 180k] ------------------ 1920| 0| { 1921| 0| return ret; /* error */ 1922| 0| } 1923| 180k| bHasStereo += (ret == 2); 1924| 180k| if ((ret > 0)) ------------------ | Branch (1924:21): [True: 146k, False: 34.2k] ------------------ 1925| 146k| { 1926| | /* ret == 0 => Empty InChI, 1=> No Stereo, 2=> Has Stereo */ 1927| 146k| num_components++; 1928| 146k| *bHasReconnected |= (iInChI == INCHI_REC); ------------------ | | 571| 146k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1929| 146k| *bHasFixedH |= (iMobileH == TAUT_NON); ------------------ | | 574| 146k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1930| 146k| } 1931| 180k| *bHasMetal |= bInChIHasReconnectedMetal(pInChI); 1932| 180k| } 1933| 20.7k| } 1934| 10.3k| } 1935| | 1936| 5.18k| if ((nModeFlagsValue & REQ_MODE_RELATIVE_STEREO) && (nModeFlagsValue & REQ_MODE_RACEMIC_STEREO)) ------------------ | | 26| 5.18k|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ if ((nModeFlagsValue & REQ_MODE_RELATIVE_STEREO) && (nModeFlagsValue & REQ_MODE_RACEMIC_STEREO)) ------------------ | | 28| 39|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (1936:9): [True: 39, False: 5.15k] | Branch (1936:57): [True: 0, False: 39] ------------------ 1937| 0| { 1938| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1939| 0| } 1940| 5.18k| if (bHasStereo && !nModeFlagsValue) /* REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU*/ ------------------ | Branch (1940:9): [True: 961, False: 4.22k] | Branch (1940:23): [True: 912, False: 49] ------------------ 1941| 912| { 1942| | /* inversion does not change the stereo or no stereo at all */ 1943| 912| nModeFlagsValue = REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; /* Abs */ ------------------ | | 19| 912|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue = REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; /* Abs */ ------------------ | | 20| 912|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 1944| 912| } 1945| | 1946| 5.18k| if (!num_known_SB && num_unk_und_SB) ------------------ | Branch (1946:9): [True: 4.82k, False: 365] | Branch (1946:26): [True: 132, False: 4.69k] ------------------ 1947| 132| { 1948| 132| ; /* full SUU option or SB part of it */ 1949| 132| } 1950| 5.05k| else 1951| 5.05k| { 1952| 5.05k| nModeFlagsValue |= REQ_MODE_SB_IGN_ALL_UU; /* ignore Unknown/Undefind SB if no well-defined SB exist */ ------------------ | | 32| 5.05k|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 1953| 5.05k| } 1954| | 1955| 5.18k| if (!num_known_SC && num_unk_und_SC) ------------------ | Branch (1955:9): [True: 4.77k, False: 410] | Branch (1955:26): [True: 62, False: 4.71k] ------------------ 1956| 62| { 1957| 62| ; /* full SUU option or SB part of it */ 1958| 62| } 1959| 5.12k| else 1960| 5.12k| { 1961| 5.12k| nModeFlagsValue |= REQ_MODE_SC_IGN_ALL_UU; /* ignore Unknown/Undefind SC if no well-defined SB exist */ ------------------ | | 30| 5.12k|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 1962| 5.12k| } 1963| | /* Phosphine and Arsine Stereo */ 1964| 5.18k| if (num_SC_PIII) ------------------ | Branch (1964:9): [True: 88, False: 5.10k] ------------------ 1965| 88| { 1966| 88| bTautFlagsValue |= TG_FLAG_PHOSPHINE_STEREO; ------------------ | | 941| 88|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ 1967| 88| } 1968| | /* Phosphine and Arsine Stereo */ 1969| 5.18k| if (num_SC_AsIII) ------------------ | Branch (1969:9): [True: 2, False: 5.18k] ------------------ 1970| 2| { 1971| 2| bTautFlagsValue |= TG_FLAG_ARSINE_STEREO; ------------------ | | 942| 2|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ 1972| 2| } 1973| | 1974| 5.18k| *nModeFlagsStereo = nModeFlagsValue; 1975| 5.18k| *bTautFlagsStereo = bTautFlagsValue; 1976| | 1977| 5.18k| return 0; 1978| 5.18k|} InChILine2Data: 2348| 12.5k|{ 2349| 12.5k| int iINChI, i, j, k, m, len1, len2, ret2 = 0, retAux = 0, stateAux = 0; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2350| 12.5k| int ret, tot_charge[INCHI_NUM][TAUT_NUM]; 2351| 12.5k| int i1, i2, i3; 2352| 12.5k| int kc; 2353| 12.5k| NUM_ELEM* num_elem[INCHI_NUM][TAUT_NUM]; 2354| | 2355| | 2356| 12.5k|#if ( FIX_I2I_STEREOCONVERSION_BUG == 1 ) 2357| | /* (2008-03-06) 1=> Fix bug of i2i conversion SAbs-->(SRel||Srac) */ 2358| | /* (converter does not placed proper stereo to output) */ 2359| | 2360| | /* set new stereo type as requested by conversion option */ 2361| 12.5k| int target_stereo_type = 1; 2362| 12.5k| if (nMode & REQ_MODE_RELATIVE_STEREO) ------------------ | | 26| 12.5k|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (2362:9): [True: 0, False: 12.5k] ------------------ 2363| 0| { 2364| 0| target_stereo_type = 2; 2365| 0| } 2366| 12.5k| else if (nMode & REQ_MODE_RACEMIC_STEREO) ------------------ | | 28| 12.5k|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (2366:14): [True: 0, False: 12.5k] ------------------ 2367| 0| { 2368| 0| target_stereo_type = 3; 2369| 0| } 2370| 12.5k|#endif 2371| | 2372| 12.5k| memset(num_elem, 0, sizeof(num_elem)); /* djb-rwth: memset_s C11/Annex K variant? */ 2373| | 2374| 12.5k| ret = ReadInChILine(pInp, pLine, pStr, pState, pInpInChI, 2375| 12.5k| nNumComponents, nNumProtons, s, bStdFormat, 2376| 12.5k| input_has_save_opt, input_save_opt_bits, 2377| 12.5k| bInchi2Struct, ppolymer, pv3000); 2378| | 2379| 12.5k|#if ( FIX_I2I_STEREOCONVERSION_BUG == 1 ) 2380| | /* modify stereo type for layers as requested */ 2381| 12.5k| if (target_stereo_type > 1) ------------------ | Branch (2381:9): [True: 0, False: 12.5k] ------------------ 2382| 0| { 2383| 0| for (i1 = 0; i1 < INCHI_NUM; i1++) ------------------ | | 569| 0|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2383:22): [True: 0, False: 0] ------------------ 2384| 0| { 2385| 0| for (i2 = 0; i2 < TAUT_NUM; i2++) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2385:26): [True: 0, False: 0] ------------------ 2386| 0| { 2387| 0| for (i3 = 0; i3 < 2; i3++) ------------------ | Branch (2387:30): [True: 0, False: 0] ------------------ 2388| 0| { 2389| 0| if (s[i1][i2][i3] != 0) ------------------ | Branch (2389:25): [True: 0, False: 0] ------------------ 2390| 0| { 2391| 0| if (target_stereo_type != 1) ------------------ | Branch (2391:29): [True: 0, False: 0] ------------------ 2392| 0| { 2393| | /* do not allow conversion SRel=>SAbs, SRac=>SAbs */ 2394| 0| s[i1][i2][i3] = target_stereo_type; 2395| 0| } 2396| 0| } 2397| 0| } 2398| 0| } 2399| 0| } 2400| 0| } 2401| 12.5k|#endif 2402| | 2403| 12.5k| * nErr = 0; 2404| | 2405| 12.5k| if ((ret == RI_ERR_EOL) && ------------------ | | 18| 12.5k|#define RI_ERR_EOL (-4) ------------------ | Branch (2405:9): [True: 1.03k, False: 11.5k] ------------------ 2406| 1.03k| nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 570| 1.03k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 575| 1.03k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2406:9): [True: 1.00k, False: 31] ------------------ 2407| 1.03k| + nNumComponents[INCHI_BAS][TAUT_NON] && bReadCoord) ------------------ | | 570| 1.03k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ + nNumComponents[INCHI_BAS][TAUT_NON] && bReadCoord) ------------------ | | 574| 1.03k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2407:50): [True: 585, False: 417] ------------------ 2408| 585| { 2409| 585| retAux = ReadInChICoord(pInp, pLine, &stateAux, pInpInChI, nNumComponents); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2410| 585| } 2411| | 2412| 12.5k| if ((ret == RI_ERR_EOL || ret == RI_ERR_EOF) && ------------------ | | 18| 25.1k|#define RI_ERR_EOL (-4) ------------------ if ((ret == RI_ERR_EOL || ret == RI_ERR_EOF) && ------------------ | | 19| 11.5k|#define RI_ERR_EOF (0) ------------------ | Branch (2412:10): [True: 1.03k, False: 11.5k] | Branch (2412:31): [True: 9.31k, False: 2.21k] ------------------ 2413| 10.3k| nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 570| 10.3k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 575| 10.3k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2413:9): [True: 10.3k, False: 31] ------------------ 2414| 10.3k| + nNumComponents[INCHI_BAS][TAUT_NON]) ------------------ | | 570| 10.3k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ + nNumComponents[INCHI_BAS][TAUT_NON]) ------------------ | | 574| 10.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2415| 10.3k| { 2416| | /* post-processing: add omitted layers */ 2417| 10.3k| *pState = IST_MATERIAL_BALANCE_ERROR; 2418| 30.8k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 30.8k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2418:26): [True: 20.5k, False: 10.2k] ------------------ 2419| 20.5k| { 2420| 61.6k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 61.6k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2420:25): [True: 41.1k, False: 20.5k] ------------------ 2421| 41.1k| { 2422| | /* for Mobile/Fixed H (j) ... */ 2423| 41.1k| int bIsotopic, bStereoType, bStereoTypeAlt; 2424| 41.1k| int nMH2FH_AltInv = 0, nFH2iFH_AltInv = 0 /*, niMH2iFH_AltInv=0, nMH2iMH_AltInv=0*/; 2425| 41.1k| int jAlt = ALT_TAUT(j); ------------------ | | 577| 41.1k|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 41.1k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 41.1k] | | ------------------ ------------------ 2426| 41.1k| INCHI_MODE nFlags = 0, nFlagsAlt = 0; 2427| | /* get stereo type: ABS, REL, RAC, or nothing */ 2428| 41.1k| tot_charge[iINChI][j] = 0; 2429| 123k| for (bIsotopic = bStereoType = bStereoTypeAlt = 0; bIsotopic < 2; bIsotopic++) ------------------ | Branch (2429:68): [True: 82.2k, False: 41.1k] ------------------ 2430| 82.2k| { 2431| 82.2k| if (!bStereoType || bStereoType < s[iINChI][j][bIsotopic]) ------------------ | Branch (2431:25): [True: 82.0k, False: 193] | Branch (2431:41): [True: 10, False: 183] ------------------ 2432| 82.0k| { 2433| 82.0k| bStereoType = s[iINChI][j][bIsotopic]; 2434| 82.0k| } 2435| 82.2k| if (!bStereoTypeAlt || bStereoTypeAlt < s[iINChI][jAlt][bIsotopic]) ------------------ | Branch (2435:25): [True: 82.0k, False: 193] | Branch (2435:44): [True: 10, False: 183] ------------------ 2436| 82.0k| { 2437| 82.0k| bStereoTypeAlt = s[iINChI][jAlt][bIsotopic]; 2438| 82.0k| } 2439| 82.2k| nFlags = bStereoType == 2 ? INCHI_FLAG_REL_STEREO : bStereoType == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 121| 136|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ nFlags = bStereoType == 2 ? INCHI_FLAG_REL_STEREO : bStereoType == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 122| 78|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2439:30): [True: 136, False: 82.1k] | Branch (2439:73): [True: 78, False: 82.0k] ------------------ 2440| 82.2k| nFlagsAlt = bStereoTypeAlt == 2 ? INCHI_FLAG_REL_STEREO : bStereoTypeAlt == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 121| 136|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ nFlagsAlt = bStereoTypeAlt == 2 ? INCHI_FLAG_REL_STEREO : bStereoTypeAlt == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 122| 78|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2440:33): [True: 136, False: 82.1k] | Branch (2440:79): [True: 78, False: 82.0k] ------------------ 2441| 82.2k| } 2442| | /* set stereo type to each component */ 2443| | /* add missing nNum_H and nConnTable */ 2444| 41.1k| if (nNumComponents[iINChI][j]) ------------------ | Branch (2444:21): [True: 13.0k, False: 28.0k] ------------------ 2445| 13.0k| { 2446| 13.0k| num_elem[iINChI][j] = (NUM_ELEM*)inchi_calloc((long long)nElDataLen + 1, sizeof(num_elem[0][0][0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 13.0k|#define inchi_calloc calloc ------------------ 2447| 13.0k| if (!num_elem[iINChI][j]) ------------------ | Branch (2447:25): [True: 0, False: 13.0k] ------------------ 2448| 0| { 2449| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2450| 0| goto exit_function; 2451| 0| } 2452| 13.0k| } 2453| 318k| for (k = 0; k < nNumComponents[iINChI][j]; k++) ------------------ | Branch (2453:29): [True: 277k, False: 41.1k] ------------------ 2454| 277k| { 2455| | /* for each component k ... */ 2456| 277k| if (pInpInChI[iINChI][j]) ------------------ | Branch (2456:25): [True: 277k, False: 0] ------------------ 2457| 277k| { 2458| 277k| INChI* pInChI = &pInpInChI[iINChI][j][k]; 2459| 277k| INChI* pInChI_Alt = (k < nNumComponents[iINChI][jAlt] && ------------------ | Branch (2459:46): [True: 66.2k, False: 211k] ------------------ 2460| 66.2k| pInpInChI[iINChI][jAlt] && ------------------ | Branch (2460:29): [True: 66.2k, False: 0] ------------------ 2461| | /*pInpInChI[iINChI][jAlt]->nNumberOfAtoms)? pInpInChI[iINChI][jAlt]:NULL;*/ /* 2007-09-25 DT */ 2462| 277k| pInpInChI[iINChI][jAlt][k].nNumberOfAtoms) ? &pInpInChI[iINChI][jAlt][k] : NULL; ------------------ | Branch (2462:29): [True: 66.2k, False: 0] ------------------ 2463| 277k| if (nFlags) ------------------ | Branch (2463:29): [True: 333, False: 277k] ------------------ 2464| 333| { 2465| 333| pInChI->nFlags |= nFlags; 2466| 333| } 2467| 277k| else 2468| 277k| { 2469| 277k| if (j == TAUT_NON && !nFlags && nFlagsAlt) ------------------ | | 574| 554k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2469:33): [True: 33.7k, False: 243k] | Branch (2469:50): [True: 33.7k, False: 0] | Branch (2469:61): [True: 633, False: 33.1k] ------------------ 2470| 633| { 2471| 633| pInChI->nFlags |= nFlagsAlt; 2472| 633| } 2473| 277k| } 2474| | /**** add empty immobile H (nNum_H) if it is missing ****/ 2475| 277k| if (!pInChI->nNum_H && ------------------ | Branch (2475:29): [True: 68.9k, False: 208k] ------------------ 2476| 68.9k| !(pInChI->nNum_H = (S_CHAR*)inchi_calloc((long long)pInChI->nNumberOfAtoms + 1, sizeof(pInChI->nNum_H[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 68.9k|#define inchi_calloc calloc ------------------ | Branch (2476:29): [True: 0, False: 68.9k] ------------------ 2477| 0| { 2478| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2479| 0| goto exit_function; 2480| 0| } 2481| | /**** add single atom nConnTable if it is missing ****/ 2482| 277k| if (!pInChI->nConnTable && pInpInChI[iINChI][TAUT_YES]) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 575| 50.2k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2482:29): [True: 50.2k, False: 227k] | Branch (2482:52): [True: 50.2k, False: 0] ------------------ 2483| 50.2k| { 2484| 50.2k| AT_NUMB* pCT; 2485| 50.2k| int lenCT; 2486| 50.2k| if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES] && ------------------ | | 574| 100k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES] && ------------------ | | 575| 33.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2486:33): [True: 33.8k, False: 16.3k] | Branch (2486:50): [True: 33.1k, False: 720] ------------------ 2487| 33.1k| (pCT = pInpInChI[iINChI][TAUT_YES][k].nConnTable) && ------------------ | | 575| 33.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2487:33): [True: 33.1k, False: 0] ------------------ 2488| 33.1k| (lenCT = pInpInChI[iINChI][TAUT_YES][k].lenConnTable) > 0) ------------------ | | 575| 33.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2488:33): [True: 33.1k, False: 0] ------------------ 2489| 33.1k| { 2490| 33.1k| if (!(pInChI->nConnTable = (AT_NUMB*)inchi_calloc((long long)lenCT + 1, sizeof(pInChI->nConnTable[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 33.1k|#define inchi_calloc calloc ------------------ | Branch (2490:37): [True: 0, False: 33.1k] ------------------ 2491| 0| { 2492| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2493| 0| goto exit_function; 2494| 0| } 2495| 33.1k| memcpy(pInChI->nConnTable, pCT, lenCT * sizeof(pInChI->nConnTable[0])); 2496| 33.1k| pInChI->lenConnTable = lenCT; 2497| 33.1k| } 2498| 17.0k| else 2499| 17.0k| { 2500| 17.0k| if (j == TAUT_YES && pInChI->nNumberOfAtoms > 1) ------------------ | | 575| 34.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2500:37): [True: 16.3k, False: 720] | Branch (2500:54): [True: 4, False: 16.3k] ------------------ 2501| 4| { 2502| 4| *pState = IST_MOBILE_H_CONNECTIONS + (iINChI == INCHI_REC ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 571| 4|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ *pState = IST_MOBILE_H_CONNECTIONS + (iINChI == INCHI_REC ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 342| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (2502:75): [True: 0, False: 4] ------------------ 2503| 4| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 2504| 4| goto exit_function; 2505| 4| } 2506| 17.0k| if (!(pInChI->nConnTable = (AT_NUMB*)inchi_calloc((long long)pInChI->nNumberOfAtoms + 1, sizeof(pInChI->nConnTable[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 17.0k|#define inchi_calloc calloc ------------------ | Branch (2506:37): [True: 0, False: 17.0k] ------------------ 2507| 0| { 2508| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2509| 0| goto exit_function; 2510| 0| } 2511| 17.0k| pInChI->lenConnTable = 1; 2512| 17.0k| pInChI->nConnTable[0] = 1; 2513| 17.0k| } 2514| 50.2k| } 2515| 227k| else 2516| 227k| { 2517| 227k| if (pInChI->nConnTable && !pInChI->lenConnTable && pInChI->nNumberOfAtoms == 1) ------------------ | Branch (2517:33): [True: 227k, False: 0] | Branch (2517:55): [True: 0, False: 227k] | Branch (2517:80): [True: 0, False: 0] ------------------ 2518| 0| { 2519| 0| pInChI->nConnTable[0] = 1; 2520| 0| pInChI->lenConnTable = 1; 2521| 0| } 2522| 227k| } 2523| | /**** copy charge: Mobile H --> Fixed H; ****/ 2524| 277k| if (j == TAUT_NON) ------------------ | | 574| 277k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2524:29): [True: 33.8k, False: 243k] ------------------ 2525| 33.8k| { 2526| | /* 2527| | if ( pInChI->nTotalCharge == NO_VALUE_INT ) 2528| | { 2529| | pInChI->nTotalCharge = 0; 2530| | } 2531| | else 2532| | */ 2533| 33.8k| if (!pInChI->nTotalCharge && k < nNumComponents[iINChI][TAUT_YES] && pInpInChI[iINChI][TAUT_YES]) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 575| 33.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (!pInChI->nTotalCharge && k < nNumComponents[iINChI][TAUT_YES] && pInpInChI[iINChI][TAUT_YES]) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 575| 33.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2533:33): [True: 33.8k, False: 10] | Branch (2533:58): [True: 33.1k, False: 720] | Branch (2533:98): [True: 33.1k, False: 0] ------------------ 2534| 33.1k| { 2535| 33.1k| INChI* pAltInChI = &pInpInChI[iINChI][TAUT_YES][k]; /* Mobile H InChI */ ------------------ | | 575| 33.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2536| 33.1k| if (pAltInChI->nTotalCharge && pAltInChI->nTotalCharge != NO_VALUE_INT) ------------------ | | 23| 95|#define NO_VALUE_INT 9999 ------------------ | Branch (2536:37): [True: 95, False: 33.0k] | Branch (2536:64): [True: 37, False: 58] ------------------ 2537| 37| { 2538| 37| pInChI->nTotalCharge = pAltInChI->nTotalCharge; 2539| 37| } 2540| 33.1k| } 2541| 33.8k| } 2542| | /***** Fixed H: add pInChI->nNum_H_fixed to pInChI->nNum_H ****/ 2543| 277k| if (j == TAUT_NON && pInChI->nNum_H && pInChI->nNum_H_fixed) ------------------ | | 574| 555k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2543:29): [True: 33.8k, False: 243k] | Branch (2543:46): [True: 33.8k, False: 0] | Branch (2543:64): [True: 1.32k, False: 32.5k] ------------------ 2544| 1.32k| { 2545| 12.6k| for (m = 0; m < pInChI->nNumberOfAtoms; m++) ------------------ | Branch (2545:41): [True: 11.3k, False: 1.32k] ------------------ 2546| 11.3k| { 2547| 11.3k| pInChI->nNum_H[m] += pInChI->nNum_H_fixed[m]; 2548| 11.3k| } 2549| 1.32k| } 2550| | /***** copy isotopic atoms: Mobile H --> Fixed H ******/ 2551| 277k| if (j == TAUT_YES && pInChI->nNumberOfIsotopicAtoms && ------------------ | | 575| 555k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2551:29): [True: 243k, False: 33.8k] | Branch (2551:46): [True: 1.28k, False: 242k] ------------------ 2552| 1.28k| k < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 574| 1.28k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2552:29): [True: 127, False: 1.15k] ------------------ 2553| 127| { 2554| 127| INChI* pAltInChI = &pInpInChI[iINChI][TAUT_NON][k]; /* Fixed H InChI */ ------------------ | | 574| 127|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2555| | 2556| 127| if (!pAltInChI->nNumberOfIsotopicAtoms) ------------------ | Branch (2556:33): [True: 118, False: 9] ------------------ 2557| 118| { 2558| 118| ret2 = CopySegment(pAltInChI, pInChI, CPY_ISO_AT, 0, 0); 2559| 118| if (ret2 < 0) ------------------ | Branch (2559:37): [True: 0, False: 118] ------------------ 2560| 0| { 2561| 0| goto exit_function; 2562| 0| } 2563| 118| } 2564| 127| } 2565| | /**** copy coordinates: Mobile H --> Fixed H ******/ 2566| 277k| if (j == TAUT_YES && pInChI->IsotopicTGroup && ------------------ | | 575| 555k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2566:29): [True: 243k, False: 33.8k] | Branch (2566:46): [True: 0, False: 243k] ------------------ 2567| 0| k < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2567:29): [True: 0, False: 0] ------------------ 2568| 0| { 2569| 0| INChI* pAltInChI = &pInpInChI[iINChI][TAUT_NON][k]; /* Fixed H InChI */ ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2570| | 2571| 0| if (!pAltInChI->IsotopicTGroup) ------------------ | Branch (2571:33): [True: 0, False: 0] ------------------ 2572| 0| { 2573| 0| XYZ_COORD* pxyz = (XYZ_COORD*)inchi_calloc(pInChI->nNumberOfAtoms, sizeof(pxyz[0])); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 2574| 0| if (pxyz) ------------------ | Branch (2574:37): [True: 0, False: 0] ------------------ 2575| 0| { 2576| 0| memcpy(pxyz, pInChI->IsotopicTGroup, pInChI->nNumberOfAtoms * sizeof(pxyz[0])); 2577| 0| pAltInChI->IsotopicTGroup = (INChI_IsotopicTGroup*)pxyz; 2578| 0| } 2579| 0| else 2580| 0| { 2581| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2582| 0| goto exit_function; 2583| 0| } 2584| 0| } 2585| 0| } 2586| | 2587| | /******************************************************** 2588| | * * 2589| | * Restore omitted stereo seqments * 2590| | * * 2591| | * order of restoring: * 2592| | * * 2593| | * 1. Fixed H (F) -> (FI) Isotopic Fixed H * 2594| | * 2. Mobile H (M) -> (F) Fixed H * 2595| | * 3. Isotopic Mobile H (MI) -> (FI) Isotopic Fixed H * 2596| | * 4. Mobile H (M) -> (MI) Isotopic Mobile H * 2597| | * * 2598| | ********************************************************/ 2599| | 2600| | /***** (4) copy stereo: Mobile H --> isotopic Mobile H ******/ 2601| 277k| if (j == TAUT_YES) ------------------ | | 575| 277k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2601:29): [True: 243k, False: 33.8k] ------------------ 2602| 243k| { 2603| 243k| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2603:40): [True: 1.28k, False: 242k] ------------------ 2604| 242k| (pInChI->StereoIsotopic && ------------------ | Branch (2604:34): [True: 564, False: 241k] ------------------ 2605| 564| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2605:37): [True: 163, False: 401] ------------------ 2606| 564| + pInChI->StereoIsotopic->nNumberOfStereoBonds) || 2607| 242k| (pInChI_Alt && pInChI_Alt->nNumberOfIsotopicAtoms); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2607:34): [True: 32.9k, False: 209k] | Branch (2607:48): [True: 165, False: 32.7k] ------------------ 2608| | 2609| | /* non-isotopic Mobile H => isotopic Mobile H */ 2610| 243k| if (bIso) ------------------ | Branch (2610:33): [True: 1.60k, False: 242k] ------------------ 2611| 1.60k| { 2612| 1.60k| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2612:37): [True: 271, False: 1.33k] | Branch (2612:55): [True: 135, False: 136] ------------------ 2613| 135| (!pInChI->StereoIsotopic || !pInChI->StereoIsotopic->t_parity)) ------------------ | Branch (2613:38): [True: 73, False: 62] | Branch (2613:65): [True: 12, False: 50] ------------------ 2614| 85| { 2615| 85| if (0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP3, 1, 0)) || ------------------ | Branch (2615:41): [True: 0, False: 85] ------------------ 2616| 85| ((!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) && ------------------ | | 23| 10|#define NO_VALUE_INT 9999 ------------------ | Branch (2616:43): [True: 75, False: 10] | Branch (2616:84): [True: 6, False: 4] ------------------ 2617| 81| 0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP3_M, 1, 0)))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2617:45): [True: 0, False: 81] ------------------ 2618| 0| { 2619| 0| goto exit_function; 2620| 0| } 2621| 85| if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 85|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 85|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2621:41): [True: 14, False: 71] ------------------ 2622| 14| { 2623| 14| if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 14|#define NO_VALUE_INT 9999 ------------------ | Branch (2623:45): [True: 12, False: 2] ------------------ 2624| 12| { 2625| 12| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2625:76): [True: 2, False: 10] ------------------ 2626| 12| } 2627| 14| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 14|#define NO_VALUE_INT 9999 ------------------ | Branch (2627:45): [True: 12, False: 2] ------------------ 2628| 12| { 2629| 12| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2629:84): [True: 10, False: 2] ------------------ 2630| 12| } 2631| 14| } 2632| 85| } 2633| 1.52k| else 2634| 1.52k| { 2635| | /* copy sp3 inversion info: non-isotopic Mobile H => isotopic Mobile H */ 2636| 1.52k| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2636:41): [True: 186, False: 1.33k] | Branch (2636:59): [True: 50, False: 136] ------------------ 2637| 50| pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters && ------------------ | Branch (2637:41): [True: 50, False: 0] | Branch (2637:67): [True: 44, False: 6] ------------------ 2638| 44| pInChI->Stereo->nCompInv2Abs) ------------------ | Branch (2638:41): [True: 44, False: 0] ------------------ 2639| 44| { 2640| 44| if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 121| 44|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 122| 44|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2640:45): [True: 20, False: 24] ------------------ 2641| 20| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 23| 64|#define NO_VALUE_INT 9999 ------------------ | Branch (2641:45): [True: 20, False: 0] ------------------ 2642| 20| pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 20|#define NO_VALUE_INT 9999 ------------------ | Branch (2642:45): [True: 20, False: 0] ------------------ 2643| 20| { 2644| 20| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2644:76): [True: 0, False: 20] ------------------ 2645| 20| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2645:84): [True: 20, False: 0] ------------------ 2646| 20| } 2647| 24| else 2648| 24| { 2649| 24| if (!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) ------------------ | | 23| 24|#define NO_VALUE_INT 9999 ------------------ | Branch (2649:49): [True: 0, False: 24] | Branch (2649:90): [True: 24, False: 0] ------------------ 2650| 24| { 2651| 24| pInChI->StereoIsotopic->nCompInv2Abs = pInChI->Stereo->nCompInv2Abs; 2652| 24| } 2653| 24| } 2654| 44| } 2655| 1.52k| } 2656| 1.60k| } 2657| 243k| if (bIso && ------------------ | Branch (2657:33): [True: 1.60k, False: 242k] ------------------ 2658| 1.60k| pInChI->Stereo && pInChI->Stereo->nNumberOfStereoBonds && ------------------ | Branch (2658:33): [True: 271, False: 1.33k] | Branch (2658:51): [True: 88, False: 183] ------------------ 2659| 88| (!pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity)) ------------------ | Branch (2659:34): [True: 74, False: 14] | Branch (2659:61): [True: 10, False: 4] ------------------ 2660| 84| { 2661| 84| if (0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP2, 1, 0))) ------------------ | Branch (2661:37): [True: 0, False: 84] ------------------ 2662| 0| { 2663| 0| goto exit_function; 2664| 0| } 2665| 84| } 2666| 243k| } 2667| | /***** (0) set nCompInv2Abs to Fixed-H *********************************/ 2668| 277k| if (j == TAUT_NON) ------------------ | | 574| 277k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2668:29): [True: 33.8k, False: 243k] ------------------ 2669| 33.8k| { 2670| 33.8k| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2670:33): [True: 678, False: 33.1k] | Branch (2670:51): [True: 221, False: 457] ------------------ 2671| 221| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 221|#define NO_VALUE_INT 9999 ------------------ | Branch (2671:33): [True: 219, False: 2] ------------------ 2672| 219| { 2673| | /* case of /sN and /t... in non-isotopic Mobile-H, no /s in non-isotopic Fixed-H */ 2674| 219| if (!s[iINChI][j][0] && s[iINChI][jAlt][0] > 0 && /* /sN is not present in F and is present in M */ ------------------ | Branch (2674:37): [True: 209, False: 10] | Branch (2674:57): [True: 24, False: 185] ------------------ 2675| 24| pInChI_Alt && pInChI_Alt->Stereo && pInChI_Alt->Stereo->nNumberOfStereoCenters) ------------------ | Branch (2675:37): [True: 24, False: 0] | Branch (2675:51): [True: 24, False: 0] | Branch (2675:73): [True: 20, False: 4] ------------------ 2676| 20| { 2677| | /* inherit from Mobile-H */ 2678| | /* /s1 in M and MI; /m1 or /m0 in MI; /m. in M; no /m in F. Inherit MI->FI. Added 10-15-2007 */ 2679| 20| if (pInChI_Alt->Stereo->nCompInv2Abs == 0 && /* M: /m. ; means no /m for this component */ ------------------ | Branch (2679:41): [True: 2, False: 18] ------------------ 2680| 2| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && /* F: no /m segment for all components */ ------------------ | | 23| 22|#define NO_VALUE_INT 9999 ------------------ | Branch (2680:41): [True: 2, False: 0] ------------------ 2681| 2| pInChI_Alt->StereoIsotopic && /* MI: present */ ------------------ | Branch (2681:41): [True: 0, False: 2] ------------------ 2682| 0| pInChI_Alt->StereoIsotopic->nCompInv2Abs != 0 && ------------------ | Branch (2682:41): [True: 0, False: 0] ------------------ 2683| 0| pInChI_Alt->StereoIsotopic->nCompInv2Abs != NO_VALUE_INT && /* MI: /m0 or /m1 */ ------------------ | | 23| 20|#define NO_VALUE_INT 9999 ------------------ | Branch (2683:41): [True: 0, False: 0] ------------------ 2684| 0| !s[iINChI][j][0] && !s[iINChI][j][1] && /* F, FI: no /s */ ------------------ | Branch (2684:41): [True: 0, False: 0] | Branch (2684:61): [True: 0, False: 0] ------------------ 2685| 0| s[iINChI][jAlt][0] == 1 && s[iINChI][jAlt][1] == 1 /* M, MI: /s1 and /s1 */ ------------------ | Branch (2685:41): [True: 0, False: 0] | Branch (2685:68): [True: 0, False: 0] ------------------ 2686| 20| ) 2687| 0| { 2688| | /* copy /m from MI to FI */ 2689| 0| if (0 > (ret2 = CopySegment(pInChI, pInChI_Alt, CPY_SP3_M, 1, 1))) ------------------ | Branch (2689:45): [True: 0, False: 0] ------------------ 2690| 0| { 2691| 0| goto exit_function; 2692| 0| } 2693| 0| } 2694| 20| else 2695| 20| { 2696| | /* the following if(){...} was added to fix m1 bug 2007-09-25 DT */ 2697| 20| if (pInChI_Alt->Stereo->nCompInv2Abs != NO_VALUE_INT && s[iINChI][jAlt][0] == 1) ------------------ | | 23| 40|#define NO_VALUE_INT 9999 ------------------ | Branch (2697:45): [True: 4, False: 16] | Branch (2697:97): [True: 2, False: 2] ------------------ 2698| 2| { 2699| 2| pInChI->Stereo->nCompInv2Abs = pInChI_Alt->Stereo->nCompInv2Abs; 2700| 2| } 2701| 18| else 2702| 18| { 2703| | /* M and MI contain /sN and /sN, N=2,3. Added 10-15-2007 */ 2704| 18| if (pInChI_Alt->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 23| 36|#define NO_VALUE_INT 9999 ------------------ | Branch (2704:49): [True: 16, False: 2] ------------------ 2705| 16| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 23| 34|#define NO_VALUE_INT 9999 ------------------ | Branch (2705:49): [True: 16, False: 0] ------------------ 2706| 16| !s[iINChI][j][0] && !s[iINChI][j][1] && ------------------ | Branch (2706:49): [True: 16, False: 0] | Branch (2706:69): [True: 14, False: 2] ------------------ 2707| 14| (s[iINChI][jAlt][0] & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 121| 14|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (s[iINChI][jAlt][0] & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 122| 14|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2707:49): [True: 8, False: 6] ------------------ 2708| 8| (s[iINChI][jAlt][1] & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 8|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (s[iINChI][jAlt][1] & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 8|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2708:49): [True: 4, False: 4] ------------------ 2709| 4| { 2710| 4| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2710:60): [True: 0, False: 4] ------------------ 2711| 4| (pInChI->StereoIsotopic && ------------------ | Branch (2711:54): [True: 2, False: 2] ------------------ 2712| 2| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2712:57): [True: 0, False: 2] ------------------ 2713| 2| + pInChI->StereoIsotopic->nNumberOfStereoBonds) || 2714| 4| (pInChI_Alt && pInChI_Alt->nNumberOfIsotopicAtoms); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2714:54): [True: 4, False: 0] | Branch (2714:68): [True: 4, False: 0] ------------------ 2715| 4| if (bIso) ------------------ | Branch (2715:53): [True: 4, False: 0] ------------------ 2716| 4| { 2717| 4| if (!pInChI_Alt->StereoIsotopic && /* create zero/NULL-initialized pInChI_Alt->StereoIsotopic */ ------------------ | Branch (2717:57): [True: 0, False: 4] ------------------ 2718| 0| 0 > (ret2 = CopySegment(pInChI_Alt, pInChI_Alt, CPY_SP3_M, 1, -1))) ------------------ | Branch (2718:57): [True: 0, False: 0] ------------------ 2719| 0| { 2720| 0| goto exit_function; 2721| 0| } 2722| 4| pInChI_Alt->StereoIsotopic->nCompInv2Abs = 2; /* MI: /m1 or /m0 */ 2723| 4| pInChI_Alt->Stereo->nCompInv2Abs = 0; /* M: /m. ; no /m for this component */ 2724| 4| pInChI->Stereo->nCompInv2Abs = NO_VALUE_INT + 1; /* FI: Stereo->CompInv2Abs=0, StereoIsotopic->CompInv2Abs=1 or -1 */ ------------------ | | 23| 4|#define NO_VALUE_INT 9999 ------------------ 2725| 4| } 2726| 0| else 2727| 0| { 2728| 0| pInChI->Stereo->nCompInv2Abs = 2; /* F: /m1 or /m0, omitted from InChI as a repetition */ 2729| 0| pInChI_Alt->Stereo->nCompInv2Abs = 2; /* M: /m1 or /m0; in Srel/SRac case the value = 2 */ 2730| 0| } 2731| 4| } 2732| 14| else 2733| 14| { 2734| 14| pInChI->Stereo->nCompInv2Abs = 2; /* F: /m1 or /m0, omitted from InChI as a repetition */ 2735| 14| pInChI_Alt->Stereo->nCompInv2Abs = 2; /* M: /m1 or /m0; in Srel/SRac case the value = 2 */ 2736| 14| } 2737| 18| } 2738| 20| } 2739| 20| } 2740| 199| else 2741| 199| { 2742| | /* case of /sN in Isotopic Fixed-H only, /t... in Fixed-H, no /m (2007-08-27 DT) */ 2743| 199| if (!s[iINChI][j][0] && !s[iINChI][jAlt][0] && /* /sN in Fixed-H isotopic only */ ------------------ | Branch (2743:41): [True: 189, False: 10] | Branch (2743:61): [True: 185, False: 4] ------------------ 2744| 185| (nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 121| 185|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 122| 185|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2744:41): [True: 18, False: 167] ------------------ 2745| 18| !(pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters) && ------------------ | Branch (2745:43): [True: 10, False: 8] | Branch (2745:69): [True: 2, False: 8] ------------------ 2746| | /*!(pInChI_Alt && pInChI_Alt->Stereo && pInChI_Alt->Stereo->nNumberOfStereoCenters) &&*/ 2747| 16| !(pInChI_Alt && pInChI_Alt->StereoIsotopic && pInChI_Alt->StereoIsotopic->nNumberOfStereoCenters)) ------------------ | Branch (2747:43): [True: 16, False: 0] | Branch (2747:57): [True: 6, False: 10] | Branch (2747:87): [True: 0, False: 6] ------------------ 2748| 16| { 2749| 16| pInChI->Stereo->nCompInv2Abs = NO_VALUE_INT + 1; /* Stereo->CompInv2Abs=0, StereoIsotopic->CompInv2Abs=1 or -1 */ ------------------ | | 23| 16|#define NO_VALUE_INT 9999 ------------------ 2750| 16| } 2751| 183| else 2752| 183| { 2753| 183| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2753:72): [True: 10, False: 173] ------------------ 2754| 183| } 2755| 199| } 2756| 219| } 2757| 33.8k| } 2758| | 2759| | /***** (1) copy stereo: non-isotopic Fixed H --> isotopic Fixed H ******/ 2760| 277k| if (j == TAUT_NON) ------------------ | | 574| 277k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2760:29): [True: 33.8k, False: 243k] ------------------ 2761| 33.8k| { 2762| 33.8k| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2762:40): [True: 174, False: 33.6k] ------------------ 2763| 33.6k| (pInChI->StereoIsotopic && ------------------ | Branch (2763:34): [True: 30.2k, False: 3.44k] ------------------ 2764| 30.2k| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2764:37): [True: 28, False: 30.1k] ------------------ 2765| 30.2k| + pInChI->StereoIsotopic->nNumberOfStereoBonds) || 2766| 33.6k| (pInChI_Alt && pInChI_Alt->nNumberOfIsotopicAtoms); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2766:34): [True: 32.9k, False: 720] | Branch (2766:48): [True: 118, False: 32.8k] ------------------ 2767| | /* non-isotopic Fixed H => isotopic Fixed H */ 2768| 33.8k| if (bIso) ------------------ | Branch (2768:33): [True: 320, False: 33.5k] ------------------ 2769| 320| { 2770| 320| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2770:37): [True: 105, False: 215] | Branch (2770:55): [True: 71, False: 34] ------------------ 2771| 71| (!pInChI->StereoIsotopic || !pInChI->StereoIsotopic->t_parity)) ------------------ | Branch (2771:38): [True: 57, False: 14] | Branch (2771:65): [True: 6, False: 8] ------------------ 2772| 63| { 2773| | /* -- replaced 2007-08-27 by (aaa), see below -- DT 2774| | if ( 0 > (ret2 = CopySegment( pInChI, pInChI, CPY_SP3, 1, 0)) || 2775| | !(pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) && 2776| | 0 > (ret2 = CopySegment( pInChI, pInChI, CPY_SP3_M, 1, 0))) { 2777| | goto exit_function; 2778| | } 2779| | */ 2780| | /*----------- replacement (aaa) begin 2007-08-27 DT */ 2781| 63| if (0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP3, 1, 0))) ------------------ | Branch (2781:41): [True: 0, False: 63] ------------------ 2782| 0| { 2783| 0| goto exit_function; 2784| 0| } 2785| 63| if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT + 1) ------------------ | | 23| 63|#define NO_VALUE_INT 9999 ------------------ | Branch (2785:41): [True: 6, False: 57] ------------------ 2786| 6| { 2787| 6| pInChI->Stereo->nCompInv2Abs = 0; 2788| 6| pInChI->StereoIsotopic->nCompInv2Abs = 2; 2789| 6| } 2790| 57| else 2791| 57| { 2792| 57| if (!(pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) && ------------------ | | 23| 55|#define NO_VALUE_INT 9999 ------------------ | Branch (2792:47): [True: 2, False: 55] | Branch (2792:87): [True: 0, False: 55] ------------------ 2793| 55| 0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP3_M, 1, 0))) ------------------ | Branch (2793:45): [True: 0, False: 55] ------------------ 2794| 0| { 2795| 0| goto exit_function; 2796| 0| } 2797| 57| } 2798| | /*----------- replacement (aaa) end 2007-08-27 DT */ 2799| 63| if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 63|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 63|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2799:41): [True: 6, False: 57] ------------------ 2800| 6| { 2801| 6| if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 6|#define NO_VALUE_INT 9999 ------------------ | Branch (2801:45): [True: 0, False: 6] ------------------ 2802| 0| { 2803| 0| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2803:76): [True: 0, False: 0] ------------------ 2804| 0| } 2805| 6| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 6|#define NO_VALUE_INT 9999 ------------------ | Branch (2805:45): [True: 2, False: 4] ------------------ 2806| 2| { 2807| 2| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2807:84): [True: 0, False: 2] ------------------ 2808| 2| } 2809| 6| } 2810| |#ifdef NEVER 2811| | if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && 2812| | !s[iINChI][j][0] && s[iINChI][j][0] > 0) 2813| | { 2814| | /* copied Rel/Rac stereo to Iso; /s is in Iso /s is not in non-Iso */ 2815| | /* this means all difference in stereo is in inversion */ 2816| | if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && 2817| | pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) 2818| | { 2819| | pInChI->Stereo->nCompInv2Abs = 0; /* missing */ 2820| | pInChI->StereoIsotopic->nCompInv2Abs = 2; /* unusual value */ 2821| | } 2822| | } 2823| |#endif 2824| 63| } 2825| 257| else 2826| 257| { 2827| | /* copy sp3 inversion info: non-isotopic Fixed H --> isotopic Fixed H */ 2828| 257| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2828:41): [True: 42, False: 215] | Branch (2828:59): [True: 8, False: 34] ------------------ 2829| 8| pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters && ------------------ | Branch (2829:41): [True: 8, False: 0] | Branch (2829:67): [True: 6, False: 2] ------------------ 2830| 6| pInChI->Stereo->nCompInv2Abs) ------------------ | Branch (2830:41): [True: 0, False: 6] ------------------ 2831| 0| { 2832| 0| if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 121| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if ((nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)) && ------------------ | | 122| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2832:45): [True: 0, False: 0] ------------------ 2833| 0| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2833:45): [True: 0, False: 0] ------------------ 2834| 0| pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2834:45): [True: 0, False: 0] ------------------ 2835| 0| { 2836| 0| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2836:76): [True: 0, False: 0] ------------------ 2837| 0| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2837:84): [True: 0, False: 0] ------------------ 2838| 0| } 2839| 0| else 2840| 0| { 2841| 0| if (!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2841:49): [True: 0, False: 0] | Branch (2841:90): [True: 0, False: 0] ------------------ 2842| 0| { 2843| 0| pInChI->StereoIsotopic->nCompInv2Abs = pInChI->Stereo->nCompInv2Abs; 2844| 0| } 2845| 0| } 2846| 0| } 2847| 257| } 2848| 320| } 2849| 33.8k| if (bIso && ------------------ | Branch (2849:33): [True: 320, False: 33.5k] ------------------ 2850| 320| pInChI->Stereo && pInChI->Stereo->nNumberOfStereoBonds && ------------------ | Branch (2850:33): [True: 105, False: 215] | Branch (2850:51): [True: 2, False: 103] ------------------ 2851| 2| (!pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity)) ------------------ | Branch (2851:34): [True: 2, False: 0] | Branch (2851:61): [True: 0, False: 0] ------------------ 2852| 2| { 2853| 2| if (0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP2, 1, 0))) ------------------ | Branch (2853:37): [True: 0, False: 2] ------------------ 2854| 0| { 2855| 0| goto exit_function; 2856| 0| } 2857| 2| } 2858| 33.8k| } 2859| | 2860| | /***** copy stereo: Mobile H --> Fixed H ******/ 2861| 277k| if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES]) ------------------ | | 574| 555k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES]) ------------------ | | 575| 33.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2861:29): [True: 33.8k, False: 243k] | Branch (2861:46): [True: 33.1k, False: 720] ------------------ 2862| 33.1k| { 2863| 33.1k| INChI* pAltInChI = &pInpInChI[iINChI][TAUT_YES][k]; /* Mobile H InChI */ ------------------ | | 575| 33.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2864| 33.1k| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2864:40): [True: 174, False: 32.9k] ------------------ 2865| 32.9k| (pInChI->StereoIsotopic && ------------------ | Branch (2865:34): [True: 30.2k, False: 2.67k] ------------------ 2866| 30.2k| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2866:37): [True: 80, False: 30.1k] ------------------ 2867| 30.2k| + pInChI->StereoIsotopic->nNumberOfStereoBonds) || 2868| 32.8k| (pAltInChI && ( ------------------ | Branch (2868:34): [True: 32.8k, False: 0] ------------------ 2869| 32.8k| pAltInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2869:37): [True: 66, False: 32.8k] ------------------ 2870| 32.8k| (pAltInChI->StereoIsotopic && ------------------ | Branch (2870:38): [True: 117, False: 32.6k] ------------------ 2871| 117| pAltInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2871:41): [True: 55, False: 62] ------------------ 2872| 117| + pAltInChI->StereoIsotopic->nNumberOfStereoBonds))); /* djb-rwth: addressing LLVM warning */ 2873| 33.1k| int bNo_InChI_t = (!pInChI->Stereo || !pInChI->Stereo->t_parity); ------------------ | Branch (2873:48): [True: 32.4k, False: 652] | Branch (2873:67): [True: 301, False: 351] ------------------ 2874| 33.1k| int bNo_InChI_m = (!pInChI->Stereo || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs); ------------------ | | 23| 652|#define NO_VALUE_INT 9999 ------------------ | Branch (2874:48): [True: 32.4k, False: 652] | Branch (2874:67): [True: 132, False: 520] ------------------ 2875| | 2876| | /* (2) non-isotopic Mobile H => non-isotopic Fixed H */ 2877| 33.1k| if (pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2877:33): [True: 537, False: 32.5k] | Branch (2877:54): [True: 213, False: 324] ------------------ 2878| 213| (!pInChI->Stereo || !pInChI->Stereo->t_parity)) ------------------ | Branch (2878:34): [True: 88, False: 125] | Branch (2878:53): [True: 42, False: 83] ------------------ 2879| 130| { 2880| 130|#if ( FIX_I2I_STEREOCONVERSION_BUG2 == 1 ) 2881| | /* (2008-04-02) 1=> Fix bug of i2i conversion SAbs-->(SRel||Srac) */ 2882| | /* (converter skipped empty '/t' or sometimes produced an excess one */ 2883| | 2884| | /* check whether t stereo is actually present */ 2885| 130| int bHave_t_stereo = 1; 2886| 130| if (pInChI->Stereo) ------------------ | Branch (2886:37): [True: 42, False: 88] ------------------ 2887| 42| bHave_t_stereo = pInChI->Stereo->nNumberOfStereoCenters; 2888| | /* account for stereobonds present */ 2889| 130| if (bHave_t_stereo < 1) ------------------ | Branch (2889:37): [True: 42, False: 88] ------------------ 2890| 42| if (pInChI->Stereo->nNumberOfStereoBonds > 0) ------------------ | Branch (2890:41): [True: 4, False: 38] ------------------ 2891| 4| bHave_t_stereo = 1; 2892| | /* copy stereo anyway ... */ 2893| 130|#endif 2894| 130| if (0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3, 0, 0)) || ------------------ | Branch (2894:37): [True: 0, False: 130] ------------------ 2895| 130| ((!pInChI->Stereo->nCompInv2Abs || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs) && ------------------ | | 23| 28|#define NO_VALUE_INT 9999 ------------------ | Branch (2895:39): [True: 102, False: 28] | Branch (2895:72): [True: 28, False: 0] ------------------ 2896| 130| 0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3_M, 0, 0)))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2896:41): [True: 0, False: 130] ------------------ 2897| 0| { 2898| 0| goto exit_function; 2899| 0| } 2900| | 2901| 130|#if ( FIX_I2I_STEREOCONVERSION_BUG2 == 1 ) 2902| | /* ... correct just copied stereo if applicable */ 2903| 130| if ((s[iINChI][j][0] < 1) && ------------------ | Branch (2903:37): [True: 118, False: 12] ------------------ 2904| 118| (bHave_t_stereo < 1) && ------------------ | Branch (2904:37): [True: 38, False: 80] ------------------ 2905| 38| (pAltInChI->Stereo->nNumberOfStereoCenters > 0) && ------------------ | Branch (2905:37): [True: 38, False: 0] ------------------ 2906| 38| (s[iINChI][jAlt][0] < 1)) ------------------ | Branch (2906:37): [True: 36, False: 2] ------------------ 2907| 36| { 2908| | /* (2010-02-28) if not all stereo centers are unknown/undefined */ 2909| | /* at which condition stereo still should present .. */ 2910| 36| int all_UU = 1; 2911| 40| for (kc = 0; kc < pAltInChI->Stereo->nNumberOfStereoCenters; kc++) ------------------ | Branch (2911:50): [True: 38, False: 2] ------------------ 2912| 38| { 2913| 38| if ((pAltInChI->Stereo->t_parity[kc] != AB_PARITY_UNKN) && ------------------ | | 221| 38|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2913:45): [True: 36, False: 2] ------------------ 2914| 36| (pAltInChI->Stereo->t_parity[kc] != AB_PARITY_UNDF)) ------------------ | | 222| 36|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2914:45): [True: 34, False: 2] ------------------ 2915| 34| { 2916| 34| all_UU = 0; 2917| 34| break; 2918| 34| } 2919| 38| } 2920| 36| if (!all_UU) ------------------ | Branch (2920:41): [True: 34, False: 2] ------------------ 2921| 34| pInChI->Stereo->nNumberOfStereoCenters = 0; 2922| 36| } 2923| 130|#endif 2924| | 2925| | /* in case of missing nCompInv2Abs, 2005-05-10 */ 2926| 130| if ((pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) && ------------------ | | 23| 130|#define NO_VALUE_INT 9999 ------------------ | Branch (2926:37): [True: 130, False: 0] ------------------ 2927| 130| (nFlagsAlt & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 130|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (nFlagsAlt & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 130|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2927:37): [True: 50, False: 80] ------------------ 2928| 50| { 2929| 50| if (s[iINChI][jAlt][0] > 0 && s[iINChI][j][0] > 0) ------------------ | Branch (2929:41): [True: 18, False: 32] | Branch (2929:67): [True: 4, False: 14] ------------------ 2930| 4| { 2931| | /* suppose once in a while only non-taut stereo changes if inverted */ 2932| 4| pAltInChI->Stereo->nCompInv2Abs = (++nMH2FH_AltInv) % 2 ? 2 : 0; ------------------ | Branch (2932:75): [True: 2, False: 2] ------------------ 2933| 4| pInChI->Stereo->nCompInv2Abs = 2; 2934| 4| } 2935| 46| else 2936| 46| { 2937| | /* Mobile-H: /t.. /sN; Mobile-H isotopic: /sN (n=2 or 3), not /t...; Fixed-H layer is present, has no /t, no /i/t */ 2938| | /* Mobile-H /sN was caused by another component that would have same /mN in all layers */ 2939| | /* therefore, in case of Abs. Stereo, Mobile-H stereo isotopic stereo would have /m1 */ 2940| | /* In case of Rel/Rac stereo, since no /m1 could occur in Mobile-H isotopic, */ 2941| | /* no pAltInChI->StereoIsotopic or pInChI->StereoIsotopic have been created yet. */ 2942| | /* added 10-11-2007 to fix i2i bug for Rel/Rac stereo */ 2943| 46| if (nNumComponents[iINChI][j] > 1 && ------------------ | Branch (2943:45): [True: 32, False: 14] ------------------ 2944| 32| bNo_InChI_t && bNo_InChI_m /* no /t... or /mN in Fixed-H */ && !nFlags && ------------------ | Branch (2944:45): [True: 32, False: 0] | Branch (2944:60): [True: 32, False: 0] | Branch (2944:109): [True: 26, False: 6] ------------------ 2945| 26| !(pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity) && ------------------ | Branch (2945:47): [True: 10, False: 16] | Branch (2945:76): [True: 8, False: 2] ------------------ 2946| 18| !(pInChI->StereoIsotopic && pInChI->StereoIsotopic->t_parity) && ------------------ | Branch (2946:47): [True: 0, False: 18] | Branch (2946:73): [True: 0, False: 0] ------------------ 2947| 18| s[iINChI][j][0] == 0 && s[iINChI][j][1] == 0 && ------------------ | Branch (2947:45): [True: 18, False: 0] | Branch (2947:69): [True: 18, False: 0] ------------------ 2948| | /* /sN, N=2 or 3 only in Mobile-H AND Mobile-H isotopic */ 2949| 18| (s[iINChI][jAlt][0] & ((INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) && ------------------ | | 121| 18|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (s[iINChI][jAlt][0] & ((INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) && ------------------ | | 122| 18|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2949:45): [True: 12, False: 6] ------------------ 2950| 12| (s[iINChI][jAlt][1] & ((INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)))) ------------------ | | 121| 12|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (s[iINChI][jAlt][1] & ((INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)))) ------------------ | | 122| 12|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2950:45): [True: 0, False: 12] ------------------ 2951| 0| { 2952| 0| if (bIso) ------------------ | Branch (2952:49): [True: 0, False: 0] ------------------ 2953| 0| { 2954| | /* create two zero/NULL-initialized isotopic stereo if they do not exist */ 2955| 0| if ((!pInChI->StereoIsotopic && 0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3_M, 1, -1))) ------------------ | Branch (2955:54): [True: 0, False: 0] | Branch (2955:81): [True: 0, False: 0] ------------------ 2956| | /* -- the following will be created later, in TAUT_YES part of the code -- */ 2957| 0| || (!pAltInChI->StereoIsotopic && 0 > (ret2 = CopySegment(pAltInChI, pAltInChI, CPY_SP3_M, 1, -1)))) /* djb-rwth: addressing LLVM warnings */ /* djb-rwth: addressing coverity ID #499533 -- unresolved issue -- revision required */ ------------------ | Branch (2957:57): [True: 0, False: 0] | Branch (2957:87): [True: 0, False: 0] ------------------ 2958| 0| { 2959| 0| goto exit_function; 2960| 0| } 2961| | /* same value = 2 for MI and FI; here we assign only FI */ 2962| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 2963| 0| pInChI->Stereo->nCompInv2Abs = 0; 2964| | /* -- the following will NOT be assigned later, in TAUT_YES part of the code -- */ 2965| 0| pAltInChI->StereoIsotopic->nCompInv2Abs = 2; 2966| 0| pAltInChI->Stereo->nCompInv2Abs = 0; 2967| | /* */ 2968| 0| } 2969| 0| else 2970| 0| { 2971| 0| if (NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs && ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2971:53): [True: 0, False: 0] ------------------ 2972| 0| NO_VALUE_INT == pAltInChI->Stereo->nCompInv2Abs) ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2972:53): [True: 0, False: 0] ------------------ 2973| 0| { 2974| 0| pInChI->Stereo->nCompInv2Abs = 2; 2975| 0| pAltInChI->Stereo->nCompInv2Abs = 2; 2976| 0| } 2977| 0| } 2978| 0| } 2979| 46| else 2980| 46| { 2981| 46| if ((s[iINChI][jAlt][0] > 0 || s[iINChI][j][0] > 0) && s[iINChI][j][0] >= 0) ------------------ | Branch (2981:50): [True: 14, False: 32] | Branch (2981:76): [True: 8, False: 24] | Branch (2981:100): [True: 22, False: 0] ------------------ 2982| 22| { 2983| 22| pInChI->Stereo->nCompInv2Abs = 2; 2984| 22| } 2985| 24| else 2986| 24| { 2987| | /* Mobile-H: /t..., no /sN; Mobile-H isotopic: /s2 or /s3, not /t; Fixed-H layer is present, has no /t, no /i/t */ 2988| | /* therefore, in case of Abs. Stereo, Mobile-H stereo isotopic stereo would have /m1 */ 2989| | /* In case of Rel/Rac stereo, since no /m1 could occur in Mobile-H isotopic, */ 2990| | /* no pAltInChI->StereoIsotopic or pInChI->StereoIsotopic have been created yet. */ 2991| | /* added 10-10-2007 to fix i2i bug for Rel/Rac stereo */ 2992| 24| if (bIso && bNo_InChI_t && bNo_InChI_m /* no /t... or /mN in Fixed-H */ && !nFlags && ------------------ | Branch (2992:53): [True: 16, False: 8] | Branch (2992:61): [True: 16, False: 0] | Branch (2992:76): [True: 16, False: 0] | Branch (2992:125): [True: 16, False: 0] ------------------ 2993| 16| !(pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity) && ------------------ | Branch (2993:55): [True: 14, False: 2] | Branch (2993:84): [True: 8, False: 6] ------------------ 2994| 8| !(pInChI->StereoIsotopic && pInChI->StereoIsotopic->t_parity) && ------------------ | Branch (2994:55): [True: 4, False: 4] | Branch (2994:81): [True: 2, False: 2] ------------------ 2995| 6| s[iINChI][jAlt][0] == 0 && s[iINChI][j][0] == 0 && s[iINChI][j][1] == 0 && ------------------ | Branch (2995:53): [True: 6, False: 0] | Branch (2995:80): [True: 6, False: 0] | Branch (2995:104): [True: 6, False: 0] ------------------ 2996| | /* /sN, N=2 or 3 only in Mobile-H isotopic */ 2997| 6| (s[iINChI][jAlt][1] & ((INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)))) ------------------ | | 121| 6|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (s[iINChI][jAlt][1] & ((INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)))) ------------------ | | 122| 6|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2997:53): [True: 6, False: 0] ------------------ 2998| 6| { 2999| | /* create two zero/NULL-initialized isotopic stereo if they do not exist */ 3000| 6| if (!pInChI->StereoIsotopic && 0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3_M, 1, -1)) ------------------ | Branch (3000:57): [True: 4, False: 2] | Branch (3000:84): [True: 0, False: 4] ------------------ 3001| | /* -- the following will be created later, in TAUT_YES part of the code -- */ 3002| 6| /*|| !pAltInChI->StereoIsotopic && 0 > (ret2 = CopySegment( pAltInChI, pAltInChI, CPY_SP3_M, 1, -1))*/) 3003| 0| { 3004| 0| goto exit_function; 3005| 0| } 3006| | /* same value = 2 for MI and FI; here we assign only FI */ 3007| 6| pInChI->StereoIsotopic->nCompInv2Abs = 2; 3008| 6| pInChI->Stereo->nCompInv2Abs = 0; 3009| | /* -- the following will be assigned later, in TAUT_YES part of the code -- */ 3010| | /* 3011| | pAltInChI->StereoIsotopic->nCompInv2Abs = 2; 3012| | pAltInChI->Stereo->nCompInv2Abs = 0; 3013| | */ 3014| 6| } 3015| 18| else 3016| 18| { 3017| 18| pInChI->Stereo->nCompInv2Abs = 0; 3018| 18| } 3019| 24| } 3020| 46| } 3021| 46| } 3022| 50| if (!(pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 50|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (!(pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 50|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3022:41): [True: 0, False: 50] ------------------ 3023| 0| { 3024| 0| pInChI->nFlags |= ((nFlagsAlt | nFlags) & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)); ------------------ | | 121| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ pInChI->nFlags |= ((nFlagsAlt | nFlags) & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)); ------------------ | | 122| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 3025| 0| } 3026| 50| } 3027| 130| } 3028| 32.9k| else 3029| 32.9k| { 3030| | /* copy sp3 inversion info: non-isotopic Mobile H => non-isotopic Fixed H */ 3031| 32.9k| if (pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (3031:37): [True: 407, False: 32.5k] | Branch (3031:58): [True: 83, False: 324] ------------------ 3032| 83| pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (3032:37): [True: 83, False: 0] | Branch (3032:55): [True: 54, False: 29] ------------------ 3033| 54| pAltInChI->Stereo->nCompInv2Abs && ------------------ | Branch (3033:37): [True: 48, False: 6] ------------------ 3034| 48| (!pInChI->Stereo->nCompInv2Abs || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs)) ------------------ | | 23| 16|#define NO_VALUE_INT 9999 ------------------ | Branch (3034:38): [True: 32, False: 16] | Branch (3034:71): [True: 0, False: 16] ------------------ 3035| 32| { 3036| 32| if (!(nFlagsAlt && !nFlags) || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs) ------------------ | | 23| 6|#define NO_VALUE_INT 9999 ------------------ | Branch (3036:43): [True: 6, False: 26] | Branch (3036:56): [True: 6, False: 0] | Branch (3036:68): [True: 0, False: 6] ------------------ 3037| 26| { 3038| | /* ??? */ 3039| 26| pInChI->Stereo->nCompInv2Abs = pAltInChI->Stereo->nCompInv2Abs; 3040| 26| } 3041| 32| } 3042| 32.9k| } 3043| | 3044| | /* use same rule to copy stereobonds */ 3045| 33.1k| if (pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoBonds && ------------------ | Branch (3045:33): [True: 537, False: 32.5k] | Branch (3045:54): [True: 174, False: 363] ------------------ 3046| 174| (!pInChI->Stereo || !pInChI->Stereo->b_parity)) ------------------ | Branch (3046:34): [True: 51, False: 123] | Branch (3046:53): [True: 6, False: 117] ------------------ 3047| 57| { 3048| 57| if (0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP2, 0, 0))) ------------------ | Branch (3048:37): [True: 0, False: 57] ------------------ 3049| 0| { 3050| 0| goto exit_function; 3051| 0| } 3052| 57| } 3053| | /* (3) isotopic Mobile H -> isotopic Fixed H */ 3054| | /* if !FH_Stereo && !MH_Stereo && MH_IsoStereo!=NULL && FH_IsoStereo==NULL */ 3055| 33.1k| if (bIso) ------------------ | Branch (3055:33): [True: 375, False: 32.7k] ------------------ 3056| 375| { 3057| 375| if (!(pInChI->Stereo && pInChI->Stereo->t_parity) && /* !FH_Stereo */ ------------------ | Branch (3057:39): [True: 158, False: 217] | Branch (3057:57): [True: 126, False: 32] ------------------ 3058| 249| !(pAltInChI->Stereo && pAltInChI->Stereo->t_parity) && /* !MH_Stereo */ ------------------ | Branch (3058:39): [True: 42, False: 207] | Branch (3058:60): [True: 21, False: 21] ------------------ 3059| 228| (pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoCenters) && /* MH_IsoStereo */ ------------------ | Branch (3059:38): [True: 37, False: 191] | Branch (3059:67): [True: 28, False: 9] ------------------ 3060| 28| (!pInChI->StereoIsotopic || !pInChI->StereoIsotopic->t_parity)) ------------------ | Branch (3060:38): [True: 17, False: 11] | Branch (3060:65): [True: 3, False: 8] ------------------ 3061| 20| { 3062| | /* !FH_IsoStereo */ 3063| | /* copy sp3 iso stereo MI->FI (/t) and, if FH nCompInv2Abs (/m) is missing, copy it, too, MI->FI */ 3064| 20| if (0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3, 1, 1)) || ------------------ | Branch (3064:41): [True: 0, False: 20] ------------------ 3065| 20| ((!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) && ------------------ | | 23| 3|#define NO_VALUE_INT 9999 ------------------ | Branch (3065:43): [True: 17, False: 3] | Branch (3065:84): [True: 3, False: 0] ------------------ 3066| 20| 0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3_M, 1, 1)))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3066:45): [True: 0, False: 20] ------------------ 3067| 0| { 3068| 0| goto exit_function; 3069| 0| } 3070| | /* in case of missing nCompInv2Abs, Relative or Racemic stereo 2005-05-10 */ 3071| 20| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 23| 40|#define NO_VALUE_INT 9999 ------------------ | Branch (3071:41): [True: 20, False: 0] ------------------ 3072| 20| (nFlagsAlt & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 20|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (nFlagsAlt & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 20|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3072:41): [True: 6, False: 14] ------------------ 3073| 6| { 3074| 6| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][jAlt][1] > 0 ? 2 : 0; ------------------ | Branch (3074:80): [True: 6, False: 0] ------------------ 3075| 6| if (!(pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 6|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (!(pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 6|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3075:45): [True: 0, False: 6] ------------------ 3076| 0| { 3077| 0| pInChI->nFlags |= (nFlagsAlt & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)); ------------------ | | 121| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ pInChI->nFlags |= (nFlagsAlt & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)); ------------------ | | 122| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 3078| 0| } 3079| 6| } 3080| 20| } 3081| 355| else 3082| 355| { 3083| | /* copy sp3 inversion info only: isotopic Mobile H -> isotopic Fixed H */ 3084| 355| if (!(pInChI->Stereo && pInChI->Stereo->t_parity) && /* !FH_Stereo /t */ ------------------ | Branch (3084:43): [True: 148, False: 207] | Branch (3084:61): [True: 126, False: 22] ------------------ 3085| 229| !(pAltInChI->Stereo && pAltInChI->Stereo->t_parity) && /* !MH_Stereo /t */ ------------------ | Branch (3085:43): [True: 32, False: 197] | Branch (3085:64): [True: 21, False: 11] ------------------ 3086| 208| (pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoCenters) && /* MH_IsoStereo /t */ ------------------ | Branch (3086:42): [True: 17, False: 191] | Branch (3086:71): [True: 8, False: 9] ------------------ 3087| 8| (pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters) && /* FH_IsoStereo /t */ ------------------ | Branch (3087:42): [True: 8, False: 0] | Branch (3087:68): [True: 7, False: 1] ------------------ 3088| 7| pAltInChI->StereoIsotopic->nCompInv2Abs && /* MH_IsoStereo /m */ ------------------ | Branch (3088:41): [True: 7, False: 0] ------------------ 3089| 7| (!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs)) ------------------ | | 23| 5|#define NO_VALUE_INT 9999 ------------------ | Branch (3089:42): [True: 2, False: 5] | Branch (3089:83): [True: 3, False: 2] ------------------ 3090| 5| { 3091| | /* !FH_IsoStereo /m */ 3092| | /* added 02-09-2006 */ 3093| 5| if (0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3_M, 1, 1))) ------------------ | Branch (3093:45): [True: 0, False: 5] ------------------ 3094| 0| { 3095| 0| goto exit_function; 3096| 0| } 3097| 5| } 3098| 355| } 3099| | /* use same rule to copy stereobonds */ 3100| 375| if (!(pInChI->Stereo && pInChI->Stereo->b_parity) && ------------------ | Branch (3100:39): [True: 158, False: 217] | Branch (3100:57): [True: 28, False: 130] ------------------ 3101| 347| !(pAltInChI->Stereo && pAltInChI->Stereo->b_parity) && ------------------ | Branch (3101:39): [True: 71, False: 276] | Branch (3101:60): [True: 2, False: 69] ------------------ 3102| 345| (pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoBonds) && ------------------ | Branch (3102:38): [True: 94, False: 251] | Branch (3102:67): [True: 8, False: 86] ------------------ 3103| 8| (!pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity)) ------------------ | Branch (3103:38): [True: 6, False: 2] | Branch (3103:65): [True: 2, False: 0] ------------------ 3104| 8| { 3105| 8| if (0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP2, 1, 1))) ------------------ | Branch (3105:41): [True: 0, False: 8] ------------------ 3106| 0| { 3107| 0| goto exit_function; 3108| 0| } 3109| 8| } 3110| | 3111| | /* (4) Copy Fixed-H -> isotopic Fixed-H */ 3112| | /* if FH_Stereo && !MH_IsoStereo && && !FH_IsoStereo */ 3113| 375| if ((pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters) && /* FH_Stereo /t */ ------------------ | Branch (3113:38): [True: 158, False: 217] | Branch (3113:56): [True: 106, False: 52] ------------------ 3114| 106| !(pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity) && /* !MH_IsoStereo /t */ ------------------ | Branch (3114:39): [True: 43, False: 63] | Branch (3114:68): [True: 33, False: 10] ------------------ 3115| 73| !(pInChI->StereoIsotopic && pInChI->StereoIsotopic->t_parity)) ------------------ | Branch (3115:39): [True: 71, False: 2] | Branch (3115:65): [True: 65, False: 6] ------------------ 3116| 8| { 3117| | /* !FH_IsoStereo /t */ 3118| | 3119| | /* added 10-10-2007 DT: copy MH_Iso /m => FH_Iso /m to fix i2i bug for Abs stereo */ 3120| | /* InChI string contains: MH(/t...), MH_Iso(/mN, no /t), FH(no /t /m), FH_Iso(no /t /m) */ 3121| 8| if (pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nCompInv2Abs && /* MH_IsoStereo /m */ ------------------ | Branch (3121:41): [True: 6, False: 2] | Branch (3121:70): [True: 4, False: 2] ------------------ 3122| 4| bNo_InChI_t && ------------------ | Branch (3122:41): [True: 4, False: 0] ------------------ 3123| 4| NO_VALUE_INT != pAltInChI->StereoIsotopic->nCompInv2Abs && /* undef FH_IsoStereo /m */ ------------------ | | 23| 4|#define NO_VALUE_INT 9999 ------------------ | Branch (3123:41): [True: 0, False: 4] ------------------ 3124| 0| !(pInChI->StereoIsotopic && NO_VALUE_INT != pInChI->StereoIsotopic->nCompInv2Abs)) ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3124:43): [True: 0, False: 0] | Branch (3124:69): [True: 0, False: 0] ------------------ 3125| 0| { 3126| 0| if (0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP3_M, 1, 1))) ------------------ | Branch (3126:45): [True: 0, False: 0] ------------------ 3127| 0| { 3128| 0| goto exit_function; 3129| 0| } 3130| 0| } 3131| | 3132| | /* added 05-09-2006: copy sp3 FH=>FH_Iso */ 3133| 8| if (0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP3, 1, 0)) || ------------------ | Branch (3133:41): [True: 0, False: 8] ------------------ 3134| 8| ((!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) && ------------------ | | 23| 6|#define NO_VALUE_INT 9999 ------------------ | Branch (3134:43): [True: 2, False: 6] | Branch (3134:84): [True: 0, False: 6] ------------------ 3135| 2| 0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP3_M, 1, 0)))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3135:45): [True: 0, False: 2] ------------------ 3136| 0| { 3137| 0| goto exit_function; 3138| 0| } 3139| | 3140| | /* in case of missing nCompInv2Abs, Relative or Racemic stereo, /sN in Fixed-H, 2005-05-10 */ 3141| 8| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 23| 16|#define NO_VALUE_INT 9999 ------------------ | Branch (3141:41): [True: 0, False: 8] ------------------ 3142| 0| (nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ (nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3142:41): [True: 0, False: 0] ------------------ 3143| 0| { 3144| 0| if (s[iINChI][j][0] > 0 && s[iINChI][j][1] > 0) ------------------ | Branch (3144:45): [True: 0, False: 0] | Branch (3144:68): [True: 0, False: 0] ------------------ 3145| 0| { 3146| | /* suppose once in a while only non-taut stereo changes if inverted */ 3147| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 3148| 0| pInChI->Stereo->nCompInv2Abs = (++nFH2iFH_AltInv) % 2 ? 2 : 0; ------------------ | Branch (3148:76): [True: 0, False: 0] ------------------ 3149| 0| } 3150| 0| else 3151| 0| { 3152| 0| if ((s[iINChI][j][0] > 0 || s[iINChI][j][1] > 0) && s[iINChI][j][1] >= 0) /* ??? != NO_VALUE_INT ??? */ ------------------ | Branch (3152:50): [True: 0, False: 0] | Branch (3152:73): [True: 0, False: 0] | Branch (3152:97): [True: 0, False: 0] ------------------ 3153| 0| { 3154| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 3155| 0| } 3156| 0| else 3157| 0| { 3158| 0| pInChI->StereoIsotopic->nCompInv2Abs = 0; 3159| 0| } 3160| 0| } 3161| 0| if (!(pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 121| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (!(pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO))) ------------------ | | 122| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3161:45): [True: 0, False: 0] ------------------ 3162| 0| { 3163| 0| pInChI->nFlags |= (nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)); ------------------ | | 121| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ pInChI->nFlags |= (nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO)); ------------------ | | 122| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 3164| 0| } 3165| 0| } 3166| 8| } 3167| 367| else 3168| 367| { 3169| | /* copy sp3 inversion info only: Fixed-H -> isotopic Fixed H */ 3170| 367| if ((pInChI->Stereo && pInChI->Stereo->t_parity) && ------------------ | Branch (3170:42): [True: 150, False: 217] | Branch (3170:60): [True: 118, False: 32] ------------------ 3171| 118| !(pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity) && ------------------ | Branch (3171:43): [True: 53, False: 65] | Branch (3171:72): [True: 33, False: 20] ------------------ 3172| 85| (pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoCenters) && ------------------ | Branch (3172:42): [True: 20, False: 65] | Branch (3172:71): [True: 0, False: 20] ------------------ 3173| 0| (pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters) && ------------------ | Branch (3173:42): [True: 0, False: 0] | Branch (3173:68): [True: 0, False: 0] ------------------ 3174| 0| pInChI->Stereo->nCompInv2Abs && ------------------ | Branch (3174:41): [True: 0, False: 0] ------------------ 3175| 0| (!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs)) ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3175:42): [True: 0, False: 0] | Branch (3175:83): [True: 0, False: 0] ------------------ 3176| 0| { 3177| | /* added 05-09-2006 */ 3178| 0| if (0 > (ret2 = CopySegment(pInChI, pInChI, CPY_SP3_M, 1, 0))) ------------------ | Branch (3178:45): [True: 0, False: 0] ------------------ 3179| 0| { 3180| 0| goto exit_function; 3181| 0| } 3182| 0| } 3183| 367| } 3184| 375| } 3185| 33.1k| if (bIso && ------------------ | Branch (3185:33): [True: 375, False: 32.7k] ------------------ 3186| 375| !(pInChI->Stereo && pInChI->Stereo->nNumberOfStereoBonds) && ------------------ | Branch (3186:35): [True: 158, False: 217] | Branch (3186:53): [True: 22, False: 136] ------------------ 3187| 353| !(pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoBonds) && ------------------ | Branch (3187:35): [True: 75, False: 278] | Branch (3187:56): [True: 2, False: 73] ------------------ 3188| 351| (pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoBonds) && ------------------ | Branch (3188:34): [True: 99, False: 252] | Branch (3188:63): [True: 10, False: 89] ------------------ 3189| 10| (!pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity)) ------------------ | Branch (3189:34): [True: 2, False: 8] | Branch (3189:61): [True: 0, False: 8] ------------------ 3190| 2| { 3191| 2| if (0 > (ret2 = CopySegment(pInChI, pAltInChI, CPY_SP2, 1, 1))) ------------------ | Branch (3191:37): [True: 0, False: 2] ------------------ 3192| 0| { 3193| 0| goto exit_function; 3194| 0| } 3195| 2| } 3196| 33.1k| } 3197| 277k| } 3198| 277k| } /* end of component cycle (k) */ 3199| 41.1k| } /* end of Mobile/Fixed H cycle (j) */ 3200| | 3201| | /**** replace NO_VALUE_INT with zeroes in all Mobile & Fixed H components ****/ 3202| 61.6k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 61.6k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3202:25): [True: 41.1k, False: 20.5k] ------------------ 3203| 41.1k| { 3204| 318k| for (k = 0; k < nNumComponents[iINChI][j]; k++) ------------------ | Branch (3204:29): [True: 277k, False: 41.1k] ------------------ 3205| 277k| { 3206| 277k| if (pInpInChI[iINChI][j]) ------------------ | Branch (3206:25): [True: 277k, False: 0] ------------------ 3207| 277k| { 3208| 277k| INChI* pInChI = &pInpInChI[iINChI][j][k]; 3209| 277k| if (pInChI->nTotalCharge == NO_VALUE_INT) ------------------ | | 23| 277k|#define NO_VALUE_INT 9999 ------------------ | Branch (3209:29): [True: 76, False: 277k] ------------------ 3210| 76| { 3211| 76| pInChI->nTotalCharge = 0; 3212| 76| } 3213| 277k| if (pInChI->Stereo && pInChI->StereoIsotopic && ------------------ | Branch (3213:29): [True: 23.0k, False: 254k] | Branch (3213:47): [True: 582, False: 22.4k] ------------------ 3214| 582| pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 582|#define NO_VALUE_INT 9999 ------------------ | Branch (3214:29): [True: 359, False: 223] ------------------ 3215| 359| { 3216| 359| if (pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (3216:33): [True: 131, False: 228] ------------------ 3217| 131| pInChI->Stereo->nCompInv2Abs != NO_VALUE_INT) ------------------ | | 23| 131|#define NO_VALUE_INT 9999 ------------------ | Branch (3217:33): [True: 14, False: 117] ------------------ 3218| 14| { 3219| 14| pInChI->StereoIsotopic->nCompInv2Abs = pInChI->Stereo->nCompInv2Abs; 3220| 14| } 3221| 359| } 3222| | /* Add special nCompInv2Abs=2 to force /s2 or /s3 in InChI output */ 3223| 277k| if (pInChI->Stereo && pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 23.0k|#define NO_VALUE_INT 9999 ------------------ | Branch (3223:29): [True: 23.0k, False: 254k] | Branch (3223:47): [True: 9.41k, False: 13.5k] ------------------ 3224| 9.41k| { 3225| 9.41k| if (pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO) && ------------------ | | 121| 9.41k|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO) && ------------------ | | 122| 9.41k|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3225:33): [True: 82, False: 9.33k] ------------------ 3226| 82| pInChI->Stereo->nNumberOfStereoCenters) ------------------ | Branch (3226:33): [True: 52, False: 30] ------------------ 3227| 52| { 3228| 52| pInChI->Stereo->nCompInv2Abs = (s[iINChI][j][0] > 0 /*|| s[iINChI][j][1]>0*/) ? 2 : 0; /* we do not know the real value */ ------------------ | Branch (3228:64): [True: 22, False: 30] ------------------ 3229| 52| } 3230| 9.36k| else 3231| 9.36k| { 3232| 9.36k| pInChI->Stereo->nCompInv2Abs = 0; 3233| 9.36k| } 3234| 9.41k| } 3235| 277k| if (pInChI->StereoIsotopic && pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 23| 31.2k|#define NO_VALUE_INT 9999 ------------------ | Branch (3235:29): [True: 31.2k, False: 246k] | Branch (3235:55): [True: 30.7k, False: 507] ------------------ 3236| 30.7k| { 3237| 30.7k| if (pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO) && ------------------ | | 121| 30.7k|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (pInChI->nFlags & (INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO) && ------------------ | | 122| 30.7k|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3237:33): [True: 40, False: 30.7k] ------------------ 3238| 40| pInChI->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3238:33): [True: 22, False: 18] ------------------ 3239| 22| { 3240| 22| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; /* we do not know the real value */ ------------------ | Branch (3240:72): [True: 22, False: 0] ------------------ 3241| 22| } 3242| 30.7k| else 3243| 30.7k| { 3244| 30.7k| pInChI->StereoIsotopic->nCompInv2Abs = 0; 3245| 30.7k| } 3246| 30.7k| } 3247| | /* added 02-07-2006 */ 3248| 277k| if ((pInChI->Stereo && pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) || ------------------ | | 23| 23.0k|#define NO_VALUE_INT 9999 ------------------ | Branch (3248:30): [True: 23.0k, False: 254k] | Branch (3248:48): [True: 0, False: 23.0k] ------------------ 3249| 277k| (pInChI->StereoIsotopic && pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT)) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 23| 31.2k|#define NO_VALUE_INT 9999 ------------------ | Branch (3249:30): [True: 31.2k, False: 246k] | Branch (3249:56): [True: 0, False: 31.2k] ------------------ 3250| 0| { 3251| 0| ret2 = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3252| 0| goto exit_function; 3253| 0| } 3254| 277k| if (!pInChI->bDeleted && pInChI->nNumberOfAtoms) ------------------ | Branch (3254:29): [True: 277k, False: 33] | Branch (3254:50): [True: 277k, False: 0] ------------------ 3255| 277k| { 3256| 277k| tot_charge[iINChI][j] += pInChI->nTotalCharge; 3257| 3.68M| for (m = 0; m < pInChI->nNumberOfAtoms; m++) ------------------ | Branch (3257:41): [True: 3.40M, False: 277k] ------------------ 3258| 3.40M| { 3259| 3.40M| if (pInChI->nAtom[m] < EL_NUMBER_H || pInChI->nAtom[m] > nElDataLen) ------------------ | | 11| 6.81M|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (3259:37): [True: 0, False: 3.40M] | Branch (3259:71): [True: 0, False: 3.40M] ------------------ 3260| 0| { 3261| 0| ret2 = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3262| 0| goto exit_function; 3263| 0| } 3264| | /* all atoms except H */ 3265| 3.40M| if (pInChI->nAtom[m] > EL_NUMBER_H) ------------------ | | 11| 3.40M|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (3265:37): [True: 3.30M, False: 102k] ------------------ 3266| 3.30M| { 3267| 3.30M| num_elem[iINChI][j][pInChI->nAtom[m]].num++; 3268| 3.30M| } 3269| 3.40M| } 3270| 277k| if (0 > (ret2 = GetInChINumH(pInChI, &m))) ------------------ | Branch (3270:33): [True: 0, False: 277k] ------------------ 3271| 0| { 3272| 0| goto exit_function; 3273| 0| } 3274| 277k| num_elem[iINChI][j][EL_NUMBER_H].num += m; ------------------ | | 11| 277k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 3275| 277k| } 3276| 277k| } 3277| 277k| } 3278| 41.1k| } 3279| | 3280| 61.6k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 61.6k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3280:25): [True: 41.1k, False: 20.5k] ------------------ 3281| 41.1k| { 3282| 318k| for (k = 0; k < nNumComponents[iINChI][j]; k++) ------------------ | Branch (3282:29): [True: 277k, False: 41.1k] ------------------ 3283| 277k| { 3284| 277k| if (pInpInChI[iINChI][j]) ------------------ | Branch (3284:25): [True: 277k, False: 0] ------------------ 3285| 277k| { 3286| 277k| INChI* pInChI = &pInpInChI[iINChI][j][k]; 3287| 277k| if (pInChI->Stereo && !pInChI->Stereo->nNumberOfStereoCenters) ------------------ | Branch (3287:29): [True: 23.0k, False: 254k] | Branch (3287:47): [True: 21.8k, False: 1.11k] ------------------ 3288| 21.8k| { 3289| 21.8k| pInChI->Stereo->nCompInv2Abs = 0; 3290| 21.8k| } 3291| 277k| if (pInChI->StereoIsotopic && !pInChI->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3291:29): [True: 31.2k, False: 246k] | Branch (3291:55): [True: 30.9k, False: 394] ------------------ 3292| 30.9k| { 3293| 30.9k| pInChI->StereoIsotopic->nCompInv2Abs = 0; 3294| 30.9k| } 3295| 277k| } 3296| 277k| } 3297| 41.1k| } 3298| | 3299| 20.5k|#if ( FIX_I2I_STEREOCONVERSION_BUG3 == 1 ) 3300| | /* (2008-04-10) 1=> Fix bug of i2i conversion */ 3301| | /* (missed repeating /s in FI after F for multi-component case) */ 3302| 20.5k| if (nNumComponents[iINChI][TAUT_NON] > 1) /* if multi-component */ ------------------ | | 574| 20.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3302:17): [True: 189, False: 20.3k] ------------------ 3303| 189| { 3304| 189| if (!s[iINChI][TAUT_YES][0] && !s[iINChI][TAUT_YES][1])/* if no /s in M, MI */ ------------------ | | 575| 189|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (!s[iINChI][TAUT_YES][0] && !s[iINChI][TAUT_YES][1])/* if no /s in M, MI */ ------------------ | | 575| 168|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3304:21): [True: 168, False: 21] | Branch (3304:48): [True: 136, False: 32] ------------------ 3305| 136| { 3306| 136| if ((s[iINChI][TAUT_NON][0] > 1) && (s[iINChI][TAUT_NON][1] > 1)) /* if /srel/srac in both F, FI */ ------------------ | | 574| 136|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if ((s[iINChI][TAUT_NON][0] > 1) && (s[iINChI][TAUT_NON][1] > 1)) /* if /srel/srac in both F, FI */ ------------------ | | 574| 2|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3306:25): [True: 2, False: 134] | Branch (3306:57): [True: 0, False: 2] ------------------ 3307| 0| { 3308| 0| if (s[iINChI][TAUT_NON][0] == s[iINChI][TAUT_NON][1]) /* if same stereo in F and FI */ ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (s[iINChI][TAUT_NON][0] == s[iINChI][TAUT_NON][1]) /* if same stereo in F and FI */ ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3308:29): [True: 0, False: 0] ------------------ 3309| 0| { 3310| | /* we assume that at least one component in F has no actual stereo */ 3311| | /* and place deliberately 0 to appropriate place */ 3312| 0| for (k = 0; k < nNumComponents[iINChI][TAUT_NON]; k++) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3312:41): [True: 0, False: 0] ------------------ 3313| 0| { 3314| 0| INChI* pInChI = &pInpInChI[iINChI][TAUT_NON][k]; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3315| 0| if (pInChI->Stereo->nCompInv2Abs != 0) ------------------ | Branch (3315:37): [True: 0, False: 0] ------------------ 3316| 0| { 3317| 0| pInChI->Stereo->nCompInv2Abs = 0; 3318| 0| goto fini; 3319| 0| } 3320| 0| } 3321| 0| } 3322| 0| } 3323| 136| } 3324| 189| } 3325| 20.5k| fini:; 3326| 20.5k|#endif 3327| 20.5k| if (num_elem[iINChI][TAUT_YES]) ------------------ | | 575| 20.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3327:17): [True: 10.3k, False: 10.1k] ------------------ 3328| 10.3k| { 3329| 10.3k| tot_charge[iINChI][TAUT_YES] += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 575| 10.3k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ tot_charge[iINChI][TAUT_YES] += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 575| 10.3k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3330| 10.3k| num_elem[iINChI][TAUT_YES][EL_NUMBER_H].num += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 575| 10.3k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ num_elem[iINChI][TAUT_YES][EL_NUMBER_H].num += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 11| 10.3k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ num_elem[iINChI][TAUT_YES][EL_NUMBER_H].num += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 575| 10.3k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3331| 10.3k| } 3332| | 3333| | /**** Count H and isotopic H in Mobile and Fixed H represntations of components */ 3334| | /* if at least one component has Fixed-H layer then all components have Fixed-H */ 3335| | /* layer; those whose Fixed-H layer is empty have Fixed-H layer same as Mobile-H layer */ 3336| 20.5k| if (nNumComponents[iINChI][TAUT_NON]) ------------------ | | 574| 20.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3336:17): [True: 2.66k, False: 17.8k] ------------------ 3337| 2.66k| { 3338| | /* only if both Mobile and Fixed H exist */ 3339| 2.66k| int nFormulaH[TAUT_NUM], nNumH[TAUT_NUM], nCharge[TAUT_NUM], nNumIsotopicH[TAUT_NUM][NUM_H_ISOTOPES]; 3340| 2.66k| int nRemovedCharge, nRemovedH, nRemovedIsotopicH[NUM_H_ISOTOPES], nFoundRemovedIsoH; 3341| 2.66k| int nTotRemovedProtons, nTotRemovedIsotopicH[NUM_H_ISOTOPES], bExists[TAUT_NUM]; 3342| 2.66k| INChI* pInChI[TAUT_NUM]; 3343| 2.66k| nTotRemovedProtons = 0; 3344| 2.66k| memset(nTotRemovedIsotopicH, 0, sizeof(nTotRemovedIsotopicH)); /* djb-rwth: memset_s C11/Annex K variant? */ 3345| 2.66k| len2 = inchi_max(nNumComponents[iINChI][TAUT_YES], nNumComponents[iINChI][TAUT_NON]); ------------------ | | 138| 2.66k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 4, False: 2.66k] | | ------------------ ------------------ 3346| | 3347| 36.2k| for (k = 0; k < len2; k++) ------------------ | Branch (3347:29): [True: 33.6k, False: 2.60k] ------------------ 3348| 33.6k| { 3349| | /* k is a component index */ 3350| 101k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 101k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3350:33): [True: 67.3k, False: 33.6k] ------------------ 3351| 67.3k| { 3352| | /* j is 0=TAUT_NON or 1=TAUT_YES */ 3353| 67.3k| pInChI[j] = NULL; /* initialization 2006-03 */ 3354| 67.3k| bExists[j] = (k < nNumComponents[iINChI][j]) && ------------------ | Branch (3354:38): [True: 66.7k, False: 596] ------------------ 3355| 66.7k| pInpInChI[iINChI][j][k].nNumberOfAtoms && ------------------ | Branch (3355:29): [True: 66.7k, False: 0] ------------------ 3356| 66.7k| !pInpInChI[iINChI][j][k].bDeleted; ------------------ | Branch (3356:29): [True: 66.7k, False: 17] ------------------ 3357| 67.3k| } 3358| 33.6k| if (!bExists[TAUT_NON]) ------------------ | | 574| 33.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3358:25): [True: 4, False: 33.6k] ------------------ 3359| 4| { 3360| | /* TAUT_YES does not exist for a proton (H+) in TAUT_NON */ 3361| 4| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 3362| 4| goto exit_function; 3363| 4| } 3364| | /* at this point at least one of Mobile[k] and Fixed[k] real InChI exists */ 3365| | /* initialize for counting removed protons and isotopic H from kth Mobile-H component */ 3366| 101k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 101k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3366:33): [True: 67.3k, False: 33.6k] ------------------ 3367| 67.3k| { 3368| 67.3k| if (bExists[j]) ------------------ | Branch (3368:29): [True: 66.7k, False: 609] ------------------ 3369| 66.7k| { 3370| 66.7k| pInChI[j] = &pInpInChI[iINChI][j][k]; /* BC: reading uninit memory (fixed?) */ 3371| 66.7k| } 3372| 67.3k| nFormulaH[j] = 0; 3373| 67.3k| nNumH[j] = 0; 3374| 67.3k| nCharge[j] = 0; 3375| 269k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 72| 269k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3375:37): [True: 202k, False: 67.3k] ------------------ 3376| 202k| { 3377| 202k| nNumIsotopicH[j][m] = 0; 3378| 202k| } 3379| 67.3k| } 3380| | /* extract number of H, isotopic H, and charge */ 3381| 101k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 101k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3381:33): [True: 67.3k, False: 33.6k] ------------------ 3382| 67.3k| { 3383| 67.3k| if (!bExists[j]) ------------------ | Branch (3383:29): [True: 609, False: 66.7k] ------------------ 3384| 609| { 3385| 609| continue; 3386| 609| } 3387| 66.7k| if (0 > (ret2 = GetInChIFormulaNumH(pInChI[j], &nFormulaH[j])) || ------------------ | Branch (3387:29): [True: 0, False: 66.7k] ------------------ 3388| 66.7k| 0 > (ret2 = GetInChINumH(pInChI[j], &nNumH[j])) || ------------------ | Branch (3388:29): [True: 0, False: 66.7k] ------------------ 3389| 66.7k| 0 > (ret2 = GetInChIIsoH(pInChI[j], nNumIsotopicH[j]))) ------------------ | Branch (3389:29): [True: 0, False: 66.7k] ------------------ 3390| 0| { 3391| 0| goto exit_function; 3392| 0| } 3393| 66.7k| nCharge[j] = pInChI[j]->nTotalCharge; 3394| 66.7k| } 3395| 100k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 100k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3395:33): [True: 67.3k, False: 33.6k] ------------------ 3396| 67.3k| { 3397| 67.3k| if (!bExists[j]) ------------------ | Branch (3397:29): [True: 609, False: 66.7k] ------------------ 3398| 609| { 3399| 609| continue; 3400| 609| } 3401| 66.7k| if (nFormulaH[j] != nNumH[j]) ------------------ | Branch (3401:29): [True: 39, False: 66.6k] ------------------ 3402| 39| { 3403| 39| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 39|#define RI_ERR_SYNTAX (-2) ------------------ 3404| 39| goto exit_function; 3405| 39| } 3406| 66.7k| } 3407| 33.6k| nFoundRemovedIsoH = 0; 3408| 33.6k| nRemovedCharge = nCharge[TAUT_NON] - nCharge[TAUT_YES]; ------------------ | | 574| 33.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nRemovedCharge = nCharge[TAUT_NON] - nCharge[TAUT_YES]; ------------------ | | 575| 33.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3409| 33.6k| nRemovedH = nNumH[TAUT_NON] - nNumH[TAUT_YES]; ------------------ | | 574| 33.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nRemovedH = nNumH[TAUT_NON] - nNumH[TAUT_YES]; ------------------ | | 575| 33.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3410| 134k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 72| 134k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3410:33): [True: 100k, False: 33.6k] ------------------ 3411| 100k| { 3412| 100k| nFoundRemovedIsoH += 0 != (nRemovedIsotopicH[m] = nNumIsotopicH[TAUT_NON][m] - ------------------ | | 574| 100k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3413| 100k| nNumIsotopicH[TAUT_YES][m]); ------------------ | | 575| 100k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3414| 100k| } 3415| 33.6k| if (nRemovedCharge != nRemovedH) ------------------ | Branch (3415:25): [True: 17, False: 33.6k] ------------------ 3416| 17| { 3417| 17| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 17|#define RI_ERR_SYNTAX (-2) ------------------ 3418| 17| goto exit_function; 3419| 17| } 3420| 33.6k| if (nRemovedCharge || nFoundRemovedIsoH) ------------------ | Branch (3420:25): [True: 0, False: 33.6k] | Branch (3420:43): [True: 13, False: 33.6k] ------------------ 3421| 13| { 3422| 13| COMPONENT_REM_PROTONS* pNumProtons; 3423| 13| if (!nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3423:29): [True: 13, False: 0] ------------------ 3424| 13| { 3425| | /* allocate only if needed */ 3426| 13| nNumProtons[iINChI][TAUT_YES].pNumProtons = ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3427| 13| (COMPONENT_REM_PROTONS*)inchi_calloc(len2, ------------------ | | 1146| 13|#define inchi_calloc calloc ------------------ 3428| 13| sizeof(nNumProtons[0][0].pNumProtons[0])); 3429| 13| if (!nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3429:33): [True: 0, False: 13] ------------------ 3430| 0| { 3431| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 3432| 0| goto exit_function; 3433| 0| } 3434| 13| } 3435| 13| pNumProtons = nNumProtons[iINChI][TAUT_YES].pNumProtons + k; ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3436| 13| pNumProtons->nNumRemovedProtons = nRemovedH; 3437| 13| nTotRemovedProtons += nRemovedH; 3438| 52| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 72| 52|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3438:37): [True: 39, False: 13] ------------------ 3439| 39| { 3440| 39| pNumProtons->nNumRemovedIsotopicH[m] = nRemovedIsotopicH[m]; 3441| 39| nTotRemovedIsotopicH[m] += nRemovedIsotopicH[m]; 3442| 39| } 3443| | /* make sure the Mobile-H InChI has nTautomer */ 3444| 13| if (pInChI[TAUT_YES] && bExists[TAUT_YES]) ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (pInChI[TAUT_YES] && bExists[TAUT_YES]) ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3444:29): [True: 13, False: 0] | Branch (3444:49): [True: 13, False: 0] ------------------ 3445| 13| { 3446| 13| if (!pInChI[TAUT_YES]->lenTautomer) ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3446:33): [True: 11, False: 2] ------------------ 3447| 11| { 3448| 11| pInChI[TAUT_YES]->lenTautomer = 1; ------------------ | | 575| 11|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3449| 11| } 3450| 13| if (!pInChI[TAUT_YES]->nTautomer) ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3450:33): [True: 11, False: 2] ------------------ 3451| 11| { 3452| 11| pInChI[TAUT_YES]->nTautomer = (AT_NUMB*)inchi_calloc(pInChI[TAUT_YES]->lenTautomer, sizeof(pInChI[0]->nTautomer[0])); ------------------ | | 575| 11|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pInChI[TAUT_YES]->nTautomer = (AT_NUMB*)inchi_calloc(pInChI[TAUT_YES]->lenTautomer, sizeof(pInChI[0]->nTautomer[0])); ------------------ | | 1146| 11|#define inchi_calloc calloc ------------------ pInChI[TAUT_YES]->nTautomer = (AT_NUMB*)inchi_calloc(pInChI[TAUT_YES]->lenTautomer, sizeof(pInChI[0]->nTautomer[0])); ------------------ | | 575| 11|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3453| 11| } 3454| 13| } 3455| 13| } 3456| 33.6k| } 3457| 2.60k| if (nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 575| 2.60k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3457:21): [True: 13, False: 2.59k] ------------------ 3458| 13| { 3459| | /* check consistency */ 3460| |#if ( FIX_ISO_FIXEDH_BUG_READ == 1 ) 3461| | int iso_diff[NUM_H_ISOTOPES], iso_diff_tot = 0; 3462| |#endif 3463| 13| if (nTotRemovedProtons != nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons) ------------------ | | 575| 13|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3463:25): [True: 0, False: 13] ------------------ 3464| 0| { 3465| 0| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 3466| 0| goto exit_function; 3467| 0| } 3468| |#if ( FIX_ISO_FIXEDH_BUG_READ == 1 ) 3469| | for (m = 0; m < NUM_H_ISOTOPES; m++) 3470| | { 3471| | iso_diff[m] = nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[m] - nTotRemovedIsotopicH[m]; 3472| | if (iso_diff[m] < 0) 3473| | { 3474| | ret2 = RI_ERR_SYNTAX; 3475| | goto exit_function; 3476| | } 3477| | else 3478| | { 3479| | /* InChI-1.02b bug: nTotRemovedIsotopicH[m] < nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[m] */ 3480| | /* in non-tautomeric components where D(+) or T(+) was removed from -NH(+)= or =OH(+) */ 3481| | iso_diff_tot += iso_diff[m]; 3482| | } 3483| | } 3484| | if (iso_diff_tot) 3485| | { 3486| | if (0 > bIsoMayBeArranged(bInchi2Struct, iso_diff, nNumProtons, pInpInChI, nNumComponents, iINChI)) 3487| | { 3488| | ret2 = RI_ERR_SYNTAX; 3489| | goto exit_function; 3490| | } 3491| | } 3492| |#else 3493| 15| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 72| 15|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3493:33): [True: 15, False: 0] ------------------ 3494| 15| { 3495| 15| if (nTotRemovedIsotopicH[m] != nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[m]) ------------------ | | 575| 15|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3495:29): [True: 13, False: 2] ------------------ 3496| 13| { 3497| 13| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 13|#define RI_ERR_SYNTAX (-2) ------------------ 3498| 13| goto exit_function; 3499| 13| } 3500| 15| } 3501| 13|#endif 3502| 13| } 3503| 2.60k| } 3504| | 3505| | /* make Mobile H and Fixed H InChI arrays have same length */ 3506| 20.4k| len2 = len1 = 0; 3507| 20.4k| if (nNumComponents[iINChI][TAUT_YES] < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 575| 20.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (nNumComponents[iINChI][TAUT_YES] < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 574| 20.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3507:17): [True: 12, False: 20.4k] ------------------ 3508| 12| { 3509| 12| j = TAUT_YES; /* less components in Mobile-H layer */ ------------------ | | 575| 12|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3510| 12| len2 = nNumComponents[iINChI][TAUT_NON]; ------------------ | | 574| 12|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3511| 12| len1 = nNumComponents[iINChI][TAUT_YES]; ------------------ | | 575| 12|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3512| 12| } 3513| 20.4k| else 3514| 20.4k| if (nNumComponents[iINChI][TAUT_YES] > nNumComponents[iINChI][TAUT_NON]) ------------------ | | 575| 20.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (nNumComponents[iINChI][TAUT_YES] > nNumComponents[iINChI][TAUT_NON]) ------------------ | | 574| 20.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3514:21): [True: 7.71k, False: 12.7k] ------------------ 3515| 7.71k| { 3516| 7.71k| j = TAUT_NON; /* less components in Fixed-H layer */ ------------------ | | 574| 7.71k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3517| 7.71k| len2 = nNumComponents[iINChI][TAUT_YES]; ------------------ | | 575| 7.71k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3518| 7.71k| len1 = nNumComponents[iINChI][TAUT_NON]; ------------------ | | 574| 7.71k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3519| 7.71k| } 3520| | /* always len1 <= len2; if Mobile-H and Fixed-H have same number of components then len1=len2=0 */ 3521| 20.4k| if (len2 && len1) ------------------ | Branch (3521:17): [True: 7.72k, False: 12.7k] | Branch (3521:25): [True: 12, False: 7.71k] ------------------ 3522| 12| { 3523| 12| INChI* pInChI = (INChI*)inchi_calloc(len2, sizeof(pInChI[0])); ------------------ | | 1146| 12|#define inchi_calloc calloc ------------------ 3524| 12| if (!pInChI) ------------------ | Branch (3524:21): [True: 0, False: 12] ------------------ 3525| 0| { 3526| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 3527| 0| goto exit_function; 3528| 0| } 3529| 12| memcpy(pInChI, pInpInChI[iINChI][j], len1 * sizeof(pInChI[0])); 3530| 12| inchi_free(pInpInChI[iINChI][j]); ------------------ | | 1152| 12|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 12, False: 0] | | | Branch (1152:50): [Folded, False: 12] | | ------------------ ------------------ 3531| 12| pInpInChI[iINChI][j] = pInChI; 3532| 12| nNumComponents[iINChI][j] = len2; 3533| 604| for (; len1 < len2; len1++) ------------------ | Branch (3533:24): [True: 592, False: 12] ------------------ 3534| 592| { 3535| 592| if (j == TAUT_YES) ------------------ | | 575| 592|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3535:25): [True: 592, False: 0] ------------------ 3536| 592| { 3537| | /* mark added to Mobile H layer components as deleted protons */ 3538| 592| if (0 > (ret2 = nFillOutProtonMobileH(pInpInChI[iINChI][j] + len1))) ------------------ | Branch (3538:29): [True: 0, False: 592] ------------------ 3539| 0| { 3540| 0| goto exit_function; 3541| 0| } 3542| 592| if (0 > (ret2 = nProtonCopyIsotopicInfo(pInpInChI[iINChI][j] + len1/* to */, ------------------ | Branch (3542:29): [True: 0, False: 592] ------------------ 3543| 592| pInpInChI[iINChI][TAUT_NON] + len1/* from */))) ------------------ | | 574| 592|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3544| 0| { 3545| 0| goto exit_function; 3546| 0| } 3547| 592| } 3548| 0| else 3549| 0| { 3550| | /* mark added to Fixed H layer components as empty deleted */ 3551| | /* this should not happen */ 3552| 0| pInChI[len1].bDeleted = 1; 3553| 0| } 3554| 592| } 3555| 12| } 3556| 20.4k| } /* end of iINChI cycle */ 3557| | 3558| | /* check balances */ 3559| 30.6k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 30.6k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3559:26): [True: 20.4k, False: 10.2k] ------------------ 3560| 20.4k| { 3561| 51.1k| for (i = iINChI; i < INCHI_NUM; i++) ------------------ | | 569| 51.1k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3561:30): [True: 30.6k, False: 20.4k] ------------------ 3562| 30.6k| { 3563| 92.0k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 92.0k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3563:29): [True: 61.3k, False: 30.6k] ------------------ 3564| 61.3k| { 3565| 153k| for (k = j; k < TAUT_NUM; k++) ------------------ | | 573| 153k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3565:33): [True: 92.0k, False: 61.3k] ------------------ 3566| 92.0k| { 3567| 92.0k| if ((iINChI != i || j != k) && num_elem[iINChI][j] && num_elem[i][k]) ------------------ | Branch (3567:30): [True: 30.6k, False: 61.3k] | Branch (3567:45): [True: 20.4k, False: 40.9k] | Branch (3567:56): [True: 17.8k, False: 33.2k] | Branch (3567:79): [True: 2.72k, False: 15.1k] ------------------ 3568| 2.72k| { 3569| 2.72k| if (tot_charge[iINChI][j] != tot_charge[i][k]) ------------------ | Branch (3569:33): [True: 1, False: 2.72k] ------------------ 3570| 1| { 3571| 1| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 3572| 1| goto exit_function; 3573| 1| } 3574| 345k| for (m = 0; m <= nElDataLen; m++) ------------------ | Branch (3574:41): [True: 342k, False: 2.69k] ------------------ 3575| 342k| { 3576| 342k| if (num_elem[iINChI][j][m].num != num_elem[i][k][m].num) ------------------ | Branch (3576:37): [True: 26, False: 342k] ------------------ 3577| 26| { 3578| 26| ret2 = RI_ERR_SYNTAX; ------------------ | | 16| 26|#define RI_ERR_SYNTAX (-2) ------------------ 3579| 26| goto exit_function; 3580| 26| } 3581| 342k| } 3582| | /* 3583| | if ( memcmp( num_elem[iINChI], num_elem[i][k], (nElDataLen+1)*sizeof(num_elem[0][0][0]) ) { 3584| | ret2 = RI_ERR_SYNTAX; 3585| | goto exit_function; 3586| | } 3587| | */ 3588| 2.72k| } 3589| 92.0k| } 3590| 61.3k| } 3591| 30.6k| } 3592| 20.4k| } 3593| | 3594| 10.2k| } 3595| 2.24k| else 3596| 2.24k| { 3597| 2.24k| ret2 = ret; 3598| 2.24k| } 3599| | 3600| 12.5k|exit_function: 3601| | 3602| 37.6k| for (i = 0; i < INCHI_NUM; i++) ------------------ | | 569| 37.6k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3602:17): [True: 25.1k, False: 12.5k] ------------------ 3603| 25.1k| { 3604| 75.3k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 75.3k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3604:21): [True: 50.2k, False: 25.1k] ------------------ 3605| 50.2k| { 3606| 50.2k| if (num_elem[i][j]) ------------------ | Branch (3606:17): [True: 13.0k, False: 37.2k] ------------------ 3607| 13.0k| { 3608| 13.0k| inchi_free(num_elem[i][j]); ------------------ | | 1152| 13.0k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 13.0k, False: 0] | | | Branch (1152:50): [Folded, False: 13.0k] | | ------------------ ------------------ 3609| 13.0k| num_elem[i][j] = NULL; 3610| 13.0k| } 3611| 50.2k| } 3612| 25.1k| } 3613| 12.5k| *nErr = (ret2 < 0 && ret2 != RI_ERR_EOL) ? ret2 : 0; ------------------ | | 18| 2.34k|#define RI_ERR_EOL (-4) ------------------ | Branch (3613:14): [True: 2.34k, False: 10.2k] | Branch (3613:26): [True: 2.31k, False: 31] ------------------ 3614| | 3615| 12.5k| return ret; 3616| 12.5k|} ReadInChICoord: 4677| 585|{ 4678| 585| int c; 4679| | /* djb-rwth: removing redundant variables */ 4680| 585| int ret = RI_ERR_ALLOC; ------------------ | | 15| 585|#define RI_ERR_ALLOC (-1) ------------------ 4681| 585| int bMobileH = TAUT_YES; ------------------ | | 575| 585|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4682| 585| int bReconn = INCHI_BAS; ------------------ | | 570| 585|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 4683| 585| int state = -1; 4684| 585| int prev_state = -1; 4685| 585| int nLenXYZ = 0; 4686| 585| int bAbc = -1; /* initially undefined */ 4687| 585| const char 4688| 585| szToken[] = INCHI_TOKEN; ------------------ | | 277| 585|#define INCHI_TOKEN "/\n\r\t\\" ------------------ 4689| 585| XYZ_COORD 4690| 585| * pXYZ = NULL; 4691| | 4692| 585| *pState = 0; 4693| 585| INCHI_HEAPCHK 4694| | 4695| | /* Get "InChI=1/" */ 4696| 585| if (pLine->len) ------------------ | Branch (4696:13): [True: 0, False: 585] ------------------ 4697| 0| { 4698| 0| c = pLine->c; 4699| 0| } 4700| 585| else 4701| 585| { 4702| 585| c = nGetInChISegment(pInp, pLine, szToken); 4703| 585| } 4704| 585| if (c == RI_ERR_EOF && !pLine->len && !pLine->str[0]) ------------------ | | 19| 1.17k|#define RI_ERR_EOF (0) ------------------ | Branch (4704:9): [True: 560, False: 25] | Branch (4704:28): [True: 559, False: 1] | Branch (4704:43): [True: 559, False: 0] ------------------ 4705| 559| { 4706| 559| ret = c; 4707| 559| pLine->len = 0; 4708| 559| goto exit_error; 4709| 559| } 4710| 26| if (pLine->len == 0 || (c != SEG_END && c != RI_ERR_EOF && !INCHI_INP_EOL(c))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 273| 2|#define SEG_END '/' ------------------ if (pLine->len == 0 || (c != SEG_END && c != RI_ERR_EOF && !INCHI_INP_EOL(c))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 19| 2|#define RI_ERR_EOF (0) ------------------ if (pLine->len == 0 || (c != SEG_END && c != RI_ERR_EOF && !INCHI_INP_EOL(c))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 275| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 0, False: 0] | | | Branch (275:40): [True: 0, False: 0] | | | Branch (275:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4710:9): [True: 25, False: 1] | Branch (4710:29): [True: 1, False: 0] | Branch (4710:45): [True: 0, False: 1] ------------------ 4711| 25| { 4712| 25| *pState = -1; 4713| 25| pLine->len = 0; 4714| 25| ret = RI_ERR_PROGR; ------------------ | | 17| 25|#define RI_ERR_PROGR (-3) ------------------ 4715| 25| goto exit_error; 4716| 25| } 4717| 1| if (memcmp(pLine->str, "AuxInfo=", 8)) ------------------ | Branch (4717:9): [True: 1, False: 0] ------------------ 4718| 1| { 4719| 1| *pState = -1; 4720| 1| return c; 4721| 1| } 4722| | 4723| 0| state = AST_VERSION; 4724| 0| ret = 1; /* means read the next segment */ 4725| 0| do 4726| 0| { 4727| | /* Read the next segment up to the '/' */ 4728| 0| INCHI_HEAPCHK 4729| 0| if (ret < 0) ------------------ | Branch (4729:17): [True: 0, False: 0] ------------------ 4730| 0| { 4731| 0| *pState = prev_state; 4732| 0| break; 4733| 0| } 4734| 0| prev_state = state + (bReconn ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 342| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (4734:31): [True: 0, False: 0] ------------------ 4735| 0| if (0 < ret) ------------------ | Branch (4735:13): [True: 0, False: 0] ------------------ 4736| 0| { 4737| | /* read next segment */ 4738| 0| if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 273| 0|#define SEG_END '/' ------------------ | Branch (4738:17): [True: 0, False: 0] | Branch (4738:36): [True: 0, False: 0] ------------------ 4739| 0| { 4740| | /* abnormal reading result; should not happen */ 4741| 0| while (c != RI_ERR_EOF && !INCHI_INP_EOL(c)) ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ while (c != RI_ERR_EOF && !INCHI_INP_EOL(c)) ------------------ | | 275| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 0, False: 0] | | | Branch (275:40): [True: 0, False: 0] | | | Branch (275:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4741:24): [True: 0, False: 0] ------------------ 4742| 0| { 4743| | /* bypass to the end of line or file */ 4744| 0| c = getInChIChar(pInp); 4745| 0| } 4746| 0| ret = (c == RI_ERR_EOF) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ ret = (c == RI_ERR_EOF) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ ret = (c == RI_ERR_EOF) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 18| 0|#define RI_ERR_EOL (-4) ------------------ | Branch (4746:23): [True: 0, False: 0] ------------------ 4747| 0| pLine->len = 0; 4748| 0| pLine->c = ret; 4749| 0| break; 4750| 0| } 4751| 0| if (c == RI_ERR_EOF) ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ | Branch (4751:17): [True: 0, False: 0] ------------------ 4752| 0| { 4753| 0| ret = RI_ERR_EOF; /* end of line */ ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ 4754| 0| break; 4755| 0| } 4756| 0| if (c == SEG_END) ------------------ | | 273| 0|#define SEG_END '/' ------------------ | Branch (4756:17): [True: 0, False: 0] ------------------ 4757| 0| { 4758| 0| c = nGetInChISegment(pInp, pLine, szToken); 4759| 0| } 4760| 0| if (c < 0) ------------------ | Branch (4760:17): [True: 0, False: 0] ------------------ 4761| 0| { 4762| 0| goto exit_error; /* error */ 4763| 0| } 4764| 0| if (!pLine->len) ------------------ | Branch (4764:17): [True: 0, False: 0] ------------------ 4765| 0| { 4766| 0| ret = RI_ERR_EOL; /* end of line */ ------------------ | | 18| 0|#define RI_ERR_EOL (-4) ------------------ 4767| 0| break; 4768| 0| } 4769| | /* djb-rwth: removing redundant code */ 4770| 0| } 4771| | 4772| | /* Process the seqment */ 4773| 0| switch (state) ------------------ | Branch (4773:17): [True: 0, False: 0] ------------------ 4774| 0| { 4775| 0| case AST_VERSION: ------------------ | Branch (4775:9): [True: 0, False: 0] ------------------ 4776| | /* Mobile H */ 4777| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4778| 0| ret = ParseAuxSegmentVersion(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4779| 0| state = AST_MOBILE_H_NUMBERS; 4780| 0| break; 4781| 0| case AST_MOBILE_H_NUMBERS: ------------------ | Branch (4781:9): [True: 0, False: 0] ------------------ 4782| 0| ret = ParseAuxSegmentNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 4783| 0| state = AST_MOBILE_H_ATOM_EQ; 4784| 0| break; 4785| 0| case AST_MOBILE_H_ATOM_EQ: ------------------ | Branch (4785:9): [True: 0, False: 0] ------------------ 4786| 0| ret = ParseAuxSegmentAtomEqu(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4787| 0| state = AST_MOBILE_H_GROUP_EQ; 4788| 0| break; 4789| 0| case AST_MOBILE_H_GROUP_EQ: ------------------ | Branch (4789:9): [True: 0, False: 0] ------------------ 4790| 0| ret = ParseAuxSegmentGroupEqu(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4791| 0| state = AST_MOBILE_H_SP3_INV; 4792| 0| break; 4793| 0| case AST_MOBILE_H_SP3_INV: ------------------ | Branch (4793:9): [True: 0, False: 0] ------------------ 4794| 0| ret = ParseAuxSegmentSp3Inv(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4795| 0| state = AST_MOBILE_H_SP3_INV_NUMBERS; 4796| 0| break; 4797| 0| case AST_MOBILE_H_SP3_INV_NUMBERS: ------------------ | Branch (4797:9): [True: 0, False: 0] ------------------ 4798| 0| ret = ParseAuxSegmentSp3InvNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4799| 0| state = AST_MOBILE_H_ISO_LAYER_FORK; 4800| 0| break; 4801| | 4802| 0| case AST_MOBILE_H_ISO_LAYER_FORK: ------------------ | Branch (4802:9): [True: 0, False: 0] ------------------ 4803| 0| if (!memcmp(pLine->str, "I:", 2)) ------------------ | Branch (4803:17): [True: 0, False: 0] ------------------ 4804| 0| { 4805| 0| state = AST_MOBILE_H_ISO_NUMBERS; 4806| 0| } 4807| 0| else if (!inchi_memicmp(pLine->str, "F:", 2)) ------------------ | Branch (4807:22): [True: 0, False: 0] ------------------ 4808| 0| { 4809| 0| state = AST_FIXED_H_NUMBERS; 4810| 0| bMobileH = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4811| 0| } 4812| 0| else if ( /*bReconn == INCHI_BAS &&*/ !inchi_memicmp(pLine->str, "CRV:", 4)) ------------------ | Branch (4812:51): [True: 0, False: 0] ------------------ 4813| 0| { 4814| 0| state = AST_REVERSE_INFO_CRV; 4815| 0| } 4816| 0| else 4817| 0| if (bReconn == INCHI_BAS && !inchi_memicmp(pLine->str, "rA:", 3)) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4817:21): [True: 0, False: 0] | Branch (4817:45): [True: 0, False: 0] ------------------ 4818| 0| { 4819| 0| state = AST_REVERSE_INFO_ATOMS; 4820| 0| } 4821| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp(pLine->str, "R:", 3)) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4821:26): [True: 0, False: 0] | Branch (4821:50): [True: 0, False: 0] ------------------ 4822| 0| { 4823| 0| ret = 1; /* read the next segment */ 4824| 0| state = AST_VERSION; 4825| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4826| 0| bReconn = INCHI_REC; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4827| 0| } 4828| 0| else 4829| 0| { 4830| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4831| 0| } 4832| 0| break; 4833| | 4834| | /* Mobile H, isotopic */ 4835| 0| case AST_MOBILE_H_ISO_NUMBERS: ------------------ | Branch (4835:9): [True: 0, False: 0] ------------------ 4836| 0| ret = ParseAuxSegmentNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 4837| 0| state = AST_MOBILE_H_ISO_ATOM_EQ; 4838| 0| break; 4839| 0| case AST_MOBILE_H_ISO_ATOM_EQ: ------------------ | Branch (4839:9): [True: 0, False: 0] ------------------ 4840| 0| ret = ParseAuxSegmentAtomEqu(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4841| 0| state = AST_MOBILE_H_ISO_GROUP_EQ; 4842| 0| break; 4843| 0| case AST_MOBILE_H_ISO_GROUP_EQ: ------------------ | Branch (4843:9): [True: 0, False: 0] ------------------ 4844| 0| ret = ParseAuxSegmentGroupEqu(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4845| 0| state = AST_MOBILE_H_ISO_SP3_INV; 4846| 0| break; 4847| 0| case AST_MOBILE_H_ISO_SP3_INV: ------------------ | Branch (4847:9): [True: 0, False: 0] ------------------ 4848| 0| ret = ParseAuxSegmentSp3Inv(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4849| 0| state = AST_MOBILE_H_ISO_SP3_INV_NUMBERS; 4850| 0| break; 4851| 0| case AST_MOBILE_H_ISO_SP3_INV_NUMBERS: ------------------ | Branch (4851:9): [True: 0, False: 0] ------------------ 4852| 0| ret = ParseAuxSegmentSp3InvNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4853| 0| state = AST_FIXED_H_LAYER_FORK; 4854| 0| break; 4855| | 4856| 0| case AST_FIXED_H_LAYER_FORK: ------------------ | Branch (4856:9): [True: 0, False: 0] ------------------ 4857| 0| if (!inchi_memicmp(pLine->str, "F:", 2)) ------------------ | Branch (4857:17): [True: 0, False: 0] ------------------ 4858| 0| { 4859| 0| state = AST_FIXED_H_NUMBERS; 4860| 0| bMobileH = TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4861| 0| } 4862| 0| else if ( /*bReconn == INCHI_BAS &&*/ !inchi_memicmp(pLine->str, "CRV:", 4)) ------------------ | Branch (4862:51): [True: 0, False: 0] ------------------ 4863| 0| { 4864| 0| state = AST_REVERSE_INFO_CRV; 4865| 0| } 4866| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp(pLine->str, "rA:", 3)) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4866:22): [True: 0, False: 0] | Branch (4866:46): [True: 0, False: 0] ------------------ 4867| 0| { 4868| 0| state = AST_REVERSE_INFO_ATOMS; 4869| 0| } 4870| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp(pLine->str, "R:", 3)) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4870:22): [True: 0, False: 0] | Branch (4870:46): [True: 0, False: 0] ------------------ 4871| 0| { 4872| 0| ret = 1; /* read the next segment */ 4873| 0| state = AST_VERSION; 4874| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4875| 0| bReconn = INCHI_REC; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4876| 0| } 4877| 0| else 4878| 0| { 4879| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4880| 0| } 4881| 0| break; 4882| | 4883| 0| case AST_FIXED_H_NUMBERS: ------------------ | Branch (4883:9): [True: 0, False: 0] ------------------ 4884| 0| ret = ParseAuxSegmentNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 4885| 0| state = AST_FIXED_H_ATOM_EQ; 4886| 0| break; 4887| 0| case AST_FIXED_H_ATOM_EQ: ------------------ | Branch (4887:9): [True: 0, False: 0] ------------------ 4888| 0| ret = ParseAuxSegmentAtomEqu(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4889| 0| state = AST_FIXED_H_SP3_INV; 4890| 0| break; 4891| 0| case AST_FIXED_H_SP3_INV: ------------------ | Branch (4891:9): [True: 0, False: 0] ------------------ 4892| 0| ret = ParseAuxSegmentSp3Inv(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4893| 0| state = AST_FIXED_H_SP3_INV_NUMBERS; 4894| 0| break; 4895| 0| case AST_FIXED_H_SP3_INV_NUMBERS: ------------------ | Branch (4895:9): [True: 0, False: 0] ------------------ 4896| 0| ret = ParseAuxSegmentSp3InvNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4897| 0| state = AST_FIXED_H_ISO_LAYER_FORK; 4898| 0| break; 4899| | 4900| 0| case AST_FIXED_H_ISO_LAYER_FORK: ------------------ | Branch (4900:9): [True: 0, False: 0] ------------------ 4901| 0| if (!memcmp(pLine->str, "I:", 2)) ------------------ | Branch (4901:17): [True: 0, False: 0] ------------------ 4902| 0| { 4903| 0| state = AST_FIXED_H_ISO_NUMBERS; 4904| 0| } 4905| 0| else if ( /*bReconn == INCHI_BAS &&*/ !inchi_memicmp(pLine->str, "CRV:", 4)) ------------------ | Branch (4905:51): [True: 0, False: 0] ------------------ 4906| 0| { 4907| 0| state = AST_REVERSE_INFO_CRV; 4908| 0| } 4909| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp(pLine->str, "rA:", 3)) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4909:22): [True: 0, False: 0] | Branch (4909:46): [True: 0, False: 0] ------------------ 4910| 0| { 4911| 0| state = AST_REVERSE_INFO_ATOMS; 4912| 0| } 4913| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp(pLine->str, "R:", 3)) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4913:22): [True: 0, False: 0] | Branch (4913:46): [True: 0, False: 0] ------------------ 4914| 0| { 4915| 0| ret = 1; /* read the next segment */ 4916| 0| state = AST_VERSION; 4917| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4918| 0| bReconn = INCHI_REC; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4919| 0| } 4920| 0| else 4921| 0| { 4922| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4923| 0| } 4924| 0| break; 4925| | 4926| 0| case AST_FIXED_H_ISO_NUMBERS: ------------------ | Branch (4926:9): [True: 0, False: 0] ------------------ 4927| 0| ret = ParseAuxSegmentNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 4928| 0| state = AST_FIXED_H_ISO_ATOM_EQ; 4929| 0| break; 4930| 0| case AST_FIXED_H_ISO_ATOM_EQ: ------------------ | Branch (4930:9): [True: 0, False: 0] ------------------ 4931| 0| ret = ParseAuxSegmentAtomEqu(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4932| 0| state = AST_FIXED_H_SP3_INV; 4933| 0| break; 4934| 0| case AST_FIXED_H_ISO_SP3_INV: ------------------ | Branch (4934:9): [True: 0, False: 0] ------------------ 4935| 0| ret = ParseAuxSegmentSp3Inv(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4936| 0| state = AST_FIXED_H_ISO_SP3_INV_NUMBERS; 4937| 0| break; 4938| 0| case AST_FIXED_H_ISO_SP3_INV_NUMBERS: ------------------ | Branch (4938:9): [True: 0, False: 0] ------------------ 4939| 0| ret = ParseAuxSegmentSp3InvNumbers(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 4940| 0| state = AST_REVERSE_INFO_CRV; 4941| 0| break; 4942| 0| case AST_REVERSE_INFO_CRV: ------------------ | Branch (4942:9): [True: 0, False: 0] ------------------ 4943| 0| ret = ParseAuxSegmentReverseCRV(pLine->str, state); 4944| | /* state = (bReconn == INCHI_BAS)? AST_REVERSE_INFO_ATOMS : AST_RECONNECTED_LAYER_FORK;*/ 4945| 0| state = AST_REVERSE_INFO_ATOMS; 4946| 0| break; 4947| 0| case AST_REVERSE_INFO_ATOMS: ------------------ | Branch (4947:9): [True: 0, False: 0] ------------------ 4948| 0| ret = ParseAuxSegmentReverseAtoms(pLine->str, state); 4949| 0| state = AST_REVERSE_INFO_BONDS; 4950| 0| break; 4951| 0| case AST_REVERSE_INFO_BONDS: ------------------ | Branch (4951:9): [True: 0, False: 0] ------------------ 4952| 0| ret = ParseAuxSegmentReverseBonds(pLine->str, state); 4953| 0| state = AST_REVERSE_INFO_XYZ; 4954| 0| break; 4955| 0| case AST_REVERSE_INFO_XYZ: ------------------ | Branch (4955:9): [True: 0, False: 0] ------------------ 4956| 0| ret = ParseAuxSegmentReverseXYZ(pLine->str, &pXYZ, state); 4957| 0| state = AST_RECONNECTED_LAYER_FORK; 4958| 0| if (ret > 0) ------------------ | Branch (4958:17): [True: 0, False: 0] ------------------ 4959| 0| { 4960| 0| nLenXYZ = ret - 1; 4961| 0| } 4962| 0| break; 4963| 0| case AST_RECONNECTED_LAYER_FORK: ------------------ | Branch (4963:9): [True: 0, False: 0] ------------------ 4964| 0| if (bReconn == INCHI_BAS && !inchi_memicmp(pLine->str, "R:", 3)) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4964:17): [True: 0, False: 0] | Branch (4964:41): [True: 0, False: 0] ------------------ 4965| 0| { 4966| 0| ret = 1; /* read the next segment */ 4967| 0| state = AST_VERSION; 4968| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4969| 0| bReconn = INCHI_REC; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4970| 0| } 4971| 0| else 4972| 0| { 4973| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4974| 0| } 4975| 0| break; 4976| 0| } 4977| 0| } while (c >= 0); ------------------ | Branch (4977:14): [True: 0, False: 0] ------------------ 4978| | 4979| 0| if (pXYZ) /* djb-rwth: fixing coverity ID #499576 */ ------------------ | Branch (4979:9): [True: 0, False: 0] ------------------ 4980| 0| { 4981| 0| ret = AddAuxSegmentCoord(ret, pXYZ, nLenXYZ, pInpInChI, nNumComponents); 4982| 0| } 4983| 0| else 4984| 0| { 4985| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 4986| 0| } 4987| | 4988| 584|exit_error: 4989| 584| if (pXYZ) ------------------ | Branch (4989:9): [True: 0, False: 584] ------------------ 4990| 0| { 4991| 0| inchi_free(pXYZ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4992| 0| } 4993| 584| if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 19| 609|#define RI_ERR_EOF (0) ------------------ if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 18| 25|#define RI_ERR_EOL (-4) ------------------ | Branch (4993:9): [True: 559, False: 25] | Branch (4993:21): [True: 0, False: 25] | Branch (4993:40): [True: 0, False: 25] ------------------ 4994| 559| { 4995| 559| pLine->len = 0; 4996| 559| } 4997| | 4998| 584| return ret; 4999| 0|} ParseSegmentReadDelimitedNumbers: 7985| 1.03k|{ 7986| 1.03k| const char* p, * pStart; 7987| 1.03k| int num, curr_atom = 0; 7988| | 7989| 1.03k| *ret = 1; 7990| | 7991| 1.03k| if (!str) ------------------ | Branch (7991:9): [True: 0, False: 1.03k] ------------------ 7992| 0| { 7993| 0| *ret = -1; 7994| 0| return NULL; 7995| 0| } 7996| | 7997| 1.03k| pStart = (char*)(str + 1); 7998| 1.03k| p = pStart; 7999| 1.03k| while (*pStart) ------------------ | Branch (7999:12): [True: 1.03k, False: 1] ------------------ 8000| 1.03k| { 8001| 3.59k| for (p = pStart, curr_atom = 0; p < pEnd && *p != c_stop; curr_atom++) ------------------ | Branch (8001:41): [True: 3.59k, False: 0] | Branch (8001:53): [True: 2.81k, False: 772] ------------------ 8002| 2.81k| { 8003| 2.81k| num = (AT_NUMB)inchi_strtol(p, &p, 10); 8004| 2.81k|#if ( CHECK_STRTOL_ATNUMB==1 ) 8005| 2.81k| if (num > MAX_ATOMS || num < 0) ------------------ | | 15| 5.63k|#define MAX_ATOMS 32766 ------------------ | Branch (8005:17): [True: 2, False: 2.81k] | Branch (8005:36): [True: 0, False: 2.81k] ------------------ 8006| 2| { 8007| 2| *ret = RI_ERR_SYNTAX; ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 8008| 2| return p; 8009| 2| } 8010| 2.81k|#endif 8011| 2.81k| { 8012| 2.81k| if (0 != IntArray_Append(numlist, num)) ------------------ | Branch (8012:21): [True: 0, False: 2.81k] ------------------ 8013| 0| { 8014| 0| *ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8015| 0| return p; 8016| 0| } 8017| 2.81k| } 8018| 2.81k| if (*p == c_delim) ------------------ | Branch (8018:17): [True: 2.55k, False: 259] ------------------ 8019| 2.55k| { 8020| 2.55k| p++; 8021| 2.55k| } 8022| 259| else if (*p == c_stop) ------------------ | Branch (8022:22): [True: 255, False: 4] ------------------ 8023| 255| { 8024| 255| return p; 8025| 255| } 8026| 4| else 8027| 4| { 8028| 4| *ret = -1; return NULL; 8029| 4| } 8030| 2.81k| } 8031| 772| if (*p == c_stop) ------------------ | Branch (8031:13): [True: 772, False: 0] ------------------ 8032| 772| { 8033| 772| return p; 8034| 772| } 8035| 772| } 8036| | 8037| 1| return p; 8038| 1.03k|} insertions_sort_AT_NUMB: 10561| 57.2k|{ 10562| 57.2k| AT_NUMB* i, * j, * pk, tmp; 10563| 57.2k| int k, num_trans = 0; 10564| 112k| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (10564:28): [True: 55.5k, False: 57.2k] ------------------ 10565| 55.5k| { 10566| 100k| for (j = (i = pk) + 1, tmp = *j; j > base && *i > tmp; j = i, i--) ------------------ | Branch (10566:42): [True: 73.3k, False: 26.7k] | Branch (10566:54): [True: 44.6k, False: 28.7k] ------------------ 10567| 44.6k| { 10568| 44.6k| *j = *i; 10569| 44.6k| num_trans++; 10570| 44.6k| } 10571| 55.5k| *j = tmp; 10572| 55.5k| } 10573| | 10574| 57.2k| return num_trans; 10575| 57.2k|} TreatErrorsInReadInChIString: 10927| 2.34k|{ 10928| 2.34k| int bInChI2Struct = (ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE) && ip->nInputType == INPUT_INCHI; ------------------ | | 991| 2.34k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (10928:25): [True: 1.09k, False: 1.25k] | Branch (10928:78): [True: 1.09k, False: 0] ------------------ 10929| | 10930| | /* InChI could not be read */ 10931| 2.34k| if (nReadStatus == RI_ERR_EOF && nErr == 0 && pState == 0) /* && !(*pstrHdr) ) */ ------------------ | | 19| 4.69k|#define RI_ERR_EOF (0) ------------------ | Branch (10931:9): [True: 92, False: 2.25k] | Branch (10931:38): [True: 0, False: 92] | Branch (10931:51): [True: 0, False: 0] ------------------ 10932| 0| { 10933| | /*if ( !(*pstrHdr) ) */ 10934| 0| ;/*inchi_ios_eprint( pLog, "\nEnd of file detected after structure %ld. \n", *num_inp );*/ 10935| 0| } 10936| 2.34k| else 10937| 2.34k| { 10938| | /* Output InChI parsing error message */ 10939| 2.34k| char szHdrSimulation[128]; 10940| 2.34k| char szMsg2[1024]; 10941| 2.34k| (*num_inp)++; 10942| 2.34k| sprintf(szHdrSimulation, "Structure: %ld", *num_inp); 10943| 2.34k| getInchiStateReadErr(pState, szMsg2); 10944| | 10945| |#ifdef TARGET_EXE_STANDALONE 10946| | if (pOneInput->polymer && 10947| | bInChI2Struct && 10948| | !(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)) 10949| | { 10950| | inchi_ios_eprint(pLog, "%s Skipping polymer InChI (only conversion to Molfile is available, use OutputSDF option)\n", 10951| | *pstrHdr ? *pstrHdr : szHdrSimulation); 10952| | } 10953| | else 10954| |#endif 10955| 2.34k| { 10956| 2.34k| if (!bInChI2Struct && ------------------ | Branch (10956:17): [True: 1.25k, False: 1.09k] ------------------ 10957| 1.25k| (pState == IST_MOBILE_H_POLYMER && !ip->bPolymers)) ------------------ | Branch (10957:18): [True: 416, False: 838] | Branch (10957:52): [True: 416, False: 0] ------------------ 10958| 416| { 10959| | /* TO DO: implement InChI2InChI for polymers in a way similar to InChI2Struct 10960| | thru an external (to ReadWriteInchi) loop */ 10961| 416| inchi_ios_eprint(pLog, "%s Skipping polymer InChI for conversion of InChI to InChI\n", 10962| 416| *pstrHdr ? *pstrHdr : szHdrSimulation); ------------------ | Branch (10962:21): [True: 0, False: 416] ------------------ 10963| 416| } 10964| 1.93k| else 10965| 1.93k| { 10966| 1.93k| inchi_ios_eprint(pLog, "\n%s %s (%d) in %s (%d)\n", 10967| 1.93k| *pstrHdr ? *pstrHdr : szHdrSimulation, ------------------ | Branch (10967:21): [True: 0, False: 1.93k] ------------------ 10968| 1.93k| getInchiErrName(nErr), nErr, 10969| 1.93k| szMsg2, pState); 10970| 1.93k| } 10971| 2.34k| } 10972| | 10973| 2.34k| if (ip->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR) ------------------ | | 149| 2.34k|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ | Branch (10973:13): [True: 0, False: 2.34k] ------------------ 10974| 0| { 10975| 0| if (!(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)) ------------------ | | 133| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (10975:17): [True: 0, False: 0] ------------------ 10976| 0| { 10977| 0| inchi_ios_eprint(pOut, "%s\n", *pstrHdr ? *pstrHdr : szHdrSimulation); ------------------ | Branch (10977:48): [True: 0, False: 0] ------------------ 10978| 0| if (ip->bINChIOutputOptions & INCHI_OUT_STDINCHI) ------------------ | | 145| 0|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (10978:21): [True: 0, False: 0] ------------------ 10979| 0| { 10980| 0| inchi_ios_eprint(pOut, "InChI=1S//\n"); 10981| 0| } 10982| 0| else 10983| 0| { 10984| 0| inchi_ios_eprint(pOut, "InChI=1N//\n"); 10985| 0| } 10986| 0| } 10987| 0| } 10988| | 10989| 2.34k| if (0 != (ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE)) ------------------ | | 991| 2.34k|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (10989:13): [True: 1.09k, False: 1.25k] ------------------ 10990| | 10991| 1.09k| (*num_errors)++; 10992| 2.34k| (*num_processed)++; 10993| 2.34k| } 10994| 2.34k| if (*pstrHdr) ------------------ | Branch (10994:9): [True: 0, False: 2.34k] ------------------ 10995| 0| { 10996| 0| inchi_free(*pstrHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10997| 0| *pstrHdr = NULL; 10998| 0| } 10999| 2.34k| if (*pszCurHdr) ------------------ | Branch (10999:9): [True: 0, False: 2.34k] ------------------ 11000| 0| { 11001| 0| inchi_free(*pszCurHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 11002| 0| *pszCurHdr = NULL; 11003| 0| } 11004| | 11005| 2.34k| FreeInpInChI(pOneInput); 11006| | 11007| 2.34k| return; 11008| 2.34k|} ConvertInChI2InChI: 11032| 5.02k|{ 11033| 5.02k| int ret, tmp; 11034| | 11035| 5.02k| InchiTimeGet(pulTStart); 11036| | 11037| 5.02k| tmp = ip->bNoStructLabels; 11038| 5.02k| ip->bNoStructLabels = 1; 11039| 5.02k| INCHI_HEAPCHK 11040| 5.02k| ip->pSdfValue = NULL; 11041| 5.02k| ip->pSdfLabel = NULL; 11042| | 11043| 5.02k|#if ( FIX_DALKE_BUGS == 1 ) 11044| 5.02k| SetHillFormFromInChI(pOneInput); 11045| 5.02k|#endif 11046| | 11047| | /* 11048| | * Legacy metal handling cannot be applied during InChI-to-InChI 11049| | * conversion because the structure is not reconstructed and the 11050| | * metal-bond processing is therefore not rerun. 11051| | */ 11052| 5.02k| if (!ip->bMolecularInorganics && (ip->bReadInChIOptions & READ_INCHI_INPUT_MI)) ------------------ | | 993| 0|#define READ_INCHI_INPUT_MI 0x00000020 ------------------ | Branch (11052:9): [True: 0, False: 5.02k] | Branch (11052:38): [True: 0, False: 0] ------------------ 11053| 0| { 11054| 0| inchi_ios_eprint(pLog, "LegacyMetalHandling cannot be used with InChI2InChI for Molecular Inorganics input\n"); 11055| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 11056| 0| } 11057| 5.02k| else 11058| 5.02k| { 11059| 5.02k| ret = OutputInChIAsRequested(pCG, pOut, pLog, ip, sd, 11060| 5.02k| pOneInput, num_components, 11061| 5.02k| nModeProtonIsoExchgH, 11062| 5.02k| num_inp, save_opt_bits); 11063| 5.02k| } 11064| | 11065| |#if ( !defined(TARGET_API_LIB) && defined(TARGET_EXE_STANDALONE) ) 11066| | 11067| | /* Calculate InChIKey if requested */ 11068| | /* However, do not calculate/write it if this function is called from within dll */ 11069| | { 11070| | char ik_string[256]; /* Resulting InChIKey string */ 11071| | int ik_ret = 0; /* InChIKey-calc result code */ 11072| | int xhash1, xhash2; 11073| | char szXtra1[65], szXtra2[65]; 11074| | 11075| | inchi_ios_flush2(pLog, stderr); 11076| | 11077| | /* post-1.02b addition - correctly treat tabbed output with InChIKey */ 11078| | if (ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT) 11079| | { 11080| | if (ip->bCalcInChIHash != INCHIHASH_NONE) 11081| | { 11082| | if (pOut->s.pStr) 11083| | { 11084| | if (pOut->s.nUsedLength > 0) 11085| | { 11086| | if (pOut->s.pStr[pOut->s.nUsedLength - 1] == '\n') 11087| | { /* replace LF with TAB */ 11088| | pOut->s.pStr[pOut->s.nUsedLength - 1] = '\t'; 11089| | } 11090| | } 11091| | } 11092| | } 11093| | } 11094| | 11095| | if (ip->bCalcInChIHash == INCHIHASH_NONE) 11096| | { 11097| | /* inchi_ios_flush(pOut); */ 11098| | } 11099| | else 11100| | { 11101| | char* buf = NULL; 11102| | size_t slen = pOut->s.nUsedLength; 11103| | extract_inchi_substring(&buf, pOut->s.pStr, slen); 11104| | 11105| | if (NULL != buf) 11106| | { 11107| | xhash1 = xhash2 = 0; 11108| | if ((ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1) || 11109| | (ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2)) 11110| | { 11111| | xhash1 = 1; 11112| | } 11113| | if ((ip->bCalcInChIHash == INCHIHASH_KEY_XTRA2) || 11114| | (ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2)) 11115| | { 11116| | xhash2 = 1; 11117| | } 11118| | 11119| | ik_ret = GetINCHIKeyFromINCHI(buf, 11120| | xhash1, 11121| | xhash2, 11122| | ik_string, 11123| | szXtra1, 11124| | szXtra2); 11125| | inchi_free(buf); 11126| | } 11127| | else 11128| | { 11129| | ik_ret = INCHIKEY_NOT_ENOUGH_MEMORY; 11130| | } 11131| | 11132| | 11133| | if (ik_ret == INCHIKEY_OK) 11134| | { 11135| | inchi_ios_print(pOut, "InChIKey=%-s\n", ik_string); 11136| | } 11137| | else 11138| | { 11139| | inchi_ios_print(pLog, "Warning (Could not compute InChIKey: ", num_inp); 11140| | switch (ik_ret) 11141| | { 11142| | case INCHIKEY_UNKNOWN_ERROR: 11143| | inchi_ios_print(pLog, "unresolved error)"); 11144| | break; 11145| | case INCHIKEY_EMPTY_INPUT: 11146| | inchi_ios_print(pLog, "got an empty string)"); 11147| | break; 11148| | case INCHIKEY_INVALID_INCHI_PREFIX: 11149| | case INCHIKEY_INVALID_INCHI: 11150| | case INCHIKEY_INVALID_STD_INCHI: 11151| | inchi_ios_print(pLog, "no valid InChI string found)"); 11152| | break; 11153| | case INCHIKEY_NOT_ENOUGH_MEMORY: 11154| | inchi_ios_print(pLog, "not enough memory to treat the string)"); 11155| | break; 11156| | default:inchi_ios_print(pLog, "internal program error)"); 11157| | break; 11158| | } 11159| | 11160| | inchi_ios_print(pLog, " structure #%-lu.\n", num_inp); 11161| | if (ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT) 11162| | { 11163| | inchi_ios_print(pOut, "\n"); 11164| | } 11165| | } /* if (ip->bCalcInChIHash!=INCHIHASH_NONE) */ 11166| | 11167| | inchi_ios_flush(pOut); 11168| | inchi_ios_flush2(pLog, stderr); 11169| | } 11170| | } /* Calculate InChIKey if requested */ 11171| |#endif 11172| | 11173| 5.02k| ip->bNoStructLabels = tmp; 11174| | 11175| |#ifndef TARGET_API_LIB 11176| | if (ret < 0) 11177| | { 11178| | 11179| | if (*pszCurHdr && (*pszCurHdr)[0]) 11180| | { 11181| | inchi_ios_eprint(pLog, "Error %d creating InChI string %s\n", ret, *pszCurHdr); 11182| | } 11183| | else 11184| | { 11185| | inchi_ios_eprint(pLog, "Error %d creating InChI string, Structure %ld\n", ret, num_inp); 11186| | } 11187| | if (ip->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR) 11188| | {/* inchi_ios_eprint( pOut, "InChICreationError!\n"); *//* emit err string */ 11189| | if (ip->bINChIOutputOptions & INCHI_OUT_STDINCHI) 11190| | { 11191| | inchi_ios_eprint(pOut, "InChI=1S//\n"); 11192| | } 11193| | else 11194| | { 11195| | inchi_ios_eprint(pOut, "InChI=1N//\n"); 11196| | } 11197| | } 11198| | 11199| | (*num_errors)++; 11200| | } 11201| | 11202| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_EXE_STANDALONE) ) 11203| | else 11204| | if (*pszCurHdr && (*pszCurHdr)[0]) 11205| | { 11206| | inchi_fprintf(stderr, "%s\r", *pszCurHdr); 11207| | } 11208| |#endif 11209| |#endif 11210| | 11211| | 11212| 5.02k| if (*pszCurHdr) ------------------ | Branch (11212:9): [True: 0, False: 5.02k] ------------------ 11213| 0| { 11214| 0| inchi_free(*pszCurHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 11215| 0| *pszCurHdr = NULL; 11216| 0| } 11217| | 11218| | INCHI_HEAPCHK 11219| | 11220| 5.02k| * ulProcessingTime += InchiTimeElapsed(ic, pulTStart); 11221| | 11222| 5.02k| return ret; 11223| 5.02k|} ConvertInChI2Struct: 11263| 5.18k|{ 11264| 5.18k| int ret, i, j; 11265| 5.18k| SRM srm; /* rules how to handle bonds to metal atoms */ 11266| 5.18k| StrFromINChI* pStruct[INCHI_NUM][TAUT_NUM]; 11267| | 11268| 5.18k| int bINChIOutputOptions = /* djb-rwth: ignoring LLVM warning: variable used */ 11269| 5.18k|#if ( I2S_MODIFY_OUTPUT != 1 ) 11270| 5.18k| 0; 11271| |#else 11272| | /* transfer user's InChI output options to serialization 10-12-2007 */ 11273| | ip_inp->bINChIOutputOptions& 11274| | ( 11275| | INCHI_OUT_NO_AUX_INFO | /* do not output Aux Info */ 11276| | INCHI_OUT_SHORT_AUX_INFO | /* output short version of Aux Info */ 11277| | INCHI_OUT_ONLY_AUX_INFO | /* output only Aux Info */ 11278| | /* INCHI_OUT_EMBED_REC |*/ /* embed reconnected INChI into disconnected INChI */ 11279| | INCHI_OUT_SDFILE_ONLY | /* save input data in a Molfile instead of creating INChI */ 11280| | INCHI_OUT_PLAIN_TEXT | /* output plain text INChI */ 11281| | INCHI_OUT_PLAIN_TEXT_COMMENTS | /* output plain text annotation */ 11282| | /* INCHI_OUT_WINCHI_WINDOW |*/ /* output into wINChI text window */ 11283| | INCHI_OUT_TABBED_OUTPUT | /* tab-delimited (only for plain text) */ 11284| | INCHI_OUT_SDFILE_ATOMS_DT | /* SDfile output H isotopes as D and T */ 11285| | INCHI_OUT_SDFILE_SPLIT | /* Split SDfile into components */ 11286| | 0 11287| | ); 11288| |#endif 11289| | 11290| | /* Preliminaries */ 11291| 5.18k| InchiTimeGet(pulTStart); 11292| | 11293| 5.18k| if ((input_is_stdinchi & INCHI_INPUT_CLASS_MASK) == INCHI_INPUT_CLASS_STANDARD || ------------------ | | 75| 5.18k|#define INCHI_INPUT_CLASS_MASK 0x03 ------------------ if ((input_is_stdinchi & INCHI_INPUT_CLASS_MASK) == INCHI_INPUT_CLASS_STANDARD || ------------------ | | 77| 10.3k|#define INCHI_INPUT_CLASS_STANDARD 0x01 ------------------ | Branch (11293:9): [True: 17, False: 5.17k] ------------------ 11294| 5.17k| (input_is_stdinchi & INCHI_INPUT_CLASS_MASK) == INCHI_INPUT_CLASS_BETA) ------------------ | | 75| 5.17k|#define INCHI_INPUT_CLASS_MASK 0x03 ------------------ (input_is_stdinchi & INCHI_INPUT_CLASS_MASK) == INCHI_INPUT_CLASS_BETA) ------------------ | | 78| 5.17k|#define INCHI_INPUT_CLASS_BETA 0x02 ------------------ | Branch (11294:9): [True: 2, False: 5.17k] ------------------ 11295| 19| { 11296| 19| if (ip_inp->bINChIOutputOptions & INCHI_OUT_STDINCHI) ------------------ | | 145| 19|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (11296:13): [True: 19, False: 0] ------------------ 11297| 19| { 11298| 19| bINChIOutputOptions |= INCHI_OUT_STDINCHI; ------------------ | | 145| 19|#define INCHI_OUT_STDINCHI 0x4000 ------------------ 11299| 19| } 11300| 19| } 11301| 5.17k| else 11302| 5.17k| { 11303| 5.17k| if (ip_inp->bINChIOutputOptions & INCHI_OUT_SAVEOPT) ------------------ | | 146| 5.17k|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (11303:13): [True: 0, False: 5.17k] ------------------ 11304| 0| { 11305| 0| bINChIOutputOptions |= INCHI_OUT_SAVEOPT; ------------------ | | 146| 0|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ 11306| 0| } 11307| 5.17k| } 11308| | 11309| 5.18k| memset(pStruct, 0, sizeof(pStruct)); /* djb-rwth: memset_s C11/Annex K variant? */ 11310| | 11311| 5.18k| SetUpSrm(&srm); /* structure restore parms */ 11312| | 11313| | /* Eliminate Fixed-H InChI that are exactly same as the corresponding Mobile-H structures */ 11314| 5.18k| RemoveFixHInChIIdentical2MobH(pOneInput); 11315| | 11316| | /* Recheck layers after thee elimination; get optional stereo flags */ 11317| 5.18k| ret = DetectInpInchiCreationOptions(pOneInput, &bHasSomeReconnected, 11318| 5.18k| &bHasMetal, &bHasSomeFixedH, 11319| 5.18k| &nModeFlagsStereo, &bTautFlags); 11320| 5.18k| if (ret < 0) ------------------ | Branch (11320:9): [True: 0, False: 5.18k] ------------------ 11321| 0| { 11322| 0| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, 11323| 0| "Error in detecting input InChI options", "; "); 11324| 0| (*num_errors)++; 11325| 0| goto dealloc; 11326| 0| } 11327| | 11328| 5.18k| if (bHasSomeFixedH && !bReqNonTaut) ------------------ | Branch (11328:9): [True: 1.23k, False: 3.95k] | Branch (11328:27): [True: 0, False: 1.23k] ------------------ 11329| 0| { 11330| 0| bHasSomeFixedH = 0; 11331| 0| } 11332| | 11333| | /* Set stereo flags */ 11334| 5.18k| ip->nMode &= ~(REQ_MODE_STEREO | ------------------ | | 19| 5.18k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 11335| 5.18k| REQ_MODE_ISO_STEREO | ------------------ | | 20| 5.18k|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 11336| 5.18k| REQ_MODE_RELATIVE_STEREO | ------------------ | | 26| 5.18k|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 11337| 5.18k| REQ_MODE_RACEMIC_STEREO | ------------------ | | 28| 5.18k|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 11338| 5.18k| REQ_MODE_CHIR_FLG_STEREO | ------------------ | | 34| 5.18k|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 11339| 5.18k| REQ_MODE_SB_IGN_ALL_UU | ------------------ | | 32| 5.18k|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 11340| 5.18k| REQ_MODE_SC_IGN_ALL_UU); ------------------ | | 30| 5.18k|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 11341| | 11342| 5.18k| ip->nMode |= nModeFlagsStereo; 11343| | 11344| | /* Remove Phosphine and Arsine Stereo Flags */ 11345| 5.18k| ip->bTautFlags &= ~TG_FLAG_PHOSPHINE_STEREO; ------------------ | | 941| 5.18k|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ 11346| 5.18k| ip->bTautFlags &= ~TG_FLAG_ARSINE_STEREO; ------------------ | | 942| 5.18k|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ 11347| 5.18k| ip->bTautFlags &= ~TG_FLAG_FIX_SP3_BUG; ------------------ | | 944| 5.18k|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ 11348| | 11349| 5.18k| ip->bTautFlags |= bTautFlags; 11350| | 11351| | /* Mark Disconnected InChI components that are exactly came as Reconnected ones */ 11352| | /* Disconnected will have a negative number of the reconnected component */ 11353| | /* Reconnected will have a positive number of the disconnected component */ 11354| | 11355| 5.18k| MarkDisconectedIdenticalToReconnected(pOneInput); 11356| | 11357| | /*****************************************************************************/ 11358| | /* Pay attention to: */ 11359| | /* 1) .nLink < 0 in Disonnected which means InChI is same as in Reconnected */ 11360| | /* The component in Reconnected has .nLink pointing to the Disconnected; */ 11361| | /* each .nLink = (1+component index) or -(1+component index) */ 11362| | /* In the future .nLink>0 in Disconnected shall point to the Reconnectrd */ 11363| | /* component from which it was created */ 11364| | /* 2) Currently reversed structures from Disconnected components are created */ 11365| | /* and abandoned if Reconnected layer exists */ 11366| | /* 3) Connect/disconnect H depends on the presence of atom/bond parity */ 11367| | /* The combined Mobile/Fixed-H parity should be set for Fixed-H components*/ 11368| | /* 4) No comparison of the Disconnected layer is done if Reconnected exists */ 11369| | /* 5) Reading InChI was not fully tested in case one component has stereo in */ 11370| | /* both Mobile-H and Fixed-H layers while another component has stereo */ 11371| | /* only in Mobile-H layer */ 11372| | /*****************************************************************************/ 11373| | 11374| | 11375| | /* Main conversion InChI->Structure for each component and */ 11376| | /* after that pStruct[iRec][iMobH][iComponent].at2 is the structure, */ 11377| | /* pStruct[iRec][iMobH][iComponent].RevInChI full InChI for the structure */ 11378| | /* In case of both Fixed-H and Mobile-H layers the results are in iMobH=0 */ 11379| | /* In case of only Mobile-H/Main layer the results are in iMobH=1 */ 11380| | 11381| 5.18k| ulProcessingTime += InchiTimeElapsed(ic, pulTStart); 11382| | 11383| 5.18k| sd->ulStructTime = 0; 11384| | 11385| 5.18k| ret = AllInchiToStructure(ic, pCG, ip, sd, num_inp, *pszCurHdr, &srm, bHasSomeFixedH, pStruct, pOneInput); 11386| | 11387| 5.18k| ulProcessingTime += sd->ulStructTime; 11388| 5.18k| InchiTimeGet(pulTStart); 11389| | 11390| | /* ret < 0 is error code; ret > 0 is number of errors */ 11391| | /* in pStruct[iInchiRec][iMobileH][iComponent].nError */ 11392| 5.18k| if (ret) ------------------ | Branch (11392:9): [True: 3.42k, False: 1.76k] ------------------ 11393| 3.42k| { 11394| 3.42k|#if ( FIX_GAF_2019_1==1 ) 11395| 3.42k| if (ret > 0) ------------------ | Branch (11395:13): [True: 3.42k, False: 0] ------------------ 11396| 3.42k| { 11397| 3.42k| ret = RI_ERR_PROGR; ------------------ | | 17| 3.42k|#define RI_ERR_PROGR (-3) ------------------ 11398| 3.42k| } 11399| 3.42k|#endif 11400| | /* conversion error */ 11401| 3.42k| (*num_errors)++; 11402| 3.42k| goto dealloc; 11403| 3.42k| } 11404| | 11405| | /* Attempt to fix the numumber of removed protons in case of Mobile-H */ 11406| 1.76k| if (!pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons && ------------------ | | 570| 1.76k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (!pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons && ------------------ | | 575| 1.76k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (11406:9): [True: 1.76k, False: 0] ------------------ 11407| 1.76k| !pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 571| 1.76k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 575| 1.76k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (11407:9): [True: 1.76k, False: 0] ------------------ 11408| 1.76k| { 11409| 1.76k| ret = AddProtonAndIsoHBalanceToMobHStruct(ic, pCG, ip, sd, num_inp, bHasSomeFixedH, *pszCurHdr, pStruct, pOneInput); 11410| | 11411| 1.76k| if (ret < 0) ------------------ | Branch (11411:13): [True: 9, False: 1.75k] ------------------ 11412| 9| { 11413| 9| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "Add/Remove protons error", "; "); 11414| 9| (*num_errors)++; 11415| 9| goto dealloc; 11416| 9| } 11417| 1.76k| } 11418| | 11419| | /* Compare InChI from the Reversed Structure to the original input InChI */ 11420| 1.75k| ret = CompareAllOrigInchiToRevInChI(pStruct, pOneInput, bHasSomeFixedH, num_inp, *pszCurHdr); 11421| 1.75k| if (ret < 0) ------------------ | Branch (11421:9): [True: 0, False: 1.75k] ------------------ 11422| 0| { 11423| 0| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "InChI compare error", "; "); 11424| 0| (*num_errors)++; 11425| 0| goto dealloc; 11426| 0| } 11427| | 11428| | /* Compare disconnected versions */ 11429| 1.75k| ret = CompareAllDisconnectedOrigInchiToRevInChI(pStruct, pOneInput, 11430| 1.75k| bHasSomeFixedH, num_inp, *pszCurHdr); 11431| 1.75k| if (ret < 0) ------------------ | Branch (11431:9): [True: 0, False: 1.75k] ------------------ 11432| 0| { 11433| 0| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "InChI compare2 error", "; "); 11434| 0| (*num_errors)++; 11435| 0| goto dealloc; 11436| 0| } 11437| | 11438| 1.75k| if (WarningFlags) ------------------ | Branch (11438:9): [True: 1.75k, False: 0] ------------------ 11439| 1.75k| { 11440| 5.26k| for (i = 0; i < 2; i++) ------------------ | Branch (11440:21): [True: 3.50k, False: 1.75k] ------------------ 11441| 3.50k| { 11442| 10.5k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 10.5k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (11442:25): [True: 7.01k, False: 3.50k] ------------------ 11443| 7.01k| { 11444| 7.01k| WarningFlags[i][j] = (unsigned long)pOneInput->CompareInchiFlags[i][j]; 11445| 7.01k| } 11446| 3.50k| } 11447| 1.75k| } 11448| | 11449| 1.75k| ulProcessingTime += InchiTimeElapsed(ic, pulTStart); 11450| | 11451| |#ifndef COMPILE_ANSI_ONLY 11452| | ret = DisplayStructureComponents(pCG, ip, sd, num_inp, *pszCurHdr, &srm, bReqNonTaut, pStruct, pOneInput); 11453| | if (ret < 0) 11454| | { 11455| | AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "Display structure error", "; "); 11456| | } 11457| |#endif 11458| | 11459| | 11460| 1.75k| InchiTimeGet(pulTStart); 11461| | 11462| 1.75k| ret = MergeStructureComponents(ip, sd, num_inp, *pszCurHdr, &srm, bReqNonTaut, pStruct, pOneInput); 11463| | 11464| 1.75k| ulProcessingTime += InchiTimeElapsed(ic, pulTStart); 11465| | 11466| 1.75k| if (ret < 0) ------------------ | Branch (11466:9): [True: 0, False: 1.75k] ------------------ 11467| 0| { 11468| 0| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "Merge Components error", "; "); 11469| 0| (*num_errors)++; 11470| 0| goto dealloc; 11471| 0| } 11472| | 11473| | 11474| 1.75k|#ifdef TARGET_API_LIB 11475| | /*------------- for debug only ------------------- 11476| | InchiTimeGet(&ulTStart); 11477| | ret = OutputInChIOutOfStrFromINChI( ic, pCG, 11478| | ip, sd, num_inp, 0, 11479| | pOut, pLog, &OneInput, 11480| | save_opt_bits); 11481| | ulProcessingTime += InchiTimeElapsed( ic, pulTStart); 11482| | if ( ret < 0 ) 11483| | { 11484| | AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "Restored structure to InChI conversion failed", "; "); 11485| | goto dealloc; 11486| | } 11487| | -------------------------------------------------*/ 11488| 1.75k| if (at && num_at) ------------------ | Branch (11488:9): [True: 1.75k, False: 0] | Branch (11488:15): [True: 1.75k, False: 0] ------------------ 11489| 1.75k| { 11490| 1.75k| *at = pOneInput->atom; 11491| 1.75k| *num_at = pOneInput->num_atoms; 11492| 1.75k| pOneInput->atom = NULL; 11493| 1.75k| *polymer = pOneInput->polymer; 11494| 1.75k| pOneInput->polymer = NULL; 11495| 1.75k| *v3000 = pOneInput->v3000; 11496| 1.75k| pOneInput->v3000 = NULL; 11497| 1.75k| } 11498| |#else 11499| | 11500| | InchiTimeGet(pulTStart); 11501| | 11502| | ret = OutputInChIOutOfStrFromINChI(ic, pCG, ip, sd, num_inp, bINChIOutputOptions, 11503| | pOut, NULL, pOneInput, bHasSomeFixedH, save_opt_bits); 11504| | 11505| | ulProcessingTime += InchiTimeElapsed(ic, pulTStart); 11506| | 11507| | if (ret < 0) 11508| | { 11509| | AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "Restored structure to InChI conversion error", "; "); 11510| | (*num_errors)++; 11511| | goto dealloc; 11512| | } 11513| |#endif 11514| | 11515| 1.75k| if (szMessage) ------------------ | Branch (11515:9): [True: 1.75k, False: 0] ------------------ 11516| 1.75k| { 11517| 1.75k| int len, retcomp = 0, retcomp1 = 0; 11518| 1.75k| InchiTimeGet(pulTStart); 11519| 1.75k| retcomp = FillOutCompareMessage(szMessage, nMessageLen, pOneInput->CompareInchiFlags[0]); 11520| | 11521| 1.75k| if (pOneInput->CompareInchiFlags[1][0] || pOneInput->CompareInchiFlags[1][1]) ------------------ | Branch (11521:13): [True: 3, False: 1.75k] | Branch (11521:51): [True: 1, False: 1.75k] ------------------ 11522| 4| { 11523| 4| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "Disconnected: ", "; "); 11524| 4| retcomp1 = FillOutCompareMessage(szMessage, nMessageLen, pOneInput->CompareInchiFlags[1]); 11525| 4| } 11526| | /* add a metal warning */ 11527| 1.75k| if (bHasMetal && nInitLenMessage < (len = (int)strlen(szMessage))) ------------------ | Branch (11527:13): [True: 754, False: 1.00k] | Branch (11527:26): [True: 641, False: 113] ------------------ 11528| 641| { 11529| 641| char szMetal[] = " (Metal compound)"; 11530| 641| int shift; 11531| 641| if (len + (int)sizeof(szMetal) > nMessageLen) ------------------ | Branch (11531:17): [True: 0, False: 641] ------------------ 11532| 0| { 11533| 0| len = nMessageLen - (int)sizeof(szMetal); 11534| 0| } 11535| 641| shift = nInitLenMessage + (int)sizeof(szMetal) - 1; 11536| 641| memmove(szMessage + shift, szMessage + nInitLenMessage, ((long long)len - nInitLenMessage) * sizeof(szMessage[0])); /* djb-rwth: cast operator added */ 11537| 641| memcpy(szMessage + nInitLenMessage, szMetal, sizeof(szMetal) - sizeof(szMessage[0])); 11538| 641| szMessage[shift + len - nInitLenMessage] = '\0'; 11539| 641| } 11540| | 11541| 1.75k| retcomp = inchi_min(retcomp, retcomp1); ------------------ | | 139| 1.75k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 1.47k, False: 283] | | ------------------ ------------------ 11542| | 11543| 1.75k| if (retcomp < 0 && ------------------ | Branch (11543:13): [True: 1.47k, False: 279] ------------------ 11544| 1.47k| (ip_inp->bINChIOutputOptions2 & INCHI_OUT_MISMATCH_AS_ERROR) ------------------ | | 150| 1.47k|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ | Branch (11544:13): [True: 0, False: 1.47k] ------------------ 11545| 1.75k| ) 11546| 0| { 11547| 0| ret = RI_ERR_MISMATCH; ------------------ | | 21| 0|#define RI_ERR_MISMATCH (-9) ------------------ 11548| | /* AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "* Treated as error by user supplied option", "; "); */ 11549| 0| (*num_errors)++; 11550| 0| goto dealloc; 11551| 0| } 11552| | 11553| 1.75k| ulProcessingTime += InchiTimeElapsed(ic, pulTStart); 11554| 1.75k| } 11555| | 11556| 1.75k| ret = 0; 11557| | 11558| 5.18k|dealloc: 11559| | /* Deallocate */ 11560| 5.18k| if (ret) ------------------ | Branch (11560:9): [True: 3.43k, False: 1.75k] ------------------ 11561| 3.43k| { 11562| 3.43k| if (ret < 0) ------------------ | Branch (11562:13): [True: 3.43k, False: 0] ------------------ 11563| 3.43k| { 11564| 3.43k| if (ret == CT_USER_QUIT_ERR) ------------------ | | 32| 3.43k|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 18| 3.43k|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (11564:17): [True: 0, False: 3.43k] ------------------ 11565| 0| { 11566| 0| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "*Terminated by the user*", "; "); 11567| 0| } 11568| 3.43k| else 11569| 3.43k| { 11570| 3.43k| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "*Conversion failed*", "; "); 11571| 3.43k| } 11572| 3.43k| } 11573| 0| else 11574| 0| { 11575| 0| int iRec, iMob, iComp, nComp, len; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 11576| 0| char szTemp[128]; 11577| 0| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "*Conversion failed on component(s)", "; "); 11578| 0| len = (int)strlen(szMessage); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 11579| 0| for (iRec = 0; iRec < INCHI_NUM; iRec++) ------------------ | | 569| 0|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (11579:28): [True: 0, False: 0] ------------------ 11580| 0| { 11581| 0| for (iMob = bHasSomeFixedH ? TAUT_NON : TAUT_YES; iMob < TAUT_NUM; iMob++) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (iMob = bHasSomeFixedH ? TAUT_NON : TAUT_YES; iMob < TAUT_NUM; iMob++) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ for (iMob = bHasSomeFixedH ? TAUT_NON : TAUT_YES; iMob < TAUT_NUM; iMob++) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (11581:29): [True: 0, False: 0] | Branch (11581:67): [True: 0, False: 0] ------------------ 11582| 0| { 11583| 0| nComp = pOneInput->nNumComponents[iRec][iMob]; 11584| 0| if (!pStruct[iRec][iMob]) ------------------ | Branch (11584:25): [True: 0, False: 0] ------------------ 11585| 0| { 11586| 0| continue; 11587| 0| } 11588| 0| for (iComp = 0; iComp < nComp; iComp++) ------------------ | Branch (11588:37): [True: 0, False: 0] ------------------ 11589| 0| { 11590| 0| if (pStruct[iRec][iMob][iComp].nError) ------------------ | Branch (11590:29): [True: 0, False: 0] ------------------ 11591| 0| { 11592| 0| char* szFormula = pOneInput->pInpInChI[iRec][iMob][iComp].szHillFormula; 11593| 0| sprintf(szTemp, 11594| 0|#if ( FIX_DALKE_BUGS == 1 ) 11595| 0| " %s%s%d(%.96s)", 11596| |#else 11597| | " %s%s%d(%s)", 11598| |#endif 11599| 0| !bHasSomeReconnected ? "" : iRec ? "R" : "D", ------------------ | Branch (11599:33): [True: 0, False: 0] | Branch (11599:61): [True: 0, False: 0] ------------------ 11600| 0| !bHasSomeFixedH ? "" : iMob ? "M" : "F", ------------------ | Branch (11600:33): [True: 0, False: 0] | Branch (11600:56): [True: 0, False: 0] ------------------ 11601| 0| iComp + 1, szFormula ? szFormula : "???"); ------------------ | Branch (11601:44): [True: 0, False: 0] ------------------ 11602| 0| AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, szTemp, NULL); 11603| 0| } 11604| 0| } 11605| 0| } 11606| 0| } 11607| 0| } /* if ( ret > 0 ) */ 11608| 3.43k| } /* if ( ret ) */ 11609| | 11610| | 11611| 5.18k| InchiTimeGet(pulTStart); 11612| | 11613| | /* Print one structure report */ 11614| 5.18k| if (szMessage && szMsg && nMsgLen > 1) /* djb-rwth: additional condition for szMessage */ ------------------ | Branch (11614:9): [True: 5.18k, False: 0] | Branch (11614:22): [True: 5.18k, False: 0] | Branch (11614:31): [True: 5.18k, False: 0] ------------------ 11615| 5.18k| { 11616| 5.18k| int len = inchi_min((int)strlen(szMessage), nMsgLen - 1); ------------------ | | 139| 5.18k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 5.18k, False: 0] | | ------------------ ------------------ 11617| 5.18k| if (len > 0) ------------------ | Branch (11617:13): [True: 4.91k, False: 279] ------------------ 11618| 4.91k| { 11619| 4.91k| memcpy(szMsg, szMessage, len); 11620| 4.91k| szMsg[len] = '\0'; 11621| 4.91k| } 11622| 279| else 11623| 279| { 11624| 279| szMsg[0] = '\0'; 11625| 279| } 11626| 5.18k| } 11627| | 11628| 5.18k| if (szMessage && (nInitLenMessage < (int)strlen(szMessage))) /* djb-rwth: additional condition for szMessage */ ------------------ | Branch (11628:9): [True: 5.18k, False: 0] | Branch (11628:22): [True: 4.91k, False: 279] ------------------ 11629| 4.91k| { 11630| 4.91k| inchi_ios_eprint(pLog, "%s\n", szMessage); 11631| 4.91k| } 11632| |#ifndef TARGET_API_LIB 11633| | else 11634| | { 11635| | /*^^^inchi_ios_eprint( stderr, "%s\r", szMessage );*/ 11636| | inchi_fprintf(stderr, "%s\r", szMessage); 11637| | } 11638| |#endif 11639| | 11640| 5.18k| FreeStrFromINChI(pStruct, pOneInput->nNumComponents); 11641| 5.18k| FreeInpInChI(pOneInput); 11642| 5.18k| if (*pszCurHdr) ------------------ | Branch (11642:9): [True: 0, False: 5.18k] ------------------ 11643| 0| { 11644| 0| inchi_free(*pszCurHdr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 11645| 0| *pszCurHdr = NULL; 11646| 0| } 11647| | 11648| | INCHI_HEAPCHK 11649| | 11650| 5.18k| ulProcessingTime += InchiTimeElapsed(ic, pulTStart); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 11651| | 11652| 5.18k| return ret; 11653| 1.75k|} DetectAndExposePolymerInternals: 11658| 6.28k|{ 11659| 6.28k| int i, j, elindex, ret = 0, nheavy = 0, 11660| 6.28k| nstars = 0, zlen = 0, star0 = 0, i_last_sym, 11661| 6.28k| slen = 0, i2 = 0, ninsert = 0, kinsert, lead_pos, nc, ntimes, nc_max; 11662| 6.28k| const char* p, * pz, * pz2, * pr, * pend, * q; 11663| 6.28k| char prev_layer_symbol = '0'; 11664| 6.28k| char element[3], * tmpstr = NULL, * edited_s = NULL; 11665| 6.28k| int* insert_pos = NULL; /* inserts go before insert_pos[k] */ 11666| 6.28k| char* s = NULL, * s2 = NULL; 11667| 6.28k| int slength; 11668| | 11669| 6.28k| slength = is->s.nUsedLength; 11670| 6.28k| s = (char*)inchi_calloc(2 * (long long)slength + 32, sizeof(char)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 6.28k|#define inchi_calloc calloc ------------------ 11671| 6.28k| if (!s) ------------------ | Branch (11671:9): [True: 0, False: 6.28k] ------------------ 11672| 0| { 11673| 0| goto endf; 11674| 0| } 11675| | 11676| | /* Remove but save a tail (AuxInfo, InChIKey, etc.) if any */ 11677| 6.28k| strcpy(s, is->s.pStr); 11678| 2.36M| for (i = 0; i < slength; i++) ------------------ | Branch (11678:17): [True: 2.35M, False: 6.13k] ------------------ 11679| 2.35M| { 11680| 2.35M| if (isspace(UCINT s[i])) ------------------ | Branch (11680:13): [True: 150, False: 2.35M] ------------------ 11681| 150| { 11682| 150| i2 = i; 11683| 150| break; 11684| 150| } 11685| 2.35M| } 11686| 6.28k| if (i2) ------------------ | Branch (11686:9): [True: 150, False: 6.13k] ------------------ 11687| 150| { 11688| 150| s2 = (char*)inchi_calloc((long long)slength - (long long)i2 + 2, sizeof(char)); /* djb-rwth: cast operators added */ ------------------ | | 1146| 150|#define inchi_calloc calloc ------------------ 11689| 150| if (!s2) goto endf; ------------------ | Branch (11689:13): [True: 0, False: 150] ------------------ 11690| 150| strcpy(s2, s + i2); 11691| 150| s[i2] = '\0'; 11692| 150| } 11693| | 11694| 6.28k| i_last_sym = strlen(s) - 1; 11695| 6.28k| p = strstr(s, "InChI=1"); 11696| 6.28k| if (!p) ------------------ | Branch (11696:9): [True: 0, False: 6.28k] ------------------ 11697| 0| { 11698| 0| goto endf; 11699| 0| } 11700| | 11701| 6.28k| pz = strstr(p, "/z"); 11702| 6.28k| if (!pz) ------------------ | Branch (11702:9): [True: 5.49k, False: 784] ------------------ 11703| 5.49k| { 11704| 5.49k| goto endf; 11705| 5.49k| } 11706| 784| pz++; 11707| | 11708| | /* Check formula */ 11709| 784| p = strchr(p, '/'); 11710| 784| if (!p) /* djb-rwth: fixing coverity ID #499505 */ ------------------ | Branch (11710:9): [True: 0, False: 784] ------------------ 11711| 0| { 11712| 0| goto endf; 11713| 0| } 11714| 784| p++; 11715| 784| pend = strchr(p, '/'); 11716| 784| ntimes = 1; 11717| 10.5k| while (p != pend) ------------------ | Branch (11717:12): [True: 9.82k, False: 744] ------------------ 11718| 9.82k| { 11719| 9.82k| if (isdigit(*p)) ------------------ | Branch (11719:13): [True: 930, False: 8.89k] ------------------ 11720| 930| { 11721| 930| ntimes = (int)inchi_strtol(p, &q, 10); 11722| 930|#if ( CHECK_STRTOL_ATNUMB==1 ) 11723| 930| if (ntimes > MAX_ATOMS || ntimes < 0) ------------------ | | 15| 1.86k|#define MAX_ATOMS 32766 ------------------ | Branch (11723:17): [True: 1, False: 929] | Branch (11723:39): [True: 17, False: 912] ------------------ 11724| 18| { 11725| 18|#if (FIX_GAF_2020_25607 == 1) 11726| 18| ret = RI_ERR_SYNTAX; ------------------ | | 16| 18|#define RI_ERR_SYNTAX (-2) ------------------ 11727| 18| goto endf; 11728| |#else 11729| | return RI_ERR_SYNTAX; /* syntax error */ 11730| |#endif 11731| 18| } 11732| 912|#endif 11733| 912| p = q; 11734| 912| } 11735| 8.89k| else 11736| 8.89k| { 11737| 8.89k| if (*p == '.') ------------------ | Branch (11737:17): [True: 0, False: 8.89k] ------------------ 11738| 0| { 11739| 0| ntimes = 1; 11740| 0| } 11741| 8.89k| } 11742| | 11743| 9.81k| if (!isupper(UCINT * p)) ------------------ | Branch (11743:13): [True: 5, False: 9.80k] ------------------ 11744| 5| { 11745| 5| ret = -1; 11746| 5| goto endf; 11747| 5| } 11748| | 11749| 9.80k| j = 0; 11750| 9.80k| element[j++] = *p++; 11751| 9.80k| if (*p && islower(UCINT * p)) ------------------ | Branch (11751:13): [True: 9.80k, False: 0] | Branch (11751:19): [True: 1.78k, False: 8.01k] ------------------ 11752| 1.78k| { 11753| 1.78k| element[j++] = *p++; 11754| 1.78k| } 11755| 9.80k| element[j++] = '\0'; 11756| 9.80k| if (*p && isdigit(UCINT * p)) ------------------ | Branch (11756:13): [True: 9.80k, False: 0] | Branch (11756:19): [True: 1.12k, False: 8.68k] ------------------ 11757| 1.12k| { 11758| 1.12k| elindex = (int)inchi_strtol(p, &q, 10); 11759| 1.12k|#if ( CHECK_STRTOL_ATNUMB==1 ) 11760| 1.12k| if (elindex > MAX_ATOMS || elindex < 0) ------------------ | | 15| 2.24k|#define MAX_ATOMS 32766 ------------------ | Branch (11760:17): [True: 1, False: 1.11k] | Branch (11760:40): [True: 12, False: 1.10k] ------------------ 11761| 13| { 11762| 13|#if (FIX_GAF_2020_25607 == 1) 11763| 13| ret = RI_ERR_SYNTAX; ------------------ | | 16| 13|#define RI_ERR_SYNTAX (-2) ------------------ 11764| 13| goto endf; 11765| |#else 11766| | return RI_ERR_SYNTAX; /* syntax error */ 11767| |#endif 11768| | 11769| 13| } 11770| 1.10k|#endif 11771| 1.10k| p = q; 11772| 1.10k| } 11773| 8.68k| else 11774| 8.68k| { 11775| 8.68k| elindex = 1; 11776| 8.68k| } 11777| 9.79k| if (!elindex) ------------------ | Branch (11777:13): [True: 0, False: 9.79k] ------------------ 11778| 0| { 11779| 0| ret = -1; 11780| 0| goto endf; 11781| 0| } 11782| 9.79k|#if ( FIX_GAF_2019_2==1 ) 11783| 9.79k| if (ERR_ELEM == get_periodic_table_number(element)) ------------------ | Branch (11783:13): [True: 4, False: 9.78k] ------------------ 11784| 4| { 11785| 4| ret = -1; 11786| 4| goto endf; 11787| 4| } 11788| 9.78k|#endif 11789| 9.78k| if (element[0] != 'H' || element[1]) ------------------ | Branch (11789:13): [True: 8.85k, False: 933] | Branch (11789:34): [True: 231, False: 702] ------------------ 11790| 9.08k| { 11791| 9.08k| nheavy += ntimes * elindex; 11792| 9.08k| } 11793| | 11794| 9.78k| if (*p == '.') ------------------ | Branch (11794:13): [True: 1.38k, False: 8.40k] ------------------ 11795| 1.38k| { 11796| 1.38k| p++; 11797| 1.38k| } 11798| 9.78k| } 11799| | 11800| 744|#if ( FIX_GAF_2019_2==1 ) 11801| 744| insert_pos = (int*)inchi_calloc((long long)is->s.nUsedLength + 1, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 744|#define inchi_calloc calloc ------------------ 11802| |#else 11803| | /* max num of insert positions is 2 in formulas + Npolymeric units, the latter may not be > nheavy */ 11804| | insert_pos = (int*)inchi_calloc(nheavy + 32, sizeof(int)); 11805| |#endif 11806| 744| if (!insert_pos) ------------------ | Branch (11806:9): [True: 0, False: 744] ------------------ 11807| 0| { 11808| 0| ret = -2; 11809| 0| goto endf; 11810| 0| } 11811| | 11812| 744| ninsert = 0; 11813| 744| if (pend) ------------------ | Branch (11813:9): [True: 744, False: 0] ------------------ 11814| 744| { 11815| 744| insert_pos[ninsert] = (int)(pend - s); 11816| 744| } 11817| 0| else 11818| 0| { 11819| 0| insert_pos[ninsert] = i_last_sym; 11820| 0| } 11821| 744| ninsert++; 11822| | 11823| | /* Check hidden stars */ 11824| 744| lead_pos = (int)(pz - s); 11825| 744| pend = strchr(pz, '/'); 11826| 744| if (pend) ------------------ | Branch (11826:9): [True: 236, False: 508] ------------------ 11827| 236| { 11828| 236| zlen = (int)(pend - pz); 11829| 236| } 11830| 508| else 11831| 508| { 11832| 508| zlen = (int)strlen(pz); 11833| 508| } 11834| 744| tmpstr = (char*)inchi_calloc((long long)zlen + 32, sizeof(char)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 744|#define inchi_calloc calloc ------------------ 11835| 744| if (!tmpstr) ------------------ | Branch (11835:9): [True: 0, False: 744] ------------------ 11836| 0| { 11837| 0| ret = -2; 11838| 0| goto endf; 11839| 0| } 11840| 744| memcpy(tmpstr, pz, zlen); 11841| 744| ret = DetectHiddenPolymerStuff(tmpstr, zlen, &ninsert, insert_pos, lead_pos, &nstars); 11842| 744| if (ret) ------------------ | Branch (11842:9): [True: 14, False: 730] ------------------ 11843| 14| { 11844| 14| goto endf; 11845| 14| } 11846| 730| if (!nstars) ------------------ | Branch (11846:9): [True: 240, False: 490] ------------------ 11847| 240| { 11848| 240| goto endf; 11849| 240| } 11850| | 11851| | /* Have second '/z' ? */ 11852| 490| pr = strstr(s, "/r"); 11853| 490| if (pr) ------------------ | Branch (11853:9): [True: 182, False: 308] ------------------ 11854| 182| { 11855| 182| pr++; 11856| | 11857| 182| pend = strchr(pr, '/'); 11858| 182| if (pend) ------------------ | Branch (11858:13): [True: 180, False: 2] ------------------ 11859| 180| { 11860| 180| insert_pos[ninsert] = (int)(pend - s); 11861| 180| } 11862| 2| else 11863| 2| { 11864| 2| insert_pos[ninsert] = i_last_sym; 11865| 2| } 11866| 182| ninsert++; 11867| | 11868| 182| pz2 = strstr(pr, "/z"); 11869| 182| if (pz2) ------------------ | Branch (11869:13): [True: 179, False: 3] ------------------ 11870| 179| { 11871| 179| pz2++; 11872| 179| lead_pos = (int)(pz2 - s); 11873| 179| pend = strchr(pz2, '/'); 11874| 179| if (pend) ------------------ | Branch (11874:17): [True: 59, False: 120] ------------------ 11875| 59| { 11876| 59| zlen = (int)(pend - pz2); 11877| 59| } 11878| 120| else 11879| 120| { 11880| 120| zlen = (int)strlen(pz2); 11881| 120| } 11882| 179| if (tmpstr) ------------------ | Branch (11882:17): [True: 179, False: 0] ------------------ 11883| 179| { 11884| 179| inchi_free(tmpstr); ------------------ | | 1152| 179|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 179, False: 0] | | | Branch (1152:50): [Folded, False: 179] | | ------------------ ------------------ 11885| 179| } 11886| 179| tmpstr = (char*)inchi_calloc((long long)zlen + 32, sizeof(char)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 179|#define inchi_calloc calloc ------------------ 11887| 179| if (!tmpstr) ------------------ | Branch (11887:17): [True: 0, False: 179] ------------------ 11888| 0| { 11889| 0| ret = -2; 11890| 0| goto endf; 11891| 0| } 11892| 179| memcpy(tmpstr, pz2, zlen); 11893| 179| nstars = 0; 11894| 179| ret = DetectHiddenPolymerStuff(tmpstr, zlen, &ninsert, insert_pos, lead_pos, &nstars); 11895| 179| if (ret) ------------------ | Branch (11895:17): [True: 3, False: 176] ------------------ 11896| 3| { 11897| 3| goto endf; 11898| 3| } 11899| 179| } 11900| 182| } 11901| | 11902| 487| slen = (int)strlen(s); 11903| 487| edited_s = (char*)inchi_calloc((long long)slen * 100 + 32 * 10 * (long long)ninsert, sizeof(char)); /* high reservation */ /* djb-rwth: cast operator added */ ------------------ | | 1146| 487|#define inchi_calloc calloc ------------------ 11904| 487| if (!edited_s) ------------------ | Branch (11904:9): [True: 0, False: 487] ------------------ 11905| 0| { 11906| 0| ret = -2; 11907| 0| goto endf; 11908| 0| } 11909| | 11910| | /* Edits */ 11911| 487| nc = 0; 11912| 487| nc_max = slen * 100 + 32 * 10 * ninsert; /* djb-rwth: fixing oss-fuzz issue #384549256 */ 11913| 487| kinsert = 0; 11914| 487| star0 = nheavy + 1; 11915| 518k| for (i = 0; i < slen; i++) ------------------ | Branch (11915:17): [True: 518k, False: 0] ------------------ 11916| 518k| { 11917| 518k| if (kinsert < ninsert && i == insert_pos[kinsert]) ------------------ | Branch (11917:13): [True: 491k, False: 26.5k] | Branch (11917:34): [True: 86.5k, False: 405k] ------------------ 11918| 86.5k| { 11919| 86.5k| if (kinsert == 0 || prev_layer_symbol == 'r') ------------------ | Branch (11919:17): [True: 487, False: 86.0k] | Branch (11919:33): [True: 18, False: 86.0k] ------------------ 11920| 505| { 11921| 505| sprintf(tmpstr, ".%dZz", nstars); 11922| 505| star0 = nheavy + 1; /* reset star numbers pool */ 11923| 505| prev_layer_symbol = '0'; /* avoid printing ';' also */ 11924| 505| } 11925| 86.0k| else 11926| 86.0k| { 11927| 86.0k| sprintf(tmpstr, "%d,%d-", star0, star0 + 1); 11928| 86.0k| star0 += 2; 11929| 86.0k| } 11930| 86.5k| kinsert++; 11931| 993k| for (j = 0; j < (int)strlen(tmpstr); j++) ------------------ | Branch (11931:25): [True: 907k, False: 86.5k] ------------------ 11932| 907k| { 11933| 907k| if (nc < nc_max) ------------------ | Branch (11933:21): [True: 907k, False: 0] ------------------ 11934| 907k| { 11935| 907k| edited_s[nc] = tmpstr[j]; 11936| 907k| nc++; 11937| 907k| } 11938| 907k| } 11939| 86.5k| } 11940| | 11941| 518k| if ((i == i_last_sym) && (nc < nc_max)) ------------------ | Branch (11941:13): [True: 487, False: 518k] | Branch (11941:34): [True: 487, False: 0] ------------------ 11942| 487| { 11943| 487| edited_s[nc++] = s[i]; 11944| 487| } 11945| | 11946| 518k| if (s[i] == '/' || i == i_last_sym) ------------------ | Branch (11946:13): [True: 24.1k, False: 494k] | Branch (11946:28): [True: 474, False: 493k] ------------------ 11947| 24.6k| { 11948| 24.6k| if (prev_layer_symbol != '0' && ------------------ | Branch (11948:17): [True: 23.6k, False: 992] ------------------ 11949| 23.6k| prev_layer_symbol != 'f' && ------------------ | Branch (11949:17): [True: 19.7k, False: 3.86k] ------------------ 11950| 19.7k| prev_layer_symbol != 'z' && ------------------ | Branch (11950:17): [True: 17.1k, False: 2.59k] ------------------ 11951| 17.1k| prev_layer_symbol != 'p' && ------------------ | Branch (11951:17): [True: 16.7k, False: 411] ------------------ 11952| 16.7k| prev_layer_symbol != 'r' && ------------------ | Branch (11952:17): [True: 14.1k, False: 2.66k] ------------------ 11953| 14.1k| prev_layer_symbol != 's' ------------------ | Branch (11953:17): [True: 12.5k, False: 1.58k] ------------------ 11954| 24.6k| ) 11955| 12.5k| { 11956| 12.5k| char addon = ';'; 11957| 12.5k| if (prev_layer_symbol == 'm') ------------------ | Branch (11957:21): [True: 6.30k, False: 6.21k] ------------------ 11958| 6.30k| { 11959| 6.30k| addon = '.'; 11960| 6.30k| } 11961| 2.37M| for (j = 0; j < nstars; j++) ------------------ | Branch (11961:29): [True: 2.35M, False: 12.5k] ------------------ 11962| 2.35M| { 11963| 2.35M| if (nc < nc_max) ------------------ | Branch (11963:25): [True: 2.35M, False: 0] ------------------ 11964| 2.35M| { 11965| 2.35M| edited_s[nc++] = addon; 11966| 2.35M| } 11967| 2.35M| } 11968| 12.5k| } 11969| 12.1k| else if (prev_layer_symbol == 'f') ------------------ | Branch (11969:22): [True: 3.86k, False: 8.24k] ------------------ 11970| 3.86k| { 11971| 3.86k| if (s[i - 1] != 'f' && s[i - 2] != '/') ------------------ | Branch (11971:21): [True: 1.72k, False: 2.13k] | Branch (11971:40): [True: 1.72k, False: 0] ------------------ 11972| 1.72k| { 11973| 1.72k| sprintf(tmpstr, ".%dZz", nstars); 11974| 9.83k| for (j = 0; j < (int)strlen(tmpstr); j++) ------------------ | Branch (11974:33): [True: 8.10k, False: 1.72k] ------------------ 11975| 8.10k| { 11976| 8.10k| if (nc < nc_max) ------------------ | Branch (11976:29): [True: 8.10k, False: 0] ------------------ 11977| 8.10k| { 11978| 8.10k| edited_s[nc] = tmpstr[j]; 11979| 8.10k| nc++; 11980| 8.10k| } 11981| 8.10k| } 11982| 1.72k| } 11983| 3.86k| } 11984| | 11985| 24.6k| if (i != i_last_sym) ------------------ | Branch (11985:17): [True: 24.1k, False: 487] ------------------ 11986| 24.1k| { 11987| 24.1k| prev_layer_symbol = s[i + 1]; 11988| 24.1k| } 11989| 487| else 11990| 487| { 11991| 487| break; 11992| 487| } 11993| 24.6k| } 11994| 518k| if (nc < nc_max) ------------------ | Branch (11994:13): [True: 518k, False: 0] ------------------ 11995| 518k| { 11996| 518k| edited_s[nc] = s[i]; 11997| 518k| nc++; 11998| 518k| } 11999| 518k| } 12000| 487| if (nc < nc_max) ------------------ | Branch (12000:9): [True: 487, False: 0] ------------------ 12001| 487| { 12002| 487| edited_s[nc] = '\0'; 12003| 487| } 12004| 487| inchi_strbuf_close(&is->s); 12005| 487| inchi_ios_print(is, "%-s%-s\n", edited_s, s2 ? s2 : ""); ------------------ | Branch (12005:47): [True: 33, False: 454] ------------------ 12006| | 12007| 6.28k|endf: 12008| 6.28k| if (s) ------------------ | Branch (12008:9): [True: 6.28k, False: 0] ------------------ 12009| 6.28k| { 12010| 6.28k| inchi_free(s); ------------------ | | 1152| 6.28k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.28k, False: 0] | | | Branch (1152:50): [Folded, False: 6.28k] | | ------------------ ------------------ 12011| 6.28k| } 12012| 6.28k| if (s2) ------------------ | Branch (12012:9): [True: 150, False: 6.13k] ------------------ 12013| 150| { 12014| 150| inchi_free(s2); ------------------ | | 1152| 150|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 150, False: 0] | | | Branch (1152:50): [Folded, False: 150] | | ------------------ ------------------ 12015| 150| } 12016| 6.28k| if (edited_s) ------------------ | Branch (12016:9): [True: 487, False: 5.79k] ------------------ 12017| 487| { 12018| 487| inchi_free(edited_s); ------------------ | | 1152| 487|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 487, False: 0] | | | Branch (1152:50): [Folded, False: 487] | | ------------------ ------------------ 12019| 487| } 12020| 6.28k| if (tmpstr) ------------------ | Branch (12020:9): [True: 744, False: 5.53k] ------------------ 12021| 744| { 12022| 744| inchi_free(tmpstr); ------------------ | | 1152| 744|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 744, False: 0] | | | Branch (1152:50): [Folded, False: 744] | | ------------------ ------------------ 12023| 744| } 12024| 6.28k| if (insert_pos) ------------------ | Branch (12024:9): [True: 744, False: 5.53k] ------------------ 12025| 744| { 12026| 744| inchi_free(insert_pos); ------------------ | | 1152| 744|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 744, False: 0] | | | Branch (1152:50): [Folded, False: 744] | | ------------------ ------------------ 12027| 744| } 12028| | 12029| 6.28k| return ret; 12030| 487|} DetectHiddenPolymerStuff: 12040| 923|{ 12041| 923| char c; 12042| 923| int opened, skip, i, i0, closed, ret = 0; 12043| | 12044| 923| *nstars = opened = skip = i0 = 0; 12045| 923| closed = 1; 12046| 662k| for (i = 0; i < tmpstrlen; i++) ------------------ | Branch (12046:17): [True: 661k, False: 906] ------------------ 12047| 661k| { 12048| 661k| c = tmpstr[i]; 12049| | 12050| 661k| if (c == '(') ------------------ | Branch (12050:13): [True: 194k, False: 467k] ------------------ 12051| 194k| { 12052| 194k| if (!closed) ------------------ | Branch (12052:17): [True: 0, False: 194k] ------------------ 12053| 0| { 12054| 0| ret = -3; goto endf; 12055| 0| } 12056| 194k| opened = 1; 12057| 194k| skip = 0; 12058| 194k| i0 = i; 12059| 194k| } 12060| 467k| else if (c == ')') ------------------ | Branch (12060:18): [True: 165k, False: 302k] ------------------ 12061| 165k| { 12062| 165k| if (!opened) ------------------ | Branch (12062:17): [True: 17, False: 165k] ------------------ 12063| 17| { 12064| 17| ret = -3; goto endf; 12065| 17| } 12066| 165k| if (!skip) ------------------ | Branch (12066:17): [True: 164k, False: 46] ------------------ 12067| 164k| { 12068| 164k| (*nstars) += 2; 12069| 164k| insert_pos[(*ninsert)] = i0 + 1 + insert_lead_offset; 12070| 164k| (*ninsert)++; 12071| 164k| } 12072| 165k| opened = 0; 12073| 165k| } 12074| 302k| else if (c == '-') ------------------ | Branch (12074:18): [True: 3.64k, False: 298k] ------------------ 12075| 3.64k| { 12076| 3.64k| skip = 1; 12077| 3.64k| } 12078| 661k| } 12079| | 12080| 923|endf: 12081| 923| return ret; 12082| 923|} ichiread.c:bInChIHasReconnectedMetal: 1983| 180k|{ 1984| 180k| int i; 1985| 180k| if (pInChI && !pInChI->bDeleted && pInChI->nNumberOfAtoms && pInChI->nAtom) ------------------ | Branch (1985:9): [True: 180k, False: 0] | Branch (1985:19): [True: 176k, False: 3.92k] | Branch (1985:40): [True: 146k, False: 30.3k] | Branch (1985:66): [True: 146k, False: 0] ------------------ 1986| 146k| { 1987| 1.07M| for (i = 0; i < pInChI->nNumberOfAtoms; i++) ------------------ | Branch (1987:21): [True: 990k, False: 82.6k] ------------------ 1988| 990k| { 1989| 990k| if (is_el_a_metal((int)pInChI->nAtom[i])) ------------------ | Branch (1989:17): [True: 65.4k, False: 925k] ------------------ 1990| 65.4k| { 1991| 65.4k| if (pInChI->nNumberOfAtoms > 1 || (pInChI->nNum_H && pInChI->nNum_H[0])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1991:21): [True: 63.9k, False: 1.52k] | Branch (1991:52): [True: 1.52k, False: 0] | Branch (1991:70): [True: 4, False: 1.51k] ------------------ 1992| 63.9k| { 1993| 63.9k| return 1; 1994| 63.9k| } 1995| 65.4k| } 1996| 990k| } 1997| 146k| } 1998| | 1999| 116k| return 0; 2000| 180k|} ichiread.c:SetProtonsAndXchgIsoH: 2012| 10.2k|{ 2013| 10.2k| int j, k, k1, ret2 = 0, iINChI; 2014| 10.2k| int bAvailableProtonsForEachComponent, bAvailableProtonsTotal; 2015| | 2016| | INCHI_HEAPCHK 2017| | 2018| 10.2k| num_components[INCHI_BAS] = num_components[INCHI_REC] = 0; ------------------ | | 570| 10.2k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ num_components[INCHI_BAS] = num_components[INCHI_REC] = 0; ------------------ | | 571| 10.2k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 2019| | 2020| 30.6k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 30.6k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2020:22): [True: 20.4k, False: 10.2k] ------------------ 2021| 20.4k| { 2022| 20.4k| nModeProtonIsoExchgH[iINChI] = MODE_PIXH_UNDEFINED; 2023| | /* are totals of /p and/or /i/h available ? */ 2024| 20.4k| bAvailableProtonsTotal = 0 != OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 575| 20.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2025| 81.7k| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 72| 81.7k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2025:22): [True: 61.2k, False: 20.4k] ------------------ 2026| 61.2k| { 2027| 61.2k| bAvailableProtonsTotal |= 0 != OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[k1]; ------------------ | | 575| 61.2k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2028| 61.2k| } 2029| | /* are /p and/or /i/h available for each component ? */ 2030| 20.4k| bAvailableProtonsForEachComponent = (NULL != OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons); ------------------ | | 575| 20.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2031| | 2032| | /* decision: add /p to each component, add total to the 1st, add total as one more component */ 2033| | /* In case of bInChI2Structure just keep totals if not available for each component */ 2034| | 2035| 20.4k| if (bInChI2Structure) ------------------ | Branch (2035:13): [True: 10.3k, False: 10.0k] ------------------ 2036| 10.3k| { 2037| 10.3k| nModeProtonIsoExchgH[iINChI] = bAvailableProtonsForEachComponent ? ------------------ | Branch (2037:44): [True: 0, False: 10.3k] ------------------ 2038| 0| MODE_PIXH_ADD_TO_EACH : 2039| 10.3k| MODE_PIXH_KEEP_TOTALS; 2040| 10.3k| } 2041| 10.0k| else 2042| 10.0k| { 2043| 10.0k| if (!bReqSplitOutputInChI) ------------------ | Branch (2043:17): [True: 10.0k, False: 0] ------------------ 2044| 10.0k| { 2045| 10.0k| nModeProtonIsoExchgH[iINChI] = bAvailableProtonsForEachComponent ? ------------------ | Branch (2045:48): [True: 0, False: 10.0k] ------------------ 2046| 0| MODE_PIXH_ADD_TO_EACH : 2047| 10.0k| MODE_PIXH_ADD_TO_FIRST; 2048| 10.0k| } 2049| 0| else 2050| 0| { 2051| 0| if (!bAvailableProtonsForEachComponent) ------------------ | Branch (2051:21): [True: 0, False: 0] ------------------ 2052| 0| { 2053| 0| nModeProtonIsoExchgH[iINChI] = bAvailableProtonsTotal ? ------------------ | Branch (2053:52): [True: 0, False: 0] ------------------ 2054| 0| MODE_PIXH_ADD_A_PIXH_COMPONENT : 2055| 0| MODE_PIXH_ADD_TO_FIRST; 2056| 0| } 2057| 0| else 2058| 0| { 2059| | /* bAvailableProtonsForEachComponent && bReqSplitOutputInChI */ 2060| 0| if (bReqProtonsForEachComponent) ------------------ | Branch (2060:25): [True: 0, False: 0] ------------------ 2061| 0| { 2062| 0| nModeProtonIsoExchgH[iINChI] = MODE_PIXH_ADD_TO_EACH; 2063| 0| } 2064| 0| else 2065| 0| { 2066| 0| nModeProtonIsoExchgH[iINChI] = bReqNonTaut ? ------------------ | Branch (2066:56): [True: 0, False: 0] ------------------ 2067| 0| MODE_PIXH_ADD_TO_EACH : 2068| 0| MODE_PIXH_ADD_A_PIXH_COMPONENT; 2069| 0| } 2070| 0| } 2071| 0| } 2072| 10.0k| } 2073| | 2074| | /* remove unneeded data: protons for each component */ 2075| 20.4k| if (bAvailableProtonsForEachComponent && ------------------ | Branch (2075:13): [True: 0, False: 20.4k] ------------------ 2076| 0| nModeProtonIsoExchgH[iINChI] != MODE_PIXH_ADD_TO_EACH) ------------------ | Branch (2076:13): [True: 0, False: 0] ------------------ 2077| 0| { 2078| 0| inchi_free(OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2079| 0| OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons = NULL; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2080| 0| bAvailableProtonsForEachComponent = 0; 2081| 0| } 2082| | /* remove unneeded data: total protons all components */ 2083| 20.4k| if (bAvailableProtonsTotal && nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_TO_EACH) ------------------ | Branch (2083:13): [True: 376, False: 20.0k] | Branch (2083:39): [True: 0, False: 376] ------------------ 2084| 0| { 2085| 0| OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons = 0; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2086| 0| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 72| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2086:26): [True: 0, False: 0] ------------------ 2087| 0| { 2088| 0| OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[k1] = 0; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2089| 0| } 2090| | /* djb-rwth: removing redundant code */ 2091| 0| } 2092| | /* remove unneeded data: Fixed-H InChI; no protons data exist for Fixed-H */ 2093| 20.4k| if (!bReqNonTaut && OneInput->nNumComponents[iINChI][TAUT_NON]) ------------------ | | 574| 10.0k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2093:13): [True: 10.0k, False: 10.3k] | Branch (2093:29): [True: 1.27k, False: 8.77k] ------------------ 2094| 1.27k| { 2095| 1.27k| j = TAUT_NON; ------------------ | | 574| 1.27k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2096| 2.62k| for (k = 0; k < OneInput->nNumComponents[iINChI][j]; k++) ------------------ | Branch (2096:25): [True: 1.35k, False: 1.27k] ------------------ 2097| 1.35k| { 2098| 1.35k| Free_INChI_Members(&OneInput->pInpInChI[iINChI][j][k]); 2099| 1.35k| } 2100| 1.27k| inchi_free(OneInput->pInpInChI[iINChI][j]); ------------------ | | 1152| 1.27k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.27k, False: 0] | | | Branch (1152:50): [Folded, False: 1.27k] | | ------------------ ------------------ 2101| 1.27k| OneInput->pInpInChI[iINChI][j] = NULL; 2102| 1.27k| OneInput->nNumComponents[iINChI][j] = 0; 2103| 1.27k| } 2104| |#ifdef NEVER 2105| | /* remove unneeded data: Mobile-H InChI ????? */ 2106| | if (bReqNonTaut && OneInput->nNumComponents[iINChI][TAUT_NON]) 2107| | { 2108| | j = TAUT_YES; 2109| | for (k = 0; k < OneInput->nNumComponents[iINChI][j]; k++) 2110| | { 2111| | Free_INChI_Members(&OneInput->pInpInChI[iINChI][j][k]); 2112| | } 2113| | inchi_free(OneInput->pInpInChI[iINChI][j]); 2114| | OneInput->pInpInChI[iINChI][j] = NULL; 2115| | OneInput->nNumComponents[iINChI][j] = 0; 2116| | nModeProtonIsoExchgH[iINChI] = MODE_PIXH_UNDEFINED; 2117| | if (OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons) 2118| | { 2119| | inchi_free(OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons); 2120| | OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons = NULL; 2121| | } 2122| | } 2123| |#endif 2124| | /* add one more component containing only /p and /i/h */ 2125| 20.4k| if ((nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_A_PIXH_COMPONENT && ------------------ | Branch (2125:14): [True: 0, False: 20.4k] ------------------ 2126| 0| OneInput->nNumComponents[iINChI][TAUT_YES]) || ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2126:13): [True: 0, False: 0] ------------------ 2127| | /* always add one deleted component if no non-taut InChI is available */ 2128| 20.4k| (bInChI2Structure && !bAvailableProtonsForEachComponent && ------------------ | Branch (2128:14): [True: 10.3k, False: 10.0k] | Branch (2128:34): [True: 10.3k, False: 0] ------------------ 2129| 10.3k| !OneInput->nNumComponents[iINChI][TAUT_NON] && ------------------ | | 574| 10.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2129:17): [True: 9.08k, False: 1.29k] ------------------ 2130| 9.08k| OneInput->nNumComponents[iINChI][TAUT_YES])) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 9.08k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2130:17): [True: 3.92k, False: 5.16k] ------------------ 2131| 3.92k| { 2132| 3.92k| int nPrevLen, nLen = 0; 2133| 3.92k| j = TAUT_YES; ------------------ | | 575| 3.92k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2134| 3.92k| nPrevLen = OneInput->nNumComponents[iINChI][j]; 2135| 117k| for (k = 0; k < nPrevLen; k++) ------------------ | Branch (2135:25): [True: 113k, False: 3.92k] ------------------ 2136| 113k| { 2137| 113k| nLen += !OneInput->pInpInChI[iINChI][j][k].bDeleted; 2138| 113k| } 2139| 3.92k| if (nLen == nPrevLen) ------------------ | Branch (2139:17): [True: 3.91k, False: 7] ------------------ 2140| 3.91k| { 2141| | /* add one more component */ 2142| 3.91k| INChI* pInChI = (INChI*)inchi_calloc((long long)nLen + 1, sizeof(*pInChI)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 3.91k|#define inchi_calloc calloc ------------------ 2143| 3.91k| if (!pInChI) ------------------ | Branch (2143:21): [True: 0, False: 3.91k] ------------------ 2144| 0| { 2145| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2146| 0| goto exit_error; 2147| 0| } 2148| 3.91k| memcpy(pInChI, OneInput->pInpInChI[iINChI][j], nLen * sizeof(*pInChI)); 2149| 3.91k| inchi_free(OneInput->pInpInChI[iINChI][j]); ------------------ | | 1152| 3.91k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 3.91k, False: 0] | | | Branch (1152:50): [Folded, False: 3.91k] | | ------------------ ------------------ 2150| 3.91k| OneInput->pInpInChI[iINChI][j] = pInChI; 2151| 3.91k| } 2152| 3.92k| OneInput->nNumComponents[iINChI][j] = nLen + 1; 2153| | 2154| 3.93k| for (k = nLen; k < nPrevLen; k++) ------------------ | Branch (2154:28): [True: 7, False: 3.92k] ------------------ 2155| 7| { 2156| 7| Free_INChI_Members(&OneInput->pInpInChI[iINChI][j][k]); 2157| 7| memset(&OneInput->pInpInChI[iINChI][j][k], 0, sizeof(OneInput->pInpInChI[iINChI][j][k])); /* djb-rwth: memset_s C11/Annex K variant? */ 2158| 7| } 2159| | /* mark the last component as a proton */ 2160| 3.92k| if (0 > (ret2 = nFillOutProtonMobileH(OneInput->pInpInChI[iINChI][j] + nLen))) ------------------ | Branch (2160:17): [True: 0, False: 3.92k] ------------------ 2161| 0| { 2162| 0| goto exit_error; 2163| 0| } 2164| 3.92k| } 2165| 20.4k| INCHI_HEAPCHK 2166| | 2167| | /* remove unneeded Stereo and/or Fixed H */ 2168| 20.4k| if (!bReqStereo) ------------------ | Branch (2168:17): [True: 0, False: 20.4k] ------------------ 2169| 0| { 2170| 0| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2170:29): [True: 0, False: 0] ------------------ 2171| 0| { 2172| 0| for (k = 0; k < OneInput->nNumComponents[iINChI][j]; k++) ------------------ | Branch (2172:33): [True: 0, False: 0] ------------------ 2173| 0| { 2174| 0| if (OneInput->pInpInChI[iINChI][j][k].Stereo) ------------------ | Branch (2174:29): [True: 0, False: 0] ------------------ 2175| 0| { 2176| 0| Free_INChI_Stereo(OneInput->pInpInChI[iINChI][j][k].Stereo); 2177| 0| inchi_free(OneInput->pInpInChI[iINChI][j][k].Stereo); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2178| 0| OneInput->pInpInChI[iINChI][j][k].Stereo = NULL; 2179| 0| } 2180| 0| if (OneInput->pInpInChI[iINChI][j][k].StereoIsotopic) ------------------ | Branch (2180:29): [True: 0, False: 0] ------------------ 2181| 0| { 2182| 0| Free_INChI_Stereo(OneInput->pInpInChI[iINChI][j][k].StereoIsotopic); 2183| 0| inchi_free(OneInput->pInpInChI[iINChI][j][k].StereoIsotopic); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2184| 0| OneInput->pInpInChI[iINChI][j][k].StereoIsotopic = NULL; 2185| 0| } 2186| 0| INCHI_HEAPCHK 2187| 0| } 2188| 0| } 2189| 0| } 2190| | 2191| 20.4k| } 2192| | 2193| 10.2k| num_components[INCHI_BAS] = inchi_max(OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 570| 10.2k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ num_components[INCHI_BAS] = inchi_max(OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 138| 10.2k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 8.94k, False: 1.27k] | | ------------------ ------------------ 2194| 10.2k| OneInput->nNumComponents[INCHI_BAS][TAUT_NON]); 2195| 10.2k| num_components[INCHI_REC] = inchi_max(OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 571| 10.2k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ num_components[INCHI_REC] = inchi_max(OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 138| 10.2k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 31, False: 10.1k] | | ------------------ ------------------ 2196| 10.2k| OneInput->nNumComponents[INCHI_REC][TAUT_NON]); 2197| | 2198| 10.2k|exit_error: 2199| 10.2k| return ret2; 2200| 10.2k|} ichiread.c:GetInChINumH: 2244| 350k|{ 2245| 350k| int i, j, nNumTautGroups, iTautGroup, nTautGroupLen, lenTautomer; 2246| 350k| *nNumH = 0; 2247| 4.98M| for (i = 0; i < pInChI->nNumberOfAtoms; i++) ------------------ | Branch (2247:17): [True: 4.63M, False: 350k] ------------------ 2248| 4.63M| { 2249| 4.63M| *nNumH += (pInChI->nAtom[i] == EL_NUMBER_H); /* bridging H */ ------------------ | | 11| 4.63M|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 2250| 4.63M| *nNumH += pInChI->nNum_H[i]; 2251| 4.63M| } 2252| | /* earlier nNum_H_fixed[] should have been added to pInChI->nNum_H[] */ 2253| | /* 2254| | if ( pInChI->nNum_H_fixed ) { 2255| | for ( i = 0; i < pInChI->nNumberOfAtoms; i ++ ) { 2256| | *nNumH += pInChI->nNum_H_fixed[i]; 2257| | } 2258| | } 2259| | */ 2260| 350k| if (pInChI->lenTautomer > 3 && pInChI->nTautomer) ------------------ | Branch (2260:9): [True: 6.22k, False: 343k] | Branch (2260:36): [True: 6.22k, False: 0] ------------------ 2261| 6.22k| { 2262| 6.22k| lenTautomer = pInChI->lenTautomer; 2263| 6.22k| j = 0; 2264| 6.22k| nNumTautGroups = pInChI->nTautomer[j++]; 2265| 16.9k| for (iTautGroup = 0; j < lenTautomer && iTautGroup < nNumTautGroups; iTautGroup++, j += nTautGroupLen) ------------------ | Branch (2265:30): [True: 10.6k, False: 6.22k] | Branch (2265:49): [True: 10.6k, False: 0] ------------------ 2266| 10.6k| { 2267| 10.6k| nTautGroupLen = pInChI->nTautomer[j] + 1; 2268| 10.6k| *nNumH += pInChI->nTautomer[j + 1]; 2269| 10.6k| } 2270| 6.22k| if (iTautGroup != nNumTautGroups || j != lenTautomer) ------------------ | Branch (2270:13): [True: 0, False: 6.22k] | Branch (2270:45): [True: 0, False: 6.22k] ------------------ 2271| 0| { 2272| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2273| 0| } 2274| 6.22k| } 2275| 350k| if (pInChI->nNum_H_fixed && (pInChI->lenTautomer || pInChI->nTautomer)) ------------------ | Branch (2275:9): [True: 4.05k, False: 346k] | Branch (2275:34): [True: 0, False: 4.05k] | Branch (2275:57): [True: 0, False: 4.05k] ------------------ 2276| 0| { 2277| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2278| 0| } 2279| | 2280| 350k| return 0; 2281| 350k|} ichiread.c:GetInChIFormulaNumH: 2205| 72.5k|{ /* get number of H including bridging hydrogen atoms */ 2206| 72.5k| const char* p, * q; 2207| 72.5k| *nNumH = 0; 2208| 72.5k| if (pInChI->szHillFormula) ------------------ | Branch (2208:9): [True: 72.5k, False: 0] ------------------ 2209| 72.5k| { 2210| 78.8k| for (p = strchr(pInChI->szHillFormula, 'H'); p; p = strchr(p, 'H')) ------------------ | Branch (2210:54): [True: 6.29k, False: 72.5k] ------------------ 2211| 6.29k| { 2212| 6.29k| p++; 2213| 6.29k| if (!islower(UCINT * p)) ------------------ | Branch (2213:17): [True: 6.18k, False: 109] ------------------ 2214| 6.18k| { 2215| | /* found hydrogen in the formula */ 2216| 6.18k| if (isdigit(UCINT * p)) ------------------ | Branch (2216:21): [True: 652, False: 5.53k] ------------------ 2217| 652| { 2218| 652|#if ( CHECK_STRTOL_ATNUMB==1 ) 2219| 652| int delta = (int)inchi_strtol(p, &q, 10); 2220| 652| if (delta > MAX_ATOMS || delta < 0) ------------------ | | 15| 1.30k|#define MAX_ATOMS 32766 ------------------ | Branch (2220:25): [True: 0, False: 652] | Branch (2220:46): [True: 0, False: 652] ------------------ 2221| 0| { 2222| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 2223| 0| } 2224| 652| *nNumH += delta; 2225| |#else 2226| | * nNumH += (int)inchi_strtol(p, &q, 10); 2227| |#endif 2228| 652| p = q; 2229| 652| } 2230| 5.53k| else 2231| 5.53k| { 2232| 5.53k| *nNumH += 1; 2233| 5.53k| } 2234| 6.18k| } 2235| 6.29k| } 2236| 72.5k| } 2237| | 2238| 72.5k| return 0; 2239| 72.5k|} ichiread.c:GetInChIIsoH: 2286| 66.7k|{ 2287| 66.7k| int i; 2288| 266k| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 72| 266k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2288:17): [True: 200k, False: 66.7k] ------------------ 2289| 200k| { 2290| 200k| nNumIsotopicH[i] = 0; 2291| 200k| } 2292| 67.4k| for (i = 0; i < pInChI->nNumberOfIsotopicAtoms; i++) ------------------ | Branch (2292:17): [True: 752, False: 66.7k] ------------------ 2293| 752| { 2294| 752| if (pInChI->IsotopicAtom[i].nIsoDifference > 0 && ------------------ | Branch (2294:13): [True: 148, False: 604] ------------------ 2295| 148| pInChI->IsotopicAtom[i].nIsoDifference <= NUM_H_ISOTOPES) ------------------ | | 72| 148|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2295:13): [True: 135, False: 13] ------------------ 2296| 135| { 2297| 135| if (!pInChI->nAtom || ------------------ | Branch (2297:17): [True: 0, False: 135] ------------------ 2298| 135| !pInChI->IsotopicAtom[i].nAtomNumber || ------------------ | Branch (2298:17): [True: 0, False: 135] ------------------ 2299| 135| pInChI->IsotopicAtom[i].nAtomNumber > pInChI->nNumberOfAtoms) ------------------ | Branch (2299:17): [True: 0, False: 135] ------------------ 2300| 0| { 2301| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2302| 0| } 2303| 135| if (pInChI->nAtom[pInChI->IsotopicAtom[i].nAtomNumber - 1] == (AT_NUMB)EL_NUMBER_H) ------------------ | | 11| 135|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (2303:17): [True: 1, False: 134] ------------------ 2304| 1| { 2305| | /* isotopic H in connection table */ 2306| 1| nNumIsotopicH[pInChI->IsotopicAtom[i].nIsoDifference - 1]++; 2307| 1| } 2308| 135| } 2309| 752| nNumIsotopicH[0] += pInChI->IsotopicAtom[i].nNum_H; 2310| 752| nNumIsotopicH[1] += pInChI->IsotopicAtom[i].nNum_D; 2311| 752| nNumIsotopicH[2] += pInChI->IsotopicAtom[i].nNum_T; 2312| 752| } 2313| | 2314| 66.7k| return 0; 2315| 66.7k|} ichiread.c:ReadInChILine: 5019| 12.5k|{ 5020| 12.5k| int c, ret = RI_ERR_ALLOC, len; /* djb-rwth: removing redundant variables */ ------------------ | | 15| 12.5k|#define RI_ERR_ALLOC (-1) ------------------ 5021| 12.5k| int bMobileH = TAUT_YES, bReconn = INCHI_BAS; ------------------ | | 575| 12.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int bMobileH = TAUT_YES, bReconn = INCHI_BAS; ------------------ | | 570| 12.5k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 5022| 12.5k| const char szToken[] = INCHI_TOKEN; ------------------ | | 277| 12.5k|#define INCHI_TOKEN "/\n\r\t\\" ------------------ 5023| 12.5k| char* p; 5024| 12.5k| int state = -1, prev_state = -1; 5025| 12.5k| int bAbc = -1; /* -1=> undefined, 0=> decimal, 1=> abc (compressed) */ 5026| | 5027| 12.5k| const int len_version_prefix = (int)(sizeof("InChI=1") - 1); 5028| 12.5k| size_t k = 0; 5029| 12.5k| unsigned char let1 = 0, let2 = 0; 5030| 12.5k| const char a2p[] = "ABCDEFGHIJKLMNOP"; 5031| | 5032| 12.5k| int na_total = 0; /* whole struct, without explH */ 5033| 12.5k| int nb_total = 0; /* whole struct, without explH */ 5034| 12.5k|#if ( DISABLE_READ_COMPRESSED_INCHI==1 ) 5035| 12.5k| bAbc = 0; 5036| | /* We do not support compressed InChI explicitly */ 5037| | /* Parsing compressed InChI easily fails on fake/fuzzing inputs */ 5038| 12.5k|#endif 5039| | /* memset( pLine, 0, sizeof( pLine[0] ) ); */ 5040| 12.5k| * pState = 0; 5041| | 5042| 12.5k|next_line: 5043| 12.5k| INCHI_HEAPCHK 5044| | /* Got "InChI=1/" */ 5045| 12.5k| if (pLine->len) ------------------ | Branch (5045:13): [True: 0, False: 12.5k] ------------------ 5046| 0| { 5047| 0| c = pLine->c; 5048| 0| } 5049| 12.5k| else 5050| 12.5k| { 5051| 12.5k| INCHI_HEAPCHK 5052| 12.5k| c = nGetInChISegment(pInp, pLine, szToken); 5053| 12.5k| INCHI_HEAPCHK 5054| 12.5k| } 5055| 12.5k| if (pLine->str && (c == RI_ERR_EOF && !pLine->len && !pLine->str[0])) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 19| 25.1k|#define RI_ERR_EOF (0) ------------------ | Branch (5055:9): [True: 12.5k, False: 0] | Branch (5055:24): [True: 0, False: 12.5k] | Branch (5055:43): [True: 0, False: 0] | Branch (5055:58): [True: 0, False: 0] ------------------ 5056| 0| { 5057| 0| ret = c; 5058| 0| goto exit_function; 5059| 0| } 5060| 12.5k| INCHI_HEAPCHK 5061| | 5062| 12.5k| if (pLine->str && (pLine->len == 0 || (c != SEG_END && c != RI_ERR_EOF) || !(p = strstr(pLine->str, "InChI=1")))) /* djb-rwth: fixing a NULL pointer dereference; addressing LLVM warning; ignoring LLVM warning: value used */ ------------------ | | 273| 25.1k|#define SEG_END '/' ------------------ if (pLine->str && (pLine->len == 0 || (c != SEG_END && c != RI_ERR_EOF) || !(p = strstr(pLine->str, "InChI=1")))) /* djb-rwth: fixing a NULL pointer dereference; addressing LLVM warning; ignoring LLVM warning: value used */ ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ | Branch (5062:13): [True: 12.5k, False: 0] | Branch (5062:28): [True: 0, False: 12.5k] | Branch (5062:48): [True: 0, False: 12.5k] | Branch (5062:64): [True: 0, False: 0] | Branch (5062:84): [True: 0, False: 12.5k] ------------------ 5063| 0| { 5064| 0| if (pLine->str && pLine->str == strstr(pLine->str, "Structure")) ------------------ | Branch (5064:17): [True: 0, False: 0] | Branch (5064:31): [True: 0, False: 0] ------------------ 5065| 0| { 5066| 0| if (*pStr) ------------------ | Branch (5066:21): [True: 0, False: 0] ------------------ 5067| 0| { 5068| 0| INCHI_HEAPCHK 5069| 0| inchi_free(*pStr); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5070| 0| } 5071| 0| *pStr = pLine->str; 5072| | /* bypass to the end of the 'Structure nnn' line */ 5073| 0| memset(pLine, 0, sizeof(pLine[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 5074| 0| while (c && !INCHI_INP_EOL(c)) ------------------ | | 275| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 0, False: 0] | | | Branch (275:40): [True: 0, False: 0] | | | Branch (275:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (5074:24): [True: 0, False: 0] ------------------ 5075| 0| { 5076| 0| c = getInChIChar(pInp); 5077| 0| } 5078| 0| goto next_line; 5079| 0| } 5080| | /* bypass to the end of unrecognized line */ 5081| 0| while (c != RI_ERR_EOF && !INCHI_INP_EOL(c)) ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ while (c != RI_ERR_EOF && !INCHI_INP_EOL(c)) ------------------ | | 275| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 0, False: 0] | | | Branch (275:40): [True: 0, False: 0] | | | Branch (275:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (5081:20): [True: 0, False: 0] ------------------ 5082| 0| { 5083| 0| c = getInChIChar(pInp); 5084| 0| } 5085| 0| pLine->len = 0; 5086| 0| INCHI_HEAPCHK 5087| 0| goto next_line; 5088| 0| } 5089| | 5090| | 5091| | /* 5092| | * Preserve the calculation-class designator and Molecular Inorganics 5093| | * subversion designator from the input prefix. Historical InChI=1/... 5094| | * remains accepted as non-standard input. 5095| | */ 5096| 12.5k| *bStdFormat = INCHI_INPUT_CLASS_NONSTANDARD; ------------------ | | 76| 12.5k|#define INCHI_INPUT_CLASS_NONSTANDARD 0x00 ------------------ 5097| | 5098| 12.5k| if (pLine->str && ------------------ | Branch (5098:9): [True: 12.5k, False: 0] ------------------ 5099| 12.5k| (pLine->len == len_version_prefix + 1 || ------------------ | Branch (5099:10): [True: 118, False: 12.4k] ------------------ 5100| 12.4k| (pLine->len == len_version_prefix + 2 && ------------------ | Branch (5100:11): [True: 0, False: 12.4k] ------------------ 5101| 0| pLine->str[len_version_prefix + 1] == 'B'))) ------------------ | Branch (5101:11): [True: 0, False: 0] ------------------ 5102| 118| { 5103| 118| switch (pLine->str[len_version_prefix]) ------------------ | Branch (5103:17): [True: 118, False: 0] ------------------ 5104| 118| { 5105| 70| case 'S': ------------------ | Branch (5105:9): [True: 70, False: 48] ------------------ 5106| 70| *bStdFormat = INCHI_INPUT_CLASS_STANDARD; ------------------ | | 77| 70|#define INCHI_INPUT_CLASS_STANDARD 0x01 ------------------ 5107| 70| break; 5108| | 5109| 48| case 'B': ------------------ | Branch (5109:9): [True: 48, False: 70] ------------------ 5110| 48| *bStdFormat = INCHI_INPUT_CLASS_BETA; ------------------ | | 78| 48|#define INCHI_INPUT_CLASS_BETA 0x02 ------------------ 5111| 48| break; 5112| | 5113| 0| case 'N': ------------------ | Branch (5113:9): [True: 0, False: 118] ------------------ 5114| 0| *bStdFormat = INCHI_INPUT_CLASS_NONSTANDARD; ------------------ | | 76| 0|#define INCHI_INPUT_CLASS_NONSTANDARD 0x00 ------------------ 5115| 0| break; 5116| 118| } 5117| | 5118| 118| if (pLine->len == len_version_prefix + 2 && ------------------ | Branch (5118:13): [True: 0, False: 118] ------------------ 5119| 0| strchr("SBN", pLine->str[len_version_prefix])) ------------------ | Branch (5119:13): [True: 0, False: 0] ------------------ 5120| 0| { 5121| 0| *bStdFormat |= INCHI_INPUT_MI_MARKER; ------------------ | | 79| 0|#define INCHI_INPUT_MI_MARKER 0x04 ------------------ 5122| 0| } 5123| 118| } 5124| | 5125| 12.5k| state = IST_MOBILE_H_FORMULA; 5126| 12.5k| ret = 1; /* means read the next segment */ 5127| 12.5k| do 5128| 110k| { 5129| | /* read the next segment up to the '/' */ 5130| 110k| INCHI_HEAPCHK 5131| 110k| if (ret < 0) ------------------ | Branch (5131:17): [True: 2.21k, False: 108k] ------------------ 5132| 2.21k| { 5133| 2.21k| *pState = prev_state; 5134| 2.21k| break; 5135| 2.21k| } 5136| 108k| prev_state = state + (bReconn ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 342| 1.88k|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5136:31): [True: 1.88k, False: 106k] ------------------ 5137| 108k| if (0 < ret) ------------------ | Branch (5137:13): [True: 46.9k, False: 61.3k] ------------------ 5138| 46.9k| { 5139| | /* read next segment */ 5140| 46.9k| if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 19| 93.9k|#define RI_ERR_EOF (0) ------------------ if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 273| 37.6k|#define SEG_END '/' ------------------ | Branch (5140:17): [True: 37.6k, False: 9.30k] | Branch (5140:36): [True: 314, False: 37.3k] ------------------ 5141| 314| { 5142| | /* abnormal reading result; should not happen */ 5143| | /* unless we got backslash-SaveOpt */ 5144| 314| if (c == '\\') ------------------ | Branch (5144:21): [True: 12, False: 302] ------------------ 5145| 12| { 5146| | /* May be SaveOpt */ 5147| 12| *input_has_save_opt = 1; 5148| 12| } 5149| 314| k = 0; 5150| 534| while (c != RI_ERR_EOF && !INCHI_INP_EOL(c)) ------------------ | | 19| 1.06k|#define RI_ERR_EOF (0) ------------------ while (c != RI_ERR_EOF && !INCHI_INP_EOL(c)) ------------------ | | 275| 522|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 198, False: 324] | | | Branch (275:40): [True: 52, False: 272] | | | Branch (275:53): [True: 52, False: 220] | | ------------------ ------------------ | Branch (5150:24): [True: 522, False: 12] ------------------ 5151| 220| { 5152| | /* bypass to the end of line or file */ 5153| 220| c = getInChIChar(pInp); 5154| 220| k++; 5155| 220| if (k == 1) ------------------ | Branch (5155:25): [True: 12, False: 208] ------------------ 5156| 12| { 5157| 12| let1 = c; 5158| 12| } 5159| 208| else 5160| 208| { 5161| 208| if (k == 2) ------------------ | Branch (5161:29): [True: 12, False: 196] ------------------ 5162| 12| { 5163| 12| let2 = c; 5164| 12| } 5165| 208| } 5166| 220| } 5167| 314| if (k != 3) ------------------ | Branch (5167:21): [True: 310, False: 4] ------------------ 5168| 310| { 5169| | /* not a valid SaveOpt which must be of two chars */ 5170| 310| *input_has_save_opt = 0; 5171| | /* djb-rwth: removing redundant code */ 5172| 310| } 5173| 4| else 5174| 4| { 5175| | /* may be SaveOpt - analyze the content */ 5176| 4| if ((let2 >= 'A') && (let2 <= 'D')) /* letter-2 OK */ ------------------ | Branch (5176:25): [True: 4, False: 0] | Branch (5176:42): [True: 4, False: 0] ------------------ 5177| 4| { 5178| 4| *input_has_save_opt = 0; 5179| 4| *input_save_opt_bits = 0; 5180| 49| for (k = 0; k < 16; k++) ------------------ | Branch (5180:37): [True: 48, False: 1] ------------------ 5181| 48| { 5182| 48| if (a2p[k] == let1) /* letter-1 OK */ ------------------ | Branch (5182:33): [True: 3, False: 45] ------------------ 5183| 3| { 5184| 3| *input_save_opt_bits = (unsigned char)k; 5185| 3| *input_has_save_opt = 1; 5186| 3| break; 5187| 3| } 5188| 48| } 5189| 4| if (*input_has_save_opt) ------------------ | Branch (5189:29): [True: 3, False: 1] ------------------ 5190| 3| { 5191| 3| if (let2 == 'B' || let2 == 'D') ------------------ | Branch (5191:33): [True: 0, False: 3] | Branch (5191:48): [True: 2, False: 1] ------------------ 5192| 2| { 5193| 2| *input_save_opt_bits |= SAVE_OPT_15T; ------------------ | | 160| 2|#define SAVE_OPT_15T 0x0020 ------------------ 5194| 2| } 5195| 3| if (let2 == 'C' || let2 == 'D') ------------------ | Branch (5195:33): [True: 1, False: 2] | Branch (5195:48): [True: 2, False: 0] ------------------ 5196| 3| { 5197| 3| *input_save_opt_bits |= SAVE_OPT_KET; ------------------ | | 159| 3|#define SAVE_OPT_KET 0x0010 ------------------ 5198| 3| } 5199| 3| } 5200| 4| } 5201| 4| } 5202| | 5203| 314| ret = (c == RI_ERR_EOF) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 19| 314|#define RI_ERR_EOF (0) ------------------ ret = (c == RI_ERR_EOF) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 19| 12|#define RI_ERR_EOF (0) ------------------ ret = (c == RI_ERR_EOF) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 18| 616|#define RI_ERR_EOL (-4) ------------------ | Branch (5203:23): [True: 12, False: 302] ------------------ 5204| 314| pLine->len = 0; 5205| 314| pLine->c = ret; 5206| 314| break; /* exit */ 5207| 314| } 5208| 46.6k| if (c == RI_ERR_EOF) ------------------ | | 19| 46.6k|#define RI_ERR_EOF (0) ------------------ | Branch (5208:17): [True: 9.30k, False: 37.3k] ------------------ 5209| 9.30k| { 5210| 9.30k| ret = RI_ERR_EOF; /* end of line */ ------------------ | | 19| 9.30k|#define RI_ERR_EOF (0) ------------------ 5211| 9.30k| break; 5212| 9.30k| } 5213| 37.3k| if (c == SEG_END) ------------------ | | 273| 37.3k|#define SEG_END '/' ------------------ | Branch (5213:17): [True: 37.3k, False: 0] ------------------ 5214| 37.3k| { 5215| 37.3k| c = nGetInChISegment(pInp, pLine, szToken); 5216| 37.3k| } 5217| 37.3k| if (c < 0) ------------------ | Branch (5217:17): [True: 0, False: 37.3k] ------------------ 5218| 0| { 5219| 0| goto exit_error; /* error */ 5220| 0| } 5221| 37.3k| if (!pLine->len) ------------------ | Branch (5221:17): [True: 731, False: 36.6k] ------------------ 5222| 731| { 5223| 731| ret = RI_ERR_EOL; /* end of line */ ------------------ | | 18| 731|#define RI_ERR_EOL (-4) ------------------ 5224| 731| break; 5225| 731| } 5226| | /* djb-rwth: removing redundant code */ 5227| | 5228| | /* 5229| | if ( fst == 'z' ) 5230| | { 5231| | ret = RI_ERR_EOL; 5232| | break; 5233| | }*/ 5234| 37.3k| } 5235| | /* process the seqment */ 5236| 97.9k| switch (state) ------------------ | Branch (5236:17): [True: 97.9k, False: 0] ------------------ 5237| 97.9k| { 5238| | /* Mobile H, M */ /* / */ 5239| 12.6k| case IST_MOBILE_H_FORMULA: ------------------ | Branch (5239:9): [True: 12.6k, False: 85.3k] ------------------ 5240| 12.6k| bMobileH = TAUT_YES; ------------------ | | 575| 12.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5241| 12.6k|#if ( FIX_GAF_2019_2==1 ) 5242| | /* hack: pass state in na_total (will be updated in ParseSegmentFormula anyway) */ 5243| 12.6k| na_total = state; 5244| 12.6k|#endif 5245| 12.6k| ret = ParseSegmentFormula(pLine->str, bMobileH, pInpInChI[bReconn], 5246| 12.6k| nNumComponents[bReconn], &na_total); 5247| 12.6k| state = IST_MOBILE_H_CONNECTIONS; 5248| 12.6k| break; 5249| 12.3k| case IST_MOBILE_H_CONNECTIONS: /* /c */ ------------------ | Branch (5249:9): [True: 12.3k, False: 85.6k] ------------------ 5250| 12.3k| ret = ParseSegmentConnections(pLine->str, bMobileH, &pInpInChI[bReconn][bMobileH], 5251| 12.3k| &nNumComponents[bReconn][bMobileH], &bAbc, &nb_total); 5252| 12.3k| state = IST_MOBILE_H; 5253| 12.3k| break; 5254| 9.03k| case IST_MOBILE_H: /* /h */ ------------------ | Branch (5254:9): [True: 9.03k, False: 88.9k] ------------------ 5255| 9.03k| ret = ParseSegmentMobileH(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], &bAbc); 5256| 9.03k| state = IST_MOBILE_H_CHARGE; 5257| 9.03k| break; 5258| 7.46k| case IST_MOBILE_H_CHARGE: /* /q */ ------------------ | Branch (5258:9): [True: 7.46k, False: 90.5k] ------------------ 5259| 7.46k| ret = ParseSegmentCharge(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn]); 5260| 7.46k| state = IST_MOBILE_H_PROTONS; 5261| 7.46k| break; 5262| 6.94k| case IST_MOBILE_H_PROTONS: /* /p */ ------------------ | Branch (5262:9): [True: 6.94k, False: 91.0k] ------------------ 5263| 6.94k| ret = ParseSegmentProtons(pLine->str, bMobileH, nNumProtons[bReconn], nNumComponents[bReconn]); 5264| 6.94k| state = IST_MOBILE_H_POLYMER; 5265| 6.94k| break; 5266| 6.74k| case IST_MOBILE_H_POLYMER: /* /z */ ------------------ | Branch (5266:9): [True: 6.74k, False: 91.2k] ------------------ 5267| 6.74k| ret = ParseSegmentPolymer(pLine->str, bMobileH, 5268| 6.74k| nNumProtons[bReconn], nNumComponents[bReconn], 5269| 6.74k| na_total, nb_total, bInchi2Struct, ppPolymer, ppV3000); 5270| 6.74k| if (*ppPolymer) ------------------ | Branch (5270:17): [True: 838, False: 5.90k] ------------------ 5271| 838| (*ppPolymer)->is_in_reconn = bReconn; 5272| 6.74k| state = IST_MOBILE_H_SP2; 5273| 6.74k| break; 5274| 5.98k| case IST_MOBILE_H_SP2: /* /b */ ------------------ | Branch (5274:9): [True: 5.98k, False: 92.0k] ------------------ 5275| 5.98k| ret = ParseSegmentSp2(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5276| 5.98k| state = IST_MOBILE_H_SP3; 5277| 5.98k| break; 5278| 5.30k| case IST_MOBILE_H_SP3: /* t */ ------------------ | Branch (5278:9): [True: 5.30k, False: 92.6k] ------------------ 5279| 5.30k| ret = ParseSegmentSp3(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5280| 5.30k| state = IST_MOBILE_H_SP3_M; 5281| 5.30k| break; 5282| 4.77k| case IST_MOBILE_H_SP3_M: /* /m */ ------------------ | Branch (5282:9): [True: 4.77k, False: 93.2k] ------------------ 5283| 4.77k| ret = ParseSegmentSp3m(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 5284| 4.77k| state = IST_MOBILE_H_SP3_S; 5285| 4.77k| break; 5286| 4.73k| case IST_MOBILE_H_SP3_S: /* /s */ ------------------ | Branch (5286:9): [True: 4.73k, False: 93.2k] ------------------ 5287| 4.73k| ret = ParseSegmentSp3s(pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state); 5288| 4.73k| state = IST_MOBILE_H_ISO_LAYER_FORK; 5289| 4.73k| break; 5290| 4.68k| case IST_MOBILE_H_ISO_LAYER_FORK: ------------------ | Branch (5290:9): [True: 4.68k, False: 93.2k] ------------------ 5291| | /* find layer type after M */ 5292| 4.68k| ret = 0; 5293| 4.68k| switch (pLine->str[0]) 5294| 4.68k| { 5295| 1.38k| case 'i': ------------------ | Branch (5295:13): [True: 1.38k, False: 3.30k] ------------------ 5296| 1.38k| state = IST_MOBILE_H_ISO_ATOMS; /* MI */ 5297| 1.38k| break; 5298| 2.87k| case 'f': ------------------ | Branch (5298:13): [True: 2.87k, False: 1.81k] ------------------ 5299| 2.87k| state = IST_FIXED_H_FORMULA; /* F */ 5300| 2.87k| break; 5301| 415| case 'r': ------------------ | Branch (5301:13): [True: 415, False: 4.27k] ------------------ 5302| 415| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5303| 415| break; 5304| 16| default: ------------------ | Branch (5304:13): [True: 16, False: 4.67k] ------------------ 5305| 16| ret = RI_ERR_SYNTAX; ------------------ | | 16| 16|#define RI_ERR_SYNTAX (-2) ------------------ 5306| 4.68k| } 5307| 4.68k| if (INCHI_INP_EOL(c) && ret == 0 && !pLine->str[1]) ------------------ | | 275| 9.37k|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 41, False: 4.64k] | | | Branch (275:40): [True: 2, False: 4.64k] | | | Branch (275:53): [True: 8, False: 4.63k] | | ------------------ ------------------ | Branch (5307:37): [True: 49, False: 2] | Branch (5307:49): [True: 0, False: 49] ------------------ 5308| 0| { 5309| 0| prev_state = state + (bReconn ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 342| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5309:39): [True: 0, False: 0] ------------------ 5310| 0| ret = RI_ERR_SYNTAX; /* empty layer /i or /f or /r at the end of InChI line */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5311| 0| } 5312| 4.68k| else 5313| 4.68k| { 5314| 4.68k| if (!ret && state != IST_MOBILE_H_ISO_ATOMS) ------------------ | Branch (5314:21): [True: 4.67k, False: 16] | Branch (5314:29): [True: 3.28k, False: 1.38k] ------------------ 5315| 3.28k| { 5316| 3.28k| len = (int)strlen(pLine->str); 5317| 3.28k| if (len > 1) ------------------ | Branch (5317:25): [True: 2.50k, False: 778] ------------------ 5318| 2.50k| { 5319| 2.50k| memmove(pLine->str, pLine->str + 1, len); 5320| 2.50k| } 5321| 778| else 5322| 778| { 5323| 778| ret = 1; /* read the next segment */ 5324| 778| } 5325| 3.28k| } 5326| 4.68k| } 5327| 4.68k| break; 5328| | /* Mobile H, isotopic, MI */ 5329| 1.38k| case IST_MOBILE_H_ISO_ATOMS: /* i */ ------------------ | Branch (5329:9): [True: 1.38k, False: 96.5k] ------------------ 5330| 1.38k| ret = ParseSegmentIsoAtoms(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5331| 1.38k| state = IST_MOBILE_H_ISO_EXCH_H; 5332| 1.38k| break; 5333| 617| case IST_MOBILE_H_ISO_EXCH_H: /* /i/h */ ------------------ | Branch (5333:9): [True: 617, False: 97.3k] ------------------ 5334| 617| ret = ParseSegmentIsoExchgH(pLine->str, bMobileH, nNumProtons[bReconn], nNumComponents[bReconn], state, &bAbc); 5335| 617| state = IST_MOBILE_H_ISO_SP2; 5336| 617| break; 5337| 504| case IST_MOBILE_H_ISO_SP2: /* /i/b */ ------------------ | Branch (5337:9): [True: 504, False: 97.4k] ------------------ 5338| 504| ret = ParseSegmentSp2(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5339| 504| state = IST_MOBILE_H_ISO_SP3; 5340| 504| break; 5341| 413| case IST_MOBILE_H_ISO_SP3: /* /i/t */ ------------------ | Branch (5341:9): [True: 413, False: 97.5k] ------------------ 5342| 413| ret = ParseSegmentSp3(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5343| 413| state = IST_MOBILE_H_ISO_SP3_M; 5344| 413| break; 5345| 303| case IST_MOBILE_H_ISO_SP3_M: /* /i/m */ ------------------ | Branch (5345:9): [True: 303, False: 97.6k] ------------------ 5346| 303| ret = ParseSegmentSp3m(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 5347| 303| state = IST_MOBILE_H_ISO_SP3_S; 5348| 303| break; 5349| 295| case IST_MOBILE_H_ISO_SP3_S: /* /i/s */ ------------------ | Branch (5349:9): [True: 295, False: 97.6k] ------------------ 5350| 295| ret = ParseSegmentSp3s(pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state); 5351| 295| state = IST_FIXED_H_LAYER_FORK; 5352| 295| break; 5353| 287| case IST_FIXED_H_LAYER_FORK: ------------------ | Branch (5353:9): [True: 287, False: 97.6k] ------------------ 5354| | /* find layer type after MI */ 5355| 287| ret = 0; 5356| 287| switch (pLine->str[0]) 5357| 287| { 5358| 251| case 'f': ------------------ | Branch (5358:13): [True: 251, False: 36] ------------------ 5359| 251| state = IST_FIXED_H_FORMULA; /* F */ 5360| 251| break; 5361| 20| case 'r': ------------------ | Branch (5361:13): [True: 20, False: 267] ------------------ 5362| 20| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5363| 20| break; 5364| 16| default: ------------------ | Branch (5364:13): [True: 16, False: 271] ------------------ 5365| 16| ret = RI_ERR_SYNTAX; ------------------ | | 16| 16|#define RI_ERR_SYNTAX (-2) ------------------ 5366| 287| } 5367| 287| if (INCHI_INP_EOL(c) && ret == 0 && !pLine->str[1]) ------------------ | | 275| 574|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 6, False: 281] | | | Branch (275:40): [True: 1, False: 280] | | | Branch (275:53): [True: 2, False: 278] | | ------------------ ------------------ | Branch (5367:37): [True: 7, False: 2] | Branch (5367:49): [True: 0, False: 7] ------------------ 5368| 0| { 5369| 0| prev_state = state + (bReconn ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 342| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5369:39): [True: 0, False: 0] ------------------ 5370| 0| ret = RI_ERR_SYNTAX; /* empty layer /f or /r at the end of InChI line */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5371| 0| } 5372| 287| else 5373| 287| { 5374| 287| if (!ret) ------------------ | Branch (5374:21): [True: 271, False: 16] ------------------ 5375| 271| { 5376| 271| len = (int)strlen(pLine->str); 5377| 271| if (len > 1) ------------------ | Branch (5377:25): [True: 206, False: 65] ------------------ 5378| 206| { 5379| 206| memmove(pLine->str, pLine->str + 1, len); 5380| 206| } 5381| 65| else 5382| 65| { 5383| 65| ret = 1; /* read the next segment */ 5384| 65| } 5385| 271| } 5386| 287| } 5387| 287| break; 5388| | 5389| | /* Fixed H, F */ 5390| 3.03k| case IST_FIXED_H_FORMULA: ------------------ | Branch (5390:9): [True: 3.03k, False: 94.9k] ------------------ 5391| 3.03k| bMobileH = TAUT_NON; ------------------ | | 574| 3.03k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5392| 3.03k|#if ( FIX_GAF_2019_2==1 ) 5393| | /* hack: pass state in na_total (will be updated in ParseSegmentFormula anyway) */ 5394| 3.03k| na_total = state; 5395| 3.03k|#endif 5396| 3.03k| ret = ParseSegmentFormula(pLine->str, bMobileH, pInpInChI[bReconn], 5397| 3.03k| nNumComponents[bReconn], &na_total); 5398| 3.03k| state = IST_FIXED_H; 5399| 3.03k| break; 5400| 2.46k| case IST_FIXED_H: /* /f/h */ ------------------ | Branch (5400:9): [True: 2.46k, False: 95.5k] ------------------ 5401| 2.46k| ret = ParseSegmentMobileH(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], &bAbc); 5402| 2.46k| state = IST_FIXED_H_CHARGE; 5403| 2.46k| break; 5404| 1.16k| case IST_FIXED_H_CHARGE: /* /f/q */ ------------------ | Branch (5404:9): [True: 1.16k, False: 96.8k] ------------------ 5405| 1.16k| ret = ParseSegmentCharge(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn]); 5406| 1.16k| state = IST_FIXED_H_SP2; 5407| 1.16k| break; 5408| 1.14k| case IST_FIXED_H_SP2: /* /f/b */ ------------------ | Branch (5408:9): [True: 1.14k, False: 96.8k] ------------------ 5409| 1.14k| ret = ParseSegmentSp2(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5410| 1.14k| state = IST_FIXED_H_SP3; 5411| 1.14k| break; 5412| 932| case IST_FIXED_H_SP3: /* /f/t */ ------------------ | Branch (5412:9): [True: 932, False: 97.0k] ------------------ 5413| 932| ret = ParseSegmentSp3(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5414| 932| state = IST_FIXED_H_SP3_M; 5415| 932| break; 5416| 750| case IST_FIXED_H_SP3_M: /* /f/m */ ------------------ | Branch (5416:9): [True: 750, False: 97.2k] ------------------ 5417| 750| ret = ParseSegmentSp3m(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 5418| 750| state = IST_FIXED_H_SP3_S; 5419| 750| break; 5420| 723| case IST_FIXED_H_SP3_S: /* /f/s */ ------------------ | Branch (5420:9): [True: 723, False: 97.2k] ------------------ 5421| 723| ret = ParseSegmentSp3s(pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state); 5422| 723| state = IST_FIXED_H_PERMUTATION; 5423| 723| break; 5424| 633| case IST_FIXED_H_PERMUTATION: /* /f/o */ ------------------ | Branch (5424:9): [True: 633, False: 97.3k] ------------------ 5425| 633| ret = ParseSegmentPerm(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5426| 633| state = IST_FIXED_H_ISO_LAYER_FORK; 5427| 633| break; 5428| 547| case IST_FIXED_H_ISO_LAYER_FORK: ------------------ | Branch (5428:9): [True: 547, False: 97.4k] ------------------ 5429| | /* find layer type after M */ 5430| 547| ret = 0; 5431| 547| switch (pLine->str[0]) 5432| 547| { 5433| 435| case 'i': ------------------ | Branch (5433:13): [True: 435, False: 112] ------------------ 5434| 435| state = IST_FIXED_H_ISO_ATOMS; /* FI */ 5435| 435| break; 5436| 79| case 'r': ------------------ | Branch (5436:13): [True: 79, False: 468] ------------------ 5437| 79| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5438| 79| break; 5439| 33| default: ------------------ | Branch (5439:13): [True: 33, False: 514] ------------------ 5440| 33| ret = RI_ERR_SYNTAX; ------------------ | | 16| 33|#define RI_ERR_SYNTAX (-2) ------------------ 5441| 547| } 5442| 547| if (INCHI_INP_EOL(c) && ret == 0 && !pLine->str[1]) ------------------ | | 275| 1.09k|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 10, False: 537] | | | Branch (275:40): [True: 3, False: 534] | | | Branch (275:53): [True: 3, False: 531] | | ------------------ ------------------ | Branch (5442:37): [True: 4, False: 12] | Branch (5442:49): [True: 0, False: 4] ------------------ 5443| 0| { 5444| 0| prev_state = state + (bReconn ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 342| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5444:39): [True: 0, False: 0] ------------------ 5445| 0| ret = RI_ERR_SYNTAX; /* empty layer /i or /r at the end of InChI line */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5446| 0| } 5447| 547| else 5448| 547| { 5449| 547| if (!ret && state != IST_FIXED_H_ISO_ATOMS) ------------------ | Branch (5449:21): [True: 514, False: 33] | Branch (5449:29): [True: 79, False: 435] ------------------ 5450| 79| { 5451| 79| len = (int)strlen(pLine->str); 5452| 79| if (len > 1) ------------------ | Branch (5452:25): [True: 33, False: 46] ------------------ 5453| 33| { 5454| 33| memmove(pLine->str, pLine->str + 1, len); 5455| 33| } 5456| 46| else 5457| 46| { 5458| 46| ret = 1; /* read the next segment */ 5459| 46| } 5460| 79| } 5461| 547| } 5462| 547| break; 5463| | 5464| | /* Fixed H, isotopic, FI */ 5465| 435| case IST_FIXED_H_ISO_ATOMS: /* /f/i */ ------------------ | Branch (5465:9): [True: 435, False: 97.5k] ------------------ 5466| 435| ret = ParseSegmentIsoAtoms(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5467| 435| state = IST_FIXED_H_ISO_SP2; 5468| 435| break; 5469| 272| case IST_FIXED_H_ISO_SP2: /* /f/i/b */ ------------------ | Branch (5469:9): [True: 272, False: 97.7k] ------------------ 5470| 272| ret = ParseSegmentSp2(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5471| 272| state = IST_FIXED_H_ISO_SP3; 5472| 272| break; 5473| 257| case IST_FIXED_H_ISO_SP3: /* /f/i/t */ ------------------ | Branch (5473:9): [True: 257, False: 97.7k] ------------------ 5474| 257| ret = ParseSegmentSp3(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5475| 257| state = IST_FIXED_H_ISO_SP3_M; 5476| 257| break; 5477| 232| case IST_FIXED_H_ISO_SP3_M: /* /f/i/m */ ------------------ | Branch (5477:9): [True: 232, False: 97.7k] ------------------ 5478| 232| ret = ParseSegmentSp3m(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state); 5479| 232| state = IST_FIXED_H_ISO_SP3_S; 5480| 232| break; 5481| 211| case IST_FIXED_H_ISO_SP3_S: /* /f/i/s */ ------------------ | Branch (5481:9): [True: 211, False: 97.7k] ------------------ 5482| 211| ret = ParseSegmentSp3s(pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state); 5483| 211| state = IST_FIXED_H_ISO_PERMUTATION; 5484| 211| break; 5485| 184| case IST_FIXED_H_ISO_PERMUTATION: /* /f/i/o */ ------------------ | Branch (5485:9): [True: 184, False: 97.8k] ------------------ 5486| 184| ret = ParseSegmentPerm(pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc); 5487| 184| state = IST_RECONNECTED_LAYER_FORK; 5488| 184| break; 5489| 178| case IST_RECONNECTED_LAYER_FORK: ------------------ | Branch (5489:9): [True: 178, False: 97.8k] ------------------ 5490| | /* find layer type after FI */ 5491| 178| ret = 0; 5492| 178| switch (pLine->str[0]) 5493| 178| { 5494| 150| case 'r': ------------------ | Branch (5494:13): [True: 150, False: 28] ------------------ 5495| 150| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5496| 150| break; 5497| 28| default: ------------------ | Branch (5497:13): [True: 28, False: 150] ------------------ 5498| 28| ret = RI_ERR_SYNTAX; ------------------ | | 16| 28|#define RI_ERR_SYNTAX (-2) ------------------ 5499| 178| } 5500| 178| if (INCHI_INP_EOL(c) && ret == 0 && !pLine->str[1]) ------------------ | | 275| 356|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (275:27): [True: 12, False: 166] | | | Branch (275:40): [True: 1, False: 165] | | | Branch (275:53): [True: 3, False: 162] | | ------------------ ------------------ | Branch (5500:37): [True: 2, False: 14] | Branch (5500:49): [True: 0, False: 2] ------------------ 5501| 0| { 5502| 0| prev_state = state + (bReconn ? IST_HAPPENED_IN_RECMET : 0); ------------------ | | 342| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5502:39): [True: 0, False: 0] ------------------ 5503| 0| ret = RI_ERR_SYNTAX; /* empty layer /r at the end of InChI line */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5504| 0| } 5505| 178| else 5506| 178| { 5507| 178| if (!ret) ------------------ | Branch (5507:21): [True: 150, False: 28] ------------------ 5508| 150| { 5509| 150| len = (int)strlen(pLine->str); 5510| 150| if (len > 1) ------------------ | Branch (5510:25): [True: 36, False: 114] ------------------ 5511| 36| { 5512| 36| memmove(pLine->str, pLine->str + 1, len); 5513| 36| } 5514| 114| else 5515| 114| { 5516| 114| ret = 1; /* read the next segment */ 5517| 114| } 5518| 150| } 5519| 178| } 5520| 178| break; 5521| 300| case IST_RECONNECTED_FORMULA: ------------------ | Branch (5521:9): [True: 300, False: 97.6k] ------------------ 5522| 300|#if ( FIX_GAF_2019_1==1 ) 5523| 300| if (bReconn == INCHI_REC) ------------------ | | 571| 300|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (5523:17): [True: 13, False: 287] ------------------ 5524| 13| { 5525| | /* reconnected layer may appear only once */ 5526| 13| ret = RI_ERR_SYNTAX; ------------------ | | 16| 13|#define RI_ERR_SYNTAX (-2) ------------------ 5527| 13| break; 5528| 13| } 5529| 287|#endif 5530| 287| bReconn = INCHI_REC; ------------------ | | 571| 287|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 5531| 287| bMobileH = TAUT_YES; ------------------ | | 575| 287|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5532| 287| state = IST_MOBILE_H_FORMULA; 5533| 287| break; 5534| 97.9k| } 5535| 97.9k| } while (c >= 0); ------------------ | Branch (5535:14): [True: 97.9k, False: 0] ------------------ 5536| | 5537| 12.5k|exit_function:; 5538| 12.5k|exit_error:; 5539| | 5540| | INCHI_HEAPCHK 5541| | 5542| 12.5k| if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 19| 15.8k|#define RI_ERR_EOF (0) ------------------ if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 18| 1.52k|#define RI_ERR_EOL (-4) ------------------ | Branch (5542:13): [True: 9.31k, False: 3.24k] | Branch (5542:25): [True: 1.72k, False: 1.52k] | Branch (5542:44): [True: 0, False: 1.52k] ------------------ 5543| 11.0k| { 5544| 11.0k| pLine->len = 0; 5545| 11.0k| } 5546| | 5547| 12.5k| return ret; 5548| 12.5k|} ichiread.c:ParseSegmentFormula: 9829| 15.7k|{ 9830| 15.7k| int i, j, mpy_component, mpy_atom, len, el_number; 9831| 15.7k| int nNumComponents = 0, iComponent, nNumAtoms, nNumAtomsAndH, iAtom, nNumH, nAltMobileH = ALT_TAUT(bMobileH); ------------------ | | 577| 15.7k|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 15.7k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 15.7k] | | ------------------ ------------------ 9832| 15.7k| const char* p, * q, * e, * pStart, * pEnd; 9833| 15.7k| INChI* pInChI; 9834| 15.7k| char szEl[3]; 9835| 15.7k|#if ( FIX_GAF_2019_2==1 ) 9836| | /* hack: state passed in *na_total (will be updated in ParseSegmentFormula anyway) */ 9837| 15.7k| int state = *na_total; 9838| 15.7k|#endif 9839| 15.7k| nNumAtoms = -999; /* impossible value */ 9840| 15.7k| *na_total = 0; 9841| | 9842| | /* Pass 1. Count components */ 9843| | 9844| 15.7k| pStart = (char*)str; 9845| 30.0k| while (1) ------------------ | Branch (9845:12): [True: 30.0k, Folded] ------------------ 9846| 30.0k| { 9847| 30.0k| if (!(pEnd = strchr(pStart, '.'))) ------------------ | Branch (9847:13): [True: 15.6k, False: 14.4k] ------------------ 9848| 15.6k| { 9849| 15.6k| pEnd = pStart + strlen(pStart); 9850| 15.6k| } 9851| 30.0k| p = pStart; 9852| 30.0k| if (isdigit(*p)) ------------------ | Branch (9852:13): [True: 8.76k, False: 21.3k] ------------------ 9853| 8.76k| { 9854| 8.76k| mpy_component = (int)inchi_strtol(p, &q, 10); 9855| 8.76k| p = q; 9856| 8.76k| } 9857| 21.3k| else 9858| 21.3k| { 9859| 21.3k| mpy_component = 1; 9860| 21.3k| } 9861| 30.0k| if (!mpy_component) ------------------ | Branch (9861:13): [True: 50, False: 30.0k] ------------------ 9862| 50| { 9863| 50| break; 9864| 50| } 9865| 30.0k| if (!isupper(UCINT * p)) ------------------ | Branch (9865:13): [True: 2.55k, False: 27.4k] ------------------ 9866| 2.55k| { 9867| 2.55k| break; /* not a formula layer */ 9868| 2.55k| } 9869| 27.4k| if (pEnd == p) ------------------ | Branch (9869:13): [True: 0, False: 27.4k] ------------------ 9870| 0| { 9871| 0| break; /* zero length formula */ 9872| 0| } 9873| 27.4k| nNumComponents += mpy_component; 9874| 27.4k| if (*pEnd) ------------------ | Branch (9874:13): [True: 14.3k, False: 13.1k] ------------------ 9875| 14.3k| { 9876| 14.3k| pStart = pEnd + 1; 9877| 14.3k| } 9878| 13.1k| else 9879| 13.1k| { 9880| 13.1k| break; 9881| 13.1k| } 9882| 27.4k| } 9883| 15.7k| pnNumComponents[bMobileH] = nNumComponents; 9884| 15.7k|#if ( FIX_GAF_2019_1==1 ) 9885| 15.7k| if (nNumComponents > MAX_ATOMS) ------------------ | | 15| 15.7k|#define MAX_ATOMS 32766 ------------------ | Branch (9885:9): [True: 3, False: 15.7k] ------------------ 9886| 3| { 9887| 3| pnNumComponents[bMobileH] = 0; 9888| 3| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 9889| 3| } 9890| | /* pnNumComponents was not reset to 0 which results 9891| | in attempt then to free() garbage at 9892| | Free_INChI_Stereo ( <-- Free_INChI_Members <-- FreeInpInChI ) */ 9893| |#elif ( FIX_DALKE_BUGS == 1 ) 9894| | if (nNumComponents > MAX_ATOMS) 9895| | { 9896| | return RI_ERR_SYNTAX; /* syntax error */ 9897| | } 9898| |#endif 9899| | /* exit or error check */ 9900| 15.7k| if (!nNumComponents) ------------------ | Branch (9900:9): [True: 2.49k, False: 13.2k] ------------------ 9901| 2.49k| { 9902| 2.49k|#if ( FIX_GAF_2019_2==1 ) 9903| 2.49k| int low_case = 0; 9904| 2.49k| if (*pStart) ------------------ | Branch (9904:13): [True: 2.49k, False: 0] ------------------ 9905| 2.49k| { 9906| 2.49k| low_case = islower(UCINT * pStart); 9907| 2.49k| } 9908| 2.49k| if (!*pStart || low_case) { ------------------ | Branch (9908:13): [True: 0, False: 2.49k] | Branch (9908:25): [True: 2.45k, False: 42] ------------------ 9909| 2.45k| if (low_case) ------------------ | Branch (9909:17): [True: 2.45k, False: 0] ------------------ 9910| 2.45k| { 9911| 2.45k| if (state == IST_MOBILE_H_FORMULA) ------------------ | Branch (9911:21): [True: 85, False: 2.37k] ------------------ 9912| 85| { 9913| 85| if (*pStart != 'q' && *pStart != 'p') ------------------ | Branch (9913:25): [True: 51, False: 34] | Branch (9913:43): [True: 25, False: 26] ------------------ 9914| 25| { 9915| 25| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 25|#define RI_ERR_SYNTAX (-2) ------------------ 9916| 25| } 9917| 85| } 9918| | /* 9919| | else if (state == IST_FIXED_H_FORMULA) 9920| | { 9921| | if (*pStart != 'h' && *pStart != 'i' && *pStart != 'b' && *pStart != 'q' && *pStart != 'p') 9922| | { 9923| | return RI_ERR_SYNTAX; 9924| | } 9925| | }*/ 9926| 2.45k| } 9927| |#else 9928| | if (!*pStart || islower(UCINT * pStart)) { 9929| |#endif 9930| | 9931| 2.43k| INCHI_HEAPCHK 9932| 2.43k| if (bMobileH == TAUT_NON && 0 < (nNumComponents = pnNumComponents[nAltMobileH])) ------------------ | | 574| 4.86k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (9932:21): [True: 2.37k, False: 60] | Branch (9932:45): [True: 2.37k, False: 0] ------------------ 9933| 2.37k| { 9934| | /* allocate InChI */ 9935| 2.37k| pInChI = (INChI*)inchi_calloc(nNumComponents, sizeof(INChI)); ------------------ | | 1146| 2.37k|#define inchi_calloc calloc ------------------ 9936| 2.37k| if (!(pInChI)) ------------------ | Branch (9936:25): [True: 0, False: 2.37k] ------------------ 9937| 0| { 9938| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9939| 0| } 9940| 2.37k| pInpInChI[bMobileH] = pInChI; 9941| 2.37k| pnNumComponents[bMobileH] = nNumComponents; 9942| | /* djb-rwth: fixing oss-fuzz issue #66985, #66718 */ 9943| | /* U_CHAR** piibmi_na = (U_CHAR**)inchi_malloc(nNumComponents * sizeof(U_CHAR*)); 9944| | char** piibmi_shf = (char**)inchi_malloc(nNumComponents * sizeof(char*)); */ 9945| 41.0k| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (9945:33): [True: 38.7k, False: 2.37k] ------------------ 9946| 38.7k| { 9947| 38.7k| U_CHAR* piibmi_na = NULL; /* copied from below to obey C syntax - 2024-09-01 DT */ 9948| 38.7k| char* piibmi_shf = NULL; /* copied from below to obey C syntax - 2024-09-01 DT */ 9949| | /* copy number of atoms */ 9950| 38.7k| len = pInpInChI[bMobileH][i].nNumberOfAtoms = pInpInChI[nAltMobileH][i].nNumberOfAtoms; 9951| | /* copy atoms */ 9952| 38.7k| len = (len + 1) * sizeof(pInpInChI[0][0].nAtom[0]); 9953| 38.7k| if (pInpInChI[bMobileH][i].nAtom) ------------------ | Branch (9953:29): [True: 0, False: 38.7k] ------------------ 9954| 0| { 9955| 0| inchi_free(pInpInChI[bMobileH][i].nAtom); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 9956| 0| } 9957| 38.7k| piibmi_na = (U_CHAR*)inchi_malloc(((long long)len + 1) * sizeof(pInpInChI[0][0].nAtom[0])); ------------------ | | 1143| 38.7k|#define inchi_malloc malloc ------------------ 9958| 38.7k| if (piibmi_na) /* djb-rwth: cast operator added; addressing LLVM warning */ ------------------ | Branch (9958:29): [True: 38.7k, False: 0] ------------------ 9959| 38.7k| { 9960| 38.7k| memcpy(piibmi_na, pInpInChI[nAltMobileH][i].nAtom, len); 9961| 38.7k| piibmi_na[len] = 0; 9962| 38.7k| pInpInChI[bMobileH][i].nAtom = piibmi_na; 9963| 38.7k| } 9964| 0| else 9965| 0| { 9966| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9967| 0| } 9968| | /* copy Hill formula */ 9969| 38.7k| len = (int)strlen(pInpInChI[nAltMobileH][i].szHillFormula) + 1; 9970| 38.7k| if (pInpInChI[bMobileH][i].szHillFormula) ------------------ | Branch (9970:29): [True: 0, False: 38.7k] ------------------ 9971| 0| { 9972| 0| inchi_free(pInpInChI[bMobileH][i].szHillFormula); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 9973| 0| } 9974| 38.7k| piibmi_shf = (char*)inchi_malloc((inchi_max(len, 2)) * sizeof(char)); ------------------ | | 1143| 38.7k|#define inchi_malloc malloc ------------------ piibmi_shf = (char*)inchi_malloc((inchi_max(len, 2)) * sizeof(char)); ------------------ | | 138| 38.7k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 37.2k, False: 1.43k] | | ------------------ ------------------ 9975| 38.7k| if (piibmi_shf) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9975:29): [True: 38.7k, False: 0] ------------------ 9976| 38.7k| { 9977| 38.7k| memcpy(piibmi_shf, pInpInChI[nAltMobileH][i].szHillFormula, len); 9978| 38.7k| pInpInChI[bMobileH][i].szHillFormula = piibmi_shf; 9979| 38.7k| } 9980| 0| else 9981| 0| { 9982| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9983| 0| } 9984| 38.7k| } 9985| 2.37k| } 9986| 60| else 9987| 60| { 9988| 60| if (bMobileH == TAUT_YES) ------------------ | | 575| 60|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (9988:25): [True: 60, False: 0] ------------------ 9989| 60| { 9990| 60| int ret; 9991| | /* allocate InChI */ 9992| 60| nNumComponents = 1; 9993| | /* InChI */ 9994| 60| pnNumComponents[bMobileH] = nNumComponents; 9995| 60| if (!(pInChI = (INChI*)inchi_calloc(nNumComponents, sizeof(INChI)))) ------------------ | | 1146| 60|#define inchi_calloc calloc ------------------ | Branch (9995:29): [True: 0, False: 60] ------------------ 9996| 0| { 9997| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9998| 0| } 9999| 60| pInpInChI[bMobileH] = pInChI; 10000| 60| ret = nFillOutProtonMobileH(pInChI); 10001| 60| if (ret < 0) ------------------ | Branch (10001:29): [True: 0, False: 60] ------------------ 10002| 0| { 10003| 0| return ret; 10004| 0| } 10005| 60| } 10006| 60| } 10007| 2.43k| return 0; 10008| 2.43k| } 10009| 42| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 42|#define RI_ERR_SYNTAX (-2) ------------------ 10010| 2.49k| } 10011| | 10012| 13.2k| if (*pEnd) ------------------ | Branch (10012:9): [True: 29, False: 13.1k] ------------------ 10013| 29| { 10014| 29| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 29|#define RI_ERR_SYNTAX (-2) ------------------ 10015| 29| } 10016| | 10017| | /* allocate InChI */ 10018| 13.1k| if (!((sizeof(INChI) > 0) && (pInpInChI[bMobileH] = (INChI*)inchi_calloc(nNumComponents, sizeof(INChI))))) /* djb-rwth: fixing GH issue #58 */ ------------------ | | 1146| 13.1k|#define inchi_calloc calloc ------------------ | Branch (10018:11): [True: 13.1k, Folded] | Branch (10018:34): [True: 13.1k, False: 31] ------------------ 10019| 31| { 10020| 31| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 31|#define RI_ERR_ALLOC (-1) ------------------ 10021| 31| } 10022| 13.1k| pInChI = pInpInChI[bMobileH]; 10023| | 10024| | /* Pass 2. Count elements, save formulas and elements */ 10025| 13.1k| pStart = (char*)str; 10026| 13.1k| iComponent = 0; 10027| 26.8k| while (1) ------------------ | Branch (10027:12): [True: 26.8k, Folded] ------------------ 10028| 26.8k| { 10029| 26.8k| if (!(pEnd = strchr(pStart, '.'))) ------------------ | Branch (10029:13): [True: 13.1k, False: 13.6k] ------------------ 10030| 13.1k| { 10031| 13.1k| pEnd = pStart + strlen(pStart); 10032| 13.1k| } 10033| 26.8k| p = pStart; 10034| 26.8k| if (isdigit(UCINT * p)) ------------------ | Branch (10034:13): [True: 8.38k, False: 18.4k] ------------------ 10035| 8.38k| { 10036| 8.38k| mpy_component = (int)inchi_strtol(p, &q, 10); 10037| 8.38k|#if ( CHECK_STRTOL_ATNUMB==1 ) 10038| 8.38k| if (mpy_component > MAX_ATOMS || mpy_component < 0) ------------------ | | 15| 16.7k|#define MAX_ATOMS 32766 ------------------ | Branch (10038:17): [True: 5, False: 8.37k] | Branch (10038:46): [True: 34, False: 8.34k] ------------------ 10039| 39| { 10040| 39| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 39|#define RI_ERR_SYNTAX (-2) ------------------ 10041| 39| } 10042| 8.34k|#endif 10043| 8.34k| p = q; 10044| 8.34k| } 10045| 18.4k| else 10046| 18.4k| { 10047| 18.4k| mpy_component = 1; 10048| 18.4k| } 10049| 26.7k|#if ( FIX_DALKE_BUGS == 1 ) 10050| 26.7k| if (iComponent + mpy_component > MAX_ATOMS) ------------------ | | 15| 26.7k|#define MAX_ATOMS 32766 ------------------ | Branch (10050:13): [True: 0, False: 26.7k] ------------------ 10051| 0| { 10052| 0|#if ( FIX_GAF_2019_1==1 ) 10053| 0| nNumComponents = 0; /* djb-rwth: ignoring LLVM warning: value used */ 10054| 0|#endif 10055| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10056| 0| } 10057| 26.7k|#endif 10058| 26.7k| len = (int)(pEnd - p); 10059| 415k| for (i = 0; i < mpy_component; i++) ------------------ | Branch (10059:21): [True: 388k, False: 26.6k] ------------------ 10060| 388k| { 10061| 388k| if (iComponent + i >= nNumComponents) ------------------ | Branch (10061:17): [True: 13, False: 388k] ------------------ 10062| 13| { 10063| 13| return RI_ERR_SYNTAX; ------------------ | | 16| 13|#define RI_ERR_SYNTAX (-2) ------------------ 10064| 13| } 10065| 388k| if (pInChI[iComponent + i].szHillFormula) ------------------ | Branch (10065:17): [True: 0, False: 388k] ------------------ 10066| 0| { 10067| 0| inchi_free(pInChI[iComponent + i].szHillFormula); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10068| 0| } 10069| 388k| pInChI[iComponent + i].szHillFormula = (char*)inchi_malloc(inchi_max((long long)len, 1) + 1); /* djb-rwth: cast operator added */ ------------------ | | 1143| 388k|#define inchi_malloc malloc ------------------ pInChI[iComponent + i].szHillFormula = (char*)inchi_malloc(inchi_max((long long)len, 1) + 1); /* djb-rwth: cast operator added */ ------------------ | | 138| 388k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 285k, False: 103k] | | ------------------ ------------------ 10070| 388k| if (pInChI[iComponent + i].szHillFormula) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (10070:17): [True: 388k, False: 0] ------------------ 10071| 388k| { 10072| 388k| memcpy(pInChI[iComponent].szHillFormula, p, len); 10073| 388k| pInChI[iComponent + i].szHillFormula[len] = '\0'; 10074| 388k| } 10075| 0| else 10076| 0| { 10077| 0| return RI_ERR_ALLOC; /* djb-rwth: memory could not be allocated */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 10078| 0| } 10079| 388k| if (!i) ------------------ | Branch (10079:17): [True: 26.7k, False: 362k] ------------------ 10080| 26.7k| { 10081| | /* Pass 2.1 Parse formula and count atoms except H */ 10082| 26.7k| nNumAtoms = 0; 10083| 26.7k| nNumH = 0; 10084| | /* djb-rwth: removing redundant code */ 10085| 26.7k| e = pInChI[iComponent].szHillFormula; 10086| 167k| while (e && *e) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (10086:24): [True: 167k, False: 0] | Branch (10086:29): [True: 140k, False: 26.6k] ------------------ 10087| 140k| { 10088| 140k| if (!isupper(UCINT * e)) ------------------ | Branch (10088:25): [True: 60, False: 140k] ------------------ 10089| 60| { 10090| 60| return RI_ERR_SYNTAX; ------------------ | | 16| 60|#define RI_ERR_SYNTAX (-2) ------------------ 10091| 60| } 10092| 140k| j = 0; 10093| 140k| szEl[j++] = *e++; 10094| 140k| if (*e && islower(UCINT * e)) ------------------ | Branch (10094:25): [True: 121k, False: 18.5k] | Branch (10094:31): [True: 21.0k, False: 100k] ------------------ 10095| 21.0k| szEl[j++] = *e++; 10096| 140k| szEl[j++] = '\0'; 10097| 140k| if (*e && isdigit(UCINT * e)) ------------------ | Branch (10097:25): [True: 119k, False: 21.2k] | Branch (10097:31): [True: 21.0k, False: 98.1k] ------------------ 10098| 21.0k| { 10099| 21.0k| mpy_atom = (int)inchi_strtol(e, &q, 10); 10100| 21.0k|#if ( CHECK_STRTOL_ATNUMB==1 ) 10101| 21.0k| if (mpy_atom > MAX_ATOMS || mpy_atom < 0) ------------------ | | 15| 42.0k|#define MAX_ATOMS 32766 ------------------ | Branch (10101:29): [True: 3, False: 21.0k] | Branch (10101:53): [True: 44, False: 20.9k] ------------------ 10102| 47| { 10103| 47| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 47|#define RI_ERR_SYNTAX (-2) ------------------ 10104| 47| } 10105| 20.9k|#endif 10106| 20.9k| e = q; 10107| 20.9k| } 10108| 119k| else 10109| 119k| { 10110| 119k| mpy_atom = 1; 10111| 119k| } 10112| 140k| if (!mpy_atom) ------------------ | Branch (10112:25): [True: 0, False: 140k] ------------------ 10113| 0| { 10114| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10115| 0| } 10116| 140k| if (szEl[0] == 'H' && !szEl[1]) ------------------ | Branch (10116:25): [True: 8.43k, False: 131k] | Branch (10116:43): [True: 6.99k, False: 1.44k] ------------------ 10117| 6.99k| { 10118| 6.99k| nNumH += mpy_atom; 10119| 6.99k| continue; /* ignore H in counting number of atoms */ 10120| 6.99k| } 10121| 133k| nNumAtoms += mpy_atom; 10122| 133k| } 10123| 26.6k|#if ( FIX_DALKE_BUGS == 1 ) 10124| 26.6k| if (nNumAtoms > MAX_ATOMS) ------------------ | | 15| 26.6k|#define MAX_ATOMS 32766 ------------------ | Branch (10124:21): [True: 0, False: 26.6k] ------------------ 10125| 0| { 10126| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10127| 0| } 10128| 26.6k|#endif 10129| 26.6k| (*na_total) += mpy_component * nNumAtoms; 10130| | 10131| 26.6k| nNumAtomsAndH = nNumAtoms ? nNumAtoms : (nNumH > 0); ------------------ | Branch (10131:33): [True: 26.3k, False: 291] ------------------ 10132| 26.6k| pInChI[iComponent + i].nNumberOfAtoms = nNumAtomsAndH; 10133| 26.6k| if (pInChI[iComponent + i].nAtom) ------------------ | Branch (10133:21): [True: 0, False: 26.6k] ------------------ 10134| 0| { 10135| 0| inchi_free(pInChI[iComponent + i].nAtom); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10136| 0| } 10137| 26.6k| pInChI[iComponent + i].nAtom = (U_CHAR*)inchi_malloc(((long long)nNumAtomsAndH + 1) * sizeof(pInChI[0].nAtom[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 26.6k|#define inchi_malloc malloc ------------------ 10138| 26.6k| if (!pInChI[iComponent + i].nAtom) ------------------ | Branch (10138:21): [True: 0, False: 26.6k] ------------------ 10139| 0| { 10140| 0| return RI_ERR_ALLOC; /* failed allocation */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 10141| 0| } 10142| | /* Pass 2.2 Store elements; this assumes no bridging H. Bridging H will be found in connection table, /c */ 10143| 26.6k| iAtom = 0; 10144| 26.6k| if (nNumAtoms > 0) ------------------ | Branch (10144:21): [True: 26.3k, False: 291] ------------------ 10145| 26.3k| { 10146| 26.3k| e = pInChI[iComponent + i].szHillFormula; 10147| 166k| while (*e) ------------------ | Branch (10147:28): [True: 139k, False: 26.3k] ------------------ 10148| 139k| { 10149| 139k| if (!isupper(UCINT * e)) ------------------ | Branch (10149:29): [True: 0, False: 139k] ------------------ 10150| 0| { 10151| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10152| 0| } 10153| 139k| j = 0; 10154| 139k| szEl[j++] = *e++; 10155| 139k| if (*e && islower(UCINT * e)) ------------------ | Branch (10155:29): [True: 121k, False: 18.3k] | Branch (10155:35): [True: 21.0k, False: 100k] ------------------ 10156| 21.0k| szEl[j++] = *e++; 10157| 139k| szEl[j++] = '\0'; 10158| 139k| if (*e && isdigit(UCINT * e)) ------------------ | Branch (10158:29): [True: 118k, False: 21.1k] | Branch (10158:35): [True: 20.7k, False: 97.7k] ------------------ 10159| 20.7k| { 10160| 20.7k| mpy_atom = (int)inchi_strtol(e, &q, 10); 10161| 20.7k|#if ( CHECK_STRTOL_ATNUMB==1 ) 10162| 20.7k| if (mpy_atom > MAX_ATOMS || mpy_atom < 0) ------------------ | | 15| 41.5k|#define MAX_ATOMS 32766 ------------------ | Branch (10162:33): [True: 0, False: 20.7k] | Branch (10162:57): [True: 0, False: 20.7k] ------------------ 10163| 0| { 10164| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10165| 0| } 10166| 20.7k|#endif 10167| 20.7k| e = q; 10168| 20.7k| } 10169| 118k| else 10170| 118k| { 10171| 118k| mpy_atom = 1; 10172| 118k| } 10173| 139k| if (!mpy_atom) ------------------ | Branch (10173:29): [True: 0, False: 139k] ------------------ 10174| 0| { 10175| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10176| 0| } 10177| 139k| if (szEl[0] == 'H' && !szEl[1]) ------------------ | Branch (10177:29): [True: 8.05k, False: 131k] | Branch (10177:47): [True: 6.62k, False: 1.43k] ------------------ 10178| 6.62k| continue; /* ignore H */ 10179| 133k| el_number = get_periodic_table_number(szEl); 10180| 133k| if (el_number == ERR_ELEM) ------------------ | Branch (10180:29): [True: 25, False: 133k] ------------------ 10181| 25| { 10182| 25| return RI_ERR_SYNTAX; /* wrong element */ ------------------ | | 16| 25|#define RI_ERR_SYNTAX (-2) ------------------ 10183| 25| } 10184| 2.37M| while (mpy_atom--) ------------------ | Branch (10184:32): [True: 2.24M, False: 133k] ------------------ 10185| 2.24M| { 10186| 2.24M| if (iAtom >= nNumAtoms) ------------------ | Branch (10186:33): [True: 0, False: 2.24M] ------------------ 10187| 0| { 10188| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 10189| 0| } 10190| 2.24M| pInChI[iComponent + i].nAtom[iAtom++] = (U_CHAR)el_number; 10191| 2.24M| } 10192| 133k| } 10193| 26.3k| } 10194| 291| else 10195| 291| { 10196| 291| if (nNumH > 0) ------------------ | Branch (10196:25): [True: 291, False: 0] ------------------ 10197| 291| { 10198| 291| pInChI[iComponent + i].nAtom[iAtom++] = EL_NUMBER_H; ------------------ | | 11| 291|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 10199| 291| nNumAtoms = 1; 10200| 291| } 10201| 291| } 10202| 26.6k| pInChI[iComponent + i].nAtom[iAtom] = '\0'; 10203| 26.6k| if (nNumAtoms != iAtom) ------------------ | Branch (10203:21): [True: 0, False: 26.6k] ------------------ 10204| 0| { 10205| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 10206| 0| } 10207| 26.6k| } 10208| 362k| else 10209| 362k| { 10210| 362k| U_CHAR* pci1 = NULL; /* copied from below to obey C syntax - 2024-09-01 DT */ 10211| | /* Copy duplicated formula */ 10212| 362k| strcpy(pInChI[iComponent + i].szHillFormula, pInChI[iComponent].szHillFormula); /* djb-rwth: unresolved issue -- revision required? */ 10213| | /* Copy atoms in the duplicated formula */ 10214| 362k| pInChI[iComponent + i].nNumberOfAtoms = nNumAtoms; 10215| | /* djb-rwth: fixing oss-fuzz issue #43420, #34772 */ 10216| 362k| pci1 = (U_CHAR*)inchi_malloc((long long)nNumAtoms + 1); /* djb-rwth: cast operator added */ ------------------ | | 1143| 362k|#define inchi_malloc malloc ------------------ 10217| 362k| if (!pci1) ------------------ | Branch (10217:21): [True: 0, False: 362k] ------------------ 10218| 0| { 10219| 0| return RI_ERR_ALLOC; /* failed allocation */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 10220| 0| } 10221| 362k| pInChI[iComponent + i].nAtom = pci1; 10222| 362k| memcpy(pci1, pInChI[iComponent].nAtom, (long long)nNumAtoms + 1); /* djb-rwth: cast operator added */ 10223| 362k| } 10224| 388k| } 10225| 26.6k| iComponent += i; 10226| 26.6k| if (*pEnd) ------------------ | Branch (10226:13): [True: 13.6k, False: 12.9k] ------------------ 10227| 13.6k| { 10228| 13.6k| if (*pEnd != '.') ------------------ | Branch (10228:17): [True: 0, False: 13.6k] ------------------ 10229| 0| { 10230| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10231| 0| } 10232| 13.6k| pStart = pEnd + 1; 10233| 13.6k| } 10234| 12.9k| else 10235| 12.9k| { 10236| 12.9k| break; 10237| 12.9k| } 10238| 26.6k| } 10239| | 10240| 12.9k| if (iComponent != nNumComponents) ------------------ | Branch (10240:9): [True: 0, False: 12.9k] ------------------ 10241| 0| { 10242| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 10243| 0| } 10244| 12.9k| if (bMobileH == TAUT_NON) ------------------ | | 574| 12.9k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (10244:9): [True: 636, False: 12.3k] ------------------ 10245| 636| { 10246| | /* at this point the exact number of atoms including bridging H is known from TAUT_YES */ 10247| 1.41k| for (i = 0; i < nNumComponents && i < pnNumComponents[nAltMobileH]; i++) ------------------ | Branch (10247:21): [True: 816, False: 595] | Branch (10247:43): [True: 775, False: 41] ------------------ 10248| 775| { 10249| 775| if (pInpInChI[bMobileH][i].nNumberOfAtoms < (len = pInpInChI[nAltMobileH][i].nNumberOfAtoms)) ------------------ | Branch (10249:17): [True: 681, False: 94] ------------------ 10250| 681| { 10251| | /* there are bridging H in this component */ 10252| 681| if (pInpInChI[nAltMobileH][i].nAtom) ------------------ | Branch (10252:21): [True: 681, False: 0] ------------------ 10253| 681| { 10254| 681| U_CHAR* nAtom = (U_CHAR*)inchi_malloc(((long long)len + 1) * sizeof(nAtom[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 681|#define inchi_malloc malloc ------------------ 10255| 681| if (!nAtom) ------------------ | Branch (10255:25): [True: 0, False: 681] ------------------ 10256| 0| { 10257| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 10258| 0| } 10259| 681| memcpy(nAtom, pInpInChI[nAltMobileH][i].nAtom, len * sizeof(nAtom[0])); 10260| 681| nAtom[len] = 0; 10261| 681| if (pInpInChI[bMobileH][i].nAtom) ------------------ | Branch (10261:25): [True: 681, False: 0] ------------------ 10262| 681| { 10263| 681| inchi_free(pInpInChI[bMobileH][i].nAtom); ------------------ | | 1152| 681|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 681, False: 0] | | | Branch (1152:50): [Folded, False: 681] | | ------------------ ------------------ 10264| 681| } 10265| 681| pInpInChI[bMobileH][i].nAtom = nAtom; 10266| 681| } 10267| 681| pInpInChI[bMobileH][i].nNumberOfAtoms = len; 10268| 681| } 10269| 775| } 10270| 636| } 10271| | 10272| 12.9k| return nNumComponents + 1; 10273| 12.9k| } ichiread.c:ParseSegmentConnections: 9104| 12.3k|{ 9105| 12.3k|#define LAST_AT_LEN 256 9106| | /* Pass 1: count bonds and find actual numbers of atom */ 9107| 12.3k| int i, j, k, m, c, mpy_component; 9108| 12.3k| int nNumComponents, iComponent, nNumAtoms, nNumBonds, lenConnTable; /* djb-rwth: removing redundant variables */ 9109| 12.3k| const char* p, * q, * pStart, * pEnd; 9110| 12.3k| AT_NUMB last_atom[LAST_AT_LEN], curAtom, maxAtom; 9111| 12.3k| int num_open, state, ret, base; 9112| 12.3k| INChI* pInChI = *pInpInChI; 9113| 12.3k| LINKED_BONDS LB; 9114| 12.3k| LINKED_BONDS* pLB = &LB; /* a list of linked lists of bonds, for each atom */ 9115| 12.3k| AT_NUMB neighbor[MAXVAL]; 9116| 12.3k| int bPrevVersion = -1; 9117| | 9118| 12.3k| *nb_total = 0; 9119| 12.3k| iComponent = 0; 9120| 12.3k| LB.pBond = NULL; /* djb-rwth: initialization required to avoid garbage values */ 9121| 12.3k| if (str[0] != 'c') ------------------ | Branch (9121:9): [True: 3.27k, False: 9.09k] ------------------ 9122| 3.27k| { 9123| 3.27k| if (!pInChI && !*pnNumComponents) ------------------ | Branch (9123:13): [True: 0, False: 3.27k] | Branch (9123:24): [True: 0, False: 0] ------------------ 9124| 0| { 9125| 0| int lenFormula = 1; 9126| | /* component has no formula; allocate InChI */ 9127| 0| lenConnTable = 0; 9128| 0| nNumComponents = 1; 9129| | /* allocate InChI */ 9130| 0| if (!(pInChI = *pInpInChI = (INChI*)inchi_calloc(nNumComponents, sizeof(INChI)))) ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ | Branch (9130:17): [True: 0, False: 0] ------------------ 9131| 0| { 9132| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9133| 0| } 9134| | /* allocate empty formula */ 9135| 0| pInChI[iComponent].szHillFormula = (char*)inchi_calloc((long long)lenFormula + 1, sizeof(pInChI[0].szHillFormula[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 9136| 0| if (!pInChI[iComponent].szHillFormula) ------------------ | Branch (9136:17): [True: 0, False: 0] ------------------ 9137| 0| { 9138| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9139| 0| goto exit_function; 9140| 0| } 9141| | /* allocate empty connection table */ 9142| 0| pInChI[iComponent].nConnTable = (AT_NUMB*)inchi_calloc((long long)lenConnTable + 1, sizeof(pInChI[0].nConnTable[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 9143| 0| if (!pInChI[iComponent].nConnTable) ------------------ | Branch (9143:17): [True: 0, False: 0] ------------------ 9144| 0| { 9145| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9146| 0| goto exit_function; 9147| 0| } 9148| 0| pInChI[iComponent].lenConnTable = lenConnTable; 9149| 0| *pnNumComponents = nNumComponents; 9150| 0| } 9151| 3.27k| else 9152| 3.27k| { 9153| 3.27k| lenConnTable = 1; 9154| 3.27k| nNumComponents = *pnNumComponents; 9155| 266k| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (9155:25): [True: 263k, False: 3.27k] ------------------ 9156| 263k| { 9157| | /* allocate 1 atom connection table */ 9158| 263k| if (pInChI) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (9158:21): [True: 263k, False: 0] ------------------ 9159| 263k| { 9160| 263k| if (pInChI[i].nConnTable) ------------------ | Branch (9160:25): [True: 60, False: 263k] ------------------ 9161| 60| { 9162| 60| inchi_free(pInChI[i].nConnTable); ------------------ | | 1152| 60|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 60, False: 0] | | | Branch (1152:50): [Folded, False: 60] | | ------------------ ------------------ 9163| 60| } 9164| 263k| pInChI[i].nConnTable = (AT_NUMB*)inchi_calloc((long long)lenConnTable + 1, sizeof(pInChI[0].nConnTable[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 263k|#define inchi_calloc calloc ------------------ 9165| 263k| if (!pInChI[i].nConnTable) ------------------ | Branch (9165:25): [True: 0, False: 263k] ------------------ 9166| 0| { 9167| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9168| 0| goto exit_function; 9169| 0| } 9170| 263k| pInChI[i].nConnTable[0] = 1; 9171| 263k| pInChI[i].lenConnTable = lenConnTable; 9172| 263k| } 9173| 263k| } 9174| 3.27k| } 9175| 3.27k| return 0; 9176| 3.27k| } 9177| | 9178| | /* Pass 1. Re-Count atoms, count bonds */ 9179| | 9180| 9.09k| pStart = (char*)str + 1; 9181| 9.09k| nNumComponents = *pnNumComponents; 9182| 9.09k|#if (FIX_DALKE_BUGS == 1) 9183| | /* prevent crash on too many components */ 9184| 9.09k| if (nNumComponents > MAX_ATOMS) ------------------ | | 15| 9.09k|#define MAX_ATOMS 32766 ------------------ | Branch (9184:9): [True: 0, False: 9.09k] ------------------ 9185| 0| { 9186| 0| ret = RI_ERR_SYNTAX; /* syntax error: extra component */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9187| 0| goto exit_function; 9188| 0| } 9189| 9.09k|#endif 9190| 9.09k| memset(pLB, 0, sizeof(pLB[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 9191| | 9192| 14.4k| while (1) ------------------ | Branch (9192:12): [True: 14.4k, Folded] ------------------ 9193| 14.4k| { 9194| | /* cycle over components */ 9195| 14.4k| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (9195:13): [True: 8.11k, False: 6.33k] ------------------ 9196| 8.11k| { 9197| 8.11k| pEnd = pStart + strlen(pStart); 9198| 8.11k| } 9199| 14.4k| if ((p = strchr(pStart, '*')) && p < pEnd) ------------------ | Branch (9199:13): [True: 2.80k, False: 11.6k] | Branch (9199:42): [True: 2.62k, False: 180] ------------------ 9200| 2.62k| { 9201| 2.62k| mpy_component = (int)inchi_strtol(pStart, &q, 10); 9202| 2.62k|#if ( CHECK_STRTOL_ATNUMB==1 ) 9203| 2.62k| if (mpy_component > MAX_ATOMS || mpy_component < 0) ------------------ | | 15| 5.25k|#define MAX_ATOMS 32766 ------------------ | Branch (9203:17): [True: 2, False: 2.62k] | Branch (9203:46): [True: 30, False: 2.59k] ------------------ 9204| 32| { 9205| 32| ret = RI_ERR_SYNTAX; ------------------ | | 16| 32|#define RI_ERR_SYNTAX (-2) ------------------ 9206| 32| goto exit_function; 9207| 32| } 9208| 2.59k|#endif 9209| 2.59k| if (p != q ------------------ | Branch (9209:17): [True: 2, False: 2.59k] ------------------ 9210| 2.59k|#if (FIX_DALKE_BUGS == 1) 9211| 2.59k| || !isdigit(UCINT * pStart) ------------------ | Branch (9211:20): [True: 0, False: 2.59k] ------------------ 9212| 2.59k|#endif 9213| 2.59k| ) 9214| 2| { 9215| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 9216| 2| goto exit_function; 9217| 2| } 9218| 2.59k| p++; 9219| 2.59k| } 9220| 11.8k| else 9221| 11.8k| { 9222| 11.8k| mpy_component = 1; 9223| 11.8k| p = pStart; 9224| 11.8k| } 9225| 14.4k|#if (FIX_DALKE_BUGS == 1) 9226| 14.4k| if (iComponent + mpy_component > MAX_ATOMS) ------------------ | | 15| 14.4k|#define MAX_ATOMS 32766 ------------------ | Branch (9226:13): [True: 0, False: 14.4k] ------------------ 9227| 0| { 9228| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9229| 0| goto exit_function; 9230| 0| } 9231| 14.4k|#endif 9232| 14.4k| pStart = p; 9233| | /* Pass 1.1 parse a component */ 9234| 14.4k| num_open = 0; 9235| 14.4k| memset(last_atom, 0, sizeof(last_atom)); /* djb-rwth: memset_s C11/Annex K variant? */ 9236| 14.4k| state = '\0'; /* initial state */ 9237| 14.4k| maxAtom = 0; 9238| 14.4k| nNumBonds = 0; 9239| | /* djb-rwth: removing redundant code */ 9240| 14.4k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (9240:13): [True: 9.52k, False: 4.88k] | Branch (9240:25): [True: 0, False: 9.52k] ------------------ 9241| 0| { 9242| | /* check if compressed InChI */ 9243| 0| *pbAbc = isupper(UCINT * p) ? 1 : 0; ------------------ | Branch (9243:22): [True: 0, False: 0] ------------------ 9244| 0| } 9245| 14.4k| base = *pbAbc ? ALPHA_BASE : 10; ------------------ | | 170| 0|#define ALPHA_BASE 27 ------------------ | Branch (9245:16): [True: 0, False: 14.4k] ------------------ 9246| | 9247| 14.4k| if (*pbAbc == 1) ------------------ | Branch (9247:13): [True: 0, False: 14.4k] ------------------ 9248| 0| { 9249| 0| nNumAtoms = 1; 9250| 0| while (p < pEnd) ------------------ | Branch (9250:20): [True: 0, False: 0] ------------------ 9251| 0| { 9252| 0| if (*p == '-') ------------------ | Branch (9252:21): [True: 0, False: 0] ------------------ 9253| 0| { 9254| 0| if (bPrevVersion == -1) ------------------ | Branch (9254:25): [True: 0, False: 0] ------------------ 9255| 0| { 9256| | /* previous InChI version */ 9257| 0| bPrevVersion = 1; 9258| 0| } 9259| 0| else 9260| 0| if (bPrevVersion != 1) ------------------ | Branch (9260:29): [True: 0, False: 0] ------------------ 9261| 0| { 9262| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9263| 0| goto exit_function; 9264| 0| } 9265| 0| nNumAtoms--; 9266| 0| p++; 9267| 0| } 9268| 0| if (isdigit(UCINT * p)) ------------------ | Branch (9268:21): [True: 0, False: 0] ------------------ 9269| 0| { 9270| 0| if (bPrevVersion == -1) ------------------ | Branch (9270:25): [True: 0, False: 0] ------------------ 9271| 0| { 9272| | /* curreny InChI, version 1 */ 9273| 0| bPrevVersion = 0; 9274| 0| } 9275| 0| else 9276| 0| if (bPrevVersion != 0) ------------------ | Branch (9276:29): [True: 0, False: 0] ------------------ 9277| 0| { 9278| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9279| 0| goto exit_function; 9280| 0| } 9281| 0| nNumAtoms -= inchi_strtol(p, &p, 10); /* bypass digits */ 9282| 0| } 9283| 0| if (*p != '-' && (curAtom = (AT_NUMB)inchi_strtol(p, &q, base))) ------------------ | Branch (9283:21): [True: 0, False: 0] | Branch (9283:34): [True: 0, False: 0] ------------------ 9284| 0| { 9285| 0| nNumAtoms++; 9286| 0| nNumBonds++; 9287| 0| p = q; 9288| 0| if (maxAtom < curAtom) ------------------ | Branch (9288:25): [True: 0, False: 0] ------------------ 9289| 0| maxAtom = curAtom; 9290| 0| } 9291| 0| else 9292| 0| { 9293| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9294| 0| goto exit_function; 9295| 0| } 9296| 0| } 9297| 0| if (maxAtom < nNumAtoms && nNumBonds) ------------------ | Branch (9297:17): [True: 0, False: 0] | Branch (9297:40): [True: 0, False: 0] ------------------ 9298| 0| { 9299| 0| maxAtom = nNumAtoms; 9300| 0| } 9301| 0| } 9302| 14.4k| else 9303| 14.4k| { 9304| 155k| while (p < pEnd) ------------------ | Branch (9304:20): [True: 140k, False: 14.3k] ------------------ 9305| 140k| { 9306| | /* atom number */ 9307| 140k| c = UCINT * p++; ------------------ | | 88| 140k|#define UCINT (int)(unsigned char) ------------------ 9308| 140k| switch (c) 9309| 140k| { 9310| 11.4k| case '(': ------------------ | Branch (9310:17): [True: 11.4k, False: 129k] ------------------ 9311| 21.3k| case ')': ------------------ | Branch (9311:17): [True: 9.91k, False: 130k] ------------------ 9312| 26.4k| case ',': ------------------ | Branch (9312:17): [True: 5.09k, False: 135k] ------------------ 9313| 66.3k| case '-': ------------------ | Branch (9313:17): [True: 39.9k, False: 100k] ------------------ 9314| 66.3k| if (state != 'N') ------------------ | Branch (9314:25): [True: 23, False: 66.3k] ------------------ 9315| 23| { 9316| 23| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 23|#define RI_ERR_SYNTAX (-2) ------------------ 9317| 23| goto exit_function; 9318| 23| } 9319| 66.3k| state = c; 9320| 66.3k| num_open += (c == '(') - (c == ')'); 9321| 66.3k| if (num_open < 0) ------------------ | Branch (9321:25): [True: 12, False: 66.3k] ------------------ 9322| 12| { 9323| 12| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 12|#define RI_ERR_SYNTAX (-2) ------------------ 9324| 12| goto exit_function; 9325| 12| } 9326| 66.3k| break; 9327| 74.3k| default: ------------------ | Branch (9327:17): [True: 74.3k, False: 66.3k] ------------------ 9328| 74.3k| if (isdigit(c) && (curAtom = (AT_NUMB)inchi_strtol(p - 1, &q, 10))) ------------------ | Branch (9328:25): [True: 74.2k, False: 29] | Branch (9328:39): [True: 74.2k, False: 5] ------------------ 9329| 74.2k| { 9330| 74.2k| p = q; 9331| 74.2k| switch (state) 9332| 74.2k| { 9333| 11.4k| case '(': ------------------ | Branch (9333:25): [True: 11.4k, False: 62.8k] ------------------ 9334| 20.6k| case ')': ------------------ | Branch (9334:25): [True: 9.24k, False: 65.0k] ------------------ 9335| 25.6k| case ',': ------------------ | Branch (9335:25): [True: 5.00k, False: 69.2k] ------------------ 9336| 64.7k| case '-': ------------------ | Branch (9336:25): [True: 39.1k, False: 35.1k] ------------------ 9337| 64.7k| nNumBonds++; 9338| 74.2k| case '\0': ------------------ | Branch (9338:25): [True: 9.50k, False: 64.7k] ------------------ 9339| 74.2k| if (maxAtom < curAtom) ------------------ | Branch (9339:33): [True: 20.6k, False: 53.6k] ------------------ 9340| 20.6k| maxAtom = curAtom; 9341| 74.2k| state = 'N'; 9342| 74.2k| break; 9343| 0| default: ------------------ | Branch (9343:25): [True: 0, False: 74.2k] ------------------ 9344| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9345| 0| goto exit_function; 9346| 74.2k| } 9347| 74.2k| } 9348| 34| else 9349| 34| { 9350| 34| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 34|#define RI_ERR_SYNTAX (-2) ------------------ 9351| 34| goto exit_function; 9352| 34| } 9353| 74.2k| break; 9354| 140k| } 9355| 140k| } 9356| 14.3k| if (num_open) ------------------ | Branch (9356:17): [True: 11, False: 14.3k] ------------------ 9357| 11| { 9358| 11| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 11|#define RI_ERR_SYNTAX (-2) ------------------ 9359| 11| goto exit_function; 9360| | /* syntax error: parentheses do not match */ 9361| 11| } 9362| 14.3k| } 9363| 14.3k| (*nb_total) += nNumBonds; 9364| | 9365| | /* Save the results and allocate memory */ 9366| 14.3k| nNumAtoms = (int)maxAtom; /* 0 if empty connection table and no bonds present */ 9367| 14.3k| lenConnTable = nNumAtoms + nNumBonds; 9368| | 9369| | /* connection table format: At1[,Neigh11,Neigh12,...],At2[,Neigh21,Neigh22,...],AtN[NeighN1,NeighN2,...] */ 9370| | /* where AtK > NeighK1 > NeighK2,...; At(K) < At(K+1); the length = num.atoms + num.bonds */ 9371| 89.1k| for (i = 0; i < mpy_component; i++) ------------------ | Branch (9371:21): [True: 74.8k, False: 14.2k] ------------------ 9372| 74.8k| { 9373| 74.8k|#if ( FIX_GAF_2019_2==1 ) 9374| 74.8k| if ((iComponent + i > nNumComponents - 1) || (iComponent + i < 0)) ------------------ | Branch (9374:17): [True: 13, False: 74.8k] | Branch (9374:58): [True: 0, False: 74.8k] ------------------ 9375| 13| { 9376| 13| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 13|#define RI_ERR_SYNTAX (-2) ------------------ 9377| 13| goto exit_function; 9378| 13| } 9379| 74.8k| if (pInChI[iComponent + i].nNumberOfAtoms <= 0 || pInChI[iComponent + i].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 15| 74.8k|#define MAX_ATOMS 32766 ------------------ | Branch (9379:17): [True: 0, False: 74.8k] | Branch (9379:63): [True: 0, False: 74.8k] ------------------ 9380| 0| { 9381| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9382| 0| goto exit_function; 9383| 0| } 9384| 74.8k|#endif 9385| | /* check number of atoms: the difference may be due to bridging H */ 9386| 74.8k| if ((j = pInChI[iComponent + i].nNumberOfAtoms) < nNumAtoms) ------------------ | Branch (9386:17): [True: 34.9k, False: 39.8k] ------------------ 9387| 34.9k| { 9388| | /* reallocate */ 9389| 34.9k| U_CHAR* nAtomTmp = (U_CHAR*)inchi_malloc((long long)nNumAtoms + 1); /* djb-rwth: cast operator added */ ------------------ | | 1143| 34.9k|#define inchi_malloc malloc ------------------ 9390| 34.9k| if (!nAtomTmp) ------------------ | Branch (9390:21): [True: 0, False: 34.9k] ------------------ 9391| 0| { 9392| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9393| 0| goto exit_function; 9394| 0| } 9395| 34.9k| memcpy(nAtomTmp, pInChI[iComponent + i].nAtom, sizeof(nAtomTmp[0]) * j); 9396| 7.68M| while (j < nNumAtoms) ------------------ | Branch (9396:24): [True: 7.64M, False: 34.9k] ------------------ 9397| 7.64M| { 9398| 7.64M| nAtomTmp[j++] = EL_NUMBER_H; /* bridging H */ ------------------ | | 11| 7.64M|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 9399| 7.64M| } 9400| 34.9k| nAtomTmp[j] = '\0'; 9401| 34.9k| INCHI_HEAPCHK 9402| 34.9k| if (pInChI[iComponent + i].nAtom) ------------------ | Branch (9402:25): [True: 34.9k, False: 0] ------------------ 9403| 34.9k| { 9404| 34.9k| inchi_free(pInChI[iComponent + i].nAtom); ------------------ | | 1152| 34.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 34.9k, False: 0] | | | Branch (1152:50): [Folded, False: 34.9k] | | ------------------ ------------------ 9405| 34.9k| } 9406| 34.9k| pInChI[iComponent + i].nAtom = nAtomTmp; 9407| 34.9k| pInChI[iComponent + i].nNumberOfAtoms = nNumAtoms; 9408| 34.9k| } 9409| 39.8k| else 9410| 39.8k| { 9411| 39.8k| if (j > nNumAtoms && (lenConnTable || j != 1)) ------------------ | Branch (9411:21): [True: 4.91k, False: 34.9k] | Branch (9411:39): [True: 24, False: 4.88k] | Branch (9411:55): [True: 7, False: 4.88k] ------------------ 9412| 31| { 9413| 31| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 31|#define RI_ERR_SYNTAX (-2) ------------------ 9414| 31| goto exit_function; 9415| 31| } 9416| 39.8k| } 9417| | /* allocate connection table */ 9418| 74.7k| if (pInChI[iComponent + i].nConnTable) ------------------ | Branch (9418:17): [True: 0, False: 74.7k] ------------------ 9419| 0| { 9420| 0| inchi_free(pInChI[iComponent + i].nConnTable); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 9421| 0| } 9422| 74.7k| if (!nNumAtoms && !nNumBonds && !lenConnTable) ------------------ | Branch (9422:17): [True: 4.88k, False: 69.8k] | Branch (9422:31): [True: 4.88k, False: 0] | Branch (9422:45): [True: 4.88k, False: 0] ------------------ 9423| 4.88k| { 9424| 4.88k| lenConnTable = 1; /* one atom, no bonds */ 9425| 4.88k| } 9426| 74.7k| pInChI[iComponent + i].nConnTable = (AT_NUMB*)inchi_calloc((long long)lenConnTable + 1, sizeof(pInChI[0].nConnTable[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 74.7k|#define inchi_calloc calloc ------------------ 9427| 74.7k| if (!pInChI[iComponent + i].nConnTable) ------------------ | Branch (9427:17): [True: 0, False: 74.7k] ------------------ 9428| 0| { 9429| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9430| 0| goto exit_function; 9431| 0| } 9432| 74.7k| pInChI[iComponent + i].lenConnTable = lenConnTable; 9433| 74.7k| } 9434| | 9435| | /* Pass 1.2 parse a component and extract the bonds */ 9436| 14.2k| num_open = 0; 9437| 14.2k| memset(last_atom, 0, sizeof(last_atom)); /* djb-rwth: memset_s C11/Annex K variant? */ 9438| 14.2k| state = '\0'; /* initial state */ 9439| | /* djb-rwth: removing redundant code */ 9440| 14.2k| p = pStart; 9441| 14.2k| pLB->len = 0; 9442| | 9443| 14.2k| if (*pbAbc == 1) ------------------ | Branch (9443:13): [True: 0, False: 14.2k] ------------------ 9444| 0| { 9445| | /* compressed */ 9446| 0| int num_neigh; 9447| 0| num_open = 0; 9448| 0| last_atom[num_open] = 2; 9449| 0| while (p < pEnd) ------------------ | Branch (9449:20): [True: 0, False: 0] ------------------ 9450| 0| { 9451| 0| if (last_atom[num_open] > maxAtom) ------------------ | Branch (9451:21): [True: 0, False: 0] ------------------ 9452| 0| { 9453| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9454| 0| goto exit_function; 9455| 0| } 9456| 0| if (isupper(UCINT * p)) ------------------ | Branch (9456:21): [True: 0, False: 0] ------------------ 9457| 0| { 9458| 0| curAtom = (AT_NUMB)inchi_strtol(p, &q, base); 9459| 0| if ((ret = AddLinkedBond(last_atom[num_open], curAtom, (AT_NUMB)nNumAtoms, pLB))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9459:25): [True: 0, False: 0] ------------------ 9460| 0| { 9461| 0| goto exit_function; 9462| 0| } 9463| 0| p = q; 9464| 0| if (bPrevVersion == 1) ------------------ | Branch (9464:25): [True: 0, False: 0] ------------------ 9465| 0| { 9466| 0| while (p < pEnd && *p == '-') ------------------ | Branch (9466:32): [True: 0, False: 0] | Branch (9466:44): [True: 0, False: 0] ------------------ 9467| 0| { 9468| 0| p++; 9469| 0| if ((curAtom = (AT_NUMB)inchi_strtol(p, &q, base))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9469:33): [True: 0, False: 0] ------------------ 9470| 0| { 9471| 0| if ((ret = AddLinkedBond(last_atom[num_open], curAtom, (AT_NUMB)nNumAtoms, pLB))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9471:37): [True: 0, False: 0] ------------------ 9472| 0| { 9473| 0| goto exit_function; 9474| 0| } 9475| 0| p = q; 9476| 0| } 9477| 0| else 9478| 0| { 9479| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9480| 0| goto exit_function; 9481| 0| } 9482| 0| } 9483| 0| } 9484| 0| else 9485| 0| { 9486| 0| if (bPrevVersion == 0 && isdigit(*p)) ------------------ | Branch (9486:29): [True: 0, False: 0] | Branch (9486:50): [True: 0, False: 0] ------------------ 9487| 0| { 9488| 0| num_neigh = (int)inchi_strtol(p, &q, 10); 9489| 0| p = q; 9490| 0| while (num_neigh-- && p < pEnd) ------------------ | Branch (9490:36): [True: 0, False: 0] | Branch (9490:51): [True: 0, False: 0] ------------------ 9491| 0| { 9492| 0| if ((curAtom = (AT_NUMB)inchi_strtol(p, &q, base))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9492:37): [True: 0, False: 0] ------------------ 9493| 0| { 9494| 0| if ((ret = AddLinkedBond(last_atom[num_open], curAtom, (AT_NUMB)nNumAtoms, pLB))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9494:41): [True: 0, False: 0] ------------------ 9495| 0| { 9496| 0| goto exit_function; 9497| 0| } 9498| 0| p = q; 9499| 0| } 9500| 0| else 9501| 0| { 9502| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9503| 0| goto exit_function; 9504| 0| } 9505| 0| } 9506| 0| } 9507| 0| } 9508| 0| last_atom[num_open]++; 9509| 0| } 9510| 0| else 9511| 0| { 9512| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9513| 0| goto exit_function; 9514| 0| } 9515| 0| } 9516| 0| } 9517| 14.2k| else 9518| 14.2k| { 9519| 149k| while (p < pEnd) ------------------ | Branch (9519:20): [True: 135k, False: 14.2k] ------------------ 9520| 135k| { 9521| | /* each atom number except the first means a new bond */ 9522| 135k| c = UCINT * p++; ------------------ | | 88| 135k|#define UCINT (int)(unsigned char) ------------------ 9523| 135k| switch (c) 9524| 135k| { 9525| 9.71k| case '(': ------------------ | Branch (9525:17): [True: 9.71k, False: 125k] ------------------ 9526| 19.4k| case ')': ------------------ | Branch (9526:17): [True: 9.71k, False: 125k] ------------------ 9527| 24.2k| case ',': ------------------ | Branch (9527:17): [True: 4.82k, False: 130k] ------------------ 9528| 63.7k| case '-': ------------------ | Branch (9528:17): [True: 39.5k, False: 95.9k] ------------------ 9529| 63.7k| switch (state) 9530| 63.7k| { 9531| 63.7k| case 'N': ------------------ | Branch (9531:21): [True: 63.7k, False: 0] ------------------ 9532| 63.7k| state = c; 9533| 63.7k| break; 9534| 0| default: ------------------ | Branch (9534:21): [True: 0, False: 63.7k] ------------------ 9535| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9536| 0| goto exit_function; 9537| 63.7k| } 9538| 63.7k| break; 9539| 71.6k| default: ------------------ | Branch (9539:17): [True: 71.6k, False: 63.7k] ------------------ 9540| 71.6k| if (isdigit(c) && (curAtom = (AT_NUMB)inchi_strtol(p - 1, &q, 10))) ------------------ | Branch (9540:25): [True: 71.6k, False: 0] | Branch (9540:39): [True: 71.6k, False: 0] ------------------ 9541| 71.6k| { 9542| 71.6k| p = q; 9543| 71.6k| switch (state) 9544| 71.6k| { 9545| 9.40k| case '\0': ------------------ | Branch (9545:25): [True: 9.40k, False: 62.2k] ------------------ 9546| 9.40k| last_atom[num_open] = curAtom; 9547| 9.40k| state = 'N'; 9548| 9.40k| break; 9549| 9.71k| case '(': ------------------ | Branch (9549:25): [True: 9.71k, False: 61.9k] ------------------ 9550| 9.71k| if ((ret = AddLinkedBond(last_atom[num_open], curAtom, (AT_NUMB)nNumAtoms, pLB))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9550:33): [True: 1, False: 9.71k] ------------------ 9551| 1| { 9552| 1| goto exit_function; 9553| 1| } 9554| 9.71k| if (++num_open >= LAST_AT_LEN) ------------------ | | 9105| 9.71k|#define LAST_AT_LEN 256 ------------------ | Branch (9554:33): [True: 0, False: 9.71k] ------------------ 9555| 0| { 9556| 0| ret = RI_ERR_PROGR; /* program error: buffer overflow */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 9557| 0| goto exit_function; 9558| 0| } 9559| 9.71k| last_atom[num_open] = curAtom; 9560| 9.71k| state = 'N'; 9561| 9.71k| break; 9562| | 9563| 9.05k| case ')': ------------------ | Branch (9563:25): [True: 9.05k, False: 62.6k] ------------------ 9564| 9.05k| if (!num_open) ------------------ | Branch (9564:33): [True: 0, False: 9.05k] ------------------ 9565| 0| { 9566| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9567| 0| goto exit_function; 9568| 0| } 9569| 9.05k| if ((ret = AddLinkedBond(last_atom[--num_open], curAtom, (AT_NUMB)nNumAtoms, pLB))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9569:33): [True: 0, False: 9.05k] ------------------ 9570| 0| { 9571| 0| goto exit_function; 9572| 0| } 9573| 9.05k| last_atom[num_open] = curAtom; 9574| 9.05k| state = 'N'; 9575| 9.05k| break; 9576| | 9577| 4.73k| case ',': ------------------ | Branch (9577:25): [True: 4.73k, False: 66.9k] ------------------ 9578| 4.73k| if (!num_open) ------------------ | Branch (9578:33): [True: 2, False: 4.73k] ------------------ 9579| 2| { 9580| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 9581| 2| goto exit_function; 9582| 2| } 9583| 4.73k| if ((ret = AddLinkedBond(last_atom[num_open - 1], curAtom, (AT_NUMB)nNumAtoms, pLB))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9583:33): [True: 0, False: 4.73k] ------------------ 9584| 0| { 9585| 0| goto exit_function; 9586| 0| } 9587| 4.73k| last_atom[num_open] = curAtom; 9588| 4.73k| state = 'N'; 9589| 4.73k| break; 9590| 38.7k| case '-': ------------------ | Branch (9590:25): [True: 38.7k, False: 32.9k] ------------------ 9591| 38.7k| if ((ret = AddLinkedBond(last_atom[num_open], curAtom, (AT_NUMB)nNumAtoms, pLB))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9591:33): [True: 9, False: 38.7k] ------------------ 9592| 9| { 9593| 9| goto exit_function; 9594| 9| } 9595| 38.7k| last_atom[num_open] = curAtom; 9596| 38.7k| state = 'N'; 9597| 38.7k| break; 9598| 0| default: ------------------ | Branch (9598:25): [True: 0, False: 71.6k] ------------------ 9599| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9600| 0| goto exit_function; 9601| 71.6k| } 9602| 71.6k| } 9603| 0| else 9604| 0| { 9605| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9606| 0| goto exit_function; 9607| 0| } 9608| 71.6k| break; 9609| 135k| } 9610| 135k| } 9611| 14.2k| } 9612| | 9613| | /* Store the bonds in connection table */ 9614| 14.2k| if (lenConnTable > 1) ------------------ | Branch (9614:13): [True: 9.38k, False: 4.89k] ------------------ 9615| 9.38k| { 9616| 65.8k| for (i = 0, m = 0; i < nNumAtoms; i++) ------------------ | Branch (9616:32): [True: 56.6k, False: 9.22k] ------------------ 9617| 56.6k| { 9618| 56.6k| k = 0; 9619| | 9620| 56.6k| if (!pLB->pBond) ------------------ | Branch (9620:21): [True: 8, False: 56.6k] ------------------ 9621| 8| { 9622| 8| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 9623| 8| goto exit_function; 9624| 8| } 9625| | 9626| 56.6k| if ((j = pLB->pBond[i + 1].prev)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (9626:21): [True: 56.5k, False: 61] ------------------ 9627| 56.5k| { 9628| 112k| while (k < MAXVAL) ------------------ | | 70| 112k|#define MAXVAL 50 /* max number of bonds per atom */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (9628:28): [True: 112k, False: 12] ------------------ 9629| 112k| { 9630| 112k| neighbor[k++] = pLB->pBond[j].neigh; 9631| 112k| if (j == i + 1) ------------------ | Branch (9631:29): [True: 56.5k, False: 55.5k] ------------------ 9632| 56.5k| break; 9633| 55.5k| j = pLB->pBond[j].prev; 9634| 55.5k| } 9635| 56.5k| } 9636| 56.6k| if (j != i + 1) ------------------ | Branch (9636:21): [True: 73, False: 56.5k] ------------------ 9637| 73| { 9638| 73| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 73|#define RI_ERR_SYNTAX (-2) ------------------ 9639| 73| goto exit_function; 9640| 73| } 9641| | 9642| | /* sort the neighbors */ 9643| | 9644| 56.5k| insertions_sort_AT_NUMB(neighbor, k); 9645| | 9646| 56.5k| if (m == pInChI[iComponent].lenConnTable) ------------------ | Branch (9646:21): [True: 12, False: 56.5k] ------------------ 9647| 12| { 9648| 12| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 12|#define RI_ERR_SYNTAX (-2) ------------------ 9649| 12| goto exit_function; 9650| 12| } 9651| | 9652| 56.5k|#if ( FIX_GAF_2020_25726==1 ) 9653| 110k| for (j = 1; j < k; j++) ------------------ | Branch (9653:29): [True: 54.3k, False: 56.5k] ------------------ 9654| 54.3k| { 9655| 54.3k| if (neighbor[j] == neighbor[j - 1]) ------------------ | Branch (9655:25): [True: 68, False: 54.2k] ------------------ 9656| 68| { 9657| 68| ret = RI_ERR_SYNTAX; /* syntax error - same nbr twice, i.e. multiple bond between same atoms */ ------------------ | | 16| 68|#define RI_ERR_SYNTAX (-2) ------------------ 9658| 68| goto exit_function; 9659| 68| } 9660| 54.3k| } 9661| 56.5k|#endif 9662| 56.5k| pInChI[iComponent].nConnTable[m++] = i + 1; /* atom number */ 9663| 111k| for (j = 0; j < k && (int)neighbor[j] <= i; j++) ------------------ | Branch (9663:29): [True: 89.8k, False: 21.9k] | Branch (9663:38): [True: 55.2k, False: 34.5k] ------------------ 9664| 55.2k| { 9665| 55.2k| if (m == pInChI[iComponent].lenConnTable) ------------------ | Branch (9665:25): [True: 5, False: 55.2k] ------------------ 9666| 5| { 9667| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 9668| 5| goto exit_function; 9669| 5| } 9670| 55.2k| pInChI[iComponent].nConnTable[m++] = neighbor[j]; 9671| 55.2k| } 9672| 56.5k| } 9673| 9.22k| if (m != lenConnTable) ------------------ | Branch (9673:17): [True: 0, False: 9.22k] ------------------ 9674| 0| { 9675| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 9676| 0| goto exit_function; 9677| 0| } 9678| 9.22k| } 9679| 4.89k| else 9680| 4.89k| { 9681| 4.89k| pInChI[iComponent].nConnTable[0] = 1; /* single atom */ 9682| 4.89k| } 9683| | 9684| | /* Duplicate if needed */ 9685| 74.1k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (9685:21): [True: 60.0k, False: 14.1k] ------------------ 9686| 60.0k| { 9687| | /* 9688| | if ( pInChI[iComponent+i].nConnTable ) { 9689| | inchi_free( pInChI[iComponent+i].nConnTable ); 9690| | } 9691| | pInChI[iComponent+i].nConnTable = (AT_NUMB *)inchi_calloc( lenConnTable+1, sizeof(pInChI[0].nConnTable[0]) ); 9692| | if ( !pInChI[iComponent+i].nConnTable ) { 9693| | ret = RI_ERR_ALLOC; 9694| | goto exit_function; 9695| | } 9696| | */ 9697| 60.0k| if (!pInChI[iComponent + i].nConnTable || pInChI[iComponent + i].lenConnTable != lenConnTable) ------------------ | Branch (9697:17): [True: 0, False: 60.0k] | Branch (9697:55): [True: 0, False: 60.0k] ------------------ 9698| 0| { 9699| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 9700| 0| goto exit_function; 9701| 0| } 9702| 60.0k| memcpy(pInChI[iComponent + i].nConnTable, pInChI[iComponent].nConnTable, lenConnTable * sizeof(pInChI[0].nConnTable[0])); 9703| 60.0k| } 9704| | /* prepare for the next connection table */ 9705| 14.1k| iComponent += i; 9706| 14.1k| if (*pEnd) ------------------ | Branch (9706:13): [True: 6.28k, False: 7.83k] ------------------ 9707| 6.28k| pStart = pEnd + 1; 9708| 7.83k| else 9709| 7.83k| break; 9710| | /* We must check if we have already read as many components as we have in the fragment. */ 9711| | /* If yes, then we break, because anything else that might follow cannot be useful information. */ 9712| | /* There are files with a trailing ";" that would cause a problem (memory allocation bug) if we did not do this. */ 9713| 6.28k| if (iComponent == nNumComponents) ------------------ | Branch (9713:13): [True: 928, False: 5.35k] ------------------ 9714| 928| break; 9715| 6.28k| } 9716| 8.76k| ret = iComponent; 9717| | 9718| 9.09k|exit_function: 9719| | 9720| 9.09k| if (pLB->pBond) ------------------ | Branch (9720:9): [True: 8.92k, False: 167] ------------------ 9721| 8.92k| { 9722| 8.92k| INCHI_HEAPCHK 9723| 8.92k| inchi_free(pLB->pBond); ------------------ | | 1152| 8.92k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 8.92k, False: 0] | | | Branch (1152:50): [Folded, False: 8.92k] | | ------------------ ------------------ 9724| 8.92k| } 9725| | 9726| 9.09k| return ret; 9727| 8.76k|#undef LAST_AT_LEN 9728| 8.76k|} ichiread.c:AddLinkedBond: 10717| 62.2k|{ 10718| 62.2k| int nReqLen = inchi_max(2 * num_at + 2, pLB->len + 2); ------------------ | | 138| 62.2k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 50.2k, False: 11.9k] | | ------------------ ------------------ 10719| 62.2k| AT_NUMB prev; 10720| 62.2k|#if ( FIX_GAF_2019_2==1 ) 10721| 62.2k| { 10722| 62.2k| if (at2 > num_at || at1 > num_at || at1 < 0 || at2<0 || num_at>MAX_ATOMS) ------------------ | | 15| 62.2k|#define MAX_ATOMS 32766 ------------------ | Branch (10722:13): [True: 0, False: 62.2k] | Branch (10722:29): [True: 0, False: 62.2k] | Branch (10722:45): [True: 0, False: 62.2k] | Branch (10722:56): [True: 0, False: 62.2k] | Branch (10722:65): [True: 10, False: 62.2k] ------------------ 10723| 10| { 10724| 10| return RI_ERR_SYNTAX; ------------------ | | 16| 10|#define RI_ERR_SYNTAX (-2) ------------------ 10725| 10| } 10726| 62.2k| } 10727| 62.2k|#endif 10728| 62.2k| if (pLB->len_alloc <= nReqLen) ------------------ | Branch (10728:9): [True: 8.97k, False: 53.2k] ------------------ 10729| 8.97k| { 10730| | /*int nNewLen = nReqLen + (nReqLen + LINKED_BOND_ADD - 1)%LINKED_BOND_ADD + LINKED_BOND_ADD;*/ 10731| 8.97k| int nNewLen = nReqLen - nReqLen % LINKED_BOND_ADD + 2 * LINKED_BOND_ADD; ------------------ | | 64| 8.97k|#define LINKED_BOND_ADD 128 ------------------ int nNewLen = nReqLen - nReqLen % LINKED_BOND_ADD + 2 * LINKED_BOND_ADD; ------------------ | | 64| 8.97k|#define LINKED_BOND_ADD 128 ------------------ 10732| 8.97k| ONE_LINKED_BOND* pBond = (ONE_LINKED_BOND*)inchi_calloc(nNewLen, sizeof(pBond[0])); ------------------ | | 1146| 8.97k|#define inchi_calloc calloc ------------------ 10733| 8.97k| if (!pBond) ------------------ | Branch (10733:13): [True: 0, False: 8.97k] ------------------ 10734| 0| { 10735| 0| return RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 10736| 0| } 10737| 8.97k| if (pLB->pBond && pLB->len) ------------------ | Branch (10737:13): [True: 42, False: 8.92k] | Branch (10737:27): [True: 40, False: 2] ------------------ 10738| 40| { 10739| 40| memcpy(pBond, pLB->pBond, pLB->len * sizeof(pBond[0])); 10740| 40| } 10741| 8.97k| if (pLB->pBond) ------------------ | Branch (10741:13): [True: 42, False: 8.92k] ------------------ 10742| 42| inchi_free(pLB->pBond); ------------------ | | 1152| 42|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 42, False: 0] | | | Branch (1152:50): [Folded, False: 42] | | ------------------ ------------------ 10743| 8.97k| pLB->pBond = pBond; 10744| 8.97k| pLB->len_alloc = nNewLen; 10745| 8.97k| } 10746| 62.2k| if (!pLB->len) ------------------ | Branch (10746:9): [True: 9.35k, False: 52.8k] ------------------ 10747| 9.35k| { 10748| 9.35k| pLB->len = num_at + 1; 10749| 9.35k| memset(pLB->pBond, 0, ((long long)num_at + 1) * sizeof(pLB->pBond[0])); /* djb-rwth: cast operator added; memset_s C11/Annex K variant? */ 10750| 9.35k| } 10751| | 10752| 62.2k| prev = pLB->pBond[at1].prev; /* position of the last neighbor of at1 in the pLB->pBond */ 10753| 62.2k| if (!prev) ------------------ | Branch (10753:9): [True: 9.35k, False: 52.8k] ------------------ 10754| 9.35k| { 10755| 9.35k| pLB->pBond[at1].neigh = at2; 10756| 9.35k| pLB->pBond[at1].prev = at1; 10757| 9.35k| } 10758| 52.8k| else 10759| 52.8k| { 10760| 52.8k| pLB->pBond[pLB->len].neigh = at2; 10761| 52.8k| pLB->pBond[pLB->len].prev = prev; 10762| 52.8k| pLB->pBond[at1].prev = pLB->len++; 10763| 52.8k| } 10764| | 10765| 62.2k| prev = pLB->pBond[at2].prev; /* position of the last neighbor of at2 in the pLB->pBond */ 10766| 62.2k| if (!prev) ------------------ | Branch (10766:9): [True: 47.6k, False: 14.6k] ------------------ 10767| 47.6k| { 10768| 47.6k| pLB->pBond[at2].neigh = at1; 10769| 47.6k| pLB->pBond[at2].prev = at2; 10770| 47.6k| } 10771| 14.6k| else 10772| 14.6k| { 10773| 14.6k| pLB->pBond[pLB->len].neigh = at1; 10774| 14.6k| pLB->pBond[pLB->len].prev = prev; 10775| 14.6k| pLB->pBond[at2].prev = pLB->len++; 10776| 14.6k| } 10777| | 10778| 62.2k| return 0; 10779| 62.2k|} ichiread.c:ParseSegmentMobileH: 8248| 11.4k|{ 8249| 11.4k|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) 8250| | 8251| | /* Pass 1: count bonds and find actual numbers of atom */ 8252| | 8253| 11.4k| int i, mpy_component, num_H, num_Minus, val, num_Atoms, numCtAtoms, tg_alloc_len, len, len2, k = 0; 8254| 11.4k| int num_H_component, num_H_formula, num_taut_H_component, num_H_InChI, ret2; 8255| 11.4k| int nNumComponents, iComponent, lenTautomer, tg_pos_Tautomer, iTGroup; /* djb-rwth: removing redundant variables */ 8256| 11.4k| const char* p, * q, * h, * t, * p1, * pTaut, * pStart, * pEnd; 8257| 11.4k| int curAtom, nxtAtom; /* djb-rwth: fixing coverity ID #499563 */ 8258| 11.4k| int state, ret, nAltMobileH = ALT_TAUT(bMobileH); /* djb-rwth: removing redundant variables */ ------------------ | | 577| 11.4k|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 11.4k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 11.4k] | | ------------------ ------------------ 8259| 11.4k| INChI* pInChI = pInpInChI[bMobileH]; 8260| 11.4k| INChI* pAltInChI = pInpInChI[nAltMobileH]; 8261| 11.4k| int base = 10; 8262| | 8263| 11.4k| num_H = -999; /* impossible value */ 8264| 11.4k| num_Minus = -999; /* impossible value */ 8265| 11.4k| tg_pos_Tautomer = -999; /* impossible value */ 8266| | 8267| | /* number of immobile H is always allocated; immobile H are present in M layer only */ 8268| 11.4k| nNumComponents = pnNumComponents[bMobileH]; 8269| | 8270| | /* djb-rwth: fixing oss-fuzz issues #66985, #66718, #43512, #43456, #43420, #42774, #34772, #30156 */ 8271| | 8272| 345k| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (8272:17): [True: 334k, False: 11.4k] ------------------ 8273| 334k| { 8274| 334k| len = pInChI[i].nNumberOfAtoms; 8275| 334k| if (bMobileH == TAUT_NON && i < pnNumComponents[nAltMobileH]) ------------------ | | 574| 668k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8275:13): [True: 42.0k, False: 292k] | Branch (8275:37): [True: 38.8k, False: 3.13k] ------------------ 8276| 38.8k| { 8277| 38.8k| if (len < pAltInChI[i].nNumberOfAtoms) ------------------ | Branch (8277:17): [True: 0, False: 38.8k] ------------------ 8278| 0| { 8279| 0| len = pAltInChI[i].nNumberOfAtoms; 8280| 0| if (pInChI[i].nNum_H) ------------------ | Branch (8280:21): [True: 0, False: 0] ------------------ 8281| 0| { 8282| 0| inchi_free(pInChI[i].nNum_H); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 8283| 0| pInChI[i].nNum_H = NULL; 8284| 0| } 8285| 0| } 8286| 38.8k| } 8287| 334k| len++; 8288| 334k| if (!pInChI[i].nNum_H) ------------------ | Branch (8288:13): [True: 334k, False: 60] ------------------ 8289| 334k| { 8290| 334k| S_CHAR* pi_nnh2 = (S_CHAR*)inchi_calloc(len, sizeof(pInChI[0].nNum_H[0])); ------------------ | | 1146| 334k|#define inchi_calloc calloc ------------------ 8291| 334k| if (!pi_nnh2) ------------------ | Branch (8291:17): [True: 0, False: 334k] ------------------ 8292| 0| { 8293| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 8294| 0| goto exit_function; 8295| 0| } 8296| 334k| pInChI[i].nNum_H = pi_nnh2; 8297| | /* pi_nnh2_init = true; */ 8298| 334k| } 8299| | /* copy immobile H from Mobile-H layer to Fixed-H layer */ 8300| 334k| if (bMobileH == TAUT_NON && i < pnNumComponents[nAltMobileH]) ------------------ | | 574| 668k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8300:13): [True: 42.0k, False: 292k] | Branch (8300:37): [True: 38.8k, False: 3.13k] ------------------ 8301| 38.8k| { 8302| 38.8k| S_CHAR* pai_nnh = (S_CHAR*)inchi_realloc(pAltInChI[i].nNum_H, len * sizeof(pAltInChI[0].nNum_H[0])); ------------------ | | 1149| 38.8k|#define inchi_realloc realloc ------------------ 8303| 38.8k| if (pai_nnh) ------------------ | Branch (8303:17): [True: 38.8k, False: 0] ------------------ 8304| 38.8k| { 8305| 38.8k| S_CHAR* pi_nnh1 = NULL; /* copied from below to satisfy C syntax 2024-09-01 DT */ 8306| 38.8k| pAltInChI[i].nNum_H = pai_nnh; 8307| | /*if (!pi_nnh2_init) 8308| | { 8309| | */ 8310| 38.8k| pi_nnh1 = (S_CHAR*)inchi_calloc(len, sizeof(pInChI[0].nNum_H[0])); ------------------ | | 1146| 38.8k|#define inchi_calloc calloc ------------------ 8311| 38.8k| if (!pi_nnh1) ------------------ | Branch (8311:21): [True: 0, False: 38.8k] ------------------ 8312| 0| { 8313| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 8314| 0| goto exit_function; 8315| 0| } 8316| 38.8k| memcpy(pi_nnh1, pai_nnh, ((long long)len - 1) * sizeof(pInChI[0].nNum_H[0])); /* djb-rwth: cast operator added */ 8317| | /* djb-rwth: alternative solution 8318| | k = memcpy_custom(&pi_nnh1[i], pAltInChI[i].nNum_H, ((long long)len - 1) * sizeof(pInChI[0].nNum_H[0])) 8319| | if (k) 8320| | { 8321| | ret = RI_ERR_ALLOC; 8322| | goto exit_function; 8323| | } 8324| | */ 8325| 38.8k| pInChI[i].nNum_H = pi_nnh1; 8326| | /* 8327| | } 8328| | else 8329| | { 8330| | memcpy(pi_nnh2, pai_nnh, ((long long)len - 1) * sizeof(pInChI[0].nNum_H[0])); * djb-rwth: cast operator added * 8331| | * djb-rwth: alternative solution * 8332| | k = memcpy_custom(&pi_nnh2[i], pAltInChI[i].nNum_H, ((long long)len - 1) * sizeof(pInChI[0].nNum_H[0])) 8333| | if (k) 8334| | { 8335| | ret = RI_ERR_ALLOC; 8336| | goto exit_function; 8337| | } 8338| | 8339| | } 8340| | */ 8341| 38.8k| } 8342| 0| else 8343| 0| { 8344| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 8345| 0| goto exit_function; 8346| 0| } 8347| 38.8k| } 8348| 334k| } 8349| | 8350| 11.4k| if (str[0] != 'h') ------------------ | Branch (8350:9): [True: 6.03k, False: 5.46k] ------------------ 8351| 6.03k| { 8352| 6.03k| return 0; 8353| 6.03k| } 8354| | 8355| | /* Read Hydrogen info in 1 pass */ 8356| | 8357| 5.46k| pStart = (char*)str + 1; 8358| 5.46k| iComponent = 0; 8359| 5.46k| nNumComponents = pnNumComponents[bMobileH]; 8360| | 8361| 5.74k| while (1) ------------------ | Branch (8361:12): [True: 5.74k, Folded] ------------------ 8362| 5.74k| { 8363| | /* cycle over components */ 8364| 5.74k| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (8364:13): [True: 5.44k, False: 292] ------------------ 8365| 5.44k| { 8366| 5.44k| pEnd = pStart + strlen(pStart); 8367| 5.44k| } 8368| 5.74k| if ((p = strchr(pStart, '*')) && p < pEnd) ------------------ | Branch (8368:13): [True: 132, False: 5.60k] | Branch (8368:42): [True: 81, False: 51] ------------------ 8369| 81| { 8370| 81| mpy_component = (int)inchi_strtol(pStart, &q, 10); 8371| 81|#if ( CHECK_STRTOL_ATNUMB==1 ) 8372| 81| if (mpy_component > MAX_ATOMS || mpy_component < 0) ------------------ | | 15| 162|#define MAX_ATOMS 32766 ------------------ | Branch (8372:17): [True: 0, False: 81] | Branch (8372:46): [True: 6, False: 75] ------------------ 8373| 6| { 8374| 6| ret = RI_ERR_SYNTAX; ------------------ | | 16| 6|#define RI_ERR_SYNTAX (-2) ------------------ 8375| 6| goto exit_function; 8376| 6| } 8377| 75|#endif 8378| 75|#if ( FIX_DALKE_BUGS == 1 ) 8379| 75| if (p != q || !isdigit(UCINT* pStart)) /* prevent non-positive multipliers */ ------------------ | Branch (8379:17): [True: 1, False: 74] | Branch (8379:27): [True: 0, False: 74] ------------------ 8380| |#else 8381| | if (p != q) 8382| |#endif 8383| 1| { 8384| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 8385| 1| goto exit_function; 8386| 1| } 8387| 74| p++; 8388| 74| } 8389| 5.65k| else 8390| 5.65k| { 8391| 5.65k| mpy_component = 1; 8392| 5.65k| p = pStart; 8393| 5.65k| } 8394| 5.73k| pStart = p; 8395| | /* Pass 1.1 parse a component */ 8396| | /* djb-rwth: removing redundant code */ 8397| | /* djb-rwth: removing redundant code */ 8398| | /* djb-rwth: removing redundant code */ 8399| 5.73k| curAtom = 0; /* djb-rwth: ignoring LLVM warning: value used */ 8400| 5.73k| numCtAtoms = pInChI[iComponent].nNumberOfAtoms; 8401| 5.73k| if (bMobileH == TAUT_NON && iComponent < pnNumComponents[nAltMobileH]) ------------------ | | 574| 11.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8401:13): [True: 1.41k, False: 4.31k] | Branch (8401:37): [True: 1.38k, False: 39] ------------------ 8402| 1.38k| { 8403| 1.38k| numCtAtoms = pAltInChI[iComponent].nNumberOfAtoms; 8404| 1.38k| } 8405| | 8406| 5.73k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (8406:13): [True: 5.18k, False: 552] | Branch (8406:25): [True: 0, False: 5.18k] ------------------ 8407| 0| { 8408| | /* check if compressed InChI */ 8409| 0| *pbAbc = (*p == ',' || isupper(UCINT* p)) ? 1 : 0; ------------------ | Branch (8409:23): [True: 0, False: 0] | Branch (8409:36): [True: 0, False: 0] ------------------ 8410| 0| } 8411| 5.73k| base = (*pbAbc == 1) ? ALPHA_BASE : 10; ------------------ | | 170| 0|#define ALPHA_BASE 27 ------------------ | Branch (8411:16): [True: 0, False: 5.73k] ------------------ 8412| | 8413| | /* immobile H */ 8414| 5.73k| t = pTaut = (*pbAbc == 1) ? strchr(p, ',') : strchr(p, '('); /* locate the first tautomer group character */ ------------------ | Branch (8414:21): [True: 0, False: 5.73k] ------------------ 8415| | 8416| 5.73k| if (t && bMobileH == TAUT_NON) ------------------ | | 574| 2.48k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8416:13): [True: 2.48k, False: 3.24k] | Branch (8416:18): [True: 1, False: 2.48k] ------------------ 8417| 1| { 8418| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 8419| 1| goto exit_function; 8420| 1| } 8421| 5.73k| if (!pTaut || pTaut > pEnd) ------------------ | Branch (8421:13): [True: 3.24k, False: 2.48k] | Branch (8421:23): [True: 10, False: 2.47k] ------------------ 8422| 3.25k| { 8423| 3.25k| pTaut = pEnd; 8424| 3.25k| t = NULL; /* found no tautomeric group for this component */ 8425| 3.25k| } 8426| | /* djb-rwth: fixing oss-fuzz issue #69489 */ 8427| 11.7k| for (i = 0; (i < mpy_component) && (iComponent + i < nNumComponents); i++) ------------------ | Branch (8427:21): [True: 6.08k, False: 5.71k] | Branch (8427:44): [True: 6.07k, False: 12] ------------------ 8428| 6.07k| { 8429| 6.07k| if (bMobileH == TAUT_NON) ------------------ | | 574| 6.07k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8429:17): [True: 1.45k, False: 4.62k] ------------------ 8430| 1.45k| { 8431| | /* allocate nNum_H_fixed */ 8432| 1.45k| if (pInChI[iComponent + i].nNum_H_fixed) ------------------ | Branch (8432:21): [True: 0, False: 1.45k] ------------------ 8433| 0| { 8434| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 8435| 0| goto exit_function; 8436| 0| } 8437| 1.45k| if (iComponent + i < pnNumComponents[nAltMobileH]) ------------------ | Branch (8437:21): [True: 1.38k, False: 69] ------------------ 8438| 1.38k| { 8439| 1.38k| len = inchi_max(pInChI[iComponent + i].nNumberOfAtoms, pAltInChI[iComponent + i].nNumberOfAtoms) + 1; ------------------ | | 138| 1.38k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 3, False: 1.37k] | | ------------------ ------------------ 8440| 1.38k| } 8441| 69| else 8442| 69| { 8443| 69| len = pInChI[iComponent + i].nNumberOfAtoms + 1; 8444| 69| } 8445| 1.45k| pInChI[iComponent + i].nNum_H_fixed = (S_CHAR*)inchi_calloc(len, sizeof(pInChI[0].nNum_H_fixed[0])); ------------------ | | 1146| 1.45k|#define inchi_calloc calloc ------------------ 8446| 1.45k| if (!pInChI[iComponent + i].nNum_H_fixed) ------------------ | Branch (8446:21): [True: 0, False: 1.45k] ------------------ 8447| 0| { 8448| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 8449| 0| goto exit_function; 8450| 0| } 8451| | /* compare nAtom */ 8452| 1.45k| if (iComponent + i < pnNumComponents[nAltMobileH]) ------------------ | Branch (8452:21): [True: 1.38k, False: 69] ------------------ 8453| 1.38k| { 8454| 1.38k| len2 = inchi_min(pInChI[iComponent + i].nNumberOfAtoms, pAltInChI[iComponent + i].nNumberOfAtoms); ------------------ | | 139| 1.38k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 1.38k] | | ------------------ ------------------ 8455| 1.38k| if (pInChI[iComponent + i].nAtom && len2) ------------------ | Branch (8455:25): [True: 1.38k, False: 0] | Branch (8455:57): [True: 1.38k, False: 0] ------------------ 8456| 1.38k| { 8457| | /* check */ 8458| 1.38k| if (memcmp(pInChI[iComponent + i].nAtom, pAltInChI[iComponent + i].nAtom, len2 * sizeof(pInChI[0].nAtom[0]))) ------------------ | Branch (8458:29): [True: 5, False: 1.37k] ------------------ 8459| 5| { 8460| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 8461| 5| goto exit_function; 8462| 5| } 8463| 1.38k| } 8464| | /* allocate and copy atom if bridging H are present */ 8465| 1.37k| if (pInChI[iComponent + i].nNumberOfAtoms < pAltInChI[iComponent + i].nNumberOfAtoms) ------------------ | Branch (8465:25): [True: 0, False: 1.37k] ------------------ 8466| 0| { 8467| 0| if (pInChI[iComponent + i].nAtom) ------------------ | Branch (8467:29): [True: 0, False: 0] ------------------ 8468| 0| inchi_free(pInChI[iComponent + i].nAtom); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 8469| 0| if (!(pInChI[iComponent + i].nAtom = (U_CHAR*)inchi_calloc(len, sizeof(pInChI[0].nAtom[0])))) ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ | Branch (8469:29): [True: 0, False: 0] ------------------ 8470| 0| { 8471| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 8472| 0| goto exit_function; 8473| 0| } 8474| 0| if (len > 1) ------------------ | Branch (8474:29): [True: 0, False: 0] ------------------ 8475| 0| { 8476| 0| memcpy(pInChI[iComponent + i].nAtom, pAltInChI[iComponent + i].nAtom, ((long long)len - 1) * sizeof(pInChI[0].nAtom[0])); /* djb-rwth: cast operator added */ 8477| 0| } 8478| | /* correct number of atoms including bridging H */ 8479| 0| pInChI[iComponent + i].nNumberOfAtoms = pAltInChI[iComponent + i].nNumberOfAtoms; 8480| 0| } 8481| 1.37k| } 8482| 1.45k| } 8483| 6.07k| } 8484| | 8485| 5.72k| if (*pbAbc == 1) ------------------ | Branch (8485:13): [True: 0, False: 5.72k] ------------------ 8486| 0| { 8487| | /* read numbers of H: XnYn... or XYn... */ 8488| 0| p = pStart; 8489| 0| tg_alloc_len = 0; 8490| 0| num_H_component = num_taut_H_component = 0; 8491| 0| while (p < pTaut) ------------------ | Branch (8491:20): [True: 0, False: 0] ------------------ 8492| 0| { 8493| | /* syntax check: atom number */ 8494| 0| if (!*p || !isupper(UCINT* p)) ------------------ | Branch (8494:21): [True: 0, False: 0] | Branch (8494:28): [True: 0, False: 0] ------------------ 8495| 0| { 8496| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8497| 0| goto exit_function; 8498| 0| } 8499| 0| if ((curAtom = nxtAtom = (int)inchi_strtol(p, &q, base))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (8499:21): [True: 0, False: 0] ------------------ 8500| 0| { 8501| 0| p = q; 8502| 0| if (isupper(UCINT* p)) ------------------ | Branch (8502:25): [True: 0, False: 0] ------------------ 8503| 0| { 8504| 0| nxtAtom = (int)inchi_strtol(p, &q, base); 8505| 0|#if ( CHECK_STRTOL_ATNUMB==1 ) 8506| 0| if (nxtAtom > MAX_ATOMS || nxtAtom < 0) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ | Branch (8506:29): [True: 0, False: 0] | Branch (8506:52): [True: 0, False: 0] ------------------ 8507| 0| { 8508| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8509| 0| goto exit_function; 8510| 0| } 8511| 0|#endif 8512| 0| p = q; 8513| 0| } 8514| 0| } 8515| 0| if (curAtom <= 0 || curAtom > nxtAtom || ------------------ | Branch (8515:21): [True: 0, False: 0] | Branch (8515:37): [True: 0, False: 0] ------------------ 8516| 0| nxtAtom > numCtAtoms || p > pTaut) ------------------ | Branch (8516:21): [True: 0, False: 0] | Branch (8516:45): [True: 0, False: 0] ------------------ 8517| 0| { 8518| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8519| 0| goto exit_function; 8520| 0| } 8521| | /* number of H, may be negative */ 8522| 0| if (!(num_H = (int)inchi_strtol(p, &q, 10)) || q > pTaut) ------------------ | Branch (8522:21): [True: 0, False: 0] | Branch (8522:64): [True: 0, False: 0] ------------------ 8523| 0| { 8524| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8525| 0| goto exit_function; 8526| 0| } 8527| 0| p = q; 8528| | /* set number of H */ 8529| | /* djb-rwth: fixing oss-fuzz issue #38399 */ 8530| 0| if (((bMobileH == TAUT_YES) && pInChI[iComponent].nNum_H) || ((bMobileH != TAUT_YES) && pInChI[iComponent].nNum_H_fixed)) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (((bMobileH == TAUT_YES) && pInChI[iComponent].nNum_H) || ((bMobileH != TAUT_YES) && pInChI[iComponent].nNum_H_fixed)) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (8530:22): [True: 0, False: 0] | Branch (8530:48): [True: 0, False: 0] | Branch (8530:79): [True: 0, False: 0] | Branch (8530:105): [True: 0, False: 0] ------------------ 8531| 0| { 8532| 0| for (i = curAtom; i <= nxtAtom; i++) ------------------ | Branch (8532:39): [True: 0, False: 0] ------------------ 8533| 0| { 8534| 0| nNum_H(iComponent)[i - 1] = num_H; ------------------ | | 8249| 0|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8249:31): [True: 0, False: 0] | | ------------------ ------------------ 8535| 0| num_H_component += num_H; 8536| 0| } 8537| 0| } 8538| 0| } 8539| 0| if (p != pTaut) ------------------ | Branch (8539:17): [True: 0, False: 0] ------------------ 8540| 0| { 8541| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8542| 0| goto exit_function; 8543| 0| } 8544| 0| } 8545| 5.72k| else 8546| 5.72k| { 8547| | /* read numbers of H: 1-2,3H2,4,5H3 */ 8548| 5.72k| p = pStart; 8549| 5.72k| tg_alloc_len = 0; 8550| 5.72k| num_H_component = num_taut_H_component = 0; 8551| 5.72k|#if ( FIX_GAF_2019_1==1 ) 8552| 5.72k| { 8553| 5.72k| char invalid; 8554| 5.72k| const char* str1 = str + 1; 8555| 5.72k| if (bMobileH == TAUT_NON) /* FixedH layer "/h"*/ ------------------ | | 574| 5.72k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8555:21): [True: 1.41k, False: 4.31k] ------------------ 8556| 1.41k| { 8557| 1.41k| invalid = str1[strspn(str1, "0123456789hDHT-,;()*")]; 8558| 1.41k| } 8559| 4.31k| else /* Main layer (mobileH) "/h"*/ 8560| 4.31k| { 8561| 4.31k| invalid = str1[strspn(str1, "0123456789DHT-,;()*")]; 8562| 4.31k| } 8563| 5.72k| if (invalid != '\0') ------------------ | Branch (8563:21): [True: 10, False: 5.71k] ------------------ 8564| 10| { 8565| 10| ret = RI_ERR_SYNTAX; ------------------ | | 16| 10|#define RI_ERR_SYNTAX (-2) ------------------ 8566| 10| goto exit_function; 8567| 10| } 8568| 5.72k| } 8569| 5.71k|#endif 8570| 9.93k| while (p < pTaut) ------------------ | Branch (8570:20): [True: 4.32k, False: 5.61k] ------------------ 8571| 4.32k| { 8572| | /* syntax check: atom number */ 8573| 4.32k| if (!*p || !isdigit(UCINT* p)) ------------------ | Branch (8573:21): [True: 0, False: 4.32k] | Branch (8573:28): [True: 11, False: 4.31k] ------------------ 8574| 11| { 8575| 11| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 11|#define RI_ERR_SYNTAX (-2) ------------------ 8576| 11| goto exit_function; 8577| 11| } 8578| | /* number of H */ 8579| 4.31k| h = p + strcspn(p, "Hh"); 8580| | /*h = strchr( p, 'H' );*/ 8581| 4.31k| if (!*h || h >= pTaut) ------------------ | Branch (8581:21): [True: 3, False: 4.31k] | Branch (8581:28): [True: 2, False: 4.31k] ------------------ 8582| 5| { 8583| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 8584| 5| goto exit_function; 8585| | /* 8586| | p = pTaut; 8587| | h = NULL; 8588| | break; */ /* no more H found */ 8589| 5| } 8590| 4.31k| num_H = (*h == 'H') ? 1 : (*h == 'h') ? -1 : 0; ------------------ | Branch (8590:25): [True: 3.03k, False: 1.27k] | Branch (8590:43): [True: 1.27k, False: 0] ------------------ 8591| 4.31k| if (!num_H) ------------------ | Branch (8591:21): [True: 0, False: 4.31k] ------------------ 8592| 0| { 8593| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8594| 0| goto exit_function; 8595| 0| } 8596| 4.31k| if (h[1] && isdigit(UCINT h[1])) ------------------ | Branch (8596:21): [True: 2.18k, False: 2.12k] | Branch (8596:29): [True: 1.00k, False: 1.18k] ------------------ 8597| 1.00k| { 8598| 1.00k| num_H *= (int)inchi_strtol(h + 1, &p1, 10); 8599| 1.00k| } 8600| 3.30k| else 8601| 3.30k| { 8602| 3.30k| p1 = h + 1; /* next set of immobile H */ 8603| 3.30k| } 8604| 4.31k| if (*p1 == ',') ------------------ | Branch (8604:21): [True: 1.67k, False: 2.64k] ------------------ 8605| 1.67k| { 8606| 1.67k| p1++; /* next H-subsegment; otherwise (H or ; or end of the segment */ 8607| 1.67k| } 8608| | /* list of atoms that have num_H */ 8609| 9.02k| while (p < h) ------------------ | Branch (8609:24): [True: 4.80k, False: 4.22k] ------------------ 8610| 4.80k| { 8611| 4.80k| if (!*p || !isdigit(UCINT* p)) ------------------ | Branch (8611:25): [True: 0, False: 4.80k] | Branch (8611:32): [True: 3, False: 4.79k] ------------------ 8612| 3| { 8613| 3| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 8614| 3| goto exit_function; 8615| 3| } 8616| 4.79k| nxtAtom = curAtom = (int)inchi_strtol(p, &q, 10); 8617| 4.79k| if (*q == '-') ------------------ | Branch (8617:25): [True: 222, False: 4.57k] ------------------ 8618| 222| { 8619| 222| nxtAtom = (int)inchi_strtol(q + 1, &q, 10); 8620| 222|#if ( CHECK_STRTOL_ATNUMB==1 ) 8621| 222| if (nxtAtom > MAX_ATOMS || nxtAtom < 0) ------------------ | | 15| 444|#define MAX_ATOMS 32766 ------------------ | Branch (8621:29): [True: 2, False: 220] | Branch (8621:52): [True: 34, False: 186] ------------------ 8622| 36| { 8623| 36| ret = RI_ERR_SYNTAX; ------------------ | | 16| 36|#define RI_ERR_SYNTAX (-2) ------------------ 8624| 36| goto exit_function; 8625| 36| } 8626| 222|#endif 8627| 222| } 8628| | /* consitency check */ 8629| 4.76k| if (curAtom <= 0 || curAtom > numCtAtoms || ------------------ | Branch (8629:25): [True: 17, False: 4.74k] | Branch (8629:41): [True: 27, False: 4.71k] ------------------ 8630| 4.71k| nxtAtom < curAtom || nxtAtom > numCtAtoms) ------------------ | Branch (8630:25): [True: 0, False: 4.71k] | Branch (8630:46): [True: 6, False: 4.71k] ------------------ 8631| 50| { 8632| 50| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 50|#define RI_ERR_SYNTAX (-2) ------------------ 8633| 50| goto exit_function; 8634| 50| } 8635| | /* set number of H */ 8636| | /* djb-rwth: fixing oss-fuzz issue #38399 */ 8637| 4.71k| if (((bMobileH == TAUT_YES) && pInChI[iComponent].nNum_H) || ((bMobileH != TAUT_YES) && pInChI[iComponent].nNum_H_fixed)) ------------------ | | 575| 4.71k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (((bMobileH == TAUT_YES) && pInChI[iComponent].nNum_H) || ((bMobileH != TAUT_YES) && pInChI[iComponent].nNum_H_fixed)) ------------------ | | 575| 2.69k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (8637:26): [True: 2.01k, False: 2.69k] | Branch (8637:52): [True: 2.01k, False: 0] | Branch (8637:83): [True: 2.69k, False: 0] | Branch (8637:109): [True: 2.68k, False: 4] ------------------ 8638| 4.70k| { 8639| 13.0k| for (i = curAtom; i <= nxtAtom; i++) ------------------ | Branch (8639:43): [True: 8.35k, False: 4.70k] ------------------ 8640| 8.35k| { 8641| 8.35k| nNum_H(iComponent)[i - 1] = num_H; ------------------ | | 8249| 8.35k|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 575| 8.35k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8249:31): [True: 5.66k, False: 2.69k] | | ------------------ ------------------ 8642| 8.35k| num_H_component += num_H; 8643| 8.35k| } 8644| 4.70k| } 8645| | /* move to the next atom number if any */ 8646| 4.71k| p = q; 8647| 4.71k| if (*p == ',') ------------------ | Branch (8647:25): [True: 503, False: 4.20k] ------------------ 8648| 503| { 8649| 503| p++; 8650| 503| } 8651| 4.71k| } 8652| | 8653| 4.22k| if (p == h) ------------------ | Branch (8653:21): [True: 4.22k, False: 0] ------------------ 8654| 4.22k| { 8655| 4.22k| p = p1; 8656| 4.22k| } 8657| 0| else 8658| 0| { 8659| 0| if (p == pTaut) ------------------ | Branch (8659:25): [True: 0, False: 0] ------------------ 8660| 0| { 8661| 0| break; 8662| 0| } 8663| 0| else 8664| 0| { 8665| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8666| 0| goto exit_function; 8667| 0| } 8668| 0| } 8669| 4.22k| } 8670| 5.71k| } 8671| | 8672| | INCHI_HEAPCHK 8673| | /* ) -> (, H, N, [-, N,], AtNum,... AtNum) */ 8674| 5.61k| lenTautomer = 0; 8675| 5.61k| if ((p = t)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (8675:13): [True: 2.47k, False: 3.13k] ------------------ 8676| 2.47k| { 8677| 2.47k| if (*pbAbc == 1) ------------------ | Branch (8677:17): [True: 0, False: 2.47k] ------------------ 8678| 0| { 8679| | /* tautomeric groups: pass 1 */ 8680| 0| iTGroup = 0; 8681| 0| state = ')'; /* init as if the prev. t-group just ended */ /* djb-rwth: ignoring LLVM warning: value used */ 8682| 0| num_Atoms = 0; 8683| | /* Tautomeric info storage */ 8684| | /* NumGroups; ((NumAt+2, NumH, Num(-), At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 2} */ 8685| | /* Allocated length: [5*nNumberOfAtoms/2+1], see Alloc_INChI(...) */ 8686| 0| if (*p == ',') ------------------ | Branch (8686:21): [True: 0, False: 0] ------------------ 8687| 0| { /* start t-group */ 8688| 0| p++; 8689| 0| } 8690| 0| else 8691| 0| { 8692| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8693| 0| goto exit_function; 8694| 0| } 8695| 0| while (p < pEnd) ------------------ | Branch (8695:24): [True: 0, False: 0] ------------------ 8696| 0| { 8697| | /* start t-group */ 8698| 0| if (!isdigit(UCINT* p) || !(num_H = (int)inchi_strtol(p, &q, 10)) || q > pEnd) ------------------ | Branch (8698:25): [True: 0, False: 0] | Branch (8698:47): [True: 0, False: 0] | Branch (8698:90): [True: 0, False: 0] ------------------ 8699| 0| { 8700| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8701| 0| goto exit_function; 8702| 0| } 8703| 0| p = q; 8704| 0| num_Minus = 0; 8705| 0| if (*p == '-') ------------------ | Branch (8705:25): [True: 0, False: 0] ------------------ 8706| 0| { 8707| 0| p++; 8708| 0| if (isdigit(UCINT* p)) ------------------ | Branch (8708:29): [True: 0, False: 0] ------------------ 8709| 0| { 8710| 0| num_Minus = (int)inchi_strtol(p, &q, 10); 8711| 0| p = q; 8712| 0| } 8713| 0| else 8714| 0| { 8715| 0| num_Minus = 1; 8716| 0| } 8717| 0| } 8718| 0| if (p >= pEnd) ------------------ | Branch (8718:25): [True: 0, False: 0] ------------------ 8719| 0| { 8720| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8721| 0| goto exit_function; 8722| 0| } 8723| 0| if (!tg_alloc_len) ------------------ | Branch (8723:25): [True: 0, False: 0] ------------------ 8724| 0| { 8725| | /* 8726| | --- header --- 8727| | [num_t_groups] 8728| | --- one t-group: --- 8729| | [len=group length no including this value] 8730| | [num_H] 8731| | [num_(-)] 8732| | [Endpoint(1),...,Endpoint(len-2)] 8733| | --- next t-group --- 8734| | ... 8735| | 8736| | Max. size = 1 + 3*max_num_t_groups + max_num_endpoints 8737| | 8738| | max_num_t_groups = num_at/2 8739| | max_num_endpoints = num_at 8740| | 8741| | Max. size = 1 + 3*(num_at/2) + num_at = 1 + (5*num_at)/2 8742| | 5 = 3 + INCHI_T_NUM_MOVABLE = 3 + num_types_of_attachments 8743| | 8744| | This does not include zero termination! 8745| | 8746| | */ 8747| 0| tg_alloc_len = ((3 + INCHI_T_NUM_MOVABLE) * pInChI[iComponent].nNumberOfAtoms) / 2 + 1; ------------------ | | 749| 0|#define INCHI_T_NUM_MOVABLE 2 ------------------ 8748| 0| for (i = 0; i < mpy_component; i++) ------------------ | Branch (8748:37): [True: 0, False: 0] ------------------ 8749| 0| { 8750| 0| pInChI[iComponent + i].nTautomer = (AT_NUMB*)inchi_calloc((long long)tg_alloc_len + 1, sizeof(pInChI->nTautomer[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 8751| 0| if (!pInChI[iComponent + i].nTautomer) ------------------ | Branch (8751:33): [True: 0, False: 0] ------------------ 8752| 0| { 8753| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 8754| 0| goto exit_function; 8755| 0| } 8756| 0| pInChI[iComponent + i].lenTautomer = 0; 8757| 0| } 8758| 0| tg_pos_Tautomer = 1; /* number atoms (NumAt+2) position */ 8759| 0| } 8760| 0| else 8761| 0| { 8762| | /* next t-group */ 8763| 0| tg_pos_Tautomer = lenTautomer; 8764| 0| } 8765| 0| if (tg_pos_Tautomer + 3 >= tg_alloc_len) ------------------ | Branch (8765:25): [True: 0, False: 0] ------------------ 8766| 0| { 8767| 0| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 8768| 0| goto exit_function; 8769| 0| } 8770| 0| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 1] = num_H; 8771| 0| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 2] = num_Minus; 8772| 0| lenTautomer = tg_pos_Tautomer + 3; /* first atom number position */ 8773| 0| num_taut_H_component += num_H; 8774| | 8775| 0| while (p < pEnd && isupper(UCINT* p)) ------------------ | Branch (8775:28): [True: 0, False: 0] | Branch (8775:40): [True: 0, False: 0] ------------------ 8776| 0| { 8777| | /* read list of tautomeric atoms */ 8778| 0| val = (int)inchi_strtol(p, &q, base); 8779| 0| if (lenTautomer >= tg_alloc_len || val > numCtAtoms) ------------------ | Branch (8779:29): [True: 0, False: 0] | Branch (8779:60): [True: 0, False: 0] ------------------ 8780| 0| { 8781| 0| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 8782| 0| goto exit_function; 8783| 0| } 8784| 0| num_Atoms++; 8785| 0| pInChI[iComponent].nTautomer[lenTautomer++] = val; 8786| 0| p = q; 8787| 0| } 8788| 0| if (!num_Atoms || (p < pEnd && !isdigit(UCINT * p))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (8788:25): [True: 0, False: 0] | Branch (8788:40): [True: 0, False: 0] | Branch (8788:52): [True: 0, False: 0] ------------------ 8789| 0| { 8790| 0| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 8791| 0| goto exit_function; 8792| 0| } 8793| 0| iTGroup++; 8794| 0| pInChI[iComponent].nTautomer[tg_pos_Tautomer] = lenTautomer - tg_pos_Tautomer - 1; /* length of the rest of the t-group */ 8795| 0| pInChI[iComponent].lenTautomer = lenTautomer; 8796| 0| } 8797| 0| if (!iTGroup || p != pEnd) ------------------ | Branch (8797:21): [True: 0, False: 0] | Branch (8797:33): [True: 0, False: 0] ------------------ 8798| 0| { 8799| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8800| 0| goto exit_function; 8801| 0| } 8802| 0| pInChI[iComponent].nTautomer[0] = iTGroup; 8803| 0| } 8804| 2.47k| else 8805| 2.47k| { 8806| | /* tautomeric groups: pass 1 */ 8807| 2.47k| iTGroup = 0; 8808| 2.47k| state = ')'; /* init as if the prev. t-group just ended */ 8809| 2.47k| num_Atoms = 0; 8810| | /* Tautomeric info storage */ 8811| | /* NumGroups; ((NumAt+2, NumH, Num(-), At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 2} */ 8812| | /* Allocated length: [5*nNumberOfAtoms/2+1], see Alloc_INChI(...) */ 8813| 100k| while (p < pEnd) ------------------ | Branch (8813:24): [True: 98.1k, False: 2.41k] ------------------ 8814| 98.1k| { 8815| | /* t-group */ 8816| 98.1k| switch (*p) 8817| 98.1k| { 8818| 4.66k| case '(': /* start t-group */ ------------------ | Branch (8818:21): [True: 4.66k, False: 93.5k] ------------------ 8819| 4.66k| switch (state) 8820| 4.66k| { 8821| 4.65k| case ')': ------------------ | Branch (8821:25): [True: 4.65k, False: 9] ------------------ 8822| 4.65k| state = *p++; 8823| 4.65k| num_H = 0; 8824| 4.65k| num_Minus = 0; 8825| 4.65k| continue; 8826| 9| default: ------------------ | Branch (8826:25): [True: 9, False: 4.65k] ------------------ 8827| 9| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 9|#define RI_ERR_SYNTAX (-2) ------------------ 8828| 9| goto exit_function; 8829| 4.66k| } 8830| 4.57k| case ')': /* end t-group */ ------------------ | Branch (8830:21): [True: 4.57k, False: 93.6k] ------------------ 8831| 4.57k| switch (state) 8832| 4.57k| { 8833| 4.56k| case 'A': /* previuos was atom number */ ------------------ | Branch (8833:25): [True: 4.56k, False: 2] ------------------ 8834| 4.56k| if (!tg_alloc_len) ------------------ | Branch (8834:33): [True: 0, False: 4.56k] ------------------ 8835| 0| { 8836| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8837| 0| goto exit_function; 8838| 0| } 8839| 4.56k| iTGroup++; 8840| 4.56k| state = *p++; 8841| 4.56k| pInChI[iComponent].nTautomer[tg_pos_Tautomer] = lenTautomer - tg_pos_Tautomer - 1; /* length of the rest of the t-group */ 8842| 4.56k| pInChI[iComponent].lenTautomer = lenTautomer; 8843| 4.56k| continue; 8844| 2| default: ------------------ | Branch (8844:25): [True: 2, False: 4.56k] ------------------ 8845| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 8846| 2| goto exit_function; 8847| 4.57k| } 8848| 4.65k| case 'H': /* number of H */ ------------------ | Branch (8848:21): [True: 4.65k, False: 93.5k] ------------------ 8849| 4.65k| switch (state) 8850| 4.65k| { 8851| 4.65k| case '(': ------------------ | Branch (8851:25): [True: 4.65k, False: 1] ------------------ 8852| 4.65k| state = *p++; 8853| 4.65k| num_H = 1; 8854| 4.65k| continue; 8855| 1| default: ------------------ | Branch (8855:25): [True: 1, False: 4.65k] ------------------ 8856| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 8857| 1| goto exit_function; 8858| 4.65k| } 8859| 1.09k| case '-': /* number of (-) */ ------------------ | Branch (8859:21): [True: 1.09k, False: 97.1k] ------------------ 8860| 1.09k| switch (state) 8861| 1.09k| { 8862| 946| case 'N': /* previous was number of H */ ------------------ | Branch (8862:25): [True: 946, False: 149] ------------------ 8863| 1.09k| case 'H': /* previous was H */ ------------------ | Branch (8863:25): [True: 144, False: 951] ------------------ 8864| 1.09k| state = *p++; 8865| 1.09k| num_Minus = 1; 8866| 1.09k| continue; 8867| 5| default: ------------------ | Branch (8867:25): [True: 5, False: 1.09k] ------------------ 8868| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 8869| 5| goto exit_function; 8870| 1.09k| } 8871| 39.0k| case ',': ------------------ | Branch (8871:21): [True: 39.0k, False: 59.1k] ------------------ 8872| 39.0k| switch (state) 8873| 39.0k| { 8874| 3.25k| case 'N': /* previous was number of H */ ------------------ | Branch (8874:25): [True: 3.25k, False: 35.8k] ------------------ 8875| 3.53k| case 'H': /* previous was H */ ------------------ | Branch (8875:25): [True: 284, False: 38.8k] ------------------ 8876| 3.81k| case '-': /* previuos was - */ ------------------ | Branch (8876:25): [True: 274, False: 38.8k] ------------------ 8877| 4.60k| case 'M': /* previous was number of (-) */ ------------------ | Branch (8877:25): [True: 797, False: 38.2k] ------------------ 8878| | /* the next must be the first tautomeric atom number; save num_H & num_Minus */ 8879| 4.60k| if (num_H <= 0 && num_Minus <= 0) ------------------ | Branch (8879:33): [True: 0, False: 4.60k] | Branch (8879:47): [True: 0, False: 0] ------------------ 8880| 0| { 8881| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8882| 0| goto exit_function; 8883| 0| } 8884| 4.60k| if (!tg_alloc_len) ------------------ | Branch (8884:33): [True: 2.43k, False: 2.17k] ------------------ 8885| 2.43k| { 8886| | /* 8887| | --- header --- 8888| | [num_t_groups] 8889| | --- one t-group: --- 8890| | [len=group length no including this value] 8891| | [num_H] 8892| | [num_(-)] 8893| | [Endpoint(1),...,Endpoint(len-2)] 8894| | --- next t-group --- 8895| | ... 8896| | 8897| | Max. size = 1 + 3*max_num_t_groups + max_num_endpoints 8898| | 8899| | max_num_t_groups = num_at/2 8900| | max_num_endpoints = num_at 8901| | 8902| | Max. size = 1 + 3*(num_at/2) + num_at = 1 + (5*num_at)/2 8903| | 5 = 3 + INCHI_T_NUM_MOVABLE = 3 + num_types_of_attachments 8904| | 8905| | This does not include zero termination! 8906| | 8907| | */ 8908| 2.43k| tg_alloc_len = ((3 + INCHI_T_NUM_MOVABLE) * pInChI[iComponent].nNumberOfAtoms) / 2 + 1; ------------------ | | 749| 2.43k|#define INCHI_T_NUM_MOVABLE 2 ------------------ 8909| 5.06k| for (i = 0; i < mpy_component; i++) ------------------ | Branch (8909:45): [True: 2.62k, False: 2.43k] ------------------ 8910| 2.62k| { 8911| | /* djb-rwth: fixing oss-fuzz issue #68314 */ 8912| 2.62k| AT_NUMB* pinchi_icint = (AT_NUMB*)inchi_calloc((long long)tg_alloc_len + 1, sizeof(pInChI->nTautomer[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 2.62k|#define inchi_calloc calloc ------------------ 8913| 2.62k| if (!pinchi_icint) ------------------ | Branch (8913:41): [True: 0, False: 2.62k] ------------------ 8914| 0| { 8915| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 8916| 0| goto exit_function; 8917| 0| } 8918| 2.62k| pInChI[iComponent + i].nTautomer = pinchi_icint; 8919| 2.62k| pInChI[iComponent + i].lenTautomer = 0; 8920| 2.62k| } 8921| 2.43k| tg_pos_Tautomer = 1; /* number atoms (NumAt+2) position */ 8922| 2.43k| } 8923| 2.17k| else 8924| 2.17k| { 8925| | /* next t-group */ 8926| 2.17k| tg_pos_Tautomer = lenTautomer; 8927| 2.17k| } 8928| 4.60k| if (tg_pos_Tautomer + 3 >= tg_alloc_len) ------------------ | Branch (8928:33): [True: 2, False: 4.60k] ------------------ 8929| 2| { 8930| 2| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 17| 2|#define RI_ERR_PROGR (-3) ------------------ 8931| 2| goto exit_function; 8932| 2| } 8933| 4.60k| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 1] = num_H; 8934| 4.60k| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 2] = num_Minus; 8935| 4.60k| lenTautomer = tg_pos_Tautomer + 3; /* first atom number position */ 8936| | /* djb-rwth: fixing GH issue #59.1 */ 8937| 4.60k| if (num_H >= INT_MIN && num_H <= INT_MAX) /* djb-rwth: addressing coverity ID #499582 -- boundary check is required */ ------------------ | Branch (8937:33): [True: 4.60k, False: 0] | Branch (8937:53): [True: 4.60k, False: 0] ------------------ 8938| 4.60k| { 8939| 4.60k| num_taut_H_component += num_H; 8940| 4.60k| } 8941| 0| else 8942| 0| { 8943| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 8944| 0| goto exit_function; 8945| 0| } 8946| 4.60k| state = *p++; 8947| 4.60k| continue; 8948| 34.4k| case 'A': ------------------ | Branch (8948:25): [True: 34.4k, False: 4.60k] ------------------ 8949| | /* previuos was atom number */ 8950| 34.4k| state = *p++; 8951| 34.4k| continue; 8952| 0| default: ------------------ | Branch (8952:25): [True: 0, False: 39.0k] ------------------ 8953| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8954| 0| goto exit_function; 8955| 39.0k| } 8956| 44.1k| default: ------------------ | Branch (8956:21): [True: 44.1k, False: 54.0k] ------------------ 8957| 44.1k| if (isdigit(UCINT* p)) ------------------ | Branch (8957:29): [True: 44.1k, False: 0] ------------------ 8958| 44.1k| { 8959| 44.1k| val = (int)inchi_strtol(p, &q, 10); 8960| 44.1k| if (val <= 0) ------------------ | Branch (8960:33): [True: 25, False: 44.0k] ------------------ 8961| 25| { 8962| 25| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 25|#define RI_ERR_SYNTAX (-2) ------------------ 8963| 25| goto exit_function; 8964| 25| } 8965| 44.0k| p = q; 8966| 44.0k| switch (state) 8967| 44.0k| { 8968| 4.20k| case 'H': ------------------ | Branch (8968:29): [True: 4.20k, False: 39.8k] ------------------ 8969| 4.20k| num_H = val; 8970| 4.20k| state = 'N'; 8971| 4.20k| continue; 8972| 803| case '-': ------------------ | Branch (8972:29): [True: 803, False: 43.2k] ------------------ 8973| 803| num_Minus = val; 8974| 803| state = 'M'; 8975| 803| continue; 8976| 39.0k| case ',': ------------------ | Branch (8976:29): [True: 39.0k, False: 5.01k] ------------------ 8977| 39.0k| if (lenTautomer >= tg_alloc_len || val > numCtAtoms) ------------------ | Branch (8977:37): [True: 0, False: 39.0k] | Branch (8977:68): [True: 13, False: 39.0k] ------------------ 8978| 13| { 8979| 13| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 17| 13|#define RI_ERR_PROGR (-3) ------------------ 8980| 13| goto exit_function; 8981| 13| } 8982| 39.0k| num_Atoms++; 8983| 39.0k| pInChI[iComponent].nTautomer[lenTautomer++] = val; 8984| 39.0k| state = 'A'; 8985| 39.0k| continue; 8986| 3| default: ------------------ | Branch (8986:29): [True: 3, False: 44.0k] ------------------ 8987| 3| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 8988| 3| goto exit_function; 8989| 44.0k| } 8990| 44.0k| } 8991| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8992| 0| goto exit_function; 8993| 98.1k| } 8994| 98.1k| } 8995| 2.41k| if (!iTGroup || state != ')') ------------------ | Branch (8995:21): [True: 17, False: 2.39k] | Branch (8995:33): [True: 17, False: 2.37k] ------------------ 8996| 34| { 8997| 34| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 34|#define RI_ERR_SYNTAX (-2) ------------------ 8998| 34| goto exit_function; 8999| 34| } 9000| 2.37k| pInChI[iComponent].nTautomer[0] = iTGroup; 9001| 2.37k| } 9002| 2.47k| } 9003| | /* check num_H in components; for bMobileH=TAUT_NON, pInChI->nNum_H_fixed[] has not been added to pInChI->nNum_H[] yet */ 9004| 5.51k| if (0 > (ret2 = GetInChIFormulaNumH(pInChI + iComponent, &num_H_formula)) || ------------------ | Branch (9004:13): [True: 0, False: 5.51k] ------------------ 9005| 5.51k| 0 > (ret2 = GetInChINumH(pInChI + iComponent, &num_H_InChI))) ------------------ | Branch (9005:13): [True: 0, False: 5.51k] ------------------ 9006| 0| { 9007| 0| ret = ret2; 9008| 0| goto exit_function; 9009| 0| } 9010| 5.51k| if (num_H_formula != num_H_InChI + (bMobileH == TAUT_NON ? num_H_component : 0)) ------------------ | | 574| 5.51k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (9010:13): [True: 74, False: 5.44k] | Branch (9010:45): [True: 1.39k, False: 4.12k] ------------------ 9011| 74| { 9012| 74| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 74|#define RI_ERR_SYNTAX (-2) ------------------ 9013| 74| goto exit_function; 9014| 74| } 9015| | 9016| | /* duplicate according to multiplication */ 9017| 5.78k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (9017:21): [True: 345, False: 5.43k] ------------------ 9018| 345| { 9019| 345|#if ( FIX_GAF_2019_2==1 ) 9020| 345| if ((iComponent + i > nNumComponents - 1) || (iComponent + i < 0)) ------------------ | Branch (9020:17): [True: 5, False: 340] | Branch (9020:58): [True: 0, False: 340] ------------------ 9021| 5| { 9022| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 9023| 5| goto exit_function; 9024| 5| } 9025| | 9026| 340| if ((pInChI[iComponent + i].nNumberOfAtoms <= 0) || (pInChI[iComponent + i].nNumberOfAtoms > MAX_ATOMS)) ------------------ | | 15| 340|#define MAX_ATOMS 32766 ------------------ | Branch (9026:17): [True: 0, False: 340] | Branch (9026:65): [True: 0, False: 340] ------------------ 9027| 0| { 9028| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9029| 0| goto exit_function; 9030| 0| } 9031| 340|#endif 9032| | /* djb-rwth: fixing oss-fuzz issue #69699 */ 9033| 340| if (nNum_H(iComponent)) /* djb-rwth: fixing GH issues #27/#28 */ ------------------ | | 8249| 340|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 575| 340|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8249:30): [True: 340, False: 0] | | | Branch (8249:31): [True: 306, False: 34] | | ------------------ ------------------ 9034| 340| { 9035| 340| memcpy(nNum_H(iComponent + i), nNum_H(iComponent), pInChI[iComponent + i].nNumberOfAtoms * sizeof(nNum_H(0)[0])); ------------------ | | 8249| 340|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 575| 340|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8249:31): [True: 306, False: 34] | | ------------------ ------------------ memcpy(nNum_H(iComponent + i), nNum_H(iComponent), pInChI[iComponent + i].nNumberOfAtoms * sizeof(nNum_H(0)[0])); ------------------ | | 8249| 340|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 575| 340|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8249:31): [True: 306, False: 34] | | ------------------ ------------------ memcpy(nNum_H(iComponent + i), nNum_H(iComponent), pInChI[iComponent + i].nNumberOfAtoms * sizeof(nNum_H(0)[0])); ------------------ | | 8249| 340|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 575| 340|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8249:31): [True: 0, False: 340] | | ------------------ ------------------ 9036| 340| } 9037| | /* 9038| | memcpy( pInChI[iComponent+i].nNum_H, pInChI[iComponent].nNum_H, 9039| | pInChI[iComponent+i].nNumberOfAtoms * sizeof(pInChI[0].nNum_H[0]) ); 9040| | */ 9041| 340| if (pInChI[iComponent + i].nTautomer && pInChI[iComponent].nTautomer && pInChI[iComponent].lenTautomer) ------------------ | Branch (9041:17): [True: 168, False: 172] | Branch (9041:53): [True: 168, False: 0] | Branch (9041:85): [True: 168, False: 0] ------------------ 9042| 168| { 9043| 168| memcpy(pInChI[iComponent + i].nTautomer, pInChI[iComponent].nTautomer, 9044| 168| pInChI[iComponent].lenTautomer * sizeof(pInChI[0].nTautomer[0])); 9045| 168| pInChI[iComponent + i].lenTautomer = pInChI[iComponent].lenTautomer; 9046| 168| } 9047| | /* check num_H in components */ 9048| 340| if (0 > (ret2 = GetInChIFormulaNumH(pInChI + iComponent + i, &num_H_formula)) || ------------------ | Branch (9048:17): [True: 0, False: 340] ------------------ 9049| 340| 0 > (ret2 = GetInChINumH(pInChI + iComponent + i, &num_H_InChI))) ------------------ | Branch (9049:17): [True: 0, False: 340] ------------------ 9050| 0| { 9051| 0| ret = ret2; 9052| 0| goto exit_function; 9053| 0| } 9054| 340| if (num_H_formula != num_H_InChI + (bMobileH == TAUT_NON ? num_H_component : 0)) ------------------ | | 574| 340|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (9054:17): [True: 0, False: 340] | Branch (9054:49): [True: 34, False: 306] ------------------ 9055| 0| { 9056| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9057| 0| goto exit_function; 9058| 0| } 9059| 340| } 9060| | 9061| | /* prepare for the next component */ 9062| 5.43k| iComponent += i; 9063| 5.43k| if (*pEnd) ------------------ | Branch (9063:13): [True: 279, False: 5.16k] ------------------ 9064| 279| { 9065| 279|#if (FIX_DALKE_BUGS == 1) 9066| | /* prevent crash on extra trailing ';' */ 9067| 279| if (iComponent >= nNumComponents) ------------------ | Branch (9067:17): [True: 1, False: 278] ------------------ 9068| 1| { 9069| 1| ret = RI_ERR_SYNTAX; /* syntax error: extra component */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 9070| 1| goto exit_function; 9071| 1| } 9072| 278|#endif 9073| 278| pStart = pEnd + 1; 9074| 278| } 9075| 5.16k| else 9076| 5.16k| { 9077| 5.16k| break; 9078| 5.16k| } 9079| 5.43k| } 9080| | 9081| 5.16k| if (nNumComponents != iComponent) ------------------ | Branch (9081:9): [True: 17, False: 5.14k] ------------------ 9082| 17| { 9083| 17| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 17|#define RI_ERR_SYNTAX (-2) ------------------ 9084| 17| goto exit_function; 9085| 17| } 9086| 5.14k| ret = iComponent + 1; 9087| | 9088| 5.46k|exit_function: 9089| 5.46k| INCHI_HEAPCHK 9090| | 9091| 5.46k| return ret; 9092| 5.14k|} ichiread.c:ParseSegmentCharge: 8049| 8.63k|{ 8050| | /* Pass 1: count bonds and find actual numbers of atom */ 8051| 8.63k| int i, mpy_component, val; 8052| 8.63k| int nNumComponents, iComponent; 8053| 8.63k| const char* p, * q, * t, * pStart, * pEnd; 8054| 8.63k| int ret; 8055| 8.63k| INChI* pInChI = pInpInChI[bMobileH]; 8056| 8.63k| const char mult_type[] = "mnMNe"; 8057| 8.63k| int if_cnd = 1; /* djb-rwth: needed for some if condition restructuring */ 8058| | 8059| 8.63k| if (str[0] != 'q') ------------------ | Branch (8059:9): [True: 7.99k, False: 640] ------------------ 8060| 7.99k| { 8061| 7.99k| return 0; 8062| 7.99k| } 8063| | 8064| 640| pStart = (char*)str + 1; 8065| 640| iComponent = 0; 8066| 640| nNumComponents = ppnNumComponents[bMobileH]; 8067| | 8068| 640| if (!*pStart && bMobileH == TAUT_NON) ------------------ | | 574| 36|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8068:9): [True: 36, False: 604] | Branch (8068:21): [True: 10, False: 26] ------------------ 8069| 10| { 8070| 20| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (8070:21): [True: 10, False: 10] ------------------ 8071| 10| { 8072| 10| pInChI[i].nTotalCharge = NO_VALUE_INT; ------------------ | | 23| 10|#define NO_VALUE_INT 9999 ------------------ 8073| 10| } 8074| 10| return nNumComponents + 1; 8075| 10| } 8076| | 8077| 1.04k| while (1) ------------------ | Branch (8077:12): [True: 1.04k, Folded] ------------------ 8078| 1.04k| { 8079| | /* cycle over components */ 8080| 1.04k| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (8080:13): [True: 611, False: 432] ------------------ 8081| 611| { 8082| 611| pEnd = pStart + strlen(pStart); 8083| 611| } 8084| | 8085| | /* djb-rwth: condition for if block had to be rewritten */ 8086| 1.04k| if ((int)inchi_strtol(pStart, &q, 10) > 0) ------------------ | Branch (8086:13): [True: 311, False: 732] ------------------ 8087| 311| { 8088| 311| val = (int)inchi_strtol(pStart, &q, 10); 8089| 311| if_cnd = isdigit(UCINT * pStart); 8090| | 8091| 311| } 8092| 732| else 8093| 732| { 8094| 732| val = 1; 8095| 732| q = pStart; 8096| 732| if_cnd = 1; 8097| 732| } 8098| | 8099| | 8100| 1.04k| if (if_cnd && (t = strchr((char*)mult_type, *q)) && q + 1 == pEnd) /* djb-rwth: if_cnd applied; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (8100:13): [True: 753, False: 290] | Branch (8100:23): [True: 42, False: 711] | Branch (8100:61): [True: 6, False: 36] ------------------ 8101| 6| { 8102| | /* process the abbreviation */ 8103| | 8104| 6| switch (bMobileH) 8105| 6| { 8106| 0| case TAUT_YES: ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (8106:13): [True: 0, False: 6] ------------------ 8107| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8108| 0| goto exit_function; 8109| 6| case TAUT_NON: ------------------ | | 574| 6|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8109:13): [True: 6, False: 0] ------------------ 8110| 6| if (*q != 'm' || ------------------ | Branch (8110:21): [True: 0, False: 6] ------------------ 8111| 6| iComponent + val > nNumComponents || ------------------ | Branch (8111:21): [True: 5, False: 1] ------------------ 8112| 1| iComponent + val > ppnNumComponents[TAUT_YES]) ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (8112:21): [True: 0, False: 1] ------------------ 8113| 5| { 8114| | 8115| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 8116| 5| goto exit_function; 8117| 5| } 8118| 5| for (i = 0; i < val; i++) ------------------ | Branch (8118:29): [True: 4, False: 1] ------------------ 8119| 4| { 8120| | /* avoid 0 which means "omitted" */ 8121| 4| pInChI[iComponent + i].nTotalCharge = pInpInChI[TAUT_YES][iComponent + i].nTotalCharge ? ------------------ | | 575| 4|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (8121:59): [True: 0, False: 4] ------------------ 8122| 0| pInpInChI[TAUT_YES][iComponent + i].nTotalCharge : ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 8123| 4| NO_VALUE_INT; ------------------ | | 23| 8|#define NO_VALUE_INT 9999 ------------------ 8124| 4| } 8125| 1| mpy_component = val; 8126| 1| goto end_main_cycle; 8127| 0| default: ------------------ | Branch (8127:13): [True: 0, False: 6] ------------------ 8128| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8129| 0| goto exit_function; 8130| 6| } 8131| 6| } 8132| 1.03k| else 8133| 1.03k| { 8134| 1.03k| if ((p = strchr(pStart, '*')) && p < pEnd) ------------------ | Branch (8134:17): [True: 102, False: 935] | Branch (8134:46): [True: 21, False: 81] ------------------ 8135| 21| { 8136| 21| mpy_component = (int)inchi_strtol(pStart, &q, 10); 8137| 21|#if ( CHECK_STRTOL_ATNUMB==1 ) 8138| 21| if (mpy_component > MAX_ATOMS || mpy_component < 0) ------------------ | | 15| 42|#define MAX_ATOMS 32766 ------------------ | Branch (8138:21): [True: 0, False: 21] | Branch (8138:50): [True: 11, False: 10] ------------------ 8139| 11| { 8140| 11| ret = RI_ERR_SYNTAX; ------------------ | | 16| 11|#define RI_ERR_SYNTAX (-2) ------------------ 8141| 11| goto exit_function; 8142| 11| } 8143| 10|#endif 8144| 10| if (p != q) ------------------ | Branch (8144:21): [True: 0, False: 10] ------------------ 8145| 0| { 8146| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8147| 0| goto exit_function; 8148| 0| } 8149| 10| p++; 8150| 10| } 8151| 1.01k| else 8152| 1.01k| { 8153| 1.01k| mpy_component = 1; 8154| 1.01k| p = pStart; 8155| 1.01k| } 8156| 1.03k| } 8157| 1.02k|#if ( FIX_DALKE_BUGS == 1 ) 8158| 1.02k| if (mpy_component + iComponent > nNumComponents || mpy_component <= 0) ------------------ | Branch (8158:13): [True: 6, False: 1.02k] | Branch (8158:60): [True: 2, False: 1.01k] ------------------ 8159| 8| { 8160| 8| ret = RI_ERR_SYNTAX; /* syntax error: too many components in charge layer */ ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 8161| 8| goto exit_function; 8162| 8| } 8163| 1.01k|#endif 8164| 1.01k| pStart = p; 8165| 1.01k| if (pStart < pEnd) ------------------ | Branch (8165:13): [True: 693, False: 325] ------------------ 8166| 693| { 8167| 693| if (pStart[0] == '+' && isdigit(UCINT pStart[1])) ------------------ | Branch (8167:17): [True: 296, False: 397] | Branch (8167:37): [True: 296, False: 0] ------------------ 8168| 296| { 8169| 296| val = (int)inchi_strtol(pStart + 1, &q, 10); 8170| 296| pStart = q; 8171| 296| } 8172| 397| else 8173| 397| { 8174| 397| if (pStart[0] == '-' && isdigit(UCINT pStart[1])) ------------------ | Branch (8174:21): [True: 378, False: 19] | Branch (8174:41): [True: 372, False: 6] ------------------ 8175| 372| { 8176| 372| val = -(int)inchi_strtol(pStart + 1, &q, 10); 8177| 372| pStart = q; 8178| 372| } 8179| 25| else 8180| 25| { 8181| 25| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 25|#define RI_ERR_SYNTAX (-2) ------------------ 8182| 25| goto exit_function; 8183| 25| } 8184| 397| } 8185| 668|#if ( FIX_DALKE_BUGS == 1 ) 8186| 668| if (val < -256 || val > 256) ------------------ | Branch (8186:17): [True: 24, False: 644] | Branch (8186:31): [True: 7, False: 637] ------------------ 8187| 31| { 8188| 31| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 31|#define RI_ERR_SYNTAX (-2) ------------------ 8189| 31| goto exit_function; 8190| 31| } 8191| 637|#endif 8192| 637| if (!val) ------------------ | Branch (8192:17): [True: 55, False: 582] ------------------ 8193| 55| { 8194| 55| if (pStart != pEnd) ------------------ | Branch (8194:21): [True: 1, False: 54] ------------------ 8195| 1| { 8196| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 8197| 1| goto exit_function; 8198| 1| } 8199| 54| if (bMobileH == TAUT_NON) ------------------ | | 574| 54|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8199:21): [True: 0, False: 54] ------------------ 8200| 0| { 8201| 0| val = NO_VALUE_INT; /* avoid 0 which means "omitted" */ ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ 8202| 0| } 8203| 54| } 8204| 637| } 8205| 325| else 8206| 325| { 8207| 325| val = NO_VALUE_INT; ------------------ | | 23| 325|#define NO_VALUE_INT 9999 ------------------ 8208| 325| } 8209| 1.96k| for (i = 0; i < mpy_component; i++) ------------------ | Branch (8209:21): [True: 1.00k, False: 961] ------------------ 8210| 1.00k| { 8211| 1.00k| pInChI[iComponent + i].nTotalCharge = val; 8212| 1.00k| } 8213| | 8214| 962| end_main_cycle: 8215| 962| iComponent += mpy_component; 8216| 962| if (*pEnd) ------------------ | Branch (8216:13): [True: 413, False: 549] ------------------ 8217| 413| { 8218| 413| pStart = pEnd + 1; 8219| 413| continue; 8220| 413| } 8221| 549| else 8222| 549| { 8223| 549| break; 8224| 549| } 8225| 962| } 8226| | 8227| 549| if (nNumComponents != iComponent) ------------------ | Branch (8227:9): [True: 8, False: 541] ------------------ 8228| 8| { 8229| 8| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 8230| 8| goto exit_function; 8231| 8| } 8232| 541| ret = iComponent + 1; 8233| | 8234| 630|exit_function: 8235| | 8236| 630| return ret; 8237| 541|} ichiread.c:ParseSegmentProtons: 7443| 6.94k|{ 7444| | /* Pass 1: count bonds and find actual numbers of atom */ 7445| 6.94k| int val; 7446| 6.94k| const char* q, * pStart, * pEnd; 7447| 6.94k| int ret; 7448| | 7449| 6.94k| if (str[0] != 'p') ------------------ | Branch (7449:9): [True: 6.60k, False: 336] ------------------ 7450| 6.60k| { 7451| 6.60k| return 0; 7452| 6.60k| } 7453| | 7454| 336| pStart = (char*)str + 1; 7455| | 7456| 336| while (1) ------------------ | Branch (7456:12): [True: 336, Folded] ------------------ 7457| 336| { 7458| | /* cycle over components */ 7459| 336| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (7459:13): [True: 332, False: 4] ------------------ 7460| 332| { 7461| 332| pEnd = pStart + strlen(pStart); 7462| 332| } 7463| | 7464| 336| if (pStart[0] == '+' && isdigit(UCINT pStart[1])) ------------------ | Branch (7464:13): [True: 202, False: 134] | Branch (7464:33): [True: 202, False: 0] ------------------ 7465| 202| { 7466| 202| val = (int)inchi_strtol(pStart + 1, &q, 10); 7467| 202| } 7468| 134| else 7469| 134| { 7470| 134| if (pStart[0] == '-' && isdigit(UCINT pStart[1])) ------------------ | Branch (7470:17): [True: 124, False: 10] | Branch (7470:37): [True: 122, False: 2] ------------------ 7471| 122| { 7472| 122| val = -(int)inchi_strtol(pStart + 1, &q, 10); 7473| 122| } 7474| 12| else 7475| 12| { 7476| 12| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 12|#define RI_ERR_SYNTAX (-2) ------------------ 7477| 12| goto exit_function; 7478| 12| } 7479| 134| } 7480| 324| if (!val) ------------------ | Branch (7480:13): [True: 0, False: 324] ------------------ 7481| 0| { 7482| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7483| 0| goto exit_function; 7484| 0| } 7485| 324| nNumProtons[bMobileH].nNumRemovedProtons = val; 7486| 324| if (*pEnd || q != pEnd) ------------------ | Branch (7486:13): [True: 4, False: 320] | Branch (7486:22): [True: 13, False: 307] ------------------ 7487| 17| { 7488| 17| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 17|#define RI_ERR_SYNTAX (-2) ------------------ 7489| 17| goto exit_function; 7490| 17| } 7491| 307| else 7492| 307| { 7493| 307| break; 7494| 307| } 7495| 324| } 7496| 307| ret = 1; 7497| | 7498| 336|exit_function: 7499| | 7500| 336| return ret; 7501| 307|} ichiread.c:ParseSegmentPolymer: 7516| 6.74k|{ 7517| 6.74k| const char* p, * q, * pStart, * pEnd, * p0; 7518| 6.74k| char comma = ',', dot = '.', dash = '-', lt_par = '(', rt_par = ')'; 7519| 6.74k| int iunit, val, ret, prev, is_range, pdn_limit; 7520| 6.74k| int curr_atom, type = -1, subtype = -1, conn = -1; 7521| 6.74k| AT_NUMB num_atom; 7522| 6.74k| INT_ARRAY alist; 7523| 6.74k| OAD_Polymer* pd = NULL; 7524| | 7525| 6.74k| if (str[0] != 'z') ------------------ | Branch (7525:9): [True: 5.90k, False: 837] ------------------ 7526| 5.90k| { 7527| 5.90k| return 0; 7528| 5.90k| } 7529| | 7530| 837| if (IntArray_Alloc(&alist, 4)) ------------------ | Branch (7530:9): [True: 0, False: 837] ------------------ 7531| 0| { 7532| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7533| 0| } 7534| | 7535| 837| if (*ppPolymer) ------------------ | Branch (7535:9): [True: 0, False: 837] ------------------ 7536| 0| { 7537| 0| OAD_Polymer_Free(*ppPolymer); 7538| 0| } 7539| | 7540| 837| pd = *ppPolymer = (OAD_Polymer*) 7541| 837| inchi_calloc(1, sizeof(OAD_Polymer)); ------------------ | | 1146| 837|#define inchi_calloc calloc ------------------ 7542| 837| (*ppPolymer)->pzz = NULL; 7543| | 7544| 837| if (!pd) ------------------ | Branch (7544:9): [True: 0, False: 837] ------------------ 7545| 0| { 7546| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7547| 0| } 7548| | 7549| | 7550| 837| if (!bInchi2Struct) ------------------ | Branch (7550:9): [True: 416, False: 421] ------------------ 7551| 416| { 7552| 416| ret = RI_ERR_SYNTAX; goto exit_function; ------------------ | | 16| 416|#define RI_ERR_SYNTAX (-2) ------------------ 7553| 416| } 7554| | 7555| | /* Count units */ 7556| 421| pd->n = 1; 7557| 421| p = (char*)str + 1; 7558| 2.30k| while ((p = strchr(p, ';'))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7558:12): [True: 1.88k, False: 421] ------------------ 7559| 1.88k| { 7560| 1.88k| p++; 7561| 1.88k| pd->n++; 7562| 1.88k| } 7563| 421| pd->units = (OAD_PolymerUnit**) 7564| 421| inchi_calloc(pd->n, sizeof(OAD_PolymerUnit*)); ------------------ | | 1146| 421|#define inchi_calloc calloc ------------------ 7565| 421| pdn_limit = pd->n; 7566| 421| if (!pd->units) ------------------ | Branch (7566:9): [True: 0, False: 421] ------------------ 7567| 0| { 7568| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7569| 0| } 7570| | 7571| 421| pStart = (char*)str; 7572| 421| pStart++; 7573| 421| if (!pStart) ------------------ | Branch (7573:9): [True: 0, False: 421] ------------------ 7574| 0| { 7575| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 7576| 0| goto exit_function; 7577| 0| } 7578| | 7579| 421| iunit = 0; 7580| | /* djb-rwth: fixing oss-fuzz issue #67678 */ 7581| 2.03k| while (pStart && (*pStart)) ------------------ | Branch (7581:12): [True: 2.03k, False: 0] | Branch (7581:22): [True: 1.79k, False: 245] ------------------ 7582| 1.79k| { 7583| 1.79k| OAD_PolymerUnit* unit = NULL; 7584| | 7585| 1.79k| if (*pStart == ';') ------------------ | Branch (7585:13): [True: 779, False: 1.01k] ------------------ 7586| 779| { 7587| 779| pStart++; 7588| 779| } 7589| | 7590| 1.79k| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (7590:13): [True: 401, False: 1.39k] ------------------ 7591| 401| { 7592| 401| pEnd = pStart + strlen(pStart); 7593| 401| } 7594| 1.79k| if (!isdigit(UCINT pStart[0])) ------------------ | Branch (7594:13): [True: 78, False: 1.71k] ------------------ 7595| 78| { 7596| 78| ret = RI_ERR_SYNTAX; ------------------ | | 16| 78|#define RI_ERR_SYNTAX (-2) ------------------ 7597| 78| goto exit_function; 7598| 78| } 7599| 1.71k| val = (int)inchi_strtol(pStart + 0, &q, 10); 7600| 1.71k| type = val / 100; 7601| 1.71k| subtype = (val - (type * 100)) / 10; 7602| 1.71k| conn = (val - (type * 100 + subtype * 10)); 7603| 1.71k| if (*q != '-') ------------------ | Branch (7603:13): [True: 17, False: 1.69k] ------------------ 7604| 17| { 7605| 17| ret = RI_ERR_SYNTAX; ------------------ | | 16| 17|#define RI_ERR_SYNTAX (-2) ------------------ 7606| 17| goto exit_function; 7607| 17| } 7608| 1.69k|#if ( FIX_OSS_FUZZ_30162_30343==1 ) 7609| 1.69k| if (val < 100) /* type should always be non-zero followed by subtype and conn, like 101 or 200 */ ------------------ | Branch (7609:13): [True: 26, False: 1.67k] ------------------ 7610| 26| { 7611| 26| ret = RI_ERR_SYNTAX; ------------------ | | 16| 26|#define RI_ERR_SYNTAX (-2) ------------------ 7612| 26| goto exit_function; 7613| 26| } 7614| 1.67k|#endif 7615| | 7616| 1.67k|#if ( FIX_GAF_2020_25741==1 ) 7617| 1.67k| { 7618| 1.67k| int valid_unit = 0; 7619| 1.67k| if (type == POLYMER_STY_NON || type == POLYMER_STY_SRU || type == POLYMER_STY_MON || ------------------ | | 179| 3.34k|#define POLYMER_STY_NON 0 ------------------ if (type == POLYMER_STY_NON || type == POLYMER_STY_SRU || type == POLYMER_STY_MON || ------------------ | | 180| 3.34k|#define POLYMER_STY_SRU 1 /**< structure-based unit or copolymer subunit */ ------------------ if (type == POLYMER_STY_NON || type == POLYMER_STY_SRU || type == POLYMER_STY_MON || ------------------ | | 181| 3.32k|#define POLYMER_STY_MON 2 /**< source-based polymer unit or copolymer subunit */ ------------------ | Branch (7619:17): [True: 0, False: 1.67k] | Branch (7619:44): [True: 24, False: 1.64k] | Branch (7619:71): [True: 203, False: 1.44k] ------------------ 7620| 1.44k| type == POLYMER_STY_COP || type == POLYMER_STY_MOD || type == POLYMER_STY_CRO || ------------------ | | 182| 3.11k|#define POLYMER_STY_COP 3 /**< copolymer unit embedding >1 subunits (may be SRU, MON, MER, CRO, MOD; others not supported yet) */ ------------------ type == POLYMER_STY_COP || type == POLYMER_STY_MOD || type == POLYMER_STY_CRO || ------------------ | | 183| 2.95k|#define POLYMER_STY_MOD 4 /**< copolymer subunit only, designates chemical modification of SRU */ ------------------ type == POLYMER_STY_COP || type == POLYMER_STY_MOD || type == POLYMER_STY_CRO || ------------------ | | 184| 2.92k|#define POLYMER_STY_CRO 5 /**< copolymer subunit only, designates cross-linked version of SRU */ ------------------ | Branch (7620:17): [True: 165, False: 1.28k] | Branch (7620:44): [True: 30, False: 1.25k] | Branch (7620:71): [True: 999, False: 252] ------------------ 7621| 252| type == POLYMER_STY_MER) ------------------ | | 185| 252|#define POLYMER_STY_MER 6 /**< copolymer subunit only, source-based with no homopolymerize */ ------------------ | Branch (7621:17): [True: 237, False: 15] ------------------ 7622| 1.65k| { 7623| 1.65k| if (subtype == POLYMER_SST_NON || subtype == POLYMER_SST_ALT || ------------------ | | 187| 3.31k|#define POLYMER_SST_NON 0 ------------------ if (subtype == POLYMER_SST_NON || subtype == POLYMER_SST_ALT || ------------------ | | 188| 2.68k|#define POLYMER_SST_ALT 1 ------------------ | Branch (7623:21): [True: 634, False: 1.02k] | Branch (7623:51): [True: 491, False: 533] ------------------ 7624| 533| subtype == POLYMER_SST_RAN || subtype == POLYMER_SST_BLK) ------------------ | | 189| 2.19k|#define POLYMER_SST_RAN 2 ------------------ subtype == POLYMER_SST_RAN || subtype == POLYMER_SST_BLK) ------------------ | | 190| 159|#define POLYMER_SST_BLK 3 ------------------ | Branch (7624:21): [True: 374, False: 159] | Branch (7624:51): [True: 156, False: 3] ------------------ 7625| 1.65k| { 7626| 1.65k| if (conn == POLYMER_CONN_NON || conn == POLYMER_CONN_HT || ------------------ | | 192| 3.31k|#define POLYMER_CONN_NON 0 ------------------ if (conn == POLYMER_CONN_NON || conn == POLYMER_CONN_HT || ------------------ | | 193| 2.80k|#define POLYMER_CONN_HT 1 ------------------ | Branch (7626:25): [True: 508, False: 1.14k] | Branch (7626:53): [True: 537, False: 610] ------------------ 7627| 610| conn == POLYMER_CONN_HH || conn == POLYMER_CONN_EU) ------------------ | | 194| 2.26k|#define POLYMER_CONN_HH 2 ------------------ conn == POLYMER_CONN_HH || conn == POLYMER_CONN_EU) ------------------ | | 195| 56|#define POLYMER_CONN_EU 3 ------------------ | Branch (7627:25): [True: 554, False: 56] | Branch (7627:52): [True: 55, False: 1] ------------------ 7628| 1.65k| { 7629| 1.65k| valid_unit = 1; 7630| 1.65k| } 7631| 1.65k| } 7632| 1.65k| } 7633| 1.67k| if (!valid_unit) ------------------ | Branch (7633:17): [True: 19, False: 1.65k] ------------------ 7634| 19| { 7635| 19| ret = RI_ERR_SYNTAX; ------------------ | | 16| 19|#define RI_ERR_SYNTAX (-2) ------------------ 7636| 19| goto exit_function; 7637| 19| } 7638| 1.67k| } 7639| 1.65k|#endif 7640| | 7641| 1.65k| q++; 7642| 1.65k| prev = 0; 7643| 1.65k| is_range = 0; 7644| 3.40k| for (p = q, curr_atom = 0; p < pEnd && *p != '('; curr_atom++) ------------------ | Branch (7644:36): [True: 2.71k, False: 685] | Branch (7644:48): [True: 1.76k, False: 949] ------------------ 7645| 1.76k| { 7646| 1.76k| num_atom = (AT_NUMB)inchi_strtol(p, &p, 10); 7647| 1.76k|#if ( ( CHECK_STRTOL_ATNUMB==1 ) || ( FIX_GAF_2019_2==1 ) ) 7648| 1.76k| if (num_atom > na_total || num_atom < 0) ------------------ | Branch (7648:17): [True: 16, False: 1.75k] | Branch (7648:40): [True: 0, False: 1.75k] ------------------ 7649| 16| { 7650| 16| ret = RI_ERR_SYNTAX; ------------------ | | 16| 16|#define RI_ERR_SYNTAX (-2) ------------------ 7651| 16| goto exit_function; 7652| 16| } 7653| 1.75k|#endif 7654| 1.75k| if (!num_atom || num_atom > na_total) ------------------ | Branch (7654:17): [True: 4, False: 1.74k] | Branch (7654:30): [True: 0, False: 1.74k] ------------------ 7655| 4| { 7656| 4| ret = RI_ERR_SYNTAX; goto exit_function; ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 7657| 4| } 7658| 1.74k| if (is_range) ------------------ | Branch (7658:17): [True: 465, False: 1.28k] ------------------ 7659| 465| { 7660| 465| int a; 7661| 4.18k| for (a = prev + 1; a <= num_atom; a++) ------------------ | Branch (7661:36): [True: 3.72k, False: 465] ------------------ 7662| 3.72k| { 7663| 3.72k| if (0 != IntArray_Append(&alist, a)) ------------------ | Branch (7663:25): [True: 0, False: 3.72k] ------------------ 7664| 0| { 7665| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7666| 0| } 7667| 3.72k| } 7668| 465| is_range = 0; 7669| 465| prev = 0; 7670| 465| } 7671| 1.28k| else 7672| 1.28k| { 7673| 1.28k| if (0 != IntArray_Append(&alist, num_atom)) ------------------ | Branch (7673:21): [True: 0, False: 1.28k] ------------------ 7674| 0| { 7675| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7676| 0| } 7677| 1.28k| prev = num_atom; 7678| 1.28k| } 7679| 1.74k| if (*p == '-') ------------------ | Branch (7679:17): [True: 507, False: 1.24k] ------------------ 7680| 507| { 7681| 507| p++; 7682| 507| is_range = 1; 7683| 507| } 7684| 1.24k| else if (*p == ',') ------------------ | Branch (7684:22): [True: 240, False: 1.00k] ------------------ 7685| 240| { 7686| 240| p++; 7687| 240| } 7688| 1.74k| } 7689| | 7690| 1.63k| if (alist.used) ------------------ | Branch (7690:13): [True: 1.16k, False: 469] ------------------ 7691| 1.16k| { 7692| 1.16k| unit = OAD_PolymerUnit_New(4, /* maxatoms */ 7693| 1.16k| 0, /* maxbonds=0 for now */ 7694| 1.16k| iunit + 1, /* id */ 7695| 1.16k| iunit + 1, /* label */ 7696| 1.16k| type, 7697| 1.16k| subtype, 7698| 1.16k| conn, 7699| 1.16k| "", /* smt */ 7700| 1.16k| alist.used, 7701| 1.16k| &alist, 7702| 1.16k| 0, /* blist.used */ 7703| 1.16k| NULL, /* &blist */ 7704| 1.16k| 0, /* nlinks */ 7705| | NULL /* **links */ 7706| 1.16k| ); 7707| | 7708| 1.16k| if (!unit) ------------------ | Branch (7708:17): [True: 0, False: 1.16k] ------------------ 7709| 0| { 7710| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7711| 0| } 7712| | /* djb-rwth: preventing buffer overrun */ 7713| 1.16k| if (iunit < pdn_limit) ------------------ | Branch (7713:17): [True: 1.16k, False: 1] ------------------ 7714| 1.16k| { 7715| 1.16k| pd->units[iunit] = unit; 7716| 1.16k| } 7717| 1| else 7718| 1| { 7719| 1| ret = RI_ERR_PROGR; ------------------ | | 17| 1|#define RI_ERR_PROGR (-3) ------------------ 7720| 1| goto exit_function; 7721| 1| } 7722| 1.16k| IntArray_Reset(&alist); 7723| 1.16k| iunit++; 7724| 1.16k| } 7725| | 7726| 1.63k| if (*p == lt_par) ------------------ | Branch (7726:13): [True: 948, False: 685] ------------------ 7727| 948| { 7728| | /* Structure-based representn, read crossing bonds information */ 7729| 948| const int nothing = 0, endgroups = 1, stars = 2, stars_ring = 3, stars_bond = 4, stars_atom = 5; 7730| 948| int have = nothing; 7731| 948| int res, ib, err = 0; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 7732| 948| INT_ARRAY numlist; 7733| | 7734| 948| if (IntArray_Alloc(&numlist, 4)) ------------------ | Branch (7734:17): [True: 0, False: 948] ------------------ 7735| 0| { 7736| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7737| 0| goto exit_function; 7738| 0| } 7739| | 7740| 948| p0 = p; 7741| 2.11k| while (*(++p)) ------------------ | Branch (7741:20): [True: 2.11k, False: 7] ------------------ 7742| 2.11k| { 7743| 2.11k| if (*p == '-') ------------------ | Branch (7743:21): [True: 808, False: 1.30k] ------------------ 7744| 808| { 7745| 808| have = endgroups; break; 7746| 808| } 7747| 1.30k| if (*p == ',') ------------------ | Branch (7747:21): [True: 133, False: 1.17k] ------------------ 7748| 133| { 7749| 133| have = stars; break; 7750| 133| } 7751| 1.30k| } 7752| 948| if (have == stars) ------------------ | Branch (7752:17): [True: 133, False: 815] ------------------ 7753| 133| { 7754| 752| while (*(++p)) ------------------ | Branch (7754:24): [True: 750, False: 2] ------------------ 7755| 750| { 7756| 750| if (*p == ',') ------------------ | Branch (7756:25): [True: 113, False: 637] ------------------ 7757| 113| { 7758| 113| have = stars_ring; break; 7759| 113| } 7760| 637| if (*p == '.') ------------------ | Branch (7760:25): [True: 7, False: 630] ------------------ 7761| 7| { 7762| 7| have = stars_bond; break; 7763| 7| } 7764| 630| if (*p == ')') ------------------ | Branch (7764:25): [True: 11, False: 619] ------------------ 7765| 11| { 7766| 11| have = stars_atom; break; 7767| 11| } 7768| 630| } 7769| 133| } 7770| 948| p = p0; 7771| | 7772| 948| if (unit) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (7772:17): [True: 921, False: 27] ------------------ 7773| 921| { 7774| 921| unit->cyclizable = CLOSING_SRU_NOT_APPLICABLE; ------------------ | | 19| 921|#define CLOSING_SRU_NOT_APPLICABLE 0 ------------------ 7775| 921| if (have == endgroups) ------------------ | Branch (7775:21): [True: 786, False: 135] ------------------ 7776| 786| { 7777| | /* Read end groups notation */ 7778| 786| p = ParseSegmentReadDelimitedNumbers(p, pEnd, &numlist, dash, comma, &res); 7779| 786| if (res == 1 && numlist.used == 2) ------------------ | Branch (7779:25): [True: 785, False: 1] | Branch (7779:37): [True: 2, False: 783] ------------------ 7780| 2| { 7781| 2| p = ParseSegmentReadDelimitedNumbers(p, pEnd, &numlist, dash, rt_par, &res); 7782| 2| } 7783| 786| if (res == 1 && numlist.used == 4) ------------------ | Branch (7783:25): [True: 785, False: 1] | Branch (7783:37): [True: 16, False: 769] ------------------ 7784| 16| { 7785| 16| pStart = p + 1; 7786| 16| unit->nb = 2; 7787| 16| unit->blist = (int*)inchi_calloc(2 * (long long)unit->nb, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 16|#define inchi_calloc calloc ------------------ 7788| 16| if (!unit->blist) ------------------ | Branch (7788:29): [True: 0, False: 16] ------------------ 7789| 0| { 7790| 0| ret = RI_ERR_ALLOC; IntArray_Free(&numlist); goto exit_function; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7791| 0| } 7792| 16| unit->blist[0] = numlist.item[0]; unit->blist[1] = numlist.item[1]; 7793| 16| unit->blist[2] = numlist.item[2]; unit->blist[3] = numlist.item[3]; 7794| 16| unit->cap1 = numlist.item[0]; /* just for GAF check belows */ 7795| 16| unit->cap2 = numlist.item[2]; 7796| 16| IntArray_Free(&numlist); 7797| 16| continue; 7798| 16| } 7799| 786| } 7800| 135| else if (have == stars_ring || ------------------ | Branch (7800:26): [True: 112, False: 23] ------------------ 7801| 23| have == stars_bond || ------------------ | Branch (7801:21): [True: 7, False: 16] ------------------ 7802| 16| have == stars_atom) ------------------ | Branch (7802:21): [True: 11, False: 5] ------------------ 7803| 130| { 7804| | /* Read star atoms - frame shiftable bonds notation */ 7805| 130| IntArray_Reset(&numlist); 7806| 130| p = ParseSegmentReadDelimitedNumbers(p, pEnd, &numlist, comma, dash, &res); 7807| 130| if (res != 1 || numlist.used != 2) ------------------ | Branch (7807:25): [True: 3, False: 127] | Branch (7807:37): [True: 0, False: 127] ------------------ 7808| 3| { 7809| 3| ret = RI_ERR_SYNTAX; IntArray_Free(&numlist); goto exit_function; ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 7810| 3| } 7811| | /* OK, we got star atom numbers */ 7812| 127| if (have == stars_ring) ------------------ | Branch (7812:25): [True: 109, False: 18] ------------------ 7813| 109| { 7814| 109| p = ParseSegmentReadDelimitedNumbers(p, pEnd, &numlist, comma, rt_par, &res); 7815| 109| if (res != 1 || numlist.used < 4) ------------------ | Branch (7815:29): [True: 1, False: 108] | Branch (7815:41): [True: 0, False: 108] ------------------ 7816| 1| { 7817| 1| ret = RI_ERR_SYNTAX; ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 7818| 1| IntArray_Free(&numlist); 7819| 1| goto exit_function; 7820| 1| } 7821| 108| unit->cyclizable = CLOSING_SRU_RING; ------------------ | | 20| 108|#define CLOSING_SRU_RING 1 ------------------ 7822| 108| unit->nbkbonds = (numlist.used - 2) / 2; 7823| 108| } 7824| 18| else if (have == stars_bond) ------------------ | Branch (7824:30): [True: 7, False: 11] ------------------ 7825| 7| { 7826| 7| p = ParseSegmentReadDelimitedNumbers(p, pEnd, &numlist, dot, rt_par, &res); 7827| 7| if (res != 1 || numlist.used < 4) ------------------ | Branch (7827:29): [True: 1, False: 6] | Branch (7827:41): [True: 1, False: 5] ------------------ 7828| 2| { 7829| 2| ret = RI_ERR_SYNTAX; ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7830| 2| IntArray_Free(&numlist); 7831| 2| goto exit_function; 7832| 2| } 7833| 5| unit->cyclizable = CLOSING_SRU_HIGHER_ORDER_BOND; ------------------ | | 21| 5|#define CLOSING_SRU_HIGHER_ORDER_BOND 2 ------------------ 7834| 5| unit->nbkbonds = 1; 7835| 5| } 7836| 11| else if (have == stars_atom) ------------------ | Branch (7836:30): [True: 11, False: 0] ------------------ 7837| 11| { 7838| 11| int num = inchi_strtol(++p, &p, 10); 7839| 11|#if ( ( CHECK_STRTOL_ATNUMB==1 ) || ( FIX_GAF_2019_2==1 ) ) 7840| 11| if (num > na_total || num < 0) ------------------ | Branch (7840:29): [True: 1, False: 10] | Branch (7840:47): [True: 1, False: 9] ------------------ 7841| 2| { 7842| 2| IntArray_Free(&numlist); 7843| 2| ret = RI_ERR_SYNTAX; ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7844| 2| goto exit_function; 7845| 2| } 7846| 9|#endif 7847| 9| if (*p != rt_par) ------------------ | Branch (7847:29): [True: 2, False: 7] ------------------ 7848| 2| { 7849| 2| ret = RI_ERR_SYNTAX; ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7850| 2| IntArray_Free(&numlist); 7851| 2| goto exit_function; 7852| 2| } 7853| 7| IntArray_Append(&numlist, num); 7854| 7| unit->cyclizable = CLOSING_SRU_DIRADICAL; ------------------ | | 22| 7|#define CLOSING_SRU_DIRADICAL 3 ------------------ 7855| 7| unit->nbkbonds = 1; 7856| 7| } 7857| 127| } 7858| 5| else 7859| 5| { 7860| 5| ret = RI_ERR_SYNTAX; IntArray_Free(&numlist); goto exit_function; ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 7861| 5| } 7862| | 7863| 890| unit->cap1 = numlist.item[0]; 7864| 890| unit->cap2 = numlist.item[1]; 7865| | 7866| 890| if (unit->bkbonds) ------------------ | Branch (7866:21): [True: 0, False: 890] ------------------ 7867| 0| { 7868| 0| imat_free(unit->maxbkbonds, unit->bkbonds); 7869| 0| unit->bkbonds = NULL; 7870| 0| } 7871| 890| unit->maxbkbonds = inchi_max(unit->maxbkbonds, unit->nbkbonds); ------------------ | | 138| 890|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 890] | | ------------------ ------------------ 7872| 890| err = imat_new(unit->maxbkbonds, 2, &(unit->bkbonds)); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 7873| 1.70k| for (ib = 0; ib < unit->nbkbonds; ib++) ------------------ | Branch (7873:30): [True: 817, False: 890] ------------------ 7874| 817| { 7875| 817| unit->bkbonds[ib][0] = numlist.item[ib * 2 + 2]; 7876| 817| if (numlist.used != 3) ------------------ | Branch (7876:25): [True: 810, False: 7] ------------------ 7877| 810| { 7878| 810| unit->bkbonds[ib][1] = numlist.item[ib * 2 + 3]; 7879| 810| } 7880| 7| else 7881| 7| { 7882| 7| unit->bkbonds[ib][1] = unit->bkbonds[ib][0]; 7883| 7| } 7884| 817| } 7885| 890| if (unit->nbkbonds > 0) ------------------ | Branch (7885:21): [True: 120, False: 770] ------------------ 7886| 120| { 7887| | /*unit->cyclizable = 1;*/ 7888| 120| unit->cap1 = numlist.item[0]; 7889| 120| unit->cap2 = numlist.item[1]; 7890| 120| } 7891| 890| } 7892| | 7893| 917| pStart = p + 1; 7894| 917| IntArray_Free(&numlist); 7895| 917| continue; 7896| 948| } 7897| | 7898| 685| if (*p == ';') ------------------ | Branch (7898:13): [True: 583, False: 102] ------------------ 7899| 583| { 7900| 583| p++; 7901| 583| } 7902| 685| q = p; 7903| 685| pStart = p; 7904| 685| } 7905| | 7906| 245| pd->really_do_frame_shift = 1; 7907| 245| pd->frame_shift_scheme = FSS_STARS_CYCLED; 7908| 245| pd->treat = POLYMERS_MODERN; ------------------ | | 1216| 245|#define POLYMERS_MODERN 1 /* v. 1.06+ way to treat polymers with Zz */ ------------------ 7909| 245| pd->is_in_reconn = 0; 7910| | 7911| | /*OAD_Polymer_DebugTrace( pd );*/ 7912| | 7913| 245| ret = pd->n; 7914| | 7915| 837|exit_function: 7916| | 7917| 837| IntArray_Free(&alist); 7918| 837| if (ret == RI_ERR_ALLOC || ret == RI_ERR_SYNTAX || ret == RI_ERR_PROGR) ------------------ | | 15| 1.67k|#define RI_ERR_ALLOC (-1) ------------------ if (ret == RI_ERR_ALLOC || ret == RI_ERR_SYNTAX || ret == RI_ERR_PROGR) ------------------ | | 16| 1.67k|#define RI_ERR_SYNTAX (-2) ------------------ if (ret == RI_ERR_ALLOC || ret == RI_ERR_SYNTAX || ret == RI_ERR_PROGR) ------------------ | | 17| 246|#define RI_ERR_PROGR (-3) ------------------ | Branch (7918:9): [True: 0, False: 837] | Branch (7918:32): [True: 591, False: 246] | Branch (7918:56): [True: 1, False: 245] ------------------ 7919| 592| { 7920| | /*FreeExtOrigAtData( pd, pv );*/ 7921| 592| } 7922| 245|#if ( FIX_GAF_2019_2==1 ) 7923| 245| else 7924| 245| { 7925| 245| if (pd) ------------------ | Branch (7925:13): [True: 245, False: 0] ------------------ 7926| 245| { 7927| 245| int iu, ipsb, maxats = na_total + pd->n_pzz; 7928| 828| for (iu = 0; iu < pd->n; iu++) ------------------ | Branch (7928:26): [True: 601, False: 227] ------------------ 7929| 601| { 7930| 601| int astar1, astar2; 7931| 601|#if ( FIX_OSS_FUZZ_25604==1 ) 7932| 601| if (NULL == pd->units[iu]) ------------------ | Branch (7932:21): [True: 14, False: 587] ------------------ 7933| 14| { 7934| 14| ret = RI_ERR_SYNTAX; ------------------ | | 16| 14|#define RI_ERR_SYNTAX (-2) ------------------ 7935| 14| break; 7936| 14| } 7937| 587|#endif 7938| 587| astar1 = pd->units[iu]->cap1; 7939| 587| astar2 = pd->units[iu]->cap2; 7940| 587| if (0 == pd->units[iu]->nb) ------------------ | Branch (7940:21): [True: 572, False: 15] ------------------ 7941| 572| { 7942| 572| continue; 7943| 572| } 7944| 15| if (ret == RI_ERR_SYNTAX) ------------------ | | 16| 15|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (7944:21): [True: 0, False: 15] ------------------ 7945| 0| { 7946| 0| break; 7947| 0| } 7948| 15| if (astar1 > maxats || astar1 <= 0 || astar2 > maxats || astar2 <= 0) ------------------ | Branch (7948:21): [True: 0, False: 15] | Branch (7948:40): [True: 4, False: 11] | Branch (7948:55): [True: 0, False: 11] | Branch (7948:74): [True: 0, False: 11] ------------------ 7949| 4| { 7950| 4| ret = RI_ERR_SYNTAX; ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 7951| 4| break; 7952| 4| } 7953| 11| for (ipsb = 0; ipsb < pd->units[iu]->nbkbonds; ipsb++) ------------------ | Branch (7953:32): [True: 0, False: 11] ------------------ 7954| 0| { 7955| 0| int a1psb, a2psb; 7956| 0| a1psb = pd->units[iu]->bkbonds[ipsb][0]; 7957| 0| a2psb = pd->units[iu]->bkbonds[ipsb][1]; 7958| 0| if (a1psb > maxats || a1psb <= 0 || a2psb > maxats || a2psb <= 0) ------------------ | Branch (7958:25): [True: 0, False: 0] | Branch (7958:43): [True: 0, False: 0] | Branch (7958:57): [True: 0, False: 0] | Branch (7958:75): [True: 0, False: 0] ------------------ 7959| 0| { 7960| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7961| 0| break; 7962| 0| } 7963| 0| } 7964| 11| } 7965| 245| } 7966| 245| } 7967| 837|#endif 7968| | 7969| 837| return ret; 7970| 245|} ichiread.c:ParseSegmentSp2: 6885| 7.90k|{ 6886| | /* Pass 1: count bonds and find actual numbers of atom */ 6887| 7.90k| int i, mpy_component, val, len_limit; 6888| 7.90k| int nNumComponents, iComponent, len, iBond; 6889| 7.90k| AT_NUMB nAtom1, nAtom2; 6890| 7.90k| int bondParity; 6891| 7.90k| const char* p, * q, * t, * pStart, * pEnd, * r; 6892| 7.90k| int ret = 0; 6893| 7.90k| INChI* pInChI = pInpInChI[bMobileH]; 6894| 7.90k| INChI* pInChIFrom = NULL; 6895| | /* 6896| | INChI_Stereo *Stereo = NULL; 6897| | INChI_Stereo *StereoOther = NULL; 6898| | */ 6899| 7.90k| INChI_Stereo** pStereo = NULL; 6900| | 6901| 7.90k| const char mult_type[] = "mnMNe"; 6902| 7.90k| const char parity_type[] = "-+u?"; 6903| 7.90k| int bIsoTo, bIsoFrom, nCpyType = CPY_SP2; 6904| 7.90k| int bIso = (state == IST_MOBILE_H_ISO_SP2 || state == IST_FIXED_H_ISO_SP2); ------------------ | Branch (6904:19): [True: 504, False: 7.39k] | Branch (6904:52): [True: 272, False: 7.12k] ------------------ 6905| 7.90k| int base = 10; 6906| 7.90k| int if_cnd = 1; /* djb-rwth: needed for some if condition restructuring */ 6907| | 6908| 7.90k| if (!bIso && state != IST_MOBILE_H_SP2 && state != IST_FIXED_H_SP2) ------------------ | Branch (6908:9): [True: 7.12k, False: 776] | Branch (6908:18): [True: 1.14k, False: 5.98k] | Branch (6908:47): [True: 0, False: 1.14k] ------------------ 6909| 0| { 6910| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 6911| 0| } 6912| | 6913| 7.90k| if (str[0] != 'b') ------------------ | Branch (6913:9): [True: 6.51k, False: 1.38k] ------------------ 6914| 6.51k| { 6915| 6.51k| return 0; 6916| 6.51k| } 6917| | 6918| 1.38k| pStart = (char*)str + 1; 6919| 1.38k| iComponent = 0; 6920| 1.38k| nNumComponents = ppnNumComponents[bMobileH]; 6921| | 6922| 1.38k| if (!*pStart) ------------------ | Branch (6922:9): [True: 169, False: 1.21k] ------------------ 6923| 169| { 6924| | /* create empty sp2 segment which means no sp2 */ 6925| 6.91k| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6925:30): [True: 6.74k, False: 169] ------------------ 6926| 6.74k| { 6927| 6.74k| INChI* pIsoInChI = &pInChI[iComponent]; 6928| 6.74k| pStereo = bIso ? &pIsoInChI->StereoIsotopic : &pIsoInChI->Stereo; ------------------ | Branch (6928:23): [True: 180, False: 6.56k] ------------------ 6929| 6.74k| if (*pStereo && (pStereo[0]->b_parity || pStereo[0]->nNumberOfStereoBonds || ------------------ | Branch (6929:17): [True: 4, False: 6.73k] | Branch (6929:30): [True: 0, False: 4] | Branch (6929:54): [True: 0, False: 4] ------------------ 6930| 4| pStereo[0]->nBondAtom1 || pStereo[0]->nBondAtom2)) ------------------ | Branch (6930:17): [True: 0, False: 4] | Branch (6930:43): [True: 0, False: 4] ------------------ 6931| 0| { 6932| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6933| 0| goto exit_function; 6934| 0| } 6935| | /* allocate empty sp2 stereo */ 6936| 6.74k| ret = CopySegment(pIsoInChI, NULL, CPY_SP2, bIso, -1); 6937| 6.74k| if (ret < 0) ------------------ | Branch (6937:17): [True: 0, False: 6.74k] ------------------ 6938| 0| { 6939| 0| goto exit_function; 6940| 0| } 6941| 6.74k| } 6942| 169| ret = nNumComponents + 1; 6943| 169| goto exit_function; 6944| 169| } 6945| | 6946| 1.83k| while (1) ------------------ | Branch (6946:12): [True: 1.83k, Folded] ------------------ 6947| 1.83k| { 6948| | /* Cycle over components */ 6949| 1.83k| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (6949:13): [True: 1.18k, False: 647] ------------------ 6950| 1.18k| { 6951| 1.18k| pEnd = pStart + strlen(pStart); 6952| 1.18k| } 6953| | 6954| | /* djb-rwth: condition for if block had to be rewritten -- GH issue #09, thanks to Istvan Ori */ 6955| 1.83k| if ((int)inchi_strtol(pStart, &q, 10) > 0) ------------------ | Branch (6955:13): [True: 1.12k, False: 706] ------------------ 6956| 1.12k| { 6957| 1.12k| val = (int)inchi_strtol(pStart, &q, 10); 6958| 1.12k| if_cnd = isdigit(*pStart); 6959| | 6960| 1.12k| } 6961| 706| else 6962| 706| { 6963| 706| val = 1; 6964| 706| q = pStart; 6965| 706| if_cnd = 1; 6966| 706| } 6967| | 6968| | 6969| 1.83k| if (if_cnd && (t = strchr((char*)mult_type, *q)) && q + 1 == pEnd) /* djb-rwth: if_cnd applied; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (6969:13): [True: 1.82k, False: 10] | Branch (6969:23): [True: 71, False: 1.75k] | Branch (6969:61): [True: 26, False: 45] ------------------ 6970| 26| { 6971| | /* process the abbreviation */ 6972| 26| ret = 0; 6973| 26|#if (FIX_DALKE_BUGS == 1) 6974| | /* djb-rwth: fixing GH issue #59.2 */ 6975| 26| if ((iComponent + val >= INT_MIN) && (iComponent + val <= INT_MAX)) ------------------ | Branch (6975:17): [True: 26, False: 0] | Branch (6975:50): [True: 26, False: 0] ------------------ 6976| 26| { 6977| 26| if ((iComponent + val > nNumComponents)) ------------------ | Branch (6977:21): [True: 8, False: 18] ------------------ 6978| 8| { 6979| 8| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 6980| 8| goto exit_function; 6981| 8| } 6982| 26| } 6983| 0| else 6984| 0| { 6985| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6986| 0| goto exit_function; 6987| 0| } 6988| 18|#endif 6989| 18| switch (bMobileH) 6990| 18| { 6991| 14| case TAUT_YES: ------------------ | | 575| 14|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (6991:13): [True: 14, False: 4] ------------------ 6992| 14| switch (state) 6993| 14| { 6994| 13| case IST_MOBILE_H_ISO_SP2: ------------------ | Branch (6994:17): [True: 13, False: 1] ------------------ 6995| 13| if (*q == 'm') ------------------ | Branch (6995:25): [True: 0, False: 13] ------------------ 6996| 0| { 6997| | /* copy from mobile H to isotopic mobile H */ 6998| 0| pInChIFrom = pInChI; 6999| 0| bIsoTo = 1; 7000| 0| bIsoFrom = 0; 7001| 0| } 7002| 13| else 7003| 13| { 7004| 13| if (*q == 'e') ------------------ | Branch (7004:29): [True: 13, False: 0] ------------------ 7005| 13| { 7006| | /* copy from mobile H to isotopic mobile H */ 7007| 13| pInChIFrom = pInChI; 7008| 13| bIsoTo = 1; 7009| 13| bIsoFrom = -1; /* empty */ 7010| 13| } 7011| 0| else 7012| 0| { 7013| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7014| 0| } 7015| 13| } 7016| 13| break; 7017| 1| default: ------------------ | Branch (7017:17): [True: 1, False: 13] ------------------ 7018| 1| ret = RI_ERR_SYNTAX; ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 7019| 1| break; 7020| 14| } 7021| 14| break; 7022| 14| case TAUT_NON: ------------------ | | 574| 4|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (7022:13): [True: 4, False: 14] ------------------ 7023| 4| switch (state) 7024| 4| { 7025| 0| case IST_FIXED_H_SP2: ------------------ | Branch (7025:17): [True: 0, False: 4] ------------------ 7026| 0| if (*q == 'm') ------------------ | Branch (7026:25): [True: 0, False: 0] ------------------ 7027| 0| { 7028| | /* copy from mobile H to fixed H */ 7029| 0|#if ( FIX_GAF_2019_2==1 ) 7030| 0| int inum = ALT_TAUT(bMobileH); ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 7031| 0| pInChIFrom = pInpInChI[inum]; 7032| |#else 7033| | pInChIFrom = pInpInChI[ALT_TAUT(bMobileH)]; 7034| |#endif 7035| 0| bIsoTo = 0; 7036| 0| bIsoFrom = 0; 7037| 0| } 7038| 0| else 7039| 0| { 7040| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7041| 0| } 7042| 0| break; 7043| 4| case IST_FIXED_H_ISO_SP2: ------------------ | Branch (7043:17): [True: 4, False: 0] ------------------ 7044| 4| if (*q == 'm') ------------------ | Branch (7044:25): [True: 0, False: 4] ------------------ 7045| 0| { 7046| | /* copy from mobile H to fixed isotopic H */ 7047| 0| pInChIFrom = pInpInChI[ALT_TAUT(bMobileH)]; ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 7048| 0| bIsoTo = 1; 7049| 0| bIsoFrom = 0; 7050| 0| } 7051| 4| else 7052| 4| { 7053| 4| if (*q == 'M') ------------------ | Branch (7053:29): [True: 0, False: 4] ------------------ 7054| 0| { 7055| | /* copy from isotopic mobile H to fixed isotopic H */ 7056| 0| pInChIFrom = pInpInChI[ALT_TAUT(bMobileH)]; ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 7057| 0| bIsoTo = 1; 7058| 0| bIsoFrom = 1; 7059| 0| } 7060| 4| else 7061| 4| { 7062| 4| if (*q == 'n') ------------------ | Branch (7062:33): [True: 0, False: 4] ------------------ 7063| 0| { 7064| | /* copy from fixed H to fixed isotopic H */ 7065| 0| pInChIFrom = pInChI; 7066| 0| bIsoTo = 1; 7067| 0| bIsoFrom = 0; 7068| 0| } 7069| 4| else 7070| 4| { 7071| 4| if (*q == 'e') ------------------ | Branch (7071:37): [True: 4, False: 0] ------------------ 7072| 4| { 7073| | /* copy from mobile H to isotopic mobile H */ 7074| 4| pInChIFrom = pInChI; 7075| 4| bIsoTo = 1; 7076| 4| bIsoFrom = -1; /* empty */ 7077| 4| } 7078| 0| else 7079| 0| { 7080| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7081| 0| } 7082| 4| } 7083| 4| } 7084| 4| } 7085| 4| break; 7086| 0| default: ------------------ | Branch (7086:17): [True: 0, False: 4] ------------------ 7087| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7088| 0| break; 7089| 4| } 7090| 4| break; 7091| | 7092| 4| default: ------------------ | Branch (7092:13): [True: 0, False: 18] ------------------ 7093| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7094| 0| break; 7095| 18| } 7096| 18| if (ret < 0) ------------------ | Branch (7096:17): [True: 1, False: 17] ------------------ 7097| 1| { 7098| 1| goto exit_function; 7099| 1| } 7100| | /* copy */ 7101| 41| for (i = 0; i < val; i++) ------------------ | Branch (7101:25): [True: 25, False: 16] ------------------ 7102| 25| { 7103| 25|#if ( FIX_GAF_2019_2==1 ) 7104| 25| if ((iComponent + i > nNumComponents - 1) || (iComponent + i < 0)) ------------------ | Branch (7104:21): [True: 0, False: 25] | Branch (7104:62): [True: 0, False: 25] ------------------ 7105| 0| { 7106| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7107| 0| goto exit_function; 7108| 0| } 7109| 25| if (NULL == pInChIFrom || NULL == pInChIFrom + iComponent + i) /* djb-rwth: ignoring GCC warning */ ------------------ | Branch (7109:21): [True: 0, False: 25] | Branch (7109:43): [True: 0, False: 25] ------------------ 7110| 0| { 7111| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7112| 0| goto exit_function; 7113| 0| } 7114| | 7115| 25| if ((pInChIFrom[iComponent + i].nNumberOfAtoms <= 0) || (pInChIFrom[iComponent + i].nNumberOfAtoms > MAX_ATOMS)) ------------------ | | 15| 25|#define MAX_ATOMS 32766 ------------------ | Branch (7115:21): [True: 0, False: 25] | Branch (7115:73): [True: 0, False: 25] ------------------ 7116| 0| { 7117| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7118| 0| goto exit_function; 7119| 0| } 7120| 25|#endif 7121| 25| ret = CopySegment(pInChI + iComponent + i, pInChIFrom + iComponent + i, nCpyType, bIsoTo, bIsoFrom); 7122| 25| if (!ret) ------------------ | Branch (7122:21): [True: 0, False: 25] ------------------ 7123| 0| { 7124| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7125| 0| } 7126| 25| if (ret < 0) ------------------ | Branch (7126:21): [True: 1, False: 24] ------------------ 7127| 1| { 7128| 1| goto exit_function; 7129| 1| } 7130| 25| } 7131| 16| mpy_component = val; 7132| 16| goto end_main_cycle; 7133| 17| } 7134| 1.80k| else 7135| | /* regular multiplier */ 7136| 1.80k| if ((p = strchr(pStart, '*')) && p < pEnd) ------------------ | Branch (7136:17): [True: 20, False: 1.78k] | Branch (7136:46): [True: 17, False: 3] ------------------ 7137| 17| { 7138| 17| mpy_component = (int)inchi_strtol(pStart, &q, 10); 7139| 17|#if ( CHECK_STRTOL_ATNUMB==1 ) 7140| 17| if (mpy_component > MAX_ATOMS || mpy_component < 0) ------------------ | | 15| 34|#define MAX_ATOMS 32766 ------------------ | Branch (7140:21): [True: 3, False: 14] | Branch (7140:50): [True: 0, False: 14] ------------------ 7141| 3| { 7142| 3| ret = RI_ERR_SYNTAX; ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 7143| 3| goto exit_function; 7144| 3| } 7145| 14|#endif 7146| 14| if (p != q) ------------------ | Branch (7146:21): [True: 1, False: 13] ------------------ 7147| 1| { 7148| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 7149| 1| goto exit_function; 7150| 1| } 7151| | 7152| 13| p++; /* move to the 1st character of the component */ 7153| 13| } 7154| 1.79k| else 7155| 1.79k| { 7156| 1.79k| mpy_component = 1; 7157| 1.79k| p = pStart; 7158| 1.79k| } 7159| 1.80k|#if (FIX_DALKE_BUGS == 1) 7160| 1.80k| if (iComponent + mpy_component > nNumComponents) ------------------ | Branch (7160:13): [True: 2, False: 1.80k] ------------------ 7161| 2| { 7162| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7163| 2| goto exit_function; 7164| 2| } 7165| 1.80k|#endif 7166| 1.80k| pStart = p; 7167| 1.80k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (7167:13): [True: 1.15k, False: 647] | Branch (7167:25): [True: 0, False: 1.15k] ------------------ 7168| 0| { 7169| | /* check if compressed InChI */ 7170| 0| *pbAbc = isupper(UCINT * p) ? 1 : 0; ------------------ | Branch (7170:22): [True: 0, False: 0] ------------------ 7171| 0| } 7172| 1.80k| base = (*pbAbc == 1) ? ALPHA_BASE : 10; ------------------ | | 170| 0|#define ALPHA_BASE 27 ------------------ | Branch (7172:16): [True: 0, False: 1.80k] ------------------ 7173| 1.80k| if (*pbAbc == 1) ------------------ | Branch (7173:13): [True: 0, False: 1.80k] ------------------ 7174| 0| { 7175| | /* process the componnt: at1-at2p,at1-at2p,... */ 7176| | /* pass 1: find number of stereobonds */ 7177| 0| for (p = pStart, iBond = 0; p < pEnd; iBond++) ------------------ | Branch (7177:41): [True: 0, False: 0] ------------------ 7178| 0| { 7179| | /* atoms 1, 2, and parity */ 7180| 0| if ((nAtom1 = (AT_NUMB)inchi_strtol(p, &p, base)) && ------------------ | Branch (7180:21): [True: 0, False: 0] ------------------ 7181| 0| (nAtom2 = (AT_NUMB)inchi_strtol(p, &p, base)) && ------------------ | Branch (7181:21): [True: 0, False: 0] ------------------ 7182| 0| (bondParity = (int)inchi_strtol(p, &p, 10), ------------------ | Branch (7182:21): [True: 0, False: 0] ------------------ 7183| 0| AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 231| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 230| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (7183:25): [True: 0, False: 0] | Branch (7183:62): [True: 0, False: 0] ------------------ 7184| 0| { 7185| 0| ; /* okay */ 7186| 0| } 7187| 0| else 7188| 0| { 7189| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7190| 0| goto exit_function; 7191| 0| } 7192| 0| if (nAtom1 <= nAtom2 || ------------------ | Branch (7192:21): [True: 0, False: 0] ------------------ 7193| 0| nAtom1 > pInChI[iComponent].nNumberOfAtoms) ------------------ | Branch (7193:21): [True: 0, False: 0] ------------------ 7194| 0| { 7195| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7196| 0| goto exit_function; 7197| 0| } 7198| 0| } 7199| 0| } 7200| 1.80k| else 7201| 1.80k| { 7202| | /* process the componnt: at1-at2p,at1-at2p,... */ 7203| | /* pass 1: find number of stereobonds */ 7204| 3.40k| for (p = pStart, iBond = 0; p < pEnd; iBond++, p += (*p == ',')) ------------------ | Branch (7204:41): [True: 1.68k, False: 1.72k] ------------------ 7205| 1.68k| { 7206| 1.68k| nAtom1 = (AT_NUMB)inchi_strtol(p, &q, 10); 7207| 1.68k|#if ( CHECK_STRTOL_ATNUMB==1 ) 7208| 1.68k| if (nAtom1 > MAX_ATOMS || nAtom1 < 0) ------------------ | | 15| 3.36k|#define MAX_ATOMS 32766 ------------------ | Branch (7208:21): [True: 4, False: 1.67k] | Branch (7208:43): [True: 0, False: 1.67k] ------------------ 7209| 4| { 7210| 4| ret = RI_ERR_SYNTAX; ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 7211| 4| goto exit_function; 7212| 4| } 7213| 1.67k|#endif 7214| 1.67k| if (*q != '-') ------------------ | Branch (7214:21): [True: 50, False: 1.62k] ------------------ 7215| 50| { 7216| 50| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 50|#define RI_ERR_SYNTAX (-2) ------------------ 7217| 50| goto exit_function; 7218| 50| } 7219| 1.62k| p = q + 1; 7220| 1.62k| nAtom2 = (AT_NUMB)inchi_strtol(p, &q, 10); 7221| 1.62k|#if ( CHECK_STRTOL_ATNUMB==1 ) 7222| 1.62k| if (nAtom2 > MAX_ATOMS || nAtom2 < 0) ------------------ | | 15| 3.25k|#define MAX_ATOMS 32766 ------------------ | Branch (7222:21): [True: 3, False: 1.62k] | Branch (7222:43): [True: 0, False: 1.62k] ------------------ 7223| 3| { 7224| 3| ret = RI_ERR_SYNTAX; ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 7225| 3| goto exit_function; 7226| 3| } 7227| 1.62k|#endif 7228| 1.62k| if (!nAtom1 || !nAtom2 || ------------------ | Branch (7228:21): [True: 0, False: 1.62k] | Branch (7228:32): [True: 0, False: 1.62k] ------------------ 7229| 1.62k| nAtom1 <= nAtom2 || ------------------ | Branch (7229:21): [True: 4, False: 1.62k] ------------------ 7230| 1.62k| nAtom1 > pInChI[iComponent].nNumberOfAtoms || ------------------ | Branch (7230:21): [True: 15, False: 1.60k] ------------------ 7231| 1.60k| !(r = strchr((char*)parity_type, *q))) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (7231:21): [True: 2, False: 1.60k] ------------------ 7232| 21| { 7233| 21| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 21|#define RI_ERR_SYNTAX (-2) ------------------ 7234| 21| goto exit_function; 7235| 21| } 7236| 1.60k| p = q + 1; 7237| 1.60k| } 7238| 1.80k| } 7239| | 7240| 1.72k| if (p != pEnd) ------------------ | Branch (7240:13): [True: 1, False: 1.72k] ------------------ 7241| 1| { 7242| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 7243| 1| goto exit_function; 7244| 1| } 7245| 1.72k| len = iBond; 7246| | 7247| 1.72k|#if ( FIX_GAF_2019_2==1 ) 7248| 1.72k| if ((iComponent > nNumComponents - 1) || (iComponent < 0)) ------------------ | Branch (7248:13): [True: 2, False: 1.72k] | Branch (7248:50): [True: 0, False: 1.72k] ------------------ 7249| 2| { 7250| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7251| 2| goto exit_function; 7252| 2| } 7253| 1.72k| if (pInChI[iComponent].nNumberOfAtoms <= 0 || pInChI[iComponent].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 15| 1.72k|#define MAX_ATOMS 32766 ------------------ | Branch (7253:13): [True: 0, False: 1.72k] | Branch (7253:55): [True: 0, False: 1.72k] ------------------ 7254| 0| { 7255| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7256| 0| goto exit_function; 7257| 0| } 7258| 1.72k|#endif 7259| | 7260| | /* memory allocation */ 7261| 1.72k| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (7261:19): [True: 124, False: 1.59k] ------------------ 7262| 1.72k| if (!*pStereo) ------------------ | Branch (7262:13): [True: 1.71k, False: 4] ------------------ 7263| 1.71k| { 7264| 1.71k| if (!(*pStereo = (INChI_Stereo*)inchi_calloc(1, sizeof(**pStereo)))) ------------------ | | 1146| 1.71k|#define inchi_calloc calloc ------------------ | Branch (7264:17): [True: 0, False: 1.71k] ------------------ 7265| 0| { 7266| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7267| 0| goto exit_function; 7268| 0| } 7269| 1.71k| } 7270| 1.72k| if (pStereo[0]->b_parity || pStereo[0]->nNumberOfStereoBonds || ------------------ | Branch (7270:13): [True: 0, False: 1.72k] | Branch (7270:37): [True: 0, False: 1.72k] ------------------ 7271| 1.72k| pStereo[0]->nBondAtom1 || pStereo[0]->nBondAtom2) ------------------ | Branch (7271:13): [True: 0, False: 1.72k] | Branch (7271:39): [True: 0, False: 1.72k] ------------------ 7272| 0| { 7273| 0| ret = RI_ERR_SYNTAX; /* syntax error: bonds have already been allocated */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7274| 0| goto exit_function; 7275| 0| } 7276| | /* allocate sp2 stereo */ 7277| 1.72k| len_limit = len + 1; 7278| 1.72k| if (!(pStereo[0]->b_parity = (S_CHAR*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->b_parity[0]))) || ------------------ | | 1146| 1.72k|#define inchi_calloc calloc ------------------ | Branch (7278:13): [True: 0, False: 1.72k] ------------------ 7279| 1.72k| !(pStereo[0]->nBondAtom1 = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->nBondAtom1[0]))) || ------------------ | | 1146| 1.72k|#define inchi_calloc calloc ------------------ | Branch (7279:13): [True: 0, False: 1.72k] ------------------ 7280| 1.72k| !(pStereo[0]->nBondAtom2 = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->nBondAtom2[0])))) /* djb-rwth: cast operators added */ ------------------ | | 1146| 1.72k|#define inchi_calloc calloc ------------------ | Branch (7280:13): [True: 0, False: 1.72k] ------------------ 7281| 0| { 7282| | /* cleanup */ 7283| 0| if (pStereo[0]->b_parity) ------------------ | Branch (7283:17): [True: 0, False: 0] ------------------ 7284| 0| { 7285| 0| INCHI_HEAPCHK 7286| 0| inchi_free(pStereo[0]->b_parity); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 7287| 0| pStereo[0]->b_parity = NULL; 7288| 0| } 7289| 0| if (pStereo[0]->nBondAtom1) ------------------ | Branch (7289:17): [True: 0, False: 0] ------------------ 7290| 0| { 7291| 0| INCHI_HEAPCHK 7292| 0| inchi_free(pStereo[0]->nBondAtom1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 7293| 0| pStereo[0]->nBondAtom1 = NULL; 7294| 0| } 7295| 0| if (pStereo[0]->nBondAtom2) ------------------ | Branch (7295:17): [True: 0, False: 0] ------------------ 7296| 0| { 7297| 0| INCHI_HEAPCHK 7298| 0| inchi_free(pStereo[0]->nBondAtom2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 7299| 0| pStereo[0]->nBondAtom2 = NULL; 7300| 0| } 7301| 0| INCHI_HEAPCHK 7302| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 7303| 0| goto exit_function; 7304| 0| } 7305| | 7306| | /* pass 2: store stereobonds */ 7307| 1.72k| if (*pbAbc == 1) ------------------ | Branch (7307:13): [True: 0, False: 1.72k] ------------------ 7308| 0| { 7309| 0| for (p = pStart, iBond = 0; p < pEnd; iBond++) ------------------ | Branch (7309:41): [True: 0, False: 0] ------------------ 7310| 0| { 7311| 0| if ((nAtom1 = (AT_NUMB)inchi_strtol(p, &p, base)) && ------------------ | Branch (7311:21): [True: 0, False: 0] ------------------ 7312| 0| (nAtom2 = (AT_NUMB)inchi_strtol(p, &p, base)) && ------------------ | Branch (7312:21): [True: 0, False: 0] ------------------ 7313| 0| (bondParity = (int)inchi_strtol(p, &p, 10), ------------------ | Branch (7313:21): [True: 0, False: 0] ------------------ 7314| 0| AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 231| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 230| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (7314:25): [True: 0, False: 0] | Branch (7314:62): [True: 0, False: 0] ------------------ 7315| 0| { 7316| 0| ; /* okay */ 7317| 0| } 7318| 0| else 7319| 0| { 7320| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7321| 0| goto exit_function; 7322| 0| } 7323| 0| pStereo[0]->b_parity[iBond] = bondParity; 7324| 0| pStereo[0]->nBondAtom1[iBond] = nAtom1; 7325| 0| pStereo[0]->nBondAtom2[iBond] = nAtom2; 7326| | 7327| 0| if (iBond && ------------------ | Branch (7327:21): [True: 0, False: 0] ------------------ 7328| 0| !(pStereo[0]->nBondAtom1[iBond - 1] < nAtom1 || ------------------ | Branch (7328:23): [True: 0, False: 0] ------------------ 7329| 0| (pStereo[0]->nBondAtom1[iBond - 1] == nAtom1 && ------------------ | Branch (7329:26): [True: 0, False: 0] ------------------ 7330| 0| pStereo[0]->nBondAtom2[iBond - 1] < nAtom2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7330:29): [True: 0, False: 0] ------------------ 7331| 0| { 7332| 0| ret = RI_ERR_SYNTAX; /* syntax error: wrong bond order */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7333| 0| goto exit_function; 7334| 0| } 7335| 0| } 7336| 0| } 7337| 1.72k| else 7338| 1.72k| { 7339| 3.29k| for (p = pStart, iBond = 0; p < pEnd; iBond++, p += (*p == ',')) ------------------ | Branch (7339:41): [True: 1.57k, False: 1.72k] ------------------ 7340| 1.57k| { 7341| 1.57k| nAtom1 = (AT_NUMB)inchi_strtol(p, &q, 10); 7342| 1.57k|#if ( CHECK_STRTOL_ATNUMB==1 ) 7343| 1.57k| if (nAtom1 > MAX_ATOMS || nAtom1 < 0) ------------------ | | 15| 3.15k|#define MAX_ATOMS 32766 ------------------ | Branch (7343:21): [True: 0, False: 1.57k] | Branch (7343:43): [True: 0, False: 1.57k] ------------------ 7344| 0| { 7345| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7346| 0| goto exit_function; 7347| 0| } 7348| 1.57k|#endif 7349| 1.57k| if (*q != '-') ------------------ | Branch (7349:21): [True: 0, False: 1.57k] ------------------ 7350| 0| { 7351| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7352| 0| goto exit_function; 7353| 0| } 7354| 1.57k| p = q + 1; 7355| 1.57k| nAtom2 = (AT_NUMB)inchi_strtol(p, &q, 10); 7356| 1.57k|#if ( CHECK_STRTOL_ATNUMB==1 ) 7357| 1.57k| if (nAtom2 > MAX_ATOMS || nAtom2 < 0) ------------------ | | 15| 3.15k|#define MAX_ATOMS 32766 ------------------ | Branch (7357:21): [True: 0, False: 1.57k] | Branch (7357:43): [True: 0, False: 1.57k] ------------------ 7358| 0| { 7359| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7360| 0| goto exit_function; 7361| 0| } 7362| 1.57k|#endif 7363| 1.57k| if (!(r = strchr((char*)parity_type, *q))) ------------------ | Branch (7363:21): [True: 0, False: 1.57k] ------------------ 7364| 0| { 7365| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7366| 0| goto exit_function; 7367| 0| } 7368| 1.57k| p = q + 1; 7369| 1.57k| bondParity = (int)(r - parity_type) + 1; 7370| | /* djb-rwth: preventing buffer overrun */ 7371| 1.57k| if (iBond < len_limit) ------------------ | Branch (7371:21): [True: 1.57k, False: 0] ------------------ 7372| 1.57k| { 7373| 1.57k| pStereo[0]->b_parity[iBond] = bondParity; 7374| 1.57k| pStereo[0]->nBondAtom1[iBond] = nAtom1; 7375| 1.57k| pStereo[0]->nBondAtom2[iBond] = nAtom2; 7376| 1.57k| } 7377| 0| else 7378| 0| { 7379| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 7380| 0| goto exit_function; 7381| 0| } 7382| | 7383| 1.57k| if (iBond && ------------------ | Branch (7383:21): [True: 500, False: 1.07k] ------------------ 7384| 500| !(pStereo[0]->nBondAtom1[iBond - 1] < nAtom1 || ------------------ | Branch (7384:23): [True: 373, False: 127] ------------------ 7385| 127| (pStereo[0]->nBondAtom1[iBond - 1] == nAtom1 && ------------------ | Branch (7385:26): [True: 126, False: 1] ------------------ 7386| 126| pStereo[0]->nBondAtom2[iBond - 1] < nAtom2))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7386:29): [True: 125, False: 1] ------------------ 7387| 2| { 7388| 2| ret = RI_ERR_SYNTAX; /* syntax error: wrong bond order */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7389| 2| goto exit_function; 7390| 2| } 7391| 1.57k| } 7392| 1.72k| } 7393| 1.72k| pStereo[0]->nNumberOfStereoBonds = iBond; 7394| | 7395| 1.72k| if (p != pEnd) ------------------ | Branch (7395:13): [True: 0, False: 1.72k] ------------------ 7396| 0| { 7397| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7398| 0| goto exit_function; 7399| 0| } 7400| | 7401| | /* multiplier */ 7402| 1.72k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (7402:21): [True: 8, False: 1.72k] ------------------ 7403| 8| { 7404| 8| ret = CopySegment(pInChI + iComponent + i, pInChI + iComponent, nCpyType, bIso, bIso); 7405| 8| if (ret < 0) ------------------ | Branch (7405:17): [True: 0, False: 8] ------------------ 7406| 0| { 7407| 0| goto exit_function; 7408| 0| } 7409| 8| } 7410| | 7411| 1.73k| end_main_cycle: 7412| 1.73k| iComponent += mpy_component; 7413| 1.73k| if (*pEnd) ------------------ | Branch (7413:13): [True: 619, False: 1.11k] ------------------ 7414| 619| { 7415| 619| pStart = pEnd + 1; 7416| 619| continue; 7417| 619| } 7418| 1.11k| else 7419| 1.11k| { 7420| 1.11k| break; 7421| 1.11k| } 7422| 1.73k|} 7423| 1.11k| if (nNumComponents != iComponent) ------------------ | Branch (7423:9): [True: 2, False: 1.11k] ------------------ 7424| 2| { 7425| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7426| 2| goto exit_function; 7427| 2| } 7428| 1.11k| ret = iComponent + 1; 7429| | 7430| 1.38k|exit_function: 7431| | 7432| 1.38k| return ret; 7433| 1.11k| } ichiread.c:ParseSegmentSp3: 6619| 6.90k|{ 6620| | /* Pass 1: count bonds and find actual numbers of atom */ 6621| 6.90k| const char mult_type[] = "mnMNe"; 6622| 6.90k| const char parity_type[] = "-+u?"; 6623| 6.90k| const char* p, * q, * t, * pStart, * pEnd, * r; 6624| 6.90k| AT_NUMB nAtom1; 6625| 6.90k| int mpy_component = 0, val; 6626| 6.90k| int nNumComponents, iComponent, len, iAtom; 6627| 6.90k| int atomParity; 6628| 6.90k| int ret = 0, retf = 0; 6629| 6.90k| int base = 10; 6630| 6.90k| int nCpyType = CPY_SP3; 6631| 6.90k| int bIso = (state == IST_MOBILE_H_ISO_SP3 || state == IST_FIXED_H_ISO_SP3); ------------------ | Branch (6631:17): [True: 413, False: 6.49k] | Branch (6631:50): [True: 257, False: 6.23k] ------------------ 6632| 6.90k| INChI* pInChI = pInpInChI[bMobileH]; 6633| 6.90k| INChI_Stereo** pStereo = NULL; 6634| 6.90k| int if_cnd = 1; /* djb-rwth: needed for some if condition restructuring */ 6635| | 6636| 6.90k| if (!bIso && state != IST_MOBILE_H_SP3 && state != IST_FIXED_H_SP3) ------------------ | Branch (6636:9): [True: 6.23k, False: 670] | Branch (6636:18): [True: 932, False: 5.30k] | Branch (6636:47): [True: 0, False: 932] ------------------ 6637| 0| { 6638| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 6639| 0| } 6640| 6.90k| if (str[0] != 't') ------------------ | Branch (6640:9): [True: 5.25k, False: 1.65k] ------------------ 6641| 5.25k| { 6642| 5.25k| return 0; /* RI_ERR_EOF - ? */ 6643| 5.25k| } 6644| | 6645| 1.65k| pStart = (char*)str + 1; 6646| 1.65k| iComponent = 0; 6647| 1.65k| nNumComponents = ppnNumComponents[bMobileH]; 6648| | 6649| | /* Pass 1: create empty segment and exit */ 6650| 1.65k| if (!*pStart) ------------------ | Branch (6650:9): [True: 233, False: 1.41k] ------------------ 6651| 233| { 6652| 233| ret = SegmentSp3CreateEmpty(str, bMobileH, pInpInChI, nNumComponents, state, pbAbc); 6653| 233| goto exit_function; 6654| 233| } 6655| | 6656| | /* Cycle over components */ 6657| 35.7k| while (1) ------------------ | Branch (6657:12): [True: 35.7k, Folded] ------------------ 6658| 35.7k| { 6659| 35.7k| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (6659:13): [True: 1.39k, False: 34.3k] ------------------ 6660| 1.39k| { 6661| 1.39k| pEnd = pStart + strlen(pStart); 6662| 1.39k| } 6663| | 6664| | /* djb-rwth: condition for if block had to be rewritten */ 6665| 35.7k| if ((int)inchi_strtol(pStart, &q, 10) > 0) ------------------ | Branch (6665:13): [True: 1.48k, False: 34.2k] ------------------ 6666| 1.48k| { 6667| 1.48k| val = (int)inchi_strtol(pStart, &q, 10); 6668| 1.48k| if_cnd = isdigit(*pStart); 6669| | 6670| 1.48k| } 6671| 34.2k| else 6672| 34.2k| { 6673| 34.2k| val = 1; 6674| 34.2k| q = pStart; 6675| 34.2k| if_cnd = 1; 6676| 34.2k| } 6677| | 6678| | /* Abbreviation? */ 6679| 35.7k| if (if_cnd && (t = strchr((char*)mult_type, *q)) && q + 1 == pEnd) /* djb-rwth: if_cnd applied; ignoring LLVM warning: variable used */ ------------------ | Branch (6679:13): [True: 35.7k, False: 10] | Branch (6679:23): [True: 231, False: 35.4k] | Branch (6679:61): [True: 22, False: 209] ------------------ 6680| 22| { 6681| | /* Process abbrebiation */ 6682| 22| retf = SegmentSp3ProcessAbbreviation(&mpy_component, iComponent, nNumComponents, 6683| 22| val, q, state, pbAbc, bMobileH, nCpyType, 6684| 22| pInChI, pInpInChI[ALT_TAUT(bMobileH)]); ------------------ | | 577| 22|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 22|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 22] | | ------------------ ------------------ 6685| 22| if (retf == RI_ERR_SYNTAX) ------------------ | | 16| 22|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (6685:17): [True: 7, False: 15] ------------------ 6686| 7| { 6687| 7| ret = RI_ERR_SYNTAX; ------------------ | | 16| 7|#define RI_ERR_SYNTAX (-2) ------------------ 6688| 7| goto exit_function; 6689| 7| } 6690| 15| goto end_main_cycle; 6691| 22| } 6692| | /* Multiplier? */ 6693| 35.6k| else if ((p = strchr(pStart, '*')) && p < pEnd) ------------------ | Branch (6693:18): [True: 124, False: 35.5k] | Branch (6693:47): [True: 105, False: 19] ------------------ 6694| 105| { 6695| | /* Process regular multiplier */ 6696| 105| mpy_component = (int)inchi_strtol(pStart, &q, 10); 6697| 105| if (p != q) ------------------ | Branch (6697:17): [True: 2, False: 103] ------------------ 6698| 2| { 6699| 2| ret = RI_ERR_SYNTAX; ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 6700| 2| goto exit_function; 6701| 2| } 6702| 103| p++; /* move to the 1st character of the component */ 6703| 103| } 6704| 35.5k| else 6705| 35.5k| { 6706| | /* Just normal sequence of centers/configs, prepare to read */ 6707| 35.5k| mpy_component = 1; 6708| 35.5k| p = pStart; 6709| 35.5k| } 6710| 35.6k|#if (FIX_DALKE_BUGS == 1) 6711| 35.6k| if (iComponent + mpy_component > nNumComponents) ------------------ | Branch (6711:13): [True: 12, False: 35.6k] ------------------ 6712| 12| { 6713| 12| ret = RI_ERR_SYNTAX; ------------------ | | 16| 12|#define RI_ERR_SYNTAX (-2) ------------------ 6714| 12| goto exit_function; 6715| 12| } 6716| 35.6k|#endif 6717| | 6718| 35.6k| pStart = p; 6719| 35.6k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (6719:13): [True: 1.40k, False: 34.2k] | Branch (6719:25): [True: 0, False: 1.40k] ------------------ 6720| 0| { 6721| | /* check if compressed InChI */ 6722| 0| *pbAbc = isupper(UCINT * p) ? 1 : 0; ------------------ | Branch (6722:22): [True: 0, False: 0] ------------------ 6723| 0| } 6724| 35.6k| base = (*pbAbc == 1) ? ALPHA_BASE : 10; ------------------ | | 170| 0|#define ALPHA_BASE 27 ------------------ | Branch (6724:16): [True: 0, False: 35.6k] ------------------ 6725| | 6726| | /* Process the component: at1p,at1p,... */ 6727| | 6728| | /* Pass 1: find number of stereoatoms len */ 6729| 35.6k| if (*pbAbc == 1) ------------------ | Branch (6729:13): [True: 0, False: 35.6k] ------------------ 6730| 0| { 6731| 0| for (p = pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (6731:41): [True: 0, False: 0] ------------------ 6732| 0| { 6733| 0| if ((nAtom1 = (AT_NUMB)inchi_strtol(p, &p, base)) && ------------------ | Branch (6733:21): [True: 0, False: 0] ------------------ 6734| 0| (atomParity = (int)inchi_strtol(p, &p, 10), ------------------ | Branch (6734:21): [True: 0, False: 0] ------------------ 6735| 0| AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 231| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 230| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (6735:25): [True: 0, False: 0] | Branch (6735:62): [True: 0, False: 0] ------------------ 6736| 0| { 6737| 0| ; /* okay */ 6738| 0| } 6739| 0| else 6740| 0| { 6741| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6742| 0| goto exit_function; 6743| 0| } 6744| 0| if (nAtom1 > pInChI[iComponent].nNumberOfAtoms) ------------------ | Branch (6744:21): [True: 0, False: 0] ------------------ 6745| 0| { 6746| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6747| 0| goto exit_function; 6748| 0| } 6749| 0| } 6750| 0| } 6751| 35.6k| else 6752| 35.6k| { 6753| 37.6k| for (p = pStart, iAtom = 0; p < pEnd; iAtom++, p += (*p == ',')) ------------------ | Branch (6753:41): [True: 1.95k, False: 35.6k] ------------------ 6754| 1.95k| { 6755| 1.95k| nAtom1 = (AT_NUMB)inchi_strtol(p, &q, 10); 6756| 1.95k| p = q + 1; 6757| 1.95k| if (!nAtom1 || ------------------ | Branch (6757:21): [True: 16, False: 1.94k] ------------------ 6758| 1.94k| nAtom1 > pInChI[iComponent].nNumberOfAtoms || ------------------ | Branch (6758:21): [True: 15, False: 1.92k] ------------------ 6759| 1.92k| !(r = strchr((char*)parity_type, *q))) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (6759:21): [True: 1, False: 1.92k] ------------------ 6760| 32| { 6761| 32| ret = RI_ERR_SYNTAX; ------------------ | | 16| 32|#define RI_ERR_SYNTAX (-2) ------------------ 6762| 32| goto exit_function; 6763| 32| } 6764| 1.95k| } 6765| 35.6k| } 6766| 35.6k| if (p != pEnd) ------------------ | Branch (6766:13): [True: 6, False: 35.6k] ------------------ 6767| 6| { 6768| 6| ret = RI_ERR_SYNTAX; ------------------ | | 16| 6|#define RI_ERR_SYNTAX (-2) ------------------ 6769| 6| goto exit_function; 6770| 6| } 6771| 35.6k| len = iAtom; 6772| | /* Found len, the number of stereo centers in /t segment for component iComponent */ 6773| | 6774| 35.6k|#if ( ( FIX_GAF_2019_1==1 ) || ( FIX_GAF_2019_2==1 ) ) 6775| 35.6k| if ((iComponent > nNumComponents - 1) || (iComponent < 0)) ------------------ | Branch (6775:13): [True: 0, False: 35.6k] | Branch (6775:50): [True: 2, False: 35.6k] ------------------ 6776| 2| { 6777| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 6778| 2| goto exit_function; 6779| 2| } 6780| 35.6k| if (pInChI[iComponent].nNumberOfAtoms <= 0 || pInChI[iComponent].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 15| 35.6k|#define MAX_ATOMS 32766 ------------------ | Branch (6780:13): [True: 0, False: 35.6k] | Branch (6780:55): [True: 0, False: 35.6k] ------------------ 6781| 0| { 6782| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6783| 0| goto exit_function; 6784| 0| } 6785| 35.6k|#endif 6786| | 6787| | /* Allocate memory for pStereo */ 6788| 35.6k| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (6788:19): [True: 33.9k, False: 1.73k] ------------------ 6789| 35.6k| if (!*pStereo) ------------------ | Branch (6789:13): [True: 35.3k, False: 296] ------------------ 6790| 35.3k| { 6791| 35.3k| if (!(*pStereo = (INChI_Stereo*)inchi_calloc(1, sizeof(**pStereo)))) ------------------ | | 1146| 35.3k|#define inchi_calloc calloc ------------------ | Branch (6791:17): [True: 0, False: 35.3k] ------------------ 6792| 0| { 6793| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6794| 0| goto exit_function; 6795| 0| } 6796| 35.3k| } 6797| 35.6k| if (pStereo[0]->t_parity || pStereo[0]->nNumberOfStereoCenters || ------------------ | Branch (6797:13): [True: 2, False: 35.6k] | Branch (6797:37): [True: 0, False: 35.6k] ------------------ 6798| 35.6k| pStereo[0]->nNumber) ------------------ | Branch (6798:13): [True: 0, False: 35.6k] ------------------ 6799| 2| { 6800| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 6801| 2| goto exit_function; 6802| 2| } 6803| | /* Allocate sp3 stereo */ 6804| 35.6k| if (!(pStereo[0]->t_parity = (S_CHAR*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->b_parity[0]))) || ------------------ | | 1146| 35.6k|#define inchi_calloc calloc ------------------ | Branch (6804:13): [True: 0, False: 35.6k] ------------------ 6805| 35.6k| !(pStereo[0]->nNumber = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->nNumber[0])))) /* djb-rwth: cast operators added */ ------------------ | | 1146| 35.6k|#define inchi_calloc calloc ------------------ | Branch (6805:13): [True: 0, False: 35.6k] ------------------ 6806| 0| { 6807| | /* cleanup */ 6808| 0| if (pStereo[0]->t_parity) ------------------ | Branch (6808:17): [True: 0, False: 0] ------------------ 6809| 0| { 6810| 0| INCHI_HEAPCHK 6811| 0| inchi_free(pStereo[0]->t_parity); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6812| 0| pStereo[0]->t_parity = NULL; 6813| 0| } 6814| 0| if (pStereo[0]->nNumber) ------------------ | Branch (6814:17): [True: 0, False: 0] ------------------ 6815| 0| { 6816| 0| INCHI_HEAPCHK 6817| 0| inchi_free(pStereo[0]->nNumber); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6818| 0| pStereo[0]->nNumber = NULL; 6819| 0| } 6820| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6821| 0| goto exit_function; 6822| 0| } 6823| | 6824| | 6825| | /* Store stereocenters (pass 2) */ 6826| 35.6k| retf = SegmentSp3StoreStereoCenters(pbAbc, pStart, pEnd, pInChI[iComponent].nNumberOfAtoms, pStereo[0]); 6827| 35.6k| if (retf == RI_ERR_SYNTAX) ------------------ | | 16| 35.6k|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (6827:13): [True: 4, False: 35.6k] ------------------ 6828| 4| { 6829| 4| ret = RI_ERR_SYNTAX; ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 6830| 4| goto exit_function; 6831| 4| } 6832| | 6833| | /* Treat multiplier-covered components */ 6834| 35.6k| retf = SegmentSp3CopyMultiplierCovered(mpy_component, iComponent, pInChI, bIso, nCpyType); 6835| 35.6k| if (retf == RI_ERR_SYNTAX) ------------------ | | 16| 35.6k|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (6835:13): [True: 0, False: 35.6k] ------------------ 6836| 0| { 6837| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6838| 0| goto exit_function; 6839| 0| } 6840| | 6841| 35.6k| end_main_cycle: 6842| 35.6k| iComponent += mpy_component; 6843| 35.6k| if (*pEnd) ------------------ | Branch (6843:13): [True: 34.2k, False: 1.35k] ------------------ 6844| 34.2k| { 6845| 34.2k| pStart = pEnd + 1; 6846| 34.2k| continue; 6847| 34.2k| } 6848| 1.35k| else 6849| 1.35k| { 6850| 1.35k| break; 6851| 1.35k| } 6852| | 6853| 35.6k| } /* Cycle over components */ 6854| | 6855| 1.35k| if (nNumComponents != iComponent) ------------------ | Branch (6855:9): [True: 11, False: 1.33k] ------------------ 6856| 11| { 6857| | /* Not all components treated, that's an error */ 6858| 11| ret = RI_ERR_SYNTAX; ------------------ | | 16| 11|#define RI_ERR_SYNTAX (-2) ------------------ 6859| 11| goto exit_function; 6860| 11| } 6861| | /* At this moment, INChI_Stereo pInChI[k].Stereo provides stereocenter parity info for k-th component 6862| | pInChI[k].Stereo. 6863| | nNumber[nNumberOfStereoCenters] cano numbers 6864| | t_parity[nNumberOfStereoCenters] tetrahedral atom parities 6865| | */ 6866| | 6867| | 6868| 1.33k| ret = iComponent + 1; 6869| | 6870| 1.65k|exit_function: 6871| | 6872| 1.65k| return ret; 6873| 1.33k|} ichiread.c:SegmentSp3CreateEmpty: 12094| 233|{ 12095| 233| int ret = 0; 12096| 233| int iComponent; 12097| 233| int len0 = 0; 12098| 233| int bIso = (state == IST_MOBILE_H_ISO_SP3 || state == IST_FIXED_H_ISO_SP3); ------------------ | Branch (12098:17): [True: 19, False: 214] | Branch (12098:50): [True: 86, False: 128] ------------------ 12099| 233| INChI_Stereo** pStereo = NULL; 12100| 233| INChI* pInChI = pInpInChI[bMobileH]; 12101| | 12102| 2.24k| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (12102:26): [True: 2.01k, False: 233] ------------------ 12103| 2.01k| { 12104| 2.01k| INChI* pIsoInChI = &pInChI[iComponent]; 12105| 2.01k| pStereo = bIso ? &pIsoInChI->StereoIsotopic : &pIsoInChI->Stereo; ------------------ | Branch (12105:19): [True: 159, False: 1.85k] ------------------ 12106| 2.01k| if (!*pStereo) ------------------ | Branch (12106:13): [True: 1.06k, False: 944] ------------------ 12107| 1.06k| { 12108| 1.06k| if (!(*pStereo = (INChI_Stereo*)inchi_calloc(1, sizeof(**pStereo)))) ------------------ | | 1146| 1.06k|#define inchi_calloc calloc ------------------ | Branch (12108:17): [True: 0, False: 1.06k] ------------------ 12109| 0| { 12110| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 12111| 0| } 12112| 1.06k| } 12113| | /* allocate empty sp3 stereo */ 12114| 2.01k| if ((!pStereo[0]->b_parity && ------------------ | Branch (12114:14): [True: 1.06k, False: 944] ------------------ 12115| 1.06k| !(pStereo[0]->b_parity = (S_CHAR*)inchi_calloc((long long)len0 + 1, sizeof(pStereo[0]->b_parity[0])))) || ------------------ | | 1146| 1.06k|#define inchi_calloc calloc ------------------ | Branch (12115:13): [True: 0, False: 1.06k] ------------------ 12116| 2.01k| (!pStereo[0]->nBondAtom1 && ------------------ | Branch (12116:14): [True: 1.06k, False: 944] ------------------ 12117| 1.06k| !(pStereo[0]->nBondAtom1 = (AT_NUMB*)inchi_calloc((long long)len0 + 1, sizeof(pStereo[0]->nBondAtom1[0])))) || ------------------ | | 1146| 1.06k|#define inchi_calloc calloc ------------------ | Branch (12117:17): [True: 0, False: 1.06k] ------------------ 12118| 2.01k| (!pStereo[0]->nBondAtom2 && ------------------ | Branch (12118:14): [True: 1.06k, False: 944] ------------------ 12119| 1.06k| !(pStereo[0]->nBondAtom2 = (AT_NUMB*)inchi_calloc((long long)len0 + 1, sizeof(pStereo[0]->nBondAtom2[0]))))) /* djb-rwth: cast operator added; addressing LLVM warnings */ ------------------ | | 1146| 1.06k|#define inchi_calloc calloc ------------------ | Branch (12119:17): [True: 0, False: 1.06k] ------------------ 12120| 0| { 12121| | /* cleanup */ 12122| 0| if (pStereo[0]->b_parity) ------------------ | Branch (12122:17): [True: 0, False: 0] ------------------ 12123| 0| { 12124| 0| INCHI_HEAPCHK 12125| 0| inchi_free(pStereo[0]->b_parity); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 12126| 0| pStereo[0]->b_parity = NULL; 12127| 0| } 12128| 0| if (pStereo[0]->nBondAtom1) ------------------ | Branch (12128:17): [True: 0, False: 0] ------------------ 12129| 0| { 12130| 0| INCHI_HEAPCHK 12131| 0| inchi_free(pStereo[0]->nBondAtom1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 12132| 0| pStereo[0]->nBondAtom1 = NULL; 12133| 0| } 12134| 0| if (pStereo[0]->nBondAtom2) ------------------ | Branch (12134:17): [True: 0, False: 0] ------------------ 12135| 0| { 12136| 0| INCHI_HEAPCHK 12137| 0| inchi_free(pStereo[0]->nBondAtom2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 12138| 0| pStereo[0]->nBondAtom2 = NULL; 12139| 0| } 12140| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 12141| 0| } 12142| 2.01k| pStereo[0]->nCompInv2Abs = NO_VALUE_INT; ------------------ | | 23| 2.01k|#define NO_VALUE_INT 9999 ------------------ 12143| 2.01k| } 12144| 233| ret = nNumComponents + 1; 12145| | 12146| 233| return ret; 12147| 233|} ichiread.c:SegmentSp3ProcessAbbreviation: 12278| 22|{ 12279| 22| int i, bIsoTo = -1, bIsoFrom = -1; 12280| 22| int ret = 0; 12281| 22| INChI* pInChIFrom = NULL; 12282| | 12283| 22|#if (FIX_DALKE_BUGS == 1) 12284| 22| if (iComponent + val > nNumComponents) ------------------ | Branch (12284:9): [True: 3, False: 19] ------------------ 12285| 3| { 12286| 3| return RI_ERR_SYNTAX; ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 12287| 3| } 12288| 19|#endif 12289| |#if (FIX_GAF_ISSUES==1) 12290| | if (iComponent < 0) 12291| | { 12292| | return RI_ERR_SYNTAX; 12293| | } 12294| |#endif 12295| | 12296| 19| switch (bMobileH) 12297| 19| { 12298| 8| case TAUT_YES: ------------------ | | 575| 8|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (12298:5): [True: 8, False: 11] ------------------ 12299| 8| switch (state) 12300| 8| { 12301| 7| case IST_MOBILE_H_ISO_SP3: ------------------ | Branch (12301:9): [True: 7, False: 1] ------------------ 12302| 7| if (*q == 'm') ------------------ | Branch (12302:17): [True: 0, False: 7] ------------------ 12303| 0| { 12304| | /* copy from mobile H to isotopic mobile H */ 12305| 0| pInChIFrom = pInChI; 12306| 0| bIsoTo = 1; 12307| 0| bIsoFrom = 0; 12308| 0| } 12309| 7| else 12310| 7| { 12311| 7| if (*q == 'e') ------------------ | Branch (12311:21): [True: 7, False: 0] ------------------ 12312| 7| { 12313| | /* copy from mobile H to isotopic mobile H */ 12314| 7| pInChIFrom = pInChI; 12315| 7| bIsoTo = 1; 12316| 7| bIsoFrom = -1; /* empty */ 12317| 7| } 12318| 0| else 12319| 0| { 12320| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12321| 0| } 12322| 7| } 12323| 7| break; 12324| 1| default: ------------------ | Branch (12324:9): [True: 1, False: 7] ------------------ 12325| 1| ret = RI_ERR_SYNTAX; ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 12326| 1| break; 12327| 8| } 12328| 8| break; 12329| 11| case TAUT_NON: ------------------ | | 574| 11|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (12329:5): [True: 11, False: 8] ------------------ 12330| 11| switch (state) 12331| 11| { 12332| 8| case IST_FIXED_H_SP3: ------------------ | Branch (12332:9): [True: 8, False: 3] ------------------ 12333| 8| if (*q == 'm') ------------------ | Branch (12333:17): [True: 2, False: 6] ------------------ 12334| 2| { 12335| | /* copy from mobile H to fixed H */ 12336| 2| pInChIFrom = pInpInChI_ALT_TAUT_bMobileH; 12337| 2| bIsoTo = 0; 12338| 2| bIsoFrom = 0; 12339| 2| } 12340| 6| else 12341| 6| { 12342| 6| if (*q == 'e') ------------------ | Branch (12342:21): [True: 6, False: 0] ------------------ 12343| 6| { 12344| | /* copy from mobile H to isotopic mobile H */ 12345| 6| pInChIFrom = pInChI; /* djb-rwth: addressing coverity ID #499498 -- definitely not a copy-paste error */ 12346| 6| bIsoTo = 1; 12347| 6| bIsoFrom = -1; /* empty */ 12348| 6| } 12349| 0| else 12350| 0| { 12351| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12352| 0| } 12353| 6| } 12354| 8| break; 12355| 3| case IST_FIXED_H_ISO_SP3: ------------------ | Branch (12355:9): [True: 3, False: 8] ------------------ 12356| 3| if (*q == 'm') ------------------ | Branch (12356:17): [True: 0, False: 3] ------------------ 12357| 0| { 12358| | /* copy from mobile H to fixed isotopic H */ 12359| 0| pInChIFrom = pInpInChI_ALT_TAUT_bMobileH; 12360| 0| bIsoTo = 1; 12361| 0| bIsoFrom = 0; 12362| 0| } 12363| 3| else 12364| 3| { 12365| 3| if (*q == 'M') ------------------ | Branch (12365:21): [True: 3, False: 0] ------------------ 12366| 3| { 12367| | /* copy from isotopic mobile H to fixed isotopic H */ 12368| 3| pInChIFrom = pInpInChI_ALT_TAUT_bMobileH; 12369| 3| bIsoTo = 1; 12370| 3| bIsoFrom = 1; 12371| 3| } 12372| 0| else 12373| 0| { 12374| 0| if (*q == 'n') ------------------ | Branch (12374:25): [True: 0, False: 0] ------------------ 12375| 0| { 12376| | /* copy from fixed H to fixed isotopic H */ 12377| 0| pInChIFrom = pInChI; 12378| 0| bIsoTo = 1; 12379| 0| bIsoFrom = 0; 12380| 0| } 12381| 0| else 12382| 0| { 12383| 0| if (*q == 'e') ------------------ | Branch (12383:29): [True: 0, False: 0] ------------------ 12384| 0| { 12385| | /* copy from mobile H to isotopic mobile H */ 12386| 0| pInChIFrom = pInChI; 12387| 0| bIsoTo = 1; 12388| 0| bIsoFrom = -1; /* empty */ 12389| 0| } 12390| 0| else 12391| 0| { 12392| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12393| 0| } 12394| 0| } 12395| 0| } 12396| 3| } 12397| 3| break; 12398| 0| default: ------------------ | Branch (12398:9): [True: 0, False: 11] ------------------ 12399| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12400| 0| break; 12401| 11| } 12402| 11| break; 12403| | 12404| 11| default: ------------------ | Branch (12404:5): [True: 0, False: 19] ------------------ 12405| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12406| 0| break; 12407| 19| } 12408| | 12409| 19| if (ret < 0) ------------------ | Branch (12409:9): [True: 1, False: 18] ------------------ 12410| 1| { 12411| 1| return ret; 12412| 1| } 12413| | 12414| | /* copy */ 12415| 45| for (i = 0; i < val; i++) ------------------ | Branch (12415:17): [True: 30, False: 15] ------------------ 12416| 30| { 12417| | /* djb-rwth: fixing oss-fuzz issue #26540 */ 12418| 30| ret = CopySegment(pInChI + iComponent + i, pInChIFrom + iComponent + i, nCpyType, bIsoTo, bIsoFrom); 12419| 30| if (!ret) ------------------ | Branch (12419:13): [True: 3, False: 27] ------------------ 12420| 3| { 12421| 3| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 12422| 3| } 12423| 30| if (ret < 0) ------------------ | Branch (12423:13): [True: 3, False: 27] ------------------ 12424| 3| { 12425| 3| return ret; 12426| 3| } 12427| 27| if (bIsoFrom >= 0) ------------------ | Branch (12427:13): [True: 4, False: 23] ------------------ 12428| 4| { 12429| 4| INChI_Stereo* pStereoTo = bIsoTo ? pInChI[iComponent + i].StereoIsotopic : pInChI[iComponent + i].Stereo; ------------------ | Branch (12429:39): [True: 0, False: 4] ------------------ 12430| 4| if (pStereoTo) ------------------ | Branch (12430:17): [True: 4, False: 0] ------------------ 12431| 4| { 12432| 4| pStereoTo->nCompInv2Abs = NO_VALUE_INT; /* in case there in no /m segment after this */ ------------------ | | 23| 4|#define NO_VALUE_INT 9999 ------------------ 12433| 4| } 12434| 4| } 12435| 27| } 12436| | 12437| 15| *mpy_component = val; 12438| | 12439| 15| return ret; 12440| 18|} ichiread.c:SegmentSp3StoreStereoCenters: 12156| 35.6k|{ 12157| 35.6k| const char parity_type[] = "-+u?"; 12158| 35.6k| const char* p, * q, * r; 12159| 35.6k| AT_NUMB nAtom1; 12160| 35.6k| int iAtom; 12161| 35.6k| int atomParity; 12162| 35.6k| int base = 10; 12163| | 12164| 35.6k| if (*pbAbc == 1) ------------------ | Branch (12164:9): [True: 0, False: 35.6k] ------------------ 12165| 0| { 12166| 0| for (p = (char*)pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (12166:44): [True: 0, False: 0] ------------------ 12167| 0| { 12168| 0| if ((nAtom1 = (AT_NUMB)inchi_strtol(p, &p, base)) && ------------------ | Branch (12168:17): [True: 0, False: 0] ------------------ 12169| 0| (atomParity = (int)inchi_strtol(p, &p, 10), ------------------ | Branch (12169:17): [True: 0, False: 0] ------------------ 12170| 0| AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 231| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY)) ------------------ | | 230| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (12170:21): [True: 0, False: 0] | Branch (12170:58): [True: 0, False: 0] ------------------ 12171| 0| { 12172| 0| ; /* okay */ 12173| 0| } 12174| 0| else 12175| 0| { 12176| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12177| 0| } 12178| 0| if (nAtom1 > pInChI_iComponent_nNumberOfAtoms) ------------------ | Branch (12178:17): [True: 0, False: 0] ------------------ 12179| 0| { 12180| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12181| 0| } 12182| 0| PStereo_0->t_parity[iAtom] = atomParity; 12183| 0| PStereo_0->nNumber[iAtom] = nAtom1; 12184| 0| if (iAtom && !(PStereo_0->nNumber[iAtom - 1] < nAtom1)) ------------------ | Branch (12184:17): [True: 0, False: 0] | Branch (12184:26): [True: 0, False: 0] ------------------ 12185| 0| { 12186| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12187| 0| } 12188| 0| } 12189| 0| } 12190| 35.6k| else 12191| 35.6k| { 12192| 37.4k| for (p = (char*)pStart, iAtom = 0; p < pEnd; iAtom++, p += (*p == ',')) ------------------ | Branch (12192:44): [True: 1.85k, False: 35.6k] ------------------ 12193| 1.85k| { 12194| 1.85k| nAtom1 = (AT_NUMB)inchi_strtol(p, &q, 10); 12195| 1.85k|#if ( CHECK_STRTOL_ATNUMB==1 ) 12196| 1.85k| if (nAtom1 > MAX_ATOMS || nAtom1 < 0) ------------------ | | 15| 3.70k|#define MAX_ATOMS 32766 ------------------ | Branch (12196:17): [True: 0, False: 1.85k] | Branch (12196:39): [True: 0, False: 1.85k] ------------------ 12197| 0| { 12198| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12199| 0| } 12200| 1.85k|#endif 12201| 1.85k| if (!(r = strchr((char*)parity_type, *q))) ------------------ | Branch (12201:17): [True: 0, False: 1.85k] ------------------ 12202| 0| { 12203| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12204| 0| } 12205| 1.85k| p = q + 1; 12206| 1.85k| atomParity = (int)(r - parity_type) + 1; 12207| 1.85k| PStereo_0->t_parity[iAtom] = atomParity; 12208| 1.85k| PStereo_0->nNumber[iAtom] = nAtom1; 12209| 1.85k| if (iAtom && !(PStereo_0->nNumber[iAtom - 1] < nAtom1)) ------------------ | Branch (12209:17): [True: 488, False: 1.36k] | Branch (12209:26): [True: 4, False: 484] ------------------ 12210| 4| { 12211| 4| return RI_ERR_SYNTAX; ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 12212| 4| } 12213| 1.85k| } 12214| 35.6k| } 12215| 35.6k| PStereo_0->nNumberOfStereoCenters = iAtom; 12216| | /*if ( iAtom ) {*/ 12217| 35.6k| PStereo_0->nCompInv2Abs = NO_VALUE_INT; /* unknown yet */ ------------------ | | 23| 35.6k|#define NO_VALUE_INT 9999 ------------------ 12218| | 12219| 35.6k| if (p != pEnd) ------------------ | Branch (12219:9): [True: 0, False: 35.6k] ------------------ 12220| 0| { 12221| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12222| 0| } 12223| | 12224| 35.6k| return 0; 12225| 35.6k|} ichiread.c:SegmentSp3CopyMultiplierCovered: 12236| 35.6k|{ 12237| 35.6k| int i, ret = 0; 12238| 35.6k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (12238:17): [True: 21, False: 35.6k] ------------------ 12239| 21| { 12240| 21| ret = CopySegment(pInChI + iComponent + i, pInChI + iComponent, nCpyType, bIso, bIso); 12241| 21| if (!ret) ------------------ | Branch (12241:13): [True: 0, False: 21] ------------------ 12242| 0| { 12243| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12244| 0| } 12245| 21| if (ret < 0) ------------------ | Branch (12245:13): [True: 0, False: 21] ------------------ 12246| 0| { 12247| 0| return ret; 12248| 0| } 12249| 21| ret = CopySegment(pInChI + iComponent + i, pInChI + iComponent, CPY_SP3_M, bIso, bIso); 12250| 21| if (!ret) ------------------ | Branch (12250:13): [True: 0, False: 21] ------------------ 12251| 0| { 12252| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 12253| 0| } 12254| 21| if (ret < 0) ------------------ | Branch (12254:13): [True: 0, False: 21] ------------------ 12255| 0| { 12256| 0| return ret; 12257| 0| } 12258| 21| } 12259| | 12260| 35.6k| return ret; 12261| 35.6k|} ichiread.c:ParseSegmentSp3m: 6396| 6.05k|{ 6397| | /* Pass 1: count bonds and find actual numbers of atom */ 6398| 6.05k| int nNumComponents, iComponent; 6399| 6.05k| const char* p, * pStart, * pEnd; 6400| 6.05k| int ret = 0; 6401| 6.05k| INChI* pInChI = pInpInChI[bMobileH]; 6402| 6.05k| INChI_Stereo** pStereo = NULL; 6403| | 6404| 6.05k| int bIso = (state == IST_MOBILE_H_ISO_SP3_M || state == IST_FIXED_H_ISO_SP3_M); ------------------ | Branch (6404:19): [True: 303, False: 5.75k] | Branch (6404:54): [True: 232, False: 5.52k] ------------------ 6405| | 6406| 6.05k| if (!bIso && state != IST_MOBILE_H_SP3_M && state != IST_FIXED_H_SP3_M) ------------------ | Branch (6406:9): [True: 5.52k, False: 535] | Branch (6406:18): [True: 750, False: 4.77k] | Branch (6406:49): [True: 0, False: 750] ------------------ 6407| 0| { 6408| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 6409| 0| } 6410| 6.05k| nNumComponents = ppnNumComponents[bMobileH]; 6411| | 6412| 6.05k| if (str[0] != 'm') ------------------ | Branch (6412:9): [True: 5.86k, False: 192] ------------------ 6413| 5.86k| { 6414| | /* /m is missing: check whether we have to inherit /m from a preceding stereo layer */ 6415| 5.86k| INChI_Stereo* pStereoFrom, * pStereoTo; 6416| 5.86k| INChI* pInChIFrom; 6417| 5.86k| int bMobileHFrom = -1, bIsoFrom = -1; /* djb-rwth: removing redundant variables */ 6418| 5.86k| if (bMobileH && !bIso) ------------------ | Branch (6418:13): [True: 4.94k, False: 917] | Branch (6418:25): [True: 4.67k, False: 275] ------------------ 6419| 4.67k| { 6420| 4.67k| return 0; /* Main non-isotopic cannot inherit: it has no preceding layer */ 6421| 4.67k| } 6422| 1.19k| else 6423| 1.19k| { 6424| 1.19k| if (!bMobileH && !bIso) ------------------ | Branch (6424:17): [True: 917, False: 275] | Branch (6424:30): [True: 706, False: 211] ------------------ 6425| 706| { 6426| | /* fixed-H non-isotopic (F) inherits from Mobile-H non-isotopic (M) */ 6427| 706| bMobileHFrom = TAUT_YES; ------------------ | | 575| 706|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6428| 706| bIsoFrom = 0; 6429| 706| } 6430| 486| else 6431| 486| { 6432| 486| if (bMobileH && bIso) ------------------ | Branch (6432:21): [True: 275, False: 211] | Branch (6432:33): [True: 275, False: 0] ------------------ 6433| 275| { 6434| | /* Mobile-H isotopic (MI) inherits from Mobile-H non-isotopic (M) */ 6435| 275| bMobileHFrom = TAUT_YES; ------------------ | | 575| 275|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6436| 275| bIsoFrom = 0; 6437| 275| } 6438| 211| else 6439| 211| { 6440| 211| if (!bMobileH && bIso) ------------------ | Branch (6440:25): [True: 211, False: 0] | Branch (6440:38): [True: 211, False: 0] ------------------ 6441| 211| { 6442| | /* Fixed-H isotopic (FI) inherits from Fixed-H non-isotopic (F) */ 6443| 211| bMobileHFrom = TAUT_NON; ------------------ | | 574| 211|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6444| 211| bIsoFrom = 0; 6445| | /* if Sp3 is empty in F as well as in M, then inherit from MI */ 6446| 211| if (!bIsSp3LayerNotEmpty(pInpInChI, TAUT_NON, 0, ppnNumComponents[TAUT_NON /*bMobileH*/]) /* F */ && ------------------ | | 574| 211|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (!bIsSp3LayerNotEmpty(pInpInChI, TAUT_NON, 0, ppnNumComponents[TAUT_NON /*bMobileH*/]) /* F */ && ------------------ | | 574| 211|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (6446:29): [True: 166, False: 45] ------------------ 6447| 166| !bIsSp3LayerNotEmpty(pInpInChI, TAUT_YES, 0, ppnNumComponents[TAUT_YES /*bMobileH*/]) /* M */) ------------------ | | 575| 166|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ !bIsSp3LayerNotEmpty(pInpInChI, TAUT_YES, 0, ppnNumComponents[TAUT_YES /*bMobileH*/]) /* M */) ------------------ | | 575| 166|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (6447:29): [True: 163, False: 3] ------------------ 6448| 163| { 6449| 163| bMobileHFrom = TAUT_YES; ------------------ | | 575| 163|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6450| 163| bIsoFrom = 1; 6451| 163| } 6452| 211| } 6453| 211| } 6454| 486| } 6455| 1.19k| } 6456| 1.19k| if (bMobileHFrom < 0 || bIsoFrom < 0) /* djb-rwth: addressing coverity ID #499556 -- check necessary due to initialisation values */ ------------------ | Branch (6456:13): [True: 0, False: 1.19k] | Branch (6456:33): [True: 0, False: 1.19k] ------------------ 6457| 0| { 6458| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 6459| 0| } 6460| 1.19k| if (!bIsSp3LayerNotEmpty(pInpInChI, bMobileHFrom, bIsoFrom, ppnNumComponents[/*bMobileH*/ bMobileHFrom])) ------------------ | Branch (6460:13): [True: 990, False: 202] ------------------ 6461| 990| { 6462| | /* nothing to copy; check whether it should have inherited from a preceding layer */ 6463| 990| if ((!bMobileHFrom && bIsoFrom) || (bMobileHFrom && !bIsoFrom)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6463:18): [True: 3, False: 987] | Branch (6463:35): [True: 0, False: 3] | Branch (6463:49): [True: 987, False: 3] | Branch (6463:65): [True: 841, False: 146] ------------------ 6464| 841| { 6465| | /* MI or F inherit stereo from M */ 6466| 841| bMobileHFrom = TAUT_YES; ------------------ | | 575| 841|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6467| 841| bIsoFrom = 0; 6468| 841| if (!bIsSp3LayerNotEmpty(pInpInChI, bMobileHFrom, bIsoFrom, ppnNumComponents[bMobileHFrom /*bMobileH*/])) ------------------ | Branch (6468:21): [True: 841, False: 0] ------------------ 6469| 841| { 6470| 841| return 0; 6471| 841| } 6472| 841| } 6473| 149| else 6474| 149| { 6475| 149| return 0; 6476| 149| } 6477| 990| } 6478| 202| nNumComponents = inchi_min(ppnNumComponents[bMobileH], ppnNumComponents[bMobileHFrom]); ------------------ | | 139| 202|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 2, False: 200] | | ------------------ ------------------ 6479| 834| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6479:30): [True: 632, False: 202] ------------------ 6480| 632| { 6481| 632| pInChIFrom = pInpInChI[bMobileHFrom] + iComponent; 6482| 632| pInChI = pInpInChI[bMobileH] + iComponent; 6483| 632| if (pInChIFrom->nNumberOfAtoms > 0 && !pInChIFrom->bDeleted && ------------------ | Branch (6483:17): [True: 632, False: 0] | Branch (6483:51): [True: 632, False: 0] ------------------ 6484| 632| pInChI->nNumberOfAtoms > 0 && !pInChI->bDeleted) ------------------ | Branch (6484:17): [True: 632, False: 0] | Branch (6484:47): [True: 632, False: 0] ------------------ 6485| 632| { 6486| 632| pStereoFrom = bIsoFrom ? pInChIFrom->StereoIsotopic : pInChIFrom->Stereo; ------------------ | Branch (6486:31): [True: 167, False: 465] ------------------ 6487| 632| pStereoTo = bIso ? pInChI->StereoIsotopic : pInChI->Stereo; ------------------ | Branch (6487:29): [True: 405, False: 227] ------------------ 6488| 632| if (pStereoFrom && pStereoTo) ------------------ | Branch (6488:21): [True: 632, False: 0] | Branch (6488:36): [True: 272, False: 360] ------------------ 6489| 272| { 6490| 272| pStereoTo->nCompInv2Abs = pStereoFrom->nCompInv2Abs; 6491| | /* djb-rwth: removing redundant code */ 6492| 272| } 6493| 632| } 6494| 632| } 6495| 202| return 0; /* return value > 0 means the non-/m segment has been processed here */ 6496| 1.19k| } 6497| | 6498| 192| pStart = str + 1; 6499| 192| iComponent = 0; 6500| | 6501| | /*if ( !(pEnd = strchr( pStart, ';' )) )*/ /* 2007-09-25 DT */ 6502| 192| if (!(strchr(pStart, '/'))) /* djb-rwth: removing redundant code */ ------------------ | Branch (6502:9): [True: 192, False: 0] ------------------ 6503| 192| { 6504| 192| pEnd = pStart + strlen(pStart); 6505| 192| } 6506| 0| else 6507| 0| { 6508| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6509| 0| goto exit_function; 6510| 0| } 6511| 192| p = pStart; 6512| 192| if (pEnd == pStart) ------------------ | Branch (6512:9): [True: 121, False: 71] ------------------ 6513| 121| { 6514| | /* create empty sp3 segment */ 6515| 121| int len = 0; 6516| 6.87k| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6516:30): [True: 6.75k, False: 121] ------------------ 6517| 6.75k| { 6518| 6.75k| INChI* pIsoInChI = &pInChI[iComponent]; 6519| 6.75k| pStereo = bIso ? &pIsoInChI->StereoIsotopic : &pIsoInChI->Stereo; ------------------ | Branch (6519:23): [True: 38, False: 6.71k] ------------------ 6520| 6.75k| if (!*pStereo) ------------------ | Branch (6520:17): [True: 6.69k, False: 52] ------------------ 6521| 6.69k| { 6522| 6.69k| if (!(*pStereo = (INChI_Stereo*)inchi_calloc(1, sizeof(**pStereo)))) ------------------ | | 1146| 6.69k|#define inchi_calloc calloc ------------------ | Branch (6522:21): [True: 0, False: 6.69k] ------------------ 6523| 0| { 6524| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6525| 0| goto exit_function; 6526| 0| } 6527| 6.69k| } 6528| 6.75k| pStereo[0]->nCompInv2Abs = NO_VALUE_INT; /* deliberately empty */ ------------------ | | 23| 6.75k|#define NO_VALUE_INT 9999 ------------------ 6529| |#ifdef NEVER 6530| | if (pStereo[0]->nNumberOfStereoCenters) 6531| | { 6532| | ret = RI_ERR_SYNTAX; /* syntax error */ 6533| | goto exit_function; 6534| | } 6535| |#endif 6536| | /* allocate empty sp3 stereo */ 6537| 6.75k| if ((!pStereo[0]->t_parity && ------------------ | Branch (6537:18): [True: 6.71k, False: 35] ------------------ 6538| 6.71k| !(pStereo[0]->t_parity = (S_CHAR*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->b_parity[0])))) || ------------------ | | 1146| 6.71k|#define inchi_calloc calloc ------------------ | Branch (6538:17): [True: 0, False: 6.71k] ------------------ 6539| 6.75k| (!pStereo[0]->nNumber && ------------------ | Branch (6539:18): [True: 6.71k, False: 35] ------------------ 6540| 6.71k| !(pStereo[0]->nNumber = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->nNumber[0]))))) /* djb-rwth: cast operators added; addressing LLVM warnings */ ------------------ | | 1146| 6.71k|#define inchi_calloc calloc ------------------ | Branch (6540:21): [True: 0, False: 6.71k] ------------------ 6541| 0| { 6542| | /* cleanup */ 6543| 0| if (pStereo[0]->t_parity) ------------------ | Branch (6543:21): [True: 0, False: 0] ------------------ 6544| 0| { 6545| 0| INCHI_HEAPCHK 6546| 0| inchi_free(pStereo[0]->t_parity); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6547| 0| pStereo[0]->t_parity = NULL; 6548| 0| } 6549| 0| if (pStereo[0]->nNumber) ------------------ | Branch (6549:21): [True: 0, False: 0] ------------------ 6550| 0| { 6551| 0| INCHI_HEAPCHK 6552| 0| inchi_free(pStereo[0]->nNumber); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6553| 0| pStereo[0]->nNumber = NULL; 6554| 0| } 6555| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6556| 0| goto exit_function; 6557| 0| } 6558| 6.75k|} 6559| 121| ret = nNumComponents + 1; 6560| 121| } 6561| 71| else 6562| 71| { 6563| 498| while (p < pEnd && iComponent < nNumComponents) ------------------ | Branch (6563:16): [True: 440, False: 58] | Branch (6563:28): [True: 434, False: 6] ------------------ 6564| 434| { 6565| | /* cycle over components */ 6566| 434| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (6566:23): [True: 79, False: 355] ------------------ 6567| 434| if (*p != '.' && !*pStereo) ------------------ | Branch (6567:17): [True: 95, False: 339] | Branch (6567:30): [True: 83, False: 12] ------------------ 6568| 83| { 6569| 83| if (!(*pStereo = (INChI_Stereo*)inchi_calloc(1, sizeof(**pStereo)))) ------------------ | | 1146| 83|#define inchi_calloc calloc ------------------ | Branch (6569:21): [True: 0, False: 83] ------------------ 6570| 0| { 6571| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6572| 0| goto exit_function; 6573| 0| } 6574| 83| } 6575| 434| switch (*p) 6576| 434| { 6577| 39| case '1': ------------------ | Branch (6577:13): [True: 39, False: 395] ------------------ 6578| 39| pStereo[0]->nCompInv2Abs = -1; 6579| 39| break; 6580| 49| case '0': ------------------ | Branch (6580:13): [True: 49, False: 385] ------------------ 6581| 49| pStereo[0]->nCompInv2Abs = 1; 6582| 49| break; 6583| 339| case '.': ------------------ | Branch (6583:13): [True: 339, False: 95] ------------------ 6584| 339| if (*pStereo) ------------------ | Branch (6584:21): [True: 46, False: 293] ------------------ 6585| 46| { 6586| 46| pStereo[0]->nCompInv2Abs = 0; 6587| 46| } 6588| 339| break; 6589| 7| default: ------------------ | Branch (6589:13): [True: 7, False: 427] ------------------ 6590| 7| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 7|#define RI_ERR_SYNTAX (-2) ------------------ 6591| 7| goto exit_function; 6592| 434| } 6593| 427| iComponent++; 6594| 427| p++; 6595| 427| } 6596| 64| if (p != pEnd || iComponent != nNumComponents) ------------------ | Branch (6596:13): [True: 6, False: 58] | Branch (6596:26): [True: 28, False: 30] ------------------ 6597| 34| { 6598| 34| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 34|#define RI_ERR_SYNTAX (-2) ------------------ 6599| 34| goto exit_function; 6600| 34| } 6601| 30| ret = nNumComponents + 1; 6602| 30| } 6603| | 6604| 192|exit_function: 6605| | 6606| 192| return ret; 6607| 192| } ichiread.c:bIsSp3LayerNotEmpty: 6363| 2.41k|{ 6364| 2.41k| INChI* pInChI; 6365| 2.41k| INChI_Stereo* pStereo; 6366| 2.41k| int iComponent, num_not_empty = 0; 6367| | 6368| 2.41k| if (pInpInChI[bMobileH]) ------------------ | Branch (6368:9): [True: 2.41k, False: 0] ------------------ 6369| 2.41k| { 6370| 178k| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6370:30): [True: 175k, False: 2.41k] ------------------ 6371| 175k| { 6372| 175k| pInChI = pInpInChI[bMobileH] + iComponent; 6373| 175k| if (pInChI->bDeleted || !pInChI->nNumberOfAtoms) ------------------ | Branch (6373:17): [True: 46, False: 175k] | Branch (6373:37): [True: 0, False: 175k] ------------------ 6374| 46| { 6375| 46| continue; 6376| 46| } 6377| 175k| pStereo = bIso ? pInChI->StereoIsotopic : pInChI->Stereo; ------------------ | Branch (6377:23): [True: 33.5k, False: 142k] ------------------ 6378| 175k| if (pStereo && pStereo->nNumberOfStereoCenters > 0 && pStereo->nNumber && pStereo->t_parity) ------------------ | Branch (6378:17): [True: 1.54k, False: 174k] | Branch (6378:28): [True: 344, False: 1.19k] | Branch (6378:67): [True: 344, False: 0] | Branch (6378:87): [True: 344, False: 0] ------------------ 6379| 344| { 6380| 344| num_not_empty++; 6381| 344| } 6382| 175k| } 6383| 2.41k| } 6384| 2.41k| return num_not_empty; 6385| 2.41k|} ichiread.c:ParseSegmentSp3s: 6254| 5.96k|{ 6255| | /* Pass 1: count bonds and find actual numbers of atom */ 6256| 5.96k| int nNumComponents, iComponent, val; 6257| 5.96k| const char* p, * q, * pStart, * pEnd; 6258| 5.96k| int ret = 0; 6259| 5.96k| INChI* pInChI = pInpInChI[bMobileH]; 6260| 5.96k| INChI_Stereo** pStereo = NULL; 6261| | 6262| 5.96k| int bIso = (state == IST_MOBILE_H_ISO_SP3_S || state == IST_FIXED_H_ISO_SP3_S); ------------------ | Branch (6262:19): [True: 295, False: 5.67k] | Branch (6262:54): [True: 211, False: 5.46k] ------------------ 6263| | 6264| 5.96k| if (!bIso && state != IST_MOBILE_H_SP3_S && state != IST_FIXED_H_SP3_S) ------------------ | Branch (6264:9): [True: 5.46k, False: 506] | Branch (6264:18): [True: 723, False: 4.73k] | Branch (6264:49): [True: 0, False: 723] ------------------ 6265| 0| { 6266| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 6267| 0| } 6268| | 6269| 5.96k| if (str[0] != 's') ------------------ | Branch (6269:9): [True: 5.61k, False: 356] ------------------ 6270| 5.61k| { 6271| 5.61k| return 0; 6272| 5.61k| } 6273| | 6274| 356| pStart = (char*)str + 1; 6275| | /* djb-rwth: removing redundant code */ 6276| 356| nNumComponents = ppnNumComponents[bMobileH]; 6277| | 6278| | /*if ( !(pEnd = strchr( pStart, ';' )) )*/ /* 2007-09-25 DT */ 6279| 356| if (!(strchr(pStart, '/'))) /* djb-rwth: removing redundant variables/code */ ------------------ | Branch (6279:9): [True: 356, False: 0] ------------------ 6280| 356| { 6281| 356| pEnd = pStart + strlen(pStart); 6282| 356| } 6283| 0| else 6284| 0| { 6285| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6286| 0| goto exit_function; 6287| 0| } 6288| 356| p = pStart; 6289| 356| if (pEnd == pStart) ------------------ | Branch (6289:9): [True: 154, False: 202] ------------------ 6290| 154| { 6291| | /* create empty sp3 segment */ 6292| 154| int len = 0; 6293| 154| s[bMobileH][bIso] = NO_VALUE_INT; /* empty */ ------------------ | | 23| 154|#define NO_VALUE_INT 9999 ------------------ 6294| | /* create empty sp3 segment */ 6295| 10.3k| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6295:30): [True: 10.1k, False: 153] ------------------ 6296| 10.1k| { 6297| 10.1k| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (6297:23): [True: 98, False: 10.0k] ------------------ 6298| 10.1k| if (!*pStereo) ------------------ | Branch (6298:17): [True: 10.0k, False: 111] ------------------ 6299| 10.0k| { 6300| 10.0k| if (!(*pStereo = (INChI_Stereo*)inchi_calloc(1, sizeof(**pStereo)))) ------------------ | | 1146| 10.0k|#define inchi_calloc calloc ------------------ | Branch (6300:21): [True: 0, False: 10.0k] ------------------ 6301| 0| { 6302| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6303| 0| goto exit_function; 6304| 0| } 6305| 10.0k| } 6306| 10.1k| pStereo[0]->nCompInv2Abs = 0; /* deliberately empty */ 6307| | 6308| 10.1k| if (pStereo[0]->nNumberOfStereoCenters) ------------------ | Branch (6308:17): [True: 1, False: 10.1k] ------------------ 6309| 1| { 6310| 1| ret = RI_ERR_SYNTAX; /* syntax error: "/s" without a digit describes "no stereo" */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 6311| 1| goto exit_function; 6312| 1| } 6313| | /* allocate empty sp3 stereo */ 6314| 10.1k| if ((!pStereo[0]->t_parity && ------------------ | Branch (6314:18): [True: 10.0k, False: 102] ------------------ 6315| 10.0k| !(pStereo[0]->t_parity = (S_CHAR*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->b_parity[0])))) || ------------------ | | 1146| 10.0k|#define inchi_calloc calloc ------------------ | Branch (6315:17): [True: 0, False: 10.0k] ------------------ 6316| 10.1k| (!pStereo[0]->nNumber && ------------------ | Branch (6316:18): [True: 10.0k, False: 102] ------------------ 6317| 10.0k| !(pStereo[0]->nNumber = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pStereo[0]->nNumber[0]))))) /* djb-rwth: cast operators added; addressing LLVM warnings */ ------------------ | | 1146| 10.0k|#define inchi_calloc calloc ------------------ | Branch (6317:21): [True: 0, False: 10.0k] ------------------ 6318| 0| { 6319| | /* cleanup */ 6320| 0| if (pStereo[0]->t_parity) ------------------ | Branch (6320:21): [True: 0, False: 0] ------------------ 6321| 0| { 6322| 0| INCHI_HEAPCHK 6323| 0| inchi_free(pStereo[0]->t_parity); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6324| 0| pStereo[0]->t_parity = NULL; 6325| 0| } 6326| 0| if (pStereo[0]->nNumber) ------------------ | Branch (6326:21): [True: 0, False: 0] ------------------ 6327| 0| { 6328| 0| INCHI_HEAPCHK 6329| 0| inchi_free(pStereo[0]->nNumber); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6330| 0| pStereo[0]->nNumber = NULL; 6331| 0| } 6332| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6333| 0| goto exit_function; 6334| 0| } 6335| 10.1k| } 6336| 153| ret = nNumComponents + 1; 6337| 153| } 6338| 202| else 6339| 202| { 6340| 202| val = (int)inchi_strtol(p, &q, 10); 6341| 202| if (q == pEnd && 1 <= val && val <= 3) ------------------ | Branch (6341:13): [True: 200, False: 2] | Branch (6341:26): [True: 190, False: 10] | Branch (6341:38): [True: 178, False: 12] ------------------ 6342| 178| { 6343| 178| s[bMobileH][bIso] = val; 6344| 178| ret = nNumComponents + 1; 6345| 178| } 6346| 24| else 6347| 24| { 6348| 24| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 24|#define RI_ERR_SYNTAX (-2) ------------------ 6349| 24| } 6350| 202| } 6351| | 6352| 356|exit_function: 6353| | 6354| 356| return ret; 6355| 356|} ichiread.c:ParseSegmentIsoAtoms: 5825| 1.82k|{ 5826| 1.82k| int i, mpy_component, val; 5827| 1.82k| int nNumComponents, iComponent, len = 0, iAtom; 5828| 1.82k| int nAtom1; /* djb-rwth: fixing coverity ID #499573 */ 5829| 1.82k| const char* p, * q, * t, * pStart, * pEnd, * r; 5830| 1.82k| int ret = 0; 5831| 1.82k| INChI* pInChI = pInpInChI[bMobileH]; 5832| 1.82k| INChI* pInChIFrom = NULL; 5833| 1.82k| INChI_IsotopicAtom** pIsotopicAtom = NULL; 5834| 1.82k| INChI_IsotopicAtom isoAtom; 5835| | 5836| 1.82k| const char mult_type[] = "mnMNe"; 5837| 1.82k| const char parity_type[] = "-+TDH"; 5838| 1.82k| int bIsoFrom, nCpyType = CPY_ISO_AT; 5839| 1.82k| int base = 10; 5840| 1.82k| int if_cnd = 1; /* djb-rwth: needed for some if condition restructuring */ 5841| | 5842| 1.82k| if (str[0] != 'i') ------------------ | Branch (5842:9): [True: 0, False: 1.82k] ------------------ 5843| 0| { 5844| 0| return 0; 5845| 0| } 5846| | 5847| 1.82k| pStart = (char*)str + 1; 5848| 1.82k| iComponent = 0; 5849| 1.82k| nNumComponents = ppnNumComponents[bMobileH]; 5850| | 5851| 1.82k| if (!((bMobileH == TAUT_YES && state == IST_MOBILE_H_ISO_ATOMS) || ------------------ | | 575| 3.64k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5851:12): [True: 1.38k, False: 435] | Branch (5851:36): [True: 1.38k, False: 0] ------------------ 5852| 435| (bMobileH == TAUT_NON && state == IST_FIXED_H_ISO_ATOMS))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 574| 870|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5852:10): [True: 435, False: 0] | Branch (5852:34): [True: 435, False: 0] ------------------ 5853| 0| { 5854| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5855| 0| } 5856| 1.82k| if (!*pStart) ------------------ | Branch (5856:9): [True: 492, False: 1.33k] ------------------ 5857| 492| { 5858| 492| return nNumComponents + 1; /* no isotopic atoms */ 5859| 492| } 5860| | 5861| 35.2k| while (1) ------------------ | Branch (5861:12): [True: 35.2k, Folded] ------------------ 5862| 35.2k| { 5863| | /* cycle over components */ 5864| 35.2k| if (!(pEnd = strchr(pStart, ';'))) ------------------ | Branch (5864:13): [True: 1.30k, False: 33.9k] ------------------ 5865| 1.30k| { 5866| 1.30k| pEnd = pStart + strlen(pStart); 5867| 1.30k| } 5868| 35.2k| if ((p = strchr(pStart, '*')) && p < pEnd) ------------------ | Branch (5868:13): [True: 153, False: 35.1k] | Branch (5868:42): [True: 129, False: 24] ------------------ 5869| 129| { 5870| 129| mpy_component = (int)inchi_strtol(pStart, &q, 10); 5871| 129| if (p != q) ------------------ | Branch (5871:17): [True: 1, False: 128] ------------------ 5872| 1| { 5873| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 5874| 1| goto exit_function; 5875| 1| } 5876| 128|#if (FIX_DALKE_BUGS == 1) 5877| 128| if (iComponent + mpy_component > nNumComponents) ------------------ | Branch (5877:17): [True: 8, False: 120] ------------------ 5878| 8| { 5879| 8| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 5880| 8| goto exit_function; 5881| 8| } 5882| 120|#endif 5883| 120| p++; /* move to the 1st character of the component */ 5884| 120| } 5885| 35.1k| else 5886| 35.1k| { 5887| | /* djb-rwth: condition for if block had to be rewritten */ 5888| 35.1k| if ((int)inchi_strtol(pStart, &q, 10) > 0) ------------------ | Branch (5888:17): [True: 1.16k, False: 33.9k] ------------------ 5889| 1.16k| { 5890| 1.16k| val = (int)inchi_strtol(pStart, &q, 10); 5891| 1.16k| if_cnd = isdigit(*pStart); 5892| | 5893| 1.16k| } 5894| 33.9k| else 5895| 33.9k| { 5896| 33.9k| val = 1; 5897| 33.9k| q = pStart; 5898| 33.9k| if_cnd = 1; 5899| 33.9k| } 5900| | 5901| 35.1k| if (if_cnd && (t = strchr((char*)mult_type, *q)) && q + 1 == pEnd) /* djb-rwth: if_cnd applied; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (5901:17): [True: 35.1k, False: 3] | Branch (5901:27): [True: 134, False: 35.0k] | Branch (5901:65): [True: 19, False: 115] ------------------ 5902| 19| { 5903| | /* process the abbreviation */ 5904| 19| ret = 0; 5905| 19|#if (FIX_DALKE_BUGS == 1) 5906| 19| if (iComponent + val > nNumComponents) ------------------ | Branch (5906:21): [True: 0, False: 19] ------------------ 5907| 0| { 5908| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5909| 0| goto exit_function; 5910| 0| } 5911| 19|#endif 5912| 19| bIsoFrom = 0; 5913| 19| switch (bMobileH) 5914| 19| { 5915| 1| case TAUT_YES: ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5915:17): [True: 1, False: 18] ------------------ 5916| 1| ret = RI_ERR_SYNTAX; ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 5917| 1| break; 5918| 18| case TAUT_NON: ------------------ | | 574| 18|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5918:17): [True: 18, False: 1] ------------------ 5919| 18| if (*q == 'm') ------------------ | Branch (5919:25): [True: 6, False: 12] ------------------ 5920| 6| { 5921| | /* copy from mobile H to fixed H */ 5922| 6| pInChIFrom = pInpInChI[ALT_TAUT(bMobileH)]; ------------------ | | 577| 6|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 6|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 6] | | ------------------ ------------------ 5923| 6| } 5924| 12| else 5925| 12| { 5926| 12| if (*q == 'e') ------------------ | Branch (5926:29): [True: 12, False: 0] ------------------ 5927| 12| { 5928| | /* copy from mobile H to isotopic mobile H */ 5929| 12| pInChIFrom = pInChI; 5930| 12| bIsoFrom = -1; /* empty */ 5931| 12| } 5932| 0| else 5933| 0| { 5934| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5935| 0| } 5936| 12| } 5937| 18| break; 5938| 0| default: ------------------ | Branch (5938:17): [True: 0, False: 19] ------------------ 5939| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5940| 0| break; 5941| 19| } 5942| 19| if (ret < 0) ------------------ | Branch (5942:21): [True: 1, False: 18] ------------------ 5943| 1| { 5944| 1| goto exit_function; 5945| 1| } 5946| | /* copy */ 5947| 58| for (i = 0; i < val; i++) ------------------ | Branch (5947:29): [True: 48, False: 10] ------------------ 5948| 48| { 5949| 48|#if ( FIX_GAF_2019_2==1 ) 5950| 48| { 5951| 48| if ((iComponent + i > nNumComponents) || (iComponent + i < 0)) ------------------ | Branch (5951:29): [True: 0, False: 48] | Branch (5951:66): [True: 8, False: 40] ------------------ 5952| 8| { 5953| 8| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 5954| 8| goto exit_function; 5955| 8| } 5956| 48| } 5957| 40|#endif 5958| 40| ret = CopySegment(pInChI + iComponent + i, pInChIFrom + iComponent + i, nCpyType, 0, bIsoFrom); 5959| 40| if (!ret) ------------------ | Branch (5959:21): [True: 0, False: 40] ------------------ 5960| 0| { 5961| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5962| 0| } 5963| 40| if (ret < 0) ------------------ | Branch (5963:21): [True: 0, False: 40] ------------------ 5964| 0| { 5965| 0| goto exit_function; 5966| 0| } 5967| 40| } 5968| 10| iComponent += val; 5969| | /* continue to the next component(s) */ 5970| 10| if (*pEnd) ------------------ | Branch (5970:21): [True: 8, False: 2] ------------------ 5971| 8| { 5972| 8| pStart = pEnd + 1; 5973| 8| continue; 5974| 8| } 5975| 2| else 5976| 2| { 5977| 2| break; 5978| 2| } 5979| 10| } 5980| 35.1k| else 5981| 35.1k| { 5982| 35.1k| mpy_component = 1; 5983| 35.1k| p = pStart; 5984| 35.1k| } 5985| 35.1k| } 5986| | 5987| 35.2k|#if ( FIX_GAF_2019_2==1 ) 5988| 35.2k| if ((iComponent > nNumComponents - 1) || (iComponent < 0)) ------------------ | Branch (5988:13): [True: 5, False: 35.2k] | Branch (5988:50): [True: 10, False: 35.2k] ------------------ 5989| 15| { 5990| 15| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 15|#define RI_ERR_SYNTAX (-2) ------------------ 5991| 15| goto exit_function; 5992| 15| } 5993| 35.2k| if (pInChI[iComponent].nNumberOfAtoms <= 0 || pInChI[iComponent].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 15| 35.2k|#define MAX_ATOMS 32766 ------------------ | Branch (5993:13): [True: 0, False: 35.2k] | Branch (5993:55): [True: 0, False: 35.2k] ------------------ 5994| 0| { 5995| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5996| 0| goto exit_function; 5997| 0| } 5998| 35.2k|#endif 5999| 35.2k| pStart = p; 6000| 35.2k| pIsotopicAtom = &pInChI[iComponent].IsotopicAtom; 6001| 35.2k| if (*pIsotopicAtom) ------------------ | Branch (6001:13): [True: 2, False: 35.2k] ------------------ 6002| 2| { 6003| 2| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 17| 2|#define RI_ERR_PROGR (-3) ------------------ 6004| 2| goto exit_function; 6005| 2| } 6006| | 6007| 35.2k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (6007:13): [True: 1.25k, False: 33.9k] | Branch (6007:25): [True: 0, False: 1.25k] ------------------ 6008| 0| { 6009| | /* check if compressed InChI */ 6010| 0| *pbAbc = isupper(UCINT * p) ? 1 : 0; ------------------ | Branch (6010:22): [True: 0, False: 0] ------------------ 6011| 0| } 6012| 35.2k| base = (*pbAbc == 1) ? ALPHA_BASE : 10; ------------------ | | 170| 0|#define ALPHA_BASE 27 ------------------ | Branch (6012:16): [True: 0, False: 35.2k] ------------------ 6013| | 6014| 70.3k| one_more_time: 6015| 70.3k| if (*pbAbc == 1) ------------------ | Branch (6015:13): [True: 0, False: 70.3k] ------------------ 6016| 0| { 6017| | /* process the componnt: At[+/-Charge]TDH,... */ 6018| | /* pass 1: find number of stereoatoms */ 6019| 0| for (p = pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (6019:41): [True: 0, False: 0] ------------------ 6020| 0| { 6021| 0| nAtom1 = (AT_NUMB)inchi_strtol(p, &p, base); 6022| 0|#if ( CHECK_STRTOL_ATNUMB==1 ) 6023| 0| if (nAtom1 > MAX_ATOMS || nAtom1 < 0) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ | Branch (6023:21): [True: 0, False: 0] | Branch (6023:43): [True: 0, False: 0] ------------------ 6024| 0| { 6025| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6026| 0| goto exit_function; 6027| 0| } 6028| 0|#endif 6029| 0| if (!nAtom1 || ------------------ | Branch (6029:21): [True: 0, False: 0] ------------------ 6030| 0| nAtom1 > pInChI[iComponent].nNumberOfAtoms) ------------------ | Branch (6030:21): [True: 0, False: 0] ------------------ 6031| 0| { 6032| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6033| 0| goto exit_function; 6034| 0| } 6035| 0| memset(&isoAtom, 0, sizeof(isoAtom)); /* djb-rwth: memset_s C11/Annex K variant? */ 6036| 0| isoAtom.nAtomNumber = nAtom1; 6037| 0| isoAtom.nIsoDifference = (NUM_H)inchi_strtol(p, &q, 10); /* alway in abc */ 6038| 0| if (p == q) ------------------ | Branch (6038:21): [True: 0, False: 0] ------------------ 6039| 0| { 6040| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6041| 0| goto exit_function; 6042| 0| } 6043| 0| p = q; 6044| 0| if (*p == 't') ------------------ | Branch (6044:21): [True: 0, False: 0] ------------------ 6045| 0| { 6046| 0| isoAtom.nNum_T = 1; 6047| 0| p++; 6048| 0| if (isdigit(UCINT * p)) ------------------ | Branch (6048:25): [True: 0, False: 0] ------------------ 6049| 0| { 6050| 0| isoAtom.nNum_T = (NUM_H)inchi_strtol(p, &q, 10); 6051| 0| p = q; 6052| 0| } 6053| 0| } 6054| 0| if (*p == 'd') ------------------ | Branch (6054:21): [True: 0, False: 0] ------------------ 6055| 0| { 6056| 0| isoAtom.nNum_D = 1; 6057| 0| p++; 6058| 0| if (isdigit(UCINT * p)) ------------------ | Branch (6058:25): [True: 0, False: 0] ------------------ 6059| 0| { 6060| 0| isoAtom.nNum_D = (NUM_H)inchi_strtol(p, &q, 10); 6061| 0| p = q; 6062| 0| } 6063| 0| } 6064| 0| if (*p == 'h') ------------------ | Branch (6064:21): [True: 0, False: 0] ------------------ 6065| 0| { 6066| 0| isoAtom.nNum_H = 1; 6067| 0| p++; 6068| 0| if (isdigit(UCINT * p)) ------------------ | Branch (6068:25): [True: 0, False: 0] ------------------ 6069| 0| { 6070| 0| isoAtom.nNum_H = (NUM_H)inchi_strtol(p, &q, 10); 6071| 0| p = q; 6072| 0| } 6073| 0| } 6074| 0| if (p > pEnd || (!isoAtom.nIsoDifference && !isoAtom.nNum_T && !isoAtom.nNum_D && !isoAtom.nNum_H)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6074:21): [True: 0, False: 0] | Branch (6074:34): [True: 0, False: 0] | Branch (6074:61): [True: 0, False: 0] | Branch (6074:80): [True: 0, False: 0] | Branch (6074:99): [True: 0, False: 0] ------------------ 6075| 0| { 6076| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6077| 0| goto exit_function; 6078| 0| } 6079| 0| if (*pIsotopicAtom) ------------------ | Branch (6079:21): [True: 0, False: 0] ------------------ 6080| 0| { 6081| 0| pIsotopicAtom[0][iAtom] = isoAtom; 6082| 0| } 6083| 0| } 6084| 0| } 6085| 70.3k| else 6086| 70.3k| { 6087| | /* process the componnt: At[+/-Charge]TDH,... */ 6088| | /* pass 1: find number of stereoatoms */ 6089| 80.3k| for (p = pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (6089:41): [True: 10.0k, False: 70.3k] ------------------ 6090| 10.0k| { 6091| 10.0k| nAtom1 = (AT_NUMB)inchi_strtol(p, &q, 10); 6092| 10.0k|#if ( CHECK_STRTOL_ATNUMB==1 ) 6093| 10.0k| if (nAtom1 > MAX_ATOMS || nAtom1 < 0) ------------------ | | 15| 20.0k|#define MAX_ATOMS 32766 ------------------ | Branch (6093:21): [True: 9, False: 10.0k] | Branch (6093:43): [True: 0, False: 10.0k] ------------------ 6094| 9| { 6095| 9| ret = RI_ERR_SYNTAX; ------------------ | | 16| 9|#define RI_ERR_SYNTAX (-2) ------------------ 6096| 9| goto exit_function; 6097| 9| } 6098| 10.0k|#endif 6099| 10.0k| p = q; 6100| 10.0k| if (!nAtom1 || ------------------ | Branch (6100:21): [True: 20, False: 9.98k] ------------------ 6101| 9.98k| nAtom1 > pInChI[iComponent].nNumberOfAtoms || ------------------ | Branch (6101:21): [True: 18, False: 9.96k] ------------------ 6102| 9.96k| !(r = strchr((char*)parity_type, *p))) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (6102:21): [True: 1, False: 9.96k] ------------------ 6103| 39| { 6104| 39| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 39|#define RI_ERR_SYNTAX (-2) ------------------ 6105| 39| goto exit_function; 6106| 39| } 6107| 9.96k| memset(&isoAtom, 0, sizeof(isoAtom)); /* djb-rwth: memset_s C11/Annex K variant? */ 6108| 9.96k| isoAtom.nAtomNumber = nAtom1; 6109| 9.96k| if (p[0] == '+' && isdigit(UCINT p[1])) ------------------ | Branch (6109:21): [True: 1.00k, False: 8.96k] | Branch (6109:36): [True: 999, False: 1] ------------------ 6110| 999| { 6111| 999| isoAtom.nIsoDifference = (NUM_H)inchi_strtol(p + 1, &q, 10); 6112| 999| if (isoAtom.nIsoDifference >= 0) isoAtom.nIsoDifference++; ------------------ | Branch (6112:25): [True: 711, False: 288] ------------------ 6113| 999| p = q; 6114| 999| } 6115| 8.96k| else 6116| 8.96k| if (p[0] == '-' && isdigit(UCINT p[1])) ------------------ | Branch (6116:25): [True: 1.68k, False: 7.28k] | Branch (6116:40): [True: 1.67k, False: 4] ------------------ 6117| 1.67k| { 6118| 1.67k| isoAtom.nIsoDifference = -(NUM_H)inchi_strtol(p + 1, &q, 10); 6119| 1.67k| if (isoAtom.nIsoDifference == 0) isoAtom.nIsoDifference++; ------------------ | Branch (6119:29): [True: 362, False: 1.31k] ------------------ 6120| 1.67k| p = q; 6121| 1.67k| } 6122| 9.96k| if (*p == 'T') ------------------ | Branch (6122:21): [True: 1.96k, False: 7.99k] ------------------ 6123| 1.96k| { 6124| 1.96k| isoAtom.nNum_T = 1; 6125| 1.96k| p++; 6126| 1.96k| if (isdigit(UCINT * p)) ------------------ | Branch (6126:25): [True: 1.39k, False: 566] ------------------ 6127| 1.39k| { 6128| 1.39k| isoAtom.nNum_T = (NUM_H)inchi_strtol(p, &q, 10); 6129| 1.39k| p = q; 6130| 1.39k| } 6131| 1.96k| } 6132| 9.96k| if (*p == 'D') ------------------ | Branch (6132:21): [True: 526, False: 9.43k] ------------------ 6133| 526| { 6134| 526| isoAtom.nNum_D = 1; 6135| 526| p++; 6136| 526| if (isdigit(UCINT * p)) ------------------ | Branch (6136:25): [True: 208, False: 318] ------------------ 6137| 208| { 6138| 208| isoAtom.nNum_D = (NUM_H)inchi_strtol(p, &q, 10); 6139| 208| p = q; 6140| 208| } 6141| 526| } 6142| 9.96k| if (*p == 'H') ------------------ | Branch (6142:21): [True: 6.34k, False: 3.61k] ------------------ 6143| 6.34k| { 6144| 6.34k| isoAtom.nNum_H = 1; 6145| 6.34k| p++; 6146| 6.34k| if (isdigit(UCINT * p)) ------------------ | Branch (6146:25): [True: 1.59k, False: 4.74k] ------------------ 6147| 1.59k| { 6148| 1.59k| isoAtom.nNum_H = (NUM_H)inchi_strtol(p, &q, 10); 6149| 1.59k| p = q; 6150| 1.59k| } 6151| 6.34k| } 6152| 9.96k| if (!isoAtom.nIsoDifference && !isoAtom.nNum_T && !isoAtom.nNum_D && !isoAtom.nNum_H) ------------------ | Branch (6152:21): [True: 7.28k, False: 2.67k] | Branch (6152:48): [True: 5.35k, False: 1.93k] | Branch (6152:67): [True: 4.89k, False: 463] | Branch (6152:86): [True: 8, False: 4.88k] ------------------ 6153| 8| { 6154| 8| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 6155| 8| goto exit_function; 6156| 8| } 6157| 9.95k| if (p < pEnd) ------------------ | Branch (6157:21): [True: 7.72k, False: 2.23k] ------------------ 6158| 7.72k| { 6159| 7.72k| if (*p == ',') ------------------ | Branch (6159:25): [True: 7.70k, False: 20] ------------------ 6160| 7.70k| { 6161| 7.70k| p++; 6162| 7.70k| } 6163| 20| else 6164| 20| { 6165| 20| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 20|#define RI_ERR_SYNTAX (-2) ------------------ 6166| 20| goto exit_function; 6167| 20| } 6168| 7.72k| } 6169| 9.93k| if (*pIsotopicAtom) ------------------ | Branch (6169:21): [True: 4.89k, False: 5.04k] ------------------ 6170| 4.89k| { 6171| 4.89k| pIsotopicAtom[0][iAtom] = isoAtom; 6172| 4.89k| } 6173| 9.93k| } 6174| 70.3k| } 6175| 70.3k| if (p != pEnd) ------------------ | Branch (6175:13): [True: 0, False: 70.3k] ------------------ 6176| 0| { 6177| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6178| 0| goto exit_function; 6179| 0| } 6180| | 6181| 70.3k| if (!*pIsotopicAtom) ------------------ | Branch (6181:13): [True: 35.1k, False: 35.1k] ------------------ 6182| 35.1k| { 6183| | /* end of the 1st pass */ 6184| 35.1k| len = iAtom; 6185| | /* memory allocation */ 6186| 35.1k| if (!(*pIsotopicAtom = (INChI_IsotopicAtom*)inchi_calloc((long long)len + 1, sizeof(**pIsotopicAtom)))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 35.1k|#define inchi_calloc calloc ------------------ | Branch (6186:17): [True: 0, False: 35.1k] ------------------ 6187| 0| { 6188| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 6189| 0| goto exit_function; 6190| 0| } 6191| 35.1k| goto one_more_time; /* goto the 2nd pass */ 6192| 35.1k| } 6193| 35.1k| else 6194| 35.1k| { 6195| | /* 2nd pass */ 6196| 35.1k| if (len != iAtom) ------------------ | Branch (6196:17): [True: 0, False: 35.1k] ------------------ 6197| 0| { 6198| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 6199| 0| goto exit_function; 6200| 0| } 6201| 35.1k| pInChI[iComponent].nNumberOfIsotopicAtoms = len; 6202| 35.1k| } 6203| | 6204| | /* multiplier */ 6205| 35.5k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (6205:21): [True: 412, False: 35.1k] ------------------ 6206| 412| { 6207| 412| ret = CopySegment(pInChI + iComponent + i, pInChI + iComponent, nCpyType, 0, 0); 6208| 412| if (!ret) ------------------ | Branch (6208:17): [True: 0, False: 412] ------------------ 6209| 0| { 6210| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6211| 0| } 6212| 412| if (ret < 0) ------------------ | Branch (6212:17): [True: 0, False: 412] ------------------ 6213| 0| { 6214| 0| goto exit_function; 6215| 0| } 6216| 412| } 6217| | 6218| 35.1k| iComponent += mpy_component; 6219| 35.1k| if (*pEnd) ------------------ | Branch (6219:13): [True: 33.9k, False: 1.21k] ------------------ 6220| 33.9k| { 6221| 33.9k| pStart = pEnd + 1; 6222| 33.9k| continue; 6223| 33.9k| } 6224| 1.21k| else 6225| 1.21k| { 6226| 1.21k| break; 6227| 1.21k| } 6228| | 6229| 35.1k| } 6230| | 6231| 1.22k| if (nNumComponents != iComponent) ------------------ | Branch (6231:9): [True: 16, False: 1.20k] ------------------ 6232| 16| { 6233| 16| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 16|#define RI_ERR_SYNTAX (-2) ------------------ 6234| 16| goto exit_function; 6235| 16| } 6236| | 6237| 1.20k| ret = iComponent + 1; 6238| | 6239| 1.33k|exit_function: 6240| | 6241| 1.33k| return ret; 6242| 1.20k|} ichiread.c:ParseSegmentIsoExchgH: 5560| 617|{ 5561| | /* Pass 1: count bonds and find actual numbers of atom */ 5562| 617| const char* p, * q, * pStart, * pEnd; 5563| 617| int ret = 0, num, i, i_prev; 5564| 617| static const char abc_h[] = "hdt"; 5565| | 5566| 617| if (str[0] != 'h') ------------------ | Branch (5566:9): [True: 436, False: 181] ------------------ 5567| 436| { 5568| 436| return 0; 5569| 436| } 5570| | 5571| 181| pStart = (char*)str + 1; 5572| | 5573| 181| if (!(bMobileH == TAUT_YES && state == IST_MOBILE_H_ISO_EXCH_H)) ------------------ | | 575| 362|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5573:11): [True: 181, False: 0] | Branch (5573:35): [True: 181, False: 0] ------------------ 5574| 0| { 5575| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5576| 0| } 5577| | 5578| 181| if (!(strchr(pStart, ';'))) /* djb-rwth: removing redundant code */ ------------------ | Branch (5578:9): [True: 179, False: 2] ------------------ 5579| 179| { 5580| 179| pEnd = pStart + strlen(pStart); 5581| 179| } 5582| 2| else 5583| 2| { 5584| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 5585| 2| goto exit_function; 5586| 2| } 5587| 179| p = pStart; 5588| | 5589| 179| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (5589:9): [True: 170, False: 9] | Branch (5589:21): [True: 0, False: 170] ------------------ 5590| 0| { 5591| | /* check if compressed InChI */ 5592| | /* compressed: /hNtNdNh where N is a decimal number */ 5593| | /* uncompressed: /hT[n]D[n]H[n] where n > 1 is a decimal number */ 5594| 0| *pbAbc = isdigit(UCINT * p) ? 1 : 0; ------------------ | Branch (5594:18): [True: 0, False: 0] ------------------ 5595| 0| } 5596| | 5597| 179| if (*pbAbc == 1) ------------------ | Branch (5597:9): [True: 0, False: 179] ------------------ 5598| 0| { 5599| 0| i_prev = (int)sizeof(abc_h); 5600| 0| while (p < pEnd) ------------------ | Branch (5600:16): [True: 0, False: 0] ------------------ 5601| 0| { 5602| 0| num = (int)inchi_strtol(p, &q, 10); 5603| 0|#if ( CHECK_STRTOL_ATNUMB==1 ) 5604| 0| if (num > MAX_ATOMS || num < 0) ------------------ | | 15| 0|#define MAX_ATOMS 32766 ------------------ | Branch (5604:17): [True: 0, False: 0] | Branch (5604:36): [True: 0, False: 0] ------------------ 5605| 0| { 5606| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5607| 0| goto exit_function; 5608| 0| } 5609| 0|#endif 5610| 0| if (0 >= num || p == q || q >= pEnd) ------------------ | Branch (5610:17): [True: 0, False: 0] | Branch (5610:29): [True: 0, False: 0] | Branch (5610:39): [True: 0, False: 0] ------------------ 5611| 0| { 5612| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5613| 0| goto exit_function; 5614| 0| } 5615| 0| p = strchr((char*)abc_h, *q); 5616| 0| if (p && (i = (int)(p - abc_h)) < i_prev && (i < NUM_H_ISOTOPES)) /* djb-rwth: additional condition for buffer overrun prevention */ ------------------ | | 72| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (5616:17): [True: 0, False: 0] | Branch (5616:22): [True: 0, False: 0] | Branch (5616:57): [True: 0, False: 0] ------------------ 5617| 0| { 5618| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[i] = (NUM_H)num; 5619| 0| p = q + 1; 5620| 0| i_prev = i; 5621| 0| } 5622| 0| else 5623| 0| { 5624| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5625| 0| goto exit_function; 5626| 0| } 5627| 0| } 5628| 0| } 5629| 179| else 5630| 179| { 5631| 179| if (*p == 'T') ------------------ | Branch (5631:13): [True: 77, False: 102] ------------------ 5632| 77| { 5633| 77| nNumProtons[bMobileH].nNumRemovedIsotopicH[2] = 1; 5634| 77| p++; 5635| 77| if (isdigit(UCINT p[0])) ------------------ | Branch (5635:17): [True: 38, False: 39] ------------------ 5636| 38| { 5637| 38| nNumProtons[bMobileH].nNumRemovedIsotopicH[2] = (NUM_H)inchi_strtol(p, &q, 10); 5638| 38| p = q; 5639| 38| } 5640| 77| } 5641| 179| if (*p == 'D') ------------------ | Branch (5641:13): [True: 51, False: 128] ------------------ 5642| 51| { 5643| 51| nNumProtons[bMobileH].nNumRemovedIsotopicH[1] = 1; 5644| 51| p++; 5645| 51| if (isdigit(UCINT p[0])) ------------------ | Branch (5645:17): [True: 13, False: 38] ------------------ 5646| 13| { 5647| 13| nNumProtons[bMobileH].nNumRemovedIsotopicH[1] = (NUM_H)inchi_strtol(p, &q, 10); 5648| 13| p = q; 5649| 13| } 5650| 51| } 5651| 179| if (*p == 'H') ------------------ | Branch (5651:13): [True: 92, False: 87] ------------------ 5652| 92| { 5653| 92| nNumProtons[bMobileH].nNumRemovedIsotopicH[0] = 1; 5654| 92| p++; 5655| 92| if (isdigit(UCINT p[0])) ------------------ | Branch (5655:17): [True: 58, False: 34] ------------------ 5656| 58| { 5657| 58| nNumProtons[bMobileH].nNumRemovedIsotopicH[0] = (NUM_H)inchi_strtol(p, &q, 10); 5658| 58| p = q; 5659| 58| } 5660| 92| } 5661| 179| } 5662| 179| if (p != pEnd) ------------------ | Branch (5662:9): [True: 5, False: 174] ------------------ 5663| 5| { 5664| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 5|#define RI_ERR_SYNTAX (-2) ------------------ 5665| 5| goto exit_function; 5666| 5| } 5667| 174| ret = 1; 5668| | 5669| 181|exit_function: 5670| | 5671| 181| return ret; 5672| 174|} ichiread.c:ParseSegmentPerm: 5682| 817|{ 5683| 817| int nNumComponents, iComponent1, iComponent2, numTrans; 5684| 817| const char* p, * q, * pStart, * pEnd, * pPermStart, * pPermEnd; 5685| 817| int ret = 0; 5686| 817| INChI* pInChI = pInpInChI[bMobileH]; /* bMobileH should be TAUT_NON = 0 */ 5687| 817| INChI tmp; 5688| 817| int base = 10; 5689| | 5690| 817| if (str[0] != 'o') ------------------ | Branch (5690:9): [True: 714, False: 103] ------------------ 5691| 714| { 5692| 714| return 0; 5693| 714| } 5694| | 5695| | /* djb-rwth: fixing oss-fuzz issue #66746 */ 5696| 103| if (!pInChI) ------------------ | Branch (5696:9): [True: 0, False: 103] ------------------ 5697| 0| { 5698| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 5699| 0| } 5700| | 5701| 103| pStart = (char*)str + 1; 5702| 103| nNumComponents = ppnNumComponents[bMobileH]; 5703| | 5704| 103| if (!(bMobileH == TAUT_NON && (state == IST_FIXED_H_PERMUTATION || state == IST_FIXED_H_ISO_PERMUTATION))) ------------------ | | 574| 206|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5704:11): [True: 103, False: 0] | Branch (5704:36): [True: 92, False: 11] | Branch (5704:72): [True: 11, False: 0] ------------------ 5705| 0| { 5706| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5707| 0| } 5708| | 5709| 103| if (!(strchr(pStart, ';'))) /* djb-rwth: removing redundant code */ ------------------ | Branch (5709:9): [True: 99, False: 4] ------------------ 5710| 99| { 5711| 99| pEnd = pStart + strlen(pStart); 5712| 99| } 5713| 4| else 5714| 4| { 5715| 4| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 5716| 4| } 5717| 115| while (pStart < pEnd) ------------------ | Branch (5717:12): [True: 41, False: 74] ------------------ 5718| 41| { 5719| | /* cycle over components; rearrange Fixed H components in order of Mobile H components */ 5720| | /* if /o(1,2,3) then reaarange Fixed H components in this way: tmp<-1, 1<-2, 2<-3, 3<-tmp */ 5721| 41| if (*pStart != '(') ------------------ | Branch (5721:13): [True: 0, False: 41] ------------------ 5722| 0| { 5723| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5724| 0| goto exit_function; 5725| 0| } 5726| 41| pPermStart = pStart + 1; 5727| 41| memset(&tmp, 0, sizeof(tmp)); /* initialization 2006-03 */ /* djb-rwth: memset_s C11/Annex K variant? */ 5728| 41| if (!(pPermEnd = strchr(pPermStart, ')')) || pPermEnd == pPermStart) ------------------ | Branch (5728:13): [True: 2, False: 39] | Branch (5728:54): [True: 1, False: 38] ------------------ 5729| 3| { 5730| 3| ret = RI_ERR_SYNTAX; ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 5731| 3| goto exit_function; 5732| 3| } 5733| | 5734| 38| if (pPermStart < pPermEnd && *pbAbc == -1) ------------------ | Branch (5734:13): [True: 38, False: 0] | Branch (5734:38): [True: 0, False: 38] ------------------ 5735| 0| { 5736| | /* check if compressed InChI */ 5737| 0| *pbAbc = isupper(UCINT * pPermStart) ? 1 : 0; ------------------ | Branch (5737:22): [True: 0, False: 0] ------------------ 5738| 0| } 5739| 38| base = (*pbAbc == 1) ? ALPHA_BASE : 10; ------------------ | | 170| 0|#define ALPHA_BASE 27 ------------------ | Branch (5739:16): [True: 0, False: 38] ------------------ 5740| | 5741| | /* permutation cycle */ 5742| 38| if (*pbAbc == 1) ------------------ | Branch (5742:13): [True: 0, False: 38] ------------------ 5743| 0| { 5744| 0| for (p = pPermStart, iComponent2 = numTrans = 0; p < pPermEnd; iComponent2 = iComponent1, p = q) ------------------ | Branch (5744:62): [True: 0, False: 0] ------------------ 5745| 0| { 5746| | /* get first atom number */ 5747| 0| if (0 >= (iComponent1 = (int)inchi_strtol(p, &q, base)) || iComponent1 > nNumComponents) ------------------ | Branch (5747:21): [True: 0, False: 0] | Branch (5747:76): [True: 0, False: 0] ------------------ 5748| 0| { 5749| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5750| 0| goto exit_function; 5751| 0| } 5752| 0|#if ( FIX_GAF_2019_2==1 ) 5753| 0| if ((iComponent1 - 1 > nNumComponents - 1) || (iComponent1 - 1 < 0)) ------------------ | Branch (5753:21): [True: 0, False: 0] | Branch (5753:63): [True: 0, False: 0] ------------------ 5754| 0| { 5755| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5756| 0| goto exit_function; 5757| 0| } 5758| 0|#endif 5759| 0| if (iComponent2) ------------------ | Branch (5759:21): [True: 0, False: 0] ------------------ 5760| 0| { 5761| 0| pInChI[iComponent2 - 1] = pInChI[iComponent1 - 1]; 5762| 0| numTrans++; 5763| 0| } 5764| 0| else 5765| 0| { 5766| 0| tmp = pInChI[iComponent1 - 1]; /* on the 1st pass save Component1 */ 5767| 0| } 5768| 0| } 5769| 0| } 5770| 38| else 5771| 38| { 5772| 101| for (p = pPermStart, iComponent2 = numTrans = 0; p < pPermEnd; iComponent2 = iComponent1, p = q + (*q == ',')) ------------------ | Branch (5772:62): [True: 85, False: 16] ------------------ 5773| 85| { 5774| | /* get first atom number */ 5775| 85| if (!isdigit(UCINT * p)) ------------------ | Branch (5775:21): [True: 2, False: 83] ------------------ 5776| 2| { 5777| 2| ret = RI_ERR_SYNTAX; ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 5778| 2| goto exit_function; 5779| 2| } 5780| 83| iComponent1 = (int)inchi_strtol(p, &q, 10); 5781| 83| if ((iComponent1 < 1) || (iComponent1 > nNumComponents)) /* djb-rwth: fixing oss-fuzz issue #66746 */ ------------------ | Branch (5781:21): [True: 10, False: 73] | Branch (5781:42): [True: 10, False: 63] ------------------ 5782| 20| { 5783| 20| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 16| 20|#define RI_ERR_SYNTAX (-2) ------------------ 5784| 20| goto exit_function; 5785| 20| } 5786| 63| if (iComponent2) ------------------ | Branch (5786:21): [True: 32, False: 31] ------------------ 5787| 32| { 5788| 32| pInChI[iComponent2 - 1] = pInChI[iComponent1 - 1]; 5789| 32| numTrans++; 5790| 32| } 5791| 31| else 5792| 31| { 5793| 31| tmp = pInChI[iComponent1 - 1]; /* on the 1st pass save Component1 */ 5794| 31| } 5795| 63| } 5796| 38| } 5797| 16| pInChI[iComponent2 - 1] = tmp; 5798| 16| if (!numTrans || p != pPermEnd) ------------------ | Branch (5798:13): [True: 0, False: 16] | Branch (5798:26): [True: 0, False: 16] ------------------ 5799| 0| { 5800| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5801| 0| goto exit_function; 5802| 0| } 5803| 16| else 5804| 16| { 5805| 16| pStart = p + 1; 5806| 16| } 5807| 16| } 5808| 74| ret = 1; 5809| | 5810| 99|exit_function: 5811| | 5812| 99| return ret; 5813| 74|} ichiread.c:nFillOutProtonMobileH: 9733| 4.57k|{ 9734| 4.57k| int len = 1; 9735| 4.57k| pInChI->bDeleted = 1; 9736| | /* formula */ 9737| 4.57k| if (!pInChI->szHillFormula && ------------------ | Branch (9737:9): [True: 4.57k, False: 0] ------------------ 9738| 4.57k| !(pInChI->szHillFormula = (char*)inchi_calloc((long long)len + 1, sizeof(pInChI->szHillFormula[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 4.57k|#define inchi_calloc calloc ------------------ | Branch (9738:9): [True: 0, False: 4.57k] ------------------ 9739| 0| { 9740| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9741| 0| } 9742| 4.57k| strcpy(pInChI->szHillFormula, "H"); 9743| 4.57k| pInChI->nNumberOfAtoms = 1; 9744| | 9745| | /* atoms */ 9746| 4.57k| if (!pInChI->nAtom && ------------------ | Branch (9746:9): [True: 4.57k, False: 0] ------------------ 9747| 4.57k| !(pInChI->nAtom = (U_CHAR*)inchi_calloc((long long)len + 1, sizeof(pInChI->nAtom[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 4.57k|#define inchi_calloc calloc ------------------ | Branch (9747:9): [True: 0, False: 4.57k] ------------------ 9748| 0| { 9749| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9750| 0| } 9751| 4.57k| pInChI->nAtom[0] = 1; 9752| | /* charge */ 9753| 4.57k| pInChI->nTotalCharge = 1; 9754| | /* connection table */ 9755| 4.57k| if (!pInChI->nConnTable && ------------------ | Branch (9755:9): [True: 4.57k, False: 0] ------------------ 9756| 4.57k| !(pInChI->nConnTable = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pInChI->nConnTable[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 4.57k|#define inchi_calloc calloc ------------------ | Branch (9756:9): [True: 0, False: 4.57k] ------------------ 9757| 0| { 9758| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9759| 0| } 9760| 4.57k| pInChI->nConnTable[0] = 1; 9761| 4.57k| pInChI->lenConnTable = len; 9762| | /* tautomer */ 9763| 4.57k| if (!pInChI->nTautomer && ------------------ | Branch (9763:9): [True: 4.57k, False: 0] ------------------ 9764| 4.57k| !(pInChI->nTautomer = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pInChI->nTautomer[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 4.57k|#define inchi_calloc calloc ------------------ | Branch (9764:9): [True: 0, False: 4.57k] ------------------ 9765| 0| { 9766| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9767| 0| } 9768| | /* nNum_H */ 9769| 4.57k| if (!pInChI->nNum_H && ------------------ | Branch (9769:9): [True: 4.57k, False: 0] ------------------ 9770| 4.57k| !(pInChI->nNum_H = (S_CHAR*)inchi_calloc((long long)len + 1, sizeof(pInChI->nNum_H[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 4.57k|#define inchi_calloc calloc ------------------ | Branch (9770:9): [True: 0, False: 4.57k] ------------------ 9771| 0| { 9772| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9773| 0| } 9774| 4.57k| pInChI->nNum_H[0] = 0; 9775| | 9776| 4.57k| pInChI->nTautomer[0] = 0; 9777| 4.57k| pInChI->lenTautomer = 1; 9778| | 9779| 4.57k| return 0; 9780| 4.57k|} ichiread.c:nProtonCopyIsotopicInfo: 9785| 592|{ 9786| 592| if (pInChI_from->nNumberOfIsotopicAtoms) ------------------ | Branch (9786:9): [True: 0, False: 592] ------------------ 9787| 0| { 9788| 0| if (pInChI_to->nNumberOfIsotopicAtoms && ------------------ | Branch (9788:13): [True: 0, False: 0] ------------------ 9789| 0| pInChI_from->nNumberOfIsotopicAtoms > pInChI_to->nNumberOfIsotopicAtoms) ------------------ | Branch (9789:13): [True: 0, False: 0] ------------------ 9790| 0| { 9791| | 9792| 0| inchi_free(pInChI_to->IsotopicAtom); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 9793| 0| pInChI_to->IsotopicAtom = NULL; 9794| 0| pInChI_to->nNumberOfIsotopicAtoms = 0; 9795| 0| } 9796| 0| if (!pInChI_to->IsotopicAtom && ------------------ | Branch (9796:13): [True: 0, False: 0] ------------------ 9797| 0| !(pInChI_to->IsotopicAtom = ------------------ | Branch (9797:13): [True: 0, False: 0] ------------------ 9798| 0| (INChI_IsotopicAtom*)inchi_calloc(pInChI_from->nNumberOfIsotopicAtoms, ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 9799| 0| sizeof(pInChI_to->IsotopicAtom[0])))) 9800| 0| { 9801| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 9802| 0| } 9803| 0| pInChI_to->nNumberOfIsotopicAtoms = pInChI_from->nNumberOfIsotopicAtoms; 9804| 0| memcpy(pInChI_to->IsotopicAtom, pInChI_from->IsotopicAtom, 9805| 0| pInChI_from->nNumberOfIsotopicAtoms * sizeof(pInChI_to->IsotopicAtom[0])); 9806| 0| } 9807| 592| else 9808| 592| { 9809| 592| if (pInChI_to->IsotopicAtom) ------------------ | Branch (9809:13): [True: 0, False: 592] ------------------ 9810| 0| { 9811| 0| inchi_free(pInChI_to->IsotopicAtom); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 9812| 0| } 9813| 592| pInChI_to->IsotopicAtom = NULL; 9814| 592| pInChI_to->nNumberOfIsotopicAtoms = 0; 9815| 592| } 9816| | 9817| 592| return 0; 9818| 592|} ichiread.c:CopySegment: 10282| 8.17k|{ 10283| 8.17k| int ret = RI_ERR_ALLOC; ------------------ | | 15| 8.17k|#define RI_ERR_ALLOC (-1) ------------------ 10284| 8.17k| int len; 10285| | 10286| 8.17k| if (SegmentType == CPY_SP2 || ------------------ | Branch (10286:9): [True: 6.92k, False: 1.24k] ------------------ 10287| 1.24k| SegmentType == CPY_SP3 || ------------------ | Branch (10287:9): [True: 357, False: 888] ------------------ 10288| 888| SegmentType == CPY_SP3_M || ------------------ | Branch (10288:9): [True: 318, False: 570] ------------------ 10289| 570| SegmentType == CPY_SP3_S) ------------------ | Branch (10289:9): [True: 0, False: 570] ------------------ 10290| 7.60k| { 10291| 7.60k| INChI_Stereo** pstereoTo = NULL; 10292| 7.60k| INChI_Stereo* stereoFrom = bIsotopicFrom == 1 ? pInChIFrom->StereoIsotopic : ------------------ | Branch (10292:36): [True: 64, False: 7.53k] ------------------ 10293| 7.60k| bIsotopicFrom == 0 ? pInChIFrom->Stereo : NULL; ------------------ | Branch (10293:13): [True: 745, False: 6.79k] ------------------ 10294| 7.60k| if (stereoFrom || bIsotopicFrom < 0) ------------------ | Branch (10294:13): [True: 806, False: 6.79k] | Branch (10294:27): [True: 6.79k, False: 3] ------------------ 10295| 7.59k| { 10296| 7.59k| if (SegmentType == CPY_SP2) ------------------ | Branch (10296:17): [True: 6.92k, False: 672] ------------------ 10297| 6.92k| { 10298| 6.92k|#if ( FIX_GAF_2019_1==1 ) 10299| 6.92k| if (bIsotopicFrom >= 0 && ------------------ | Branch (10299:21): [True: 161, False: 6.76k] ------------------ 10300| 161| (pInChIFrom->nNumberOfAtoms > MAX_ATOMS || pInChIFrom->nNumberOfAtoms < 0)) ------------------ | | 15| 322|#define MAX_ATOMS 32766 ------------------ | Branch (10300:22): [True: 0, False: 161] | Branch (10300:64): [True: 0, False: 161] ------------------ 10301| 0| { 10302| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10303| 0| goto exit_function; 10304| 0| } 10305| 6.92k|#endif 10306| 6.92k| if (bIsotopicFrom < 0 || ------------------ | Branch (10306:21): [True: 6.76k, False: 161] ------------------ 10307| 161| (stereoFrom->b_parity && ------------------ | Branch (10307:22): [True: 161, False: 0] ------------------ 10308| 161| stereoFrom->nBondAtom1 && ------------------ | Branch (10308:25): [True: 161, False: 0] ------------------ 10309| 161| stereoFrom->nBondAtom2)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (10309:25): [True: 161, False: 0] ------------------ 10310| 6.92k| { 10311| 6.92k| S_CHAR* pst0_bp = NULL; /* copied from below to obey C syntax - 2024-09-01 DT */ 10312| 6.92k| AT_NUMB* pst0_nba1 = NULL; /* copied from below to obey C syntax - 2024-09-01 DT */ 10313| 6.92k| AT_NUMB* pst0_nba2 = NULL; /* copied from below to obey C syntax - 2024-09-01 DT */ 10314| | 10315| 6.92k| len = (bIsotopicFrom < 0) ? 0 : stereoFrom->nNumberOfStereoBonds; ------------------ | Branch (10315:27): [True: 6.76k, False: 161] ------------------ 10316| 6.92k| pstereoTo = bIsotopicTo ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (10316:33): [True: 307, False: 6.62k] ------------------ 10317| 6.92k| if (!pstereoTo[0]) ------------------ | Branch (10317:25): [True: 6.90k, False: 23] ------------------ 10318| 6.90k| { 10319| | /* djb-rwth: fixing oss-fuzz issue #66985 */ 10320| 6.90k| INChI_Stereo* pst0 = (INChI_Stereo*)inchi_calloc(1, sizeof(**pstereoTo)); ------------------ | | 1146| 6.90k|#define inchi_calloc calloc ------------------ 10321| 6.90k| pstereoTo[0] = pst0; 10322| 6.90k| if (!pst0) ------------------ | Branch (10322:29): [True: 0, False: 6.90k] ------------------ 10323| 0| { 10324| 0| goto exit_function; 10325| 0| } 10326| 6.90k| } 10327| 6.92k| if (pstereoTo[0]->nNumberOfStereoBonds > 0 || pstereoTo[0]->b_parity || ------------------ | Branch (10327:25): [True: 0, False: 6.92k] | Branch (10327:67): [True: 1, False: 6.92k] ------------------ 10328| 6.92k| pstereoTo[0]->nBondAtom1 || pstereoTo[0]->nBondAtom2) ------------------ | Branch (10328:25): [True: 0, False: 6.92k] | Branch (10328:53): [True: 0, False: 6.92k] ------------------ 10329| 1| { 10330| 1| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 10331| 1| goto exit_function; 10332| 1| } 10333| | /* allocate sp2 stereo */ 10334| | /* djb-rwth: fixing oss-fuzz issue #66985 */ 10335| | /* djb-rwth: cast operators added */ 10336| 6.92k| pst0_bp = (S_CHAR*)inchi_calloc((long long)len + 1, sizeof(pstereoTo[0]->b_parity[0])); ------------------ | | 1146| 6.92k|#define inchi_calloc calloc ------------------ 10337| 6.92k| pst0_nba1 = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pstereoTo[0]->nBondAtom1[0])); ------------------ | | 1146| 6.92k|#define inchi_calloc calloc ------------------ 10338| 6.92k| pst0_nba2 = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pstereoTo[0]->nBondAtom2[0])); ------------------ | | 1146| 6.92k|#define inchi_calloc calloc ------------------ 10339| 6.92k| pstereoTo[0]->b_parity = pst0_bp; 10340| 6.92k| pstereoTo[0]->nBondAtom1 = pst0_nba1; 10341| 6.92k| pstereoTo[0]->nBondAtom2 = pst0_nba2; 10342| 6.92k| if (!pst0_bp || !pst0_nba1 || !pst0_nba2) ------------------ | Branch (10342:25): [True: 0, False: 6.92k] | Branch (10342:37): [True: 0, False: 6.92k] | Branch (10342:51): [True: 0, False: 6.92k] ------------------ 10343| 0| { 10344| | /* cleanup */ 10345| 0| if (pst0_bp) ------------------ | Branch (10345:29): [True: 0, False: 0] ------------------ 10346| 0| { 10347| 0| INCHI_HEAPCHK 10348| 0| inchi_free(pst0_bp); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10349| 0| pst0_bp = NULL; 10350| 0| } 10351| 0| if (pst0_nba1) ------------------ | Branch (10351:29): [True: 0, False: 0] ------------------ 10352| 0| { 10353| 0| INCHI_HEAPCHK 10354| 0| inchi_free(pst0_nba1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10355| 0| pst0_nba1 = NULL; 10356| 0| } 10357| 0| if (pstereoTo[0]->nBondAtom2) ------------------ | Branch (10357:29): [True: 0, False: 0] ------------------ 10358| 0| { 10359| 0| INCHI_HEAPCHK 10360| 0| inchi_free(pst0_nba2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10361| 0| pst0_nba2 = NULL; 10362| 0| } 10363| 0| INCHI_HEAPCHK 10364| 0| goto exit_function; 10365| 0| } 10366| | /* copy stereo */ 10367| 6.92k| if (bIsotopicFrom >= 0 && len) ------------------ | Branch (10367:25): [True: 161, False: 6.76k] | Branch (10367:47): [True: 157, False: 4] ------------------ 10368| 157| { 10369| 157|#if ( FIX_GAF_2019_1==1 ) 10370| 157| if (pInChIFrom->nNumberOfAtoms > MAX_ATOMS || pInChIFrom->nNumberOfAtoms < 0) ------------------ | | 15| 314|#define MAX_ATOMS 32766 ------------------ | Branch (10370:29): [True: 0, False: 157] | Branch (10370:71): [True: 0, False: 157] ------------------ 10371| 0| { 10372| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10373| 0| goto exit_function; 10374| 0| } 10375| 157|#endif 10376| 157| memcpy(pst0_bp, stereoFrom->b_parity, ((long long)len + 1) * sizeof(pst0_bp[0])); /* djb-rwth: cast operator added */ 10377| 157| memcpy(pst0_nba1, stereoFrom->nBondAtom1, ((long long)len + 1) * sizeof(pst0_nba1[0])); /* djb-rwth: cast operator added */ 10378| 157| memcpy(pst0_nba2, stereoFrom->nBondAtom2, ((long long)len + 1) * sizeof(pst0_nba2[0])); /* djb-rwth: cast operator added */ 10379| 157| } 10380| 6.92k| pstereoTo[0]->nNumberOfStereoBonds = len; 10381| | 10382| 6.92k| return len + 1; 10383| 6.92k| } 10384| 0| else 10385| 0| { 10386| 0| return 0; 10387| 0| } 10388| 6.92k| } 10389| 672| else 10390| 672| { 10391| 672| if (SegmentType == CPY_SP3) ------------------ | Branch (10391:21): [True: 354, False: 318] ------------------ 10392| 354| { 10393| 354| if (bIsotopicFrom < 0 || ------------------ | Branch (10393:25): [True: 23, False: 331] ------------------ 10394| 331| (stereoFrom->t_parity && ------------------ | Branch (10394:26): [True: 331, False: 0] ------------------ 10395| 331| stereoFrom->nNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (10395:29): [True: 331, False: 0] ------------------ 10396| 354| { 10397| | 10398| 354| len = (bIsotopicFrom < 0) ? 0 : stereoFrom->nNumberOfStereoCenters; ------------------ | Branch (10398:31): [True: 23, False: 331] ------------------ 10399| | 10400| 354| pstereoTo = bIsotopicTo ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (10400:37): [True: 199, False: 155] ------------------ 10401| 354| if (!pstereoTo[0]) ------------------ | Branch (10401:29): [True: 268, False: 86] ------------------ 10402| 268| { 10403| 268| if (!(pstereoTo[0] = (INChI_Stereo*)inchi_calloc(1, sizeof(**pstereoTo)))) ------------------ | | 1146| 268|#define inchi_calloc calloc ------------------ | Branch (10403:33): [True: 0, False: 268] ------------------ 10404| 0| { 10405| 0| goto exit_function; 10406| 0| } 10407| 268| } 10408| 354| if (pstereoTo[0]->nNumberOfStereoCenters > 0 || pstereoTo[0]->t_parity || ------------------ | Branch (10408:29): [True: 0, False: 354] | Branch (10408:73): [True: 0, False: 354] ------------------ 10409| 354| pstereoTo[0]->nNumber) ------------------ | Branch (10409:29): [True: 0, False: 354] ------------------ 10410| 0| { 10411| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10412| 0| goto exit_function; 10413| 0| } 10414| | /* allocate sp3 stereo */ 10415| 354| if (!(pstereoTo[0]->t_parity = (S_CHAR*)inchi_calloc((long long)len + 1, sizeof(pstereoTo[0]->b_parity[0]))) || ------------------ | | 1146| 354|#define inchi_calloc calloc ------------------ | Branch (10415:29): [True: 0, False: 354] ------------------ 10416| 354| !(pstereoTo[0]->nNumber = (AT_NUMB*)inchi_calloc((long long)len + 1, sizeof(pstereoTo[0]->nBondAtom1[0])))) /* djb-rwth: cast operators added */ ------------------ | | 1146| 354|#define inchi_calloc calloc ------------------ | Branch (10416:29): [True: 0, False: 354] ------------------ 10417| 0| { 10418| | /* cleanup */ 10419| 0| if (pstereoTo[0]->t_parity) ------------------ | Branch (10419:33): [True: 0, False: 0] ------------------ 10420| 0| { 10421| 0| inchi_free(pstereoTo[0]->t_parity); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10422| 0| pstereoTo[0]->t_parity = NULL; 10423| 0| } 10424| 0| if (pstereoTo[0]->nNumber) ------------------ | Branch (10424:33): [True: 0, False: 0] ------------------ 10425| 0| { 10426| 0| inchi_free(pstereoTo[0]->nNumber); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 10427| 0| pstereoTo[0]->nNumber = NULL; 10428| 0| } 10429| 0| goto exit_function; 10430| 0| } 10431| | /* copy stereo */ 10432| 354| if (bIsotopicFrom >= 0 && len) ------------------ | Branch (10432:29): [True: 331, False: 23] | Branch (10432:51): [True: 306, False: 25] ------------------ 10433| 306| { 10434| 306| memcpy(pstereoTo[0]->t_parity, stereoFrom->t_parity, ((long long)len + 1) * sizeof(pstereoTo[0]->t_parity[0])); /* djb-rwth: cast operator added */ 10435| 306| memcpy(pstereoTo[0]->nNumber, stereoFrom->nNumber, ((long long)len + 1) * sizeof(pstereoTo[0]->nNumber[0])); /* djb-rwth: cast operator added */ 10436| 306| } 10437| 354| pstereoTo[0]->nNumberOfStereoCenters = len; 10438| 354| return len + 1; 10439| 354| } 10440| 0| else 10441| 0| { 10442| 0| return 0; 10443| 0| } 10444| 354| } 10445| 318| else 10446| 318| { 10447| 318| if (SegmentType == CPY_SP3_M) ------------------ | Branch (10447:25): [True: 318, False: 0] ------------------ 10448| 318| { 10449| 318| pstereoTo = bIsotopicTo ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (10449:37): [True: 167, False: 151] ------------------ 10450| 318| if (!pstereoTo[0]) ------------------ | Branch (10450:29): [True: 4, False: 314] ------------------ 10451| 4| { 10452| 4| if (!(pstereoTo[0] = (INChI_Stereo*)inchi_calloc(1, sizeof(**pstereoTo)))) ------------------ | | 1146| 4|#define inchi_calloc calloc ------------------ | Branch (10452:33): [True: 0, False: 4] ------------------ 10453| 0| { 10454| 0| goto exit_function; 10455| 0| } 10456| 4| } 10457| 318| if (pstereoTo[0]->nCompInv2Abs && NO_VALUE_INT != pstereoTo[0]->nCompInv2Abs) ------------------ | | 23| 40|#define NO_VALUE_INT 9999 ------------------ | Branch (10457:29): [True: 40, False: 278] | Branch (10457:59): [True: 0, False: 40] ------------------ 10458| 0| { 10459| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10460| 0| goto exit_function; 10461| 0| } 10462| 318| if (bIsotopicFrom < 0) ------------------ | Branch (10462:29): [True: 4, False: 314] ------------------ 10463| 4| { 10464| 4| pstereoTo[0]->nCompInv2Abs = 0; 10465| 4| } 10466| 314| else 10467| 314| { 10468| 314| pstereoTo[0]->nCompInv2Abs = stereoFrom->nCompInv2Abs; 10469| 314| } 10470| 318| return 1; 10471| 318| } 10472| 0| else 10473| 0| { 10474| | /* use bTrivialInv to save /s1, /s2, /s3 */ 10475| 0| if (SegmentType == CPY_SP3_S) ------------------ | Branch (10475:29): [True: 0, False: 0] ------------------ 10476| 0| { 10477| 0| pstereoTo = bIsotopicFrom ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (10477:41): [True: 0, False: 0] ------------------ 10478| 0| if (!pstereoTo[0]) ------------------ | Branch (10478:33): [True: 0, False: 0] ------------------ 10479| 0| { 10480| 0| if (!(pstereoTo[0] = (INChI_Stereo*)inchi_calloc(1, sizeof(**pstereoTo)))) ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ | Branch (10480:37): [True: 0, False: 0] ------------------ 10481| 0| { 10482| 0| goto exit_function; 10483| 0| } 10484| 0| } 10485| 0| if (pstereoTo[0]->bTrivialInv) ------------------ | Branch (10485:33): [True: 0, False: 0] ------------------ 10486| 0| { 10487| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10488| 0| goto exit_function; 10489| 0| } 10490| 0| if (stereoFrom) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (10490:33): [True: 0, False: 0] ------------------ 10491| 0| pstereoTo[0]->bTrivialInv = stereoFrom->bTrivialInv; 10492| 0| if (bIsotopicFrom < 0) ------------------ | Branch (10492:33): [True: 0, False: 0] ------------------ 10493| 0| { 10494| 0| pstereoTo[0]->bTrivialInv = 0; 10495| 0| } 10496| 0| else 10497| 0| { 10498| 0| pstereoTo[0]->bTrivialInv = stereoFrom->bTrivialInv; 10499| 0| } 10500| 0| return 1; 10501| 0| } 10502| 0| } 10503| 318| } 10504| 672| } 10505| 7.59k| } 10506| | 10507| 3| return 0; /* nothing to copy */ 10508| 7.60k| } 10509| | 10510| 570| else if (SegmentType == CPY_ISO_AT) ------------------ | Branch (10510:14): [True: 570, False: 0] ------------------ 10511| 570| { 10512| 570| int nNumberOfIsotopicAtoms = pInChIFrom->nNumberOfIsotopicAtoms; 10513| 570| INChI_IsotopicAtom** pIsotopicAtomTo = NULL; 10514| 570| INChI_IsotopicAtom* IsotopicAtomFrom = pInChIFrom->IsotopicAtom; 10515| 570| if (bIsotopicFrom < 0 || IsotopicAtomFrom) ------------------ | Branch (10515:13): [True: 38, False: 532] | Branch (10515:34): [True: 532, False: 0] ------------------ 10516| 570| { 10517| 570| len = (bIsotopicFrom < 0) ? 0 : nNumberOfIsotopicAtoms; ------------------ | Branch (10517:19): [True: 38, False: 532] ------------------ 10518| 570|#if ( FIX_GAF_2019_3==1 ) 10519| 570| if (pInChITo->nNumberOfIsotopicAtoms < 1) ------------------ | Branch (10519:17): [True: 570, False: 0] ------------------ 10520| 570| { 10521| | /* forcibly free iso-related memory and set to NULL */ 10522| 570| qzfree(pInChITo->IsotopicAtom); ------------------ | | 1176| 570|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 16|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 16, False: 0] | | | | | Branch (1152:50): [Folded, False: 16] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 16, False: 554] | | | Branch (1176:61): [Folded, False: 570] | | ------------------ ------------------ 10523| 570| } 10524| 570|#endif 10525| 570| pIsotopicAtomTo = &pInChITo->IsotopicAtom; 10526| 570| if (!*pIsotopicAtomTo) ------------------ | Branch (10526:17): [True: 570, False: 0] ------------------ 10527| 570| { 10528| 570| if (!(*pIsotopicAtomTo = (INChI_IsotopicAtom*)inchi_calloc((long long)len + 1, sizeof(**pIsotopicAtomTo)))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 570|#define inchi_calloc calloc ------------------ | Branch (10528:21): [True: 0, False: 570] ------------------ 10529| 0| { 10530| 0| goto exit_function; 10531| 0| } 10532| 570| } 10533| 570| if (pInChITo->nNumberOfIsotopicAtoms) ------------------ | Branch (10533:17): [True: 0, False: 570] ------------------ 10534| 0| { 10535| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10536| 0| goto exit_function; 10537| 0| } 10538| 570| if (bIsotopicFrom >= 0 && len) ------------------ | Branch (10538:17): [True: 532, False: 38] | Branch (10538:39): [True: 486, False: 46] ------------------ 10539| 486| { 10540| 486| memcpy(*pIsotopicAtomTo, IsotopicAtomFrom, ((long long)len + 1) * sizeof(**pIsotopicAtomTo)); /* djb-rwth: cast operator added */ 10541| 486| } 10542| 570| pInChITo->nNumberOfIsotopicAtoms = len; 10543| 570| return len + 1; 10544| 570| } 10545| | 10546| 0| return 0; 10547| 570| } 10548| | 10549| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 10550| | 10551| 1|exit_function: 10552| | 10553| 1| return ret; 10554| 0|} ichiread.c:getInChIChar: 10580| 4.44M|{ 10581| 4.44M| if (pInp->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1016| 4.44M|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (10581:9): [True: 4.44M, False: 0] ------------------ 10582| 4.44M| { 10583| | /* input from string */ 10584| 4.44M| if (pInp->s.nPtr < pInp->s.nUsedLength) ------------------ | Branch (10584:13): [True: 4.43M, False: 6.00k] ------------------ 10585| 4.43M| { 10586| 4.43M| return (int)pInp->s.pStr[pInp->s.nPtr++]; 10587| 4.43M| } 10588| 6.00k| return RI_ERR_EOF; ------------------ | | 19| 6.00k|#define RI_ERR_EOF (0) ------------------ 10589| 4.44M| } 10590| 0| else 10591| 0| { 10592| | /* input from plain file */ 10593| 0| int c; 10594| |#if ( defined(_MSC_VER)&&defined(_WIN32) || defined(__BORLANDC__)&&defined(__WIN32__) || defined(__GNUC__)&&defined(__MINGW32__)&&defined(_WIN32) ) 10595| | do 10596| | { 10597| | c = getc(pInp->f); 10598| | if (c == EOF) 10599| | { 10600| | c = RI_ERR_EOF; 10601| | break; 10602| | } 10603| | } while (c == '\r'); 10604| |#else 10605| 0| c = getc(pInp->f); 10606| 0| if (c == EOF) ------------------ | Branch (10606:13): [True: 0, False: 0] ------------------ 10607| 0| { 10608| 0| c = RI_ERR_EOF; ------------------ | | 19| 0|#define RI_ERR_EOF (0) ------------------ 10609| 0| } 10610| 0|#endif 10611| 0| return c; 10612| 0| } 10613| 4.44M|} ichiread.c:nGetInChISegment: 10693| 50.5k|{ 10694| 50.5k| int c; 10695| 50.5k| Line->len = 0; 10696| 4.44M| while (0 < (c = AddInChIChar(pInp, Line, pszToken))) ------------------ | Branch (10696:12): [True: 4.39M, False: 50.5k] ------------------ 10697| 4.39M| { 10698| 4.39M| ; 10699| 4.39M| } 10700| 50.5k| if (c < -2) ------------------ | Branch (10700:9): [True: 38.9k, False: 11.5k] ------------------ 10701| 38.9k| { 10702| 38.9k| c = -(c + 2); 10703| 38.9k| } 10704| 50.5k| Line->c = c; 10705| | 10706| 50.5k| return c; 10707| 50.5k|} ichiread.c:AddInChIChar: 10620| 4.44M|{ 10621| 4.44M| int c = getInChIChar(pInp); 10622| | /* 10623| | while ( c == '\r' ) { 10624| | c = getInChIChar( pInp ); 10625| | } 10626| | */ 10627| | 10628| | INCHI_HEAPCHK 10629| | 10630| 4.44M| if (Line->len + 2 >= Line->len_alloc) ------------------ | Branch (10630:13): [True: 42.5k, False: 4.39M] ------------------ 10631| 42.5k| { 10632| 42.5k| char* str = (char*)inchi_calloc((long long)Line->len_alloc + SEGM_LINE_ADD, sizeof(str[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 42.5k|#define inchi_calloc calloc ------------------ char* str = (char*)inchi_calloc((long long)Line->len_alloc + SEGM_LINE_ADD, sizeof(str[0])); /* djb-rwth: cast operator added */ ------------------ | | 50| 42.5k|#define SEGM_LINE_ADD 128 ------------------ 10633| 42.5k| INCHI_HEAPCHK 10634| 42.5k| if (str) ------------------ | Branch (10634:21): [True: 42.5k, False: 0] ------------------ 10635| 42.5k| { 10636| 42.5k| if (Line->len > 0 && Line->str) ------------------ | Branch (10636:25): [True: 29.9k, False: 12.5k] | Branch (10636:42): [True: 29.9k, False: 0] ------------------ 10637| 29.9k| { 10638| 29.9k| memcpy(str, Line->str, sizeof(str[0]) * Line->len); 10639| 29.9k| Line->len_alloc += SEGM_LINE_ADD; ------------------ | | 50| 29.9k|#define SEGM_LINE_ADD 128 ------------------ 10640| 29.9k| inchi_free(Line->str); ------------------ | | 1152| 29.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 29.9k, False: 0] | | | Branch (1152:50): [Folded, False: 29.9k] | | ------------------ ------------------ 10641| 29.9k| INCHI_HEAPCHK 10642| 29.9k| } 10643| 12.5k| else 10644| 12.5k| { 10645| 12.5k| Line->len_alloc += SEGM_LINE_ADD; ------------------ | | 50| 12.5k|#define SEGM_LINE_ADD 128 ------------------ 10646| 12.5k| } 10647| 42.5k| Line->str = str; 10648| 42.5k| } 10649| 0| else 10650| 0| { 10651| 0| c = RI_ERR_ALLOC; /* fatal error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 10652| 0| goto exit_function; 10653| 0| } 10654| 42.5k| } 10655| 4.44M| INCHI_HEAPCHK 10656| 4.44M| if (c < 0) ------------------ | Branch (10656:13): [True: 0, False: 4.44M] ------------------ 10657| 0| { 10658| 0| Line->str[Line->len] = '\0'; 10659| 0| INCHI_HEAPCHK 10660| 0| c = RI_ERR_SYNTAX; /* fatal error: wrong char */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10661| 0| goto exit_function; 10662| 0| } 10663| | 10664| 4.44M| if (c && strchr(pszToken, c)) /* /\ */ ------------------ | Branch (10664:9): [True: 4.43M, False: 11.5k] | Branch (10664:14): [True: 38.9k, False: 4.39M] ------------------ 10665| 38.9k| { 10666| 38.9k| Line->str[Line->len] = '\0'; 10667| 38.9k| INCHI_HEAPCHK 10668| 38.9k| c = -(c + 2); 10669| 38.9k| goto exit_function; 10670| 38.9k| } 10671| 4.40M| else if (!c && !Line->len) ------------------ | Branch (10671:14): [True: 11.5k, False: 4.39M] | Branch (10671:20): [True: 1.23k, False: 10.3k] ------------------ 10672| 1.23k| { 10673| 1.23k| Line->str[Line->len] = c; 10674| 1.23k| INCHI_HEAPCHK 10675| 1.23k| } 10676| 4.40M| else 10677| 4.40M| { 10678| 4.40M| Line->str[Line->len++] = c; 10679| 4.40M| INCHI_HEAPCHK 10680| 4.40M| } 10681| | 10682| 4.44M|exit_function: 10683| | 10684| | INCHI_HEAPCHK 10685| | 10686| 4.44M| return c; /* djb-rwth: addressing coverity ID #499500 -- c = getInChIChar(pInp) cannot be tainted */ 10687| 4.44M|} ichiread.c:getInchiStateReadErr: 509| 2.34k|{ 510| 2.34k| int i, bRecMet = 0; 511| | 512| 2.34k| if (stat >= IST_HAPPENED_IN_RECMET) ------------------ | | 342| 2.34k|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (512:9): [True: 82, False: 2.26k] ------------------ 513| 82| { 514| 82| bRecMet = 1; 515| 82| stat -= IST_HAPPENED_IN_RECMET; ------------------ | | 342| 82|#define IST_HAPPENED_IN_RECMET 100 ------------------ 516| 82| } 517| 39.2k| for (i = 0; 0 <= irErrMsg[i].stat && stat != irErrMsg[i].stat; i++) ------------------ | Branch (517:17): [True: 39.2k, False: 0] | Branch (517:42): [True: 36.8k, False: 2.34k] ------------------ 518| 36.8k| { 519| 36.8k| ; 520| 36.8k| } 521| 2.34k| sprintf(szMsg, 522| 2.34k|#if ( FIX_DALKE_BUGS == 1 ) 523| 2.34k| "%s%.100s", 524| |#else 525| | "%s%s", 526| |#endif 527| 2.34k| irErrMsg[i].msg, bRecMet ? ", Reconnected layer" : ""); ------------------ | Branch (527:26): [True: 82, False: 2.26k] ------------------ 528| | 529| 2.34k|} ichiread.c:getInchiErrName: 534| 1.93k|{ 535| 1.93k| switch (nErr) ------------------ | Branch (535:13): [True: 1.89k, False: 31] ------------------ 536| 1.93k| { 537| 31| case RI_ERR_ALLOC: ------------------ | | 15| 31|#define RI_ERR_ALLOC (-1) ------------------ | Branch (537:5): [True: 31, False: 1.89k] ------------------ 538| 31| return "Allocation failed"; 539| 18| case RI_ERR_PROGR: ------------------ | | 17| 18|#define RI_ERR_PROGR (-3) ------------------ | Branch (539:5): [True: 18, False: 1.91k] ------------------ 540| 18| return "Program error"; 541| 1.85k| case RI_ERR_SYNTAX: ------------------ | | 16| 1.85k|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (541:5): [True: 1.85k, False: 80] ------------------ 542| 1.85k| return "Syntax error"; 543| 0| case RI_ERR_EOL: ------------------ | | 18| 0|#define RI_ERR_EOL (-4) ------------------ | Branch (543:5): [True: 0, False: 1.93k] ------------------ 544| 0| return "End of line"; 545| 1.93k| } 546| 31| return "Unknown error"; 547| 1.93k|} ichiread.c:SetHillFormFromInChI: 555| 5.02k|{ 556| 5.02k| int iINChI, iTaut, iComp, num_diff; 557| 5.02k| INChI* pINChI; 558| 5.02k| char* szHillFormulaOld; 559| 15.0k| for (iINChI = 0, num_diff = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 15.0k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (559:36): [True: 10.0k, False: 5.02k] ------------------ 560| 10.0k| { 561| 30.1k| for (iTaut = TAUT_NON; iTaut < TAUT_NUM; iTaut++) ------------------ | | 574| 10.0k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (iTaut = TAUT_NON; iTaut < TAUT_NUM; iTaut++) ------------------ | | 573| 30.1k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (561:32): [True: 20.1k, False: 10.0k] ------------------ 562| 20.1k| { 563| 117k| for (iComp = 0; iComp < OneInput->nNumComponents[iINChI][iTaut]; iComp++) ------------------ | Branch (563:29): [True: 97.5k, False: 20.1k] ------------------ 564| 97.5k| { 565| 97.5k| pINChI = &OneInput->pInpInChI[iINChI][iTaut][iComp]; 566| 97.5k| if (!pINChI->nNumberOfAtoms || pINChI->bDeleted || !pINChI->szHillFormula || !pINChI->szHillFormula[0]) ------------------ | Branch (566:21): [True: 0, False: 97.5k] | Branch (566:48): [True: 7, False: 97.5k] | Branch (566:68): [True: 0, False: 97.5k] | Branch (566:94): [True: 0, False: 97.5k] ------------------ 567| 7| { 568| 7| continue; 569| 7| } 570| 97.5k| szHillFormulaOld = pINChI->szHillFormula; 571| 97.5k| pINChI->szHillFormula = AllocateAndFillHillFormula(pINChI); 572| 97.5k| num_diff += !pINChI->szHillFormula || !pINChI->szHillFormula[0] || strcmp(pINChI->szHillFormula, szHillFormulaOld); ------------------ | Branch (572:29): [True: 35.2k, False: 62.2k] | Branch (572:55): [True: 0, False: 62.2k] | Branch (572:84): [True: 44.1k, False: 18.1k] ------------------ 573| 97.5k| inchi_free(szHillFormulaOld); ------------------ | | 1152| 97.5k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 97.5k, False: 0] | | | Branch (1152:50): [Folded, False: 97.5k] | | ------------------ ------------------ 574| 97.5k| } 575| 20.1k| } 576| 10.0k| } 577| | 578| 5.02k| return num_diff; 579| 5.02k|} ichiread.c:OutputInChIAsRequested: 1212| 5.02k|{ 1213| 5.02k| int j, k, k1, k2, ret2 = 0, iINChI, iINChI1; /* djb-rwth: removing redundant variables */ 1214| 5.02k| PINChI2* pINChI[INCHI_NUM], * newPTR1; 1215| 5.02k| PINChI_Aux2* pINChI_Aux[INCHI_NUM], * newPTR2; 1216| 5.02k| int bReqNonTaut; 1217| 5.02k| int bHasSomeReconnected; 1218| | 1219| 5.02k| INPUT_PARMS ip_local; 1220| 5.02k| STRUCT_DATA sd_local; 1221| 5.02k| INPUT_PARMS* ip = &ip_local; 1222| 5.02k| STRUCT_DATA* sd = &sd_local; 1223| 5.02k| NORM_CANON_FLAGS ncFlags; 1224| 5.02k| NORM_CANON_FLAGS* pncFlags = &ncFlags; 1225| 5.02k| int nRet1, bSortPrintINChIFlags; 1226| 5.02k| int bReqSplitOutputInChI; 1227| 5.02k| int nNumOutputComponents; 1228| | 1229| 5.02k| INCHI_IOS_STRING temp_string_container; 1230| 5.02k| INCHI_IOS_STRING* strbuf = &temp_string_container; 1231| 5.02k| memset(strbuf, 0, sizeof(*strbuf)); /* djb-rwth: memset_s C11/Annex K variant? */ 1232| | 1233| 5.02k| if (0 >= inchi_strbuf_init(strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT)) ------------------ | | 65| 5.02k|#define INCHI_STRBUF_INITIAL_SIZE 262144 ------------------ if (0 >= inchi_strbuf_init(strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT)) ------------------ | | 66| 5.02k|#define INCHI_STRBUF_SIZE_INCREMENT 262144 ------------------ | Branch (1233:9): [True: 0, False: 5.02k] ------------------ 1234| 0| { 1235| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1236| 0| goto exit_error; 1237| 0| } 1238| | 1239| 5.02k| nRet1 = 0; 1240| 5.02k| k1 = k2 = 0; 1241| 5.02k| memset(pncFlags, 0, sizeof(*pncFlags)); /* djb-rwth: memset_s C11/Annex K variant? */ 1242| 5.02k| memset(pINChI, 0, sizeof(pINChI)); /* djb-rwth: memset_s C11/Annex K variant? */ 1243| 5.02k| memset(pINChI_Aux, 0, sizeof(pINChI_Aux)); /* djb-rwth: memset_s C11/Annex K variant? */ 1244| | 1245| 5.02k| *ip = *ip_inp; 1246| 5.02k| *sd = *sd_inp; 1247| 5.02k| bHasSomeReconnected = 0; 1248| 5.02k| bSortPrintINChIFlags = 0; 1249| | /* djb-rwth: removing redundant code */ 1250| 5.02k| bReqNonTaut = (0 != (ip->nMode & REQ_MODE_BASIC)); ------------------ | | 15| 5.02k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1251| 5.02k| bReqSplitOutputInChI = (0 != (ip->bReadInChIOptions & READ_INCHI_SPLIT_OUTPUT)); ------------------ | | 989| 5.02k|#define READ_INCHI_SPLIT_OUTPUT 0x00000002 ------------------ 1252| | 1253| | INCHI_HEAPCHK 1254| | 1255| 5.02k| if (num_components[INCHI_BAS]) ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1255:13): [True: 5.02k, False: 0] ------------------ 1256| 5.02k| { 1257| | /* djb-rwth: MYREALLOC2( PINChI2, PINChI_Aux2, pINChI[INCHI_BAS], pINChI_Aux[INCHI_BAS], num_components[INCHI_BAS], (long long)num_components[INCHI_BAS], k1 ); has been replaced and the whole block rewritten to address memory leaks and reading from freed memory locations */ 1258| | 1259| 5.02k| do { 1260| 5.02k| if ((num_components[INCHI_BAS]) <= ((long long)num_components[INCHI_BAS])) ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ((num_components[INCHI_BAS]) <= ((long long)num_components[INCHI_BAS])) ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1260:21): [True: 5.02k, False: 0] ------------------ 1261| 5.02k| { 1262| 5.02k| newPTR1 = (PINChI2*)inchi_calloc(((long long)num_components[INCHI_BAS]) + 1, sizeof(PINChI2)); ------------------ | | 1146| 5.02k|#define inchi_calloc calloc ------------------ newPTR1 = (PINChI2*)inchi_calloc(((long long)num_components[INCHI_BAS]) + 1, sizeof(PINChI2)); ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1263| 5.02k| newPTR2 = (PINChI_Aux2*)inchi_calloc(((long long)num_components[INCHI_BAS]) + 1, sizeof(PINChI_Aux2)); ------------------ | | 1146| 5.02k|#define inchi_calloc calloc ------------------ newPTR2 = (PINChI_Aux2*)inchi_calloc(((long long)num_components[INCHI_BAS]) + 1, sizeof(PINChI_Aux2)); ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1264| 5.02k| if (newPTR1 && newPTR2) { ------------------ | Branch (1264:25): [True: 5.02k, False: 0] | Branch (1264:36): [True: 5.02k, False: 0] ------------------ 1265| 5.02k| if ((pINChI[INCHI_BAS]) && (num_components[INCHI_BAS]) > 0) ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ((pINChI[INCHI_BAS]) && (num_components[INCHI_BAS]) > 0) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1265:29): [True: 0, False: 5.02k] | Branch (1265:52): [True: 0, False: 0] ------------------ 1266| 0| memcpy(newPTR1, (pINChI[INCHI_BAS]), (num_components[INCHI_BAS]) * sizeof(PINChI2)); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ memcpy(newPTR1, (pINChI[INCHI_BAS]), (num_components[INCHI_BAS]) * sizeof(PINChI2)); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1267| 5.02k| if ((pINChI_Aux[INCHI_BAS]) && (num_components[INCHI_BAS]) > 0) ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ((pINChI_Aux[INCHI_BAS]) && (num_components[INCHI_BAS]) > 0) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1267:29): [True: 0, False: 5.02k] | Branch (1267:56): [True: 0, False: 0] ------------------ 1268| 0| memcpy(newPTR2, (pINChI_Aux[INCHI_BAS]), (num_components[INCHI_BAS]) * sizeof(PINChI_Aux2)); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ memcpy(newPTR2, (pINChI_Aux[INCHI_BAS]), (num_components[INCHI_BAS]) * sizeof(PINChI_Aux2)); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1269| 5.02k| if (pINChI[INCHI_BAS]) ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1269:29): [True: 0, False: 5.02k] ------------------ 1270| 0| inchi_free(pINChI[INCHI_BAS]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1271| 5.02k| if (pINChI_Aux[INCHI_BAS]) ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1271:29): [True: 0, False: 5.02k] ------------------ 1272| 0| inchi_free(pINChI_Aux[INCHI_BAS]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1273| 5.02k| pINChI[INCHI_BAS] = newPTR1; ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1274| 5.02k| pINChI_Aux[INCHI_BAS] = newPTR2; ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1275| 5.02k| num_components[INCHI_BAS] = (long long)num_components[INCHI_BAS]; ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ num_components[INCHI_BAS] = (long long)num_components[INCHI_BAS]; ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1276| 5.02k| k1 = 0; 1277| 5.02k| } 1278| 0| else 1279| 0| { 1280| 0| inchi_free(newPTR1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1281| 0| inchi_free(newPTR2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1282| 0| k1 = 1; 1283| 0| } 1284| 5.02k| } 1285| 0| else { k1 = 0; } 1286| 5.02k| } while (0); ------------------ | Branch (1286:22): [Folded, False: 5.02k] ------------------ 1287| 5.02k| } 1288| | 1289| 5.02k| if (num_components[INCHI_REC]) ------------------ | | 571| 5.02k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1289:9): [True: 25, False: 5.00k] ------------------ 1290| 25| { 1291| | /* djb-rwth: MYREALLOC2( PINChI2, PINChI_Aux2, pINChI[INCHI_REC], pINChI_Aux[INCHI_REC], num_components[INCHI_REC], (long long)num_components[INCHI_REC], k2 ); has been replaced and the whole block rewritten to address memory leaks and reading from freed memory locations */ 1292| | 1293| 25| do { 1294| 25| if ((num_components[INCHI_REC]) <= ((long long)num_components[INCHI_REC])) ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if ((num_components[INCHI_REC]) <= ((long long)num_components[INCHI_REC])) ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1294:17): [True: 25, False: 0] ------------------ 1295| 25| { 1296| 25| newPTR1 = (PINChI2*)inchi_calloc(((long long)num_components[INCHI_REC]) + 1, sizeof(PINChI2)); ------------------ | | 1146| 25|#define inchi_calloc calloc ------------------ newPTR1 = (PINChI2*)inchi_calloc(((long long)num_components[INCHI_REC]) + 1, sizeof(PINChI2)); ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1297| 25| newPTR2 = (PINChI_Aux2*)inchi_calloc(((long long)num_components[INCHI_REC]) + 1, sizeof(PINChI_Aux2)); ------------------ | | 1146| 25|#define inchi_calloc calloc ------------------ newPTR2 = (PINChI_Aux2*)inchi_calloc(((long long)num_components[INCHI_REC]) + 1, sizeof(PINChI_Aux2)); ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1298| 25| if (newPTR1 && newPTR2) { ------------------ | Branch (1298:21): [True: 25, False: 0] | Branch (1298:32): [True: 25, False: 0] ------------------ 1299| 25| if ((pINChI[INCHI_REC]) && (num_components[INCHI_REC]) > 0) ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if ((pINChI[INCHI_REC]) && (num_components[INCHI_REC]) > 0) ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1299:25): [True: 0, False: 25] | Branch (1299:48): [True: 0, False: 0] ------------------ 1300| 0| memcpy(newPTR1, (pINChI[INCHI_REC]), (num_components[INCHI_REC]) * sizeof(PINChI2)); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ memcpy(newPTR1, (pINChI[INCHI_REC]), (num_components[INCHI_REC]) * sizeof(PINChI2)); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1301| 25| if ((pINChI_Aux[INCHI_REC]) && (num_components[INCHI_REC]) > 0) ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if ((pINChI_Aux[INCHI_REC]) && (num_components[INCHI_REC]) > 0) ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1301:25): [True: 0, False: 25] | Branch (1301:52): [True: 0, False: 0] ------------------ 1302| 0| memcpy(newPTR2, (pINChI_Aux[INCHI_REC]), (num_components[INCHI_REC]) * sizeof(PINChI_Aux2)); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ memcpy(newPTR2, (pINChI_Aux[INCHI_REC]), (num_components[INCHI_REC]) * sizeof(PINChI_Aux2)); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1303| 25| if (pINChI[INCHI_REC]) ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1303:25): [True: 0, False: 25] ------------------ 1304| 0| inchi_free(pINChI[INCHI_REC]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1305| 25| if (pINChI_Aux[INCHI_REC]) ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1305:25): [True: 0, False: 25] ------------------ 1306| 0| inchi_free(pINChI_Aux[INCHI_REC]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1307| 25| pINChI[INCHI_REC] = newPTR1; ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1308| 25| pINChI_Aux[INCHI_REC] = newPTR2; ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1309| 25| num_components[INCHI_REC] = (long long)num_components[INCHI_REC]; ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ num_components[INCHI_REC] = (long long)num_components[INCHI_REC]; ------------------ | | 571| 25|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1310| 25| k2 = 0; 1311| 25| } 1312| 0| else 1313| 0| { 1314| 0| inchi_free(newPTR1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1315| 0| inchi_free(newPTR2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1316| 0| k2 = 1; 1317| 0| } 1318| 25| } 1319| 0| else { k2 = 0; } 1320| 25| } while (0); ------------------ | Branch (1320:18): [Folded, False: 25] ------------------ 1321| 25| } 1322| | 1323| | 1324| | INCHI_HEAPCHK 1325| | 1326| 5.02k| if (k1 || k2 /*|| !pStr*/) ------------------ | Branch (1326:13): [True: 0, False: 5.02k] | Branch (1326:19): [True: 0, False: 5.02k] ------------------ 1327| 0| { 1328| | /* djb-rwth: avoiding memory leak */ 1329| 0| free(pINChI[INCHI_BAS]); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1330| 0| free(pINChI_Aux[INCHI_BAS]); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1331| 0| free(pINChI[INCHI_REC]); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1332| 0| free(pINChI_Aux[INCHI_REC]); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1333| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1334| 0| goto exit_error; 1335| 0| } 1336| | 1337| 5.02k| if (num_components[INCHI_REC] && ------------------ | | 571| 5.02k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1337:9): [True: 25, False: 5.00k] ------------------ 1338| 25| (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) && ------------------ | | 932| 25|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1338:9): [True: 0, False: 25] ------------------ 1339| 0| (ip->bTautFlags & TG_FLAG_DISCONNECT_COORD)) ------------------ | | 931| 0|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (1339:9): [True: 0, False: 0] ------------------ 1340| 0| { 1341| 0| sd->bTautFlagsDone[0] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 975| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 1342| 0| bHasSomeReconnected = 1; 1343| 0| } 1344| | 1345| 15.0k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 15.0k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1345:22): [True: 10.0k, False: 5.02k] ------------------ 1346| 10.0k| { 1347| 30.1k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 30.1k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1347:21): [True: 20.1k, False: 10.0k] ------------------ 1348| 20.1k| { 1349| 20.1k| if (bReqNonTaut || (j != TAUT_NON && OneInput->pInpInChI[iINChI][j])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 40.2k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1349:17): [True: 0, False: 20.1k] | Branch (1349:33): [True: 10.0k, False: 10.0k] | Branch (1349:50): [True: 5.05k, False: 5.00k] ------------------ 1350| 5.05k| { 1351| 102k| for (k = 0; k < num_components[iINChI]; k++) ------------------ | Branch (1351:29): [True: 97.5k, False: 5.05k] ------------------ 1352| 97.5k| { 1353| | /* allocate InChI & AuxInfo */ 1354| 97.5k| if (!(pINChI[iINChI][k][j] = (INChI*)inchi_calloc(1, sizeof(INChI)))) ------------------ | | 1146| 97.5k|#define inchi_calloc calloc ------------------ | Branch (1354:25): [True: 0, False: 97.5k] ------------------ 1355| 0| { 1356| | /* djb-rwth: avoiding memory leak */ 1357| 0| free(pINChI[INCHI_BAS]); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1358| 0| free(pINChI_Aux[INCHI_BAS]); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1359| 0| free(pINChI[INCHI_REC]); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1360| 0| free(pINChI_Aux[INCHI_REC]); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1361| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1362| 0| goto exit_error; 1363| 0| } 1364| 97.5k| if (!(pINChI_Aux[iINChI][k][j] = (INChI_Aux*)inchi_calloc(1, sizeof(INChI_Aux)))) ------------------ | | 1146| 97.5k|#define inchi_calloc calloc ------------------ | Branch (1364:25): [True: 0, False: 97.5k] ------------------ 1365| 0| { 1366| | /* djb-rwth: avoiding memory leak */ 1367| 0| free(pINChI[INCHI_BAS]); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1368| 0| free(pINChI_Aux[INCHI_BAS]); ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1369| 0| free(pINChI[INCHI_REC]); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1370| 0| free(pINChI_Aux[INCHI_REC]); ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1371| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1372| 0| goto exit_error; 1373| 0| } 1374| | /* copy InChI & AuxInfo */ 1375| 97.5k| if (k < OneInput->nNumComponents[iINChI][j]) ------------------ | Branch (1375:25): [True: 97.5k, False: 0] ------------------ 1376| 97.5k| { 1377| | 1378| | /* copy InChI */ 1379| 97.5k| *pINChI[iINChI][k][j] = OneInput->pInpInChI[iINChI][j][k]; 1380| 97.5k| memset(&OneInput->pInpInChI[iINChI][j][k], 0, sizeof(OneInput->pInpInChI[iINChI][j][k])); /* djb-rwth: memset_s C11/Annex K variant? */ 1381| | INCHI_HEAPCHK 1382| | /* take care of protons in AuxInfo */ 1383| | 1384| 97.5k| if (nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_TO_EACH && j == TAUT_YES) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1384:33): [True: 0, False: 97.5k] | Branch (1384:90): [True: 0, False: 0] ------------------ 1385| 0| { 1386| 0| pINChI_Aux[iINChI][k][j]->nNumRemovedProtons = 1387| 0| OneInput->nNumProtons[iINChI][j].pNumProtons[k].nNumRemovedProtons; 1388| 0| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 72| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (1388:46): [True: 0, False: 0] ------------------ 1389| 0| { 1390| 0| pINChI_Aux[iINChI][k][j]->nNumRemovedIsotopicH[k1] = 1391| 0| OneInput->nNumProtons[iINChI][j].pNumProtons[k].nNumRemovedIsotopicH[k1]; 1392| 0| } 1393| 0| INCHI_HEAPCHK 1394| 0| } 1395| 97.5k| else if ((!k && nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_TO_FIRST) || ------------------ | Branch (1395:39): [True: 5.05k, False: 92.4k] | Branch (1395:45): [True: 5.05k, False: 0] ------------------ 1396| 92.4k| (k + 1 == OneInput->nNumComponents[iINChI][j] && ------------------ | Branch (1396:34): [True: 1.34k, False: 91.1k] ------------------ 1397| 1.34k| nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_A_PIXH_COMPONENT)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1397:37): [True: 0, False: 1.34k] ------------------ 1398| 5.05k| { 1399| | /* add protons and exchangeable isotopic H to the first component's AuxInfo */ 1400| 5.05k| pINChI_Aux[iINChI][k][j]->nNumRemovedProtons = OneInput->nNumProtons[iINChI][j].nNumRemovedProtons; 1401| 20.2k| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 72| 20.2k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (1401:46): [True: 15.1k, False: 5.05k] ------------------ 1402| 15.1k| { 1403| 15.1k| pINChI_Aux[iINChI][k][j]->nNumRemovedIsotopicH[k1] = 1404| 15.1k| OneInput->nNumProtons[iINChI][j].nNumRemovedIsotopicH[k1]; 1405| 15.1k| } 1406| 5.05k| INCHI_HEAPCHK 1407| 5.05k| } 1408| 92.4k| else 1409| 92.4k| { 1410| 92.4k| pINChI_Aux[iINChI][k][j]->bDeleted = pINChI[iINChI][k][j]->bDeleted; 1411| 92.4k| } 1412| | 1413| 97.5k| if (j == TAUT_YES && pINChI[iINChI][k][j] && pINChI[iINChI][k][j]->nNumberOfAtoms && ------------------ | | 575| 195k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1413:29): [True: 97.5k, False: 0] | Branch (1413:46): [True: 97.5k, False: 0] | Branch (1413:70): [True: 97.5k, False: 0] ------------------ 1414| 97.5k| !pINChI[iINChI][k][j]->nNum_H_fixed) ------------------ | Branch (1414:29): [True: 97.5k, False: 0] ------------------ 1415| 97.5k| { 1416| | /* serializer crashes if it is not allocated */ 1417| 97.5k| pINChI[iINChI][k][j]->nNum_H_fixed = (S_CHAR*)inchi_calloc((long long)pINChI[iINChI][k][j]->nNumberOfAtoms + 1, sizeof(pINChI[0][0][0]->nNum_H_fixed[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 97.5k|#define inchi_calloc calloc ------------------ 1418| 97.5k| } 1419| | 1420| 97.5k| if (j == TAUT_YES && k < OneInput->nNumComponents[iINChI][TAUT_NON] && ------------------ | | 575| 195k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (j == TAUT_YES && k < OneInput->nNumComponents[iINChI][TAUT_NON] && ------------------ | | 574| 97.5k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1420:29): [True: 97.5k, False: 0] | Branch (1420:46): [True: 0, False: 97.5k] ------------------ 1421| 0| pINChI[iINChI][k][j] && pINChI[iINChI][k][j]->nNumberOfAtoms && ------------------ | Branch (1421:29): [True: 0, False: 0] | Branch (1421:53): [True: 0, False: 0] ------------------ 1422| 0| pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms && ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms && ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1422:29): [True: 0, False: 0] | Branch (1422:60): [True: 0, False: 0] ------------------ 1423| 0| !CompareReversedINChI(pINChI[iINChI][k][j], pINChI[iINChI][k][TAUT_NON], NULL, NULL)) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1423:29): [True: 0, False: 0] ------------------ 1424| 0| { 1425| 0| pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms = 0; /* eliminate non-taut equal to taut */ ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1426| 0| } 1427| 97.5k| } 1428| 0| else 1429| 0| { 1430| | /* extra component, usually it is a Mobile H component */ 1431| | /* corresponding to a free proton component in Fixed H */ 1432| 0| pINChI[iINChI][k][j]->bDeleted = 1; 1433| 0| pINChI_Aux[iINChI][k][j]->bDeleted = 1; 1434| 0| } 1435| 97.5k| } /* k */ 1436| 5.05k| } /* if ( bReqNonTaut || j != TAUT_NON && OneInput->pInpInChI[iINChI][j] ) */ 1437| | 1438| 20.1k| if (OneInput->pInpInChI[iINChI][j]) ------------------ | Branch (1438:17): [True: 5.05k, False: 15.0k] ------------------ 1439| 5.05k| { 1440| 5.05k| INCHI_HEAPCHK 1441| 5.05k| inchi_free(OneInput->pInpInChI[iINChI][j]); ------------------ | | 1152| 5.05k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 5.05k, False: 0] | | | Branch (1152:50): [Folded, False: 5.05k] | | ------------------ ------------------ 1442| 5.05k| OneInput->pInpInChI[iINChI][j] = NULL; 1443| 5.05k| } 1444| 20.1k| } /* j */ 1445| 10.0k| } /* iINChI */ 1446| | 1447| 5.02k| if (bReqSplitOutputInChI) ------------------ | Branch (1447:9): [True: 0, False: 5.02k] ------------------ 1448| 0| { 1449| 0| if (bHasSomeReconnected) ------------------ | Branch (1449:13): [True: 0, False: 0] ------------------ 1450| 0| { 1451| 0| iINChI1 = INCHI_REC; /* only reconnected */ ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1452| | /* djb-rwth: removing redundant code */ 1453| 0| sd->num_components[INCHI_BAS] = sd->num_components[INCHI_REC]; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->num_components[INCHI_BAS] = sd->num_components[INCHI_REC]; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1454| 0| } 1455| 0| else 1456| 0| { 1457| 0| iINChI1 = 0; /* only disconnected */ 1458| | /* djb-rwth: removing redundant code */ 1459| 0| } 1460| 0| sd->num_components[INCHI_REC] = 0; /* treat reconnected as connected */ ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1461| 0| nNumOutputComponents = sd->num_components[INCHI_BAS]; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1462| 0| } 1463| 5.02k| else 1464| 5.02k| { 1465| 5.02k| iINChI1 = 0; 1466| | /* djb-rwth: removing redundant code */ 1467| 5.02k| nNumOutputComponents = 1; 1468| 5.02k| } 1469| | 1470| 10.0k| for (k1 = 0, k2 = (bReqSplitOutputInChI ? k1 + 1 : nNumOutputComponents); k1 < k2 && k1 < nNumOutputComponents; k1 = k2, k2++) ------------------ | Branch (1470:24): [True: 0, False: 5.02k] | Branch (1470:79): [True: 10.0k, False: 0] | Branch (1470:90): [True: 5.02k, False: 5.02k] ------------------ 1471| 5.02k| { 1472| | 1473| 5.02k| if (bReqSplitOutputInChI) ------------------ | Branch (1473:13): [True: 0, False: 5.02k] ------------------ 1474| 0| { 1475| 0| sd->num_components[INCHI_BAS] = 1; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1476| 0| sd->num_components[INCHI_REC] = 0; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1477| | /* additional data */ 1478| 0| sd->num_non_taut[INCHI_BAS] = ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1479| 0| sd->num_taut[INCHI_BAS] = ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1480| 0| sd->num_non_taut[INCHI_REC] = ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1481| 0| sd->num_taut[INCHI_REC] = 0; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1482| 0| iINChI = iINChI1; 1483| 0| for (j = 0; j < TAUT_NUM && sd->num_components[iINChI]; j++) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1483:25): [True: 0, False: 0] | Branch (1483:41): [True: 0, False: 0] ------------------ 1484| 0| { 1485| 0| for (k = k1; k < k2; k++) ------------------ | Branch (1485:30): [True: 0, False: 0] ------------------ 1486| 0| { 1487| | /* find where the current processed structure is located */ 1488| 0| int cur_is_in_non_taut = (pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms > 0); ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ int cur_is_in_non_taut = (pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms > 0); ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1488:47): [True: 0, False: 0] | Branch (1488:78): [True: 0, False: 0] ------------------ 1489| 0| int cur_is_in_taut = (pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0); ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int cur_is_in_taut = (pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0); ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1489:43): [True: 0, False: 0] | Branch (1489:74): [True: 0, False: 0] ------------------ 1490| 0| int cur_is_non_taut = (cur_is_in_non_taut && 0 == pINChI[iINChI][k][TAUT_NON]->lenTautomer) || ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1490:44): [True: 0, False: 0] | Branch (1490:66): [True: 0, False: 0] ------------------ 1491| 0| (cur_is_in_taut && 0 == pINChI[iINChI][k][TAUT_YES]->lenTautomer); /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1491:26): [True: 0, False: 0] | Branch (1491:44): [True: 0, False: 0] ------------------ 1492| 0| int cur_is_taut = cur_is_in_taut && 0 < pINChI[iINChI][k][TAUT_YES]->lenTautomer; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1492:39): [True: 0, False: 0] | Branch (1492:57): [True: 0, False: 0] ------------------ 1493| 0| if (cur_is_non_taut + cur_is_taut) ------------------ | Branch (1493:25): [True: 0, False: 0] ------------------ 1494| 0| { 1495| | /* count tautomeric and non-tautomeric components of the structures */ 1496| | /* 1497| | int j1 = cur_is_in_non_taut? TAUT_NON:TAUT_YES; 1498| | int j2 = cur_is_in_taut? TAUT_YES:TAUT_NON; 1499| | */ 1500| 0| sd->num_non_taut[INCHI_BAS] += cur_is_non_taut; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1501| 0| sd->num_taut[INCHI_BAS] += cur_is_taut; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1502| 0| } 1503| 0| } 1504| 0| } 1505| 0| INCHI_HEAPCHK 1506| 0| } 1507| 5.02k| else 1508| 5.02k| { 1509| 5.02k| sd->num_components[INCHI_BAS] = inchi_max(OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->num_components[INCHI_BAS] = inchi_max(OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 138| 5.02k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 5.02k, False: 0] | | ------------------ ------------------ 1510| 5.02k| OneInput->nNumComponents[INCHI_BAS][TAUT_NON]); 1511| 5.02k| sd->num_components[INCHI_REC] = inchi_max(OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 571| 5.02k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->num_components[INCHI_REC] = inchi_max(OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 138| 5.02k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 25, False: 5.00k] | | ------------------ ------------------ 1512| 5.02k| OneInput->nNumComponents[INCHI_REC][TAUT_NON]); 1513| | /* additional data needed for SortAndPrintINChI() */ 1514| 15.0k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 15.0k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1514:30): [True: 10.0k, False: 5.02k] ------------------ 1515| 10.0k| { 1516| 10.0k| sd->num_non_taut[iINChI] = 1517| 10.0k| sd->num_taut[iINChI] = 0; 1518| 20.1k| for (j = 0; j < TAUT_NUM && sd->num_components[iINChI]; j++) ------------------ | | 573| 40.3k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1518:29): [True: 15.1k, False: 5.05k] | Branch (1518:45): [True: 10.1k, False: 5.00k] ------------------ 1519| 10.1k| { 1520| 20.2k| for (k = k1; k < k2; k++) ------------------ | Branch (1520:34): [True: 10.1k, False: 10.1k] ------------------ 1521| 10.1k| { 1522| | /* find where the current processed structure is located */ 1523| 10.1k| int cur_is_in_non_taut = (pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms > 0); ------------------ | | 574| 10.1k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ int cur_is_in_non_taut = (pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms > 0); ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1523:51): [True: 0, False: 10.1k] | Branch (1523:82): [True: 0, False: 0] ------------------ 1524| 10.1k| int cur_is_in_taut = (pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0); ------------------ | | 575| 10.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int cur_is_in_taut = (pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0); ------------------ | | 575| 10.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1524:47): [True: 10.1k, False: 0] | Branch (1524:78): [True: 10.1k, False: 0] ------------------ 1525| 10.1k| int cur_is_non_taut = (cur_is_in_non_taut && 0 == pINChI[iINChI][k][TAUT_NON]->lenTautomer) || ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1525:48): [True: 0, False: 10.1k] | Branch (1525:70): [True: 0, False: 0] ------------------ 1526| 10.1k| (cur_is_in_taut && 0 == pINChI[iINChI][k][TAUT_YES]->lenTautomer); /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 10.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1526:30): [True: 10.1k, False: 0] | Branch (1526:48): [True: 7.76k, False: 2.33k] ------------------ 1527| 10.1k| int cur_is_taut = cur_is_in_taut && 0 < pINChI[iINChI][k][TAUT_YES]->lenTautomer; ------------------ | | 575| 10.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1527:43): [True: 10.1k, False: 0] | Branch (1527:61): [True: 2.33k, False: 7.76k] ------------------ 1528| 10.1k| if (cur_is_non_taut + cur_is_taut) ------------------ | Branch (1528:29): [True: 10.1k, False: 0] ------------------ 1529| 10.1k| { 1530| | /* count tautomeric and non-tautomeric components of the structures */ 1531| | /* 1532| | int j1 = cur_is_in_non_taut? TAUT_NON:TAUT_YES; 1533| | int j2 = cur_is_in_taut? TAUT_YES:TAUT_NON; 1534| | */ 1535| 10.1k| sd->num_non_taut[iINChI] += cur_is_non_taut; 1536| 10.1k| sd->num_taut[iINChI] += cur_is_taut; 1537| 10.1k| } 1538| 10.1k| } 1539| 10.1k| } 1540| 10.0k| } 1541| 5.02k| INCHI_HEAPCHK 1542| 5.02k| } 1543| 5.02k| if (bReqSplitOutputInChI) ------------------ | Branch (1543:13): [True: 0, False: 5.02k] ------------------ 1544| 0| { 1545| | /* output components one by one (for splitting input InChI into components) */ 1546| 0| PINChI2* pInChI_2[INCHI_NUM]; 1547| 0| PINChI_Aux2* pInChI_Aux_2[INCHI_NUM]; 1548| 0| INChI* pInChI_1[1][2]; 1549| 0| INChI_Aux* pInChI_Aux_1[1][2]; 1550| 0| memset(pInChI_2, 0, sizeof(pInChI_2)); /* djb-rwth: memset_s C11/Annex K variant? */ 1551| 0| memset(pInChI_Aux_2, 0, sizeof(pInChI_Aux_2)); /* djb-rwth: memset_s C11/Annex K variant? */ 1552| 0| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1552:25): [True: 0, False: 0] ------------------ 1553| 0| { 1554| 0| pInChI_1[0][j] = pINChI[iINChI1][k1][j]; 1555| 0| pInChI_Aux_1[0][j] = pINChI_Aux[iINChI1][k1][j]; 1556| 0| } 1557| 0| pInChI_2[INCHI_BAS] = pInChI_1; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1558| 0| pInChI_Aux_2[INCHI_BAS] = pInChI_Aux_1; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1559| | /* make sure purely reconnected InChI is marked as ReChI, not InChI */ 1560| 0| if (bHasSomeReconnected && ------------------ | Branch (1560:17): [True: 0, False: 0] ------------------ 1561| 0| (bInChIHasReconnectedMetal(pInChI_1[0][TAUT_YES]) || ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1561:18): [True: 0, False: 0] ------------------ 1562| 0| bInChIHasReconnectedMetal(pInChI_1[0][TAUT_NON]))) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1562:21): [True: 0, False: 0] ------------------ 1563| 0| { 1564| 0| bSortPrintINChIFlags = FLAG_SORT_PRINT_ReChI_PREFIX; ------------------ | | 666| 0|#define FLAG_SORT_PRINT_ReChI_PREFIX 64 /* Output ReChI instead of InChI */ ------------------ 1565| 0| } 1566| 0| else 1567| 0| { 1568| 0| bSortPrintINChIFlags = 0; 1569| 0| } 1570| 0| INCHI_HEAPCHK 1571| 0| nRet1 = SortAndPrintINChI(pCG, pOut, strbuf, pLog, ip, 1572| 0| NULL /*orig_inp_data*/, 1573| 0| NULL /*prep_inp_data*/, 1574| 0| NULL /*composite_norm_data*/, 1575| 0| NULL /*pOrigStruct*/, 1576| 0| sd->num_components, sd->num_non_taut, 1577| 0| sd->num_taut, sd->bTautFlags, 1578| 0| sd->bTautFlagsDone, pncFlags, num_inp, 1579| 0| pInChI_2, pInChI_Aux_2, 1580| 0| &bSortPrintINChIFlags, save_opt_bits); 1581| 0| INCHI_HEAPCHK 1582| 0| } 1583| 5.02k| else 1584| 5.02k| { 1585| 5.02k| INCHI_HEAPCHK 1586| | 1587| 5.02k| bSortPrintINChIFlags = 0; 1588| 5.02k| nRet1 = SortAndPrintINChI(pCG, pOut, strbuf, pLog, ip, 1589| 5.02k| NULL /*orig_inp_data*/, NULL /*prep_inp_data*/, 1590| 5.02k| NULL /*composite_norm_data*/, NULL /*pOrigStruct*/, 1591| 5.02k| sd->num_components, sd->num_non_taut, sd->num_taut, 1592| 5.02k| sd->bTautFlags, sd->bTautFlagsDone, pncFlags, num_inp, 1593| 5.02k| pINChI, pINChI_Aux, &bSortPrintINChIFlags, 1594| 5.02k| save_opt_bits); 1595| 5.02k| INCHI_HEAPCHK 1596| 5.02k| } 1597| 5.02k| if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 13| 10.0k|#define _IS_FATAL 3 ------------------ if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 12| 5.02k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1597:13): [True: 0, False: 5.02k] | Branch (1597:35): [True: 0, False: 5.02k] ------------------ 1598| 0| { 1599| 0| break; 1600| 0| } 1601| 5.02k| } 1602| | 1603| 5.02k| INCHI_HEAPCHK 1604| 5.02k| FreeAllINChIArrays(pINChI, pINChI_Aux, num_components); 1605| 5.02k| INCHI_HEAPCHK 1606| | 1607| 15.0k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 15.0k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1607:26): [True: 10.0k, False: 5.02k] ------------------ 1608| 10.0k| { 1609| 30.1k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 30.1k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1609:25): [True: 20.1k, False: 10.0k] ------------------ 1610| 20.1k| { 1611| 20.1k| if (OneInput->nNumProtons[iINChI][j].pNumProtons) ------------------ | Branch (1611:21): [True: 0, False: 20.1k] ------------------ 1612| 0| { 1613| 0| inchi_free(OneInput->nNumProtons[iINChI][j].pNumProtons); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1614| 0| OneInput->nNumProtons[iINChI][j].pNumProtons = NULL; 1615| 0| } 1616| 20.1k| } 1617| 10.0k| } 1618| | 1619| | INCHI_HEAPCHK 1620| | 1621| 5.02k| if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 13| 10.0k|#define _IS_FATAL 3 ------------------ if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 12| 5.02k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1621:13): [True: 0, False: 5.02k] | Branch (1621:35): [True: 0, False: 5.02k] ------------------ 1622| 0| { 1623| 0| ret2 = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1624| 0| } 1625| | 1626| 5.02k|exit_error: 1627| | 1628| 5.02k| inchi_strbuf_close(strbuf); 1629| | 1630| 5.02k| return ret2; 1631| 5.02k|} QueueCreate: 33| 376k|{ 34| 376k| QUEUE *q = NULL; 35| 376k| QINT_TYPE *Val = NULL; ------------------ | | 16| 376k|#define QINT_TYPE qInt ------------------ 36| 376k| if (nTotLength < 1 || nSize != ( int )sizeof( QINT_TYPE ) || ------------------ | Branch (36:9): [True: 0, False: 376k] | Branch (36:27): [True: 0, False: 376k] ------------------ 37| 376k| !( q = (QUEUE *) inchi_calloc( 1, sizeof( QUEUE ) ) ) || ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (37:10): [True: 0, False: 376k] ------------------ 38| 376k| !( Val = (QINT_TYPE *) inchi_calloc( nTotLength, nSize ) )) ------------------ | | 1146| 376k|#define inchi_calloc calloc ------------------ | Branch (38:10): [True: 0, False: 376k] ------------------ 39| 0| { 40| 0| if (q) inchi_free( q ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ | Branch (40:13): [True: 0, False: 0] ------------------ 41| 0| return NULL; 42| 0| } 43| 376k| q->Val = Val; 44| | /* q->nSize = nSize; */ 45| 376k| q->nTotLength = nTotLength; 46| | 47| 376k| return q; 48| 376k|} QueueAdd: 53| 352k|{ 54| 352k| if (q && Val && q->nLength < q->nTotLength) ------------------ | Branch (54:9): [True: 352k, False: 0] | Branch (54:14): [True: 352k, False: 0] | Branch (54:21): [True: 352k, False: 0] ------------------ 55| 352k| { 56| 352k| q->Val[( q->nFirst + q->nLength ) % q->nTotLength] = *Val; 57| 352k| q->nLength++; 58| 352k| return q->nLength; 59| 352k| } 60| | 61| 0| return -1; 62| 352k|} QueueGet: 67| 352k|{ 68| 352k| if (q && Val && q->nLength > 0) ------------------ | Branch (68:9): [True: 352k, False: 0] | Branch (68:14): [True: 352k, False: 0] | Branch (68:21): [True: 352k, False: 0] ------------------ 69| 352k| { 70| 352k| *Val = q->Val[q->nFirst]; 71| | /* new: do not allow to overwrite the retrieved value */ 72| 352k| q->nFirst = ( q->nFirst == q->nTotLength - 1 ) ? 0 : q->nFirst + 1; ------------------ | Branch (72:21): [True: 0, False: 352k] ------------------ 73| 352k| q->nLength--; 74| | /* -- old -- 75| | if ( -- q->nLength ) { 76| | q->nFirst = (q->nFirst == q->nTotLength - 1)? 0 : q->nFirst + 1; 77| | } 78| | */ 79| 352k| return q->nLength; 80| 352k| } 81| | 82| 0| return -1; 83| 352k|} QueueGetAny: 88| 352k|{ 89| 352k| if (0 <= ord && ord < q->nTotLength) ------------------ | Branch (89:9): [True: 352k, False: 0] | Branch (89:21): [True: 352k, False: 0] ------------------ 90| 352k| { 91| 352k| *Val = q->Val[ord]; 92| 352k| return 1; /* success */ 93| 352k| } 94| 0| else 95| 0| { 96| 0| return -1; /* error */ 97| 0| } 98| 352k|} QueueDelete: 169| 376k|{ 170| 376k| if (q) ------------------ | Branch (170:9): [True: 376k, False: 0] ------------------ 171| 376k| { 172| 376k| if (q->Val) inchi_free( q->Val ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ | Branch (172:13): [True: 376k, False: 0] ------------------ 173| 376k| inchi_free( q ); ------------------ | | 1152| 376k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 376k, False: 0] | | | Branch (1152:50): [Folded, False: 376k] | | ------------------ ------------------ 174| 376k| } 175| | 176| | return NULL; 177| 376k|} QueueReinit: 182| 77.5k|{ 183| 77.5k| if (q) ------------------ | Branch (183:9): [True: 77.5k, False: 0] ------------------ 184| 77.5k| { 185| 77.5k| q->nFirst = 0; 186| 77.5k| q->nLength = 0; 187| | /* memset( q->Val, 0, q->nTotLength*sizeof(q->Val[0])); */ /* for debug only */ 188| 77.5k| return q->nTotLength; 189| 77.5k| } 190| | 191| 0| return -1; 192| 77.5k|} QueueLength: 197| 274k|{ 198| 274k| if (q) ------------------ | Branch (198:9): [True: 274k, False: 0] ------------------ 199| 274k| { 200| 274k| return q->nLength; 201| 274k| } 202| 0| else 203| 0| { 204| 0| return 0; 205| 0| } 206| 274k|} QueueWrittenLength: 211| 77.5k|{ 212| 77.5k| if (q) ------------------ | Branch (212:9): [True: 77.5k, False: 0] ------------------ 213| 77.5k| { 214| 77.5k| int len = q->nFirst + q->nLength; 215| 77.5k| return ( len > q->nTotLength ) ? q->nTotLength : len; ------------------ | Branch (215:16): [True: 0, False: 77.5k] ------------------ 216| 77.5k| } 217| 0| else 218| 0| { 219| 0| return 0; 220| 0| } 221| 77.5k|} GetMinRingSize: 232| 77.5k|{ 233| 77.5k| int qLen, i, j; 234| 77.5k| AT_RANK nCurLevel, nRingSize, nMinRingSize = MAX_ATOMS + 1; ------------------ | | 15| 77.5k|#define MAX_ATOMS 32766 ------------------ 235| 77.5k| qInt at_no, next; 236| 77.5k| int iat_no, inext; 237| | 238| 274k| while ((qLen = QueueLength( q ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (238:12): [True: 196k, False: 77.3k] ------------------ 239| 196k| { 240| | /* traverse the next level (next outer ring) */ 241| 548k| for (i = 0; i < qLen; i++) ------------------ | Branch (241:21): [True: 352k, False: 196k] ------------------ 242| 352k| { 243| 352k| if (0 <= QueueGet( q, &at_no )) ------------------ | Branch (243:17): [True: 352k, False: 0] ------------------ 244| 352k| { 245| 352k| iat_no = (int) at_no; 246| 352k| nCurLevel = nAtomLevel[iat_no] + 1; 247| 352k| if (2 * nCurLevel > nMaxRingSize + 4) ------------------ | Branch (247:21): [True: 230, False: 351k] ------------------ 248| 230| { 249| | /* 2*nCurLevel = nRingSize + 3 + k, k = 0 or 1 */ 250| 230| if (nMinRingSize < MAX_ATOMS + 1) ------------------ | | 15| 230|#define MAX_ATOMS 32766 ------------------ | Branch (250:25): [True: 80, False: 150] ------------------ 251| 80| { 252| 80| return ( nMinRingSize >= nMaxRingSize ) ? 0 : nMinRingSize; ------------------ | Branch (252:32): [True: 53, False: 27] ------------------ 253| 80| } 254| 150| return 0; /* min. ring size > nMaxRingSize */ 255| 230| } 256| 1.00M| for (j = 0; j < atom[iat_no].valence; j++) ------------------ | Branch (256:29): [True: 650k, False: 351k] ------------------ 257| 650k| { 258| 650k| next = (qInt) atom[iat_no].neighbor[j]; 259| 650k| inext = (int) next; 260| 650k| if (!nAtomLevel[inext]) ------------------ | Branch (260:25): [True: 194k, False: 456k] ------------------ 261| 194k| { 262| | /* the at_no neighbor has not been traversed yet. Add it to the queue */ 263| 194k| if (0 <= QueueAdd( q, &next )) ------------------ | Branch (263:29): [True: 194k, False: 0] ------------------ 264| 194k| { 265| 194k| nAtomLevel[inext] = nCurLevel; 266| 194k| cSource[inext] = cSource[iat_no]; /* keep the path number */ 267| 194k| } 268| 0| else 269| 0| { 270| 0| return -1; /* error */ 271| 0| } 272| 194k| } 273| 456k| else 274| 456k| { 275| 456k| if (nAtomLevel[inext] + 1 >= nCurLevel && ------------------ | Branch (275:29): [True: 83.6k, False: 372k] ------------------ 276| 83.6k| cSource[inext] != cSource[iat_no] ------------------ | Branch (276:33): [True: 73.4k, False: 10.2k] ------------------ 277| | /* && cSource[(int)next] != -1 */ 278| 456k| ) 279| 73.4k| { 280| | /* found a ring closure */ 281| | /* debug */ 282| 73.4k| if (cSource[inext] == -1) ------------------ | Branch (282:33): [True: 0, False: 73.4k] ------------------ 283| 0| { 284| 0| return -1; /* error */ 285| 0| } 286| 73.4k| if (( nRingSize = nAtomLevel[inext] + nCurLevel - 2 ) < nMinRingSize) ------------------ | Branch (286:33): [True: 42.2k, False: 31.1k] ------------------ 287| 42.2k| { 288| 42.2k| nMinRingSize = nRingSize; 289| 42.2k| } 290| | /* return (nRingSize >= nMaxRingSize)? 0 : nRingSize; */ 291| 73.4k| } 292| 456k| } 293| 650k| } 294| 351k| } 295| 0| else 296| 0| { 297| 0| return -1; /* error */ 298| 0| } 299| 352k| } 300| 196k| } 301| | 302| 77.3k| if (nMinRingSize < MAX_ATOMS + 1) ------------------ | | 15| 77.3k|#define MAX_ATOMS 32766 ------------------ | Branch (302:9): [True: 42.2k, False: 35.1k] ------------------ 303| 42.2k| { 304| 42.2k| return ( nMinRingSize >= nMaxRingSize ) ? 0 : nMinRingSize; ------------------ | Branch (304:16): [True: 1.46k, False: 40.7k] ------------------ 305| 42.2k| } 306| | 307| 35.1k| return 0; 308| 77.3k|} is_bond_in_Nmax_memb_ring: 334| 77.5k|{ 335| 77.5k| int nMinRingSize = -1, i; 336| 77.5k| qInt n; 337| 77.5k| int nTotLen; 338| | 339| 77.5k| if (nMaxRingSize < 3) ------------------ | Branch (339:9): [True: 0, False: 77.5k] ------------------ 340| 0| { 341| 0| return 0; 342| 0| } 343| | 344| 77.5k| QueueReinit( q ); 345| | 346| | /* mark the starting atom */ 347| 77.5k| nAtomLevel[at_no] = 1; 348| 77.5k| cSource[at_no] = -1; 349| | /* add neighbors */ 350| 235k| for (i = 0; i < atom[at_no].valence; i++) ------------------ | Branch (350:17): [True: 158k, False: 77.5k] ------------------ 351| 158k| { 352| 158k| n = (qInt) atom[at_no].neighbor[i]; 353| 158k| nAtomLevel[(int) n] = 2; 354| 158k| cSource[(int) n] = 1 + ( i == neigh_ord ); 355| 158k| QueueAdd( q, &n ); 356| 158k| } 357| | 358| 77.5k| nMinRingSize = GetMinRingSize( atom, q, nAtomLevel, cSource, nMaxRingSize ); 359| | /* cleanup */ 360| 77.5k| nTotLen = QueueWrittenLength( q ); 361| 429k| for (i = 0; i < nTotLen; i++) ------------------ | Branch (361:17): [True: 352k, False: 77.5k] ------------------ 362| 352k| { 363| 352k| if (0 < QueueGetAny( q, &n, i )) ------------------ | Branch (363:13): [True: 352k, False: 0] ------------------ 364| 352k| { 365| 352k| nAtomLevel[(int) n] = 0; 366| 352k| cSource[(int) n] = 0; 367| 352k| } 368| 352k| } 369| 77.5k| nAtomLevel[at_no] = 0; 370| 77.5k| cSource[at_no] = 0; 371| | 372| | /* 373| | if ( nAtomLevel ) 374| | inchi_free ( nAtomLevel ); 375| | if ( cSource ) 376| | inchi_free ( cSource ); 377| | QueueDelete( q ); 378| | */ 379| | 380| 77.5k| return nMinRingSize; 381| 77.5k|} is_atom_in_3memb_ring: 386| 7.90k|{ 387| 7.90k| AT_NUMB neigh_neigh; 388| 7.90k| int i, j, k, val, val_neigh, neigh; 389| | 390| 7.90k| if (atom[at_no].nNumAtInRingSystem < 3) ------------------ | Branch (390:9): [True: 1.43k, False: 6.46k] ------------------ 391| 1.43k| { 392| 1.43k| return 0; 393| 1.43k| } 394| | 395| 13.3k| for (i = 0, val = atom[at_no].valence; i < val; i++) ------------------ | Branch (395:44): [True: 10.7k, False: 2.60k] ------------------ 396| 10.7k| { 397| 10.7k| neigh = (int) atom[at_no].neighbor[i]; 398| 10.7k| if (atom[at_no].nRingSystem != atom[neigh].nRingSystem) ------------------ | Branch (398:13): [True: 1.29k, False: 9.41k] ------------------ 399| 1.29k| { 400| 1.29k| continue; 401| 1.29k| } 402| 25.6k| for (j = 0, val_neigh = atom[neigh].valence; j < val_neigh; j++) ------------------ | Branch (402:54): [True: 20.0k, False: 5.55k] ------------------ 403| 20.0k| { 404| 20.0k| neigh_neigh = atom[neigh].neighbor[j]; 405| 20.0k| if ((int) neigh_neigh == at_no) ------------------ | Branch (405:17): [True: 8.44k, False: 11.6k] ------------------ 406| 8.44k| { 407| 8.44k| continue; 408| 8.44k| } 409| 36.5k| for (k = 0; k < val; k++) ------------------ | Branch (409:25): [True: 28.7k, False: 7.78k] ------------------ 410| 28.7k| { 411| 28.7k| if (atom[at_no].neighbor[k] == neigh_neigh) ------------------ | Branch (411:21): [True: 3.86k, False: 24.8k] ------------------ 412| 3.86k| { 413| 3.86k| return 1; 414| 3.86k| } 415| 28.7k| } 416| 11.6k| } 417| 9.41k| } 418| | 419| 2.60k| return 0; 420| 6.46k|} clear_t_group_info: 475| 146k|{ 476| 146k| if (!ti) ------------------ | Branch (476:9): [True: 0, False: 146k] ------------------ 477| 0| { 478| 0| return; 479| 0| } 480| 146k| else 481| 146k| { 482| 146k| T_GROUP *t_group = ti->t_group; 483| 146k| int max_num_t_groups = ti->max_num_t_groups; 484| 146k| AT_NUMB *tGroupNumber = ti->tGroupNumber; 485| 146k| int num_t_groups = ti->num_t_groups; 486| 146k| AT_NUMB *nEndpointAtomNumber = ti->nEndpointAtomNumber; 487| 146k| int nNumEndpoints = ti->nNumEndpoints; 488| 146k| AT_NUMB *nIsotopicEndpointAtomNumber = ti->nIsotopicEndpointAtomNumber; 489| 146k| int nNumIsotopicEndpoints = ti->nNumIsotopicEndpoints; 490| 146k| memset( ti, 0, sizeof( *ti ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 491| 146k| if (t_group) ------------------ | Branch (491:13): [True: 0, False: 146k] ------------------ 492| 0| { 493| 0| memset( t_group, 0, sizeof( t_group[0] )*max_num_t_groups ); /* djb-rwth: memset_s C11/Annex K variant? */ 494| 0| } 495| 146k| else 496| 146k| { 497| 146k| max_num_t_groups = 0; 498| 146k| } 499| 146k| if (tGroupNumber) ------------------ | Branch (499:13): [True: 0, False: 146k] ------------------ 500| 0| { 501| 0| memset( tGroupNumber, 0, sizeof( tGroupNumber[0] )*num_t_groups ); /* djb-rwth: memset_s C11/Annex K variant? */ 502| 0| } 503| 146k| else 504| 146k| { 505| 146k| num_t_groups = 0; 506| 146k| } 507| 146k| if (nEndpointAtomNumber) ------------------ | Branch (507:13): [True: 0, False: 146k] ------------------ 508| 0| { 509| 0| memset( nEndpointAtomNumber, 0, sizeof( nEndpointAtomNumber[0] )*nNumEndpoints ); /* djb-rwth: memset_s C11/Annex K variant? */ 510| 0| } 511| 146k| else 512| 146k| { 513| 146k| nNumEndpoints = 0; 514| 146k| } 515| 146k| if (nIsotopicEndpointAtomNumber) ------------------ | Branch (515:13): [True: 0, False: 146k] ------------------ 516| 0| { 517| 0| memset( nIsotopicEndpointAtomNumber, 0, sizeof( nIsotopicEndpointAtomNumber[0] )*nNumIsotopicEndpoints ); /* djb-rwth: memset_s C11/Annex K variant? */ 518| 0| } 519| 146k| else 520| 146k| { 521| 146k| nNumIsotopicEndpoints = 0; 522| 146k| } 523| | 524| 146k| ti->t_group = t_group; 525| 146k| ti->max_num_t_groups = max_num_t_groups; 526| 146k| ti->tGroupNumber = tGroupNumber; 527| 146k| ti->num_t_groups = num_t_groups; 528| 146k| ti->nEndpointAtomNumber = nEndpointAtomNumber; 529| 146k| ti->nNumEndpoints = nNumEndpoints; 530| 146k| ti->nIsotopicEndpointAtomNumber = nIsotopicEndpointAtomNumber; 531| | 532| 146k| ti->nNumIsotopicEndpoints = nNumIsotopicEndpoints; 533| 146k| } 534| | 535| 146k| return; 536| 146k|} GetTgroupInfoFromInChI: 544| 146k|{ 545| 146k| int ret, i, j, k, itg, num_atoms, len_tg, num_t_groups; /* djb-rwth: removing redundant variables */ 546| 146k| AT_NUMB *tGroupNumber = NULL; 547| | /* djb-rwth: removing redundant variables */ 548| 146k| AT_NUMB *tiGroupNumber = NULL; 549| | 550| 146k| ret = 0; 551| | 552| 146k| clear_t_group_info( ti ); 553| 146k| if (pInChI && pInChI->lenTautomer > 1 && ------------------ | Branch (553:9): [True: 146k, False: 0] | Branch (553:19): [True: 1.24k, False: 145k] ------------------ 554| 1.24k| pInChI->nTautomer && pInChI->nTautomer[0] > 0) ------------------ | Branch (554:10): [True: 1.24k, False: 0] | Branch (554:31): [True: 1.24k, False: 0] ------------------ 555| 1.24k| { 556| 1.24k| num_atoms = pInChI->nNumberOfAtoms; 557| | /* djb-rwth: removing redundant code */ 558| 1.24k| num_t_groups = pInChI->nTautomer[0]; 559| 1.24k| len_tg = pInChI->lenTautomer - T_GROUP_HDR_LEN*pInChI->nTautomer[0] - 1; /* number of endpoints */ ------------------ | | 72| 1.24k|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 1.24k|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 560| | 561| | /* allocation ti->t_group */ 562| 1.24k| if (ti->max_num_t_groups != num_atoms / 2 + 1 || !ti->t_group) ------------------ | Branch (562:13): [True: 1.24k, False: 0] | Branch (562:58): [True: 0, False: 0] ------------------ 563| 1.24k| { 564| 1.24k| ti->max_num_t_groups = num_atoms / 2 + 1; 565| 1.24k| if (ti->t_group) ------------------ | Branch (565:17): [True: 0, False: 1.24k] ------------------ 566| 0| inchi_free( ti->t_group ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 567| 1.24k| ti->t_group = (T_GROUP *) inchi_calloc( (long long)ti->max_num_t_groups + 1, sizeof( ti->t_group[0] ) ); /* djb-rwth: correcting 0 bytes allocation */ ------------------ | | 1146| 1.24k|#define inchi_calloc calloc ------------------ 568| 1.24k| } 569| | 570| | /* allocation ti->tGroupNumber */ 571| 1.24k| if (ti->num_t_groups != num_t_groups || !ti->tGroupNumber) ------------------ | Branch (571:13): [True: 1.24k, False: 0] | Branch (571:49): [True: 0, False: 0] ------------------ 572| 1.24k| { 573| 1.24k| ti->num_t_groups = num_t_groups; 574| 1.24k| if (ti->tGroupNumber) ------------------ | Branch (574:17): [True: 0, False: 1.24k] ------------------ 575| 0| inchi_free( ti->tGroupNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 576| 1.24k| ti->tGroupNumber = (AT_NUMB *) inchi_calloc( ( (long long)ti->num_t_groups + 1 )*TGSO_TOTAL_LEN, sizeof( ti->tGroupNumber[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 1.24k|#define inchi_calloc calloc ------------------ ti->tGroupNumber = (AT_NUMB *) inchi_calloc( ( (long long)ti->num_t_groups + 1 )*TGSO_TOTAL_LEN, sizeof( ti->tGroupNumber[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 141| 1.24k|#define TGSO_TOTAL_LEN 4 ------------------ 577| 1.24k| } 578| | 579| | /* allocation ti->tGroupNumber */ 580| 1.24k| if (len_tg != ti->nNumEndpoints || !ti->nEndpointAtomNumber) ------------------ | Branch (580:13): [True: 1.24k, False: 0] | Branch (580:44): [True: 0, False: 0] ------------------ 581| 1.24k| { 582| 1.24k| ti->nNumEndpoints = len_tg; 583| 1.24k| if (ti->nEndpointAtomNumber) ------------------ | Branch (583:17): [True: 0, False: 1.24k] ------------------ 584| 0| inchi_free( ti->nEndpointAtomNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 585| 1.24k| ti->nEndpointAtomNumber = (AT_NUMB *) inchi_calloc( (long long)len_tg + 1, sizeof( ti->nEndpointAtomNumber[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 1.24k|#define inchi_calloc calloc ------------------ 586| 1.24k| } 587| | 588| | /* check */ 589| 1.24k| if (!ti->t_group || !ti->tGroupNumber || !ti->nEndpointAtomNumber) ------------------ | Branch (589:13): [True: 0, False: 1.24k] | Branch (589:29): [True: 0, False: 1.24k] | Branch (589:50): [True: 0, False: 1.24k] ------------------ 590| 0| { 591| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 592| 0| goto exit_function; 593| 0| } 594| | 595| 1.24k| tGroupNumber = ti->tGroupNumber; 596| | /* djb-rwth: removing redundant code */ 597| 1.24k| tiGroupNumber = tGroupNumber + TGSO_SYMM_IORDER * (long long)ti->num_t_groups; /* djb-rwth: cast operator added */ ------------------ | | 139| 1.24k|#define TGSO_SYMM_IORDER 2 /* tiGroupNumber: isotopic symmetry rank sorting order */ ------------------ 598| | 599| | 600| | INCHI_HEAPCHK 601| | 602| 1.24k| j = 1; /* index in pInChI->nTautomer[] */ 603| 1.24k| i = 0; /* index in ti->nEndpointAtomNumber[] */ 604| | 605| | /* djb-rwth: fixing oss-fuzz issues #67681, #67641 */ 606| 3.52k| for (itg = 0; itg < pInChI->nTautomer[0] && itg <= ti->max_num_t_groups; itg++) ------------------ | Branch (606:23): [True: 2.28k, False: 1.23k] | Branch (606:53): [True: 2.28k, False: 4] ------------------ 607| 2.28k| { 608| 2.28k| len_tg = pInChI->nTautomer[j]; /* t-group length not including pInChI->nTautomer[j] */ 609| 2.28k| ti->t_group[itg].num[0] = pInChI->nTautomer[j + 1] + pInChI->nTautomer[j + 2]; /* num mobile H & (-) */ 610| 2.28k| ti->t_group[itg].num[1] = pInChI->nTautomer[j + 2]; /* num mobile (-) */ 611| 2.28k| tGroupNumber[itg] = tiGroupNumber[itg] = itg; /* index */ 612| 2.28k| ti->t_group[itg].nGroupNumber = /*tSymmRank[itg] = tiSymmRank[itg] =*/ itg + 1; /* t-group number */ 613| 2.28k| j += T_GROUP_HDR_LEN; /* skip t-group header */ ------------------ | | 72| 2.28k|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 2.28k|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 614| 2.28k| len_tg -= T_GROUP_HDR_LEN - 1; ------------------ | | 72| 2.28k|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 2.28k|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 615| | 616| 2.28k| ti->t_group[itg].nNumEndpoints = len_tg; 617| 2.28k| ti->t_group[itg].nFirstEndpointAtNoPos = i; 618| | 619| 20.8k| while (len_tg > 0) ------------------ | Branch (619:20): [True: 18.5k, False: 2.28k] ------------------ 620| 18.5k| { 621| 18.5k| k = ti->nEndpointAtomNumber[i] = pInChI->nTautomer[j] - 1; /* djb-rwth: buffer overrun avoided implicitly in loop condition */ 622| 18.5k|#if ( FIX_GAF_2019_1==1 ) 623| 18.5k| if (k<0 || k>num_atoms) ------------------ | Branch (623:21): [True: 0, False: 18.5k] | Branch (623:28): [True: 0, False: 18.5k] ------------------ 624| 0| { 625| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 626| 0| goto exit_function; 627| 0| } 628| 18.5k|#endif 629| 18.5k| if (at) ------------------ | Branch (629:21): [True: 16.5k, False: 2.01k] ------------------ 630| 16.5k| { 631| 16.5k| at[k].endpoint = itg + 1; 632| 16.5k| } 633| 18.5k| if (endpoint) ------------------ | Branch (633:21): [True: 2.01k, False: 16.5k] ------------------ 634| 2.01k| { 635| 2.01k| endpoint[k] = itg + 1; 636| 2.01k| } 637| 18.5k| len_tg--; 638| 18.5k| j++; 639| 18.5k| i++; 640| 18.5k| } 641| 2.28k| } 642| | 643| 1.24k| if (i != ti->nNumEndpoints) ------------------ | Branch (643:13): [True: 4, False: 1.23k] ------------------ 644| 4| { 645| 4| ret = RI_ERR_PROGR; ------------------ | | 17| 4|#define RI_ERR_PROGR (-3) ------------------ 646| 4| } 647| | 648| 1.24k| INCHI_HEAPCHK 649| 1.24k| } 650| | 651| 146k|exit_function: 652| 146k| return ret; 653| 146k|} FillOutpStructEndpointFromInChI: 658| 1.14k|{ 659| 1.14k| int num_at = pInChI->nNumberOfAtoms; 660| 1.14k| AT_NUMB *endpoint = *pEndpoint; 661| 1.14k| int itg, i, j, k, len_tg; 662| | 663| 1.14k| if (!endpoint && !( endpoint = (AT_NUMB*) inchi_malloc( num_at * sizeof( endpoint[0] ) ) )) ------------------ | | 1143| 1.14k|#define inchi_malloc malloc ------------------ | Branch (663:9): [True: 1.14k, False: 0] | Branch (663:22): [True: 0, False: 1.14k] ------------------ 664| 0| { 665| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 666| 0| } 667| | 668| 1.14k| memset( endpoint, 0, num_at * sizeof( endpoint[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 669| 1.14k| if (pInChI->lenTautomer <= 1 || !pInChI->nTautomer) ------------------ | Branch (669:9): [True: 548, False: 594] | Branch (669:37): [True: 0, False: 594] ------------------ 670| 548| { 671| 548| goto exit_function; 672| 548| } 673| | 674| 594| j = 1; /* index in pInChI->nTautomer[] */ 675| 594| i = 0; /* index in ti->nEndpointAtomNumber[] */ 676| 1.30k| for (itg = 0; itg < pInChI->nTautomer[0]; itg++) ------------------ | Branch (676:19): [True: 715, False: 594] ------------------ 677| 715| { 678| 715| len_tg = pInChI->nTautomer[j]; /* t-group length not including pInChI->nTautomer[j] */ 679| 715| j += T_GROUP_HDR_LEN; /* skip t-group header */ ------------------ | | 72| 715|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 715|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 680| 715| len_tg -= T_GROUP_HDR_LEN - 1; ------------------ | | 72| 715|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 715|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 681| | /* ti->t_group[itg].nNumEndpoints = len_tg; */ 682| 2.73k| for (; 0 < len_tg--; j++, i++) ------------------ | Branch (682:16): [True: 2.02k, False: 715] ------------------ 683| 2.02k| { 684| 2.02k| k = pInChI->nTautomer[j] - 1; 685| 2.02k| endpoint[k] = itg + 1; 686| 2.02k| } 687| 715| } 688| | 689| 1.14k|exit_function: 690| 1.14k| *pEndpoint = endpoint; 691| | 692| 1.14k| return 0; 693| 594|} cmp_charge_val: 698| 1.00M|{ 699| 1.00M| const CHARGE_VAL *p1 = (const CHARGE_VAL *) a1; 700| 1.00M| const CHARGE_VAL *p2 = (const CHARGE_VAL *) a2; 701| 1.00M| int diff; 702| | 703| 1.00M| if ((diff = (int) p1->nValence - (int) p2->nValence)) /* smaller valence first */ /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (703:9): [True: 803k, False: 199k] ------------------ 704| 803k| return diff; 705| 199k| if ((diff = abs( (int) p1->nCharge ) - abs( (int) p2->nCharge ))) /* smaller abs charge first */ /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (705:9): [True: 99.3k, False: 100k] ------------------ 706| 99.3k| return diff; 707| 100k| if ((diff = (int) p2->nCharge - (int) p1->nCharge)) /* (+) first, (-) second */ /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (707:9): [True: 100k, False: 0] ------------------ 708| 100k| return diff; 709| 0| return (int) p1->nValenceOrderingNumber - (int) p2->nValenceOrderingNumber; 710| 100k|} bMayBeACationInMobileHLayer: 715| 307k|{ 716| 307k| int j, neigh; 717| 307k| U_CHAR cVal; /* moved from below 2024-09-01 DT */ 718| 307k| if (!bMobileH || !at[iat].num_H) ------------------ | Branch (718:9): [True: 15.6k, False: 291k] | Branch (718:22): [True: 290k, False: 1.72k] ------------------ 719| 305k| { 720| 305k| return 1; 721| 305k| } 722| | 723| | /* cVal, cation valence */ 724| 1.72k| switch ( at[iat].el_number ) { 725| 333| case EL_NUMBER_N: /* fallthrough */ ------------------ | | 14| 333|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (725:9): [True: 333, False: 1.39k] ------------------ 726| 358| case EL_NUMBER_P: ------------------ | | 18| 358|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (726:9): [True: 25, False: 1.69k] ------------------ 727| 358| cVal = 4; 728| 358| break; 729| 156| case EL_NUMBER_O: /* fallthrough */ ------------------ | | 15| 156|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (729:9): [True: 156, False: 1.56k] ------------------ 730| 387| case EL_NUMBER_S: ------------------ | | 19| 387|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (730:9): [True: 231, False: 1.49k] ------------------ 731| 522| case EL_NUMBER_SE: ------------------ | | 23| 522|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (731:9): [True: 135, False: 1.58k] ------------------ 732| 671| case EL_NUMBER_TE: ------------------ | | 26| 671|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (732:9): [True: 149, False: 1.57k] ------------------ 733| 671| cVal = 3; 734| 671| break; 735| 694| default: ------------------ | Branch (735:9): [True: 694, False: 1.02k] ------------------ 736| 694| return 1; 737| 1.72k| } 738| | 739| 1.02k| if (at[iat].valence + at[iat].num_H <= cVal) ------------------ | Branch (739:9): [True: 986, False: 43] ------------------ 740| 986| { 741| 1.80k| for (j = 0; j < at[iat].valence; j++) ------------------ | Branch (741:21): [True: 825, False: 978] ------------------ 742| 825| { 743| 825| neigh = at[iat].neighbor[j]; 744| 825| if (at[neigh].valence == 4 && at[neigh].chem_bonds_valence == 4 && !at[neigh].num_H && ------------------ | Branch (744:17): [True: 66, False: 759] | Branch (744:43): [True: 66, False: 0] | Branch (744:80): [True: 66, False: 0] ------------------ 745| 66| pVA[neigh].cNumValenceElectrons == 3 && pVA[neigh].cPeriodicRowNumber == 1) ------------------ | Branch (745:21): [True: 14, False: 52] | Branch (745:61): [True: 8, False: 6] ------------------ 746| 8| { 747| 8| return 1; 748| 8| } 749| 825| } 750| 978| return 0; 751| 986| } 752| 43| return 1; 753| 1.02k|} clean_charge_val: 759| 147k|{ 760| 147k| inp_ATOM *at = atom + iat; 761| 147k| int nPeriodicNum = at->el_number; 762| 147k| int num_bonds = at->valence; 763| 147k| int min_valence = at->valence + at->num_H; 764| | /* in fixed-H case treat tautomeric -O as tautomeric to avoid #O(+) */ 765| 147k| int bTautomeric = ( at->endpoint != 0 ); 766| 147k| int bFixedHTautomeric = !bMobileH && ( endpoint && endpoint[iat] && ------------------ | Branch (766:29): [True: 7.53k, False: 140k] | Branch (766:44): [True: 7.53k, False: 0] | Branch (766:56): [True: 1.57k, False: 5.96k] ------------------ 767| 1.57k| pVA[iat].cNumValenceElectrons == 6 && 1 == num_bonds && ------------------ | Branch (767:29): [True: 715, False: 857] | Branch (767:67): [True: 621, False: 94] ------------------ 768| 621| !at->num_H && !bIsMetal ); ------------------ | Branch (768:29): [True: 549, False: 72] | Branch (768:43): [True: 549, False: 0] ------------------ 769| | /* int bIsMetal = is_el_a_metal( nPeriodicNum );*/ 770| 147k| int bDoNotAddH = if_skip_add_H( nPeriodicNum ); 771| 147k| int nPeriod, nNumEqAbsCharges; 772| 147k| int nNumValenceEl = get_sp_element_type( nPeriodicNum, &nPeriod ) - 1; 773| | 774| 147k| int i, j; 775| | 776| 147k| if (!len) ------------------ | Branch (776:9): [True: 486, False: 147k] ------------------ 777| 486| return len; 778| | 779| 147k| insertions_sort( pCG, pChargeVal, len, sizeof( pChargeVal[0] ), cmp_charge_val ); 780| | 781| | /* metals -- very preliminary code */ 782| 147k| if (bIsMetal && bDoNotAddH) ------------------ | Branch (782:9): [True: 0, False: 147k] | Branch (782:21): [True: 0, False: 0] ------------------ 783| 0| { 784| |/* keep the 1st found */ 785| 0| return inchi_min( 1, len ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 786| 0| } 787| | /* Mobile-H layer cannot have H on positively charged N, P (all IV), O, S, Se, Te (all III) */ 788| | 789| | /* 790| | if ( abs( pChargeVal[0].nCharge ) > 1 && pChargeVal[0].nValence >= min_valence ) { 791| | return inchi_min( 1, len ); 792| | } 793| | */ 794| 147k| nNumEqAbsCharges = 0; 795| 779k| for (i = j = 0; i < len && j < ( nNumEqAbsCharges ? 3 + nNumEqAbsCharges : 4 ); i++) ------------------ | Branch (795:21): [True: 657k, False: 122k] | Branch (795:32): [True: 641k, False: 15.7k] | Branch (795:38): [True: 16.2k, False: 640k] ------------------ 796| 641k| { 797| | /* for now accept only charge = 0, -1, +1 */ 798| 641k| if (abs( pChargeVal[i].nCharge ) > 1) ------------------ | Branch (798:13): [True: 184k, False: 457k] ------------------ 799| 184k| { 800| 184k| continue; 801| 184k| } 802| 457k| if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( min_valence - 1 ) < pChargeVal[i].nValence) ------------------ | | 34| 457k|#define BOND_TYPE_TRIPLE 3 ------------------ if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( min_valence - 1 ) < pChargeVal[i].nValence) ------------------ | | 33| 457k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (802:13): [True: 342, False: 456k] ------------------ 803| 342| { 804| 342| continue; /* not more than one triple and the rest - double bonds per atom */ 805| 342| } 806| 456k| if (( bTautomeric || (j && bFixedHTautomeric) ) && pChargeVal[i].nCharge < 0) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (806:15): [True: 3.61k, False: 453k] | Branch (806:31): [True: 308k, False: 145k] | Branch (806:36): [True: 1.44k, False: 306k] | Branch (806:60): [True: 1.58k, False: 3.47k] ------------------ 807| 1.58k| { 808| 1.58k| continue; /* negative charge must be included in the tautomeric group */ 809| 1.58k| } 810| 455k| if (( bTautomeric || bFixedHTautomeric ) && pChargeVal[i].nCharge > 0) ------------------ | Branch (810:15): [True: 2.37k, False: 453k] | Branch (810:30): [True: 1.64k, False: 451k] | Branch (810:53): [True: 1.50k, False: 2.51k] ------------------ 811| 1.50k| { 812| 1.50k| continue; /* positive charge for now cannot reach a tautomeric group */ 813| 1.50k| } 814| 453k| if (j && !bMayBeACationInMobileHLayer( atom, pVA, iat, bMobileH ) && pChargeVal[i].nCharge > 0) ------------------ | Branch (814:13): [True: 307k, False: 146k] | Branch (814:18): [True: 978, False: 306k] | Branch (814:78): [True: 286, False: 692] ------------------ 815| 286| { 816| 286| if (i + 1 < len && ------------------ | Branch (816:17): [True: 234, False: 52] ------------------ 817| 234| pChargeVal[i].nValence == pChargeVal[i + 1].nValence && ------------------ | Branch (817:18): [True: 81, False: 153] ------------------ 818| 81| pChargeVal[i].nCharge == -pChargeVal[i + 1].nCharge) ------------------ | Branch (818:18): [True: 81, False: 0] ------------------ 819| 81| { 820| | /* (-) if exists is always after (+) */ 821| 81| i += 1; /* also skip the next element */ 822| 81| } 823| 286| continue; /* in case of Mobile-H, a hydrogen cannot be on a (+)-charged heteroatom */ 824| 286| } 825| | 826| | /* accept same valence opposite charges only for C and its group in Periodic Table */ 827| 453k| if (j && !bTautomeric && ------------------ | Branch (827:13): [True: 307k, False: 146k] | Branch (827:18): [True: 306k, False: 341] ------------------ 828| 306k| pChargeVal[i].nValence == pChargeVal[j - 1].nValence && ------------------ | Branch (828:14): [True: 59.4k, False: 247k] ------------------ 829| 59.4k| pChargeVal[i].nCharge == -pChargeVal[j - 1].nCharge) ------------------ | Branch (829:14): [True: 59.4k, False: 0] ------------------ 830| 59.4k| { 831| 59.4k| if (nNumValenceEl == VALUE_OCTET / 2 && pChargeVal[i].nCharge && !nNumEqAbsCharges) ------------------ | | 26| 59.4k|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ | Branch (831:17): [True: 30.6k, False: 28.8k] | Branch (831:53): [True: 30.6k, False: 0] | Branch (831:78): [True: 30.6k, False: 0] ------------------ 832| 30.6k| { 833| 30.6k| pChargeVal[j++] = pChargeVal[i]; 834| 30.6k| nNumEqAbsCharges++; 835| 30.6k| } 836| 59.4k| continue; 837| 59.4k| } 838| | /* do not accept valence=5 for neutral NHn in case of not Mobile-H 2005-01-26 ???? */ 839| 394k| if (nNumValenceEl == 5 && nPeriod == 1 && at->num_H && ------------------ | Branch (839:13): [True: 195k, False: 198k] | Branch (839:35): [True: 147k, False: 48.5k] | Branch (839:51): [True: 2.56k, False: 144k] ------------------ 840| 2.56k| j && !bMobileH && ------------------ | Branch (840:14): [True: 1.42k, False: 1.14k] | Branch (840:19): [True: 1.24k, False: 175] ------------------ 841| 1.24k| pChargeVal[i].nValence == 5 && !pChargeVal[i].nCharge) ------------------ | Branch (841:14): [True: 521, False: 727] | Branch (841:45): [True: 521, False: 0] ------------------ 842| 521| { 843| 521| continue; 844| 521| } 845| | /* do not accept gaps in allowed valences */ 846| 393k| if (j && pChargeVal[i].nValence > pChargeVal[j - 1].nValence + 1) ------------------ | Branch (846:13): [True: 247k, False: 146k] | Branch (846:18): [True: 9.07k, False: 238k] ------------------ 847| 9.07k| { 848| 9.07k| break; 849| 9.07k| } 850| 384k| pChargeVal[j++] = pChargeVal[i]; 851| 384k| } 852| 147k| len = j; 853| 147k| if (!nNumEqAbsCharges && num_bonds < 3 && len == 4) ------------------ | Branch (853:9): [True: 116k, False: 30.6k] | Branch (853:30): [True: 92.5k, False: 23.9k] | Branch (853:47): [True: 34.5k, False: 57.9k] ------------------ 854| 34.5k| { 855| 34.5k| len--; /* prohibit =S# where # is a triple bond */ 856| 34.5k| } 857| 147k| return len; 858| 147k|} GetAtomRestoreInfo: 880| 1.13M|{ 881| | /* #defines from util.c */ 882| 1.13M|#define MIN_ATOM_CHARGE (-2) 883| 1.13M|#define MAX_ATOM_CHARGE 2 884| 1.13M|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) 885| 1.13M|#define NUM_ATOM_CHARGES (MAX_ATOM_CHARGE - MIN_ATOM_CHARGE + 1) 886| 1.13M|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ 887| | 888| 1.13M| int i, j, j2, k, k2, charge, cur_charge, num_non_bonding_electrons; 889| 1.13M| int nNumStates, nNumSelectedStates, num_H, num_bonds; 890| 1.13M| int nOctetNeutralValenceExcess, nFirstNeutralValenceExcess; 891| 1.13M| int nFoundNeutralValenceExcess, nFoundNeutralValenceOrdNumber; 892| 1.13M| int nLastFoundValenceOrdNumber, nLastFoundValenceState; 893| 1.13M| int cn_bits, cn_bits_array[5], len_cn_bits_array; 894| 1.13M| inp_ATOM* at = atom + iat; 895| 1.13M| VAL_AT* pVA = pVArray + iat; 896| 1.13M| int nPeriodicNum = at->el_number; 897| 1.13M| int cur_chem_valence, cur_chem_valence_fixed, min_chem_valence, known_chem_valence; 898| 1.13M| int metal_bonds_chem_valence, not_metal_bonds_chem_valence, alt_bonds_delta_valence, bonds_chem_valence, bond_type; 899| 1.13M| CHARGE_VAL ChargeVal[NUM_ATOM_CHARGES * MAX_NUM_VALENCES]; 900| | 901| 1.13M| memset(ChargeVal, 0, sizeof(ChargeVal)); 902| | 903| 1.13M| pVA->cDoNotAddH = if_skip_add_H(nPeriodicNum); /* InChI never adds H to this atom */ 904| | /*pVA->cMetal = is_el_a_metal( nPeriodicNum );*/ /* the atom is a metal */ 905| | 906| | /* count bonds to metal atoms; metals have already been marked */ 907| 1.13M| metal_bonds_chem_valence = not_metal_bonds_chem_valence = alt_bonds_delta_valence = 0; 908| | 909| 1.13M| if (pVA->cMetal) ------------------ | Branch (909:9): [True: 449k, False: 683k] ------------------ 910| 449k| { 911| 449k| j = at->valence; /* all bonds to metal */ 912| 496k| for (i = k = j2 = k2 = 0; i < at->valence; i++) ------------------ | Branch (912:35): [True: 47.0k, False: 449k] ------------------ 913| 47.0k| { 914| 47.0k| bond_type = (at->bond_type[i] & BOND_TYPE_MASK); ------------------ | | 189| 47.0k|#define BOND_TYPE_MASK 0x0f ------------------ 915| 47.0k| if (bond_type <= BOND_TYPE_TRIPLE) ------------------ | | 34| 47.0k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (915:17): [True: 46.9k, False: 80] ------------------ 916| 46.9k| { 917| 46.9k| metal_bonds_chem_valence += inchi_max(BOND_TYPE_SINGLE, bond_type); ------------------ | | 138| 46.9k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 46.9k] | | ------------------ ------------------ 918| 46.9k| } 919| 80| else 920| 80| { 921| 80| metal_bonds_chem_valence += BOND_TYPE_SINGLE; ------------------ | | 32| 80|#define BOND_TYPE_SINGLE 1 ------------------ 922| 80| k++; /* count alternating bonds */ 923| 80| } 924| 47.0k| } 925| 449k| } 926| 683k| else 927| 683k| { 928| 1.00M| for (i = j = j2 = k = k2 = 0; i < at->valence; i++) ------------------ | Branch (928:39): [True: 325k, False: 683k] ------------------ 929| 325k| { 930| 325k| bond_type = (at->bond_type[i] & BOND_TYPE_MASK); ------------------ | | 189| 325k|#define BOND_TYPE_MASK 0x0f ------------------ 931| 325k| if (pVArray[(int)at->neighbor[i]].cMetal) ------------------ | Branch (931:17): [True: 40.5k, False: 285k] ------------------ 932| 40.5k| { 933| 40.5k| j++; /* number of bonds to metal atoms */ 934| 40.5k| if (bond_type <= BOND_TYPE_TRIPLE) ------------------ | | 34| 40.5k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (934:21): [True: 40.4k, False: 73] ------------------ 935| 40.4k| { 936| 40.4k| metal_bonds_chem_valence += inchi_max(BOND_TYPE_SINGLE, bond_type); ------------------ | | 138| 40.4k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 40.4k] | | ------------------ ------------------ 937| 40.4k| } 938| 73| else 939| 73| { 940| 73| metal_bonds_chem_valence += BOND_TYPE_SINGLE; ------------------ | | 32| 73|#define BOND_TYPE_SINGLE 1 ------------------ 941| 73| k++; /* count alternating bonds */ 942| 73| } 943| 40.5k| } 944| 285k| else 945| 285k| { 946| 285k| j2++; 947| 285k| if (bond_type <= BOND_TYPE_TRIPLE) ------------------ | | 34| 285k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (947:21): [True: 284k, False: 331] ------------------ 948| 284k| { 949| 284k| not_metal_bonds_chem_valence += inchi_max(BOND_TYPE_SINGLE, bond_type); ------------------ | | 138| 284k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 284k] | | ------------------ ------------------ 950| 284k| } 951| 331| else 952| 331| { 953| 331| not_metal_bonds_chem_valence += BOND_TYPE_SINGLE; ------------------ | | 32| 331|#define BOND_TYPE_SINGLE 1 ------------------ 954| 331| k2++; /* count alternating bonds */ 955| 331| } 956| 285k| } 957| 325k| } 958| 683k| } 959| | 960| 1.13M| bonds_chem_valence = metal_bonds_chem_valence + not_metal_bonds_chem_valence; 961| | 962| 1.13M| if (at->chem_bonds_valence > bonds_chem_valence) ------------------ | Branch (962:9): [True: 302, False: 1.13M] ------------------ 963| 302| { 964| 302| if (at->chem_bonds_valence - bonds_chem_valence > 1) ------------------ | Branch (964:13): [True: 0, False: 302] ------------------ 965| 0| { 966| 0| at->chem_bonds_valence = bonds_chem_valence + 1; /* should not happen */ 967| 0| } 968| 302| alt_bonds_delta_valence = at->chem_bonds_valence - bonds_chem_valence; 969| 302| } 970| | 971| 1.13M| pVA->cNumBondsToMetal = j; 972| | 973| 1.13M| if (nPeriodicNum == EL_NUMBER_H) ------------------ | | 11| 1.13M|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (973:9): [True: 46.4k, False: 1.08M] ------------------ 974| 46.4k| { 975| | /* ignore bridging H; ??? later add ??? */ 976| 46.4k| return 0; 977| 46.4k| } 978| | 979| 1.08M| num_H = at->num_H; 980| 1.08M| num_bonds = at->valence; 981| | 982| 1.08M| if (!num_bonds && !num_H) ------------------ | Branch (982:9): [True: 912k, False: 174k] | Branch (982:23): [True: 909k, False: 2.39k] ------------------ 983| 909k| { 984| 909k| return 0; /* do not know the answer: isolated atom */ 985| 909k| } 986| | /* at the beginning all bonds are single */ 987| 176k| min_chem_valence = num_bonds + num_H; 988| 176k| cur_chem_valence = bonds_chem_valence + alt_bonds_delta_valence + num_H; /* includes double & alternating bond contribution */ 989| | 990| | /* number of non-bonding electrons in case of all single bonds */ 991| 176k| num_non_bonding_electrons = (int)pVA->cNumValenceElectrons - min_chem_valence; 992| | /* Octet rule: charge = bonds_valence + NumValenceElectrons - 8 */ 993| 176k| charge = min_chem_valence + (int)pVA->cNumValenceElectrons - VALUE_OCTET; /* wrong */ ------------------ | | 26| 176k|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ 994| | 995| | /* typical (ad hoc) minimal neutral valence */ 996| 176k| known_chem_valence = (pVA->cNumValenceElectrons > VALUE_OCTET / 2) ? ------------------ | | 26| 176k|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ | Branch (996:26): [True: 113k, False: 62.9k] ------------------ 997| 113k| VALUE_OCTET - pVA->cNumValenceElectrons : ------------------ | | 26| 113k|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ 998| 176k| pVA->cNumValenceElectrons; 999| | /* excess of typical valence over all-single-bonds valence */ 1000| 176k| nOctetNeutralValenceExcess = known_chem_valence - min_chem_valence; 1001| | /* (NB=num.bonds, NV=neutral valence, NVX=neutral valence excess, LFVS=last found valence state, val.=valence) 1002| | 1003| | element NB knownFst octet Last octetNVX firstNVX foundNVX chargeLFVS LFVS 1004| | valence val. NV>= 1005| | 1006| | -B 1 3 3 3 2 2 = 2 +2 1007| | >B 2 3 3 3 1 1 = 1 +1 1008| | >B- 3 3 3 3 0 0 = 0 0 1009| | >B< 4 3 3 3 -1 -1 <> N/A -1 1010| | 1011| | -C 1 4 4 4 3 3 = 3 N/A 1012| | >C 2 4 4 4 2 2 = 2 +2 (-2) 1013| | >C- 3 4 4 4 1 1 = 1 +1 (-1) 1014| | >C< 4 4 4 4 0 0 = 0 0 1015| | C(V) 5 4 4 N/A -1 -1 <> N/A N/A 1016| | 1017| | -Si 1 4 4 4 3 3 = 3 N/A 1018| | >Si 2 4 4 4 2 2 = 2 +2 (-2) 1019| | >Si- 3 4 4 4 1 1 = 1 +1 (-1) 1020| | >Si- 4 4 4 4 0 0 = 0 0 1021| | Si(V) 5 4 4 N/A -1 -1 <> N/A -1 1022| | 1023| | -N 1 3 3 3 2 2 = 2 -2 1024| | >N 2 3 3 3 1 1 = 1 -1 1025| | >N- 3 3 3 3 0 0 = 0 0 (+2) 1026| | >N< 4 3 3 5 -1 -1 <> 1 +1 1027| | N(V) 5 3 3 5 -2 -2 <> 0 0 1028| | N(VI) 6 3 3 N/A -3 -3 <> N/A N/A 1029| | N(VII) 7 3 3 N/A -4 -4 <> N/A N/A 1030| | 1031| | -P 1 3 3 3 2 2 = 2 -2 1032| | >P 2 3 3 3 1 1 = 1 -1 1033| | >P- 3 3 3 3 0 0 = 0 0 (-2, +2) 1034| | >P< 4 3 3 5 -1 -1 <> 1 +1 (-1) 1035| | P(V) 5 3 3 5 -2 -2 <> 0 0 (-2) 1036| | P(VI) 6 3 3 N/A -3 -3 <> N/A -1 1037| | P(VII) 7 3 3 N/A -4 -4 <> N/A -2 1038| | P(VIII) 8 3 3 N/A -5 -5 <> N/A N/A 1039| | 1040| | -O 1 2 2 2 1 1 = 1 -1 1041| | >O 2 2 2 2 0 0 = 0 0 1042| | >O- 3 2 2 N/A -1 -1 <> N/A +1 1043| | >O< 4 2 2 N/A -2 -2 <> N/A +2 1044| | O(V) 5 2 2 N/A -3 -3 <> N/A +1 1045| | O(VI) 6 2 2 N/A -4 -4 <> N/A N/A 1046| | 1047| | -S 1 2 2 2 1 1 = 1 -1 1048| | >S 2 2 2 2 0 0 = 0 0 NPNP - prohibit 1049| | >S- 3 2 2 4 -1 -1 <> 1 +1 (-1) PNPN 1050| | >S< 4 2 2 4 -2 -2 <> 0 0 (+2) 1051| | S(V) 5 2 2 6 -3 -3 <> 1 +1 (-1) 1052| | S(VI) 6 2 2 6 -4 -4 <> 0 0 1053| | S(VII) 7 2 2 N/A -5 -5 <> 0 -1 1054| | S(VIII) 8 2 2 N/A -6 -6 <> N/A N/A 1055| | 1056| | -F 1 1 1 1 0 0 = 0 0 1057| | >F 2 1 1 1 -1 -1 <> N/A +1 1058| | >F- 3 1 1 1 -2 -2 <> N/A +2 1059| | >F< 4 1 1 1 -3 -3 <> N/A N/A 1060| | F(V) 5 1 1 1 -4 -4 <> N/A +2 1061| | F(VI) 6 1 1 1 -5 -5 <> N/A N/A 1062| | 1063| | -Cl 1 1 1 1 0 0 = 0 0 NPNP - prohibit 1064| | >Cl 2 1 1 3 -1 -1 <> 1 +1 PNPN - prohibit 1065| | >Cl- 3 1 1 3 -2 -2 <> 0 0 (+2) NPNP 1066| | >Cl< 4 1 1 5 -3 -3 <> 1 +1 PNPN 1067| | Cl(V) 5 1 1 5 -4 -4 <> 0 0 1068| | Cl(VI) 6 1 1 7 -5 -5 <> 1 +1 1069| | Cl(VII) 7 1 1 7 -6 -6 <> 0 0 1070| | Cl(VIII) 8 1 1 N/A -7 -7 <> N/A N/A 1071| | 1072| | 1073| | NB = num_bonds+num_H 1074| | 1075| | knownFst valence = nFirstNeutralValenceExcess + min_chem_valence 1076| | octet val. = nOctetNeutralValenceExcess + min_chem_valence 1077| | Last NV>= = nFoundNeutralValenceExcess + min_chem_valence 1078| | 1079| | octetNVX = nOctetNeutralValenceExcess 1080| | firstNVX = nFirstNeutralValenceExcess 1081| | foundNVX = nFoundNeutralValenceExcess 1082| | 1083| | chargeLFVS = ChargeVal[nLastFoundValenceState].nCharge 1084| | 1085| | */ 1086| | /* minimal known neutral atom valence; different for Sn(2/4), Tl(1/3), Pb(2/4): (known/typical ad hoc) */ 1087| 176k| known_chem_valence = get_el_valence( nPeriodicNum, 0, 0 ); 1088| | 1089| 176k| if (pSrm->bMetalAddFlower) ------------------ | Branch (1089:9): [True: 176k, False: 0] ------------------ 1090| 176k| { 1091| | /* bond orders of bonds to metal may be as they are (pSrm->nMetalInitBondOrder==1) 1092| | or decreased by one (pSrm->nMetalInitBondOrder==0) 1093| | nMetalInitBondOrder == nMetalMinBondOrder + nMetalInitEdgeFlow 1094| | */ 1095| 176k| cur_chem_valence_fixed = cur_chem_valence - pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitBondOrder ); 1096| 176k| pVA->cInitOrigValenceToMetal = metal_bonds_chem_valence; 1097| 176k| pVA->cInitValenceToMetal = metal_bonds_chem_valence - pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitBondOrder ); 1098| 176k| pVA->cInitFlowToMetal = pVA->cInitValenceToMetal - pVA->cNumBondsToMetal * pSrm->nMetalMinBondOrder; 1099| 176k| if (pVA->cMetal) ------------------ | Branch (1099:13): [True: 26.9k, False: 149k] ------------------ 1100| 26.9k| { 1101| 26.9k| pVA->cInitFreeValences += alt_bonds_delta_valence; 1102| 26.9k| } 1103| 176k| if (pSrm->nMetalInitEdgeFlow < pSrm->nMetalInitBondOrder - pSrm->nMetalMinBondOrder) ------------------ | Branch (1103:13): [True: 0, False: 176k] ------------------ 1104| 0| { 1105| | /* single bond has zero initial flow + 2 radicals at incident atoms */ 1106| 0| if (pVA->cInitFlowToMetal <= pVA->cNumBondsToMetal) ------------------ | Branch (1106:17): [True: 0, False: 0] ------------------ 1107| 0| { 1108| 0| if (pVA->cMetal) ------------------ | Branch (1108:21): [True: 0, False: 0] ------------------ 1109| 0| { 1110| 0| pVA->cInitFreeValences += pVA->cInitFlowToMetal; 1111| 0| } 1112| 0| pVA->cInitFlowToMetal = 0; 1113| 0| } 1114| 0| else 1115| 0| { 1116| 0| if (pVA->cMetal) ------------------ | Branch (1116:21): [True: 0, False: 0] ------------------ 1117| 0| { 1118| 0| pVA->cInitFreeValences += pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitEdgeFlow ); 1119| 0| } 1120| 0| pVA->cInitFlowToMetal -= pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitEdgeFlow ); 1121| 0| } 1122| 0| } 1123| 176k| } 1124| 0| else 1125| 0| { 1126| | /* treat metal atoms as ordinary non-metal atoms */ 1127| 0| cur_chem_valence_fixed = cur_chem_valence; 1128| 0| pVA->cInitFlowToMetal = metal_bonds_chem_valence - pVA->cNumBondsToMetal; 1129| 0| pVA->cInitValenceToMetal = metal_bonds_chem_valence; 1130| 0| pVA->cInitOrigValenceToMetal = metal_bonds_chem_valence; 1131| 0| } 1132| | 1133| | 1134| 176k| if (pVA->cMetal && pSrm->bMetalAddFlower) ------------------ | Branch (1134:9): [True: 26.9k, False: 149k] | Branch (1134:24): [True: 26.9k, False: 0] ------------------ 1135| 26.9k| { 1136| 26.9k| pVA->cnListIndex = cnListIndexMe + 1; ------------------ | | 467| 26.9k|#define cnListIndexMe (17) /* index of {cnMe, cn_bits_Me,... } element of cnList[] */ ------------------ 1137| | /* 1138| | pVA->cInitOrigValenceToMetal += alt_bonds_delta_valence; 1139| | pVA->cInitValenceToMetal += alt_bonds_delta_valence; 1140| | pVA->cInitFreeValences = (pSrm->nMetalInitBondOrder + alt_bonds_delta_valence 1141| | - (pSrm->nMetalMinBondOrder + pSrm->nMetalInitEdgeFlow)) * pVA->cNumBondsToMetal; 1142| | */ 1143| 26.9k| return 0; /* metal */ 1144| 26.9k| } 1145| | 1146| 149k| if (!known_chem_valence) ------------------ | Branch (1146:9): [True: 2.23k, False: 147k] ------------------ 1147| 2.23k| { 1148| | /* a noble gas like He, Ne, ... */ 1149| 2.23k| pVA->cInitFreeValences = at->chem_bonds_valence - at->valence; 1150| 2.23k| return TREAT_ATOM_AS_METAL; /* do not know anything about this atom; needs 2nd pass */ ------------------ | | 258| 2.23k|#define TREAT_ATOM_AS_METAL 99 ------------------ 1151| 2.23k| } 1152| | 1153| 147k| nFirstNeutralValenceExcess = known_chem_valence - min_chem_valence; 1154| | 1155| 147k| nFoundNeutralValenceExcess = NO_VALUE_INT; ------------------ | | 23| 147k|#define NO_VALUE_INT 9999 ------------------ 1156| 147k| nFoundNeutralValenceOrdNumber = NO_VALUE_INT; ------------------ | | 23| 147k|#define NO_VALUE_INT 9999 ------------------ 1157| 147k| nLastFoundValenceOrdNumber = NO_VALUE_INT; ------------------ | | 23| 147k|#define NO_VALUE_INT 9999 ------------------ 1158| 147k| nLastFoundValenceState = NO_VALUE_INT; ------------------ | | 23| 147k|#define NO_VALUE_INT 9999 ------------------ 1159| | 1160| | /* find the lowest known valence >= all-single-bonds valence */ 1161| 886k| for (cur_charge = MIN_ATOM_CHARGE, nNumStates = 0; cur_charge <= MAX_ATOM_CHARGE; cur_charge++) ------------------ | | 882| 147k|#define MIN_ATOM_CHARGE (-2) ------------------ for (cur_charge = MIN_ATOM_CHARGE, nNumStates = 0; cur_charge <= MAX_ATOM_CHARGE; cur_charge++) ------------------ | | 883| 886k|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (1161:56): [True: 738k, False: 147k] ------------------ 1162| 738k| { 1163| 4.43M| for (i = 0; i < MAX_NUM_VALENCES; i++) ------------------ | | 886| 4.43M|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (1163:21): [True: 3.69M, False: 738k] ------------------ 1164| 3.69M| { 1165| 3.69M| known_chem_valence = get_el_valence(nPeriodicNum, cur_charge, i); 1166| 3.69M| if (cur_chem_valence_fixed > known_chem_valence || !known_chem_valence) ------------------ | Branch (1166:17): [True: 2.83M, False: 855k] | Branch (1166:64): [True: 3.96k, False: 851k] ------------------ 1167| 2.84M| { 1168| 2.84M| continue; /* known valence < all-single-bonds valence */ 1169| 2.84M| } 1170| 851k| if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * (num_bonds - 1) + num_H < known_chem_valence) ------------------ | | 34| 851k|#define BOND_TYPE_TRIPLE 3 ------------------ if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * (num_bonds - 1) + num_H < known_chem_valence) ------------------ | | 33| 851k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1170:17): [True: 193k, False: 657k] ------------------ 1171| 193k| { 1172| 193k| continue; /* not more than one triple and the rest - double bonds per atom */ 1173| 193k| } 1174| | 1175| | /* keep all found */ 1176| 657k| ChargeVal[nNumStates].nValence = known_chem_valence; 1177| 657k| ChargeVal[nNumStates].nCharge = cur_charge; 1178| 657k| ChargeVal[nNumStates].nValenceOrderingNumber = i; 1179| 657k| if (!cur_charge && nFoundNeutralValenceExcess == NO_VALUE_INT) ------------------ | | 23| 174k|#define NO_VALUE_INT 9999 ------------------ | Branch (1179:17): [True: 174k, False: 483k] | Branch (1179:32): [True: 124k, False: 50.2k] ------------------ 1180| 124k| { 1181| | /* neutral state; compare to the lowest typical valence */ 1182| 124k| nFoundNeutralValenceExcess = known_chem_valence - min_chem_valence; 1183| 124k| nFoundNeutralValenceOrdNumber = i; 1184| 124k| } 1185| 657k| if (min_chem_valence == known_chem_valence) ------------------ | Branch (1185:17): [True: 165k, False: 492k] ------------------ 1186| 165k| { 1187| 165k| if (nLastFoundValenceState == NO_VALUE_INT) ------------------ | | 23| 165k|#define NO_VALUE_INT 9999 ------------------ | Branch (1187:21): [True: 130k, False: 35.1k] ------------------ 1188| 130k| { 1189| | /* accept the first found */ 1190| 130k| nLastFoundValenceState = nNumStates; 1191| 130k| } 1192| 35.1k| else 1193| 35.1k| if (abs(ChargeVal[nLastFoundValenceState].nCharge) >= abs(cur_charge)) ------------------ | Branch (1193:25): [True: 24.0k, False: 11.0k] ------------------ 1194| 24.0k| { 1195| | /* accept smaller abs(charge); if abs(charges) are same, accept (+) */ 1196| 24.0k| nLastFoundValenceState = nNumStates; 1197| 24.0k| } 1198| 165k| } 1199| | 1200| 657k| nNumStates++; 1201| 657k| } 1202| 738k| } 1203| | 1204| | /***********************************************************************************/ 1205| | /* select only appropriate charge & valence so that a suitable ChargeStruct exists */ 1206| | /***********************************************************************************/ 1207| | 1208| 147k| nNumSelectedStates = clean_charge_val( pCG, ChargeVal, nNumStates, atom, 1209| 147k| pVArray, iat, pVA->cMetal, 1210| 147k| bMobileH, endpoint ); 1211| | 1212| 147k| if (!nNumSelectedStates) ------------------ | Branch (1212:9): [True: 1.41k, False: 146k] ------------------ 1213| 1.41k| { 1214| 1.41k| return TREAT_ATOM_AS_METAL; /* nothing to do */ ------------------ | | 258| 1.41k|#define TREAT_ATOM_AS_METAL 99 ------------------ 1215| 1.41k| } 1216| | 1217| | /***********************************************************************************/ 1218| | /* Find an appropriate ChargeStruct index for the ChargeVal found */ 1219| | /***********************************************************************************/ 1220| 146k| cn_bits = 0; 1221| 146k| memset( cn_bits_array, 0, sizeof( cn_bits_array ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1222| | /***** set bits identifying a suitable ChargeStruct ******/ 1223| 526k| for (i = len_cn_bits_array = 0; i < nNumSelectedStates && len_cn_bits_array < 4; i++) ------------------ | Branch (1223:37): [True: 380k, False: 146k] | Branch (1223:63): [True: 380k, False: 0] ------------------ 1224| 380k| { 1225| 380k| switch (ChargeVal[i].nCharge) 1226| 380k| { 1227| 109k| case -1: ------------------ | Branch (1227:13): [True: 109k, False: 271k] ------------------ 1228| 109k| cn_bits_array[len_cn_bits_array] |= cn_bits_M; /* Minus 1 */ ------------------ | | 418| 109k|#define cn_bits_M 4 /* Minus 1: charge = -1 */ ------------------ 1229| 109k| break; 1230| 141k| case 0: ------------------ | Branch (1230:13): [True: 141k, False: 238k] ------------------ 1231| 141k| cn_bits_array[len_cn_bits_array] |= cn_bits_N; /* Neutral */ ------------------ | | 416| 141k|#define cn_bits_N 1 /* Neutral: charge = 0 */ ------------------ 1232| 141k| break; 1233| 129k| case 1: ------------------ | Branch (1233:13): [True: 129k, False: 251k] ------------------ 1234| 129k| cn_bits_array[len_cn_bits_array] |= cn_bits_P; /* Plus 1 */ ------------------ | | 417| 129k|#define cn_bits_P 2 /* Plus 1: charge = +1 */ ------------------ 1235| 129k| break; 1236| 0| default: ------------------ | Branch (1236:13): [True: 0, False: 380k] ------------------ 1237| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1238| 380k| } 1239| 380k| if (i + 1 < nNumSelectedStates && ------------------ | Branch (1239:13): [True: 234k, False: 146k] ------------------ 1240| 234k| ChargeVal[i].nValence == ChargeVal[i + 1].nValence && ------------------ | Branch (1240:14): [True: 30.6k, False: 203k] ------------------ 1241| 30.6k| ChargeVal[i].nCharge && ------------------ | Branch (1241:14): [True: 30.6k, False: 0] ------------------ 1242| 30.6k| ChargeVal[i].nCharge == -ChargeVal[i + 1].nCharge) ------------------ | Branch (1242:14): [True: 30.6k, False: 0] ------------------ 1243| 30.6k| { 1244| 30.6k| ; /* add opposite charge to the same element of cn_bits_array[] */ 1245| 30.6k| } 1246| 349k| else 1247| 349k| { 1248| 349k| len_cn_bits_array++; 1249| 349k| } 1250| 380k| } 1251| 146k| if (!len_cn_bits_array || len_cn_bits_array > 4) ------------------ | Branch (1251:9): [True: 0, False: 146k] | Branch (1251:31): [True: 0, False: 146k] ------------------ 1252| 0| { 1253| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1254| 0| } 1255| | /* accommodate added 4-state ChargeStruct: +/- cannot be in case of 4 states */ 1256| 146k| if (len_cn_bits_array + 1 == nNumSelectedStates && nNumSelectedStates == 4) ------------------ | Branch (1256:9): [True: 30.6k, False: 115k] | Branch (1256:56): [True: 711, False: 29.9k] ------------------ 1257| 711| { 1258| 711| len_cn_bits_array--; 1259| 711| nNumSelectedStates--; 1260| 711| cn_bits_array[len_cn_bits_array] = 0; 1261| 711| } 1262| | /* fix for terminal hydrogenless -C as in isocyano or CO: there is no just cnE_[] ChargeStruct */ 1263| 146k| if (len_cn_bits_array == 1 && ------------------ | Branch (1263:9): [True: 24.9k, False: 121k] ------------------ 1264| 24.9k| cn_bits_array[0] == ( cn_bits_P | cn_bits_M ) && ------------------ | | 417| 24.9k|#define cn_bits_P 2 /* Plus 1: charge = +1 */ ------------------ cn_bits_array[0] == ( cn_bits_P | cn_bits_M ) && ------------------ | | 418| 24.9k|#define cn_bits_M 4 /* Minus 1: charge = -1 */ ------------------ | Branch (1264:10): [True: 15.6k, False: 9.30k] ------------------ 1265| 15.6k| ChargeVal[0].nValence + 1 > BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( num_bonds - 1 ) + num_H) ------------------ | | 34| 15.6k|#define BOND_TYPE_TRIPLE 3 ------------------ ChargeVal[0].nValence + 1 > BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( num_bonds - 1 ) + num_H) ------------------ | | 33| 15.6k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1265:10): [True: 15.6k, False: 1] ------------------ 1266| 15.6k| { 1267| 15.6k| cn_bits_array[len_cn_bits_array++] = cn_bits_N; ------------------ | | 416| 15.6k|#define cn_bits_N 1 /* Neutral: charge = 0 */ ------------------ 1268| 15.6k| ChargeVal[nNumSelectedStates].nValence = ChargeVal[nNumSelectedStates - 1].nValence; 1269| 15.6k| ChargeVal[nNumSelectedStates].nCharge = 0; 1270| 15.6k| ChargeVal[nNumSelectedStates].nValenceOrderingNumber = 0; 1271| 15.6k| } 1272| | 1273| 149k|make_cn_bits: 1274| 149k| cn_bits = MAKE_CN_BITS( cn_bits_array[0], cn_bits_array[1], cn_bits_array[2], cn_bits_array[3] ); ------------------ | | 421| 149k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 149k|#define cn_bits_shift 3 | | ------------------ | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 149k|#define cn_bits_shift 3 | | ------------------ | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 149k|#define cn_bits_shift 3 | | ------------------ ------------------ 1275| | 1276| | /*********** find ChargeStructure **************/ 1277| 1.16M| for (i = 0, j = -1; i < cnListNumEl; i++) ------------------ | Branch (1277:25): [True: 1.16M, False: 3.55k] ------------------ 1278| 1.16M| { 1279| 1.16M| if (cnList[i].bits == cn_bits) ------------------ | Branch (1279:13): [True: 146k, False: 1.01M] ------------------ 1280| 146k| { 1281| 146k| j = i; 1282| 146k| break; /* found */ 1283| 146k| } 1284| 1.16M| } 1285| | 1286| 149k| if (j < 0) ------------------ | Branch (1286:9): [True: 3.55k, False: 146k] ------------------ 1287| 3.55k| { 1288| | /* ChargeStructure was not found */ 1289| 3.55k| if (1 < len_cn_bits_array && len_cn_bits_array + 1 == nNumSelectedStates) ------------------ | Branch (1289:13): [True: 3.55k, False: 1] | Branch (1289:38): [True: 0, False: 3.55k] ------------------ 1290| 0| { 1291| |/* a pair of opposite charges was combined */ 1292| 0| len_cn_bits_array--; 1293| 0| cn_bits_array[len_cn_bits_array] = 0; 1294| 0| goto make_cn_bits; 1295| 0| } 1296| 3.55k| else if (nNumSelectedStates == 4) ------------------ | Branch (1296:18): [True: 3.55k, False: 1] ------------------ 1297| 3.55k| { 1298| | /* reduce number of states */ 1299| 3.55k| len_cn_bits_array--; 1300| 3.55k| cn_bits_array[len_cn_bits_array] = 0; 1301| 3.55k| nNumSelectedStates--; 1302| 3.55k| goto make_cn_bits; 1303| 3.55k| } 1304| 1| return RI_ERR_PROGR; /* charge structure not found */ ------------------ | | 17| 1|#define RI_ERR_PROGR (-3) ------------------ 1305| 3.55k| } 1306| | 1307| | /********** ChargeStructure has been found **********/ 1308| 146k| pVA->cnListIndex = j + 1; /* charge structure index + 1 */ 1309| 146k| pVA->cInitCharge = cnList[j].nInitialCharge; 1310| | /********** Calculate "Free Valence" ****************/ 1311| 146k|#if ( ALLOW_METAL_BOND_ZERO == 1 ) 1312| | 1313| |#if ( INIT_METAL_BOND_ZERO == 1 ) 1314| | if (pVA->cMetal) 1315| | { 1316| | j = 0; 1317| | } 1318| | else 1319| | { 1320| | j = ChargeVal[0].nValence - cur_chem_valence_fixed; 1321| | } 1322| |#else 1323| 146k| j = ChargeVal[0].nValence - cur_chem_valence_fixed; 1324| 146k|#endif 1325| | 1326| |#else 1327| | j = ChargeVal[0].nValence - cur_chem_valence_fixed; 1328| |#endif 1329| 146k| if (j < 0) ------------------ | Branch (1329:9): [True: 0, False: 146k] ------------------ 1330| 0| { 1331| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1332| 0| } 1333| 146k| pVA->cInitFreeValences = j; /* number of initial unsatisfied valences; should be combined with */ 1334| | /* (cap - flow) of vertex=0 in the charge structure[pVA->cnListIndex-1] */ 1335| 146k| return 1; /* success */ 1336| | 1337| 146k|#undef MIN_ATOM_CHARGE 1338| 146k|#undef MAX_ATOM_CHARGE 1339| 146k|#undef NEUTRAL_STATE 1340| 146k|#undef NUM_ATOM_CHARGES 1341| 146k|#undef MAX_NUM_VALENCES 1342| 146k|} get_sp_element_type: 1395| 1.24M|{ 1396| 1.24M| int row = 0, type = 0; 1397| 1.24M| if (nPeriodicNumber == 1) ------------------ | Branch (1397:9): [True: 44.3k, False: 1.20M] ------------------ 1398| 44.3k| { 1399| 44.3k| type = 1; /* H: 1 */ 1400| 44.3k| row = 0; 1401| 44.3k| } 1402| 1.20M| else if (nPeriodicNumber == 2) ------------------ | Branch (1402:14): [True: 2.44k, False: 1.19M] ------------------ 1403| 2.44k| { 1404| 2.44k| type = 0; row = 0; 1405| 2.44k| } 1406| 1.19M| else if (nPeriodicNumber <= 10) ------------------ | Branch (1406:14): [True: 519k, False: 679k] ------------------ 1407| 519k| { 1408| | /* Li: 2, Be: 3, B: 4, C: 5, N: 6, O: 7, F: 8, Ne: 9; later subtract 1 */ 1409| 519k| type = nPeriodicNumber - 1; row = 1; 1410| 519k| } 1411| 679k| else if (nPeriodicNumber <= 18) ------------------ | Branch (1411:14): [True: 212k, False: 467k] ------------------ 1412| 212k| { 1413| 212k| type = nPeriodicNumber - 9; row = 2; 1414| 212k| } 1415| 467k| else if (nPeriodicNumber <= 20) ------------------ | Branch (1415:14): [True: 11.8k, False: 455k] ------------------ 1416| 11.8k| { 1417| 11.8k| type = nPeriodicNumber - 17; row = 3; 1418| 11.8k| } 1419| 455k| else if (nPeriodicNumber <= 30) ------------------ | Branch (1419:14): [True: 83.4k, False: 371k] ------------------ 1420| 83.4k| { 1421| 83.4k| type = 0; row = 3; 1422| 83.4k| } 1423| 371k| else if (nPeriodicNumber <= 36) ------------------ | Branch (1423:14): [True: 11.8k, False: 360k] ------------------ 1424| 11.8k| { 1425| 11.8k| type = nPeriodicNumber - 27; row = 3; 1426| 11.8k| } 1427| 360k| else if (nPeriodicNumber <= 38) ------------------ | Branch (1427:14): [True: 532, False: 359k] ------------------ 1428| 532| { 1429| 532| type = nPeriodicNumber - 35; row = 4; 1430| 532| } 1431| 359k| else if (nPeriodicNumber <= 48) ------------------ | Branch (1431:14): [True: 154k, False: 204k] ------------------ 1432| 154k| { 1433| 154k| type = 0; row = 4; 1434| 154k| } 1435| 204k| else if (nPeriodicNumber <= 54) ------------------ | Branch (1435:14): [True: 20.7k, False: 184k] ------------------ 1436| 20.7k| { 1437| 20.7k| type = nPeriodicNumber - 45; row = 4; 1438| 20.7k| } 1439| 184k| else if (nPeriodicNumber <= 56) ------------------ | Branch (1439:14): [True: 1.04k, False: 183k] ------------------ 1440| 1.04k| { 1441| 1.04k| type = nPeriodicNumber - 53; row = 5; 1442| 1.04k| } 1443| 183k| else if (nPeriodicNumber <= 80) ------------------ | Branch (1443:14): [True: 79.6k, False: 103k] ------------------ 1444| 79.6k| { 1445| 79.6k| type = 0; row = 5; 1446| 79.6k| } 1447| 103k| else if (nPeriodicNumber <= 86) ------------------ | Branch (1447:14): [True: 2.16k, False: 101k] ------------------ 1448| 2.16k| { 1449| 2.16k| type = nPeriodicNumber - 77; row = 5; 1450| 2.16k| } 1451| 101k| else if (nPeriodicNumber <= 88) ------------------ | Branch (1451:14): [True: 1.60k, False: 99.7k] ------------------ 1452| 1.60k| { 1453| 1.60k| type = nPeriodicNumber - 85; row = 6; 1454| 1.60k| } 1455| 99.7k| else 1456| 99.7k| { 1457| 99.7k| type = 0; row = 6; 1458| 99.7k| } 1459| | 1460| 1.24M| *nRow = row; 1461| | 1462| 1.24M| return type == 9 ? 0 : type; ------------------ | Branch (1462:12): [True: 999, False: 1.24M] ------------------ 1463| 1.24M|} ReallocTCGroups: 1468| 34.4k|{ 1469| 34.4k| TC_GROUP *pTCGroup = (TC_GROUP *) inchi_malloc( sizeof( pTCGroup[0] )*( (long long)pTCGroups->max_tc_groups + nAdd ) ); /* djb-rwth: cast operator added */ ------------------ | | 1143| 34.4k|#define inchi_malloc malloc ------------------ 1470| | 1471| 34.4k| if (pTCGroup) ------------------ | Branch (1471:9): [True: 34.4k, False: 0] ------------------ 1472| 34.4k| { 1473| 34.4k| if (pTCGroups->num_tc_groups) ------------------ | Branch (1473:13): [True: 30, False: 34.3k] ------------------ 1474| 30| { 1475| 30| memcpy(pTCGroup, pTCGroups->pTCG, sizeof(pTCGroup[0]) * pTCGroups->num_tc_groups); 1476| 30| } 1477| 34.4k| memset( pTCGroup + pTCGroups->max_tc_groups, 0, sizeof( pTCGroup[0] )*nAdd ); /* djb-rwth: memset_s C11/Annex K variant? */ 1478| 34.4k| if (pTCGroups->pTCG) ------------------ | Branch (1478:13): [True: 30, False: 34.3k] ------------------ 1479| 30| { 1480| 30| inchi_free( pTCGroups->pTCG ); ------------------ | | 1152| 30|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 30, False: 0] | | | Branch (1152:50): [Folded, False: 30] | | ------------------ ------------------ 1481| 30| } 1482| 34.4k| pTCGroups->pTCG = pTCGroup; 1483| 34.4k| pTCGroups->max_tc_groups += nAdd; 1484| 34.4k| return 0; 1485| 34.4k| } 1486| | 1487| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1488| 34.4k|} RegisterTCGroup: 1494| 812k|{ 1495| 812k| int i, ret = 0; 1496| | 1497| | /* search */ 1498| 2.80M| for (i = 0; i < pTCGroups->num_tc_groups; i++) ------------------ | Branch (1498:17): [True: 2.53M, False: 268k] ------------------ 1499| 2.53M| { 1500| 2.53M| if (pTCGroups->pTCG[i].type == nGroupType && ------------------ | Branch (1500:13): [True: 674k, False: 1.85M] ------------------ 1501| 674k| pTCGroups->pTCG[i].ord_num == nGroupOrdNum) ------------------ | Branch (1501:14): [True: 543k, False: 131k] ------------------ 1502| 543k| { 1503| 543k| break; 1504| 543k| } 1505| 2.53M| } 1506| | 1507| 812k| if (i == pTCGroups->num_tc_groups) ------------------ | Branch (1507:9): [True: 268k, False: 543k] ------------------ 1508| 268k| { 1509| | /* add one more group */ 1510| 268k| if (pTCGroups->num_tc_groups == pTCGroups->max_tc_groups) ------------------ | Branch (1510:13): [True: 34.4k, False: 234k] ------------------ 1511| 34.4k| { 1512| 34.4k| ret = ReallocTCGroups( pTCGroups, INC_NUM_TCGROUPS ); ------------------ | | 158| 34.4k|#define INC_NUM_TCGROUPS 16 ------------------ 1513| 34.4k| if (ret) ------------------ | Branch (1513:17): [True: 0, False: 34.4k] ------------------ 1514| 0| { 1515| 0| goto exit_function; 1516| 0| } 1517| 34.4k| } 1518| | 1519| 268k| ret = i + 1; /* added new group */ 1520| 268k| pTCGroups->num_tc_groups++; 1521| 268k| pTCGroups->pTCG[i].type = nGroupType; 1522| 268k| pTCGroups->pTCG[i].ord_num = nGroupOrdNum; 1523| 268k| } 1524| | 1525| 812k| pTCGroups->pTCG[i].num_edges += nNumEdges; 1526| | 1527| 812k| pTCGroups->pTCG[i].st_cap += nVertexCap; 1528| 812k| pTCGroups->pTCG[i].st_flow += nVertexFlow; 1529| | 1530| 812k| pTCGroups->pTCG[i].edges_cap += nEdgeCap; 1531| 812k| pTCGroups->pTCG[i].edges_flow += nEdgeFlow; 1532| | 1533| 812k|exit_function: 1534| 812k| return ret; 1535| 812k|} nTautEndpointEdgeCap: 1540| 2.04k|{ 1541| | /* There are 3 sources of cap-flow = number of unsatisfied valences: 1542| | ----------------------------------------------------------------- 1543| | 1. pVA[i].cInitFreeValences 1544| | 2. pCN[0].v.cap - pCN[0].v.flow 1545| | 3. st[i].chem_bonds_valence - SUM(SINGLE, DOUBLE, TRIPLE bond orders) 1546| | Reasons: (a) This sum will not include 'ALTERN' bonds 1547| | (b) until now at[i].chem_bonds_valence was used as a 1548| | number of satisfied valences. In case of adjacent 1549| | stereobonds marked as BOND_TYPE_ALTERN the value of 1550| | at[i].chem_bonds_valence may be = at[i].valence+1. 1551| | 4. Since tautomerism is defined for a neutral atom, do not add 1552| | initial flows from the atom to the ChargeStruct 1553| | CORRECTION: tautomeric endpoints do not have ChargeStruct. 1554| | 1555| | */ 1556| 2.04k| int j, k, nEdgeCap, bonds_valence, stereo_bond_excess_valence; 1557| 2.04k| MY_CONST C_NODE *pCN = pVA[i].cnListIndex > 0 ? cnList[pVA[i].cnListIndex - 1].pCN : NULL; ------------------ | | 268| 2.04k|#define MY_CONST const ------------------ | Branch (1557:28): [True: 1.02k, False: 1.01k] ------------------ 1558| | 1559| | 1560| | /* 1: free valences to reach the minimum known atom valence */ 1561| 2.04k| nEdgeCap = pVA[i].cInitFreeValences; 1562| | 1563| | /* 2: atom free valence in the ChargeStruct */ 1564| 2.04k| if (pCN) ------------------ | Branch (1564:9): [True: 1.02k, False: 1.01k] ------------------ 1565| 1.02k| { 1566| 1.02k| nEdgeCap += pCN[0].v.cap - pCN[0].v.flow; /* normally should not happen */ 1567| 1.02k| } 1568| | 1569| | /* 3: atom free valence due to known from stereochemistry stereogenic bond types */ 1570| | /* 1571| | for ( j = 0, bonds_valence = 0; j < at[i].valence; j ++ ) 1572| | { 1573| | if ( at[i].bond_type[j] <= BOND_TYPE_TRIPLE ) 1574| | { 1575| | bonds_valence += at[i].bond_type[j]; 1576| | } 1577| | } 1578| | */ 1579| | 1580| | /* bonds > SINGLE are assumed fixed stereobonds; fixed bond cannot increase t-group edge flow */ 1581| 2.07k| for (stereo_bond_excess_valence = 0, j = 0; j < MAX_NUM_STEREO_BONDS && at[i].sb_parity[j]; j++) ------------------ | | 873| 4.14k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1581:49): [True: 2.07k, False: 0] | Branch (1581:77): [True: 27, False: 2.04k] ------------------ 1582| 27| { 1583| 27| k = at[i].sb_ord[j]; 1584| 27| if (at[i].bond_type[k] < BOND_TYPE_TRIPLE) ------------------ | | 34| 27|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1584:13): [True: 16, False: 11] ------------------ 1585| 16| { 1586| 16| stereo_bond_excess_valence += at[i].bond_type[k] - BOND_TYPE_SINGLE; ------------------ | | 32| 16|#define BOND_TYPE_SINGLE 1 ------------------ 1587| 16| } 1588| 27| } 1589| | 1590| | /* 1591| | bonds_valence = (at[i].chem_bonds_valence - bonds_valence) + (bonds_valence -at[i].valence - stereo_bond_excess_valence); 1592| | */ 1593| 2.04k| bonds_valence = ( at[i].chem_bonds_valence - at[i].valence ) - stereo_bond_excess_valence; 1594| | 1595| | 1596| | /*---- add 1, 2, 3 ----*/ 1597| 2.04k| if (bonds_valence >= 0) ------------------ | Branch (1597:9): [True: 2.04k, False: 0] ------------------ 1598| 2.04k| { 1599| 2.04k| nEdgeCap += bonds_valence; 1600| 2.04k| } 1601| 0| else 1602| 0| { 1603| 0| nEdgeCap = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1604| 0| } 1605| | 1606| 2.04k| return nEdgeCap; 1607| 2.04k|} BondFlowMaxcapMinorder: 1663| 6.72M|{ 1664| | 1665| 6.72M| int nFlow, nMaxcap, nMinorder, nInitorder, bNeedsFlower = 0; 1666| 6.72M| inp_ATOM *at = atom + iat; 1667| 6.72M| int neigh = at->neighbor[ineigh]; 1668| 6.72M| int bond_type = at->bond_type[ineigh] & BOND_TYPE_MASK; ------------------ | | 189| 6.72M|#define BOND_TYPE_MASK 0x0f ------------------ 1669| 6.72M| int nMetal = ( 0 != pVA[iat].cMetal ) + ( 0 != pVA[neigh].cMetal ); 1670| 6.72M| int nEndpoint = ( 0 != at->endpoint ) + ( 0 != atom[neigh].endpoint ); 1671| 6.72M| int nStereo = ( at->p_parity || at->sb_parity[0] ) + ( atom[neigh].p_parity || atom[neigh].sb_parity[0] ); ------------------ | Branch (1671:27): [True: 36.3k, False: 6.69M] | Branch (1671:43): [True: 46.2k, False: 6.64M] | Branch (1671:66): [True: 35.2k, False: 6.69M] | Branch (1671:90): [True: 45.5k, False: 6.64M] ------------------ 1672| | 1673| 6.72M| if (bond_type > BOND_TYPE_TRIPLE) ------------------ | | 34| 6.72M|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1673:9): [True: 1.08k, False: 6.72M] ------------------ 1674| 1.08k| { 1675| 1.08k| bond_type = BOND_TYPE_SINGLE; ------------------ | | 32| 1.08k|#define BOND_TYPE_SINGLE 1 ------------------ 1676| 1.08k| } 1677| | 1678| | /* M=metal, A=non-metal atom, e=endpoint */ 1679| 6.72M| if ((nStereo && pSrm->bFixStereoBonds) || !nMetal || !pSrm->bMetalAddFlower) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1679:10): [True: 127k, False: 6.60M] | Branch (1679:21): [True: 0, False: 127k] | Branch (1679:47): [True: 5.00M, False: 1.71M] | Branch (1679:58): [True: 0, False: 1.71M] ------------------ 1680| 5.00M| { 1681| | /* atom-atom rules, no metal atoms involved (1: A-A, A-Ae, Ae-Ae) */ 1682| 5.00M| nMinorder = BOND_TYPE_SINGLE; ------------------ | | 32| 5.00M|#define BOND_TYPE_SINGLE 1 ------------------ 1683| 5.00M| nInitorder = bond_type; 1684| 5.00M| nFlow = nInitorder - nMinorder; 1685| 5.00M| } 1686| 1.71M| else if (nMetal && !nEndpoint) ------------------ | Branch (1686:14): [True: 1.71M, False: 0] | Branch (1686:24): [True: 1.71M, False: 5.44k] ------------------ 1687| 1.71M| { 1688| | /* M-a, M-M */ 1689| | /* atom - metal or metal-metal, none of them is an endpoint (2: M-M, M-A) */ 1690| 1.71M| nMinorder = pSrm->nMetalMinBondOrder; 1691| 1.71M| nInitorder = pSrm->nMetalInitBondOrder + bond_type - BOND_TYPE_SINGLE; ------------------ | | 32| 1.71M|#define BOND_TYPE_SINGLE 1 ------------------ 1692| 1.71M| nFlow = nInitorder - nMinorder; 1693| 1.71M| if (!pSrm->nMetalInitEdgeFlow && ------------------ | Branch (1693:13): [True: 0, False: 1.71M] ------------------ 1694| 0| pSrm->nMetalInitBondOrder > pSrm->nMetalMinBondOrder && ------------------ | Branch (1694:14): [True: 0, False: 0] ------------------ 1695| 0| nFlow > 0) ------------------ | Branch (1695:14): [True: 0, False: 0] ------------------ 1696| 0| { 1697| | /* reduce initial flow by 1 and increase st_cap on metal by 1 */ 1698| 0| nFlow--; 1699| 0| } 1700| 1.71M| bNeedsFlower = ( 0 != pVA[iat].cMetal ); 1701| 1.71M| } 1702| 5.44k| else 1703| 5.44k| if ((pVA[iat].cMetal && !at->endpoint && !pVA[neigh].cMetal && atom[neigh].endpoint) || ------------------ | Branch (1703:14): [True: 2.93k, False: 2.50k] | Branch (1703:33): [True: 2.88k, False: 50] | Branch (1703:50): [True: 2.87k, False: 17] | Branch (1703:72): [True: 2.87k, False: 0] ------------------ 1704| 2.57k| (pVA[neigh].cMetal && !atom[neigh].endpoint && !pVA[iat].cMetal && at->endpoint)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1704:15): [True: 2.54k, False: 29] | Branch (1704:36): [True: 2.52k, False: 17] | Branch (1704:61): [True: 2.50k, False: 21] | Branch (1704:81): [True: 2.50k, False: 0] ------------------ 1705| 5.37k| { 1706| | /* M-ae */ 1707| | /* metal connected to a non-metal endpoint (3: M-Ae) */ 1708| 5.37k| nMinorder = pSrm->nMetal2EndpointMinBondOrder; 1709| 5.37k| nInitorder = pSrm->nMetal2EndpointInitBondOrder + bond_type - BOND_TYPE_SINGLE; ------------------ | | 32| 5.37k|#define BOND_TYPE_SINGLE 1 ------------------ 1710| 5.37k| nFlow = nInitorder - nMinorder; 1711| 5.37k| if (!pSrm->nMetal2EndpointInitEdgeFlow && ------------------ | Branch (1711:17): [True: 5.37k, False: 0] ------------------ 1712| 5.37k| pSrm->nMetal2EndpointInitBondOrder > pSrm->nMetal2EndpointMinBondOrder && ------------------ | Branch (1712:18): [True: 0, False: 5.37k] ------------------ 1713| 0| nFlow > 0) ------------------ | Branch (1713:18): [True: 0, False: 0] ------------------ 1714| 0| { 1715| | /* reduce initial flow by 1 and increase st_cap on metal by 1 */ 1716| 0| nFlow--; 1717| 0| } 1718| 5.37k| bNeedsFlower = ( 0 != pVA[iat].cMetal ); 1719| 5.37k| } 1720| 67| else 1721| 67| { 1722| | /* endpoint is metal => no flower (4: M-Me, Me-Me, Me-A, Me-Ae) */ 1723| 67| nMinorder = pSrm->nMetal2EndpointMinBondOrder; 1724| 67| nInitorder = pSrm->nMetal2EndpointInitBondOrder + bond_type - BOND_TYPE_SINGLE; ------------------ | | 32| 67|#define BOND_TYPE_SINGLE 1 ------------------ 1725| 67| nFlow = nInitorder - nMinorder; 1726| 67| if (!pSrm->nMetal2EndpointInitEdgeFlow && ------------------ | Branch (1726:17): [True: 67, False: 0] ------------------ 1727| 67| pSrm->nMetal2EndpointInitBondOrder > pSrm->nMetal2EndpointMinBondOrder && ------------------ | Branch (1727:18): [True: 0, False: 67] ------------------ 1728| 0| nFlow > 0) ------------------ | Branch (1728:18): [True: 0, False: 0] ------------------ 1729| 0| { 1730| |/* reduce initial flow by 1 and increase st_cap on metal by 1 */ 1731| 0| nFlow--; 1732| 0| } 1733| 67| bNeedsFlower = ( pVA[iat].cMetal && !at->endpoint ); ------------------ | Branch (1733:30): [True: 67, False: 0] | Branch (1733:49): [True: 17, False: 50] ------------------ 1734| 67| } 1735| | 1736| 6.72M| nMaxcap = BOND_TYPE_TRIPLE - nMinorder; ------------------ | | 34| 6.72M|#define BOND_TYPE_TRIPLE 3 ------------------ 1737| 6.72M| if (pnMaxcap) ------------------ | Branch (1737:9): [True: 1.36M, False: 5.36M] ------------------ 1738| 1.36M| { 1739| 1.36M| *pnMaxcap = nMaxcap; 1740| 1.36M| } 1741| 6.72M| if (pnMinorder) ------------------ | Branch (1741:9): [True: 6.72M, False: 0] ------------------ 1742| 6.72M| { 1743| 6.72M| *pnMinorder = nMinorder; 1744| 6.72M| } 1745| 6.72M| if (pbNeedsFlower) ------------------ | Branch (1745:9): [True: 1.19M, False: 5.53M] ------------------ 1746| 1.19M| { 1747| 1.19M| *pbNeedsFlower = bNeedsFlower; 1748| 1.19M| } 1749| | 1750| 6.72M| return nFlow; 1751| 6.72M|} AtomStcapStflow: 1757| 1.22M|{ 1758| 1.22M| int ineigh, bFlower; 1759| 1.22M| int nStflow = 0, nMaxBondCap, nMinBondOrder, bNeedsFlower = 0; 1760| 1.22M| int valence = atom[iat].valence; 1761| 1.22M| int nStcap = atom[iat].chem_bonds_valence; 1762| 1.22M| int nMGroupEdgeCap = 0, nMGroupEdgeFlow = 0, nFlow; 1763| | 1764| 1.22M| if (pSrm->bMetalAddFlower) ------------------ | Branch (1764:9): [True: 1.22M, False: 0] ------------------ 1765| 1.22M| { 1766| 1.22M| nStcap -= pVA[iat].cInitOrigValenceToMetal - pVA[iat].cInitValenceToMetal; 1767| 1.22M| } 1768| | 1769| 2.41M| for (ineigh = 0; ineigh < valence; ineigh++) ------------------ | Branch (1769:22): [True: 1.19M, False: 1.22M] ------------------ 1770| 1.19M| { 1771| 1.19M| nFlow = BondFlowMaxcapMinorder( atom, pVA, pSrm, iat, ineigh, &nMaxBondCap, &nMinBondOrder, &bFlower ); 1772| 1.19M| nStflow += nFlow; 1773| 1.19M| nStcap -= nMinBondOrder; 1774| 1.19M| if (bFlower) ------------------ | Branch (1774:13): [True: 226k, False: 967k] ------------------ 1775| 226k| { 1776| 226k| bNeedsFlower++; 1777| 226k| nMGroupEdgeFlow += nFlow; 1778| 226k| nMGroupEdgeCap += BOND_TYPE_TRIPLE - nMinBondOrder + pSrm->nMetalMaxCharge_D; ------------------ | | 34| 226k|#define BOND_TYPE_TRIPLE 3 ------------------ 1779| 226k| } 1780| 1.19M| } 1781| | 1782| 1.22M| if (pnStcap) ------------------ | Branch (1782:9): [True: 1.19M, False: 24.3k] ------------------ 1783| 1.19M| { 1784| 1.19M| *pnStcap = bNeedsFlower ? nStflow : nStcap; /* initially, metal atoms are not radicals */ ------------------ | Branch (1784:20): [True: 91.8k, False: 1.10M] ------------------ 1785| 1.19M| } 1786| 1.22M| if (pnStflow) ------------------ | Branch (1786:9): [True: 1.19M, False: 24.3k] ------------------ 1787| 1.19M| { 1788| 1.19M| *pnStflow = nStflow; 1789| 1.19M| } 1790| 1.22M| if (pnMGroupEdgeFlow) ------------------ | Branch (1790:9): [True: 48.7k, False: 1.17M] ------------------ 1791| 48.7k| { 1792| 48.7k| *pnMGroupEdgeFlow = nMGroupEdgeCap - nMGroupEdgeFlow; 1793| 48.7k| } 1794| 1.22M| if (pnMGroupEdgeCap) ------------------ | Branch (1794:9): [True: 48.7k, False: 1.17M] ------------------ 1795| 48.7k| { 1796| 48.7k| *pnMGroupEdgeCap = nMGroupEdgeCap; 1797| 48.7k| } 1798| | 1799| 1.22M| return bNeedsFlower; /* number of variable bonds to metal */ 1800| 1.22M|} nCountBnsSizes: 1837| 87.9k|{ 1838| 87.9k| int i, j, n, k, ret = 0, nBonds, nOtherEdges, nVertices, bMetalAtoms, bNeedsFlower; 1839| 87.9k| int nTgroupEdges, nTgroupEdgesFromTg, nTotNegChargInTgroups, cap, flow; 1840| 87.9k| MY_CONST C_NODE *pCN = NULL; ------------------ | | 268| 87.9k|#define MY_CONST const ------------------ 1841| 87.9k| nVertices = nBonds = nOtherEdges = nTgroupEdges = nTgroupEdgesFromTg = nTotNegChargInTgroups = 0; 1842| | 1843| | /* count metal atoms and electrons */ 1844| 1.18M| for (i = 0; i < num_at; i++) ------------------ | Branch (1844:17): [True: 1.09M, False: 87.9k] ------------------ 1845| 1.09M| { 1846| 1.09M| pTCGroups->num_metal_atoms += ( pVA[i].cMetal != 0 ); 1847| 1.09M| pTCGroups->num_metal_bonds += pVA[i].cNumBondsToMetal; 1848| 1.09M| pTCGroups->total_electrons += at[i].el_number; 1849| 1.09M| pTCGroups->total_electrons_metals += pVA[i].cMetal ? at[i].el_number : 0; ------------------ | Branch (1849:46): [True: 438k, False: 659k] ------------------ 1850| 1.09M| } 1851| 87.9k| pTCGroups->total_electrons -= pTCGroups->total_charge; 1852| 87.9k| pTCGroups->num_metal_bonds /= 2; 1853| | 1854| | /* register tautomeric groups */ 1855| 89.4k| for (i = 0; i < ti->num_t_groups; i++) ------------------ | Branch (1855:17): [True: 1.45k, False: 87.9k] ------------------ 1856| 1.45k| { 1857| 1.45k| ret = RegisterTCGroup( pTCGroups, 1858| 1.45k| BNS_VERT_TYPE_TGROUP, ------------------ | | 47| 1.45k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 1859| 1.45k| ti->t_group[i].nGroupNumber, 1860| 1.45k| ti->t_group[i].num[0] /* st_cap */, 1861| 1.45k| 0 /* st_flow */, 1862| 1.45k| 0 /* edge cap */, 1863| 1.45k| 0 /* edge flow */, 1864| 1.45k| ti->t_group[i].nNumEndpoints /* num Edges */ 1865| 1.45k| ); 1866| 1.45k| if (ret < 0) ------------------ | Branch (1866:13): [True: 0, False: 1.45k] ------------------ 1867| 0| { 1868| 0| goto exit_function; 1869| 0| } 1870| | 1871| | /* edges to tautomeric groups */ 1872| 1.45k| nOtherEdges += ti->t_group[i].nNumEndpoints; 1873| 1.45k| nTgroupEdgesFromTg += ti->t_group[i].nNumEndpoints; 1874| | /* total negative charge in t-groups */ 1875| 1.45k| nTotNegChargInTgroups += ti->t_group[i].num[1]; 1876| 1.45k| if (ret > 0) ------------------ | Branch (1876:13): [True: 1.45k, False: 0] ------------------ 1877| 1.45k| { 1878| | /* should always happen since this is the first time this t-group is added */ 1879| 1.45k| j = ret - 1; 1880| 1.45k| pTCGroups->pTCG[j].tg_num_H = ti->t_group[i].num[0] - ti->t_group[i].num[1]; 1881| 1.45k| pTCGroups->pTCG[j].tg_num_Minus = ti->t_group[i].num[1]; 1882| 1.45k| } 1883| 1.45k| } 1884| | 1885| 87.9k| bMetalAtoms = 0; 1886| | 1887| 153k|repeat_for_metals: 1888| | 1889| | /* count vertices and register ChargeValence groups */ 1890| | /* for now an atom may belong either to a t-group or to a ChargeValence group, but not to both */ 1891| 2.08M| for (i = 0; i < num_at; i++) ------------------ | Branch (1891:17): [True: 1.93M, False: 153k] ------------------ 1892| 1.93M| { 1893| | /* number of bonds */ 1894| 1.93M| nBonds += at[i].valence; 1895| | /* Process ChargeStruct vertices and edges */ 1896| 1.93M| if (pVA[i].cnListIndex) ------------------ | Branch (1896:13): [True: 241k, False: 1.69M] ------------------ 1897| 241k| { 1898| | /* count vertices & edges in the ChargeValence Substructure attached to an atom */ 1899| | /* Important: unlike inp_ATOM, each edge e appears in pCN[*].e[*] only ONE time */ 1900| 241k| int len = cnList[j = pVA[i].cnListIndex - 1].len; 1901| 241k| int bits = cnList[j].bits; 1902| 241k| int type, neigh_type; /* djb-rwth: removing redundant variables */ 1903| 241k| pCN = cnList[j].pCN; 1904| | 1905| | /* first process all non-metals, after that -- all metals */ 1906| 241k| if (( bits != cn_bits_Me ) != !bMetalAtoms) ------------------ | | 440| 241k|#define cn_bits_Me (-1) ------------------ | Branch (1906:17): [True: 81.8k, False: 159k] ------------------ 1907| 81.8k| { 1908| 81.8k| continue; 1909| 81.8k| } 1910| | /* djb-rwth: removing redundant code */ 1911| 777k| for (j = 0; j < len; j++) ------------------ | Branch (1911:25): [True: 618k, False: 159k] ------------------ 1912| 618k| { 1913| 618k| type = pCN[j].v.type; /* ChargeStruct vertex type: atom is the first, c-groups are last */ 1914| | 1915| | /* process all pCN[j] neighbors */ 1916| 1.09M| for (k = 0; k < MAX_CN_VAL && ( n = pCN[j].e[k].neigh ); k++) ------------------ | | 397| 2.19M|#define MAX_CN_VAL 3 ------------------ | Branch (1916:29): [True: 1.09M, False: 0] | Branch (1916:47): [True: 478k, False: 618k] ------------------ 1917| 478k| { 1918| 478k| nOtherEdges++; /* edges inside ChargeStruct */ 1919| 478k| n--; /* neighbor vertex position inside cnList[j].pCN */ 1920| 478k| neigh_type = pCN[n].v.type; /* type of the neighboring atom */ 1921| | 1922| 478k| if (IS_BNS_VT_C_GR( neigh_type )) ------------------ | | 78| 478k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 478k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 478k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 258k, False: 220k] | | ------------------ ------------------ 1923| 258k| { 1924| | /* register this edge to a CN-group vertex */ 1925| 258k| cap = !bMetalAtoms ? pCN[j].e[k].cap : pCN[j].e[k].cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1925:31): [True: 209k, False: 48.7k] | Branch (1925:64): [True: 48.7k, False: 0] ------------------ 1926| 258k| flow = !bMetalAtoms ? pCN[j].e[k].flow : pCN[j].e[k].flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1926:32): [True: 209k, False: 48.7k] | Branch (1926:66): [True: 24.3k, False: 24.3k] ------------------ 1927| | 1928| 258k| ret = RegisterTCGroup( pTCGroups, 1929| 258k| neigh_type, 1930| 258k| 0 /* ord_num*/, 1931| 258k| 0 /* st_cap */, 1932| 258k| 0 /* st_flow */, 1933| 258k| cap /* edge cap*/, 1934| 258k| flow /* edge flow */, 1935| 258k| 1 /* nNumEdges*/ ); 1936| 258k| if (ret < 0) ------------------ | Branch (1936:29): [True: 0, False: 258k] ------------------ 1937| 0| { 1938| 0| goto exit_function; 1939| 0| } 1940| 258k| if (ret > 0) ------------------ | Branch (1940:29): [True: 131k, False: 127k] ------------------ 1941| 131k| { 1942| | /* the group has just been created; add one more edge to (+/-) or supergroup */ 1943| 131k| ret = RegisterTCGroup( pTCGroups, 1944| 131k| neigh_type, 1945| 131k| 0 /* ord_num*/, 1946| 131k| 0 /* st_cap */, 1947| 131k| 0 /* st_flow */, 1948| 131k| 0 /* edge cap*/, 1949| 131k| 0/* edge flow*/, 1950| 131k| 1 /* nNumEdges*/ ); 1951| 131k| if (ret < 0) ------------------ | Branch (1951:33): [True: 0, False: 131k] ------------------ 1952| 0| { 1953| 0| goto exit_function; 1954| 0| } 1955| 131k| nOtherEdges++; 1956| 131k| } 1957| 258k| } 1958| | 1959| 478k| if (IS_BNS_VT_C_GR( type )) ------------------ | | 78| 478k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 478k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 478k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 0, False: 478k] | | ------------------ ------------------ 1960| 0| { 1961| | /* register this edge to a CN-group vertex; normally this does not happen */ 1962| | 1963| 0| cap = !bMetalAtoms ? pCN[j].e[k].cap : pCN[j].e[k].cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1963:31): [True: 0, False: 0] | Branch (1963:64): [True: 0, False: 0] ------------------ 1964| 0| flow = !bMetalAtoms ? pCN[j].e[k].flow : pCN[j].e[k].flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1964:32): [True: 0, False: 0] | Branch (1964:66): [True: 0, False: 0] ------------------ 1965| | 1966| 0| ret = RegisterTCGroup( pTCGroups, type, 0 /* ord_num*/, 1967| 0| 0 /* st_cap */, 0 /* st_flow */, 1968| 0| cap /* edge cap*/, flow /* edge flow */, 1 /* nNumEdges*/ ); 1969| 0| if (ret < 0) ------------------ | Branch (1969:29): [True: 0, False: 0] ------------------ 1970| 0| { 1971| 0| goto exit_function; 1972| 0| } 1973| 0| if (ret > 0) ------------------ | Branch (1973:29): [True: 0, False: 0] ------------------ 1974| 0| { 1975| | /* the group has just been created; add one more edge to (+/-) or supergroup */ 1976| 0| ret = RegisterTCGroup( pTCGroups, type, 0 /* ord_num*/, 1977| 0| 0 /* st_cap */, 0 /* st_flow */, 1978| 0| 0 /* edge cap*/, 0/* edge flow*/, 1 /* nNumEdges*/ ); 1979| 0| if (ret < 0) ------------------ | Branch (1979:33): [True: 0, False: 0] ------------------ 1980| 0| { 1981| 0| goto exit_function; 1982| 0| } 1983| 0| nOtherEdges++; 1984| 0| } 1985| 0| } 1986| 478k| } /* end of the current vertex pCN[j] neighbors */ 1987| | 1988| | /* process pCN[j] vertex */ 1989| | 1990| 618k| if (type & BNS_VERT_TYPE_ATOM) ------------------ | | 45| 618k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (1990:21): [True: 159k, False: 458k] ------------------ 1991| 159k| { 1992| 159k| continue; /* do not count regular atoms here */ 1993| 159k| } 1994| 458k| if (IS_BNS_VT_CHRG_STRUCT( type )) ------------------ | | 82| 458k|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 53| 458k|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ | | #define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 51| 175k|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (82:38): [True: 175k, False: 283k] | | | Branch (82:69): [True: 175k, False: 0] | | ------------------ ------------------ 1995| 175k| { 1996| 175k| nVertices++; 1997| 175k| continue; 1998| 175k| } 1999| | 2000| 283k| if (pSrm->bMetalAddFlower && IS_BNS_VT_M_GR( type )) ------------------ | | 80| 283k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 283k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ | | | Branch (80:37): [True: 24.3k, False: 258k] | | ------------------ ------------------ | Branch (2000:21): [True: 283k, False: 0] ------------------ 2001| 24.3k| { 2002| | /* special treatment: flow and cap are known as well as structure */ 2003| | /* initial bond valence to metal is either 0 or 1 */ 2004| 24.3k| EdgeFlow nEdgeFlow, nEdgeCap; 2005| | 2006| 24.3k| bNeedsFlower = AtomStcapStflow( at, pVA, pSrm, i, NULL /*pnStcap*/, NULL /*pnStflow*/, 2007| 24.3k| &nEdgeCap, &nEdgeFlow ); 2008| 24.3k| if (!bNeedsFlower) ------------------ | Branch (2008:25): [True: 39, False: 24.3k] ------------------ 2009| 39| { 2010| 39| ret = RI_ERR_PROGR; ------------------ | | 17| 39|#define RI_ERR_PROGR (-3) ------------------ 2011| 39| goto exit_function; 2012| 39| } 2013| | /* 2014| | GetAtomToMCGroupInitEdgeCapFlow( &nEdgeCap, &nEdgeFlow, pSrm, at, pVA, i ); 2015| | GetAtomToMCGroupInitEdgeCapFlow( &nEdgeCap, &nEdgeFlow, pSrm ); 2016| | */ 2017| | /* the 1st is the flower base */ 2018| | /* atom - G0 edge and G0 vertex */ 2019| 24.3k| ret = RegisterTCGroup( pTCGroups, 2020| 24.3k| type, 2021| 24.3k| 0 /* ord_num*/, 2022| | /*pVA[i].cInitFreeValences*/ 2023| 24.3k| 0 /* st_cap */, 2024| 24.3k| 0 /* st_flow */, 2025| 24.3k| (int) nEdgeCap, 2026| 24.3k| (int) nEdgeFlow, 2027| 24.3k| 1 /* nNumEdges*/ ); 2028| 24.3k| if (ret < 0) ------------------ | Branch (2028:25): [True: 0, False: 24.3k] ------------------ 2029| 0| { 2030| 0| goto exit_function; 2031| 0| } 2032| | /* count edge atom-G0 */ 2033| 24.3k| nOtherEdges++; 2034| 24.3k| if (ret > 0) ------------------ | Branch (2034:25): [True: 17.1k, False: 7.22k] ------------------ 2035| 17.1k| { 2036| | /* first time registration: add G0-G1 and G0-G2 edges to G0 */ 2037| | 2038| 17.1k| ret = RegisterTCGroup( pTCGroups, 2039| 17.1k| type, 2040| 17.1k| 0 /* ord_num*/, 2041| 17.1k| 0 /* st_cap */, 2042| 17.1k| 0 /* st_flow */, 2043| 17.1k| 0,/* edge cap*/ 2044| 17.1k| 0 /*edge flow*/, 2045| 17.1k| 2 /* nNumEdges*/ ); 2046| | 2047| 17.1k| if (ret < 0) ------------------ | Branch (2047:29): [True: 0, False: 17.1k] ------------------ 2048| 0| { 2049| 0| goto exit_function; 2050| 0| } 2051| | 2052| | /* first time registration: add G1; it has 3 edges */ 2053| | 2054| 17.1k| ret = RegisterTCGroup( pTCGroups, 2055| 17.1k| type, 2056| 17.1k| 1 /* ord_num*/, 2057| 17.1k| 0 /* st_cap */, 2058| 17.1k| 0 /* st_flow */, 2059| 17.1k| 0,/* edge cap*/ 2060| 17.1k| 0 /*edge flow*/, 2061| 17.1k| 3 /* nNumEdges*/ ); 2062| | 2063| 17.1k| if (ret <= 0) ------------------ | Branch (2063:29): [True: 0, False: 17.1k] ------------------ 2064| 0| { 2065| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2065:35): [True: 0, False: 0] ------------------ 2066| 0| goto exit_function; 2067| 0| } 2068| | 2069| | /* first time registration: add G2; it has 3 edges */ 2070| | 2071| 17.1k| ret = RegisterTCGroup( pTCGroups, 2072| 17.1k| type, 2073| 17.1k| 2 /* ord_num*/, 2074| 17.1k| 0 /* st_cap */, 2075| 17.1k| 0 /* st_flow */, 2076| 17.1k| 0,/* edge cap*/ 2077| 17.1k| 0 /*edge flow*/, 2078| 17.1k| 3 /* nNumEdges*/ ); 2079| | 2080| 17.1k| if (ret <= 0) ------------------ | Branch (2080:29): [True: 0, False: 17.1k] ------------------ 2081| 0| { 2082| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2082:35): [True: 0, False: 0] ------------------ 2083| 0| goto exit_function; 2084| 0| } 2085| | 2086| | /* first time registration: add G3; it has 2 edges */ 2087| | 2088| 17.1k| ret = RegisterTCGroup( pTCGroups, 2089| 17.1k| type, 2090| 17.1k| 3 /* ord_num*/, 2091| 17.1k| 0 /* st_cap */, 2092| 17.1k| 0 /* st_flow */, 2093| 17.1k| 0,/* edge cap*/ 2094| 17.1k| 0 /*edge flow*/, 2095| 17.1k| 2 /* nNumEdges*/ ); 2096| | 2097| 17.1k| if (ret <= 0) ------------------ | Branch (2097:29): [True: 0, False: 17.1k] ------------------ 2098| 0| { 2099| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2099:35): [True: 0, False: 0] ------------------ 2100| 0| goto exit_function; 2101| 0| } 2102| | /* count added metal flower vertices: G0, G1, G2, G3 */ 2103| 17.1k| nVertices += 4; 2104| | /* count added metal flower edges: C0-C1, C0-C2, C1-C2, C1-C3, C2-C3 */ 2105| 17.1k| nOtherEdges += 5; 2106| | /* add connections of G0 to G1 and G2 */ 2107| 17.1k| } 2108| 24.3k| continue; 2109| 24.3k| } 2110| | 2111| 258k| nVertices++; /* count BNS_VT_C_POS* types; all contain BNS_VERT_TYPE_C_GROUP bit */ 2112| 258k| if (!IS_BNS_VT_C_GR( type )) ------------------ | | 78| 258k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 258k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 258k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 258k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 258k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (2112:21): [True: 0, False: 258k] ------------------ 2113| 0| { /* check */ 2114| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2115| 0| goto exit_function; 2116| 0| } 2117| | /* add st_cap and st_flow for a charge group */ 2118| 258k| cap = !bMetalAtoms ? pCN[j].v.cap : pCN[j].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (2118:23): [True: 209k, False: 48.7k] | Branch (2118:53): [True: 48.7k, False: 0] ------------------ 2119| 258k| flow = !bMetalAtoms ? pCN[j].v.flow : pCN[j].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (2119:24): [True: 209k, False: 48.7k] | Branch (2119:55): [True: 24.3k, False: 24.3k] ------------------ 2120| | 2121| 258k| ret = RegisterTCGroup( pTCGroups, type, 0 /* ord_num*/, 2122| 258k| cap /* st-cap*/, flow /* st-flow */, 2123| 258k| 0 /* edge cap */, 0 /* edge flow */, 0 /* edges already counted */ ); 2124| 258k| if (ret < 0) ------------------ | Branch (2124:21): [True: 0, False: 258k] ------------------ 2125| 0| { 2126| 0| goto exit_function; 2127| 0| } 2128| 258k| } 2129| 159k| } 2130| 1.69M| else 2131| 1.69M| { 2132| 1.69M| pCN = NULL; 2133| 1.69M| } 2134| | 2135| | /* count edge caps to t-groups */ 2136| 1.85M| if (at[i].endpoint) ------------------ | Branch (2136:13): [True: 2.04k, False: 1.84M] ------------------ 2137| 2.04k| { 2138| 2.04k| int nEdgeCap = nTautEndpointEdgeCap( at, pVA, i ); 2139| 2.04k| nTgroupEdges++; 2140| 2.04k| if (nEdgeCap < 0) ------------------ | Branch (2140:17): [True: 0, False: 2.04k] ------------------ 2141| 0| { 2142| 0| ret = nEdgeCap; 2143| 0| goto exit_function; 2144| 0| } 2145| | 2146| | /* add number of unsatisfied valences for a t-group; the unknown flow = 0 */ 2147| 2.04k| ret = RegisterTCGroup( pTCGroups, 2148| 2.04k| BNS_VERT_TYPE_TGROUP, ------------------ | | 47| 2.04k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 2149| 2.04k| at[i].endpoint, 2150| 2.04k| 0 /* st_cap */, 2151| 2.04k| 0 /* st_flow */, 2152| 2.04k| nEdgeCap /* edge cap */, 2153| 2.04k| 0 /* edge flow */, 2154| 2.04k| 0 /* t-group edges have already been counted */ ); 2155| 2.04k| if (ret < 0) ------------------ | Branch (2155:17): [True: 0, False: 2.04k] ------------------ 2156| 0| { 2157| 0| goto exit_function; 2158| 0| } 2159| 2.04k| } 2160| 1.85M| } 2161| | 2162| 153k| if (!bMetalAtoms && pTCGroups->num_metal_atoms) ------------------ | Branch (2162:9): [True: 87.9k, False: 65.4k] | Branch (2162:25): [True: 65.5k, False: 22.4k] ------------------ 2163| 65.5k| { 2164| 65.5k| bMetalAtoms = 1; 2165| 65.5k| nBonds = 0; /* added 2006-05-15 */ 2166| 65.5k| goto repeat_for_metals; 2167| 65.5k| } 2168| | 2169| | /* count real atoms and bonds */ 2170| 87.9k| nBonds /= 2; 2171| 87.9k| pTCGroups->num_atoms = num_at; 2172| 87.9k| pTCGroups->num_bonds = nBonds; 2173| | 2174| 87.9k| pTCGroups->num_tgroups = ti->num_t_groups; 2175| 87.9k| pTCGroups->num_tgroup_edges = nTgroupEdges; 2176| 87.9k| pTCGroups->tgroup_charge = -nTotNegChargInTgroups; 2177| | 2178| 87.9k| if (0 <= ret && nTgroupEdgesFromTg != nTgroupEdges) ------------------ | Branch (2178:9): [True: 87.9k, False: 0] | Branch (2178:21): [True: 89, False: 87.8k] ------------------ 2179| 89| { 2180| 89| ret = BNS_PROGRAM_ERR; ------------------ | | 50| 89|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 89|#define BNS_ERR -9999 | | ------------------ ------------------ 2181| 89| } 2182| | 2183| 87.9k| nVertices += num_at; 2184| | 2185| | 2186| | /* count other vertices */ 2187| 87.9k| nVertices += ti->num_t_groups; 2188| 87.9k| nBonds += nOtherEdges; 2189| | 2190| | /* return edges and vertices */ 2191| 87.9k| pTCGroups->nVertices = nVertices; 2192| 87.9k| pTCGroups->nEdges = nBonds; 2193| | 2194| | 2195| 87.9k|exit_function: 2196| 87.9k| return ret; 2197| 87.9k|} nAddSuperCGroups: 2245| 87.8k|{ 2246| 87.8k| int i, k, n, n1, n2, n3, ret = 0, nNumToConnect; /* djb-rwth: removing redundant variables */ 2247| | 2248| 287k| for (i = 0; i < pTCGroups->num_tc_groups; i++) ------------------ | Branch (2248:17): [True: 200k, False: 87.8k] ------------------ 2249| 200k| { 2250| 200k| if (pTCGroups->pTCG[i].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 200k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (2250:13): [True: 594, False: 199k] ------------------ 2251| 594| { 2252| | /* djb-rwth: removing redundant code */ 2253| 594| continue; /* t-group */ 2254| 594| } 2255| 199k| if (IS_BNS_VT_C_GR( pTCGroups->pTCG[i].type ) || ------------------ | | 78| 398k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 199k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 199k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 199k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 199k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 131k, False: 68.4k] | | ------------------ ------------------ 2256| 68.4k| IS_BNS_VT_M_GR( pTCGroups->pTCG[i].type )) ------------------ | | 80| 68.4k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 68.4k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ | | | Branch (80:37): [True: 68.4k, False: 0] | | ------------------ ------------------ 2257| 199k| { 2258| | /* ChargeValence (cn) group */ 2259| 199k| switch (pTCGroups->pTCG[i].type) 2260| 199k| { 2261| 30.5k| case BNS_VT_C_POS: ------------------ | | 63| 30.5k|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | ------------------ | | | | 49| 30.5k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (2261:17): [True: 30.5k, False: 168k] ------------------ 2262| 30.5k| k = TCG_Plus0; 2263| 30.5k| break; 2264| 27.7k| case BNS_VT_C_NEG: ------------------ | | 64| 27.7k|#define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | ------------------ | | | | 49| 27.7k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | #define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | ------------------ | | | | 54| 27.7k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ | | ------------------ ------------------ | Branch (2264:17): [True: 27.7k, False: 171k] ------------------ 2265| 27.7k| k = TCG_Minus0; 2266| 27.7k| break; 2267| 19.2k| case BNS_VT_C_POS_C: ------------------ | | 65| 19.2k|#define BNS_VT_C_POS_C (BNS_VT_C_POS | BNS_VERT_TYPE_CARBON_GR) /* positive charge group, C, Si, Ge, Sn */ | | ------------------ | | | | 63| 19.2k|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 49| 19.2k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define BNS_VT_C_POS_C (BNS_VT_C_POS | BNS_VERT_TYPE_CARBON_GR) /* positive charge group, C, Si, Ge, Sn */ | | ------------------ | | | | 56| 19.2k|#define BNS_VERT_TYPE_CARBON_GR 0x0400 /* charge of carbon atom; should be used with BNS_VT_C_POS, BNS_VT_C_NEG */ | | ------------------ ------------------ | Branch (2267:17): [True: 19.2k, False: 180k] ------------------ 2268| 19.2k| k = TCG_Plus_C0; 2269| 19.2k| break; 2270| 19.2k| case BNS_VT_C_NEG_C: ------------------ | | 66| 19.2k|#define BNS_VT_C_NEG_C (BNS_VT_C_NEG | BNS_VERT_TYPE_CARBON_GR) /* negative charge group, C, Si, Ge, Sn */ | | ------------------ | | | | 64| 19.2k|#define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | | | ------------------ | | | | | | 49| 19.2k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | | | #define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | | | ------------------ | | | | | | 54| 19.2k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ | | | | ------------------ | | ------------------ | | #define BNS_VT_C_NEG_C (BNS_VT_C_NEG | BNS_VERT_TYPE_CARBON_GR) /* negative charge group, C, Si, Ge, Sn */ | | ------------------ | | | | 56| 19.2k|#define BNS_VERT_TYPE_CARBON_GR 0x0400 /* charge of carbon atom; should be used with BNS_VT_C_POS, BNS_VT_C_NEG */ | | ------------------ ------------------ | Branch (2270:17): [True: 19.2k, False: 180k] ------------------ 2271| 19.2k| k = TCG_Minus_C0; 2272| 19.2k| break; 2273| 17.1k| case BNS_VT_C_POS_M: ------------------ | | 67| 17.1k|#define BNS_VT_C_POS_M (BNS_VT_C_POS | BNS_VERT_TYPE_METAL_GR) /* positive charge group, metal */ | | ------------------ | | | | 63| 17.1k|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 49| 17.1k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define BNS_VT_C_POS_M (BNS_VT_C_POS | BNS_VERT_TYPE_METAL_GR) /* positive charge group, metal */ | | ------------------ | | | | 57| 17.1k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ ------------------ | Branch (2273:17): [True: 17.1k, False: 182k] ------------------ 2274| 17.1k| k = TCG_Plus_M0; 2275| 17.1k| break; 2276| 17.1k| case BNS_VT_C_NEG_M: ------------------ | | 68| 17.1k|#define BNS_VT_C_NEG_M (BNS_VT_C_NEG | BNS_VERT_TYPE_METAL_GR) /* negative charge group, metal */ | | ------------------ | | | | 64| 17.1k|#define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | | | ------------------ | | | | | | 49| 17.1k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | | | #define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | | | ------------------ | | | | | | 54| 17.1k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ | | | | ------------------ | | ------------------ | | #define BNS_VT_C_NEG_M (BNS_VT_C_NEG | BNS_VERT_TYPE_METAL_GR) /* negative charge group, metal */ | | ------------------ | | | | 57| 17.1k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ ------------------ | Branch (2276:17): [True: 17.1k, False: 182k] ------------------ 2277| 17.1k| k = TCG_Minus_M0; 2278| 17.1k| break; 2279| 68.4k| case BNS_VT_M_GROUP: ------------------ | | 69| 68.4k|#define BNS_VT_M_GROUP BNS_VERT_TYPE_METAL_GR /* metal-group, flower vertex */ | | ------------------ | | | | 57| 68.4k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ ------------------ | Branch (2279:17): [True: 68.4k, False: 131k] ------------------ 2280| 68.4k| switch (pTCGroups->pTCG[i].ord_num) 2281| 68.4k| { 2282| 17.1k| case 0: ------------------ | Branch (2282:25): [True: 17.1k, False: 51.3k] ------------------ 2283| 17.1k| k = TCG_MeFlower0; 2284| 17.1k| break; 2285| 17.1k| case 1: ------------------ | Branch (2285:25): [True: 17.1k, False: 51.3k] ------------------ 2286| 17.1k| k = TCG_MeFlower1; 2287| 17.1k| break; 2288| 17.1k| case 2: ------------------ | Branch (2288:25): [True: 17.1k, False: 51.3k] ------------------ 2289| 17.1k| k = TCG_MeFlower2; 2290| 17.1k| break; 2291| 17.1k| case 3: ------------------ | Branch (2291:25): [True: 17.1k, False: 51.3k] ------------------ 2292| 17.1k| k = TCG_MeFlower3; 2293| 17.1k| break; 2294| 0| default: ------------------ | Branch (2294:25): [True: 0, False: 68.4k] ------------------ 2295| 0| ret = RI_ERR_PROGR; /* unexpected group type */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2296| 0| goto exit_function; 2297| 68.4k| } 2298| 68.4k| break; 2299| | 2300| 68.4k| default: ------------------ | Branch (2300:17): [True: 0, False: 199k] ------------------ 2301| 0| ret = RI_ERR_PROGR; /* unexpected group type */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2302| 0| goto exit_function; 2303| 199k| } 2304| | 2305| 199k| if (pTCGroups->nGroup[k] >= 0 || (pTCGroups->pTCG[i].ord_num && !IS_BNS_VT_M_GR( pTCGroups->pTCG[i].type ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 80| 51.3k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 51.3k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ ------------------ | Branch (2305:17): [True: 0, False: 199k] | Branch (2305:47): [True: 51.3k, False: 148k] | Branch (2305:77): [True: 0, False: 51.3k] ------------------ 2306| 0| { 2307| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2308| 0| goto exit_function; 2309| 0| } 2310| 199k| pTCGroups->nGroup[k] = i; /* ordering number of the Charge group, starting from 0 */ 2311| 199k| } 2312| 199k| } 2313| | 2314| | /* add (+) supergroup */ 2315| 87.8k| n1 = pTCGroups->nGroup[TCG_Plus0]; 2316| 87.8k| n2 = pTCGroups->nGroup[TCG_Plus_C0]; 2317| 87.8k| n3 = pTCGroups->nGroup[TCG_Plus_M0]; 2318| 87.8k| nNumToConnect = ( n1 >= 0 ) + ( n2 >= 0 ) + ( n3 >= 0 ); 2319| | 2320| 87.8k| if (nNumToConnect) ------------------ | Branch (2320:9): [True: 33.9k, False: 53.8k] ------------------ 2321| 33.9k| { 2322| | /* if both groups are present then add a supergroup */ 2323| 33.9k| ret = RegisterTCGroup( pTCGroups, 2324| 33.9k| BNS_VT_C_POS_ALL, ------------------ | | 71| 33.9k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | ------------------ | | | | 50| 33.9k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | ------------------ | | | | 49| 33.9k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ 2325| 33.9k| 0, 2326| 33.9k| 0 /* st_cap */, 2327| 33.9k| 0 /* st_flow */, 2328| 33.9k| 0 /* edge cap */, 2329| 33.9k| 0 /* edge flow */, 2330| 33.9k| 1 + nNumToConnect 2331| | /* one more edge to connect to */ 2332| 33.9k| /* an additional (+/-) vertex */ ); 2333| | 2334| 33.9k| if (ret <= 0) ------------------ | Branch (2334:13): [True: 0, False: 33.9k] ------------------ 2335| 0| { 2336| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2336:19): [True: 0, False: 0] ------------------ 2337| 0| goto exit_function; 2338| 0| } 2339| | 2340| 33.9k| pTCGroups->nGroup[TCG_Plus] = ret - 1; /* newly added group number */ 2341| 33.9k| pTCGroups->nVertices += 2; /* two vertices including itself */ 2342| 33.9k| pTCGroups->nEdges += 1 + nNumToConnect; /* one more edge to connect to an additional (+/-) vertex */ 2343| 33.9k| } 2344| | 2345| | /* add (-) supergroup */ 2346| 87.8k| n1 = pTCGroups->nGroup[TCG_Minus0]; 2347| 87.8k| n2 = pTCGroups->nGroup[TCG_Minus_C0]; 2348| 87.8k| n3 = pTCGroups->nGroup[TCG_Minus_M0]; 2349| 87.8k| nNumToConnect = ( n1 >= 0 ) + ( n2 >= 0 ) + ( n3 >= 0 ); 2350| 87.8k| if (nNumToConnect) ------------------ | Branch (2350:9): [True: 33.2k, False: 54.5k] ------------------ 2351| 33.2k| { 2352| | /* if both groups are present then add a supergroup */ 2353| | 2354| 33.2k| ret = RegisterTCGroup( pTCGroups, 2355| 33.2k| BNS_VT_C_NEG_ALL, ------------------ | | 72| 33.2k|#define BNS_VT_C_NEG_ALL (BNS_VT_C_POS_ALL | BNS_VERT_TYPE_C_NEGATIVE) /* supergroup (-) */ | | ------------------ | | | | 71| 33.2k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 33.2k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 33.2k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define BNS_VT_C_NEG_ALL (BNS_VT_C_POS_ALL | BNS_VERT_TYPE_C_NEGATIVE) /* supergroup (-) */ | | ------------------ | | | | 54| 33.2k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ | | ------------------ ------------------ 2356| 33.2k| 0, 2357| 33.2k| 0 /* st_cap */, 2358| 33.2k| 0 /* st_flow */, 2359| 33.2k| 0 /* edge cap */, 2360| 33.2k| 0 /* edge flow */, 2361| 33.2k| 1 + nNumToConnect /* one more edge to connect to an additional (+/-) vertex */ ); 2362| | 2363| 33.2k| if (ret < 0) ------------------ | Branch (2363:13): [True: 0, False: 33.2k] ------------------ 2364| 0| { 2365| 0| goto exit_function; 2366| 0| } 2367| 33.2k| pTCGroups->nGroup[TCG_Minus] = ret - 1; /* newly added group number */ 2368| 33.2k| pTCGroups->nVertices += 2; /* needs two vertices including itself */ 2369| 33.2k| pTCGroups->nEdges += 1 + nNumToConnect; /* one more edge to connect to an additional (+/-) vertex */ 2370| 33.2k| } 2371| | 2372| | /* add neutralization vertex: (+)-()=(-) connection */ 2373| 87.8k| k = pTCGroups->nGroup[TCG_Minus]; 2374| 87.8k| n = pTCGroups->nGroup[TCG_Plus]; 2375| 87.8k| nNumToConnect = ( k >= 0 ) + ( n >= 0 ); 2376| 87.8k| if (nNumToConnect) ------------------ | Branch (2376:9): [True: 34.1k, False: 53.6k] ------------------ 2377| 34.1k| { 2378| 34.1k| pTCGroups->nVertices += 1; 2379| 34.1k| pTCGroups->nEdges += nNumToConnect; /* one edge per super-c-group */ 2380| 34.1k| } 2381| | 2382| 87.8k| ret = 0; 2383| | 2384| 87.8k|exit_function: 2385| 87.8k| return ret; 2386| 87.8k|} AddTGroups2TCGBnStruct: 2395| 87.8k|{ 2396| 87.8k| int ret = 0; 2397| 87.8k| inp_ATOM *at = pStruct->at; 2398| 87.8k| int num_atoms = pStruct->num_atoms; 2399| 87.8k| int tot_st_cap, tot_st_flow; 2400| | /* ret = ReInitBnStruct( pBNS ); */ 2401| | 2402| 87.8k| if (pTCGroups->num_tgroups /* tgi && tgi->num_t_groups && tgi->t_group*/) ------------------ | Branch (2402:9): [True: 523, False: 87.2k] ------------------ 2403| 523| { 2404| 523| int i, k, endpoint, /*centerpoint,*/ fictpoint; 2405| 523| int num_tg = pTCGroups->num_tgroups; 2406| 523| int num_edges = pBNS->num_edges; 2407| 523| int num_vertices = pBNS->num_vertices; 2408| 523| BNS_VERTEX *vert_ficpoint, *vert_ficpoint_prev; /* fictitious vertex describing t-group */ 2409| 523| BNS_VERTEX *vert_endpoint; 2410| 523| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 2411| 523| int nMaxTGroupNumber = 0; 2412| | /*ENDPOINT_INFO eif;*/ 2413| | 2414| | /* Debug: check overflow */ 2415| 523| if (num_vertices + num_tg >= pBNS->max_vertices) ------------------ | Branch (2415:13): [True: 0, False: 523] ------------------ 2416| 0| { 2417| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2418| 0| } 2419| 523| if (num_edges + pTCGroups->num_tgroup_edges >= pBNS->max_edges) ------------------ | Branch (2419:13): [True: 0, False: 523] ------------------ 2420| 0| { 2421| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2422| 0| } 2423| | 2424| | /* find the largest t-group ID */ 2425| 1.11k| for (i = 0; i < pTCGroups->num_tc_groups; i++) ------------------ | Branch (2425:21): [True: 1.05k, False: 60] ------------------ 2426| 1.05k| { 2427| 1.05k| if (pTCGroups->pTCG[i].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 1.05k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (2427:17): [True: 594, False: 463] ------------------ 2428| 594| { 2429| 594| k = pTCGroups->pTCG[i].ord_num; 2430| 594| if (k <= 0) ------------------ | Branch (2430:21): [True: 0, False: 594] ------------------ 2431| 0| { 2432| 0| return BNS_CPOINT_ERR; /* t-group does not have a number or has a wrong number */ ------------------ | | 56| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2433| 0| } 2434| 594| if (k > pTCGroups->num_tc_groups) ------------------ | Branch (2434:21): [True: 0, False: 594] ------------------ 2435| 0| { 2436| 0| return BNS_CPOINT_ERR; /* t-group has a wrong number */ ------------------ | | 56| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2437| 0| } 2438| 594| if (k != nMaxTGroupNumber + 1) ------------------ | Branch (2438:21): [True: 0, False: 594] ------------------ 2439| 0| { 2440| 0| return BNS_CPOINT_ERR; /* t-group numbers are not contiguously ascending */ ------------------ | | 56| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2441| 0| } 2442| 594| nMaxTGroupNumber = k; 2443| 594| } 2444| 463| else 2445| 463| { 2446| 463| break; /* t-groups are contiguous and first in the list */ 2447| 463| } 2448| 1.05k| } 2449| | 2450| 523| if (i != num_tg) ------------------ | Branch (2450:13): [True: 0, False: 523] ------------------ 2451| 0| { 2452| 0| return BNS_CPOINT_ERR; /* number of t-groups is wrong */ ------------------ | | 56| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2453| 0| } 2454| | 2455| | /* since t-group IDs may be not contiguous, clear all vertices that will be added. 2456| | all-zeroes-vertex will be ignored by the BNS 2457| | */ 2458| 523| memset( pBNS->vert + num_vertices, 0, nMaxTGroupNumber * sizeof( pBNS->vert[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2459| | 2460| | /* initialize new fictitious vertices */ 2461| 523| vert_ficpoint_prev = pBNS->vert + num_vertices - 1; 2462| | 2463| 523| tot_st_cap = tot_st_flow = 0; 2464| | 2465| 1.11k| for (i = 0; i < num_tg; i++, vert_ficpoint_prev = vert_ficpoint) ------------------ | Branch (2465:21): [True: 594, False: 523] ------------------ 2466| 594| { 2467| | /* 2468| | vert_ficpoint-1 is the last vertex; 2469| | vert_ficpoint is the vertex that is being added 2470| | Note: nGroupNumber are not contiguous 2471| | */ 2472| 594| vert_ficpoint = pBNS->vert + num_vertices + pTCGroups->pTCG[i].ord_num - 1; 2473| 594| vert_ficpoint->iedge = vert_ficpoint_prev->iedge + vert_ficpoint_prev->max_adj_edges; 2474| 594| vert_ficpoint->max_adj_edges = pTCGroups->pTCG[i].num_edges + nMaxAddEdges + BNS_ADD_SUPER_TGROUP; ------------------ | | 85| 594|#define BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */ ------------------ 2475| 594| vert_ficpoint->num_adj_edges = 0; 2476| 594| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 2477| 594| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = pTCGroups->pTCG[i].st_cap; 2478| 594| tot_st_cap += pTCGroups->pTCG[i].st_cap; 2479| 594| vert_ficpoint->type = pTCGroups->pTCG[i].type; 2480| 594| pTCGroups->pTCG[i].nVertexNumber = (int) ( vert_ficpoint - pBNS->vert ); 2481| 594| } 2482| | 2483| 4.83k| for (endpoint = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (2483:28): [True: 4.30k, False: 523] ------------------ 2484| 4.30k| { 2485| 4.30k| if (!at[endpoint].endpoint) ------------------ | Branch (2485:17): [True: 3.17k, False: 1.13k] ------------------ 2486| 3.17k| continue; 2487| 1.13k| fictpoint = at[endpoint].endpoint + num_vertices - 1; 2488| 1.13k| vert_ficpoint = pBNS->vert + fictpoint; /* t-group vertex */ 2489| 1.13k| vert_endpoint = pBNS->vert + endpoint; /* endpoint vertex */ 2490| | /* Debug: check overflow */ 2491| 1.13k| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (2491:17): [True: 0, False: 1.13k] ------------------ 2492| 1.13k| num_edges >= pBNS->max_edges || ------------------ | Branch (2492:18): [True: 0, False: 1.13k] ------------------ 2493| 1.13k| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (2493:18): [True: 0, False: 1.13k] ------------------ 2494| 1.13k| vert_endpoint->num_adj_edges >= vert_endpoint->max_adj_edges) ------------------ | Branch (2494:18): [True: 0, False: 1.13k] ------------------ 2495| 0| { 2496| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2497| 0| break; 2498| 0| } 2499| | 2500| |#ifdef NEVER 2501| | /* obtain donor/acceptor info */ 2502| | if (!nGetEndpointInfo( at, endpoint, &eif )) 2503| | { 2504| | ret = BNS_BOND_ERR; 2505| | break; 2506| | } 2507| |#endif 2508| | 2509| 1.13k| vert_endpoint->type |= BNS_VERT_TYPE_ENDPOINT; ------------------ | | 46| 1.13k|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 2510| | 2511| |#ifdef NEVER 2512| | /* set capacity = 1 to the edges from the endpoint to the centerpoint(s) */ 2513| | for (k = 0; k < vert_endpoint->num_adj_edges; k++) 2514| | { 2515| | int iedge = vert_endpoint->iedge[k]; 2516| | if (!pBNS->edge[iedge].cap) 2517| | { 2518| |/* single bond, possibly between endpoint and centerpoint */ 2519| | centerpoint = ( pBNS->edge[iedge].neighbor12 ^ endpoint ); 2520| | if (centerpoint < pBNS->num_atoms && 2521| | pBNS->vert[centerpoint].st_edge.cap >= 1) 2522| | { 2523| | int bond_type = ( at[endpoint].bond_type[k] & BOND_TYPE_MASK ); 2524| | if (bond_type == BOND_TAUTOM || 2525| | bond_type == BOND_ALTERN || 2526| | bond_type == BOND_ALT12NS || 2527| | bond_type == BOND_SINGLE) 2528| | { 2529| | pBNS->edge[iedge].cap = 1; 2530| | } 2531| | } 2532| | } 2533| | } 2534| |#endif 2535| | 2536| | /* create a new edge connecting endpoint to the new fictitious t-group vertex vert_ficpoint */ 2537| 1.13k| edge = pBNS->edge + num_edges; 2538| 1.13k| edge->cap = vert_endpoint->st_edge.cap - vert_endpoint->st_edge.flow; 2539| 1.13k| edge->cap = inchi_min( edge->cap, MAX_TGROUP_EDGE_CAP ); ------------------ | | 139| 1.13k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 876, False: 255] | | ------------------ ------------------ 2540| 1.13k| edge->cap = inchi_max( edge->cap, 0 ); ------------------ | | 138| 1.13k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 911, False: 220] | | ------------------ ------------------ 2541| 1.13k| edge->flow = 0; 2542| 1.13k| edge->pass = 0; 2543| | 2544| |#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 2545| | edge->forbidden &= pBNS->edge_forbidden_mask; 2546| |#endif 2547| | 2548| |#ifdef NEVER 2549| | /* later include case when the charge change allows the endpoint to become tautomeric */ 2550| | /* mark endoint having moveable H atom with flow=1 */ 2551| | 2552| | /* -- old "no charges" version -- */ 2553| | /* if (at[endpoint].chem_bonds_valence == at[endpoint].valence) */ 2554| | /* -- the following line takes charges into account -- */ 2555| | if (eif.cDonor) /* means the endpoint has an H-atom to donate */ 2556| | { 2557| | /* increment edge flow */ 2558| | edge->flow++; 2559| | /* increment one vertex st-flow & cap */ 2560| | vert_ficpoint->st_edge.flow++; 2561| | vert_ficpoint->st_edge.cap++; 2562| | /* increment another vertex st-flow & cap */ 2563| | vert_endpoint->st_edge.flow++; 2564| | vert_endpoint->st_edge.cap++; 2565| | } 2566| |#endif 2567| | 2568| | /* connect edge to endpoint and fictpoint and increment the counters of neighbors and edges */ 2569| 1.13k| ret = ConnectTwoVertices( vert_endpoint, vert_ficpoint, edge, pBNS, 0 ); 2570| 1.13k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 1.13k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.13k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.13k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.13k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.13k, False: 0] | | | Branch (67:44): [True: 0, False: 1.13k] | | ------------------ ------------------ 2571| 0| { 2572| 0| break; 2573| 0| } 2574| 1.13k| num_edges++; 2575| 1.13k| edge->cap0 = edge->cap; 2576| 1.13k| edge->flow0 = edge->flow; 2577| 1.13k| pVA[endpoint].nTautGroupEdge = num_edges; /* edge index + 1 */ 2578| 1.13k| } 2579| | 2580| 523| pBNS->num_edges = num_edges; 2581| 523| pBNS->num_vertices += nMaxTGroupNumber; 2582| 523| pBNS->num_t_groups = num_tg; 2583| 523| pBNS->tot_st_cap += tot_st_cap; 2584| 523| pBNS->tot_st_flow += tot_st_flow; 2585| 523| } 2586| | 2587| 87.8k| return ret; 2588| 87.8k|} ConnectTwoVertices: 2593| 830k|{ 2594| 830k| int ip1 = (int) ( p1 - pBNS->vert ); 2595| 830k| int ip2 = (int) ( p2 - pBNS->vert ); 2596| 830k| int ie = (int) ( e - pBNS->edge ); 2597| | 2598| | /* debug: check bounds */ 2599| 830k| if (ip1 >= pBNS->max_vertices || ip1 < 0 || ------------------ | Branch (2599:9): [True: 0, False: 830k] | Branch (2599:38): [True: 0, False: 830k] ------------------ 2600| 830k| ip2 >= pBNS->max_vertices || ip2 < 0 || ------------------ | Branch (2600:10): [True: 0, False: 830k] | Branch (2600:39): [True: 0, False: 830k] ------------------ 2601| 830k| ie >= pBNS->max_edges || ie < 0 || ------------------ | Branch (2601:10): [True: 0, False: 830k] | Branch (2601:35): [True: 0, False: 830k] ------------------ 2602| 830k| ( p1->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (2602:10): [True: 0, False: 830k] ------------------ 2603| 830k| ( p1->iedge - pBNS->iedge ) + p1->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (2603:10): [True: 0, False: 830k] ------------------ 2604| 830k| ( p2->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (2604:10): [True: 0, False: 830k] ------------------ 2605| 830k| ( p2->iedge - pBNS->iedge ) + p2->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (2605:10): [True: 0, False: 830k] ------------------ 2606| 830k| p1->num_adj_edges >= p1->max_adj_edges || ------------------ | Branch (2606:10): [True: 0, False: 830k] ------------------ 2607| 830k| p2->num_adj_edges >= p2->max_adj_edges) ------------------ | Branch (2607:10): [True: 0, False: 830k] ------------------ 2608| 0| { 2609| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2610| 0| } 2611| | /* clear the edge */ 2612| 830k| if (bClearEdge) ------------------ | Branch (2612:9): [True: 351k, False: 479k] ------------------ 2613| 351k| { 2614| 351k| memset( e, 0, sizeof( *e ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2615| 351k| } 2616| 479k| else 2617| 479k| if (e->neighbor1 || e->neighbor12) ------------------ | Branch (2617:13): [True: 0, False: 479k] | Branch (2617:29): [True: 0, False: 479k] ------------------ 2618| 0| { 2619| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2620| 0| } 2621| | 2622| | /* connect */ 2623| 830k| e->neighbor1 = inchi_min( ip1, ip2 ); ------------------ | | 139| 830k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 427k, False: 403k] | | ------------------ ------------------ 2624| 830k| e->neighbor12 = ip1 ^ ip2; 2625| 830k| p1->iedge[p1->num_adj_edges] = ie; 2626| 830k| p2->iedge[p2->num_adj_edges] = ie; 2627| 830k| e->neigh_ord[ip1 > ip2] = p1->num_adj_edges++; 2628| | 2629| 830k| e->neigh_ord[ip1 < ip2] = p2->num_adj_edges++; 2630| 830k| return 0; 2631| 830k|} AddRadicalToMetal: 2672| 34.1k|{ 2673| 34.1k| int iG0 = pTCGroups->nGroup[TCG_MeFlower0]; /* index in pTCGroups->pTCG[] */ 2674| 34.1k| int iG1 = pTCGroups->nGroup[TCG_MeFlower1]; 2675| 34.1k| int iG2 = pTCGroups->nGroup[TCG_MeFlower2]; 2676| 34.1k| int iG3 = pTCGroups->nGroup[TCG_MeFlower3]; 2677| 34.1k| int n = (iG0 >= 0) + (iG1 >= 0) + (iG2 >= 0) + (iG3 >= 0); 2678| 34.1k| int vG0, vG1, vG2, vG3; /* M-vertex number */ 2679| 34.1k| BNS_VERTEX* pG0 = NULL, * pG1 = NULL, * pG2 = NULL, * pG3 = NULL; 2680| | 2681| 34.1k| if (pTCGroups->num_metal_atoms && ------------------ | Branch (2681:9): [True: 17.2k, False: 16.9k] ------------------ 2682| 17.2k| pSrm->bMetalAddFlower && ------------------ | Branch (2682:9): [True: 17.2k, False: 0] ------------------ 2683| 17.2k| *tot_st_cap % 2 && ------------------ | Branch (2683:9): [True: 9.58k, False: 7.62k] ------------------ 2684| 9.58k| n == 4) ------------------ | Branch (2684:9): [True: 9.53k, False: 46] ------------------ 2685| 9.53k| { 2686| 9.53k| vG0 = pTCGroups->pTCG[iG0].nVertexNumber; 2687| 9.53k| vG1 = pTCGroups->pTCG[iG1].nVertexNumber; 2688| 9.53k| vG2 = pTCGroups->pTCG[iG2].nVertexNumber; 2689| 9.53k| vG3 = pTCGroups->pTCG[iG3].nVertexNumber; 2690| | 2691| 9.53k| pG0 = pBNS->vert + vG0; 2692| 9.53k| pG1 = pBNS->vert + vG1; 2693| 9.53k| pG2 = pBNS->vert + vG2; 2694| 9.53k| pG3 = pBNS->vert + vG3; 2695| | 2696| | /* add 1 unit to metal flower st_cap */ 2697| 9.53k| pG3->st_edge.cap++; 2698| 9.53k| pG3->st_edge.cap0++; 2699| 9.53k| (*tot_st_cap)++; 2700| 9.53k| return 1; 2701| 9.53k| } 2702| | 2703| 24.6k| return 0; 2704| 34.1k|} ConnectMetalFlower: 2711| 34.1k|{ 2712| 34.1k| int iG0 = pTCGroups->nGroup[TCG_MeFlower0]; /* index in pTCGroups->pTCG[] */ 2713| 34.1k| int iG1 = pTCGroups->nGroup[TCG_MeFlower1]; 2714| 34.1k| int iG2 = pTCGroups->nGroup[TCG_MeFlower2]; 2715| 34.1k| int iG3 = pTCGroups->nGroup[TCG_MeFlower3]; 2716| 34.1k| int n = ( iG0 >= 0 ) + ( iG1 >= 0 ) + ( iG2 >= 0 ) + ( iG3 >= 0 ); 2717| 34.1k| int vG0, vG1, vG2, vG3; /* M-vertex number */ 2718| 34.1k| int cur_num_edges = *pcur_num_edges; 2719| 34.1k| int cur_num_vertices = *pcur_num_vertices; 2720| 34.1k| BNS_VERTEX *pG0 = NULL, *pG1 = NULL, *pG2 = NULL, *pG3 = NULL; 2721| 34.1k| BNS_EDGE *ea = NULL, *eb = NULL, *ed = NULL, *ex = NULL, *ey = NULL, *e; 2722| 34.1k| int ia, ib, id, ix, iy; 2723| 34.1k| int c, f, dc, df, ca, fa, cb, fb, cd, fd, cx, fx, cy, fy; 2724| 34.1k| int C0, F0, C1, F1, C2, F2, C3, F3, D; 2725| 34.1k| int ret = 0, i; 2726| | 2727| 34.1k| if (0 == n) ------------------ | Branch (2727:9): [True: 17.0k, False: 17.1k] ------------------ 2728| 17.0k| { 2729| 17.0k| goto exit_function; 2730| 17.0k| } 2731| | 2732| 17.1k| if (4 != n) ------------------ | Branch (2732:9): [True: 0, False: 17.1k] ------------------ 2733| 0| { 2734| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2735| 0| goto exit_function; 2736| 0| } 2737| | 2738| 17.1k| vG0 = pTCGroups->pTCG[iG0].nVertexNumber; 2739| 17.1k| vG1 = pTCGroups->pTCG[iG1].nVertexNumber; 2740| 17.1k| vG2 = pTCGroups->pTCG[iG2].nVertexNumber; 2741| 17.1k| vG3 = pTCGroups->pTCG[iG3].nVertexNumber; 2742| | 2743| 17.1k| pG0 = pBNS->vert + vG0; 2744| 17.1k| pG1 = pBNS->vert + vG1; 2745| 17.1k| pG2 = pBNS->vert + vG2; 2746| 17.1k| pG3 = pBNS->vert + vG3; 2747| | 2748| | /* count G0 edges cap and flow (currently only atoms are connected to G0) */ 2749| 41.4k| for (i = 0, c = 0, f = 0; i < pG0->num_adj_edges; i++) ------------------ | Branch (2749:31): [True: 24.3k, False: 17.1k] ------------------ 2750| 24.3k| { 2751| 24.3k| e = pBNS->edge + pG0->iedge[i]; 2752| 24.3k| c += e->cap; 2753| 24.3k| f += e->flow; 2754| 24.3k| } 2755| | 2756| | /* consistency checks */ 2757| 17.1k| if (!IS_BNS_VT_M_GR( pTCGroups->pTCG[iG0].type ) && ------------------ | | 80| 34.2k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 17.1k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ ------------------ | Branch (2757:9): [True: 0, False: 17.1k] ------------------ 2758| 0| ( pTCGroups->pTCG[iG0].edges_cap != pG0->st_edge.cap || ------------------ | Branch (2758:11): [True: 0, False: 0] ------------------ 2759| 0| pTCGroups->pTCG[iG0].edges_flow != pG0->st_edge.flow )) ------------------ | Branch (2759:13): [True: 0, False: 0] ------------------ 2760| 0| { 2761| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2762| 0| goto exit_function; 2763| 0| } 2764| | 2765| 17.1k| if (pTCGroups->pTCG[iG0].edges_cap != c || ------------------ | Branch (2765:9): [True: 0, False: 17.1k] ------------------ 2766| 17.1k| pTCGroups->pTCG[iG0].edges_flow != f) ------------------ | Branch (2766:10): [True: 0, False: 17.1k] ------------------ 2767| 0| { 2768| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2769| 0| goto exit_function; 2770| 0| } 2771| | 2772| | /* get new edges */ 2773| | 2774| 17.1k| ea = pBNS->edge + (ia = cur_num_edges++); 2775| 17.1k| eb = pBNS->edge + (ib = cur_num_edges++); 2776| 17.1k| ed = pBNS->edge + (id = cur_num_edges++); 2777| 17.1k| ex = pBNS->edge + (ix = cur_num_edges++); 2778| 17.1k| ey = pBNS->edge + (iy = cur_num_edges++); 2779| | 2780| | /* connect vertices with edges */ 2781| 17.1k| ret = ConnectTwoVertices( pG0, pG1, eb, pBNS, 1 ); 2782| 17.1k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 17.1k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 17.1k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 17.1k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 17.1k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 17.1k, False: 0] | | | Branch (67:44): [True: 0, False: 17.1k] | | ------------------ ------------------ 2783| 0| { 2784| 0| goto exit_function; 2785| 0| } 2786| | 2787| 17.1k| ret = ConnectTwoVertices( pG0, pG2, ea, pBNS, 1 ); 2788| | 2789| 17.1k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 17.1k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 17.1k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 17.1k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 17.1k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 17.1k, False: 0] | | | Branch (67:44): [True: 0, False: 17.1k] | | ------------------ ------------------ 2790| 0| { 2791| 0| goto exit_function; 2792| 0| } 2793| | 2794| 17.1k| ret = ConnectTwoVertices( pG1, pG2, ed, pBNS, 1 ); 2795| | 2796| 17.1k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 17.1k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 17.1k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 17.1k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 17.1k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 17.1k, False: 0] | | | Branch (67:44): [True: 0, False: 17.1k] | | ------------------ ------------------ 2797| 0| { 2798| 0| goto exit_function; 2799| 0| } 2800| | 2801| 17.1k| ret = ConnectTwoVertices( pG1, pG3, ey, pBNS, 1 ); 2802| | 2803| 17.1k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 17.1k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 17.1k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 17.1k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 17.1k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 17.1k, False: 0] | | | Branch (67:44): [True: 0, False: 17.1k] | | ------------------ ------------------ 2804| 0| { 2805| 0| goto exit_function; 2806| 0| } 2807| | 2808| 17.1k| ret = ConnectTwoVertices( pG2, pG3, ex, pBNS, 1 ); 2809| | 2810| 17.1k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 17.1k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 17.1k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 17.1k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 17.1k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 17.1k, False: 0] | | | Branch (67:44): [True: 0, False: 17.1k] | | ------------------ ------------------ 2811| 0| { 2812| 0| goto exit_function; 2813| 0| } 2814| | 2815| | /* calculate caps and flows */ 2816| | 2817| 17.1k| dc = c % 2; 2818| 17.1k| c /= 2; 2819| 17.1k| df = f % 2; 2820| 17.1k| f /= 2; 2821| | 2822| 17.1k| D = pSrm->nMetalFlowerParam_D; 2823| | 2824| 17.1k| C0 = F0 = 2 * c + 2 * D + dc; 2825| 17.1k| C1 = F1 = c + 2 * D + dc - df; 2826| 17.1k| C2 = F2 = c + 2 * D; 2827| 17.1k| C3 = F3 = 0; 2828| | 2829| 17.1k| ca = c + 2 * D; 2830| 17.1k| fa = c + D - f; 2831| | 2832| 17.1k| cb = c + 2 * D + dc; 2833| 17.1k| fb = c + D + dc - ( f + df ); 2834| | 2835| 17.1k| cd = c + 2 * D; 2836| 17.1k| fd = f + D; 2837| | 2838| 17.1k| cx = cy = D; 2839| 17.1k| fx = fy = 0; 2840| | 2841| | /* check overflow */ 2842| 17.1k| if (C0 >= EDGE_FLOW_ST_MASK || F0 >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 34.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ if (C0 >= EDGE_FLOW_ST_MASK || F0 >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 34.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2842:9): [True: 0, False: 17.1k] | Branch (2842:36): [True: 0, False: 17.1k] ------------------ 2843| 17.1k| C1 >= EDGE_FLOW_ST_MASK || F1 >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 34.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ C1 >= EDGE_FLOW_ST_MASK || F1 >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 34.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2843:10): [True: 0, False: 17.1k] | Branch (2843:37): [True: 0, False: 17.1k] ------------------ 2844| 17.1k| C2 >= EDGE_FLOW_ST_MASK || F2 >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 34.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ C2 >= EDGE_FLOW_ST_MASK || F2 >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 34.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2844:10): [True: 0, False: 17.1k] | Branch (2844:37): [True: 0, False: 17.1k] ------------------ 2845| 17.1k| C3 >= EDGE_FLOW_ST_MASK || F3 >= EDGE_FLOW_ST_MASK) ------------------ | | 128| 34.2k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ C3 >= EDGE_FLOW_ST_MASK || F3 >= EDGE_FLOW_ST_MASK) ------------------ | | 128| 17.1k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2845:10): [True: 0, False: 17.1k] | Branch (2845:37): [True: 0, False: 17.1k] ------------------ 2846| 0| { 2847| 0| return BNS_PROGRAM_ERR; /* cannot handle too large st-cap or st-flow */ ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2848| 0| } 2849| | 2850| | /* set st caps and flows */ 2851| | 2852| 17.1k| SetStCapFlow( pG0, tot_st_flow, tot_st_cap, C0, F0 ); 2853| 17.1k| SetStCapFlow( pG1, tot_st_flow, tot_st_cap, C1, F1 ); 2854| 17.1k| SetStCapFlow( pG2, tot_st_flow, tot_st_cap, C2, F2 ); 2855| 17.1k| SetStCapFlow( pG3, tot_st_flow, tot_st_cap, C3, F3 ); 2856| | 2857| 17.1k| SetEdgeCapFlow( ea, ca, fa ); 2858| 17.1k| SetEdgeCapFlow( eb, cb, fb ); 2859| 17.1k| SetEdgeCapFlow( ed, cd, fd ); 2860| 17.1k| SetEdgeCapFlow( ex, cx, fx ); 2861| 17.1k| SetEdgeCapFlow( ey, cy, fy ); 2862| | 2863| | 2864| 17.1k| *pcur_num_edges = cur_num_edges; 2865| 17.1k| *pcur_num_vertices = cur_num_vertices; 2866| | 2867| 17.1k| ret = 0; 2868| | 2869| 34.1k|exit_function: 2870| | 2871| 34.1k| return ret; 2872| 17.1k|} SetEdgeCapFlow: 2877| 85.5k|{ 2878| 85.5k| e->cap = e->cap0 = edge_cap; 2879| 85.5k| e->flow = e->flow0 = edge_flow; 2880| 85.5k|} AddEdgeFlow: 2890| 265k|{ 2891| | 2892| | /* overflow check */ 2893| 265k| if (e01->cap < 0 || edge_cap < 0 || (int) e01->cap + edge_cap >= EDGE_FLOW_MASK) ------------------ | | 133| 265k|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2893:9): [True: 0, False: 265k] | Branch (2893:25): [True: 0, False: 265k] | Branch (2893:41): [True: 0, False: 265k] ------------------ 2894| 0| { 2895| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2896| 0| } 2897| | 2898| 265k| if (pDst->st_edge.cap < 0 || (int) pDst->st_edge.cap + edge_cap >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 531k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2898:9): [True: 0, False: 265k] | Branch (2898:34): [True: 0, False: 265k] ------------------ 2899| 265k| pDst->st_edge.flow < 0 || (int) pDst->st_edge.flow + edge_flow >= EDGE_FLOW_ST_MASK || ------------------ | | 128| 531k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2899:10): [True: 0, False: 265k] | Branch (2899:36): [True: 0, False: 265k] ------------------ 2900| 265k| pSrc->st_edge.cap < 0 || pSrc->st_edge.flow < 0 || ------------------ | Branch (2900:10): [True: 0, False: 265k] | Branch (2900:35): [True: 0, False: 265k] ------------------ 2901| 265k| (int) pSrc->st_edge.flow + edge_flow >= EDGE_FLOW_ST_MASK) ------------------ | | 128| 265k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2901:10): [True: 0, False: 265k] ------------------ 2902| 0| { 2903| 0| return BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2904| 0| } 2905| | 2906| | /* add flow */ 2907| 265k| e01->cap += edge_cap; 2908| 265k| e01->flow += edge_flow; 2909| 265k| e01->cap0 = e01->cap; 2910| 265k| e01->flow0 = e01->flow; 2911| | 2912| 265k| pDst->st_edge.cap += edge_cap; 2913| 265k| pDst->st_edge.cap0 = pDst->st_edge.cap; 2914| 265k| *tot_st_cap += edge_cap; 2915| | 2916| 265k| pDst->st_edge.flow += edge_flow; 2917| 265k| pDst->st_edge.flow0 = pDst->st_edge.flow; 2918| 265k| *tot_st_flow += edge_flow; 2919| | 2920| 265k| pSrc->st_edge.flow += edge_flow; 2921| 265k| pSrc->st_edge.flow0 = pSrc->st_edge.flow; 2922| 265k| *tot_st_flow += edge_flow; 2923| | 2924| |/* 2925| | pDst->st_edge.cap += e01->cap; 2926| | pDst->st_edge.cap0 = pDst->st_edge.cap; 2927| | *tot_st_cap += e01->cap; 2928| | 2929| | pDst->st_edge.flow += e01->flow; 2930| | pDst->st_edge.flow0 = pDst->st_edge.flow; 2931| | *tot_st_flow += e01->flow; 2932| | 2933| | pSrc->st_edge.flow += e01->flow; 2934| | pSrc->st_edge.flow0 = pSrc->st_edge.flow; 2935| | *tot_st_flow += e01->flow; 2936| |*/ 2937| 265k| return 0; 2938| 265k|} ConnectSuperCGroup: 3027| 102k|{ 3028| 102k| BNS_EDGE **e0X = NULL, *e; 3029| 102k| BNS_VERTEX **pvX = NULL, *pv0 = NULL, *pv1 = NULL, *pv = NULL; 3030| 102k| int *jX = NULL, *iX = NULL; 3031| 102k| int i, j, num_groups, j0, i1, j1, iXX, ret = 0, fst = 0; 3032| 102k| int cur_num_vertices = *pcur_num_vertices; 3033| 102k| int cur_num_edges = *pcur_num_edges; 3034| | 3035| 102k| if (nSuperCGroup >= 0) ------------------ | Branch (3035:9): [True: 68.3k, False: 34.1k] ------------------ 3036| 68.3k| { 3037| 68.3k| i1 = pTCGroups->nGroup[nSuperCGroup]; /* the supergroup */ 3038| 68.3k| if (i1 < 0) ------------------ | Branch (3038:13): [True: 1.10k, False: 67.2k] ------------------ 3039| 1.10k| return 0; 3040| 68.3k| } 3041| 34.1k| else 3042| 34.1k| { 3043| 34.1k| i1 = -1; 3044| 34.1k| fst = 1; 3045| 34.1k| } 3046| | 3047| 371k| for (i = num_groups = 0; i < num_add; i++) ------------------ | Branch (3047:30): [True: 270k, False: 101k] ------------------ 3048| 270k| { 3049| 270k| iXX = pTCGroups->nGroup[nAddGroups[i]]; 3050| 270k| num_groups += ( iXX >= 0 && iXX != i1 ); ------------------ | Branch (3050:25): [True: 198k, False: 71.8k] | Branch (3050:37): [True: 198k, False: 0] ------------------ 3051| 270k| } 3052| 101k| if (num_groups < 1) ------------------ | Branch (3052:9): [True: 0, False: 101k] ------------------ 3053| 0| { /* Y connect only 2 or more groups; V connects even 1 group */ 3054| 0| return 0; 3055| 0| } 3056| | 3057| 101k| e0X = (BNS_EDGE **) inchi_calloc( (long long)num_groups + 1, sizeof( e0X[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 101k|#define inchi_calloc calloc ------------------ 3058| 101k| pvX = (BNS_VERTEX **) inchi_calloc( (long long)num_groups + 1, sizeof( pvX[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 101k|#define inchi_calloc calloc ------------------ 3059| 101k| jX = (int *) inchi_calloc( (long long)num_groups + 1, sizeof( jX[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 101k|#define inchi_calloc calloc ------------------ 3060| 101k| iX = (int *) inchi_calloc( (long long)num_groups + 1, sizeof( iX[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 101k|#define inchi_calloc calloc ------------------ 3061| | 3062| 101k| if (!e0X || !pvX || !jX || !iX) ------------------ | Branch (3062:9): [True: 0, False: 101k] | Branch (3062:17): [True: 0, False: 101k] | Branch (3062:25): [True: 0, False: 101k] | Branch (3062:32): [True: 0, False: 101k] ------------------ 3063| 0| { 3064| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 3065| 0| goto exit_function; 3066| 0| } 3067| | 3068| | /* create vert_ficpoint -- central Y-connection vertex */ 3069| | 3070| 101k| j0 = cur_num_vertices; 3071| 101k| pv0 = pBNS->vert + j0; /* center of the Y-connection; has number j0 */ 3072| 101k| pv0->iedge = ( pv0 - 1 )->iedge + ( pv0 - 1 )->max_adj_edges; 3073| 101k| pv0->max_adj_edges = num_groups + 1 + BNS_ADD_EDGES; /* Y-connection num. edges */ ------------------ | | 89| 101k|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 3074| 101k| pv0->num_adj_edges = 0; /* nothing connected yet */ 3075| 101k| pv0->type = BNS_VT_YVCONNECTOR; ------------------ | | 75| 101k|#define BNS_VT_YVCONNECTOR BNS_VERT_TYPE__AUX /* group connection */ | | ------------------ | | | | 53| 101k|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ ------------------ 3076| 101k| cur_num_vertices++; 3077| | 3078| 101k| if (fst == 0) ------------------ | Branch (3078:9): [True: 67.2k, False: 34.1k] ------------------ 3079| 67.2k| { 3080| | /* find super c-group vertex pv1, number j1 */ 3081| 67.2k| jX[0] = j1 = pTCGroups->pTCG[i1].nVertexNumber; 3082| 67.2k| iX[0] = i1; 3083| 67.2k| pvX[0] = pv1 = pBNS->vert + j1; 3084| 67.2k| } 3085| | 3086| | /* find other c-group vertices */ 3087| 371k| for (i = 0, j = 1; i < num_add; i++) ------------------ | Branch (3087:24): [True: 270k, False: 101k] ------------------ 3088| 270k| { 3089| 270k| iXX = pTCGroups->nGroup[nAddGroups[i]]; 3090| 270k| if (( iXX >= 0 ) && ( iXX != i1 )) ------------------ | Branch (3090:13): [True: 198k, False: 71.8k] | Branch (3090:29): [True: 198k, False: 0] ------------------ 3091| 198k| { 3092| 198k| iX[j] = iXX; 3093| 198k| jX[j] = pTCGroups->pTCG[iXX].nVertexNumber; 3094| 198k| pvX[j] = pBNS->vert + jX[j]; 3095| 198k| j++; 3096| 198k| } 3097| 270k| } 3098| | 3099| | /* grab (num_groups+1) free edges */ 3100| 367k| for (i = fst; i <= num_groups; i++) ------------------ | Branch (3100:19): [True: 265k, False: 101k] ------------------ 3101| 265k| { 3102| 265k| e = e0X[i] = pBNS->edge + cur_num_edges; 3103| 265k| pv = pvX[i]; 3104| 265k| j = jX[i]; 3105| 265k| iXX = iX[i]; 3106| | /* connect all to pv0 */ 3107| 265k| ret = ConnectTwoVertices( pv0, pv, e, pBNS, 1 ); 3108| 265k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 265k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 265k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 265k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 265k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 265k, False: 0] | | | Branch (67:44): [True: 0, False: 265k] | | ------------------ ------------------ 3109| 0| { 3110| 0| goto exit_function; 3111| 0| } 3112| 265k| if (i) ------------------ | Branch (3112:13): [True: 198k, False: 67.2k] ------------------ 3113| 198k| { 3114| | /* from c-group to central Y-connecting vertex of from supergroup to (+/-) vertex */ 3115| 198k| pTCGroups->pTCG[iX[i]].nForwardEdge = cur_num_edges; 3116| 198k| } 3117| 67.2k| else 3118| 67.2k| { 3119| | /* from central Y-connecting vertex to supergroup */ 3120| 67.2k| pTCGroups->pTCG[iX[i]].nBackwardEdge = cur_num_edges; 3121| 67.2k| } 3122| 265k| cur_num_edges++; 3123| 265k| } 3124| | 3125| | /* set flow and cap for incoming into pv0 edges */ 3126| 299k| for (i = 1; i <= num_groups; i++) ------------------ | Branch (3126:17): [True: 198k, False: 101k] ------------------ 3127| 198k| { 3128| 198k| int nDelta = pTCGroups->pTCG[iX[i]].st_cap - pTCGroups->pTCG[iX[i]].edges_cap; 3129| 198k| int edge_cap = pTCGroups->pTCG[iX[i]].edges_cap + nDelta; /* added nDelta */ 3130| 198k| int edge_flow = pTCGroups->pTCG[iX[i]].edges_cap - pTCGroups->pTCG[iX[i]].edges_flow /*-nDelta*/; 3131| | 3132| 198k| ret = AddEdgeFlow( edge_cap, edge_flow, 3133| 198k| e0X[i], pvX[i]/*src*/, pv0 /* dest*/, tot_st_cap, tot_st_flow ); 3134| | 3135| 198k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 198k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 198k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 198k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 198k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 198k, False: 0] | | | Branch (67:44): [True: 0, False: 198k] | | ------------------ ------------------ 3136| 0| { 3137| 0| goto exit_function; 3138| 0| } 3139| 198k| } 3140| | 3141| 101k| if (fst == 0) ------------------ | Branch (3141:9): [True: 67.2k, False: 34.1k] ------------------ 3142| 67.2k| { 3143| | /* set flow and cap for going out of pv0 and into pv1 edge */ 3144| 67.2k| int edge_cap = pv0->st_edge.cap; 3145| 67.2k| int edge_flow = pv0->st_edge.cap - pv0->st_edge.flow; 3146| | 3147| 67.2k| ret = AddEdgeFlow( pv0->st_edge.cap, pv0->st_edge.cap - pv0->st_edge.flow, 3148| 67.2k| e0X[0], pv0/*src*/, pv1 /* dest*/, tot_st_cap, tot_st_flow ); 3149| | 3150| 67.2k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 67.2k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 67.2k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 67.2k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 67.2k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 67.2k, False: 0] | | | Branch (67:44): [True: 0, False: 67.2k] | | ------------------ ------------------ 3151| 0| { 3152| 0| goto exit_function; 3153| 0| } 3154| | 3155| 67.2k| pTCGroups->pTCG[iX[0]].edges_cap += edge_cap; 3156| 67.2k| pTCGroups->pTCG[iX[0]].edges_flow += edge_flow; 3157| 67.2k| pTCGroups->pTCG[iX[0]].st_cap += edge_cap; 3158| 67.2k| pTCGroups->pTCG[iX[0]].st_flow += edge_flow; 3159| 67.2k| } 3160| 34.1k| else 3161| 34.1k| { 3162| | /* no supergroup => change cap to flow */ 3163| 34.1k| *tot_st_cap += pv0->st_edge.flow - pv0->st_edge.cap; 3164| 34.1k| pv0->st_edge.cap += pv0->st_edge.flow - pv0->st_edge.cap; 3165| 34.1k| pv0->st_edge.cap0 = pv0->st_edge.cap; 3166| 34.1k| } 3167| | 3168| 101k| *pcur_num_vertices = cur_num_vertices; 3169| 101k| *pcur_num_edges = cur_num_edges; 3170| 101k| ret = num_groups; 3171| | 3172| 101k|exit_function: 3173| 101k| if (e0X) inchi_free( e0X ); ------------------ | | 1152| 101k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 101k, False: 0] | | | Branch (1152:50): [Folded, False: 101k] | | ------------------ ------------------ | Branch (3173:9): [True: 101k, False: 0] ------------------ 3174| 101k| if (pvX) inchi_free( pvX ); ------------------ | | 1152| 101k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 101k, False: 0] | | | Branch (1152:50): [Folded, False: 101k] | | ------------------ ------------------ | Branch (3174:9): [True: 101k, False: 0] ------------------ 3175| 101k| if (jX) inchi_free( jX ); ------------------ | | 1152| 101k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 101k, False: 0] | | | Branch (1152:50): [Folded, False: 101k] | | ------------------ ------------------ | Branch (3175:9): [True: 101k, False: 0] ------------------ 3176| 101k| if (iX) inchi_free( iX ); ------------------ | | 1152| 101k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 101k, False: 0] | | | Branch (1152:50): [Folded, False: 101k] | | ------------------ ------------------ | Branch (3176:9): [True: 101k, False: 0] ------------------ 3177| | 3178| 101k| return ret; 3179| 101k|} AddStCapFlow: 3184| 358k|{ 3185| 358k| vert_ficpoint->st_edge.flow += flow; 3186| 358k| *tot_st_flow += flow; 3187| 358k| vert_ficpoint->st_edge.cap += cap; 3188| 358k| *tot_st_cap += cap; 3189| | 3190| 358k| vert_ficpoint->st_edge.flow0 = vert_ficpoint->st_edge.flow; 3191| 358k| vert_ficpoint->st_edge.cap0 = vert_ficpoint->st_edge.cap; 3192| 358k|} SetStCapFlow: 3197| 68.4k|{ 3198| 68.4k| *tot_st_flow += flow - vert_ficpoint->st_edge.flow; 3199| 68.4k| vert_ficpoint->st_edge.flow = flow; 3200| 68.4k| *tot_st_cap += cap - vert_ficpoint->st_edge.cap; 3201| 68.4k| vert_ficpoint->st_edge.cap = cap; 3202| | 3203| 68.4k| vert_ficpoint->st_edge.flow0 = vert_ficpoint->st_edge.flow; 3204| 68.4k| vert_ficpoint->st_edge.cap0 = vert_ficpoint->st_edge.cap; 3205| 68.4k|} AddCGroups2TCGBnStruct: 3216| 87.8k|{ 3217| 87.8k| int ret = 0, ret1, ret2, ret3, bNeedsFlower; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3218| 87.8k| inp_ATOM *at = pStruct->at; 3219| 87.8k| int num_atoms = pStruct->num_atoms; 3220| | /*int num_tg = pTCGroups->num_tgroups;*/ 3221| 87.8k| int num_cg = pTCGroups->num_tc_groups - pTCGroups->num_tgroups; 3222| 87.8k| int fst_cg_vertex = pBNS->num_vertices; 3223| 87.8k| int fst_cg_group = pTCGroups->num_tgroups; 3224| 87.8k| int num_vertices = pBNS->num_vertices; 3225| 87.8k| int num_edges = pBNS->num_edges; 3226| 87.8k| int cg_charge = 0; 3227| 87.8k| ICHICONST SRM *pSrm = pStruct->pSrm; ------------------ | | 13| 87.8k|#define ICHICONST const ------------------ 3228| | 3229| | /* ret = ReInitBnStruct( pBNS ); */ 3230| | 3231| 87.8k| if (num_cg > 0) ------------------ | Branch (3231:9): [True: 34.1k, False: 53.6k] ------------------ 3232| 34.1k| { 3233| | /* if ( cgi && cgi->num_c_groups && cgi->c_group ) */ 3234| 34.1k| int i, i1, i2, j, j1, j2, k, k1, k2, n, c_point, c_neigh, cap, flow; 3235| 34.1k| int cur_num_vertices, cur_num_edges; 3236| 34.1k| BNS_VERTEX *vert_ficpoint, *vert_ficpoint_prev, *vert_ficpoint_base; /* fictitious vertex describing charge c-group */ 3237| 34.1k| BNS_VERTEX *pv1, *pv2; 3238| 34.1k| BNS_EDGE *edge; /* edge between that vertex and the tautomeric c_point */ 3239| 34.1k| int nMaxCGroupNumber = 0; 3240| 34.1k| MY_CONST C_NODE *pCN; ------------------ | | 268| 34.1k|#define MY_CONST const ------------------ 3241| 34.1k| int cn_len, cn_bits, bMetalAtoms; 3242| 34.1k| int type; 3243| 34.1k| int tot_st_cap, tot_st_flow; 3244| 34.1k| int nAddGroups[16]; 3245| | 3246| | 3247| | /* Debug: check overflow */ 3248| 34.1k| if (num_vertices >= pBNS->max_vertices) ------------------ | Branch (3248:13): [True: 0, False: 34.1k] ------------------ 3249| 0| { 3250| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3251| 0| } 3252| | 3253| 34.1k| nMaxCGroupNumber = num_cg; 3254| | /* clear all vertices not used until now */ 3255| 34.1k| memset( pBNS->vert + num_vertices, 0, ( (long long)pBNS->max_vertices - num_vertices ) * sizeof( pBNS->vert[0] ) ); /* djb-rwth: cast operator added; memset_s C11/Annex K variant? */ 3256| 34.1k| tot_st_cap = pBNS->tot_st_cap; 3257| 34.1k| tot_st_flow = pBNS->tot_st_flow; 3258| | 3259| | /*****************************************/ 3260| | /* initialize new fictitious vertices */ 3261| | /* representing c-point groups, c-groups */ 3262| | /*****************************************/ 3263| 34.1k| vert_ficpoint_prev = pBNS->vert + fst_cg_vertex - 1; 3264| | 3265| 300k| for (i = 0; i < num_cg; i++) ------------------ | Branch (3265:21): [True: 266k, False: 34.1k] ------------------ 3266| 266k| { 3267| | /* 3268| | vert_ficpoint-1 is the last vertex; 3269| | vert_ficpoint is the being added vertex 3270| | Note: nGroupNumber are not contiguous 3271| | */ 3272| 266k| vert_ficpoint = vert_ficpoint_prev + 1; 3273| 266k| vert_ficpoint->iedge = vert_ficpoint_prev->iedge + vert_ficpoint_prev->max_adj_edges; 3274| 266k| vert_ficpoint->max_adj_edges = pTCGroups->pTCG[i + fst_cg_group].num_edges + nMaxAddEdges; 3275| 266k| vert_ficpoint->num_adj_edges = 0; 3276| | 3277| 266k| vert_ficpoint->st_edge.flow += pTCGroups->pTCG[i + fst_cg_group].st_flow; 3278| 266k| tot_st_flow += pTCGroups->pTCG[i + fst_cg_group].st_flow; 3279| 266k| vert_ficpoint->st_edge.cap += pTCGroups->pTCG[i + fst_cg_group].st_cap; 3280| 266k| tot_st_cap += pTCGroups->pTCG[i + fst_cg_group].st_cap; 3281| | 3282| 266k| vert_ficpoint->st_edge.flow0 = vert_ficpoint->st_edge.flow; 3283| 266k| vert_ficpoint->st_edge.cap0 = vert_ficpoint->st_edge.cap; 3284| | 3285| 266k| vert_ficpoint->type = pTCGroups->pTCG[i + fst_cg_group].type; 3286| | /* save the vertex number */ 3287| 266k| pTCGroups->pTCG[i + fst_cg_group].nVertexNumber = (int) ( vert_ficpoint - pBNS->vert ); 3288| | 3289| 266k| vert_ficpoint_prev = vert_ficpoint; /* keep track of iedges */ 3290| 266k| } 3291| | 3292| 34.1k| cur_num_vertices = (int) ( vert_ficpoint_prev - pBNS->vert ) + 1; 3293| 34.1k| cur_num_edges = num_edges; 3294| | 3295| | /*************************************************************/ 3296| | /* pass 1: */ 3297| | /* create ChargeStruct for c-points and connect them to */ 3298| | /* the vertices representing c-point groups; */ 3299| | /* set final atom st_cap, st_flow */ 3300| | /*************************************************************/ 3301| 228k| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3301:27): [True: 194k, False: 34.1k] ------------------ 3302| 194k| { 3303| 194k| if (!( k = pVA[c_point].cnListIndex )) ------------------ | Branch (3303:17): [True: 35.0k, False: 158k] ------------------ 3304| 35.0k| continue; /* not a c-point */ 3305| | 3306| 158k| k--; 3307| 158k| pCN = cnList[k].pCN; /* pointer to the ChargeStruct */ 3308| 158k| cn_len = cnList[k].len; /* length of the ChargeStruct */ 3309| 158k| cn_bits = cnList[k].bits; /* bits: for M-recognition */ 3310| | /* cn_bits = cnList[k].bits; */ /* ChargeStruct type */ 3311| 158k| bMetalAtoms = ( cn_bits == cn_bits_Me ); ------------------ | | 440| 158k|#define cn_bits_Me (-1) ------------------ 3312| 158k| vert_ficpoint_base = vert_ficpoint_prev; /* add aux vertices after this */ 3313| | 3314| | /* create disconnected auxiliary vertices of the at[c_point] ChargeStruct; add to them st_flow & st_cap */ 3315| 775k| for (i1 = 0; i1 < cn_len; i1++) ------------------ | Branch (3315:26): [True: 617k, False: 158k] ------------------ 3316| 617k| { 3317| 617k| if (!IS_BNS_VT_CHRG_STRUCT( pCN[i1].v.type )) ------------------ | | 82| 617k|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 53| 617k|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ | | #define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 51| 175k|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (82:38): [True: 175k, False: 441k] | | | Branch (82:69): [True: 175k, False: 0] | | ------------------ ------------------ 3318| 441k| { 3319| 441k| continue; 3320| 441k| } 3321| | /* the atom is always the first; the attached c-points are always the last */ 3322| 175k| vert_ficpoint = vert_ficpoint_base + i1; /* i1 = 1, 2,.. less number of attached c-points */ 3323| 175k| vert_ficpoint->iedge = vert_ficpoint_prev->iedge + vert_ficpoint_prev->max_adj_edges; 3324| 175k| vert_ficpoint->max_adj_edges = pCN[i1].v.valence; /* do not add additional edges to aux vertices */ 3325| 175k| vert_ficpoint->num_adj_edges = 0; 3326| | 3327| 175k| cap = !bMetalAtoms ? pCN[i1].v.cap : pCN[i1].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3327:23): [True: 151k, False: 24.3k] | Branch (3327:54): [True: 24.3k, False: 0] ------------------ 3328| 175k| flow = !bMetalAtoms ? pCN[i1].v.flow : pCN[i1].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3328:24): [True: 151k, False: 24.3k] | Branch (3328:56): [True: 24.3k, False: 0] ------------------ 3329| | 3330| 175k| AddStCapFlow( vert_ficpoint, &tot_st_flow, &tot_st_cap, cap, flow ); 3331| 175k| vert_ficpoint->type = pCN[i1].v.type; /* =BNS_VERT_TYPE__AUX */ 3332| | 3333| 175k| vert_ficpoint_prev = vert_ficpoint; /* the last one will be vert_ficpoint for the next c-point */ 3334| 175k| cur_num_vertices = (int) ( vert_ficpoint - pBNS->vert ) + 1; 3335| | 3336| 175k| if (vert_ficpoint->iedge + vert_ficpoint->max_adj_edges - pBNS->iedge >= pBNS->max_iedges) ------------------ | Branch (3336:21): [True: 0, False: 175k] ------------------ 3337| 0| { 3338| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3339| 0| } 3340| 175k| if (cur_num_vertices >= pBNS->max_vertices) ------------------ | Branch (3340:21): [True: 0, False: 175k] ------------------ 3341| 0| { 3342| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3343| 0| } 3344| 175k| } 3345| | 3346| | /* connect the vertices with new edges, add edge flow and cap */ 3347| 775k| for (i1 = 0; i1 < cn_len; i1++) ------------------ | Branch (3347:26): [True: 617k, False: 158k] ------------------ 3348| 617k| { 3349| 617k| pv1 = NULL; 3350| 617k| k1 = -1; 3351| | 3352| | /* find vertex corresponding to i1 */ 3353| | 3354| 617k| if (pCN[i1].v.type & BNS_VERT_TYPE_ATOM) ------------------ | | 45| 617k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (3354:21): [True: 158k, False: 458k] ------------------ 3355| 158k| { 3356| 158k| pv1 = pBNS->vert + c_point; /* may be only one atom -- the current c_point at i1==0 */ 3357| | /* add atom vertex st_cap and st_flow */ 3358| 158k| cap = !bMetalAtoms ? pCN[i1].v.cap : pCN[i1].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3358:27): [True: 134k, False: 24.3k] | Branch (3358:58): [True: 0, False: 24.3k] ------------------ 3359| 158k| flow = !bMetalAtoms ? pCN[i1].v.flow : pCN[i1].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3359:28): [True: 134k, False: 24.3k] | Branch (3359:60): [True: 0, False: 24.3k] ------------------ 3360| 158k| AddStCapFlow( pv1, &tot_st_flow, &tot_st_cap, cap, flow ); 3361| 158k| } 3362| | 3363| 458k| else if (IS_BNS_VT_C_GR( pCN[i1].v.type )) ------------------ | | 78| 458k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 458k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 458k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 458k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 458k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 258k, False: 199k] | | ------------------ ------------------ 3364| 258k| { 3365| | /* find c-group vertex by looking for its type */ 3366| 639k| for (j = 0; j < num_cg; j++) ------------------ | Branch (3366:33): [True: 639k, False: 0] ------------------ 3367| 639k| { 3368| 639k| if (pCN[i1].v.type == pBNS->vert[fst_cg_vertex + j].type) ------------------ | Branch (3368:29): [True: 258k, False: 381k] ------------------ 3369| 258k| { 3370| 258k| pv1 = pBNS->vert + fst_cg_vertex + j; 3371| 258k| break; 3372| 258k| } 3373| 639k| } 3374| | /* index of the pTCGroups->pTCG[] */ 3375| 258k| if (pv1) ------------------ | Branch (3375:25): [True: 258k, False: 0] ------------------ 3376| 258k| { 3377| 258k| k1 = j + fst_cg_group; 3378| 258k| if (pTCGroups->pTCG[k1].type != pCN[i1].v.type || ------------------ | Branch (3378:29): [True: 0, False: 258k] ------------------ 3379| 258k| pTCGroups->pTCG[k1].ord_num) ------------------ | Branch (3379:30): [True: 0, False: 258k] ------------------ 3380| 0| { 3381| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3382| 0| } 3383| 258k| } 3384| 258k| } 3385| | 3386| 199k| else if (IS_BNS_VT_M_GR( pCN[i1].v.type )) ------------------ | | 80| 199k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 199k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ | | | Branch (80:37): [True: 24.3k, False: 175k] | | ------------------ ------------------ 3387| 24.3k| { 3388| 24.3k| k1 = pTCGroups->nGroup[TCG_MeFlower0]; 3389| 24.3k| if (k1 < 0 || ------------------ | Branch (3389:25): [True: 0, False: 24.3k] ------------------ 3390| 24.3k| pTCGroups->pTCG[k1].type != pCN[i1].v.type || ------------------ | Branch (3390:26): [True: 0, False: 24.3k] ------------------ 3391| 24.3k| pTCGroups->pTCG[k1].ord_num || ------------------ | Branch (3391:30): [True: 0, False: 24.3k] ------------------ 3392| 24.3k| !pSrm->bMetalAddFlower) ------------------ | Branch (3392:30): [True: 0, False: 24.3k] ------------------ 3393| 0| { 3394| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3395| 0| } 3396| 24.3k| pv1 = pBNS->vert + pTCGroups->pTCG[k1].nVertexNumber; 3397| 24.3k| } 3398| | 3399| 175k| else if (IS_BNS_VT_CHRG_STRUCT( pCN[i1].v.type )) ------------------ | | 82| 175k|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 53| 175k|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ | | #define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 51| 175k|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (82:38): [True: 175k, False: 0] | | | Branch (82:69): [True: 175k, False: 0] | | ------------------ ------------------ 3400| 175k| { 3401| | /* aux vertex */ 3402| 175k| pv1 = vert_ficpoint_base + i1; 3403| 175k| } 3404| | 3405| 617k| if (!pv1) ------------------ | Branch (3405:21): [True: 0, False: 617k] ------------------ 3406| 0| { 3407| 0| return BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3408| 0| } 3409| | 3410| | /* connect pairs of vertices with new edges */ 3411| 1.09M| for (k = 0; k < MAX_CN_VAL && ( i2 = pCN[i1].e[k].neigh ); k++) ------------------ | | 397| 2.19M|#define MAX_CN_VAL 3 ------------------ | Branch (3411:29): [True: 1.09M, False: 0] | Branch (3411:47): [True: 478k, False: 617k] ------------------ 3412| 478k| { 3413| 478k| pv2 = NULL; 3414| 478k| k2 = -1; 3415| 478k| i2--; /* neighbor */ 3416| | 3417| | /* find vertex corresponding to i2 */ 3418| | 3419| 478k| if (pCN[i2].v.type & BNS_VERT_TYPE_ATOM) ------------------ | | 45| 478k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (3419:25): [True: 24.3k, False: 453k] ------------------ 3420| 24.3k| { 3421| 24.3k| pv2 = pBNS->vert + c_point; 3422| 24.3k| cap = !bMetalAtoms ? pCN[i2].v.cap : pCN[i2].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3422:31): [True: 0, False: 24.3k] | Branch (3422:62): [True: 0, False: 24.3k] ------------------ 3423| 24.3k| flow = !bMetalAtoms ? pCN[i2].v.flow : pCN[i2].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3423:32): [True: 0, False: 24.3k] | Branch (3423:64): [True: 0, False: 24.3k] ------------------ 3424| | /* add atom vertex st_cap and st_flow; this normally should not happen */ 3425| 24.3k| AddStCapFlow( pv2, &tot_st_flow, &tot_st_cap, cap, flow ); 3426| 24.3k| } 3427| | 3428| 453k| else if (IS_BNS_VT_C_GR( pCN[i2].v.type )) ------------------ | | 78| 453k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 453k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 453k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 453k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 453k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 258k, False: 195k] | | ------------------ ------------------ 3429| 258k| { 3430| | /* find c-group vertex by looking for its type */ 3431| 639k| for (j = 0; j < num_cg; j++) ------------------ | Branch (3431:37): [True: 639k, False: 0] ------------------ 3432| 639k| { 3433| 639k| if (pCN[i2].v.type == pBNS->vert[fst_cg_vertex + j].type) ------------------ | Branch (3433:33): [True: 258k, False: 381k] ------------------ 3434| 258k| { 3435| 258k| pv2 = pBNS->vert + fst_cg_vertex + j; 3436| 258k| break; 3437| 258k| } 3438| 639k| } 3439| 258k| if (pv2) ------------------ | Branch (3439:29): [True: 258k, False: 0] ------------------ 3440| 258k| { 3441| 258k| k2 = j + fst_cg_group; 3442| 258k| if (pTCGroups->pTCG[k2].type != pCN[i2].v.type || ------------------ | Branch (3442:33): [True: 0, False: 258k] ------------------ 3443| 258k| pTCGroups->pTCG[k2].ord_num) ------------------ | Branch (3443:34): [True: 0, False: 258k] ------------------ 3444| 0| { 3445| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3446| 0| } 3447| 258k| } 3448| 258k| } 3449| | 3450| 195k| else if (IS_BNS_VT_M_GR( pCN[i2].v.type )) ------------------ | | 80| 195k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 195k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ | | | Branch (80:37): [True: 0, False: 195k] | | ------------------ ------------------ 3451| 0| { 3452| 0| k2 = pTCGroups->nGroup[TCG_MeFlower0]; 3453| 0| if (k2 < 0 || ------------------ | Branch (3453:29): [True: 0, False: 0] ------------------ 3454| 0| pTCGroups->pTCG[k2].type != pCN[i2].v.type || ------------------ | Branch (3454:30): [True: 0, False: 0] ------------------ 3455| 0| pTCGroups->pTCG[k2].ord_num || ------------------ | Branch (3455:34): [True: 0, False: 0] ------------------ 3456| 0| !pSrm->bMetalAddFlower) ------------------ | Branch (3456:34): [True: 0, False: 0] ------------------ 3457| 0| { 3458| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3459| 0| } 3460| 0| pv2 = pBNS->vert + pTCGroups->pTCG[k2].nVertexNumber; 3461| 0| } 3462| | 3463| 195k| else if (IS_BNS_VT_CHRG_STRUCT( pCN[i2].v.type )) ------------------ | | 82| 195k|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 53| 195k|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ | | #define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 51| 195k|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (82:38): [True: 195k, False: 0] | | | Branch (82:69): [True: 195k, False: 0] | | ------------------ ------------------ 3464| 195k| { 3465| 195k| pv2 = vert_ficpoint_base + i2; 3466| 195k| } 3467| | 3468| | /* connect pv1 and pv2 */ 3469| 478k| if (!pv1 || !pv2 || pv1 == pv2) ------------------ | Branch (3469:25): [True: 0, False: 478k] | Branch (3469:33): [True: 0, False: 478k] | Branch (3469:41): [True: 0, False: 478k] ------------------ 3470| 0| { 3471| 0| return BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3472| 0| } 3473| | 3474| 478k| j1 = (int)(pv1 - pBNS->vert); 3475| 478k| j2 = (int)(pv2 - pBNS->vert); 3476| | 3477| | /* create a new edge connecting pv1 and pv2 */ 3478| 478k| edge = pBNS->edge + cur_num_edges; 3479| 478k| if ((IS_BNS_VT_M_GR( pCN[i1].v.type ) && IS_BNS_VT_ATOM( pCN[i2].v.type )) || ------------------ | | 80| 956k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 478k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ | | | Branch (80:37): [True: 24.3k, False: 453k] | | ------------------ ------------------ if ((IS_BNS_VT_M_GR( pCN[i1].v.type ) && IS_BNS_VT_ATOM( pCN[i2].v.type )) || ------------------ | | 83| 24.3k|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 45| 24.3k|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (83:37): [True: 24.3k, False: 0] | | ------------------ ------------------ 3480| 453k| (IS_BNS_VT_M_GR( pCN[i2].v.type ) && IS_BNS_VT_ATOM( pCN[i1].v.type ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 80| 907k|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 57| 453k|#define BNS_VERT_TYPE_METAL_GR 0x0800 /* metal atom group; may be used alone or with BNS_VT_M_POS, BNS_VT_M_NEG */ | | ------------------ | | | Branch (80:37): [True: 0, False: 453k] | | ------------------ ------------------ (IS_BNS_VT_M_GR( pCN[i2].v.type ) && IS_BNS_VT_ATOM( pCN[i1].v.type ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 83| 0|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 45| 0|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (83:37): [True: 0, False: 0] | | ------------------ ------------------ 3481| 24.3k| { 3482| | /* at[c_point] is a metal or is treated as a metal; connect it to M-group */ 3483| | /* metal - M-group (i.e. Metal-Flower) edge */ 3484| 24.3k| int nStCap, nStFlow; 3485| 24.3k| bNeedsFlower = AtomStcapStflow( at, pVA, pSrm, c_point, &nStCap, &nStFlow, &edge->cap, &edge->flow ); 3486| | /* GetAtomToMCGroupInitEdgeCapFlow( &edge->cap, &edge->flow, pSrm, at, pVA, c_point ); */ 3487| 24.3k| if (!bNeedsFlower) ------------------ | Branch (3487:29): [True: 0, False: 24.3k] ------------------ 3488| 0| { 3489| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3490| 0| } 3491| 24.3k| pVA[c_point].nMetalGroupEdge = cur_num_edges + 1; 3492| | /* pBNS->vert[c_point].st_edge.cap += edge->flow;*/ /* where was this done ???*/ 3493| 24.3k| pBNS->vert[c_point].st_edge.flow += edge->flow; 3494| 24.3k| pBNS->vert[c_point].st_edge.cap += edge->flow + pVA[c_point].cInitFreeValences; 3495| 24.3k| pBNS->vert[c_point].st_edge.flow0 = pBNS->vert[c_point].st_edge.flow; 3496| 24.3k| pBNS->vert[c_point].st_edge.cap0 = pBNS->vert[c_point].st_edge.cap; 3497| 24.3k| tot_st_flow += edge->flow; 3498| 24.3k| tot_st_cap += edge->flow + pVA[c_point].cInitFreeValences; 3499| 24.3k| } 3500| 453k| else 3501| 453k| { 3502| 453k| edge->cap = !bMetalAtoms ? pCN[i1].e[k].cap : pCN[i1].e[k].cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3502:37): [True: 380k, False: 72.9k] | Branch (3502:71): [True: 72.9k, False: 0] ------------------ 3503| 453k| edge->flow = !bMetalAtoms ? pCN[i1].e[k].flow : pCN[i1].e[k].flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3503:38): [True: 380k, False: 72.9k] | Branch (3503:73): [True: 24.3k, False: 48.6k] ------------------ 3504| 453k| } 3505| | 3506| 478k| edge->forbidden = pCN[i1].e[k].bForbiddenEdge ? BNS_EDGE_FORBIDDEN_MASK : 0; ------------------ | | 39| 5.04k|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ | Branch (3506:39): [True: 5.04k, False: 473k] ------------------ 3507| | 3508| | /* c-group incoming edges cap and flow needed in ConnectSuperCGroup() */ 3509| | /* 3510| | if ( k1 >= 0 ) { 3511| | pTCGroups->pTCG[k1].edges_cap += pCN[i1].e[k].cap; 3512| | pTCGroups->pTCG[k1].edges_flow += pCN[i1].e[k].flow; 3513| | } 3514| | if ( k2 >= 0 ) { 3515| | pTCGroups->pTCG[k2].edges_cap += pCN[i1].e[k].cap; 3516| | pTCGroups->pTCG[k2].edges_flow += pCN[i1].e[k].flow; 3517| | } 3518| | */ 3519| | 3520| 478k| edge->pass = 0; 3521| | 3522| |#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 3523| | edge->forbidden &= pBNS->edge_forbidden_mask; 3524| |#endif 3525| | 3526| | /* check edge overflow */ 3527| 478k| if (pv1->num_adj_edges >= pv1->max_adj_edges || ------------------ | Branch (3527:25): [True: 0, False: 478k] ------------------ 3528| 478k| pv2->num_adj_edges >= pv2->max_adj_edges || ------------------ | Branch (3528:26): [True: 0, False: 478k] ------------------ 3529| 478k| cur_num_edges >= pBNS->max_edges) ------------------ | Branch (3529:26): [True: 0, False: 478k] ------------------ 3530| 0| { 3531| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3532| 0| } 3533| | 3534| | /* connect edge to the incident vertices and increment the counters of neighbors and edges */ 3535| | 3536| 478k| ret = ConnectTwoVertices( pv1, pv2, edge, pBNS, 0 ); 3537| | 3538| 478k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 478k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 478k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 478k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 478k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 478k, False: 0] | | | Branch (67:44): [True: 0, False: 478k] | | ------------------ ------------------ 3539| 0| { 3540| 0| return ret; 3541| 0| } 3542| | 3543| 478k| edge->cap0 = edge->cap; 3544| 478k| edge->flow0 = edge->flow; 3545| | 3546| | /* save the edge index */ 3547| 478k| type = IS_BNS_VT_C_GR( pv1->type ) ? pv1->type : ------------------ | | 78| 478k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 478k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 478k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 0, False: 478k] | | ------------------ ------------------ 3548| 478k| IS_BNS_VT_C_GR( pv2->type ) ? pv2->type : 0; ------------------ | | 78| 478k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 478k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 478k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 478k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 258k, False: 220k] | | ------------------ ------------------ 3549| 478k| if (type) ------------------ | Branch (3549:25): [True: 258k, False: 220k] ------------------ 3550| 258k| { 3551| | /* the edge connects to a c-group */ 3552| 258k| if (type & BNS_VERT_TYPE_C_NEGATIVE) ------------------ | | 54| 258k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (3552:29): [True: 120k, False: 138k] ------------------ 3553| 120k| { 3554| 120k| pVA[c_point].nCMinusGroupEdge = cur_num_edges + 1; 3555| 120k| } 3556| 138k| else 3557| 138k| { 3558| 138k| pVA[c_point].nCPlusGroupEdge = cur_num_edges + 1; 3559| 138k| } 3560| 258k| } 3561| 478k| cur_num_edges++; /* end of new edge creation */ 3562| 478k| } 3563| 617k| } 3564| 158k| } 3565| | 3566| | 3567| | /*************************************************************/ 3568| | /* pass 2: */ 3569| | /* adjust bond cap, flow from the final atom st_cap, st_flow */ 3570| | /*************************************************************/ 3571| 228k| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3571:27): [True: 194k, False: 34.1k] ------------------ 3572| 194k| { 3573| 194k| int st_cap, st_cap2, max_edge_flow; 3574| 194k| pv1 = pBNS->vert + c_point; /* atom vertex */ 3575| 194k| st_cap = pv1->st_edge.cap; 3576| 782k| for (k = 0; k < pv1->num_adj_edges; k++) ------------------ | Branch (3576:25): [True: 588k, False: 194k] ------------------ 3577| 588k| { 3578| 588k| edge = pBNS->edge + pv1->iedge[k]; /* incident edge */ 3579| 588k| c_neigh = edge->neighbor12 ^ c_point; /* adjacent vertex */ 3580| 588k| pv2 = pBNS->vert + c_neigh; 3581| 588k| if (c_neigh > c_point || !( pv2->type & BNS_VERT_TYPE_ATOM )) ------------------ | | 45| 168k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (3581:21): [True: 419k, False: 168k] | Branch (3581:42): [True: 0, False: 168k] ------------------ 3582| 419k| { 3583| 419k| continue; 3584| 419k| } 3585| | /* adjacent vertex is an atom; the edge is a bond; process each bond only once */ 3586| 168k| st_cap2 = pv2->st_edge.cap; 3587| | /* the edge flow <= min( incident atom st_caps) */ 3588| 168k| max_edge_flow = inchi_min( st_cap, st_cap2 ); ------------------ | | 139| 168k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 68.9k, False: 99.8k] | | ------------------ ------------------ 3589| | /* bond order <= triple bond (flow=2) */ 3590| 168k| if (((pSrm->bMetalAddFlower && !pSrm->nMetalMinBondOrder && ------------------ | Branch (3590:23): [True: 168k, False: 0] | Branch (3590:48): [True: 168k, False: 0] ------------------ 3591| 168k| ( pVA[c_point].cMetal && pVA[c_point].cNumBondsToMetal)) || ------------------ | Branch (3591:23): [True: 22.0k, False: 146k] | Branch (3591:46): [True: 22.0k, False: 0] ------------------ 3592| 146k| (pVA[c_neigh].cMetal && pVA[c_neigh].cNumBondsToMetal) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3592:26): [True: 16.6k, False: 130k] | Branch (3592:49): [True: 16.6k, False: 0] ------------------ 3593| 38.7k| { 3594| 38.7k| max_edge_flow = inchi_min( max_edge_flow, MAX_BOND_EDGE_CAP + 1 ); ------------------ | | 139| 38.7k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 11.9k, False: 26.7k] | | ------------------ ------------------ 3595| 38.7k| } 3596| 130k| else 3597| 130k| { 3598| 130k| max_edge_flow = inchi_min( max_edge_flow, MAX_BOND_EDGE_CAP ); ------------------ | | 139| 130k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 64.9k, False: 65.0k] | | ------------------ ------------------ 3599| 130k| } 3600| 168k| if (at[c_point].bond_type[k] == BOND_TYPE_SINGLE) ------------------ | | 32| 168k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (3600:21): [True: 168k, False: 464] ------------------ 3601| 168k| { 3602| | /* the bond has not been changed due to stereo */ 3603| 168k| edge->cap = edge->cap0 = max_edge_flow; 3604| 168k| } 3605| 168k| } 3606| 194k| } 3607| | 3608| | /***********************************************************/ 3609| | /************** ************/ 3610| | /************** connect M-flower with new edges ************/ 3611| | /************** ************/ 3612| | /***********************************************************/ 3613| | 3614| 34.1k| ret = ConnectMetalFlower( &cur_num_vertices, &cur_num_edges, &tot_st_cap, &tot_st_flow, pSrm, pBNS, pTCGroups ); 3615| | 3616| 34.1k| if (ret < 0) ------------------ | Branch (3616:13): [True: 0, False: 34.1k] ------------------ 3617| 0| { 3618| 0| goto exit_function; 3619| 0| } 3620| | 3621| | /***********************************************************/ 3622| | /************** ************/ 3623| | /************** add additional vertices & edges ************/ 3624| | /************** to connect c-groups ************/ 3625| | /************** ************/ 3626| | /***********************************************************/ 3627| | 3628| | /* (+) supergroup, Y-connection */ 3629| | 3630| 34.1k| k = 0; 3631| 34.1k| nAddGroups[k++] = TCG_Plus0; 3632| 34.1k| nAddGroups[k++] = TCG_Plus_C0; 3633| 34.1k| nAddGroups[k++] = TCG_Plus_M0; 3634| | 3635| 34.1k| ret1 = ConnectSuperCGroup( TCG_Plus, 3636| 34.1k| nAddGroups, 3637| 34.1k| k, 3638| 34.1k| &cur_num_vertices, 3639| 34.1k| &cur_num_edges, 3640| 34.1k| &tot_st_cap, 3641| 34.1k| &tot_st_flow, 3642| 34.1k| pBNS, 3643| 34.1k| pTCGroups ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3644| | 3645| | /* (-) supergroup, Y-connection */ 3646| | 3647| 34.1k| k = 0; 3648| 34.1k| nAddGroups[k++] = TCG_Minus0; 3649| 34.1k| nAddGroups[k++] = TCG_Minus_C0; 3650| 34.1k| nAddGroups[k++] = TCG_Minus_M0; 3651| | 3652| 34.1k| ret2 = ConnectSuperCGroup( TCG_Minus, 3653| 34.1k| nAddGroups, 3654| 34.1k| k, 3655| 34.1k| &cur_num_vertices, 3656| 34.1k| &cur_num_edges, 3657| 34.1k| &tot_st_cap, 3658| 34.1k| &tot_st_flow, 3659| 34.1k| pBNS, 3660| 34.1k| pTCGroups ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3661| | 3662| | /******** connect (+) and (-) ***************/ 3663| | 3664| 34.1k| k = 0; 3665| 34.1k| nAddGroups[k++] = TCG_Plus; 3666| 34.1k| nAddGroups[k++] = TCG_Minus; 3667| | 3668| 34.1k| ret3 = ConnectSuperCGroup( -1, 3669| 34.1k| nAddGroups, 3670| 34.1k| k, 3671| 34.1k| &cur_num_vertices, 3672| 34.1k| &cur_num_edges, 3673| 34.1k| &tot_st_cap, 3674| 34.1k| &tot_st_flow, 3675| 34.1k| pBNS, 3676| 34.1k| pTCGroups ); 3677| | 3678| | /* Take care of the full charge */ 3679| | 3680| 34.1k| cg_charge = pTCGroups->total_charge - pTCGroups->tgroup_charge - pTCGroups->charge_on_atoms; 3681| 34.1k| ret = 1; 3682| 34.1k| if (ret3 > 0) ------------------ | Branch (3682:13): [True: 34.1k, False: 0] ------------------ 3683| 34.1k| { 3684| | /* (+) and (-) or at least one of them have been connected */ 3685| 34.1k| int nVertPlusMinus = cur_num_vertices - 1; 3686| 34.1k| BNS_VERTEX *pVertPlusMinus = pBNS->vert + nVertPlusMinus; 3687| 34.1k| BNS_VERTEX *pVertPlus = NULL, *pVertMinus = NULL, *pVert = NULL; 3688| 34.1k| BNS_EDGE *pEdgePlus = NULL, *pEdgeMinus = NULL, *pEdge = NULL; 3689| 34.1k| n = pTCGroups->nGroup[TCG_Plus] >= 0; /* (+)-supergroup exists */ 3690| 34.1k| k = pTCGroups->nGroup[TCG_Minus] >= 0; /* (-)-supergroup exists */ 3691| | 3692| 34.1k| if (pVertPlusMinus->num_adj_edges == 2 && k + n == 2) ------------------ | Branch (3692:17): [True: 33.0k, False: 1.10k] | Branch (3692:55): [True: 33.0k, False: 0] ------------------ 3693| 33.0k| { 3694| 33.0k| pEdgePlus = pBNS->edge + pVertPlusMinus->iedge[0]; /* TCG_Plus was the 1st */ 3695| 33.0k| pEdgeMinus = pBNS->edge + pVertPlusMinus->iedge[1]; /* TCG_Minus was the 2nd */ 3696| 33.0k| } 3697| | 3698| 1.10k| else if (pVertPlusMinus->num_adj_edges == 1 && k + n == 1) ------------------ | Branch (3698:22): [True: 1.10k, False: 0] | Branch (3698:60): [True: 1.10k, False: 0] ------------------ 3699| 1.10k| { 3700| 1.10k| if (pTCGroups->nGroup[TCG_Plus] >= 0) ------------------ | Branch (3700:21): [True: 901, False: 203] ------------------ 3701| 901| { 3702| 901| pEdgePlus = pBNS->edge + pVertPlusMinus->iedge[0]; 3703| 901| } 3704| 203| else if (pTCGroups->nGroup[TCG_Minus] >= 0) ------------------ | Branch (3704:26): [True: 203, False: 0] ------------------ 3705| 203| { 3706| 203| pEdgeMinus = pBNS->edge + pVertPlusMinus->iedge[0]; 3707| 203| } 3708| 1.10k| } 3709| | 3710| 0| else if (k + n) ------------------ | Branch (3710:22): [True: 0, False: 0] ------------------ 3711| 0| { 3712| | /* program error check */ 3713| 0| ret = BNS_BOND_ERR; ------------------ | | 52| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3714| 0| goto exit_function; 3715| 0| } 3716| | 3717| 34.1k| if (pEdgePlus) ------------------ | Branch (3717:17): [True: 33.9k, False: 203] ------------------ 3718| 33.9k| { 3719| 33.9k| pVertPlus = pBNS->vert + ( pEdgePlus->neighbor12 ^ nVertPlusMinus ); 3720| 33.9k| } 3721| 34.1k| if (pEdgeMinus) ------------------ | Branch (3721:17): [True: 33.2k, False: 901] ------------------ 3722| 33.2k| { 3723| 33.2k| pVertMinus = pBNS->vert + ( pEdgeMinus->neighbor12 ^ nVertPlusMinus ); 3724| 33.2k| } 3725| | 3726| 34.1k| pVert = pVertPlus ? pVertPlus : pVertMinus ? pVertMinus : NULL; ------------------ | Branch (3726:21): [True: 33.9k, False: 203] | Branch (3726:45): [True: 203, False: 0] ------------------ 3727| 34.1k| pEdge = pEdgePlus ? pEdgePlus : pEdgeMinus ? pEdgeMinus : NULL; ------------------ | Branch (3727:21): [True: 33.9k, False: 203] | Branch (3727:45): [True: 203, False: 0] ------------------ 3728| 34.1k| if (pEdgeMinus) ------------------ | Branch (3728:17): [True: 33.2k, False: 901] ------------------ 3729| 33.2k| { 3730| 33.2k| pTCGroups->nEdgeMinus = (int) ( pEdgeMinus - pBNS->edge ); 3731| 33.2k| } 3732| 34.1k| if (pEdgePlus) ------------------ | Branch (3732:17): [True: 33.9k, False: 203] ------------------ 3733| 33.9k| { 3734| 33.9k| pTCGroups->nEdgePlus = (int) ( pEdgePlus - pBNS->edge ); 3735| 33.9k| } 3736| 34.1k| if (pEdge) ------------------ | Branch (3736:17): [True: 34.1k, False: 0] ------------------ 3737| 34.1k| { 3738| 34.1k| pTCGroups->nEdge4charge = (int) ( pEdge - pBNS->edge ); 3739| 34.1k| } 3740| | 3741| | /* set total charge */ 3742| | 3743| 34.1k| if (pVert && pEdge) ------------------ | Branch (3743:17): [True: 34.1k, False: 0] | Branch (3743:26): [True: 34.1k, False: 0] ------------------ 3744| 34.1k| { 3745| | /* do not check rescaps for now */ 3746| 34.1k| if (cg_charge > 0) ------------------ | Branch (3746:21): [True: 604, False: 33.5k] ------------------ 3747| 604| { 3748| 604| pVertPlusMinus->st_edge.cap += cg_charge; 3749| 604| tot_st_cap += cg_charge; 3750| 604| pVertPlusMinus->st_edge.cap0 = pVertPlusMinus->st_edge.cap; 3751| 604| } 3752| | 3753| 34.1k| if (cg_charge < 0) ------------------ | Branch (3753:21): [True: 111, False: 34.0k] ------------------ 3754| 111| { 3755| 111| pVert->st_edge.cap -= cg_charge; 3756| 111| tot_st_cap -= cg_charge; 3757| 111| pVert->st_edge.cap0 = pVert->st_edge.cap; 3758| | 3759| 111| if (pEdge->cap - pEdge->flow + cg_charge < 0) ------------------ | Branch (3759:25): [True: 38, False: 73] ------------------ 3760| 38| { 3761| | /* 2006-02-06: increase edge capacity to avoid clogging */ 3762| 38| pEdge->cap = pEdge->flow - cg_charge; 3763| 38| } 3764| 111| } 3765| 34.1k| pTCGroups->added_charge = cg_charge; 3766| 34.1k| } 3767| 34.1k| if (!cg_charge || ( pVert && pEdge )) ------------------ | Branch (3767:17): [True: 33.4k, False: 715] | Branch (3767:33): [True: 715, False: 0] | Branch (3767:42): [True: 715, False: 0] ------------------ 3768| 34.1k| { 3769| 34.1k| ret = 2; 3770| 34.1k| } 3771| 34.1k| } 3772| | 3773| 34.1k| AddRadicalToMetal( &tot_st_cap, &tot_st_flow, pSrm, pBNS, pTCGroups ); 3774| | 3775| | 3776| 34.1k| pBNS->num_edges = cur_num_edges; 3777| 34.1k| pBNS->num_vertices = cur_num_vertices; 3778| 34.1k| pBNS->num_c_groups = num_cg; 3779| 34.1k| pBNS->tot_st_cap = tot_st_cap; 3780| 34.1k| pBNS->tot_st_flow = tot_st_flow; 3781| 34.1k| } 3782| | 3783| 87.8k|exit_function: 3784| 87.8k| return ret; 3785| 87.8k|} nNumEdgesToCnVertex: 3790| 159k|{ 3791| 159k| int i, j, n, num_edges, v1 = v + 1; 3792| 776k| for (i = 0, num_edges = 0; i < len; i++) ------------------ | Branch (3792:32): [True: 617k, False: 159k] ------------------ 3793| 617k| { 3794| 1.09M| for (j = 0; j < MAX_CN_VAL && ( n = pCN[i].e[j].neigh ); j++) ------------------ | | 397| 2.19M|#define MAX_CN_VAL 3 ------------------ | Branch (3794:21): [True: 1.09M, False: 0] | Branch (3794:39): [True: 478k, False: 617k] ------------------ 3795| 478k| { 3796| 478k| num_edges += ( i == v || n == v1 ); ------------------ | Branch (3796:28): [True: 225k, False: 252k] | Branch (3796:38): [True: 24.3k, False: 228k] ------------------ 3797| 478k| } 3798| 617k| } 3799| 159k| return num_edges; 3800| 159k|} AllocateAndInitTCGBnStruct: 3848| 87.8k|{ 3849| 87.8k| inp_ATOM *at = pStruct->at; 3850| 87.8k| int num_atoms = pStruct->num_atoms; 3851| 87.8k| ICHICONST SRM *pSrm = pStruct->pSrm; ------------------ | | 13| 87.8k|#define ICHICONST const ------------------ 3852| | 3853| 87.8k| BN_STRUCT *pBNS = NULL; 3854| 87.8k| BNS_VERTEX *vert; 3855| 87.8k| BNS_IEDGE *iedge; 3856| | 3857| 87.8k| int neigh, num_changed_bonds = 0; 3858| 87.8k| U_CHAR bond_type, bond_mark; 3859| 87.8k| int bNeedsFlower1, bNeedsFlower2, min_order; 3860| | 3861| 87.8k| int i, j, k, m, n_edges, num_bonds, num_edges; 3862| 87.8k| int f1, f2, c1, c2, edge_cap, edge_flow, st_cap, st_flow, flag_alt_bond; 3863| 87.8k| int tot_st_cap, tot_st_flow; 3864| 87.8k| int max_tg, max_edges, max_vertices, len_alt_path, max_iedges, num_iedges, num_altp; 3865| | 3866| | /* count vertices */ 3867| 87.8k| max_tg = pTCGroups->num_tgroups; 3868| | /* +1 for a super-tautomeric group */ 3869| | /* max_vertices = num_atoms + nMaxAddAtoms + max_tg + 1; */ 3870| 87.8k| max_vertices = pTCGroups->nVertices + nMaxAddAtoms; 3871| | 3872| | /* count edges */ 3873| 87.8k| num_changed_bonds = 0; 3874| 87.8k| num_bonds = pTCGroups->num_bonds; 3875| | 3876| | /* each atom has enough edges to belong to a tautomeric group + nMaxAddEdges */ 3877| | /* number of atoms is large enough to accommodate max. possible number of t-groups + nMaxAddAtoms */ 3878| | /* max_altp cannot be larger than BN_MAX_ALTP = 16 */ 3879| 87.8k| num_edges = pTCGroups->nEdges; 3880| | 3881| | /* +max_tg for edges between t-groups and super-tautomeric group */ 3882| 87.8k| max_edges = num_edges + ( nMaxAddEdges + NUM_KINDS_OF_GROUPS )*max_vertices; ------------------ | | 86| 87.8k|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 3883| 87.8k| max_iedges = 2 * max_edges + pTCGroups->nAddIedges; 3884| 87.8k| len_alt_path = max_vertices + iALTP_HDR_LEN + 1; /* may overflow if an edge is traversed in 2 directions */ 3885| 87.8k| len_alt_path += inchi_max( max_vertices / 2, 16 ); /* to avoid the overflow */ ------------------ | | 138| 87.8k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 7.07k, False: 80.7k] | | ------------------ ------------------ 3886| | 3887| 87.8k| if (!(pBNS = (BN_STRUCT*)inchi_calloc(1, sizeof(BN_STRUCT))) || ------------------ | | 1146| 87.8k|#define inchi_calloc calloc ------------------ | Branch (3887:9): [True: 0, False: 87.8k] ------------------ 3888| 87.8k| !(pBNS->edge = (BNS_EDGE*)inchi_calloc(max_edges, sizeof(BNS_EDGE))) || ------------------ | | 1146| 87.8k|#define inchi_calloc calloc ------------------ | Branch (3888:9): [True: 0, False: 87.8k] ------------------ 3889| 87.8k| !(pBNS->vert = (BNS_VERTEX*)inchi_calloc(max_vertices, sizeof(BNS_VERTEX))) || ------------------ | | 1146| 87.8k|#define inchi_calloc calloc ------------------ | Branch (3889:9): [True: 0, False: 87.8k] ------------------ 3890| 87.8k| !(pBNS->iedge = (BNS_IEDGE*)inchi_calloc(max_iedges, sizeof(BNS_IEDGE)))) ------------------ | | 1146| 87.8k|#define inchi_calloc calloc ------------------ | Branch (3890:9): [True: 0, False: 87.8k] ------------------ 3891| 0| { 3892| 0| return DeAllocateBnStruct( pBNS ); 3893| 0| } 3894| | 3895| | /* alt path init (standard spell) */ 3896| 1.49M| for (num_altp = 0; num_altp < max_altp && num_altp < BN_MAX_ALTP; num_altp++) ------------------ | | 17| 1.40M|#define BN_MAX_ALTP 16 ------------------ | Branch (3896:24): [True: 1.40M, False: 87.8k] | Branch (3896:47): [True: 1.40M, False: 0] ------------------ 3897| 1.40M| { 3898| 1.40M| if (!( pBNS->altp[num_altp] = (BNS_ALT_PATH*) inchi_calloc( len_alt_path, sizeof( BNS_ALT_PATH ) ) )) ------------------ | | 1146| 1.40M|#define inchi_calloc calloc ------------------ | Branch (3898:13): [True: 0, False: 1.40M] ------------------ 3899| 0| { 3900| 0| return DeAllocateBnStruct( pBNS ); 3901| 0| } 3902| 1.40M| ALTP_ALLOCATED_LEN( pBNS->altp[num_altp] ) = len_alt_path; ------------------ | | 111| 1.40M|#define ALTP_ALLOCATED_LEN(altp) (altp)[iALTP_MAX_LEN].number ------------------ 3903| 1.40M| pBNS->len_alt_path = len_alt_path; /* ??? duplication ??? */ 3904| | /* re-init */ 3905| 1.40M| ALTP_DELTA( pBNS->altp[num_altp] ) = 0; ------------------ | | 112| 1.40M|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 3906| 1.40M| ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 103| 1.40M|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 118| 1.40M|#define NO_VERTEX -2 ------------------ 3907| 1.40M| ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 102| 1.40M|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 118| 1.40M|#define NO_VERTEX -2 ------------------ 3908| 1.40M| ALTP_PATH_LEN( pBNS->altp[num_altp] ) = 0; ------------------ | | 101| 1.40M|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 3909| 1.40M| } 3910| 87.8k| pBNS->alt_path = NULL; 3911| 87.8k| pBNS->num_altp = 0; 3912| 87.8k| pBNS->max_altp = num_altp; 3913| | 3914| | 3915| | /* fill vertices (no connectivity) */ 3916| 87.8k| iedge = pBNS->iedge; 3917| 87.8k| num_iedges = 0; 3918| 87.8k| tot_st_cap = tot_st_flow = 0; 3919| 920k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3919:17): [True: 832k, False: 87.8k] ------------------ 3920| 832k| { 3921| | /* count edges incident to pBNS->vert[i] */ 3922| 832k| k = at[i].valence + ( at[i].endpoint != 0 ) + ( nMaxAddEdges /*+ NUM_KINDS_OF_GROUPS*/ ); 3923| 832k| if (( j = pVA[i].cnListIndex - 1 ) >= 0) ------------------ | Branch (3923:13): [True: 159k, False: 673k] ------------------ 3924| 159k| { 3925| | /* add number of neighbors in the ChargeStruct */ 3926| 159k| k += nNumEdgesToCnVertex( cnList[j].pCN, cnList[j].len, 0 ); 3927| 159k| } 3928| | /* set max number of edges for the vertex */ 3929| 832k| pBNS->vert[i].max_adj_edges = k; 3930| 832k| pBNS->vert[i].iedge = iedge; 3931| 832k| iedge += k; 3932| | /* add atom vertex cap */ 3933| 832k| st_cap = 0; 3934| 832k| st_flow = 0; 3935| 832k| bNeedsFlower1 = AtomStcapStflow( at, pVA, pSrm, i, &c1, &f1, NULL, NULL ); 3936| | /* pVA[i].cNumBondsToMetal = bNeedsFlower1; */ 3937| | /* GetAtomStCapFlow( at, pVA, pSrm, i, &c1, &f1 ); */ 3938| 832k| st_cap += c1; 3939| 832k| st_cap += bNeedsFlower1 ? 0 : pVA[i].cInitFreeValences; ------------------ | Branch (3939:19): [True: 24.3k, False: 808k] ------------------ 3940| 832k| pBNS->vert[i].st_edge.cap = st_cap; /* the 1st time st_cap is set */ 3941| 832k| pBNS->vert[i].st_edge.cap0 = pBNS->vert[i].st_edge.cap; 3942| 832k| tot_st_cap += st_cap; 3943| 832k| } 3944| | 3945| 87.8k| num_iedges = (int) ( iedge - pBNS->iedge ); 3946| 87.8k| if (max_iedges - num_iedges < ( nMaxAddEdges + NUM_KINDS_OF_GROUPS )*max_vertices) ------------------ | | 86| 87.8k|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ | Branch (3946:9): [True: 0, False: 87.8k] ------------------ 3947| 0| { 3948| 0| return DeAllocateBnStruct( pBNS ); 3949| 0| } 3950| | 3951| 87.8k| pBNS->num_atoms = num_atoms; /* number of real atoms */ 3952| 87.8k| pBNS->num_added_atoms = 0; 3953| 87.8k| pBNS->num_t_groups = 0; /* number of added t-groups */ 3954| 87.8k| pBNS->num_c_groups = 0; 3955| 87.8k| pBNS->nMaxAddAtoms = nMaxAddAtoms; 3956| 87.8k| pBNS->nMaxAddEdges = nMaxAddEdges; 3957| | 3958| 87.8k| pBNS->num_vertices = num_atoms; /* current number of vertices, in general a sum of 3959| | pBNS->num_atoms 3960| | pBNS->num_t_groups 3961| | number of c-groups 3962| | number of auxiliary vertices 3963| | pBNS->num_added_atoms 3964| | */ 3965| 87.8k| pBNS->max_vertices = max_vertices; 3966| | 3967| | 3968| 87.8k| pBNS->num_bonds = num_bonds; /* number of real edges (bonds) */ 3969| 87.8k| pBNS->max_edges = max_edges; 3970| 87.8k| pBNS->max_iedges = max_iedges; 3971| | 3972| | 3973| | /* 3974| | To remove t-groups and added atoms: 3975| | 3976| | for ( i = 0; i < pBNS->num_atoms; i ++ ) 3977| | { 3978| | for ( j = pBNS->vert[i].num_adj_edges-1; 0 <= j; j -- ) 3979| | { 3980| | k = pBNS->edge[pBNS->vert[i].iedge[j]].neighbor12 ^ i; 3981| | if ( pBNS->vert[k].type & BNS_VERT_TYPE_ATOM ) 3982| | { 3983| | pBNS->vert[i].num_adj_edges = j+1; 3984| | break; 3985| | } 3986| | } 3987| | } 3988| | 3989| | pBNS->num_vertices = pBNS->num_atoms; 3990| | pBNS->num_edges = pBNS->num_bonds; 3991| | pBNS->num_added_atoms = 0; 3992| | pBNS->num_t_groups = 0; 3993| | pBNS->num_added_edges = 0; 3994| | 3995| | ALTP_DELTA(pBNS->alt_path) = 0; 3996| | ALTP_START_ATOM(pBNS->alt_path) = NO_VERTEX; 3997| | ALTP_END_ATOM(pBNS->alt_path) = NO_VERTEX; 3998| | ALTP_PATH_LEN(pBNS->alt_path) = 0; 3999| | 4000| | */ 4001| | 4002| | 4003| | /* add and fill edges and connectivity */ 4004| 920k| for (i = 0, n_edges = 0; i < num_atoms; i++) ------------------ | Branch (4004:30): [True: 832k, False: 87.8k] ------------------ 4005| 832k| { 4006| 832k| vert = pBNS->vert + i; /* pointer to the ith vertex */ 4007| 832k| st_cap = 0; 4008| 832k| st_flow = 0; 4009| 832k| flag_alt_bond = 0; 4010| 1.17M| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4010:21): [True: 339k, False: 832k] ------------------ 4011| 339k| { 4012| 339k| neigh = at[i].neighbor[j]; 4013| | /* find this bond at the neighbor */ 4014| 553k| for (k = 0; k < at[neigh].valence; k++) ------------------ | Branch (4014:25): [True: 553k, False: 0] ------------------ 4015| 553k| { 4016| 553k| if (at[neigh].neighbor[k] == i) ------------------ | Branch (4016:21): [True: 339k, False: 214k] ------------------ 4017| 339k| { 4018| 339k| break; 4019| 339k| } 4020| 553k| } 4021| 339k| bond_type = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 339k|#define BOND_TYPE_MASK 0x0f ------------------ 4022| 339k| bond_mark = ( at[i].bond_type[j] & ~BOND_TYPE_MASK ); ------------------ | | 189| 339k|#define BOND_TYPE_MASK 0x0f ------------------ 4023| 339k| if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && bond_type != BOND_TRIPLE) ------------------ | | 177| 339k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 678k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && bond_type != BOND_TRIPLE) ------------------ | | 178| 1.35k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 340k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && bond_type != BOND_TRIPLE) ------------------ | | 179| 418|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 418|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (4023:17): [True: 1.35k, False: 337k] | Branch (4023:45): [True: 418, False: 932] | Branch (4023:73): [True: 418, False: 0] ------------------ 4024| 418| { 4025| | /* make unknown bonds single */ 4026| 418| bond_type = BOND_SINGLE; ------------------ | | 177| 418|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 418|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ 4027| 418| at[i].bond_type[j] = bond_mark | bond_type; 4028| 418| num_changed_bonds++; 4029| 418| } 4030| 339k| if (neigh > i) ------------------ | Branch (4030:17): [True: 169k, False: 169k] ------------------ 4031| 169k| { 4032| | /* this is the first time we encounter this bond */ 4033| 169k| bNeedsFlower1 = AtomStcapStflow( at, pVA, pSrm, i, &c1, &f1, NULL, NULL ); 4034| | /* GetAtomStCapFlow( at, pVA, pSrm, i, &c1, &f1 ); */ 4035| 169k| c1 += bNeedsFlower1 ? 0 : pVA[i].cInitFreeValences; /* elevate cap to the lowest valence in ChargeStruct */ ------------------ | Branch (4035:23): [True: 21.1k, False: 148k] ------------------ 4036| 169k| bNeedsFlower2 = AtomStcapStflow( at, pVA, pSrm, neigh, &c2, &f2, NULL, NULL ); 4037| | /* GetAtomStCapFlow( at, pVA, pSrm, neigh, &c2, &f2 ); */ 4038| 169k| c2 += bNeedsFlower2 ? 0 : pVA[neigh].cInitFreeValences; /* elevate cap to the lowest valence in ChargeStruct */ ------------------ | Branch (4038:23): [True: 22.0k, False: 147k] ------------------ 4039| | 4040| | /* at this point -O would have st_cap=st_flow=0 because the lowest valence=1 for charge=-1 */ 4041| | /* however, if -O belongs to a t-group its cap would be 1, flow = 0 */ 4042| | /*f1 = MAX_AT_FLOW(at[i]);*/ 4043| | /*f2 = MAX_AT_FLOW(at[neigh]);*/ 4044| | 4045| 169k| edge_flow = BondFlowMaxcapMinorder( at, pVA, pSrm, i, j, &edge_cap, &min_order, NULL ); 4046| | 4047| 169k| pBNS->edge[n_edges].neighbor1 = (AT_NUMB) i; 4048| 169k| pBNS->edge[n_edges].neighbor12 = (AT_NUMB) ( i ^ neigh ); 4049| 169k| pBNS->edge[n_edges].flow = 4050| 169k| pBNS->edge[n_edges].flow0 = edge_flow; 4051| 169k| pBNS->edge[n_edges].cap = 4052| 169k| pBNS->edge[n_edges].cap0 = edge_cap; 4053| 169k| pBNS->edge[n_edges].neigh_ord[0] = j; /* iedge to neigh index at vertex[i], i < neigh */ 4054| 169k| pBNS->edge[n_edges].neigh_ord[1] = k; /* iedge to i index at vertex[neigh], i < neigh */ 4055| 169k| pBNS->edge[n_edges].pass = 0; 4056| 169k| pBNS->edge[n_edges].forbidden = 0; /* may be forbidden if edge_flow = 1: stereogenic fixed double bond */ 4057| 169k| if (bond_type == BOND_TYPE_DOUBLE) ------------------ | | 33| 169k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (4057:21): [True: 466, False: 169k] ------------------ 4058| 466| { 4059| | /* forbid changing stereogenic double bonds */ 4060| 478| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) ------------------ | | 873| 956|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (4060:33): [True: 478, False: 0] | Branch (4060:61): [True: 437, False: 41] ------------------ 4061| 437| { 4062| 437| if (at[i].sb_ord[m] == j) ------------------ | Branch (4062:29): [True: 425, False: 12] ------------------ 4063| 425| { 4064| 425| pBNS->edge[n_edges].forbidden |= BNS_EDGE_FORBIDDEN_MASK; ------------------ | | 39| 425|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 4065| 425| break; 4066| 425| } 4067| 437| } 4068| 466| } 4069| 169k| if (pBNS->vert[neigh].iedge) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (4069:21): [True: 169k, False: 0] ------------------ 4070| 169k| { 4071| 169k| vert->iedge[j] = pBNS->vert[neigh].iedge[k] = n_edges++; /* same iedge index as neighbor index in at[] */ 4072| 169k| } 4073| 169k| } 4074| 169k| else 4075| 169k| { 4076| | /* this is the second time we encounter this bond. It was stored at */ 4077| 169k| int iedge2 = pBNS->vert[neigh].iedge[k]; 4078| 169k| edge_cap = pBNS->edge[iedge2].cap; 4079| 169k| edge_flow = pBNS->edge[iedge2].flow; 4080| 169k| } 4081| 339k| st_flow += edge_flow; 4082| | /* 4083| | st_cap += edge_cap; 4084| | */ 4085| 339k| } 4086| | 4087| 832k| vert->num_adj_edges = j; 4088| | /* 4089| | vert->st_edge.cap = 4090| | vert->st_edge.cap0 = st_cap; 4091| | */ 4092| 832k| vert->st_edge.flow = 4093| 832k| vert->st_edge.flow0 = st_flow; 4094| 832k| vert->type = BNS_VERT_TYPE_ATOM; ------------------ | | 45| 832k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ 4095| | /* 4096| | tot_st_cap += vert->st_edge.cap; 4097| | */ 4098| 832k| tot_st_flow += vert->st_edge.flow; 4099| 832k| } 4100| | 4101| 87.8k| *pNum_changed_bonds = num_changed_bonds / 2; 4102| | 4103| 87.8k| pBNS->num_edges = n_edges; /* number of edges */ 4104| 87.8k| pBNS->num_iedges = num_iedges; 4105| 87.8k| pBNS->num_added_edges = 0; 4106| | 4107| 87.8k| pBNS->tot_st_cap = tot_st_cap; 4108| 87.8k| pBNS->tot_st_flow = tot_st_flow; 4109| | 4110| |/* exit_function: */ 4111| | 4112| 87.8k| return pBNS; 4113| 87.8k|} IncrZeroBondsAndClearEndpts: 4118| 146k|{ 4119| 146k| int i, j; 4120| 1.04M| for (i = 0; i < num_at; i++) ------------------ | Branch (4120:17): [True: 898k, False: 146k] ------------------ 4121| 898k| { 4122| 898k| at[i].endpoint = 0; 4123| 898k| at[i].component = iComponent; 4124| 1.25M| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4124:21): [True: 354k, False: 898k] ------------------ 4125| 354k| { 4126| 354k| if (!at[i].bond_type[j]) ------------------ | Branch (4126:17): [True: 12.5k, False: 341k] ------------------ 4127| 12.5k| { 4128| 12.5k| at[i].bond_type[j] = BOND_TYPE_SINGLE; ------------------ | | 32| 12.5k|#define BOND_TYPE_SINGLE 1 ------------------ 4129| 12.5k| at[i].chem_bonds_valence += BOND_TYPE_SINGLE; ------------------ | | 32| 12.5k|#define BOND_TYPE_SINGLE 1 ------------------ 4130| 12.5k| } 4131| 354k| } 4132| 898k| } 4133| 146k|} IncrZeroBonds: 4138| 70.4k|{ 4139| 70.4k| int i, j; 4140| 229k| for (i = 0; i < num_at; i++) ------------------ | Branch (4140:17): [True: 159k, False: 70.4k] ------------------ 4141| 159k| { 4142| 159k| at[i].component = iComponent; 4143| 283k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4143:21): [True: 123k, False: 159k] ------------------ 4144| 123k| { 4145| 123k| if (!at[i].bond_type[j]) ------------------ | Branch (4145:17): [True: 4.03k, False: 119k] ------------------ 4146| 4.03k| { 4147| 4.03k| at[i].bond_type[j] = BOND_TYPE_SINGLE; ------------------ | | 32| 4.03k|#define BOND_TYPE_SINGLE 1 ------------------ 4148| 4.03k| at[i].chem_bonds_valence += BOND_TYPE_SINGLE; ------------------ | | 32| 4.03k|#define BOND_TYPE_SINGLE 1 ------------------ 4149| 4.03k| } 4150| 123k| } 4151| 159k| } 4152| 70.4k|} ClearEndpts: 4157| 70.4k|{ 4158| 70.4k| int i; 4159| 229k| for (i = 0; i < num_at; i++) ------------------ | Branch (4159:17): [True: 159k, False: 70.4k] ------------------ 4160| 159k| { 4161| 159k| at[i].endpoint = 0; 4162| 159k| } 4163| 70.4k|} GetDeltaChargeFromVF: 4195| 69.1k|{ 4196| 69.1k| int i, v = NO_VERTEX; ------------------ | | 118| 69.1k|#define NO_VERTEX -2 ------------------ 4197| 69.1k| int ieIn1 = ( !( vf->bUsed & VF_USED_IN ) && vf->e_In >= 0 && vf->delta_In ) ? vf->e_In + 1 : NO_VERTEX; ------------------ | | 4183| 69.1k|#define VF_USED_IN 1 ------------------ int ieIn1 = ( !( vf->bUsed & VF_USED_IN ) && vf->e_In >= 0 && vf->delta_In ) ? vf->e_In + 1 : NO_VERTEX; ------------------ | | 118| 50.6k|#define NO_VERTEX -2 ------------------ | Branch (4197:19): [True: 35.4k, False: 33.6k] | Branch (4197:50): [True: 18.4k, False: 17.0k] | Branch (4197:67): [True: 18.4k, False: 0] ------------------ 4198| 69.1k| int ieOut1 = ( !( vf->bUsed & VF_USED_OUT ) && vf->e_Out >= 0 && vf->delta_Out ) ? vf->e_Out + 1 : NO_VERTEX; ------------------ | | 4184| 69.1k|#define VF_USED_OUT 2 ------------------ int ieOut1 = ( !( vf->bUsed & VF_USED_OUT ) && vf->e_Out >= 0 && vf->delta_Out ) ? vf->e_Out + 1 : NO_VERTEX; ------------------ | | 118| 52.2k|#define NO_VERTEX -2 ------------------ | Branch (4198:20): [True: 38.7k, False: 30.4k] | Branch (4198:52): [True: 16.9k, False: 21.7k] | Branch (4198:70): [True: 16.9k, False: 0] ------------------ 4199| 69.1k| int nInitCharge, nPlusFlow, nMinusFlow, nDeltaCharge, nNumDeltaCharge, eCPlus, eCMinus; 4200| | 4201| 69.1k| if (!( vf->type & BNS_VERT_TYPE_C_GROUP ) || ------------------ | | 49| 69.1k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (4201:9): [True: 41.4k, False: 27.6k] ------------------ 4202| 27.6k| ( vf->type & BNS_VERT_TYPE_SUPER_TGROUP ) || ------------------ | | 50| 27.6k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 ------------------ | Branch (4202:9): [True: 0, False: 27.6k] ------------------ 4203| 27.6k| ( ieIn1 == NO_VERTEX && ieOut1 == NO_VERTEX )) ------------------ | | 118| 55.3k|#define NO_VERTEX -2 ------------------ ( ieIn1 == NO_VERTEX && ieOut1 == NO_VERTEX )) ------------------ | | 118| 13.0k|#define NO_VERTEX -2 ------------------ | Branch (4203:11): [True: 13.0k, False: 14.6k] | Branch (4203:33): [True: 1.20k, False: 11.7k] ------------------ 4204| 42.6k| { 4205| 42.6k| return 0; 4206| 42.6k| } 4207| 26.4k| if (vf->type & BNS_VERT_TYPE_C_NEGATIVE) ------------------ | | 54| 26.4k|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (4207:9): [True: 12.3k, False: 14.1k] ------------------ 4208| 12.3k| { 4209| | /* negative charge edge */ 4210| 73.1k| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (4210:21): [True: 64.1k, False: 8.97k] ------------------ 4211| 64.1k| { 4212| 64.1k| if (pVA[i].nCMinusGroupEdge == ieIn1 || pVA[i].nCMinusGroupEdge == ieOut1) ------------------ | Branch (4212:17): [True: 823, False: 63.3k] | Branch (4212:53): [True: 2.54k, False: 60.8k] ------------------ 4213| 3.37k| { 4214| 3.37k| v = i; 4215| 3.37k| break; 4216| 3.37k| } 4217| 64.1k| } 4218| 12.3k| } 4219| 14.1k| else 4220| 14.1k| { 4221| | /* positive charge edge */ 4222| 87.1k| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (4222:21): [True: 75.8k, False: 11.3k] ------------------ 4223| 75.8k| { 4224| 75.8k| if (pVA[i].nCPlusGroupEdge == ieIn1 || pVA[i].nCPlusGroupEdge == ieOut1) ------------------ | Branch (4224:17): [True: 1.46k, False: 74.3k] | Branch (4224:52): [True: 1.32k, False: 73.0k] ------------------ 4225| 2.78k| { 4226| 2.78k| v = i; 4227| 2.78k| break; 4228| 2.78k| } 4229| 75.8k| } 4230| 14.1k| } 4231| | 4232| 26.4k| if (v == NO_VERTEX) ------------------ | | 118| 26.4k|#define NO_VERTEX -2 ------------------ | Branch (4232:9): [True: 20.3k, False: 6.15k] ------------------ 4233| 20.3k| return 0; 4234| | 4235| 6.15k| nInitCharge = pVA[v].cInitCharge; 4236| 6.15k| nPlusFlow = nMinusFlow = 0; 4237| 6.15k| nNumDeltaCharge = 0; 4238| | 4239| 6.15k| if (( eCPlus = pVA[v].nCPlusGroupEdge - 1 ) >= 0) ------------------ | Branch (4239:9): [True: 5.54k, False: 610] ------------------ 4240| 5.54k| { 4241| 5.54k| nPlusFlow = pBNS->edge[eCPlus].cap 4242| 5.54k| - pBNS->edge[eCPlus].flow; 4243| 5.54k| } 4244| | 4245| 6.15k| if (( eCMinus = pVA[v].nCMinusGroupEdge - 1 ) >= 0) ------------------ | Branch (4245:9): [True: 4.33k, False: 1.82k] ------------------ 4246| 4.33k| { 4247| 4.33k| nMinusFlow = -pBNS->edge[eCMinus].flow; 4248| 4.33k| } 4249| 6.15k| nInitCharge += nPlusFlow + nMinusFlow; 4250| | 4251| 6.15k| nDeltaCharge = 0; 4252| | 4253| 6.15k| if (!( vf[0].bUsed & VF_USED_OUT )) ------------------ | | 4184| 6.15k|#define VF_USED_OUT 2 ------------------ | Branch (4253:9): [True: 5.87k, False: 289] ------------------ 4254| 5.87k| { 4255| 5.87k| if (vf[0].e_Out == eCPlus || vf[0].e_Out == eCMinus) ------------------ | Branch (4255:13): [True: 1.32k, False: 4.54k] | Branch (4255:38): [True: 2.54k, False: 1.99k] ------------------ 4256| 3.87k| { 4257| 3.87k| nDeltaCharge -= vf[0].delta_Out; 4258| 3.87k| vf[0].bUsed |= VF_USED_OUT; ------------------ | | 4184| 3.87k|#define VF_USED_OUT 2 ------------------ 4259| 3.87k| } 4260| 5.87k| } 4261| | 4262| 6.15k| if (!( vf[0].bUsed & VF_USED_IN )) ------------------ | | 4183| 6.15k|#define VF_USED_IN 1 ------------------ | Branch (4262:9): [True: 5.43k, False: 726] ------------------ 4263| 5.43k| { 4264| 5.43k| if (vf[0].e_In == eCPlus || vf[0].e_In == eCMinus) ------------------ | Branch (4264:13): [True: 1.46k, False: 3.97k] | Branch (4264:37): [True: 823, False: 3.14k] ------------------ 4265| 2.28k| { 4266| 2.28k| nDeltaCharge -= vf[0].delta_In; 4267| 2.28k| vf[0].bUsed |= VF_USED_IN; ------------------ | | 4183| 2.28k|#define VF_USED_IN 1 ------------------ 4268| 2.28k| } 4269| 5.43k| } 4270| | 4271| 6.15k| if (!nInitCharge && nDeltaCharge) ------------------ | Branch (4271:9): [True: 4.81k, False: 1.34k] | Branch (4271:25): [True: 4.81k, False: 0] ------------------ 4272| 4.81k| { 4273| 4.81k| nNumDeltaCharge++; 4274| 4.81k| } 4275| 1.34k| else if (nInitCharge && 0 == nInitCharge + nDeltaCharge) ------------------ | Branch (4275:14): [True: 1.34k, False: 0] | Branch (4275:29): [True: 1.33k, False: 7] ------------------ 4276| 1.33k| { 4277| 1.33k| nNumDeltaCharge--; 4278| 1.33k| } 4279| | 4280| 6.15k| return nNumDeltaCharge; 4281| 26.4k|} EvaluateChargeChanges: 4286| 19.1k|{ 4287| 19.1k| int pass, i, j, v0, v1, v2, v, ineigh1, /*ineigh2,*/ vLast, n, delta, ret, ie, err = 0; 4288| 19.1k| BNS_EDGE *edge; 4289| 19.1k| int nDeltaH, nDeltaCharge, iPrev, nInitCharge, nPlusFlow, nMinusFlow; 4290| 19.1k| int nNumDeltaH = 0; 4291| 19.1k| int nNumDeltaCharge = 0; 4292| 19.1k| int nNumVisitedAtoms = 0; 4293| 19.1k| VF vf[NUM_VF + 1]; 4294| | 4295| 19.1k| *pnDeltaH = 0; 4296| 19.1k| *pnDeltaCharge = 0; 4297| 19.1k| *pnNumVisitedAtoms = 0; 4298| | 4299| 38.2k| for (pass = pBNS->num_altp - 1, ret = 0; 0 <= pass; pass--) ------------------ | Branch (4299:46): [True: 19.1k, False: 19.1k] ------------------ 4300| 19.1k| { 4301| | 4302| 19.1k| pBNS->alt_path = pBNS->altp[pass]; 4303| 19.1k| v1 = ALTP_START_ATOM( pBNS->alt_path ); ------------------ | | 103| 19.1k|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 4304| 19.1k| n = ALTP_PATH_LEN( pBNS->alt_path ); ------------------ | | 101| 19.1k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 4305| 19.1k| delta = ALTP_DELTA( pBNS->alt_path ); ------------------ | | 112| 19.1k|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 4306| 19.1k| vLast = ALTP_END_ATOM( pBNS->alt_path ); ------------------ | | 102| 19.1k|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 4307| 19.1k| v0 = v2 = NO_VERTEX; ------------------ | | 118| 19.1k|#define NO_VERTEX -2 ------------------ 4308| | 4309| 19.1k| memset( vf, 0, sizeof( vf ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4310| 95.5k| for (i = 0; i < (int) ( sizeof( vf ) / sizeof( vf[0] ) ); i++) ------------------ | Branch (4310:21): [True: 76.4k, False: 19.1k] ------------------ 4311| 76.4k| { 4312| 76.4k| vf[i].v = NO_VERTEX; /* = -2 */ ------------------ | | 118| 76.4k|#define NO_VERTEX -2 ------------------ 4313| 76.4k| vf[i].e_In = NO_VERTEX; ------------------ | | 118| 76.4k|#define NO_VERTEX -2 ------------------ 4314| 76.4k| vf[i].e_Out = NO_VERTEX; ------------------ | | 118| 76.4k|#define NO_VERTEX -2 ------------------ 4315| 76.4k| } 4316| 19.1k| iPrev = 0; 4317| | /* add to the queue */ 4318| 19.1k| if (ANY_VERT_TYPE( pBNS->vert[v1].type )) ------------------ | | 4167| 19.1k|#define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 45| 19.1k|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | #define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 47| 19.1k|#define BNS_VERT_TYPE_TGROUP 0x0004 | | ------------------ | | #define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 49| 19.1k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (4167:27): [True: 9.36k, False: 9.74k] | | ------------------ | | 4168| 19.1k| !((X) & (BNS_VERT_TYPE_SUPER_TGROUP))) | | ------------------ | | | | 50| 9.36k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ | | | Branch (4168:28): [True: 6.50k, False: 2.86k] | | ------------------ ------------------ 4319| 6.50k| { 4320| 6.50k| if (pBNS->vert[v1].type & BNS_VERT_TYPE_ATOM) ------------------ | | 45| 6.50k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (4320:17): [True: 5.65k, False: 851] ------------------ 4321| 5.65k| { 4322| 5.65k| nNumVisitedAtoms++; 4323| 5.65k| } 4324| 6.50k| vf[2].type = pBNS->vert[v1].type; 4325| 6.50k| vf[2].v = v1; 4326| 6.50k| iPrev = 2; 4327| 6.50k| } 4328| | 4329| 19.1k| nNumDeltaH = 0; 4330| 19.1k| nNumDeltaCharge = 0; 4331| 19.1k| nNumVisitedAtoms = 0; 4332| | 4333| 199k| for (i = 0; i < n; i++, delta = -delta, v0 = v1, v1 = v2) /* djb-rwth: removing redundant code */ ------------------ | Branch (4333:21): [True: 180k, False: 19.1k] ------------------ 4334| 180k| { 4335| 180k| ineigh1 = ALTP_THIS_ATOM_NEIGHBOR( pBNS->alt_path, i ); /* v1->v2 neighbor */ ------------------ | | 104| 180k|#define ALTP_THIS_ATOM_NEIGHBOR(altp,X) (altp)[iALTP_NEIGHBOR+(X)].ineigh[0] /* 0 <= X < path_len */ ------------------ 4336| | /*ineigh2 = ALTP_NEXT_ATOM_NEIGHBOR(pBNS->alt_path, i);*/ /* v2->v1 neighbor */ 4337| 180k| edge = pBNS->edge + ( ie = pBNS->vert[v1].iedge[ineigh1] ); 4338| | /* follow the BN Structure, not the inp_ATOM, to take care of swithching to 4339| | t-groups, c-groups or other fictitious edges/vertices 4340| | */ 4341| | 4342| 180k| if (iPrev) ------------------ | Branch (4342:17): [True: 73.0k, False: 107k] ------------------ 4343| 73.0k| { 4344| | /* add exit delta and edge */ 4345| 73.0k| vf[2].e_Out = ie; 4346| 73.0k| vf[2].delta_Out = delta; 4347| 73.0k| } 4348| | 4349| 180k| v2 = edge->neighbor12 ^ v1; /* next vertex */ 4350| 180k| if (pBNS->vert[v2].type & BNS_VERT_TYPE_ATOM) ------------------ | | 45| 180k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (4350:17): [True: 44.4k, False: 135k] ------------------ 4351| 44.4k| { 4352| 44.4k| nNumVisitedAtoms++; 4353| 44.4k| } 4354| | 4355| 180k| if (( ANY_VERT_TYPE( pBNS->vert[v2].type ) || i == n - 1 ) && ------------------ | | 4167| 360k|#define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 45| 180k|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | #define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 47| 180k|#define BNS_VERT_TYPE_TGROUP 0x0004 | | ------------------ | | #define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 49| 180k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (4167:27): [True: 90.9k, False: 89.4k] | | ------------------ | | 4168| 360k| !((X) & (BNS_VERT_TYPE_SUPER_TGROUP))) | | ------------------ | | | | 50| 90.9k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ | | | Branch (4168:28): [True: 72.1k, False: 18.8k] | | ------------------ ------------------ | Branch (4355:59): [True: 13.5k, False: 94.7k] ------------------ 4356| 85.6k| ( vf[0].type & BNS_VERT_TYPE_C_GROUP ) && vf[0].bUsed != VF_USED_ALL) ------------------ | | 49| 85.6k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ ( vf[0].type & BNS_VERT_TYPE_C_GROUP ) && vf[0].bUsed != VF_USED_ALL) ------------------ | | 4185| 12.5k|#define VF_USED_ALL (VF_USED_IN | VF_USED_OUT) | | ------------------ | | | | 4183| 12.5k|#define VF_USED_IN 1 | | ------------------ | | #define VF_USED_ALL (VF_USED_IN | VF_USED_OUT) | | ------------------ | | | | 4184| 12.5k|#define VF_USED_OUT 2 | | ------------------ ------------------ | Branch (4356:17): [True: 12.5k, False: 73.1k] | Branch (4356:59): [True: 11.7k, False: 757] ------------------ 4357| 11.7k| { 4358| | /* unused vertex is about to be discarded */ 4359| 11.7k| nNumDeltaCharge += GetDeltaChargeFromVF( pBNS, pVA, &vf[0] ); 4360| 11.7k| } 4361| | 4362| 180k| if (ANY_VERT_TYPE( pBNS->vert[v2].type )) ------------------ | | 4167| 180k|#define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 45| 180k|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | #define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 47| 180k|#define BNS_VERT_TYPE_TGROUP 0x0004 | | ------------------ | | #define ANY_VERT_TYPE(X) (((X) & (BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_TGROUP | BNS_VERT_TYPE_C_GROUP)) && \ | | ------------------ | | | | 49| 180k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (4167:27): [True: 90.9k, False: 89.4k] | | ------------------ | | 4168| 180k| !((X) & (BNS_VERT_TYPE_SUPER_TGROUP))) | | ------------------ | | | | 50| 90.9k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ | | | Branch (4168:28): [True: 72.1k, False: 18.8k] | | ------------------ ------------------ 4363| 72.1k| { 4364| | /* shift the queue */ 4365| 72.1k| vf[0] = vf[1]; 4366| 72.1k| vf[1] = vf[2]; 4367| 72.1k| vf[2] = vf[3]; /* make vf[2] empty */ 4368| | /* add next vertex */ 4369| 72.1k| vf[2].v = v2; 4370| 72.1k| vf[2].type = pBNS->vert[v2].type; 4371| 72.1k| vf[2].e_In = ie; 4372| 72.1k| vf[2].delta_In = delta; 4373| 72.1k| iPrev = 2; /* indicates a newly added vertex */ 4374| 72.1k| } 4375| 108k| else if (i == n - 1) ------------------ | Branch (4375:22): [True: 13.5k, False: 94.7k] ------------------ 4376| 13.5k| { 4377| | /* shift the queue */ 4378| 13.5k| vf[0] = vf[1]; 4379| 13.5k| vf[1] = vf[2]; 4380| 13.5k| vf[2] = vf[3]; /* make vf[2] empty */ 4381| 13.5k| iPrev = 1; /* indicates the last vertex */ 4382| 13.5k| } 4383| 94.7k| else 4384| 94.7k| { 4385| 94.7k| iPrev = 0; /* no new vertex has been added */ 4386| 94.7k| } 4387| | 4388| 180k| if (iPrev && ( vf[1].type & BNS_VERT_TYPE_ATOM )) ------------------ | | 45| 85.6k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (4388:17): [True: 85.6k, False: 94.7k] | Branch (4388:26): [True: 46.3k, False: 39.3k] ------------------ 4389| 46.3k| { 4390| | /* a new vertex has just been added and */ 4391| | /* an atom is in the middle of the queue */ 4392| 46.3k| EdgeIndex eCPlus, eCMinus; 4393| 46.3k| v = vf[1].v; 4394| 46.3k| nInitCharge = pVA[v].cInitCharge; 4395| 46.3k| nPlusFlow = nMinusFlow = 0; 4396| 46.3k| if (( eCPlus = pVA[v].nCPlusGroupEdge - 1 ) >= 0) ------------------ | Branch (4396:21): [True: 42.7k, False: 3.65k] ------------------ 4397| 42.7k| { 4398| 42.7k| nPlusFlow = pBNS->edge[eCPlus].cap 4399| 42.7k| - pBNS->edge[eCPlus].flow; 4400| 42.7k| } 4401| 46.3k| if (( eCMinus = pVA[v].nCMinusGroupEdge - 1 ) >= 0) ------------------ | Branch (4401:21): [True: 34.8k, False: 11.5k] ------------------ 4402| 34.8k| { 4403| 34.8k| nMinusFlow = -pBNS->edge[eCMinus].flow; 4404| 34.8k| } 4405| 46.3k| nInitCharge += nPlusFlow + nMinusFlow; 4406| | 4407| 46.3k| nDeltaH = nDeltaCharge = 0; 4408| | 4409| 46.3k| if (vf[0].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 46.3k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (4409:21): [True: 53, False: 46.3k] ------------------ 4410| 53| { 4411| 53| nDeltaH -= delta; 4412| 53| } 4413| 46.3k| else if (( vf[0].type & BNS_VERT_TYPE_C_GROUP ) && ------------------ | | 49| 46.3k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (4413:26): [True: 9.71k, False: 36.5k] ------------------ 4414| 9.71k| !( vf[0].bUsed & VF_USED_OUT )) ------------------ | | 4184| 9.71k|#define VF_USED_OUT 2 ------------------ | Branch (4414:26): [True: 9.71k, False: 0] ------------------ 4415| 9.71k| { 4416| 9.71k| if (vf[0].e_Out == eCPlus || vf[0].e_Out == eCMinus) ------------------ | Branch (4416:25): [True: 5.51k, False: 4.19k] | Branch (4416:50): [True: 4.19k, False: 0] ------------------ 4417| 9.71k| { 4418| 9.71k| nDeltaCharge -= vf[0].delta_Out; 4419| 9.71k| vf[0].bUsed |= VF_USED_OUT; ------------------ | | 4184| 9.71k|#define VF_USED_OUT 2 ------------------ 4420| 9.71k| } 4421| 9.71k| } 4422| | 4423| 46.3k| if (vf[2].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 47| 46.3k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (4423:21): [True: 22, False: 46.3k] ------------------ 4424| 22| { 4425| 22| nDeltaH += delta; 4426| 22| } 4427| 46.3k| else if (( vf[2].type & BNS_VERT_TYPE_C_GROUP ) && ------------------ | | 49| 46.3k|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (4427:26): [True: 12.9k, False: 33.3k] ------------------ 4428| 12.9k| !( vf[2].bUsed & VF_USED_IN )) ------------------ | | 4183| 12.9k|#define VF_USED_IN 1 ------------------ | Branch (4428:26): [True: 12.9k, False: 0] ------------------ 4429| 12.9k| { 4430| 12.9k| if (vf[2].e_In == eCPlus || vf[2].e_In == eCMinus) ------------------ | Branch (4430:25): [True: 6.36k, False: 6.59k] | Branch (4430:49): [True: 6.59k, False: 0] ------------------ 4431| 12.9k| { 4432| 12.9k| nDeltaCharge -= vf[2].delta_In; 4433| 12.9k| vf[2].bUsed |= VF_USED_IN; ------------------ | | 4183| 12.9k|#define VF_USED_IN 1 ------------------ 4434| 12.9k| } 4435| 12.9k| } 4436| | 4437| 46.3k| if (!nInitCharge && nDeltaCharge) ------------------ | Branch (4437:21): [True: 29.3k, False: 17.0k] | Branch (4437:37): [True: 11.8k, False: 17.5k] ------------------ 4438| 11.8k| { 4439| 11.8k| nNumDeltaCharge++; 4440| 11.8k| } 4441| 34.5k| else if (nInitCharge && 0 == nInitCharge + nDeltaCharge) ------------------ | Branch (4441:26): [True: 17.0k, False: 17.5k] | Branch (4441:41): [True: 9.74k, False: 7.29k] ------------------ 4442| 9.74k| { 4443| 9.74k| nNumDeltaCharge--; 4444| 9.74k| } 4445| | 4446| 46.3k| nNumDeltaH += abs( nDeltaH ); 4447| | /* nNumDeltaCharge += abs(nDeltaCharge); */ 4448| 46.3k| vf[1].bUsed = VF_USED_ALL; ------------------ | | 4185| 46.3k|#define VF_USED_ALL (VF_USED_IN | VF_USED_OUT) | | ------------------ | | | | 4183| 46.3k|#define VF_USED_IN 1 | | ------------------ | | #define VF_USED_ALL (VF_USED_IN | VF_USED_OUT) | | ------------------ | | | | 4184| 46.3k|#define VF_USED_OUT 2 | | ------------------ ------------------ 4449| 46.3k| } 4450| 180k| } 4451| | 4452| 76.4k| for (j = 0; j < 3; j++) ------------------ | Branch (4452:21): [True: 57.3k, False: 19.1k] ------------------ 4453| 57.3k| { 4454| 57.3k| nNumDeltaCharge += GetDeltaChargeFromVF( pBNS, pVA, &vf[j] ); 4455| 57.3k| } 4456| | 4457| 19.1k| *pnDeltaH += nNumDeltaH; 4458| 19.1k| *pnDeltaCharge += nNumDeltaCharge; 4459| 19.1k| *pnNumVisitedAtoms += nNumVisitedAtoms; 4460| | 4461| | 4462| 19.1k| if (v2 != vLast) ------------------ | Branch (4462:13): [True: 0, False: 19.1k] ------------------ 4463| 0| { 4464| 0| err = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4465| 0| } 4466| 19.1k| } 4467| 19.1k| return err ? err : ret; ------------------ | Branch (4467:12): [True: 0, False: 19.1k] ------------------ 4468| 19.1k|} RunBnsTestOnce: 4474| 40.9k|{ 4475| 40.9k| int bChangeFlow = 0; /* do not change flow */ 4476| 40.9k| int delta, ret, ret2, pass; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 4477| | 4478| 40.9k| ReInitBnStructAltPaths( pBNS ); 4479| 40.9k| pass = 0; 4480| 40.9k| pBNS->alt_path = pBNS->altp[pass]; 4481| 40.9k| pBNS->num_altp = 0; 4482| 40.9k| pBNS->bChangeFlow = 0; 4483| 40.9k| delta = BalancedNetworkSearch( pBNS, pBD, bChangeFlow ); 4484| 40.9k| if (delta > 0) ------------------ | Branch (4484:9): [True: 19.1k, False: 21.8k] ------------------ 4485| 19.1k| { 4486| 19.1k| pBNS->alt_path = pBNS->altp[pass]; 4487| 19.1k| *pvFirst = ALTP_START_ATOM( pBNS->alt_path ); ------------------ | | 103| 19.1k|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 4488| 19.1k| *pPathLen = ALTP_PATH_LEN( pBNS->alt_path ); ------------------ | | 101| 19.1k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 4489| 19.1k| *pvLast = ALTP_END_ATOM( pBNS->alt_path ); ------------------ | | 102| 19.1k|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 4490| 19.1k| pBNS->num_altp++; 4491| 19.1k| ret2 = EvaluateChargeChanges( pBNS, pVA, pnDeltaH, pnDeltaCharge, pnNumVisitedAtoms ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 4492| 19.1k| } 4493| 21.8k| else 4494| 21.8k| { 4495| 21.8k| *pvFirst = NO_VERTEX; ------------------ | | 118| 21.8k|#define NO_VERTEX -2 ------------------ 4496| 21.8k| *pPathLen = 0; 4497| 21.8k| *pvLast = NO_VERTEX; ------------------ | | 118| 21.8k|#define NO_VERTEX -2 ------------------ 4498| 21.8k| ret2 = 0; 4499| 21.8k| } 4500| | 4501| 40.9k| ReInitBnStructAltPaths( pBNS ); 4502| | 4503| 40.9k| ret = ReInitBnData( pBD ); 4504| | 4505| 40.9k| return ( delta >= 0 && ret > 0 ) ? -ret ------------------ | Branch (4505:14): [True: 40.9k, False: 0] | Branch (4505:28): [True: 0, False: 40.9k] ------------------ 4506| 40.9k| : delta; 4507| 40.9k|} RunBnsRestoreOnce: 4512| 138k|{ 4513| | /* run BNS for the first time */ 4514| 138k| int nTotalDelta = 0, ret = 0; 4515| 138k| int nDelta; 4516| | 4517| 138k| ReInitBnStructAltPaths( pBNS ); 4518| | 4519| 138k| do 4520| 199k| { 4521| 199k| nDelta = RunBalancedNetworkSearch( pBNS, pBD, BNS_EF_CHNG_FLOW ); ------------------ | | 370| 199k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ 4522| 199k| if (IS_BNS_ERROR( nDelta )) ------------------ | | 67| 199k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 199k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 199k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 199k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 199k, False: 0] | | | Branch (67:44): [True: 0, False: 199k] | | ------------------ ------------------ 4523| 0| { 4524| 0| ret = nDelta; 4525| 0| goto exit_function; 4526| 0| } 4527| 199k| nTotalDelta += nDelta; 4528| 199k| ReInitBnStructAltPaths( pBNS ); 4529| 199k| ret = ReInitBnData( pBD ); 4530| 199k| if (ret > 0) ------------------ | Branch (4530:13): [True: 0, False: 199k] ------------------ 4531| 0| { 4532| 0| ret = -ret; 4533| 0| goto exit_function; 4534| 0| } 4535| 199k| } 4536| 199k| while (nDelta > 0 && ret == 0); ------------------ | Branch (4536:12): [True: 60.9k, False: 138k] | Branch (4536:26): [True: 60.9k, False: 0] ------------------ 4537| | 4538| 138k| pBNS->tot_st_flow += 2 * nTotalDelta; 4539| | 4540| 138k| ret = nTotalDelta; 4541| | 4542| 138k|exit_function: 4543| 138k| return ret; 4544| 138k|} comp_cc_cand: 4550| 1.78k|{ 4551| 1.78k| const CC_CAND *p1 = (const CC_CAND *) a1; 4552| 1.78k| const CC_CAND *p2 = (const CC_CAND *) a2; 4553| 1.78k| int ret; 4554| | 4555| 1.78k| if ((ret = (int) p2->cMetal - (int) p1->cMetal)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4555:9): [True: 72, False: 1.71k] ------------------ 4556| 72| return ret; /* metal first */ 4557| 1.71k| if ((ret = (int) p2->cNumBondsToMetal - (int) p1->cNumBondsToMetal)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4557:9): [True: 55, False: 1.65k] ------------------ 4558| 55| return ret; /* connected to metal first */ 4559| 1.65k| if ((ret = (int) p2->cPeriodicRowNumber - (int) p1->cPeriodicRowNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4559:9): [True: 271, False: 1.38k] ------------------ 4560| 271| return ret; /* heaviest first */ 4561| 1.38k| if ((ret = (int) p2->num_bonds - (int) p1->num_bonds)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4561:9): [True: 19, False: 1.36k] ------------------ 4562| 19| return ret; /* more bonds first */ 4563| 1.36k| if ((ret = (int) p1->chem_valence - (int) p2->chem_valence)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4563:9): [True: 16, False: 1.35k] ------------------ 4564| 16| return ret; /* less bond order first */ 4565| 1.35k| if ((!p1->cNumValenceElectrons && p2->cNumValenceElectrons)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4565:10): [True: 13, False: 1.33k] | Branch (4565:39): [True: 0, False: 13] ------------------ 4566| 0| return -1; /* no valence electrons first */ 4567| 1.35k| if ((!p2->cNumValenceElectrons && p1->cNumValenceElectrons)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4567:10): [True: 13, False: 1.33k] | Branch (4567:39): [True: 0, False: 13] ------------------ 4568| 0| return -1; /* no valence electrons first */ 4569| 1.35k| if (((int) p2->cNumValenceElectrons - (int) p1->cNumValenceElectrons)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4569:9): [True: 306, False: 1.04k] ------------------ 4570| 306| return ret; /* more valence electrons first */ 4571| 1.04k| ret = (int) p2->iat - (int) p1->iat; /* greater canon number first */ 4572| | 4573| 1.04k| return ret; 4574| 1.35k|} get_pVA_atom_type: 4594| 1.42k|{ 4595| 1.42k| int type = 0, val; 4596| 1.42k| if (pVA[iat].cNumValenceElectrons == 4) ------------------ | Branch (4596:9): [True: 150, False: 1.27k] ------------------ 4597| 150| { 4598| 150| if (pVA[iat].cPeriodicRowNumber == 1) ------------------ | Branch (4598:13): [True: 133, False: 17] ------------------ 4599| 133| { 4600| 133| type |= EL_TYPE_C; ------------------ | | 390| 133|#define EL_TYPE_C 0x0010 ------------------ 4601| 133| } 4602| 150| } 4603| | 4604| 1.27k| else if (pVA[iat].cNumValenceElectrons == 6) ------------------ | Branch (4604:14): [True: 438, False: 833] ------------------ 4605| 438| { 4606| 438| if (pVA[iat].cPeriodicRowNumber == 1) ------------------ | Branch (4606:13): [True: 138, False: 300] ------------------ 4607| 138| { 4608| 138| type |= EL_TYPE_O; ------------------ | | 386| 138|#define EL_TYPE_O 0x0001 ------------------ 4609| 138| } 4610| 300| else if (pVA[iat].cPeriodicRowNumber < 5) ------------------ | Branch (4610:18): [True: 300, False: 0] ------------------ 4611| 300| { 4612| 300| type |= EL_TYPE_S; ------------------ | | 387| 300|#define EL_TYPE_S 0x0002 ------------------ 4613| 300| } 4614| 438| if (bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 876|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (4614:13): [True: 114, False: 324] ------------------ 4615| 114| ( type & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 386| 114|#define EL_TYPE_O 0x0001 ------------------ ( type & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 387| 114|#define EL_TYPE_S 0x0002 ------------------ | Branch (4615:13): [True: 114, False: 0] ------------------ 4616| 114| 1 == nNoMetalBondsValence( at, iat ) && ------------------ | Branch (4616:14): [True: 54, False: 60] ------------------ 4617| 54| 1 == nNoMetalNumBonds( at, iat )) ------------------ | Branch (4617:14): [True: 51, False: 3] ------------------ 4618| 51| { 4619| 51| type |= EL_TYPE_OSt; ------------------ | | 393| 51|#define EL_TYPE_OSt 0x0100 /* terminal -OH, -O(-), -SH, -S(-), ... from fix_special_bonds(...) */ ------------------ 4620| 51| } 4621| 438| } 4622| | 4623| 833| else if (pVA[iat].cNumValenceElectrons == 5) ------------------ | Branch (4623:14): [True: 633, False: 200] ------------------ 4624| 633| { 4625| 633| if (pVA[iat].cPeriodicRowNumber == 1) ------------------ | Branch (4625:13): [True: 513, False: 120] ------------------ 4626| 513| { 4627| 513| type |= EL_TYPE_N; ------------------ | | 388| 513|#define EL_TYPE_N 0x0004 ------------------ 4628| 513| } 4629| 120| else 4630| 120| { 4631| 120| type |= EL_TYPE_P; ------------------ | | 389| 120|#define EL_TYPE_P 0x0008 ------------------ 4632| 120| } 4633| 633| } 4634| | 4635| 200| else if (!is_el_a_metal( pVA[iat].cPeriodicNumber )) ------------------ | Branch (4635:14): [True: 158, False: 42] ------------------ 4636| 158| { 4637| 158| type |= EL_TYPE_X; ------------------ | | 391| 158|#define EL_TYPE_X 0x0020 /* any not metal */ ------------------ 4638| 158| } 4639| | 4640| | /* check for possibility to be a tautomeric endpoint (that is, be a Mobile H site) */ 4641| 1.42k| val = get_endpoint_valence( at[iat].el_number ); 4642| | 4643| 1.42k| if (val && val > at[iat].valence && !at[iat].radical && ------------------ | Branch (4643:9): [True: 951, False: 470] | Branch (4643:16): [True: 621, False: 330] | Branch (4643:41): [True: 587, False: 34] ------------------ 4644| 587| -1 <= at[iat].charge && at[iat].charge <= 0 && ------------------ | Branch (4644:10): [True: 587, False: 0] | Branch (4644:34): [True: 580, False: 7] ------------------ 4645| 580| val == at[iat].chem_bonds_valence - at[iat].charge + at[iat].num_H) ------------------ | Branch (4645:10): [True: 579, False: 1] ------------------ 4646| 579| { 4647| 579| type |= EL_TYPE_PT; ------------------ | | 394| 579|#define EL_TYPE_PT 0x0200 /* may be a tautomeric endpoint */ ------------------ 4648| 579| } 4649| | 4650| 1.42k| return type; 4651| 1.42k|} AllocEdgeList: 4656| 5.58M|{ 4657| 5.58M| switch (nLen) 4658| 5.58M| { 4659| 2.59M| case EDGE_LIST_FREE: ------------------ | | 243| 2.59M|#define EDGE_LIST_FREE (-2) ------------------ | Branch (4659:9): [True: 2.59M, False: 2.99M] ------------------ 4660| 2.59M| if (NULL != pEdges->pnEdges) ------------------ | Branch (4660:17): [True: 350k, False: 2.24M] ------------------ 4661| 350k| { 4662| 350k| inchi_free( pEdges->pnEdges ); ------------------ | | 1152| 350k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 350k, False: 0] | | | Branch (1152:50): [Folded, False: 350k] | | ------------------ ------------------ 4663| 350k| } 4664| | /* fall through */ 4665| 5.23M| case EDGE_LIST_CLEAR: ------------------ | | 242| 5.23M|#define EDGE_LIST_CLEAR (-1) ------------------ | Branch (4665:9): [True: 2.63M, False: 2.94M] ------------------ 4666| 5.23M| memset( pEdges, 0, sizeof( *pEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4667| 5.23M| break; 4668| 351k| default: ------------------ | Branch (4668:9): [True: 351k, False: 5.23M] ------------------ 4669| 351k| if (nLen > 0 && nLen != pEdges->num_alloc) ------------------ | Branch (4669:17): [True: 351k, False: 19] | Branch (4669:29): [True: 351k, False: 1] ------------------ 4670| 351k| { 4671| 351k| EdgeIndex *tmp_edges = pEdges->pnEdges; 4672| 351k| int tmp_num = pEdges->num_edges; 4673| 351k| pEdges->pnEdges = (EdgeIndex *) inchi_calloc( nLen, sizeof( pEdges->pnEdges[0] ) ); ------------------ | | 1146| 351k|#define inchi_calloc calloc ------------------ 4674| 351k| if (!pEdges->pnEdges) ------------------ | Branch (4674:21): [True: 0, False: 351k] ------------------ 4675| 0| { 4676| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 4677| 0| } 4678| 351k| tmp_num = inchi_min( tmp_num, nLen ); ------------------ | | 139| 351k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 351k, False: 0] | | ------------------ ------------------ 4679| 351k| if (tmp_edges && tmp_num > 0) ------------------ | Branch (4679:21): [True: 902, False: 350k] | Branch (4679:34): [True: 373, False: 529] ------------------ 4680| 373| { 4681| 373| memcpy(pEdges->pnEdges, tmp_edges, tmp_num * sizeof(pEdges->pnEdges[0])); 4682| 373| pEdges->num_edges = tmp_num; 4683| 373| } 4684| 350k| else 4685| 350k| { 4686| 350k| pEdges->num_edges = 0; 4687| 350k| } 4688| 351k| if (tmp_edges) ------------------ | Branch (4688:21): [True: 902, False: 350k] ------------------ 4689| 902| { 4690| 902| inchi_free( tmp_edges ); ------------------ | | 1152| 902|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 902, False: 0] | | | Branch (1152:50): [Folded, False: 902] | | ------------------ ------------------ 4691| 902| } 4692| 351k| pEdges->num_alloc = nLen; 4693| 351k| return 0; 4694| 351k| } 4695| 20| break; 4696| 5.58M| } 4697| | 4698| 5.23M| return 0; 4699| 5.58M|} AddToEdgeList: 4704| 823k|{ 4705| 823k| if (pEdges->num_alloc == pEdges->num_edges) ------------------ | Branch (4705:9): [True: 143k, False: 680k] ------------------ 4706| 143k| { 4707| 143k| int ret; 4708| 143k| if (nAddLen <= 0) ------------------ | Branch (4708:13): [True: 0, False: 143k] ------------------ 4709| 0| { 4710| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 4711| 0| } 4712| 143k| if ((ret = AllocEdgeList( pEdges, pEdges->num_alloc + nAddLen ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4712:13): [True: 0, False: 143k] ------------------ 4713| 0| { 4714| 0| return ret; 4715| 0| } 4716| 143k| } 4717| | 4718| 823k| pEdges->pnEdges[pEdges->num_edges++] = (EdgeIndex) iedge; 4719| 823k| return 0; 4720| 823k|} RemoveFromEdgeListByIndex: 4725| 293|{ 4726| 293| int len; 4727| 293| if (0 <= ( len = pEdges->num_edges - index - 1 )) ------------------ | Branch (4727:9): [True: 293, False: 0] ------------------ 4728| 293| { 4729| 293| if (len) ------------------ | Branch (4729:13): [True: 72, False: 221] ------------------ 4730| 72| { 4731| 72| memmove(pEdges->pnEdges + index, pEdges->pnEdges + index + 1, len * sizeof(pEdges->pnEdges[0])); 4732| 72| } 4733| 293| pEdges->num_edges--; 4734| 293| pEdges->pnEdges[pEdges->num_edges] = 0; 4735| 293| return 0; 4736| 293| } 4737| 0| return -1; 4738| 293|} FindInEdgeList: 4743| 542|{ 4744| 542| int i; 4745| 542| EdgeIndex ie = iedge; 4746| 1.64k| for (i = pEdges->num_edges - 1; 0 <= i; i--) ------------------ | Branch (4746:37): [True: 1.16k, False: 487] ------------------ 4747| 1.16k| { 4748| 1.16k| if (ie == pEdges->pnEdges[i]) ------------------ | Branch (4748:13): [True: 55, False: 1.10k] ------------------ 4749| 55| { 4750| 55| return i; 4751| 55| } 4752| 1.16k| } 4753| | 4754| 487| return -1; 4755| 542|} RemoveFromEdgeListByValue: 4760| 1.08k|{ 4761| 1.08k| int i, ret, n = 0; 4762| 1.08k| EdgeIndex ie = iedge; 4763| 2.10k| for (i = pEdges->num_edges - 1; 0 <= i; i--) ------------------ | Branch (4763:37): [True: 1.01k, False: 1.08k] ------------------ 4764| 1.01k| { 4765| 1.01k| if (ie == pEdges->pnEdges[i]) ------------------ | Branch (4765:13): [True: 293, False: 722] ------------------ 4766| 293| { 4767| 293| if ((ret = RemoveFromEdgeListByIndex( pEdges, i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4767:17): [True: 0, False: 293] ------------------ 4768| 0| { 4769| 0| return ret; 4770| 0| } 4771| 293| n++; 4772| 293| } 4773| 1.01k| } 4774| | 4775| 1.08k| return n; 4776| 1.08k|} AllocBfsQueue: 4781| 263k|{ 4782| 263k| int ret = 0; 4783| 263k| switch (num_at) 4784| 263k| { 4785| 87.9k| case BFS_Q_FREE: ------------------ | | 61| 87.9k|#define BFS_Q_FREE (-2) ------------------ | Branch (4785:9): [True: 87.9k, False: 175k] ------------------ 4786| 87.9k| if (pQ->q) ------------------ | Branch (4786:17): [True: 87.9k, False: 0] ------------------ 4787| 87.9k| { 4788| 87.9k| pQ->q = QueueDelete( pQ->q ); 4789| 87.9k| } 4790| 87.9k| if (pQ->nAtomLevel) ------------------ | Branch (4790:17): [True: 87.9k, False: 0] ------------------ 4791| 87.9k| { 4792| 87.9k| inchi_free( pQ->nAtomLevel ); ------------------ | | 1152| 87.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 87.9k, False: 0] | | | Branch (1152:50): [Folded, False: 87.9k] | | ------------------ ------------------ 4793| 87.9k| } 4794| 87.9k| if (pQ->cSource) ------------------ | Branch (4794:17): [True: 87.9k, False: 0] ------------------ 4795| 87.9k| { 4796| 87.9k| inchi_free( pQ->cSource ); ------------------ | | 1152| 87.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 87.9k, False: 0] | | | Branch (1152:50): [Folded, False: 87.9k] | | ------------------ ------------------ 4797| 87.9k| } 4798| | /* fall through */ 4799| 175k| case BFS_Q_CLEAR: ------------------ | | 60| 175k|#define BFS_Q_CLEAR (-1) ------------------ | Branch (4799:9): [True: 87.9k, False: 175k] ------------------ 4800| 175k| memset( pQ, 0, sizeof( *pQ ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4801| 175k| return 0; 4802| | 4803| 87.9k| default: ------------------ | Branch (4803:9): [True: 87.9k, False: 175k] ------------------ 4804| 87.9k| if (num_at <= 0) ------------------ | Branch (4804:17): [True: 0, False: 87.9k] ------------------ 4805| 0| { 4806| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 4807| 0| goto exit_function; 4808| 0| } 4809| 87.9k| if (num_at > pQ->num_at) ------------------ | Branch (4809:17): [True: 87.9k, False: 0] ------------------ 4810| 87.9k| { 4811| 87.9k| if (pQ->num_at) ------------------ | Branch (4811:21): [True: 0, False: 87.9k] ------------------ 4812| 0| { 4813| 0| AllocBfsQueue( pQ, BFS_Q_FREE, 0 ); ------------------ | | 61| 0|#define BFS_Q_FREE (-2) ------------------ 4814| 0| } 4815| 87.9k| pQ->q = QueueCreate( num_at + 1, sizeof( qInt ) ); 4816| 87.9k| pQ->nAtomLevel = (AT_RANK*) inchi_calloc( num_at, sizeof( pQ->nAtomLevel[0] ) ); ------------------ | | 1146| 87.9k|#define inchi_calloc calloc ------------------ 4817| 87.9k| pQ->cSource = (S_CHAR *) inchi_calloc( num_at, sizeof( pQ->cSource[0] ) ); ------------------ | | 1146| 87.9k|#define inchi_calloc calloc ------------------ 4818| 87.9k| if (!pQ->q || !pQ->cSource || !pQ->nAtomLevel) ------------------ | Branch (4818:21): [True: 0, False: 87.9k] | Branch (4818:31): [True: 0, False: 87.9k] | Branch (4818:47): [True: 0, False: 87.9k] ------------------ 4819| 0| { 4820| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 4821| 0| goto exit_function; 4822| 0| } 4823| 87.9k| pQ->num_at = num_at; 4824| 87.9k| } 4825| 87.9k| pQ->min_ring_size = min_ring_size; 4826| 263k| } 4827| | 4828| 87.9k|exit_function: 4829| 87.9k| return ret; 4830| 263k|} RemoveForbiddenEdgeMask: 4835| 1.07M|{ 4836| 1.07M| int i, mask = ~forbidden_edge_mask; 4837| 1.55M| for (i = 0; i < pEdges->num_edges; i++) ------------------ | Branch (4837:17): [True: 477k, False: 1.07M] ------------------ 4838| 477k| { 4839| 477k| pBNS->edge[pEdges->pnEdges[i]].forbidden &= mask; 4840| 477k| } 4841| 1.07M|} SetForbiddenEdgeMask: 4846| 192k|{ 4847| 192k| int i; 4848| 403k| for (i = 0; i < pEdges->num_edges; i++) ------------------ | Branch (4848:17): [True: 211k, False: 192k] ------------------ 4849| 211k| { 4850| 211k| pBNS->edge[pEdges->pnEdges[i]].forbidden |= forbidden_edge_mask; 4851| 211k| } 4852| 192k|} RemoveForbiddenBondFlowBits: 4857| 1.90k|{ 4858| 1.90k| BNS_EDGE *e; 4859| 1.90k| int i; 4860| 1.90k| int inv_forbidden_edge_mask = ~forbidden_edge_mask_int; 4861| 12.5k| for (i = 0, e = pBNS->edge; i < pBNS->num_bonds; i++, e++) ------------------ | Branch (4861:33): [True: 10.6k, False: 1.90k] ------------------ 4862| 10.6k| { 4863| 10.6k| e->forbidden &= inv_forbidden_edge_mask; 4864| 10.6k| } 4865| 1.90k|} GetChargeFlowerUpperEdge: 4881| 620k|{ 4882| 620k| int ret = NO_VERTEX, i, j, k, i0, i1; ------------------ | | 118| 620k|#define NO_VERTEX -2 ------------------ 4883| 620k| Vertex v0, v1[3], vc, v_t, v; 4884| 620k| BNS_EDGE *pe, *pe1[3], *pe_t; 4885| 620k| BNS_VERTEX *pv0, *pv1[3], *pv_t; 4886| | 4887| 620k| if (nChargeEdge < 0) ------------------ | Branch (4887:9): [True: 366k, False: 254k] ------------------ 4888| 366k| { 4889| 366k| goto exit_function; 4890| 366k| } 4891| | 4892| 254k| pe = pBNS->edge + nChargeEdge; 4893| 254k| vc = pe->neighbor1; /* charge vertex */ 4894| 254k| if (!IS_BNS_VT_C_GR( pBNS->vert[vc].type )) ------------------ | | 78| 254k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 254k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 254k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 254k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 254k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (4894:9): [True: 170k, False: 83.5k] ------------------ 4895| 170k| { 4896| 170k| vc = vc ^ pe->neighbor12; 4897| 170k| } 4898| | 4899| 254k| v0 = vc ^ pe->neighbor12; /* ChargeStruct vertex ? */ 4900| 254k| pv0 = pBNS->vert + v0; 4901| 254k| if (IS_BNS_VT_ATOM( pv0->type )) ------------------ | | 83| 254k|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 45| 254k|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (83:37): [True: 170k, False: 83.5k] | | ------------------ ------------------ 4902| 170k| { 4903| 170k| goto exit_function; /* no charge flower exists */ 4904| 170k| } 4905| | 4906| | /* 2 edges from v0 */ 4907| 320k| for (i = j = 0; i < pv0->num_adj_edges && j < 3; i++) ------------------ | Branch (4907:21): [True: 236k, False: 83.5k] | Branch (4907:47): [True: 236k, False: 0] ------------------ 4908| 236k| { 4909| 236k| pe1[j] = pBNS->edge + pv0->iedge[i]; 4910| 236k| if (vc != ( v1[j] = pe1[j]->neighbor12 ^ v0 ) && ------------------ | Branch (4910:13): [True: 153k, False: 83.5k] ------------------ 4911| 153k| ( pv1[j] = pBNS->vert + v1[j], ------------------ | Branch (4911:13): [True: 104k, False: 48.8k] ------------------ 4912| 153k| !IS_BNS_VT_ATOM( pv1[j]->type ) && !IS_BNS_VT_C_GR( pv1[j]->type ) )) ------------------ | | 83| 306k|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 45| 153k|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ ------------------ !IS_BNS_VT_ATOM( pv1[j]->type ) && !IS_BNS_VT_C_GR( pv1[j]->type ) )) ------------------ | | 78| 274k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 121k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 121k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 121k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 121k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (4912:17): [True: 121k, False: 31.4k] | Branch (4912:52): [True: 104k, False: 17.4k] ------------------ 4913| 104k| { 4914| 104k| j++; 4915| 104k| } 4916| 236k| } 4917| | 4918| 83.5k| if (j != 2 || i != pv0->num_adj_edges) ------------------ | Branch (4918:9): [True: 31.4k, False: 52.1k] | Branch (4918:19): [True: 0, False: 52.1k] ------------------ 4919| 31.4k| { 4920| 31.4k| goto exit_function; 4921| 31.4k| } 4922| | 4923| 52.1k| if (pv1[1]->num_adj_edges == 2 && ------------------ | Branch (4923:9): [True: 52.1k, False: 0] ------------------ 4924| 52.1k| pv1[0]->num_adj_edges == 3) ------------------ | Branch (4924:10): [True: 52.1k, False: 0] ------------------ 4925| 52.1k| { 4926| 52.1k| i0 = 1; 4927| 52.1k| i1 = 0; 4928| 52.1k| } 4929| 0| else if (pv1[0]->num_adj_edges == 2 && ------------------ | Branch (4929:14): [True: 0, False: 0] ------------------ 4930| 0| pv1[1]->num_adj_edges == 3) ------------------ | Branch (4930:10): [True: 0, False: 0] ------------------ 4931| 0| { 4932| 0| i0 = 0; 4933| 0| i1 = 1; 4934| 0| } 4935| 0| else 4936| 0| { 4937| 0| goto exit_function; 4938| 0| } 4939| | 4940| | /* additional check: traverse edges around v1[i1] */ 4941| 52.1k| pv_t = pv1[i1]; 4942| 52.1k| v_t = v1[i1]; 4943| 208k| for (i = k = 0; i < pv_t->num_adj_edges; i++) ------------------ | Branch (4943:21): [True: 156k, False: 52.1k] ------------------ 4944| 156k| { 4945| 156k| pe_t = pBNS->edge + pv_t->iedge[i]; 4946| 156k| v = pe_t->neighbor12 ^ v_t; /* v1[i1] neighbor */ 4947| 156k| if (v == v0) ------------------ | Branch (4947:13): [True: 52.1k, False: 104k] ------------------ 4948| 52.1k| { 4949| 52.1k| k += 1; 4950| 52.1k| } 4951| 156k| if (v == v1[i0]) ------------------ | Branch (4951:13): [True: 52.1k, False: 104k] ------------------ 4952| 52.1k| { 4953| 52.1k| k += 2; 4954| 52.1k| } 4955| 156k| if (IS_BNS_VT_ATOM( pBNS->vert[v].type )) ------------------ | | 83| 156k|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 45| 156k|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (83:37): [True: 52.1k, False: 104k] | | ------------------ ------------------ 4956| 52.1k| { 4957| 52.1k| k += 4; 4958| 52.1k| } 4959| 156k| } 4960| 52.1k| if (k != 7) ------------------ | Branch (4960:9): [True: 0, False: 52.1k] ------------------ 4961| 0| { 4962| 0| goto exit_function; 4963| 0| } 4964| | 4965| 52.1k| ret = (int) ( pe1[i0] - pBNS->edge ); 4966| | 4967| 620k|exit_function: 4968| 620k| return ret; 4969| 52.1k|} MakeOneInChIOutOfStrFromINChI2: 5061| 88.9k|{ 5062| 88.9k| int ret; 5063| 88.9k| INPUT_PARMS ip_loc, *ip; 5064| 88.9k| STRUCT_DATA sd_loc, *sd; 5065| | 5066| 88.9k| ip_loc = *ip_inp; 5067| 88.9k| sd_loc = *sd_inp; 5068| 88.9k| ip = &ip_loc; 5069| 88.9k| sd = &sd_loc; 5070| | 5071| 88.9k| memset( sd, 0, sizeof( *sd ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5072| | 5073| | /* create structure out of BNS */ 5074| 88.9k| memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operator added */ 5075| 88.9k| pStruct->at = at2; 5076| 88.9k| ret = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 5077| 88.9k| pStruct->at = at; 5078| 88.9k| if (ret < 0) ------------------ | Branch (5078:9): [True: 0, False: 88.9k] ------------------ 5079| 0| { 5080| 0| goto exit_function;/* out of RAM or other normalization problem */ 5081| 0| } 5082| | 5083| 88.9k| pStruct->at = at; 5084| | 5085| 88.9k| ret = MakeOneInChIOutOfStrFromINChI( pCG, ic, ip, sd, pStruct, 5086| 88.9k| at2, at3, pTCGroups ); 5087| | 5088| 88.9k| if (ret < 0) ------------------ | Branch (5088:9): [True: 52, False: 88.8k] ------------------ 5089| 52| { 5090| 52| goto exit_function;/* out of RAM or other normalization problem */ 5091| 52| } 5092| 88.8k| if (at_norm) ------------------ | Branch (5092:9): [True: 88.8k, False: 0] ------------------ 5093| 88.8k| { 5094| 88.8k| *at_norm = pStruct->pOne_norm_data[0]->at; 5095| 88.8k| } 5096| 88.8k| if (at_prep) ------------------ | Branch (5096:9): [True: 88.8k, False: 0] ------------------ 5097| 88.8k| { 5098| 88.8k| if (pStruct->pOne_norm_data[0]->bTautPreprocessed && pStruct->pOne_norm_data[0]->at_fixed_bonds) ------------------ | Branch (5098:13): [True: 2.86k, False: 85.9k] | Branch (5098:62): [True: 2.86k, False: 0] ------------------ 5099| 2.86k| { 5100| 2.86k| *at_prep = pStruct->pOne_norm_data[0]->at_fixed_bonds; 5101| 2.86k| } 5102| 85.9k| else 5103| | /* get preprocessed structure in case of Fixed-H */ 5104| 85.9k| if (pStruct->iMobileH == TAUT_NON && pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->bTautPreprocessed) ------------------ | | 574| 171k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5104:17): [True: 1.89k, False: 84.0k] | Branch (5104:50): [True: 893, False: 1.00k] | Branch (5104:80): [True: 593, False: 300] ------------------ 5105| 593| { 5106| 593| *at_prep = pStruct->pOne_norm_data[1]->at_fixed_bonds; 5107| 593| } 5108| 85.3k| else 5109| 85.3k| { 5110| 85.3k| *at_prep = NULL; 5111| 85.3k| } 5112| 88.8k| } 5113| 88.8k| if (t_group_info) ------------------ | Branch (5113:9): [True: 88.8k, False: 0] ------------------ 5114| 88.8k| { 5115| 88.8k| if (pStruct->iMobileH == TAUT_YES && ------------------ | | 575| 177k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5115:13): [True: 86.9k, False: 1.89k] ------------------ 5116| 86.9k| pStruct->One_ti.num_t_groups && ------------------ | Branch (5116:14): [True: 1.80k, False: 85.1k] ------------------ 5117| 1.80k| pStruct->One_ti.t_group && pStruct->One_ti.nEndpointAtomNumber) ------------------ | Branch (5117:14): [True: 1.80k, False: 0] | Branch (5117:41): [True: 1.80k, False: 0] ------------------ 5118| 1.80k| { 5119| 1.80k| *t_group_info = &pStruct->One_ti; 5120| 1.80k| } 5121| 87.0k| else 5122| 87.0k| { 5123| 87.0k| *t_group_info = NULL; 5124| 87.0k| } 5125| 88.8k| } 5126| | 5127| 88.9k|exit_function: 5128| 88.9k| return ret; 5129| 88.8k|} MakeOneInChIOutOfStrFromINChI: 5141| 146k|{ 5142| | 5143| 146k| INCHI_MODE bTautFlags = ip->bTautFlags | TG_FLAG_H_ALREADY_REMOVED; ------------------ | | 943| 146k|#define TG_FLAG_H_ALREADY_REMOVED 0x00020000 /* processing structure restored from InChI */ ------------------ 5144| 146k| INCHI_MODE bTautFlagsDone = 0; /*(ip->bTautFlagsDone | sd->bTautFlagsDone[INCHI_BAS]);*/ 5145| 146k| INChI *cur_INChI[TAUT_NUM]; 5146| 146k| INChI_Aux *cur_INChI_Aux[TAUT_NUM]; 5147| 146k| int i, j, k; 5148| 146k| int iComponent = pTCGroups->iComponent; 5149| 146k| int len_at = pStruct->num_atoms + pStruct->num_deleted_H; 5150| 146k| int num_atoms = pStruct->num_atoms; 5151| 146k| long ulStructTime; 5152| | 5153| 146k| INP_ATOM_DATA InpCurAtData; 5154| 146k| INP_ATOM_DATA *inp_cur_data; 5155| | 5156| 146k| INP_ATOM_DATA InpNormAtData, InpNormTautData; 5157| 146k| INP_ATOM_DATA *inp_norm_data[TAUT_NUM]; /* = { &InpNormAtData, &InpNormTautData }; */ 5158| | 5159| 146k| int bOrigCoord = 0; 5160| 146k| int num_at, ret = RI_ERR_PROGR; ------------------ | | 17| 146k|#define RI_ERR_PROGR (-3) ------------------ 5161| 146k| struct tagInchiTime ulMaxTime; 5162| | 5163| 146k| T_GROUP_INFO *t_group_info = NULL; 5164| | /* initialization */ 5165| 146k| inp_cur_data = &InpCurAtData; 5166| 146k| inp_norm_data[TAUT_NON] = &InpNormAtData; ------------------ | | 574| 146k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5167| 146k| inp_norm_data[TAUT_YES] = &InpNormTautData; ------------------ | | 575| 146k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5168| | 5169| 146k| memset( inp_cur_data, 0, sizeof( *inp_cur_data ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5170| 146k| memset( inp_norm_data[TAUT_NON], 0, sizeof( *inp_norm_data[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 574| 146k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5171| 146k| memset( inp_norm_data[TAUT_YES], 0, sizeof( *inp_norm_data[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 575| 146k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5172| 146k| ulStructTime = sd->ulStructTime; 5173| 146k| memset( sd, 0, sizeof( *sd ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5174| | 5175| | /* deallocate old results */ 5176| 146k| free_t_group_info( &pStruct->One_ti ); 5177| 438k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 438k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (5177:17): [True: 292k, False: 146k] ------------------ 5178| 292k| { 5179| 292k| Free_INChI( &pStruct->pOneINChI[k] ); 5180| 292k| Free_INChI_Aux( &pStruct->pOneINChI_Aux[k] ); 5181| 292k| if (pStruct->pOne_norm_data[k]) ------------------ | Branch (5181:13): [True: 1.53k, False: 290k] ------------------ 5182| 1.53k| { 5183| 1.53k| FreeInpAtomData( pStruct->pOne_norm_data[k] ); 5184| 1.53k| inchi_free( pStruct->pOne_norm_data[k] ); ------------------ | | 1152| 1.53k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.53k, False: 0] | | | Branch (1152:50): [Folded, False: 1.53k] | | ------------------ ------------------ 5185| 1.53k| pStruct->pOne_norm_data[k] = NULL; 5186| 1.53k| } 5187| 292k| cur_INChI[k] = NULL; 5188| 292k| cur_INChI_Aux[k] = NULL; 5189| 292k| } 5190| | 5191| 146k| memcpy(at3, at2, sizeof(at3[0]) * len_at); 5192| | 5193| | /* prepare the structure */ 5194| 146k| IncrZeroBondsAndClearEndpts( at3, num_atoms, iComponent + 1 ); 5195| | 5196| 146k| CopySt2At( at3, pStruct->st, pStruct->num_atoms ); 5197| | 5198| 146k| FixUnkn0DStereoBonds( at3, pStruct->num_atoms ); 5199| | 5200| 146k| ret = ReconcileAllCmlBondParities( at3, pStruct->num_atoms, 0 ); 5201| | 5202| 146k| if (ret < 0) ------------------ | Branch (5202:9): [True: 0, False: 146k] ------------------ 5203| 0| { 5204| 0| goto exit_function; 5205| 0| } 5206| | 5207| 146k| if (0 < fix_odd_things( num_atoms, at3, 1, ip->bFixNonUniformDraw )) ------------------ | Branch (5207:9): [True: 2.99k, False: 143k] ------------------ 5208| 2.99k| { 5209| 2.99k| if (sd->nErrorType < _IS_WARNING) ------------------ | | 11| 2.99k|#define _IS_WARNING 1 ------------------ | Branch (5209:13): [True: 2.99k, False: 0] ------------------ 5210| 2.99k| { 5211| 2.99k| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 2.99k|#define _IS_WARNING 1 ------------------ 5212| 2.99k| } 5213| 2.99k| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 570| 2.99k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 978| 2.99k|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 5214| 2.99k| } 5215| | 5216| | /* allocate and set parameters */ 5217| 146k| inp_cur_data->at = at3; 5218| 146k| inp_cur_data->num_at = num_atoms; 5219| 146k| inp_cur_data->num_removed_H = pStruct->num_deleted_H; 5220| | 5221| 146k| bTautFlagsDone &= ~( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ); ------------------ | | 981| 146k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ bTautFlagsDone &= ~( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ); ------------------ | | 982| 146k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5222| | 5223| 146k| if ((i = bNumHeterAtomHasIsotopicH( at3, num_atoms ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5223:9): [True: 679, False: 145k] ------------------ 5224| 679| { 5225| 679| if (i & 1) ------------------ | Branch (5225:13): [True: 56, False: 623] ------------------ 5226| 56| { 5227| 56| bTautFlagsDone |= TG_FLAG_FOUND_ISOTOPIC_H_DONE; ------------------ | | 981| 56|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5228| 56| } 5229| 679| if (i & 2) ------------------ | Branch (5229:13): [True: 646, False: 33] ------------------ 5230| 646| { 5231| 646| bTautFlagsDone |= TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE; ------------------ | | 982| 646|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5232| 646| } 5233| 679| } 5234| | 5235| 146k| memset( &ulMaxTime, 0, sizeof( ulMaxTime ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5236| | 5237| | /* allocate memory for non-tautimeric (k=0) and tautomeric (k=1) results */ 5238| 438k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 438k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (5238:17): [True: 292k, False: 146k] ------------------ 5239| 292k| { 5240| | 5241| 292k| if (!pStruct->bMobileH || k == pStruct->bMobileH) ------------------ | Branch (5241:13): [True: 3.92k, False: 288k] | Branch (5241:35): [True: 144k, False: 144k] ------------------ 5242| 148k| { 5243| | /* pStruct->bMobileH=0: k = 0, 1 => allow allocation of both Fixed-H and Mobile-H InChI 5244| | pStruct->bMobileH=1: k = 1 only => allow allocation of only Mobile-H InChI */ 5245| | 5246| | /* djb-rwth: introducing variables for correct nAllocMode expression */ 5247| 148k| int nAM1 = 0, nAM2 = 0; 5248| 148k| int nAllocMode = 0; /* copied from below 2024-09-01 DT */ 5249| | 5250| 148k| if (k == TAUT_YES) ------------------ | | 575| 148k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5250:17): [True: 146k, False: 1.96k] ------------------ 5251| 146k| nAM1 = REQ_MODE_TAUT; ------------------ | | 16| 146k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 5252| | 5253| 148k| if (bTautFlagsDone & (TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE)) ------------------ | | 981| 148k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ if (bTautFlagsDone & (TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE)) ------------------ | | 982| 148k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5253:17): [True: 782, False: 147k] ------------------ 5254| 782| nAM2 = ip->nMode & REQ_MODE_ISO; ------------------ | | 17| 782|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 5255| | 5256| 148k| nAllocMode = nAM1 | nAM2; /* djb-rwth: original sequence of bit-wise operations had to be rewritten */ 5257| | 5258| 148k| if ((k == TAUT_NON && ( ip->nMode & REQ_MODE_BASIC )) || ------------------ | | 574| 296k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if ((k == TAUT_NON && ( ip->nMode & REQ_MODE_BASIC )) || ------------------ | | 15| 1.96k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (5258:18): [True: 1.96k, False: 146k] | Branch (5258:35): [True: 1.96k, False: 0] ------------------ 5259| 146k| (k == TAUT_YES && ( ip->nMode & REQ_MODE_TAUT ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 292k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ (k == TAUT_YES && ( ip->nMode & REQ_MODE_TAUT ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 16| 146k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (5259:19): [True: 146k, False: 0] | Branch (5259:36): [True: 146k, False: 0] ------------------ 5260| 148k| { 5261| | /* alloc INChI and INChI_Aux only if ip->nMode allows this */ 5262| 148k| cur_INChI[k] = Alloc_INChI( inp_cur_data->at, inp_cur_data->num_at, &inp_cur_data->num_bonds, 5263| 148k| &inp_cur_data->num_isotopic, nAllocMode ); 5264| 148k| cur_INChI_Aux[k] = Alloc_INChI_Aux( inp_cur_data->num_at, 5265| 148k| inp_cur_data->num_isotopic, nAllocMode, bOrigCoord ); 5266| 148k| if (cur_INChI_Aux[k]) ------------------ | Branch (5266:21): [True: 148k, False: 0] ------------------ 5267| 148k| { 5268| 148k| cur_INChI_Aux[k]->bIsIsotopic = inp_cur_data->num_isotopic; 5269| 148k| } 5270| | 5271| | /* alloc memory for the output structure: non-tautomeric and tautomeric (for displaying) */ 5272| 148k| CreateInpAtomData( inp_norm_data[k], inp_cur_data->num_at + inp_cur_data->num_removed_H, k ); 5273| | 5274| 148k| inp_norm_data[k]->num_removed_H = inp_cur_data->num_removed_H; 5275| 148k| } 5276| 0| else 5277| 0| { 5278| 0| FreeInpAtomData( inp_norm_data[k] ); 5279| 0| } 5280| 148k| } 5281| 144k| else 5282| 144k| { 5283| 144k| FreeInpAtomData( inp_norm_data[k] ); 5284| 144k| } 5285| 292k| } 5286| | 5287| 146k| k = pStruct->bMobileH; 5288| | 5289| | /* In case of Fixed-H we have to create InChI for both Fixed-H and Mobile-H */ 5290| | 5291| 146k| num_at = Create_INChI( pCG, 5292| 146k| ic, 5293| 146k| (INPUT_PARMS *) ip, 5294| 146k| cur_INChI, 5295| 146k| cur_INChI_Aux, 5296| 146k| NULL, 5297| 146k| inp_cur_data->at, 5298| 146k| inp_norm_data, 5299| 146k| inp_cur_data->num_at + inp_cur_data->num_removed_H, 5300| 146k| NULL, 5301| 146k| ip->nMode, 5302| 146k| &bTautFlags, 5303| 146k| &bTautFlagsDone, 5304| 146k| NULL /* &ulMaxTime*/, 5305| 146k| &pStruct->One_ti, 5306| 146k| sd->pStrErrStruct ); 5307| | 5308| 146k| SetConnectedComponentNumber( inp_cur_data->at, inp_cur_data->num_at, iComponent + 1 ); /* normalization alters structure component number */ 5309| | 5310| | /* Detect InChI errors */ 5311| | 5312| 146k| if (num_at < 0) ------------------ | Branch (5312:9): [True: 52, False: 145k] ------------------ 5313| 52| { 5314| 52| ret = num_at; 5315| 52| } 5316| 145k| else if (cur_INChI[k] && cur_INChI[k]->nErrorCode) ------------------ | Branch (5316:14): [True: 145k, False: 0] | Branch (5316:30): [True: 0, False: 145k] ------------------ 5317| 0| { 5318| 0| ret = cur_INChI[k]->nErrorCode; 5319| 0| } 5320| 145k| else if (cur_INChI_Aux[k] && cur_INChI_Aux[k]->nErrorCode) ------------------ | Branch (5320:14): [True: 145k, False: 0] | Branch (5320:34): [True: 0, False: 145k] ------------------ 5321| 0| { 5322| 0| ret = cur_INChI_Aux[k]->nErrorCode; 5323| 0| } 5324| 145k| else 5325| 145k| { 5326| 145k| ret = 0; 5327| 145k| } 5328| | 5329| | /* Fill out the output */ 5330| | 5331| 146k| if (!ret) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (5331:9): [True: 145k, False: 52] ------------------ 5332| 145k| { 5333| 145k| int bMobileH = pStruct->bMobileH; 5334| 145k| if (bMobileH == TAUT_NON && ------------------ | | 574| 291k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5334:13): [True: 1.92k, False: 144k] ------------------ 5335| 1.92k| 0 == cur_INChI[TAUT_NON]->nNumberOfAtoms && ------------------ | | 574| 1.92k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5335:14): [True: 1.02k, False: 893] ------------------ 5336| 1.02k| 0 < cur_INChI[TAUT_YES]->nNumberOfAtoms) ------------------ | | 575| 1.02k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5336:14): [True: 1.02k, False: 0] ------------------ 5337| 1.02k| { 5338| | /* tautomerism or H(+) removal/addition was not discovered */ 5339| 1.02k| bMobileH = TAUT_YES; ------------------ | | 575| 1.02k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5340| 1.02k| } 5341| | 5342| 145k| if (cur_INChI[1]) ------------------ | Branch (5342:13): [True: 145k, False: 0] ------------------ 5343| 145k| pStruct->nChargeRevrs = cur_INChI[TAUT_YES]->nTotalCharge; /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 575| 145k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5344| | 5345| 145k| pStruct->pOneINChI[0] = cur_INChI[bMobileH]; 5346| 145k| pStruct->pOneINChI_Aux[0] = cur_INChI_Aux[bMobileH]; 5347| 145k| pStruct->nOneINChI_bMobileH = bMobileH; 5348| 145k| cur_INChI[bMobileH] = NULL; /* remove pointer to avoid deallocation at exit_function */ 5349| 145k| cur_INChI_Aux[bMobileH] = NULL; /* remove pointer to avoid deallocation at exit_function */ 5350| | 5351| 145k| pStruct->nNumRemovedProtons = ( pStruct->iMobileH == TAUT_YES ) ? pStruct->One_ti.tni.nNumRemovedProtons : 0; ------------------ | | 575| 145k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5351:39): [True: 144k, False: 1.92k] ------------------ 5352| | 5353| | 5354| | /* set correct t-group numbers to endpoints */ 5355| | 5356| 145k| t_group_info = &pStruct->One_ti; 5357| | 5358| 145k| if (t_group_info->num_t_groups && t_group_info->t_group && t_group_info->nEndpointAtomNumber) ------------------ | Branch (5358:13): [True: 2.44k, False: 143k] | Branch (5358:43): [True: 2.44k, False: 0] | Branch (5358:68): [True: 2.44k, False: 0] ------------------ 5359| 2.44k| { 5360| 2.44k| inp_ATOM *at_norm = inp_norm_data[TAUT_YES]->at; ------------------ | | 575| 2.44k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5361| 2.44k| int num_at_norm = inp_norm_data[TAUT_YES]->num_at; ------------------ | | 575| 2.44k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5362| 19.6k| for (i = 0; i < num_at_norm; i++) ------------------ | Branch (5362:25): [True: 17.2k, False: 2.44k] ------------------ 5363| 17.2k| { 5364| 17.2k| at_norm[i].endpoint = 0; 5365| 17.2k| } 5366| 4.97k| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (5366:25): [True: 2.53k, False: 2.44k] ------------------ 5367| 2.53k| { 5368| 2.53k| k = t_group_info->t_group[i].nFirstEndpointAtNoPos; 5369| | /* add number of mobile (-) to the number of mobile H */ 5370| 2.53k| t_group_info->t_group[i].num[0] += t_group_info->t_group[i].num[1]; 5371| 8.64k| for (j = 0; j < t_group_info->t_group[i].nNumEndpoints; j++, k++) ------------------ | Branch (5371:29): [True: 6.11k, False: 2.53k] ------------------ 5372| 6.11k| { 5373| 6.11k| at_norm[t_group_info->nEndpointAtomNumber[k]].endpoint = t_group_info->t_group[i].nGroupNumber; 5374| 6.11k| } 5375| 2.53k| } 5376| 2.44k| } 5377| | 5378| 145k| pStruct->pOne_norm_data[0] = (INP_ATOM_DATA *) inchi_malloc( sizeof( pStruct->pOne_norm_data[0][0] ) ); ------------------ | | 1143| 145k|#define inchi_malloc malloc ------------------ 5379| | 5380| 145k| if (pStruct->pOne_norm_data[0]) ------------------ | Branch (5380:13): [True: 145k, False: 0] ------------------ 5381| 145k| { 5382| 145k| memcpy(pStruct->pOne_norm_data[0], inp_norm_data[bMobileH], sizeof(pStruct->pOne_norm_data[0][0])); 5383| 145k| memset( inp_norm_data[bMobileH], 0, sizeof( *inp_norm_data[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5384| 145k| } 5385| 0| else 5386| 0| { 5387| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 5388| 0| } 5389| | 5390| 145k| if (bMobileH == TAUT_NON && cur_INChI[TAUT_YES]->nNumberOfAtoms > 0) ------------------ | | 574| 291k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (bMobileH == TAUT_NON && cur_INChI[TAUT_YES]->nNumberOfAtoms > 0) ------------------ | | 575| 893|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5390:13): [True: 893, False: 145k] | Branch (5390:37): [True: 893, False: 0] ------------------ 5391| 893| { 5392| 893| int bMobileHalt = ALT_TAUT( bMobileH ); /* = TAUT_YES */ ------------------ | | 577| 893|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 893|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 893] | | ------------------ ------------------ 5393| 893| pStruct->pOneINChI[1] = cur_INChI[bMobileHalt]; 5394| 893| pStruct->pOneINChI_Aux[1] = cur_INChI_Aux[bMobileHalt]; 5395| 893| cur_INChI[bMobileHalt] = NULL; 5396| 893| cur_INChI_Aux[bMobileHalt] = NULL; 5397| 893| pStruct->pOne_norm_data[1] = (INP_ATOM_DATA *) inchi_malloc( sizeof( pStruct->pOne_norm_data[0][0] ) ); ------------------ | | 1143| 893|#define inchi_malloc malloc ------------------ 5398| 893| if (pStruct->pOne_norm_data[1]) ------------------ | Branch (5398:17): [True: 893, False: 0] ------------------ 5399| 893| { 5400| 893| memcpy(pStruct->pOne_norm_data[1], inp_norm_data[bMobileHalt], sizeof(pStruct->pOne_norm_data[0][0])); 5401| 893| memset( inp_norm_data[bMobileHalt], 0, sizeof( *inp_norm_data[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5402| 893| } 5403| 0| else 5404| 0| { 5405| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 5406| 0| } 5407| 893| } 5408| 145k| } 5409| 52| else 5410| 52| { 5411| |#if ( bRELEASE_VERSION != 1 ) 5412| |#ifndef TARGET_API_LIB 5413| | fprintf( stdout, "ERROR: Create_INChI returned %d\n", ret ); 5414| |#endif 5415| |#endif 5416| 52| } 5417| | 5418| 146k|exit_function: 5419| | /* deallocate unused */ 5420| 438k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 438k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (5420:17): [True: 292k, False: 146k] ------------------ 5421| 292k| { 5422| 292k| Free_INChI( &cur_INChI[k] ); 5423| 292k| Free_INChI_Aux( &cur_INChI_Aux[k] ); 5424| 292k| FreeInpAtomData( inp_norm_data[k] ); 5425| 292k| } 5426| 146k| sd->ulStructTime = ulStructTime; 5427| | 5428| 146k| return ret; 5429| 146k|} ConnectDisconnectedH: 5447| 71.7k|{ 5448| 71.7k| int i, j, k, n, m, num_H; 5449| 71.7k| int tot_atoms = num_atoms + num_deleted_H; 5450| | 5451| 71.7k| for (i = num_atoms; i < tot_atoms; i = j) ------------------ | Branch (5451:25): [True: 61, False: 71.7k] ------------------ 5452| 61| { 5453| 61| k = at[i].neighbor[0]; /* a[k] is the atom connected to the explicit hydrogen at[i] */ 5454| | 5455| 137| for (j = i; j < tot_atoms && at[j].neighbor[0] == k; j++) ------------------ | Branch (5455:21): [True: 77, False: 60] | Branch (5455:38): [True: 76, False: 1] ------------------ 5456| 76| { 5457| 76| ; 5458| 76| } 5459| | 5460| 61| num_H = j - i; /* number of explicit H for at[k] */ 5461| 61| if (num_H > at[k].num_H) ------------------ | Branch (5461:13): [True: 0, False: 61] ------------------ 5462| 0| { 5463| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5464| 0| } 5465| 61| if (num_H + at[k].valence > MAXVAL) ------------------ | | 60| 61|#define MAXVAL 50 /* maximum valence */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (5465:13): [True: 0, False: 61] ------------------ 5466| 0| { 5467| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5468| 0| } 5469| | 5470| | /* insert links to explicit H before all other links in the connection list */ 5471| 61| n = at[k].valence; 5472| 61| memmove(at[k].neighbor + num_H, at[k].neighbor, sizeof(at[k].neighbor[0]) * n); 5473| 61| memmove(at[k].bond_stereo + num_H, at[k].bond_stereo, sizeof(at[k].bond_stereo[0]) * n); 5474| 61| memmove(at[k].bond_type + num_H, at[k].bond_type, sizeof(at[k].bond_type[0]) * n); 5475| 137| for (n = 0; n < num_H; n++) ------------------ | Branch (5475:21): [True: 76, False: 61] ------------------ 5476| 76| { 5477| 76| at[k].neighbor[n] = i + n; 5478| 76| at[k].bond_stereo[n] = 0; 5479| 76| at[k].bond_type[n] = BOND_TYPE_SINGLE; ------------------ | | 32| 76|#define BOND_TYPE_SINGLE 1 ------------------ 5480| 76| } 5481| | 5482| 119| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[k].sb_parity[m]; m++) ------------------ | | 873| 238|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (5482:21): [True: 119, False: 0] | Branch (5482:49): [True: 58, False: 61] ------------------ 5483| 58| { 5484| 58| at[k].sb_ord[m] += num_H; 5485| 58| if (at[k].sn_ord[m] < 0) ------------------ | Branch (5485:17): [True: 58, False: 0] ------------------ 5486| 58| { 5487| 58| for (n = i; n < j; n++) ------------------ | Branch (5487:29): [True: 58, False: 0] ------------------ 5488| 58| { 5489| 58| if (at[n].orig_at_number == at[k].sn_orig_at_num[m]) ------------------ | Branch (5489:25): [True: 58, False: 0] ------------------ 5490| 58| { 5491| 58| at[k].sn_ord[m] = n - i; 5492| 58| break; 5493| 58| } 5494| 58| } 5495| | 5496| 58| if (n == j) ------------------ | Branch (5496:21): [True: 0, False: 58] ------------------ 5497| 0| { 5498| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5499| 0| } 5500| 58| } 5501| 0| else 5502| 0| { 5503| 0| at[k].sn_ord[m] += num_H; 5504| 0| } 5505| 58| } 5506| | 5507| 61| at[k].valence += num_H; 5508| 61| at[k].chem_bonds_valence += num_H; 5509| 61| at[k].num_H -= num_H; /* cannot be negative */ 5510| | 5511| | /*memset( at[k].num_iso_H, 0, sizeof(at[0].num_iso_H) );*/ /* attached H must carry all isotopic shifts */ 5512| 137| for (n = i; n < j; n++) ------------------ | Branch (5512:21): [True: 76, False: 61] ------------------ 5513| 76| { 5514| 76| at[n].chem_bonds_valence = BOND_TYPE_SINGLE; ------------------ | | 32| 76|#define BOND_TYPE_SINGLE 1 ------------------ 5515| 76| } 5516| | 5517| | /* isotopic H */ 5518| 76| for (m = j - 1; i <= m && at[m].iso_atw_diff > 0; m--) ------------------ | Branch (5518:25): [True: 70, False: 6] | Branch (5518:35): [True: 15, False: 55] ------------------ 5519| 15| { 5520| 15| if (at[m].iso_atw_diff > NUM_H_ISOTOPES) ------------------ | | 25| 15|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5520:17): [True: 0, False: 15] ------------------ 5521| 0| { 5522| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5523| 0| } 5524| 15| if (0 >= at[k].num_iso_H[(int) at[m].iso_atw_diff - 1] --) ------------------ | Branch (5524:17): [True: 0, False: 15] ------------------ 5525| 0| { 5526| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5527| 0| } 5528| 15| } 5529| 61| } 5530| | 5531| | /* subtract isotopic H */ 5532| 236k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5532:17): [True: 165k, False: 71.3k] ------------------ 5533| 165k| { 5534| 660k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 25| 660k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5534:21): [True: 495k, False: 165k] ------------------ 5535| 495k| { 5536| 495k| at[i].num_H -= at[i].num_iso_H[m]; 5537| 495k| } 5538| 165k| if (0 > at[i].num_H) ------------------ | Branch (5538:13): [True: 386, False: 164k] ------------------ 5539| 386| { 5540| 386| return RI_ERR_PROGR; ------------------ | | 17| 386|#define RI_ERR_PROGR (-3) ------------------ 5541| 386| } 5542| 165k| } 5543| | 5544| 71.3k| return tot_atoms; 5545| 71.7k|} DisconnectedConnectedH: 5561| 1.21k|{ 5562| 1.21k| int i, j, k, n, m, num_H, num_iso_H; 5563| 1.21k| int tot_atoms = num_atoms + num_deleted_H; 5564| 1.21k| S_CHAR ctmp = '0'; 5565| | 5566| | /* add implicit isotopic H to total implicit H */ 5567| 11.2k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5567:17): [True: 10.0k, False: 1.21k] ------------------ 5568| 10.0k| { 5569| 40.2k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 25| 40.2k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5569:21): [True: 30.1k, False: 10.0k] ------------------ 5570| 30.1k| { 5571| 30.1k| at[i].num_H += at[i].num_iso_H[m]; 5572| 30.1k| } 5573| 10.0k| } 5574| | 5575| 1.22k| for (i = num_atoms; i < tot_atoms; i = j) ------------------ | Branch (5575:25): [True: 6, False: 1.21k] ------------------ 5576| 6| { 5577| 6| k = at[i].neighbor[0]; /* a[k] is the atom connected to the explicit hydrogen at[i] */ 5578| | 5579| 14| for (j = i; j < tot_atoms && at[j].neighbor[0] == k; j++) ------------------ | Branch (5579:21): [True: 8, False: 6] | Branch (5579:38): [True: 8, False: 0] ------------------ 5580| 8| { 5581| 8| at[j].chem_bonds_valence = 0; 5582| 8| } 5583| 6| num_H = j - i; /* number of explicit H for at[k] */ 5584| | 5585| | /* verify correct number of explicit H */ 5586| 14| for (n = 0; n < at[k].valence && at[k].neighbor[n] >= num_atoms; n++) ------------------ | Branch (5586:21): [True: 14, False: 0] | Branch (5586:42): [True: 8, False: 6] ------------------ 5587| 8| { 5588| 8| ; 5589| 8| } 5590| 6| if (n != num_H) ------------------ | Branch (5590:13): [True: 0, False: 6] ------------------ 5591| 0| { 5592| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5593| 0| } 5594| | 5595| | /* remove bonds to explicit H located in front of all other bonds in the connection list */ 5596| 6| at[k].valence -= num_H; /* djb-rwth: use of cast operators avoided */ 5597| 6| n = at[k].valence; /* new number of bonds */ 5598| 6| at[k].chem_bonds_valence -= num_H; /* new no-H valence */ 5599| 6| if (n) ------------------ | Branch (5599:13): [True: 6, False: 0] ------------------ 5600| 6| { 5601| 6| memmove(at[k].neighbor, at[k].neighbor + num_H, sizeof(at[k].neighbor[0]) * n); 5602| 6| memmove(at[k].bond_stereo, at[k].bond_stereo + num_H, sizeof(at[k].bond_stereo[0]) * n); 5603| 6| memmove(at[k].bond_type, at[k].bond_type + num_H, sizeof(at[k].bond_type[0]) * n); 5604| 6| } 5605| | /* clear the 'tails' */ 5606| 6| memset( at[k].neighbor + n, 0, sizeof( at[k].neighbor[0] ) * num_H ); /* djb-rwth: memset_s C11/Annex K variant? */ 5607| 6| memset( at[k].bond_stereo + n, 0, sizeof( at[k].bond_stereo[0] ) * num_H ); /* djb-rwth: memset_s C11/Annex K variant? */ 5608| 6| memset( at[k].bond_type + n, 0, sizeof( at[k].bond_type[0] ) * num_H ); /* djb-rwth: memset_s C11/Annex K variant? */ 5609| | 5610| 11| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[k].sb_parity[m]; m++) ------------------ | | 873| 22|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (5610:21): [True: 11, False: 0] | Branch (5610:49): [True: 5, False: 6] ------------------ 5611| 5| { 5612| 5| at[k].sb_ord[m] -= num_H; 5613| 5| if (0 <= at[k].sn_ord[m] && at[k].sn_ord[m] < num_H) ------------------ | Branch (5613:17): [True: 5, False: 0] | Branch (5613:41): [True: 5, False: 0] ------------------ 5614| 5| { 5615| 5| at[k].sn_ord[m] = -1; /* disconnected explicit H */ 5616| 5| } 5617| 5| } 5618| | /* add explicit isotopic H (already included in num_H) */ 5619| 10| for (num_iso_H = 0, m = j - 1; i <= m && at[m].iso_atw_diff > 0; m--) ------------------ | Branch (5619:40): [True: 8, False: 2] | Branch (5619:50): [True: 4, False: 4] ------------------ 5620| 4| { 5621| 4| if (at[m].iso_atw_diff > NUM_H_ISOTOPES) ------------------ | | 25| 4|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5621:17): [True: 0, False: 4] ------------------ 5622| 0| { 5623| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5624| 0| } 5625| 4| at[k].num_iso_H[(int) at[m].iso_atw_diff - 1] ++; 5626| 4| } 5627| 6| at[k].num_H += num_H; /* add all explicit H including isotopic */ 5628| 6| } 5629| | 5630| 1.21k| return tot_atoms; 5631| 1.21k|} MakeInChIOutOfStrFromINChI2: 5643| 70.8k|{ 5644| 70.8k| char szTitle[MAX_SDF_HEADER + MAX_SDF_VALUE + 256]; 5645| | 5646| 70.8k| int len, ret; 5647| | /* 5648| | PINChI2 *pINChI[INCHI_NUM]; 5649| | PINChI_Aux2 *pINChI_Aux[INCHI_NUM]; 5650| | */ 5651| 70.8k| INPUT_PARMS local_ip; 5652| 70.8k| STRUCT_DATA local_sd; 5653| 70.8k| INPUT_PARMS *ip = &local_ip; 5654| 70.8k| STRUCT_DATA *sd = &local_sd; 5655| | 5656| 70.8k| ORIG_ATOM_DATA OrigAtData; /* 0=> disconnected, 1=> original */ 5657| 70.8k| ORIG_ATOM_DATA *orig_inp_data = &OrigAtData; 5658| 70.8k| ORIG_ATOM_DATA PrepAtData[2]; /* 0=> disconnected, 1=> original */ 5659| 70.8k| ORIG_ATOM_DATA *prep_inp_data = PrepAtData; 5660| | 5661| 70.8k| INCHI_IOS_STRING temp_string_container; 5662| 70.8k| INCHI_IOS_STRING *strbuf = &temp_string_container; 5663| 70.8k| memset( strbuf, 0, sizeof( *strbuf ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5664| | 5665| 70.8k| if (0 >= inchi_strbuf_init(strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT)) ------------------ | | 65| 70.8k|#define INCHI_STRBUF_INITIAL_SIZE 262144 ------------------ if (0 >= inchi_strbuf_init(strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT)) ------------------ | | 66| 70.8k|#define INCHI_STRBUF_SIZE_INCREMENT 262144 ------------------ | Branch (5665:9): [True: 0, False: 70.8k] ------------------ 5666| 0| { 5667| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 5668| 0| goto early_exit_error; /* djb-rwth: avoiding garbage value */ 5669| 0| } 5670| | 5671| | /* djb-rwth: fixing oss-fuzz issue #70552 */ 5672| 70.8k| if (!ip_inp || !sd_inp || !pStruct) ------------------ | Branch (5672:9): [True: 0, False: 70.8k] | Branch (5672:20): [True: 0, False: 70.8k] | Branch (5672:31): [True: 0, False: 70.8k] ------------------ 5673| 0| { 5674| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 5675| 0| goto early_exit_error; /* djb-rwth: avoiding garbage value */ 5676| 0| } 5677| | 5678| 70.8k| *ip = *ip_inp; 5679| 70.8k| ip->bDisplay = 0; 5680| 70.8k| ip->bDisplayCompositeResults = 0; 5681| 70.8k| ip->bDisplayEachComponentINChI = 0; 5682| 70.8k| ip->bDisplayIfRestoreWarnings = 0; 5683| 70.8k| ip->bINChIOutputOptions = INCHI_OUT_NO_AUX_INFO; ------------------ | | 129| 70.8k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 5684| | 5685| | /* 5686| | if ( pStruct->bMobileH ) { 5687| | ip->nMode &= ~REQ_MODE_BASIC; 5688| | ip->nMode |= REQ_MODE_TAUT; 5689| | } else { 5690| | ip->nMode |= (REQ_MODE_TAUT | REQ_MODE_BASIC); 5691| | } 5692| | */ 5693| | 5694| 70.8k| memset( sd, 0, sizeof( *sd ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5695| 70.8k| sd->fPtrStart = -1; 5696| 70.8k| sd->fPtrEnd = -1; 5697| | 5698| | /* 5699| | if ( ip->nMode & REQ_MODE_STEREO ) { 5700| | if ( ip->nMode & (REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO) ) { 5701| | sd->bChiralFlag |= FLAG_INP_AT_NONCHIRAL; 5702| | } else { 5703| | sd->bChiralFlag |= FLAG_INP_AT_CHIRAL; 5704| | } 5705| | } 5706| | */ 5707| | 5708| 70.8k| memset( orig_inp_data, 0, sizeof( *orig_inp_data ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5709| 70.8k| memset( prep_inp_data, 0, 2 * sizeof( *prep_inp_data ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5710| 70.8k| memset( pStruct->RevInChI.pINChI, 0, sizeof( pStruct->RevInChI.pINChI ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5711| 70.8k| memset( pStruct->RevInChI.pINChI_Aux, 0, sizeof( pStruct->RevInChI.pINChI_Aux ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5712| 70.8k| memset( szTitle, 0, sizeof( szTitle ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5713| | 5714| 70.8k| len = sizeof( orig_inp_data->at[0] )*( (long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H ); /* djb-rwth: cast operators added */ 5715| | 5716| 70.8k| orig_inp_data->at = (inp_ATOM *) inchi_malloc( len ); ------------------ | | 1143| 70.8k|#define inchi_malloc malloc ------------------ 5717| | 5718| 70.8k| if (orig_inp_data->at) ------------------ | Branch (5718:9): [True: 70.8k, False: 0] ------------------ 5719| 70.8k| { 5720| | /*memcpy( orig_inp_data->at, pStruct->at2, len );*/ 5721| | /*ret = ConnectDisconnectedH( orig_inp_data->at, pStruct->num_atoms, pStruct->num_deleted_H );*/ 5722| | 5723| 70.8k| CopySt2At( pStruct->at2, pStruct->st, pStruct->num_atoms ); 5724| | 5725| 70.8k| ret = ConnectDisconnectedH( pStruct->at2, pStruct->num_atoms, pStruct->num_deleted_H ); 5726| 70.8k| if (ret < 0) ------------------ | Branch (5726:13): [True: 386, False: 70.4k] ------------------ 5727| 386| { 5728| 386| goto exit_error; 5729| 386| } 5730| | 5731| 70.4k| orig_inp_data->num_inp_atoms = ret; 5732| | /* connections changed => reconcile parities even if they were reconciled before */ 5733| | /* remove t-group markings and increment zero-order bonds, 5734| | otherwise MakeInChIOutOfStrFromINChI2() woild fail */ 5735| | /* 5736| | IncrZeroBondsAndClearEndpts(pStruct->at2, pStruct->num_atoms, iComponent+1); 5737| | */ 5738| | 5739| 70.4k| IncrZeroBonds( pStruct->at2, pStruct->num_atoms, iComponent + 1 ); 5740| | 5741| | /* CopySt2At() moved to the position before ConnectDisconnectedH() because 5742| | in case stereo exists only in Mobile-H layer and the processd here 5743| | component is restored in Fixed-H layer the parities needed by 5744| | ConnectDisconnectedH() must be there before calling 5745| | ConnectDisconnectedH() 5746| | */ 5747| | /*CopySt2At( pStruct->at2, pStruct->st, pStruct->num_atoms );*/ 5748| | 5749| 70.4k| ret = ReconcileAllCmlBondParities( pStruct->at2, orig_inp_data->num_inp_atoms, 0 ); 5750| 70.4k| if (ret < 0) ------------------ | Branch (5750:13): [True: 0, False: 70.4k] ------------------ 5751| 0| { 5752| 0| goto exit_error; 5753| 0| } 5754| | 5755| |#if USE_BCF 5756| | memcpy_s( orig_inp_data->at, (long long)len, pStruct->at2, len ); /* djb-rwth: function replaced with its safe C11 variant */ 5757| |#else 5758| 70.4k| memcpy(orig_inp_data->at, pStruct->at2, len); 5759| 70.4k|#endif 5760| | 5761| 70.4k| ClearEndpts( orig_inp_data->at, pStruct->num_atoms ); 5762| | 5763| 70.4k| if (FixUnkn0DStereoBonds( orig_inp_data->at, pStruct->num_atoms )) ------------------ | Branch (5763:13): [True: 35, False: 70.4k] ------------------ 5764| 35| { 5765| 35| ret = ReconcileAllCmlBondParities( pStruct->at2, orig_inp_data->num_inp_atoms, 0 ); 5766| 35| if (ret < 0) ------------------ | Branch (5766:17): [True: 0, False: 35] ------------------ 5767| 0| { 5768| 0| goto exit_error; 5769| 0| } 5770| 35| } 5771| | /* keep endpoint[] markings in at2[] for subsequent add/remove protons */ 5772| 70.4k| } 5773| 0| else 5774| 0| { 5775| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 5776| 0| goto exit_error; 5777| 0| } 5778| | 5779| 70.4k| memset( sd->num_components, 0, sizeof( sd->num_components ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5780| 70.4k| memset( sd->num_taut, 0, sizeof( sd->num_taut ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5781| 70.4k| memset( sd->num_non_taut, 0, sizeof( sd->num_non_taut ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5782| 70.4k| memset( sd->bTautFlagsDone, 0, sizeof( sd->bTautFlagsDone ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5783| 70.4k| memset( sd->bTautFlags, 0, sizeof( sd->bTautFlags ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5784| | 5785| | 5786| 70.4k| ret = ProcessOneStructure( ic, pCG, sd, ip, szTitle, 5787| 70.4k| pStruct->RevInChI.pINChI, 5788| 70.4k| pStruct->RevInChI.pINChI_Aux, 5789| 70.4k| NULL /*inp_file*/, 5790| 70.4k| NULL /*log_file*/, 5791| 70.4k| NULL /*out_file*/, 5792| 70.4k| NULL /*prb_file*/, 5793| 70.4k| orig_inp_data, prep_inp_data, 5794| 70.4k| num_inp, strbuf, 5795| 70.4k| 0 /* save_opt_bits */ ); 5796| | 5797| 70.4k| memcpy(pStruct->RevInChI.num_components, sd->num_components, sizeof(pStruct->RevInChI.num_components)); 5798| 70.4k| memcpy(sd_inp->pStrErrStruct, sd->pStrErrStruct, sizeof(sd_inp->pStrErrStruct)); 5799| 70.4k| pStruct->RevInChI.nRetVal = ret; 5800| | 5801| | /* translate returned value */ 5802| 70.4k| if (ret == _IS_ERROR || ret == _IS_FATAL || ret == _IS_UNKNOWN) ------------------ | | 12| 140k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ if (ret == _IS_ERROR || ret == _IS_FATAL || ret == _IS_UNKNOWN) ------------------ | | 13| 140k|#define _IS_FATAL 3 ------------------ if (ret == _IS_ERROR || ret == _IS_FATAL || ret == _IS_UNKNOWN) ------------------ | | 14| 70.4k|#define _IS_UNKNOWN 4 /* unknown error: used in INChI DLL only */ ------------------ | Branch (5802:9): [True: 2, False: 70.4k] | Branch (5802:29): [True: 2, False: 70.4k] | Branch (5802:49): [True: 0, False: 70.4k] ------------------ 5803| 4| { 5804| 4| ret = RI_ERR_PROGR; ------------------ | | 17| 4|#define RI_ERR_PROGR (-3) ------------------ 5805| 4| } 5806| 70.4k| else if (ret == _IS_OKAY) ------------------ | | 10| 70.4k|#define _IS_OKAY 0 ------------------ | Branch (5806:14): [True: 60.9k, False: 9.45k] ------------------ 5807| 60.9k| { 5808| 60.9k| ret = 0; 5809| 60.9k| } 5810| 9.45k| else if (ret == _IS_WARNING) ------------------ | | 11| 9.45k|#define _IS_WARNING 1 ------------------ | Branch (5810:14): [True: 9.45k, False: 0] ------------------ 5811| 9.45k| { 5812| 9.45k| ret = 1; 5813| 9.45k| } 5814| 0| else 5815| 0| { 5816| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5817| 0| } 5818| | 5819| | /* save total charge from Mobile-H layer */ 5820| | 5821| 70.4k| pStruct->nChargeRevrs = 0; 5822| 70.4k| if (ret >= 0) ------------------ | Branch (5822:9): [True: 70.4k, False: 4] ------------------ 5823| 70.4k| { 5824| 70.4k| if (bRevInchiComponentExists( pStruct, INCHI_REC, TAUT_YES, 0 )) ------------------ | | 571| 70.4k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bRevInchiComponentExists( pStruct, INCHI_REC, TAUT_YES, 0 )) ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5824:13): [True: 0, False: 70.4k] ------------------ 5825| 0| { 5826| 0| pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_REC][0][TAUT_YES]->nTotalCharge; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_REC][0][TAUT_YES]->nTotalCharge; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5827| 0| } 5828| 70.4k| else if (bRevInchiComponentExists( pStruct, INCHI_BAS, TAUT_YES, 0 )) ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ else if (bRevInchiComponentExists( pStruct, INCHI_BAS, TAUT_YES, 0 )) ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5828:18): [True: 70.2k, False: 156] ------------------ 5829| 70.2k| { 5830| 70.2k| pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_BAS][0][TAUT_YES]->nTotalCharge; ------------------ | | 570| 70.2k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_BAS][0][TAUT_YES]->nTotalCharge; ------------------ | | 575| 70.2k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5831| 70.2k| } 5832| 70.4k| } 5833| | 5834| | /* free structure data */ 5835| 70.4k| FreeOrigAtData( orig_inp_data ); 5836| 70.4k| FreeOrigAtData( prep_inp_data ); 5837| 70.4k| FreeOrigAtData( prep_inp_data + 1 ); 5838| | 5839| 70.8k|exit_error: 5840| 70.8k|#if ( FIX_GAF_2019_2==1 ) 5841| 70.8k| if (orig_inp_data->at) ------------------ | Branch (5841:9): [True: 386, False: 70.4k] ------------------ 5842| 386| { 5843| 386| FreeInpAtom(&orig_inp_data->at); 5844| 386| } 5845| 70.8k|#endif 5846| 70.8k|early_exit_error: 5847| 70.8k| inchi_strbuf_close( strbuf ); 5848| | 5849| 70.8k| return ret; 5850| 70.8k|} CopyAt2St: 23| 100|{ 24| 100| int i; 25| 66.2k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (25:17): [True: 66.1k, False: 100] ------------------ 26| 66.1k| { 27| 66.1k| if (at[i].p_parity) ------------------ | Branch (27:13): [True: 10, False: 66.1k] ------------------ 28| 10| { 29| 10| memcpy(st[i].p_orig_at_num, at[i].p_orig_at_num, sizeof(st[0].p_orig_at_num)); 30| 10| st[i].p_parity = at[i].p_parity; 31| 10| } 32| 66.1k| if (at[i].sb_parity[0]) ------------------ | Branch (32:13): [True: 53, False: 66.0k] ------------------ 33| 53| { 34| 53| memcpy(st[i].sb_ord, at[i].sb_ord, sizeof(st[0].sb_ord)); 35| 53| memcpy(st[i].sb_parity, at[i].sb_parity, sizeof(st[0].sb_parity)); 36| 53| memcpy(st[i].sn_ord, at[i].sn_ord, sizeof(st[0].sn_ord)); 37| 53| memcpy(st[i].sn_orig_at_num, at[i].sn_orig_at_num, sizeof(st[0].sn_orig_at_num)); 38| 53| } 39| 66.1k| } 40| 100|} CopySt2At: 45| 216k|{ 46| 216k| int i; 47| 216k| if (!st) ------------------ | Branch (47:9): [True: 216k, False: 152] ------------------ 48| 216k| { 49| 216k| return; 50| 216k| } 51| | 52| 889| for (i = 0; i < num_atoms; i++) ------------------ | Branch (52:17): [True: 737, False: 152] ------------------ 53| 737| { 54| 737| if (st[i].p_parity) ------------------ | Branch (54:13): [True: 44, False: 693] ------------------ 55| 44| { 56| 44| memcpy(at[i].p_orig_at_num, st[i].p_orig_at_num, sizeof(at[0].p_orig_at_num)); 57| 44| at[i].p_parity = st[i].p_parity; 58| 44| } 59| 737| if (st[i].sb_parity[0]) ------------------ | Branch (59:13): [True: 335, False: 402] ------------------ 60| 335| { 61| 335| memcpy(at[i].sb_ord, st[i].sb_ord, sizeof(st[0].sb_ord)); 62| 335| memcpy(at[i].sb_parity, st[i].sb_parity, sizeof(at[0].sb_parity)); 63| 335| memcpy(at[i].sn_ord, st[i].sn_ord, sizeof(at[0].sn_ord)); 64| 335| memcpy(at[i].sn_orig_at_num, st[i].sn_orig_at_num, sizeof(at[0].sn_orig_at_num)); 65| 335| } 66| 737| } 67| 152|} RestoreAtomConnectionsSetStereo: 76| 145k|{ 77| 145k| inp_ATOM_STEREO *st = NULL; 78| 145k| int num_atoms, i, jv, jn, n_vertex, n_neigh, num_H, parity, num_atoms_limit; 79| 145k| int nNumDeletedH = 0, iDeletedH = 0, idelH1, idelH2, ret = 0, len; 80| 145k| int num_stereo_bonds2, num_stereo_centers2; /* djb-rwth: removing redundant variables */ 81| 145k| INChI_Stereo *pStereo = NULL, *pStereo2 = NULL; 82| 145k| AT_NUMB nCumulene[MAX_CUMULENE_LEN + 2]; 83| 145k| inp_ATOM* at = NULL; /* copied from below 2024-09-01 DT */ 84| | 85| 145k| num_atoms = pInChI->nNumberOfAtoms; 86| 145k| if (num_atoms <= 0) ------------------ | Branch (86:9): [True: 0, False: 145k] ------------------ 87| 0| { 88| 0| return 0; 89| 0| } 90| | 91| | INCHI_HEAPCHK 92| | 93| | /* atoms */ 94| 145k| at = (inp_ATOM*)inchi_calloc(num_atoms, sizeof(pStruct->at[0])); ------------------ | | 1146| 145k|#define inchi_calloc calloc ------------------ 95| 145k| num_atoms_limit = num_atoms; 96| 145k| if (!at) ------------------ | Branch (96:9): [True: 0, False: 145k] ------------------ 97| 0| { 98| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 99| 0| goto exit_function; 100| 0| } 101| 145k| pStruct->at = at; 102| 145k| pStruct->num_atoms = num_atoms; 103| | 104| | /* charge */ 105| 145k| pStruct->charge = pInChI->nTotalCharge; 106| | 107| | /* elements, terminal atoms H */ 108| 1.69M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (108:17): [True: 1.55M, False: 145k] ------------------ 109| 1.55M| { 110| 1.55M| at[i].el_number = pInChI->nAtom[i]; 111| 1.55M| if (-1 == get_element_chemical_symbol( UCINT pInChI->nAtom[i], at[i].elname )) ------------------ | | 88| 1.55M|#define UCINT (int)(unsigned char) ------------------ | Branch (111:13): [True: 0, False: 1.55M] ------------------ 112| 0| { 113| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 114| 0| goto exit_function; 115| 0| } 116| 1.55M| at[i].orig_at_number = iAtNoOffset + i + 1; 117| 1.55M| at[i].orig_compt_at_numb = i + 1; 118| 1.55M| at[i].component = iComponent + 1; 119| 1.55M| num_H = pInChI->nNum_H[i]; 120| | /* --- pInChI->nNum_H_fixed[i] was added to pInChI->nNum_H[i] --- 121| | if ( pInChI->nNum_H_fixed ) { 122| | num_H += pInChI->nNum_H_fixed[i]; 123| | } 124| | */ 125| |#if 0 126| | ( FIX_GAF_ISSUES == 1 ) 127| | if (num_H < 0) 128| | { 129| | ret = RI_ERR_PROGR; 130| | goto exit_function; 131| | } 132| |#endif 133| 1.55M| at[i].num_H = num_H; 134| 1.55M| } 135| | 136| | INCHI_HEAPCHK 137| | 138| | /* connections */ 139| 467k| for (i = 1, n_vertex = pInChI->nConnTable[0] - 1; i < pInChI->lenConnTable; i++) ------------------ | Branch (139:55): [True: 321k, False: 145k] ------------------ 140| 321k| { 141| 321k| if (( n_neigh = pInChI->nConnTable[i] - 1 ) < n_vertex) ------------------ | Branch (141:13): [True: 170k, False: 151k] ------------------ 142| 170k| { 143| | /* vertex - neighbor connection */ 144| 170k| jv = at[n_vertex].valence++; 145| 170k| at[n_vertex].neighbor[jv] = n_neigh; 146| 170k| at[n_vertex].bond_type[jv] = BOND_TYPE_SINGLE; ------------------ | | 32| 170k|#define BOND_TYPE_SINGLE 1 ------------------ 147| 170k| at[n_vertex].chem_bonds_valence += at[n_vertex].bond_type[jv]; 148| | /* neighbor - vertex connection */ 149| 170k| jn = at[n_neigh].valence++; 150| 170k| at[n_neigh].neighbor[jn] = n_vertex; 151| 170k| at[n_neigh].bond_type[jn] = BOND_TYPE_SINGLE; ------------------ | | 32| 170k|#define BOND_TYPE_SINGLE 1 ------------------ 152| 170k| at[n_neigh].chem_bonds_valence += at[n_neigh].bond_type[jn]; 153| 170k| } 154| 151k| else if (( n_vertex = n_neigh ) >= num_atoms) ------------------ | Branch (154:18): [True: 0, False: 151k] ------------------ 155| 0| { 156| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 157| 0| goto exit_function; 158| 0| } 159| 321k| } 160| | 161| | INCHI_HEAPCHK 162| | 163| | /* isotopic atoms */ 164| 145k| if (pInChI->IsotopicAtom && pInChI->nNumberOfIsotopicAtoms) ------------------ | Branch (164:9): [True: 902, False: 144k] | Branch (164:33): [True: 698, False: 204] ------------------ 165| 698| { 166| 3.20k| for (i = 0; i < pInChI->nNumberOfIsotopicAtoms; i++) ------------------ | Branch (166:21): [True: 2.50k, False: 698] ------------------ 167| 2.50k| { 168| 2.50k| n_vertex = pInChI->IsotopicAtom[i].nAtomNumber - 1; 169| | /* djb-rwth: fixing oss-fuzz issues #68742, #30956 */ 170| 2.50k| if (n_vertex < num_atoms) ------------------ | Branch (170:17): [True: 2.46k, False: 39] ------------------ 171| 2.46k| { 172| 2.46k| at[n_vertex].iso_atw_diff = (char)pInChI->IsotopicAtom[i].nIsoDifference; 173| 2.46k| at[n_vertex].num_iso_H[0] = (char)pInChI->IsotopicAtom[i].nNum_H; 174| 2.46k| at[n_vertex].num_iso_H[1] = (char)pInChI->IsotopicAtom[i].nNum_D; 175| 2.46k| at[n_vertex].num_iso_H[2] = (char)pInChI->IsotopicAtom[i].nNum_T; 176| 2.46k| } 177| 2.50k| } 178| 698| pStruct->bIsotopic |= 1; 179| 698| } 180| | 181| | INCHI_HEAPCHK 182| | 183| | /* tautomeric groups */ 184| 145k| if ((ret = GetTgroupInfoFromInChI( &pStruct->ti, at, NULL, pInChI ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (184:9): [True: 2, False: 145k] ------------------ 185| 2| { 186| 2| goto exit_function; 187| 2| } 188| | 189| | /* coordinates: data from unused members: pInChI->IsotopicTGroup and InChI->nNumberOfIsotopicTGroups */ 190| 145k| if (pInChI->IsotopicTGroup && !pInChI->nNumberOfIsotopicTGroups) ------------------ | Branch (190:9): [True: 0, False: 145k] | Branch (190:35): [True: 0, False: 0] ------------------ 191| 0| { 192| 0| pStruct->pXYZ = (XYZ_COORD *) pInChI->IsotopicTGroup; 193| 0| pInChI->IsotopicTGroup = NULL; 194| 0| } 195| | 196| | /* stereo */ 197| 145k| if (pInChI->StereoIsotopic && ------------------ | Branch (197:9): [True: 580, False: 144k] ------------------ 198| 580| ( pInChI->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (198:9): [True: 232, False: 348] ------------------ 199| 580| pInChI->StereoIsotopic->nNumberOfStereoCenters )) 200| 232| { 201| 232| pStereo = pInChI->StereoIsotopic; 202| 232| } 203| 145k| else if (pInChI->Stereo && ------------------ | Branch (203:14): [True: 12.0k, False: 133k] ------------------ 204| 12.0k| ( pInChI->Stereo->nNumberOfStereoBonds + ------------------ | Branch (204:9): [True: 726, False: 11.3k] ------------------ 205| 12.0k| pInChI->Stereo->nNumberOfStereoCenters )) 206| 726| { 207| 726| pStereo = pInChI->Stereo; 208| 726| } 209| 144k| else 210| 144k| { 211| 144k| pStereo = NULL; 212| 144k| } 213| | 214| | /* stereo2: Mobile-H in addition to Fixed-H*/ 215| 145k| pStereo2 = NULL; 216| 145k| if (pInChIMobH && pInChIMobH->nNumberOfAtoms) ------------------ | Branch (216:9): [True: 1.28k, False: 144k] | Branch (216:23): [True: 1.28k, False: 0] ------------------ 217| 1.28k| { 218| 1.28k| if (pInChIMobH->StereoIsotopic && ------------------ | Branch (218:13): [True: 35, False: 1.25k] ------------------ 219| 35| ( pInChIMobH->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (219:13): [True: 20, False: 15] ------------------ 220| 35| pInChIMobH->StereoIsotopic->nNumberOfStereoCenters )) 221| 20| { 222| 20| pStereo2 = pInChIMobH->StereoIsotopic; 223| 20| } 224| 1.26k| else 225| 1.26k| { 226| 1.26k| if (pInChIMobH->Stereo && ------------------ | Branch (226:17): [True: 193, False: 1.07k] ------------------ 227| 193| ( pInChIMobH->Stereo->nNumberOfStereoBonds + ------------------ | Branch (227:17): [True: 143, False: 50] ------------------ 228| 193| pInChIMobH->Stereo->nNumberOfStereoCenters )) 229| 143| { 230| 143| pStereo2 = pInChIMobH->Stereo; 231| 143| } 232| 1.26k| } 233| 1.28k| } 234| | 235| | INCHI_HEAPCHK 236| | 237| 145k| num_stereo_bonds2 = 0; /* djb-rwth: removing redundant code */ 238| 145k| num_stereo_centers2 = 0; /* djb-rwth: removing redundant code */ 239| | /* -- have already been done in the initialization -- 240| | iDeletedH = 0; 241| | nNumDeletedH = 0; 242| | */ 243| 145k| if (pStereo || pStereo2) ------------------ | Branch (243:9): [True: 958, False: 144k] | Branch (243:20): [True: 72, False: 144k] ------------------ 244| 1.03k| { 245| | /* count implicit H needed for parities and reallocate at[]; set at[n_vertex].at_type=1 for these atoms */ 246| 1.03k| int len1 = pStereo ? pStereo->nNumberOfStereoCenters : 0; ------------------ | Branch (246:20): [True: 958, False: 72] ------------------ 247| 1.03k| int len2 = pStereo2 ? pStereo2->nNumberOfStereoCenters : 0; ------------------ | Branch (247:20): [True: 163, False: 867] ------------------ 248| 1.03k| int i2, diff, diff2; 249| 1.81k| for (i = i2 = 0; i < len1 || i2 < len2; ) ------------------ | Branch (249:26): [True: 724, False: 1.09k] | Branch (249:38): [True: 65, False: 1.03k] ------------------ 250| 789| { 251| 789| if (i < len1 && i2 < len2) ------------------ | Branch (251:17): [True: 724, False: 65] | Branch (251:29): [True: 66, False: 658] ------------------ 252| 66| { 253| 66| diff = (int) pStereo->nNumber[i] - (int) pStereo2->nNumber[i2]; 254| 66| if (diff <= 0) ------------------ | Branch (254:21): [True: 58, False: 8] ------------------ 255| 58| { 256| 58| n_vertex = pStereo->nNumber[i] - 1; 257| 58| i++; 258| 58| i2 += !diff; 259| 58| } 260| 8| else 261| 8| { 262| 8| n_vertex = pStereo2->nNumber[i2] - 1; 263| 8| num_stereo_centers2++; 264| 8| i2++; 265| 8| } 266| 66| } 267| 723| else if (i < len1) ------------------ | Branch (267:22): [True: 658, False: 65] ------------------ 268| 658| { 269| 658| n_vertex = pStereo->nNumber[i] - 1; 270| 658| i++; 271| 658| } 272| 65| else 273| 65| { 274| 65| n_vertex = pStereo2->nNumber[i2] - 1; 275| 65| num_stereo_centers2++; 276| 65| i2++; 277| 65| } 278| | 279| 789| jv = at[n_vertex].neighbor[0]; /* djb-rwth: avoiding unsequenced modification and access */ 280| 789| jn = at[n_vertex].neighbor[1]; /* djb-rwth: avoiding unsequenced modification and access */ 281| | /* find whether it is an allene */ 282| 789| if (at[n_vertex].valence == 2 && ------------------ | Branch (282:17): [True: 83, False: 706] ------------------ 283| 83| at[n_vertex].num_H == 0 && ------------------ | Branch (283:18): [True: 73, False: 10] ------------------ 284| 73| bCanAtomBeMiddleAllene( at[n_vertex].elname, 0, 0 ) && ------------------ | Branch (284:18): [True: 56, False: 17] ------------------ 285| 56| at[jv].valence + at[jv].num_H == 3 && ------------------ | Branch (285:18): [True: 47, False: 9] ------------------ 286| 47| bCanAtomBeTerminalAllene( at[jv].elname, 0, 0 ) && ------------------ | Branch (286:18): [True: 39, False: 8] ------------------ 287| 39| at[jn].valence + at[jn].num_H == 3 && ------------------ | Branch (287:18): [True: 31, False: 8] ------------------ 288| 31| bCanAtomBeTerminalAllene( at[jn].elname, 0, 0 )) ------------------ | Branch (288:18): [True: 26, False: 5] ------------------ 289| 26| { 290| | /* allene */ 291| 26| if (!at[jv].at_type && at[jv].num_H) ------------------ | Branch (291:21): [True: 26, False: 0] | Branch (291:40): [True: 0, False: 26] ------------------ 292| 0| { 293| 0| nNumDeletedH += at[jv].num_H; 294| 0| at[jv].at_type++; /* H should be added as an explicit H */ 295| 0| } 296| | 297| 26| if (!at[jn].at_type && at[jn].num_H) ------------------ | Branch (297:21): [True: 26, False: 0] | Branch (297:40): [True: 0, False: 26] ------------------ 298| 0| { 299| 0| nNumDeletedH += at[jn].num_H; 300| 0| at[jn].at_type++; /* H should be added as an explicit H */ 301| 0| } 302| 26| } 303| 763| else 304| 763| { 305| | /* stereogenic atom - sp3 */ 306| 763| if (!at[n_vertex].at_type && at[n_vertex].num_H) ------------------ | Branch (306:21): [True: 763, False: 0] | Branch (306:46): [True: 18, False: 745] ------------------ 307| 18| { 308| 18| nNumDeletedH += at[n_vertex].num_H; 309| 18| at[n_vertex].at_type++; /* H should be added as an explicit H */ 310| 18| } 311| 763| } 312| 789| } 313| | 314| | INCHI_HEAPCHK 315| | 316| 1.03k| len1 = pStereo ? pStereo->nNumberOfStereoBonds : 0; ------------------ | Branch (316:16): [True: 958, False: 72] ------------------ 317| 1.03k| len2 = pStereo2 ? pStereo2->nNumberOfStereoBonds : 0; ------------------ | Branch (317:16): [True: 163, False: 867] ------------------ 318| 1.75k| for (i = i2 = 0; i < len1 || i2 < len2; ) ------------------ | Branch (318:26): [True: 696, False: 1.05k] | Branch (318:38): [True: 54, False: 1.00k] ------------------ 319| 750| { 320| 750| if (i < len1 && i2 < len2) ------------------ | Branch (320:17): [True: 696, False: 54] | Branch (320:29): [True: 68, False: 628] ------------------ 321| 68| { 322| 68| diff = (int) pStereo->nBondAtom1[i] - (int) pStereo2->nBondAtom1[i2]; 323| 68| diff2 = (int) pStereo->nBondAtom2[i] - (int) pStereo2->nBondAtom2[i2]; 324| 68| if (diff < 0 || (diff == 0 && diff2 <= 0)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (324:21): [True: 10, False: 58] | Branch (324:34): [True: 38, False: 20] | Branch (324:47): [True: 32, False: 6] ------------------ 325| 42| { 326| 42| n_vertex = pStereo->nBondAtom1[i] - 1; 327| 42| n_neigh = pStereo->nBondAtom2[i] - 1; 328| 42| i++; 329| 42| i2 += !diff && !diff2; ------------------ | Branch (329:27): [True: 32, False: 10] | Branch (329:36): [True: 32, False: 0] ------------------ 330| 42| } 331| 26| else 332| 26| { 333| 26| n_vertex = pStereo2->nBondAtom1[i2] - 1; 334| 26| n_neigh = pStereo2->nBondAtom2[i2] - 1; 335| 26| num_stereo_bonds2++; 336| 26| i2++; 337| 26| } 338| 68| } 339| 682| else if (i < len1) ------------------ | Branch (339:22): [True: 628, False: 54] ------------------ 340| 628| { 341| 628| n_vertex = pStereo->nBondAtom1[i] - 1; 342| 628| n_neigh = pStereo->nBondAtom2[i] - 1; 343| 628| i++; 344| 628| } 345| 54| else 346| 54| { 347| 54| n_vertex = pStereo2->nBondAtom1[i2] - 1; 348| 54| n_neigh = pStereo2->nBondAtom2[i2] - 1; 349| 54| num_stereo_bonds2++; 350| 54| i2++; 351| 54| } 352| | 353| | /* djb-rwth: fixing oss-fuzz issue #67650 */ 354| 750| if ((n_vertex < num_atoms) && !is_in_the_list( at[n_vertex].neighbor, ------------------ | Branch (354:17): [True: 750, False: 0] | Branch (354:43): [True: 74, False: 676] ------------------ 355| 750| (AT_NUMB) n_neigh, at[n_vertex].valence )) 356| 74| { 357| | /* must be a cumulene */ 358| 74| if (!bFindCumuleneChain( at, (AT_NUMB) n_vertex, (AT_NUMB) n_neigh, ------------------ | Branch (358:21): [True: 30, False: 44] ------------------ 359| 74| nCumulene, MAX_CUMULENE_LEN + 1 )) ------------------ | | 207| 74|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ 360| 30| { 361| 30| ret = RI_ERR_SYNTAX; /* not a cumulene */ ------------------ | | 16| 30|#define RI_ERR_SYNTAX (-2) ------------------ 362| 30| goto exit_function; 363| 30| } 364| 74| } 365| | 366| 720| if ((n_vertex < num_atoms) && !at[n_vertex].at_type && at[n_vertex].num_H) ------------------ | Branch (366:17): [True: 720, False: 0] | Branch (366:43): [True: 720, False: 0] | Branch (366:68): [True: 49, False: 671] ------------------ 367| 49| { 368| 49| nNumDeletedH += at[n_vertex].num_H; 369| 49| at[n_vertex].at_type++; /* H should be added as an explicit H */ 370| 49| } 371| | 372| 720| if (!at[n_neigh].at_type && at[n_neigh].num_H) ------------------ | Branch (372:17): [True: 714, False: 6] | Branch (372:41): [True: 30, False: 684] ------------------ 373| 30| { 374| 30| nNumDeletedH += at[n_neigh].num_H; 375| 30| at[n_neigh].at_type++; /* H should be added as an explicit H */ 376| 30| } 377| 720| } 378| | 379| | INCHI_HEAPCHK 380| | 381| 1.00k| if (nNumDeletedH) ------------------ | Branch (381:13): [True: 89, False: 911] ------------------ 382| 89| { 383| | /* add explicit H */ 384| 89|#if ( FIX_GAF_2019_2==1 ) 385| 89| inp_ATOM *at2 = (inp_ATOM *)inchi_calloc(nNumDeletedH>0 ? num_atoms + nNumDeletedH : num_atoms, ------------------ | | 1146| 89|#define inchi_calloc calloc ------------------ | Branch (385:54): [True: 88, False: 1] ------------------ 386| 89| sizeof(at2[0])); 387| |#else 388| | /* add explicit H */ 389| | inp_ATOM *at2 = (inp_ATOM *)inchi_calloc(num_atoms + nNumDeletedH, sizeof(at2[0])); 390| |#endif 391| 89| if (!at2) ------------------ | Branch (391:17): [True: 0, False: 89] ------------------ 392| 0| { 393| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 394| 0| goto exit_function; 395| 0| } 396| 89| pStruct->num_deleted_H = nNumDeletedH; 397| |#if USE_BCF 398| | memcpy_s( at2, sizeof(at2[0])*num_atoms, at, num_atoms * sizeof(at2[0])); /* djb-rwth: function replaced with its safe C11 variant */ 399| |#else 400| 89| memcpy(at2, at, num_atoms * sizeof(at2[0])); 401| 89|#endif 402| 89| inchi_free( at ); ------------------ | | 1152| 89|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 89, False: 0] | | | Branch (1152:50): [Folded, False: 89] | | ------------------ ------------------ 403| 89| pStruct->at = at = at2; 404| | /* fill out deleted H atom info */ 405| 223| for (i = num_atoms; i < num_atoms + nNumDeletedH; i++) /* djb-rwth: unresolved issue -- revision required? -- buffer overrun cannot happen, loop not executed for nNumDeletedH <= 0 */ ------------------ | Branch (405:33): [True: 134, False: 89] ------------------ 406| 134| { 407| 134| strcpy( at[i].elname, "H" ); 408| 134| at[i].el_number = EL_NUMBER_H; ------------------ | | 11| 134|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 409| 134| at[i].orig_at_number = iAtNoOffset + i + 1; 410| 134| at[i].orig_compt_at_numb = i + 1; 411| 134| at[i].component = iComponent + 1; 412| 134| } 413| | 414| | /* connect deleted H */ 415| 1.48k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (415:25): [True: 1.40k, False: 84] ------------------ 416| 1.40k| { 417| 1.40k| if (at[i].at_type == 1) ------------------ | Branch (417:21): [True: 91, False: 1.31k] ------------------ 418| 91| { 419| 91| if (0 > ( ret = AddExplicitDeletedH( at, i, num_atoms, ------------------ | Branch (419:25): [True: 5, False: 86] ------------------ 420| 91| &iDeletedH, &idelH1, 421| 91| nNumDeletedH, pStereo2 != NULL ) )) 422| 5| { 423| 5| goto exit_function; 424| 5| } 425| 91| } 426| 1.40k| } 427| 89| } 428| | 429| 1.00k| INCHI_HEAPCHK 430| 1.00k| } 431| | 432| 145k| if (pStereo) ------------------ | Branch (432:9): [True: 923, False: 144k] ------------------ 433| 923| { 434| | /* mark stereo centers, they have already been connected the added explicit H, if any */ 435| 923| int bInvertedParity = ( pStereo->nCompInv2Abs == -1 ); 436| 1.43k| for (i = 0; i < pStereo->nNumberOfStereoCenters; i++) ------------------ | Branch (436:21): [True: 678, False: 759] ------------------ 437| 678| { 438| 678| n_vertex = pStereo->nNumber[i] - 1; 439| 678| parity = pStereo->t_parity[i]; 440| 678| if (bInvertedParity) ------------------ | Branch (440:17): [True: 0, False: 678] ------------------ 441| 0| { 442| 0| parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 220| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 219| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 219| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 220| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (442:26): [True: 0, False: 0] | Branch (442:73): [True: 0, False: 0] ------------------ 443| 0| } 444| | /* find whether it is allene */ 445| 678| if (at[n_vertex].valence == 2 && ------------------ | Branch (445:17): [True: 44, False: 634] ------------------ 446| 44| at[n_vertex].num_H == 0 && ------------------ | Branch (446:18): [True: 39, False: 5] ------------------ 447| 39| bCanAtomBeMiddleAllene( at[n_vertex].elname, 0, 0 ) && ------------------ | Branch (447:18): [True: 33, False: 6] ------------------ 448| | /* allene has exactly 2 double bonds */ 449| 33| ( jv = at[n_vertex].neighbor[0], at[jv].valence + at[jv].num_H == 3 ) && ------------------ | Branch (449:18): [True: 29, False: 4] ------------------ 450| 29| bCanAtomBeTerminalAllene( at[jv].elname, 0, 0 ) && ------------------ | Branch (450:18): [True: 24, False: 5] ------------------ 451| 24| ( jn = at[n_vertex].neighbor[1], at[jn].valence + at[jn].num_H == 3 ) && ------------------ | Branch (451:18): [True: 22, False: 2] ------------------ 452| 22| bCanAtomBeTerminalAllene( at[jn].elname, 0, 0 )) ------------------ | Branch (452:18): [True: 20, False: 2] ------------------ 453| 20| { 454| | /* allene: add explicit H if implicit H are present */ 455| | /* iDeletedH = current number of already added explicit H */ 456| | /* idelH1 = index in at[] of the explicit H added to atom jv */ 457| 20| if (at[jv].num_H) ------------------ | Branch (457:21): [True: 0, False: 20] ------------------ 458| 0| { 459| 0| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, ------------------ | Branch (459:25): [True: 0, False: 0] ------------------ 460| 0| &idelH1, nNumDeletedH, 461| 0| pStereo2 != NULL ) )) 462| 0| { 463| 0| goto exit_function; 464| 0| } 465| 0| } 466| 20| else 467| 20| { 468| | /* index of the stereo atom neighbor */ 469| 20| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == n_vertex]; 470| 20| } 471| | 472| 20| if (at[jn].num_H) ------------------ | Branch (472:21): [True: 0, False: 20] ------------------ 473| 0| { 474| | /* iDeletedH = current number of already added explicit H */ 475| | /* idelH2 = index of the explicit H added to atom jn */ 476| 0| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (476:25): [True: 0, False: 0] ------------------ 477| 0| { 478| 0| goto exit_function; 479| 0| } 480| 0| } 481| 20| else 482| 20| { 483| 20| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == n_vertex]; 484| 20| } 485| | /* allene: set bond types to double */ 486| | /* 487| | if ( 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jv, BOND_TYPE_DOUBLE ) ) || 488| | 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jn, BOND_TYPE_DOUBLE ) ) ) { 489| | goto exit_function; 490| | } 491| | */ 492| | /* allene: make 0D parity */ 493| 20| ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, 2 ); 494| 20| if (ret < 0) ------------------ | Branch (494:21): [True: 0, False: 20] ------------------ 495| 0| { 496| 0| goto exit_function; 497| 0| } 498| 20| } 499| 658| else 500| 658| { 501| | /* stereogenic sp3 atom */ 502| 658| if (at[n_vertex].num_H) ------------------ | Branch (502:21): [True: 6, False: 652] ------------------ 503| 6| { 504| 6| if (0 > ( ret = AddExplicitDeletedH( at, n_vertex, num_atoms, ------------------ | Branch (504:25): [True: 0, False: 6] ------------------ 505| 6| &iDeletedH, &idelH1, nNumDeletedH, 506| 6| pStereo2 != NULL ) )) 507| 0| { 508| 0| goto exit_function; 509| 0| } 510| 6| } 511| | 512| 658| ret = set_atom_0D_parity( at, st, num_atoms, nNumDeletedH, n_vertex, parity ); 513| | 514| 658| if (ret < 0) ------------------ | Branch (514:21): [True: 164, False: 494] ------------------ 515| 164| { 516| 164| goto exit_function; 517| 164| } 518| | /* djb-rwth: removing redundant code */ 519| 658| } 520| | 521| 514| if (ret < 0) ------------------ | Branch (521:17): [True: 0, False: 514] ------------------ 522| 0| { 523| 0| goto exit_function; 524| 0| } 525| 514| } 526| | 527| | INCHI_HEAPCHK 528| | 529| | /* mark stereobonds */ 530| 1.39k| for (i = 0; i < pStereo->nNumberOfStereoBonds; i++) ------------------ | Branch (530:21): [True: 639, False: 751] ------------------ 531| 639| { 532| 639| jv = pStereo->nBondAtom1[i] - 1; 533| 639| jn = pStereo->nBondAtom2[i] - 1; 534| 639| parity = pStereo->b_parity[i]; 535| 639| if ((jv < num_atoms) && !is_in_the_list( at[jv].neighbor, (AT_NUMB) jn, at[jv].valence )) /* djb-rwth: fixing GHI #126/16 */ ------------------ | Branch (535:17): [True: 639, False: 0] | Branch (535:37): [True: 37, False: 602] ------------------ 536| 37| { 537| | /* must be a cumulene */ 538| 37| if (!bFindCumuleneChain( at, (AT_NUMB) jv, (AT_NUMB) jn, nCumulene, MAX_CUMULENE_LEN + 1 )) ------------------ | | 207| 37|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ | Branch (538:21): [True: 0, False: 37] ------------------ 539| 0| { 540| 0| return RI_ERR_SYNTAX; /* not a cumulene */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 541| 0| } 542| 37| len = MAX_CUMULENE_LEN + 1; ------------------ | | 207| 37|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ 543| 37| } 544| 602| else 545| 602| { 546| | /* a regular double or alt bond */ 547| 602| nCumulene[0] = jv; 548| 602| nCumulene[1] = jn; 549| 602| len = 1; /* cumulene length is number of bonds, not number of atoms */ 550| 602| } 551| | 552| | /* cumulene or double bond: add explicit H if implicit H are present */ 553| 639| if (at[jv].num_H) ------------------ | Branch (553:17): [True: 39, False: 600] ------------------ 554| 39| { 555| 39| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (555:21): [True: 1, False: 38] ------------------ 556| 1| { 557| 1| goto exit_function; 558| 1| } 559| 39| } 560| 600| else 561| 600| { 562| | /* double bond neighbor that has the smallest canonical number; it is either 0th or 1st */ 563| 600| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == nCumulene[1]]; 564| 600| } 565| 638| if (at[jn].num_H) ------------------ | Branch (565:17): [True: 16, False: 622] ------------------ 566| 16| { 567| 16| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (567:21): [True: 1, False: 15] ------------------ 568| 1| { 569| 1| goto exit_function; 570| 1| } 571| 16| } 572| 622| else 573| 622| { 574| 622| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == nCumulene[len - 1]]; 575| 622| } 576| 637| if (0 > ( ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, len ) )) ------------------ | Branch (576:17): [True: 6, False: 631] ------------------ 577| 6| { 578| 6| goto exit_function; 579| 6| } 580| 637| } 581| | 582| 759| INCHI_HEAPCHK 583| 759| } 584| | 585| | /* allocate memory for Mobile-H-only stereo */ 586| 145k| if (num_stereo_centers2 + num_stereo_bonds2) ------------------ | Branch (586:9): [True: 100, False: 145k] ------------------ 587| 100| { 588| 100| if (!( st = (inp_ATOM_STEREO *) inchi_calloc( num_atoms, sizeof( st[0] ) ) )) ------------------ | | 1146| 100|#define inchi_calloc calloc ------------------ | Branch (588:13): [True: 0, False: 100] ------------------ 589| 0| { 590| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 591| 0| goto exit_function; 592| 0| } 593| 100| CopyAt2St( at, st, num_atoms ); 594| 100| } 595| | 596| 145k| pStruct->st = st; 597| 145k| if (num_stereo_centers2) ------------------ | Branch (597:9): [True: 47, False: 145k] ------------------ 598| 47| { 599| | /* In case of Fixed-H */ 600| | /* mark additional Mobile-H stereo centers, they have already been connected the added explicit H, if any */ 601| 47| int bInvertedParity = ( pStereo2->nCompInv2Abs == -1 ); 602| 88| for (i = 0; i < pStereo2->nNumberOfStereoCenters; i++) ------------------ | Branch (602:21): [True: 64, False: 24] ------------------ 603| 64| { 604| 64| n_vertex = pStereo2->nNumber[i] - 1; 605| 64| parity = pStereo2->t_parity[i]; 606| 64| if (at[n_vertex].p_parity) ------------------ | Branch (606:17): [True: 3, False: 61] ------------------ 607| 3| { 608| 3| continue; /* the parity has already been set for Fixed-H */ 609| 3| } 610| 61| if (bInvertedParity) ------------------ | Branch (610:17): [True: 0, False: 61] ------------------ 611| 0| { 612| 0| parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 220| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 219| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 219| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 220| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (612:26): [True: 0, False: 0] | Branch (612:73): [True: 0, False: 0] ------------------ 613| 0| } 614| | /* find whether it is allene */ 615| 61| if (at[n_vertex].valence == 2 && ------------------ | Branch (615:17): [True: 17, False: 44] ------------------ 616| 17| at[n_vertex].num_H == 0 && ------------------ | Branch (616:18): [True: 12, False: 5] ------------------ 617| 12| bCanAtomBeMiddleAllene( at[n_vertex].elname, 0, 0 ) && ------------------ | Branch (617:18): [True: 11, False: 1] ------------------ 618| | /* allene has exactly 2 double bonds */ 619| 11| ( jv = at[n_vertex].neighbor[0], at[jv].valence + at[jv].num_H == 3 ) && ------------------ | Branch (619:18): [True: 10, False: 1] ------------------ 620| 10| bCanAtomBeTerminalAllene( at[jv].elname, 0, 0 ) && ------------------ | Branch (620:18): [True: 9, False: 1] ------------------ 621| 9| ( jn = at[n_vertex].neighbor[1], at[jn].valence + at[jn].num_H == 3 ) && ------------------ | Branch (621:18): [True: 8, False: 1] ------------------ 622| 8| bCanAtomBeTerminalAllene( at[jn].elname, 0, 0 )) ------------------ | Branch (622:18): [True: 7, False: 1] ------------------ 623| 7| { 624| | /* allene: add explicit H if implicit H are present */ 625| | /* iDeletedH = current number of already added explicit H */ 626| | /* idelH1 = index in at[] of the explicit H added to atom jv */ 627| 7| if (at[jv].num_H) ------------------ | Branch (627:21): [True: 0, False: 7] ------------------ 628| 0| { 629| 0| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (629:25): [True: 0, False: 0] ------------------ 630| 0| { 631| 0| goto exit_function; 632| 0| } 633| 0| } 634| 7| else 635| 7| { 636| | /* index of the stereo atom neighbor */ 637| 7| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == n_vertex]; 638| 7| } 639| 7| if (at[jn].num_H) ------------------ | Branch (639:21): [True: 0, False: 7] ------------------ 640| 0| { 641| | /* iDeletedH = current number of already added explicit H */ 642| | /* idelH2 = index of the explicit H added to atom jn */ 643| 0| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (643:25): [True: 0, False: 0] ------------------ 644| 0| { 645| 0| goto exit_function; 646| 0| } 647| 0| } 648| 7| else 649| 7| { 650| 7| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == n_vertex]; 651| 7| } 652| | /* allene: set bond types to double */ 653| | /* 654| | if ( 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jv, BOND_TYPE_DOUBLE ) ) || 655| | 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jn, BOND_TYPE_DOUBLE ) ) ) { 656| | goto exit_function; 657| | } 658| | */ 659| | /* allene: make 0D parity */ 660| 7| ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, 2 ); 661| 7| if (ret < 0) ------------------ | Branch (661:21): [True: 0, False: 7] ------------------ 662| 0| { 663| 0| goto exit_function; 664| 0| } 665| 7| } 666| 54| else 667| 54| { 668| | /* stereogenic sp3 atom */ 669| 54| if (at[n_vertex].num_H) ------------------ | Branch (669:21): [True: 11, False: 43] ------------------ 670| 11| { 671| 11| if (0 > ( ret = AddExplicitDeletedH( at, n_vertex, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (671:25): [True: 0, False: 11] ------------------ 672| 0| { 673| 0| goto exit_function; 674| 0| } 675| 11| } 676| 54| ret = set_atom_0D_parity( at, st, num_atoms, nNumDeletedH, n_vertex, parity ); 677| 54| if (ret < 0) ------------------ | Branch (677:21): [True: 23, False: 31] ------------------ 678| 23| { 679| 23| goto exit_function; 680| 23| } 681| | /* djb-rwth: removing redundant code */ 682| 54| } 683| 38| if (ret < 0) ------------------ | Branch (683:17): [True: 0, False: 38] ------------------ 684| 0| { 685| 0| goto exit_function; 686| 0| } 687| 38| } 688| 47| } 689| | 690| 145k| if (num_stereo_bonds2) ------------------ | Branch (690:9): [True: 53, False: 145k] ------------------ 691| 53| { 692| | /* In case of Fixed-H */ 693| | /* mark additional Mobile-H stereobonds, they have already been connected the added explicit H, if any */ 694| 121| for (i = 0; i < pStereo2->nNumberOfStereoBonds; i++) ------------------ | Branch (694:21): [True: 73, False: 48] ------------------ 695| 73| { 696| 73| jv = pStereo2->nBondAtom1[i] - 1; 697| 73| jn = pStereo2->nBondAtom2[i] - 1; 698| 73| parity = pStereo2->b_parity[i]; 699| 73| if (!is_in_the_list( at[jv].neighbor, (AT_NUMB) jn, at[jv].valence )) ------------------ | Branch (699:17): [True: 5, False: 68] ------------------ 700| 5| { 701| | /* must be a cumulene */ 702| 5| if (!bFindCumuleneChain( at, (AT_NUMB) jv, (AT_NUMB) jn, nCumulene, MAX_CUMULENE_LEN + 1 )) ------------------ | | 207| 5|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ | Branch (702:21): [True: 0, False: 5] ------------------ 703| 0| { 704| 0| return RI_ERR_SYNTAX; /* not a cumulene */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 705| 0| } 706| 5| len = MAX_CUMULENE_LEN + 1; ------------------ | | 207| 5|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ 707| 5| } 708| 68| else 709| 68| { 710| | /* a regular double or alt bond */ 711| 68| nCumulene[0] = jv; 712| 68| nCumulene[1] = jn; 713| 68| len = 1; /* cumulene length is number of bonds, not number of atoms */ 714| 68| } 715| | /* cumulene or double bond: add explicit H if implicit H are present */ 716| 73| if (at[jv].num_H) ------------------ | Branch (716:17): [True: 6, False: 67] ------------------ 717| 6| { 718| 6| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (718:21): [True: 0, False: 6] ------------------ 719| 0| { 720| 0| goto exit_function; 721| 0| } 722| 6| } 723| 67| else 724| 67| { 725| | /* double bond neighbor that has the smallest canonical number */ 726| 67| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == nCumulene[1]]; 727| 67| } 728| 73| if (at[jn].num_H) ------------------ | Branch (728:17): [True: 16, False: 57] ------------------ 729| 16| { 730| 16| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (730:21): [True: 0, False: 16] ------------------ 731| 0| { 732| 0| goto exit_function; 733| 0| } 734| 16| } 735| 57| else 736| 57| { 737| 57| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == nCumulene[len - 1]]; 738| 57| } 739| 73| if (0 > ( ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, len ) )) ------------------ | Branch (739:17): [True: 5, False: 68] ------------------ 740| 5| { 741| 5| goto exit_function; 742| 5| } 743| 73| } 744| 53| } 745| | 746| 145k| ret = num_atoms; 747| | 748| 145k|exit_function: 749| | 750| 145k| return ret; 751| 145k|} SetStereoBondTypeFor0DParity: 756| 1.28k|{ 757| 1.28k| AT_NUMB nCumulene[MAX_CUMULENE_LEN + 2]; 758| 1.28k| int j, n1, n2, k1, m2, ret, nLenCumulene = 0, bond_type; 759| 1.28k| k1 = at[i1].sb_ord[m1]; 760| 1.28k| n1 = i1; 761| 1.28k| nCumulene[nLenCumulene++] = n1; 762| 1.28k| do 763| 1.40k| { 764| 1.40k| n2 = at[n1].neighbor[k1]; /* next atom */ 765| 1.40k| nCumulene[nLenCumulene++] = n2; 766| 1.61k| for (m2 = 0; m2 < MAX_NUM_STEREO_BONDS && at[n2].sb_parity[m2]; m2++) ------------------ | | 873| 3.23k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (766:22): [True: 1.61k, False: 0] | Branch (766:51): [True: 1.48k, False: 128] ------------------ 767| 1.48k| { 768| 1.48k| if (n1 == at[n2].neighbor[(int) at[n2].sb_ord[m2]]) ------------------ | Branch (768:17): [True: 1.27k, False: 209] ------------------ 769| 1.27k| { 770| | /* found the endatom */ 771| 1.27k| goto found; 772| 1.27k| } 773| 1.48k| } 774| 128| if (at[n2].num_H || at[n2].valence != 2 || at[n2].endpoint) ------------------ | Branch (774:13): [True: 0, False: 128] | Branch (774:29): [True: 0, False: 128] | Branch (774:52): [True: 4, False: 124] ------------------ 775| 4| { 776| 4| break; /* not a middle cumulene */ 777| 4| } 778| 124| k1 = ( at[n2].neighbor[0] == n1 ); 779| 124| n1 = n2; 780| 124| } 781| 1.28k| while (at[n1].valence == 2 && !at[n1].num_H && nLenCumulene < MAX_CUMULENE_LEN + 2 && ------------------ | | 207| 124|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ | Branch (781:12): [True: 124, False: 0] | Branch (781:35): [True: 124, False: 0] | Branch (781:52): [True: 124, False: 0] ------------------ 782| 124| bCanAtomBeMiddleAllene( at[n1].elname, at[n1].charge, at[n1].radical )); ------------------ | Branch (782:12): [True: 124, False: 0] ------------------ 783| 4| return RI_ERR_SYNTAX; /* failed */ ------------------ | | 16| 4|#define RI_ERR_SYNTAX (-2) ------------------ 784| | 785| 1.27k|found: 786| 1.27k| if (nLenCumulene == 2) ------------------ | Branch (786:9): [True: 1.18k, False: 91] ------------------ 787| 1.18k| { 788| 1.18k| bond_type = BOND_TYPE_STEREO; /* double bond or alternating bond */ ------------------ | | 253| 1.18k|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 32| 1.18k|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 252| 1.18k|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ 789| 1.18k| } 790| 91| else 791| 91| { 792| 91| bond_type = BOND_TYPE_DOUBLE; /* cumulene or allene */ ------------------ | | 33| 91|#define BOND_TYPE_DOUBLE 2 ------------------ 793| 91| } 794| | 795| 2.68k| for (j = 1; j < nLenCumulene; j++) ------------------ | Branch (795:17): [True: 1.40k, False: 1.27k] ------------------ 796| 1.40k| { 797| | /* if bond_type = BOND_TYPE_DOUBLE then increments at->cham_bonds_valence: */ 798| | /* at->cham_bonds_valence += BOND_TYPE_DOUBLE-BOND_TYPE_SINGLE */ 799| 1.40k| if (0 > ( ret = set_bond_type( at, (AT_NUMB) nCumulene[j - 1], (AT_NUMB) nCumulene[j], bond_type ) )) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (799:13): [True: 0, False: 1.40k] ------------------ 800| 0| { 801| 0| return RI_ERR_PROGR; /* failed */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 802| 0| } 803| 1.40k| } 804| 1.27k| return nLenCumulene; 805| 1.27k|} SetStereoBondTypesFrom0DStereo: 810| 145k|{ 811| 145k| INChI_Stereo *pStereo; 812| 145k| inp_ATOM *at = pStruct->at; 813| 145k| int num_atoms = pStruct->num_atoms; 814| 145k| int i, j, num_stereo_bonds, ret; 815| | 816| 145k| if (pInChI->StereoIsotopic && ------------------ | Branch (816:9): [True: 498, False: 144k] ------------------ 817| 498| ( pInChI->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (817:9): [True: 164, False: 334] ------------------ 818| 498| pInChI->StereoIsotopic->nNumberOfStereoCenters )) 819| 164| { 820| 164| pStereo = pInChI->StereoIsotopic; 821| 164| } 822| 144k| else 823| 144k| if (pInChI->Stereo && ------------------ | Branch (823:13): [True: 11.8k, False: 133k] ------------------ 824| 11.8k| ( pInChI->Stereo->nNumberOfStereoBonds + ------------------ | Branch (824:13): [True: 581, False: 11.3k] ------------------ 825| 11.8k| pInChI->Stereo->nNumberOfStereoCenters )) 826| 581| { 827| 581| pStereo = pInChI->Stereo; 828| 581| } 829| 144k| else 830| 144k| { 831| 144k| pStereo = NULL; 832| 144k| } 833| | 834| | /************************ set bond types separately from stereo *******************/ 835| 145k| if (pStereo) ------------------ | Branch (835:9): [True: 745, False: 144k] ------------------ 836| 745| { 837| 745| num_stereo_bonds = 0; 838| 5.08k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (838:21): [True: 4.34k, False: 741] ------------------ 839| 4.34k| { 840| | /* set BOND_TYPE_DOUBLE in allenes and cumulenes */ 841| | /* set BOND_TYPE_STEREO in double bond stereo */ 842| 5.62k| for (j = 0; j < MAX_NUM_STEREO_BONDS && at[i].sb_parity[j]; j++) ------------------ | | 873| 11.2k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (842:25): [True: 5.60k, False: 17] | Branch (842:53): [True: 1.28k, False: 4.32k] ------------------ 843| 1.28k| { 844| 1.28k| num_stereo_bonds++; 845| 1.28k| if (0 > ( ret = SetStereoBondTypeFor0DParity( at, i, j ) )) ------------------ | Branch (845:21): [True: 4, False: 1.27k] ------------------ 846| 4| { 847| 4| goto exit_function; 848| 4| } 849| 1.28k| } 850| 4.34k| } 851| 741| if (num_stereo_bonds) ------------------ | Branch (851:13): [True: 434, False: 307] ------------------ 852| 434| { 853| 434| int num_bond_type_stereo; 854| 434| int num_bond_type_altern; 855| 434| AT_NUMB neigh; 856| | /* replace adjacent BOND_TYPE_STEREO with BOND_TYPE_ALTERN */ 857| 3.05k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (857:25): [True: 2.61k, False: 434] ------------------ 858| 2.61k| { 859| 2.61k| num_bond_type_stereo = 0; 860| 2.61k| num_bond_type_altern = 0; 861| 7.81k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (861:29): [True: 5.19k, False: 2.61k] ------------------ 862| 5.19k| { 863| 5.19k| num_bond_type_stereo += ( at[i].bond_type[j] == BOND_TYPE_STEREO ); ------------------ | | 253| 5.19k|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 32| 5.19k|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 252| 5.19k|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ 864| 5.19k| num_bond_type_altern += ( at[i].bond_type[j] == BOND_TYPE_ALTERN ); ------------------ | | 35| 5.19k|#define BOND_TYPE_ALTERN 4 ------------------ 865| 5.19k| } 866| 2.61k| if (num_bond_type_stereo + num_bond_type_altern > 1 && num_bond_type_stereo) ------------------ | Branch (866:21): [True: 143, False: 2.47k] | Branch (866:72): [True: 121, False: 22] ------------------ 867| 121| { 868| 425| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (868:33): [True: 304, False: 121] ------------------ 869| 304| { 870| 304| if (at[i].bond_type[j] == BOND_TYPE_STEREO) ------------------ | | 253| 304|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 32| 304|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 252| 304|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ | Branch (870:29): [True: 215, False: 89] ------------------ 871| 215| { 872| 215| neigh = at[i].neighbor[j]; 873| | /* does not change at[i].chem_bond_valence in case of BOND_TYPE_ALTERN */ 874| 215| if (0 > ( ret = set_bond_type( at, (AT_NUMB) i, neigh, BOND_TYPE_ALTERN ) )) ------------------ | | 35| 215|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (874:33): [True: 0, False: 215] ------------------ 875| 0| { 876| 0| goto exit_function; 877| 0| } 878| 215| } 879| 304| } 880| 121| } 881| | /* at this point only isolated stereo bonds have type BOND_TYPE_STEREO */ 882| 2.61k| } 883| | /* increment at[i].chem_bonds_valence if at[i] has an altern. bond */ 884| | /* replace BOND_TYPE_STEREO with BOND_TYPE_DOUBLE and increment */ 885| | /* chem_bonds_valence of the adjacent atoms */ 886| 3.05k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (886:25): [True: 2.61k, False: 434] ------------------ 887| 2.61k| { 888| 2.61k| num_bond_type_stereo = 0; 889| 2.61k| num_bond_type_altern = 0; 890| 7.81k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (890:29): [True: 5.19k, False: 2.61k] ------------------ 891| 5.19k| { 892| 5.19k| num_bond_type_stereo += ( at[i].bond_type[j] == BOND_TYPE_STEREO ); ------------------ | | 253| 5.19k|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 32| 5.19k|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 252| 5.19k|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ 893| 5.19k| num_bond_type_altern += ( at[i].bond_type[j] == BOND_TYPE_ALTERN ); ------------------ | | 35| 5.19k|#define BOND_TYPE_ALTERN 4 ------------------ 894| 5.19k| } 895| 2.61k| if (!num_bond_type_stereo && num_bond_type_altern) ------------------ | Branch (895:21): [True: 2.23k, False: 378] | Branch (895:46): [True: 270, False: 1.96k] ------------------ 896| 270| { 897| | /* an atom has only BOND_TYPE_ALTERN => adjacent BOND_TYPE_ALTERN case */ 898| 270| at[i].chem_bonds_valence += 1; 899| 270| } 900| 2.34k| else 901| 2.34k| { 902| 2.34k| if (num_bond_type_stereo == 1) ------------------ | Branch (902:25): [True: 378, False: 1.96k] ------------------ 903| 378| { 904| | /* isolated BOND_TYPE_STEREO => replace with BOND_TYPE_DOUBLE */ 905| 1.20k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (905:37): [True: 822, False: 378] ------------------ 906| 822| { 907| 822| if (at[i].bond_type[j] == BOND_TYPE_STEREO) ------------------ | | 253| 822|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 32| 822|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 252| 822|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ | Branch (907:33): [True: 378, False: 444] ------------------ 908| 378| { 909| 378| neigh = at[i].neighbor[j]; 910| | /* replacing BOND_TYPE_STEREO with BOND_TYPE_DOUBLE */ 911| | /* does not change at->chem_bonds_valence */ 912| 378| if (0 > ( ret = set_bond_type( at, (AT_NUMB) i, neigh, BOND_TYPE_DOUBLE ) )) ------------------ | | 33| 378|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (912:37): [True: 0, False: 378] ------------------ 913| 0| { 914| 0| goto exit_function; 915| 0| } 916| 378| at[i].chem_bonds_valence++; 917| 378| at[(int) neigh].chem_bonds_valence++; 918| 378| } 919| 822| } 920| 378| } 921| 1.96k| else 922| 1.96k| { 923| 1.96k| if (num_bond_type_stereo + num_bond_type_altern) ------------------ | Branch (923:29): [True: 0, False: 1.96k] ------------------ 924| 0| { 925| | /* an atom still has both BOND_TYPE_STEREO and BOND_TYPE_ALTERN */ 926| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 927| 0| goto exit_function; 928| 0| } 929| 1.96k| } 930| 2.34k| } 931| 2.61k| } 932| 434| INCHI_HEAPCHK 933| 434| } 934| 741| } 935| 145k| ret = 0; /* success */ 936| | 937| 145k|exit_function: 938| | 939| 145k| return ret; 940| 145k|} CopyBnsToAtom: 949| 1.33M|{ 950| 1.33M| int i, j, charge, ret = 0, v1, nMinorder; /* djb-rwth: removing redundant variables */ 951| 1.33M| int num_at = pStruct->num_atoms; 952| 1.33M| inp_ATOM *at = pStruct->at; 953| 1.33M| ICHICONST SRM *pSrm = pStruct->pSrm; ------------------ | | 13| 1.33M|#define ICHICONST const ------------------ 954| 1.33M| BNS_VERTEX *pv; 955| 1.33M| BNS_EDGE *pe; 956| 1.33M| int chem_bonds_valence, bond_order; 957| | 958| | /* djb-rwth: removing redundant code */ 959| 13.9M| for (i = 0; i < num_at; i++) ------------------ | Branch (959:17): [True: 12.6M, False: 1.33M] ------------------ 960| 12.6M| { 961| 12.6M| pv = pBNS->vert + i; 962| | /* bonds */ 963| 12.6M| chem_bonds_valence = 0; 964| 17.9M| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (964:21): [True: 5.36M, False: 12.6M] ------------------ 965| 5.36M| { 966| 5.36M| pe = pBNS->edge + pv->iedge[j]; 967| 5.36M| BondFlowMaxcapMinorder( at, pVA, pSrm, i, j, NULL, &nMinorder, NULL ); 968| 5.36M| bond_order = pe->flow + nMinorder; 969| 5.36M| if (!bAllowZeroBondOrder && !bond_order) ------------------ | Branch (969:17): [True: 0, False: 5.36M] | Branch (969:41): [True: 0, False: 0] ------------------ 970| 0| { 971| 0| bond_order = 1; 972| 0| } 973| 5.36M| chem_bonds_valence += bond_order; 974| 5.36M| at[i].bond_type[j] = bond_order; /* BOND_MARK_HIGHLIGHT */ 975| 5.36M| } 976| 12.6M| at[i].chem_bonds_valence = chem_bonds_valence; 977| | /* charges (both may be present resulting in zero) */ 978| 12.6M| at[i].charge = pVA[i].cInitCharge; 979| 12.6M| if (pVA[i].nCMinusGroupEdge) ------------------ | Branch (979:13): [True: 1.90M, False: 10.7M] ------------------ 980| 1.90M| { 981| 1.90M| pe = pBNS->edge + pVA[i].nCMinusGroupEdge - 1; 982| 1.90M| if ((charge = pe->flow)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (982:17): [True: 507k, False: 1.39M] ------------------ 983| 507k| { 984| 507k| at[i].charge -= charge; 985| | /* djb-rwth: removing redundant code */ 986| 507k| } 987| 1.90M| } 988| 12.6M| if (pVA[i].nCPlusGroupEdge) ------------------ | Branch (988:13): [True: 2.19M, False: 10.4M] ------------------ 989| 2.19M| { 990| 2.19M| pe = pBNS->edge + pVA[i].nCPlusGroupEdge - 1; 991| 2.19M| if ((charge = pe->cap - pe->flow)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (991:17): [True: 509k, False: 1.68M] ------------------ 992| 509k| { 993| 509k| at[i].charge += charge; 994| | /* djb-rwth: removing redundant code */ 995| 509k| } 996| 2.19M| } 997| 12.6M| if (pv->st_edge.cap > pv->st_edge.flow) ------------------ | Branch (997:13): [True: 277k, False: 12.3M] ------------------ 998| 277k| { 999| 277k| at[i].radical = RADICAL_SINGLET + ( pv->st_edge.cap - pv->st_edge.flow ); ------------------ | | 75| 277k|#define RADICAL_SINGLET 1 ------------------ 1000| 277k| } 1001| 12.6M| } 1002| | /* find charge excess */ 1003| | /* djb-rwth: removing redundant variables/code */ 1004| | /* tautomeric H and (-) */ 1005| 1.34M| for (i = 0; i < pBNS->num_t_groups; i++) ------------------ | Branch (1005:17): [True: 9.08k, False: 1.33M] ------------------ 1006| 9.08k| { 1007| | /* tautomeric groups are first non-atom vertices; 1008| | order of them is same as in pTCGroups->pTCG[] */ 1009| 9.08k| int num_H = pTCGroups->pTCG[i].tg_num_H; 1010| 9.08k| int num_Minus = pTCGroups->pTCG[i].tg_num_Minus; 1011| 9.08k| int bMinusFirst = ( pTCGroups->pTCG[i].tg_RestoreFlags & TGRF_MINUS_FIRST ); 1012| 9.08k| int num_at_add; 1013| 9.08k| Vertex vMinus = NO_VERTEX; ------------------ | | 118| 9.08k|#define NO_VERTEX -2 ------------------ 1014| 9.08k| pv = pBNS->vert + num_at + i; /* t-group vertex */ 1015| 9.08k| if (!( pv->type & BNS_VERT_TYPE_TGROUP )) ------------------ | | 47| 9.08k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (1015:13): [True: 0, False: 9.08k] ------------------ 1016| 0| { 1017| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1018| 0| } 1019| 9.08k| if (pTCGroups->pTCG[i].tg_set_Minus > 0 && num_Minus > 0) ------------------ | Branch (1019:13): [True: 12, False: 9.07k] | Branch (1019:52): [True: 12, False: 0] ------------------ 1020| 12| { 1021| 12| vMinus = pTCGroups->pTCG[i].tg_set_Minus - 1; 1022| 12| num_Minus--; 1023| 12| } 1024| | 1025| 9.08k| if (bMinusFirst) ------------------ | Branch (1025:13): [True: 76, False: 9.01k] ------------------ 1026| 76| { 1027| 264| for (j = 0; j < pv->num_adj_edges; j++) ------------------ | Branch (1027:25): [True: 188, False: 76] ------------------ 1028| 188| { 1029| 188| pe = pBNS->edge + pv->iedge[j]; 1030| 188| v1 = pe->neighbor1; 1031| 188| num_at_add = pe->flow; 1032| 188| if (v1 == vMinus) ------------------ | Branch (1032:21): [True: 12, False: 176] ------------------ 1033| 12| { 1034| 12| if (num_at_add) ------------------ | Branch (1034:25): [True: 12, False: 0] ------------------ 1035| 12| { 1036| 12| at[v1].charge = -1; /* no checking at[v1].charge == 0 for now ??? */ 1037| 12| num_at_add--; /* no checking num_at_add > 0 for now ??? */ 1038| 12| } 1039| 0| else 1040| 0| { 1041| 0| num_Minus++; /* error ??? */ 1042| 0| } 1043| 12| vMinus = NO_VERTEX; ------------------ | | 118| 12|#define NO_VERTEX -2 ------------------ 1044| 12| } 1045| 188| if (num_at_add > 0) ------------------ | Branch (1045:21): [True: 146, False: 42] ------------------ 1046| 146| { 1047| | /* atom has tautomeric attachment; do not allow =N(-) */ 1048| 146| if (num_Minus && !at[v1].charge && ------------------ | Branch (1048:25): [True: 140, False: 6] | Branch (1048:38): [True: 140, False: 0] ------------------ 1049| 140| at[v1].valence == at[v1].chem_bonds_valence) ------------------ | Branch (1049:26): [True: 136, False: 4] ------------------ 1050| 136| { 1051| 136| at[v1].charge--; 1052| 136| num_at_add--; 1053| 136| num_Minus--; 1054| 136| } 1055| 146| if (num_at_add > 0) ------------------ | Branch (1055:25): [True: 22, False: 124] ------------------ 1056| 22| { 1057| 22| at[v1].num_H += num_at_add; 1058| 22| num_H -= num_at_add; 1059| | /* djb-rwth: removing redundant code */ 1060| 22| } 1061| 146| } 1062| 188| at[v1].endpoint = i + 1; 1063| 188| } 1064| 76| if (( num_H + num_Minus != pv->st_edge.cap - pv->st_edge.flow ) && ( num_H || num_Minus || vMinus != NO_VERTEX )) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (1064:17): [True: 0, False: 76] | Branch (1064:82): [True: 0, False: 0] | Branch (1064:91): [True: 0, False: 0] | Branch (1064:104): [True: 0, False: 0] ------------------ 1065| 0| { 1066| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1067| 0| } 1068| 76| } 1069| 9.01k| else 1070| 9.01k| { 1071| 26.6k| for (j = pv->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (1071:45): [True: 17.6k, False: 9.01k] ------------------ 1072| 17.6k| { 1073| 17.6k| pe = pBNS->edge + pv->iedge[j]; 1074| 17.6k| v1 = pe->neighbor1; 1075| 17.6k| num_at_add = pe->flow; 1076| 17.6k| if (v1 == vMinus) ------------------ | Branch (1076:21): [True: 0, False: 17.6k] ------------------ 1077| 0| { 1078| 0| if (num_at_add) ------------------ | Branch (1078:25): [True: 0, False: 0] ------------------ 1079| 0| { 1080| 0| at[v1].charge = -1; /* no checking at[v1].charge == 0 for now ??? */ 1081| 0| num_at_add--; /* no checking num_at_add > 0 for now ??? */ 1082| 0| } 1083| 0| else 1084| 0| { 1085| 0| num_Minus++; /* error ??? */ 1086| 0| } 1087| 0| vMinus = NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 1088| 0| } 1089| 17.6k| if (num_at_add > 0) ------------------ | Branch (1089:21): [True: 6.82k, False: 10.7k] ------------------ 1090| 6.82k| { 1091| | /* atom has tautomeric attachment; do not allow =N(-) */ 1092| 6.82k| if (num_Minus && !at[v1].charge && ------------------ | Branch (1092:25): [True: 5.00k, False: 1.82k] | Branch (1092:38): [True: 5.00k, False: 0] ------------------ 1093| 5.00k| at[v1].valence == at[v1].chem_bonds_valence) ------------------ | Branch (1093:26): [True: 4.62k, False: 371] ------------------ 1094| 4.62k| { 1095| 4.62k| at[v1].charge--; 1096| 4.62k| num_at_add--; 1097| 4.62k| num_Minus--; 1098| 4.62k| } 1099| 6.82k| if (num_at_add > 0) ------------------ | Branch (1099:25): [True: 3.63k, False: 3.19k] ------------------ 1100| 3.63k| { 1101| 3.63k| at[v1].num_H += num_at_add; 1102| 3.63k| num_H -= num_at_add; 1103| | /* djb-rwth: removing redundant code */ 1104| 3.63k| } 1105| 6.82k| } 1106| 17.6k| at[v1].endpoint = i + 1; 1107| 17.6k| } 1108| 9.01k| if (( num_H + num_Minus != pv->st_edge.cap - pv->st_edge.flow ) && ( num_H || num_Minus || vMinus != NO_VERTEX )) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (1108:17): [True: 21, False: 8.99k] | Branch (1108:82): [True: 6, False: 15] | Branch (1108:91): [True: 15, False: 0] | Branch (1108:104): [True: 0, False: 0] ------------------ 1109| 21| { 1110| 21| return RI_ERR_PROGR; ------------------ | | 17| 21|#define RI_ERR_PROGR (-3) ------------------ 1111| 21| } 1112| 9.01k| } 1113| 9.08k| } 1114| | 1115| 1.33M| return ret; 1116| 1.33M|} CheckBnsConsistency: 1125| 101k|{ 1126| 101k| int nOutput = 0; 1127| |#ifndef TARGET_API_LIB 1128| |#if ( bRELEASE_VERSION == 0 ) 1129| | char s[128]; 1130| | int i, j, atom_charge, left_charge, charge, excess_charge, ret = 0; 1131| | int v1, v2, flow, tot_st_flow, tot_st_cap, num_electrons, nNumMetalAtoms; 1132| | int num_at = pStruct->num_atoms; 1133| | inp_ATOM *at = pStruct->at; 1134| | BNS_VERTEX *pv; 1135| | BNS_EDGE *pe; 1136| |#ifdef _DEBUG 1137| | int bDebugOutput = 0; 1138| | bNoRad = 1; 1139| | bDebugOutput = 1; 1140| |#endif 1141| | /* count electrons and metals */ 1142| | num_electrons = -pTCGroups->total_charge; 1143| | nNumMetalAtoms = 0; 1144| | for (i = 0; i < pTCGroups->num_tgroups; i++) 1145| | { 1146| | num_electrons += pTCGroups->pTCG[i].tg_num_H; 1147| | } 1148| | for (i = 0; i < num_at; i++) 1149| | { 1150| | num_electrons += at[i].el_number + at[i].num_H; 1151| | nNumMetalAtoms += pVA[i].cMetal; 1152| | } 1153| | /* create output string */ 1154| | sprintf( s, "%d:%d%sM%02dv%da%de%db%d* ", 1155| | bNoRad, pTCGroups->iComponent + 1, num_electrons % 2 ? "O" : "E", nNumMetalAtoms, 1156| | pBNS->num_vertices, num_at, pBNS->num_edges, pBNS->num_bonds ); 1157| | 1158| | 1159| | tot_st_flow = tot_st_cap = 0; 1160| | atom_charge = left_charge = 0; 1161| | if (pBNS->num_atoms != num_at) 1162| | { 1163| | fprintf( stdout, "\n%sNum. atoms discrepancy: %d(BNS) vs. %d(at) ", s, pBNS->num_atoms, num_at ); 1164| | nOutput++; 1165| | } 1166| | /* check edges */ 1167| |#ifdef _DEBUG 1168| | if (bDebugOutput && bNoRad) 1169| | { 1170| | fprintf( stderr, "\n\n------begin------------------------------------------------\n" ); 1171| | fprintf( stderr, "\n\fedge cap flow v1 v2\n\n" ); 1172| | /* xxxx xxxx/xxxx xxxx/xxxx xxxx xxxx */ 1173| | } 1174| |#endif 1175| | for (i = 0; i < pBNS->num_edges; i++) 1176| | { 1177| | pe = pBNS->edge + i; 1178| | v1 = pe->neighbor1; 1179| | v2 = v1 ^ pe->neighbor12; 1180| | if (pe->cap < pe->flow || pe->flow < 0) 1181| | { 1182| | fprintf( stdout, "\n%sedge %d (%d-%d) has cap=%d flow=%d ", s, i, v1, v2, pe->cap, pe->flow ); 1183| | nOutput++; 1184| | } 1185| |#ifdef _DEBUG 1186| | if (bDebugOutput && bNoRad) 1187| | { 1188| | /* xxxx xxxx/xxxx xxxx/xxxx xxxx xxxx */ 1189| | fprintf( stderr, "%4d %4d/%-4d %4d/%-4d %4d %4d\n", i, pe->cap, pe->cap0, pe->flow, pe->flow0, v1, v2 ); 1190| | } 1191| |#endif 1192| | } 1193| | 1194| | 1195| | /* check vertices */ 1196| |#ifdef _DEBUG 1197| | if (bDebugOutput && bNoRad) 1198| | { 1199| | fprintf( stderr, "\n\fvert st-cap st-flow type iedge : neigh\n\n" ); 1200| | /* xxxx xxxx/xxxx xxxx/xxxx 0xXXX xxxx : xxx */ 1201| | } 1202| |#endif 1203| | for (i = 0; i < pBNS->num_vertices; i++) 1204| | { 1205| | pv = pBNS->vert + i; 1206| |#ifdef _DEBUG 1207| | if (bDebugOutput && bNoRad) 1208| | { 1209| | /* xxxx xxxx/xxxx xxxx/xxxx 0xXXX xxxx : xxx */ 1210| | int j; 1211| | const char *s; 1212| | char sAtom[6]; 1213| | switch (pv->type) 1214| | { 1215| | case BNS_VERT_TYPE_ATOM: 1216| | sprintf( sAtom, "At %-2.2s", i < num_at ? at[i].elname : "??" ); 1217| | s = sAtom; 1218| | break; 1219| | case BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_ENDPOINT: 1220| | s = "Endpt"; 1221| | break; 1222| | case BNS_VT_C_POS: 1223| | s = "(+) "; 1224| | break; 1225| | case BNS_VT_C_NEG: 1226| | s = "(-) "; 1227| | break; 1228| | case BNS_VT_C_POS_C: 1229| | s = "(+C) "; 1230| | break; 1231| | case BNS_VT_C_NEG_C: 1232| | s = "(-C) "; 1233| | break; 1234| | case BNS_VT_C_POS_M: 1235| | s = "(+M) "; 1236| | break; 1237| | case BNS_VT_C_NEG_M: 1238| | s = "(-M) "; 1239| | break; 1240| | case BNS_VT_C_POS_ALL: 1241| | s = "(+)Sg"; 1242| | break; 1243| | case BNS_VT_C_NEG_ALL: 1244| | s = "(-)Sg"; 1245| | break; 1246| | case BNS_VT_M_GROUP: 1247| | s = "M-grp"; 1248| | break; 1249| | case BNS_VERT_TYPE__AUX | BNS_VERT_TYPE_TEMP: 1250| | s = "ChStr"; 1251| | break; 1252| | case BNS_VERT_TYPE__AUX: 1253| | s = "Yconn"; 1254| | break; 1255| | case BNS_VERT_TYPE_TGROUP: 1256| | s = "T-grp"; 1257| | break; 1258| | default: 1259| | s = "Unkn."; 1260| | break; 1261| | } 1262| | fprintf( stderr, "%4d %4d/%-4d %4d/%-4d 0x%03X %5s", 1263| | i, pv->st_edge.cap, pv->st_edge.cap0, pv->st_edge.flow, pv->st_edge.flow0, 1264| | pv->type, s ); 1265| | for (j = 0; j < pv->num_adj_edges; j++) 1266| | { 1267| | fprintf( stderr, " %2d", pv->iedge[j] ); 1268| | } 1269| | fprintf( stderr, ":" ); 1270| | for (j = 0; j < pv->num_adj_edges; j++) 1271| | { 1272| | pe = pBNS->edge + pv->iedge[j]; 1273| | fprintf( stderr, " %2d", pe->neighbor12 ^ i ); 1274| | } 1275| | fprintf( stderr, "\n" ); 1276| | } 1277| |#endif 1278| | tot_st_flow += pv->st_edge.flow; 1279| | tot_st_cap += pv->st_edge.cap; 1280| | if (pv->num_adj_edges > pv->max_adj_edges) 1281| | { 1282| | fprintf( stdout, "\n%s%s %d type 0x%X \"%s\" num_edges=%d > max=%d ", s, 1283| | i < num_at ? "atom" : "vertex", i, 1284| | pv->type, at[i].elname, pv->num_adj_edges, pv->max_adj_edges ); 1285| | nOutput++; 1286| | } 1287| | if (i < num_at) 1288| | { 1289| | /* charge on atoms */ 1290| | charge = pVA[i].cInitCharge; 1291| | if (pVA[i].nCMinusGroupEdge) 1292| | { 1293| | pe = pBNS->edge + pVA[i].nCMinusGroupEdge - 1; 1294| | if (pe->flow > 0) 1295| | { 1296| | charge -= pe->flow; 1297| | } 1298| | } 1299| | if (pVA[i].nCPlusGroupEdge) 1300| | { 1301| | pe = pBNS->edge + pVA[i].nCPlusGroupEdge - 1; 1302| | if (pe->cap > pe->flow) 1303| | { 1304| | charge += pe->cap - pe->flow; 1305| | } 1306| | } 1307| | if (bNoRad && pv->st_edge.flow != pv->st_edge.cap) 1308| | { 1309| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" unexpected st_cap=%d st_flow=%d ", s, 1310| | i < num_at ? "atom" : "vertex", i, 1311| | pv->type, at[i].elname, pv->st_edge.cap, pv->st_edge.flow ); 1312| | nOutput++; 1313| | } 1314| | else 1315| | if (bNoRad && charge && !strcmp( at[i].elname, "C" )) 1316| | { 1317| | /* ignore carbonyls */ 1318| | if (i == 0 && num_at == 2 && !strcmp( at[1].elname, "O" ) && 1319| | !at[0].num_H && !at[1].num_H && !pTCGroups->total_charge) 1320| | { 1321| | ; /* C(-)#O(+) structure */ 1322| | } 1323| | else 1324| | { 1325| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" charge=%d ", s, 1326| | i < num_at ? "atom" : "vertex", i, 1327| | pv->type, at[i].elname, charge ); 1328| | nOutput++; 1329| | } 1330| | } 1331| | atom_charge += charge; 1332| | } 1333| | else 1334| | if (( charge = pv->st_edge.cap - pv->st_edge.flow ) > 0) 1335| | { 1336| | /* excess charge */ 1337| | if (!bNoRad && IS_BNS_VT_C_OR_CSUPER_GR( pv->type )) 1338| | { 1339| | left_charge -= charge; 1340| | } 1341| | else 1342| | if (!bNoRad && IS_BNS_VT_YVCONNECTOR( pv->type )) 1343| | { 1344| | left_charge += charge; 1345| | } 1346| | else 1347| | if (!bNoRad && IS_BNS_VT_M_GR( pv->type ) && 1348| | 0 <= ( j = pTCGroups->nGroup[TCG_MeFlower3] ) && 1349| | i == pTCGroups->pTCG[j].nVertexNumber) 1350| | { 1351| | ; /* additional "radical" on metal flower */ 1352| | } 1353| | else 1354| | if (!( pv->type & BNS_VERT_TYPE_TGROUP ) || bNoRad) 1355| | { 1356| | /* t-groups before running BFS should have st_cap > st_flow */ 1357| | fprintf( stdout, "\n%s%s %d: type 0x%X unexpected st_cap=%d st_flow=%d ", s, 1358| | i < num_at ? "atom" : "vertex", i, 1359| | pv->type, pv->st_edge.cap, pv->st_edge.flow ); 1360| | nOutput++; 1361| | } 1362| | } 1363| | if (pv->st_edge.cap < pv->st_edge.flow || pv->st_edge.flow < 0) 1364| | { 1365| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" st_cap=%d st_flow=%d ", s, 1366| | i < num_at ? "atom" : "vertex", i, 1367| | pv->type, i < num_at ? at[i].elname : "", pv->st_edge.cap, pv->st_edge.flow ); 1368| | nOutput++; 1369| | } 1370| | /* check edge_flow vs. st_flow consistency */ 1371| | for (j = 0, flow = 0; j < pv->num_adj_edges; j++) 1372| | { 1373| | pe = pBNS->edge + pv->iedge[j]; 1374| | flow += pe->flow; 1375| | } 1376| | if (flow != pv->st_edge.flow) 1377| | { 1378| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" st_flow=%d edge_flow=%d ", s, 1379| | i < num_at ? "atom" : "vertex", i, 1380| | pv->type, i < num_at ? at[i].elname : "", pv->st_edge.flow, flow ); 1381| | nOutput++; 1382| | } 1383| | } 1384| |#ifdef _DEBUG 1385| | if (bDebugOutput && bNoRad) 1386| | { 1387| | fprintf( stderr, "\n------end--------------------------------------------------\n" ); 1388| | } 1389| |#endif 1390| | /* 1391| | if ( num_electrons %= 2 ) { 1392| | fprintf( stdout, "\n%d*Odd number of electrons (%d atoms) ", bNoRad, num_at ); 1393| | nOutput ++; 1394| | } 1395| | */ 1396| | /* tautomeric groups charge */ 1397| | for (i = 0, charge = 0; i < pTCGroups->num_tgroups; i++) 1398| | { 1399| | charge -= pTCGroups->pTCG[i].tg_num_Minus; 1400| | } 1401| | /* compare */ 1402| | if (charge != pTCGroups->tgroup_charge) 1403| | { 1404| | fprintf( stdout, "\n%sCounted t-group charge=%d while %d was saved ", s, 1405| | charge, pTCGroups->tgroup_charge ); 1406| | nOutput++; 1407| | } 1408| | /* add other charges */ 1409| | charge += atom_charge + left_charge; 1410| | excess_charge = pTCGroups->total_charge - pTCGroups->added_charge - pTCGroups->tgroup_charge; 1411| | if (charge != pTCGroups->total_charge && excess_charge != pTCGroups->total_charge - charge) 1412| | { 1413| | fprintf( stdout, "\n%sCounted total charge=%d while %d was saved; excess charge=%d ", s, 1414| | charge, pTCGroups->total_charge, excess_charge ); 1415| | nOutput++; 1416| | } 1417| | if (tot_st_cap != pBNS->tot_st_cap || tot_st_flow != pBNS->tot_st_flow) 1418| | { 1419| | fprintf( stdout, "\n%sCounted/saved total st_flow=%d/%d st_cap=%d/%d ", s, 1420| | tot_st_flow, pBNS->tot_st_flow, tot_st_cap, pBNS->tot_st_cap ); 1421| | nOutput++; 1422| | } 1423| | if (nOutput) 1424| | { 1425| | fprintf( stdout, "\n" ); 1426| | } 1427| |#endif 1428| |#endif 1429| | 1430| 101k| return nOutput; 1431| 101k|} AddExplicitDeletedH: 1442| 185|{ 1443| 185| inp_ATOM *cur_H, *cur_at = at + jv; 1444| 185| int tot_num_iso_H = NUM_ISO_H( cur_at, 0 ); ------------------ | | 55| 185|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) ------------------ 1445| 185| int num_H = cur_at->num_H; 1446| 185| int iso_H = 0; 1447| 185| S_CHAR num_iso_H[NUM_H_ISOTOPES]; 1448| 185| int i; 1449| | 1450| 185| if (!at[jv].at_type) ------------------ | Branch (1450:9): [True: 0, False: 185] ------------------ 1451| 0| { 1452| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1453| 0| } 1454| | 1455| 185| if (at[jv].at_type > 1) ------------------ | Branch (1455:9): [True: 92, False: 93] ------------------ 1456| 92| { 1457| | /* explicit hydrogens have already been added; find them */ 1458| 94| for (i = 0; i < *iDeletedH; i++) ------------------ | Branch (1458:21): [True: 94, False: 0] ------------------ 1459| 94| { 1460| 94| if (at[num_at + i].neighbor[0] == jv) ------------------ | Branch (1460:17): [True: 92, False: 2] ------------------ 1461| 92| { 1462| 92| *iH = num_at + i; /* return the first found H, it has the smallest canonical pseudo rank */ 1463| 92| return 0; 1464| 92| } 1465| 94| } 1466| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1467| 92| } 1468| | /* add all explicit H disconnected from at[jv] in order H, 1H, D, T */ 1469| 93| *iH = *iDeletedH + num_at; /* num_H includes all H, both isotopic and normal */ 1470| 372| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 25| 372|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1470:17): [True: 279, False: 93] ------------------ 1471| 279| { 1472| 279| num_iso_H[i] = at[jv].num_iso_H[i]; 1473| 279| } 1474| 200| for (; num_H && ( *iDeletedH ) < nNumDeletedH; ( *iDeletedH )++) ------------------ | Branch (1474:12): [True: 114, False: 86] | Branch (1474:21): [True: 111, False: 3] ------------------ 1475| 111| { 1476| 111| cur_H = at + num_at + ( *iDeletedH ); /* first available empty atom will be this explicit H */ 1477| 111| cur_H->neighbor[cur_H->valence] = jv; /* connect this new atom H to the real atom */ 1478| 111| cur_H->bond_type[cur_H->valence] = BOND_TYPE_SINGLE; ------------------ | | 32| 111|#define BOND_TYPE_SINGLE 1 ------------------ 1479| 111| cur_H->valence++; 1480| 111| if (num_H > tot_num_iso_H) ------------------ | Branch (1480:13): [True: 97, False: 14] ------------------ 1481| 97| { 1482| 97| num_H--; 1483| 97| if (num_H != tot_num_iso_H) ------------------ | Branch (1483:17): [True: 15, False: 82] ------------------ 1484| 15| { 1485| | /* may happen when Mobile-H stereo included in Fixed-H processing */ 1486| 15| if (bTwoStereo) ------------------ | Branch (1486:21): [True: 13, False: 2] ------------------ 1487| 13| { 1488| 13| continue; 1489| 13| } 1490| 2| else 1491| 2| { 1492| 2| return RI_ERR_SYNTAX; /* two identical H neighbors of a stereo atom/bond */ ------------------ | | 16| 2|#define RI_ERR_SYNTAX (-2) ------------------ 1493| 2| } 1494| 15| } 1495| 97| } 1496| 14| else 1497| 14| { 1498| 26| while (iso_H < NUM_H_ISOTOPES && !num_iso_H[iso_H]) ------------------ | | 25| 52|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1498:20): [True: 25, False: 1] | Branch (1498:46): [True: 12, False: 13] ------------------ 1499| 12| { 1500| 12| iso_H++; 1501| 12| } 1502| 14| if (iso_H < NUM_H_ISOTOPES) ------------------ | | 25| 14|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1502:17): [True: 13, False: 1] ------------------ 1503| 13| { 1504| 13| cur_H->iso_atw_diff = iso_H + 1; /* isotopic shift + 1 */ 1505| 13| num_H--; 1506| 13| tot_num_iso_H--; 1507| 13| num_iso_H[iso_H] --; 1508| 13| if (num_iso_H[iso_H]) ------------------ | Branch (1508:21): [True: 1, False: 12] ------------------ 1509| 1| { 1510| 1| return RI_ERR_SYNTAX; /* two identical isotopic H neighbors of a stereo atom/bond */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 1511| 1| } 1512| 13| } 1513| 1| else 1514| 1| { 1515| 1| return RI_ERR_SYNTAX; /* not enough isotopic H */ ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 1516| 1| } 1517| 14| } 1518| 111| } 1519| 89| if (num_H) ------------------ | Branch (1519:9): [True: 3, False: 86] ------------------ 1520| 3| { 1521| 3| return RI_ERR_SYNTAX; ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 1522| 3| } 1523| 86| at[jv].at_type++; /* at[jv].at_type==2 => explicit hydrogens have already been added */ 1524| | 1525| 86| return 0; /* success */ 1526| 89|} bFindCumuleneChain: 1538| 853|{ 1539| 853| int i, len, iat, nat; 1540| 853| nCumulene[0] = i1; 1541| 1.16k| for (i = 0; i < at[i1].valence; i++) ------------------ | Branch (1541:17): [True: 1.13k, False: 30] ------------------ 1542| 1.13k| { 1543| 1.13k| len = 0; 1544| 1.13k| iat = i1; /* current */ 1545| 1.13k| nat = at[i1].neighbor[i]; /* next */ 1546| 1.13k| if (len + 1 == nMaxLen) ------------------ | Branch (1546:13): [True: 837, False: 300] ------------------ 1547| 837| { 1548| 837| if (nat == i2) ------------------ | Branch (1548:17): [True: 668, False: 169] ------------------ 1549| 668| { 1550| 668| nCumulene[++len] = nat; 1551| 668| return 1; /* success */ 1552| 668| } 1553| 169| continue; /* check next at[i1] neighbor */ 1554| 837| } 1555| 483| while (at[nat].valence == 2 && ------------------ | Branch (1555:16): [True: 435, False: 48] ------------------ 1556| 435| at[nat].num_H == 0 && ------------------ | Branch (1556:17): [True: 434, False: 1] ------------------ 1557| 434| bCanAtomBeMiddleAllene( at[nat].elname, 0, 0 )) ------------------ | Branch (1557:17): [True: 361, False: 73] ------------------ 1558| 361| { 1559| 361| nCumulene[++len] = nat; 1560| 361| nat = at[nat].neighbor[at[nat].neighbor[0] == iat]; /* new next */ 1561| 361| if (len + 1 == nMaxLen) ------------------ | Branch (1561:17): [True: 178, False: 183] ------------------ 1562| 178| { 1563| 178| if (nat == i2) ------------------ | Branch (1563:21): [True: 155, False: 23] ------------------ 1564| 155| { 1565| 155| nCumulene[++len] = nat; 1566| 155| return 1; /* success */ 1567| 155| } 1568| 23| break; /* check next at[i1] neighbor */ 1569| 178| } 1570| 183| iat = nCumulene[len]; /* new current */ 1571| 183| } 1572| 300| } 1573| | 1574| 30| return 0; /* failed */ 1575| 853|} set_bond_type: 1580| 1.99k|{ 1581| 1.99k| AT_NUMB *p1 = is_in_the_list( at[i1].neighbor, i2, at[i1].valence ); 1582| 1.99k| AT_NUMB *p2 = is_in_the_list( at[i2].neighbor, i1, at[i2].valence ); 1583| 1.99k| if (p1 && p2) ------------------ | Branch (1583:9): [True: 1.99k, False: 0] | Branch (1583:15): [True: 1.99k, False: 0] ------------------ 1584| 1.99k| { 1585| 1.99k| int j1 = (int) ( p1 - at[i1].neighbor ); 1586| 1.99k| int j2 = (int) ( p2 - at[i2].neighbor ); 1587| 1.99k| int bTypePrev = at[i1].bond_type[j1]; 1588| 1.99k| at[i1].bond_type[j1] = bType; 1589| 1.99k| at[i2].bond_type[j2] = bType; 1590| 1.99k| if (bTypePrev && bTypePrev <= BOND_TYPE_TRIPLE && ------------------ | | 34| 3.99k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1590:13): [True: 1.99k, False: 0] | Branch (1590:26): [True: 808, False: 1.18k] ------------------ 1591| 808| bType && bType <= BOND_TYPE_TRIPLE) ------------------ | | 34| 808|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1591:14): [True: 808, False: 0] | Branch (1591:27): [True: 212, False: 596] ------------------ 1592| 212| { 1593| 212| at[i1].chem_bonds_valence += bType - bTypePrev; 1594| 212| at[i2].chem_bonds_valence += bType - bTypePrev; 1595| 212| } 1596| 1.99k| return 0; 1597| 1.99k| } 1598| | 1599| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1600| 1.99k|} set_cumulene_0D_parity: 1613| 737|{ 1614| 737| AT_NUMB nCumulene[MAX_CUMULENE_LEN + 2]; 1615| 737| AT_NUMB *p1, *p2; 1616| 737| int m1, m2, parity1, parity2, sb_ord_m1, sb_ord_m2, k1, k2, num_neigh1, num_neigh2; 1617| | /* the following types must exactly match types in inp_ATOM and inp_ATOM_STEREO */ 1618| 737| S_CHAR *sb_ord1, *sn_ord1, *sb_parity1; 1619| 737| S_CHAR *sb_ord2, *sn_ord2, *sb_parity2; 1620| 737| AT_NUMB *sn_orig_at_num1; 1621| 737| AT_NUMB *sn_orig_at_num2; 1622| | 1623| | 1624| 737| if (!bFindCumuleneChain( at, (AT_NUMB) i1, (AT_NUMB) i2, nCumulene, len )) ------------------ | Branch (1624:9): [True: 0, False: 737] ------------------ 1625| 0| { 1626| 0| return RI_ERR_SYNTAX; /* not an allene */ ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1627| 0| } 1628| | /* stereo bond neighbors: index of a stereo bond in its end-atom adjacency lists */ 1629| 737| if (( p1 = is_in_the_list( at[i1].neighbor, nCumulene[1], at[i1].valence ) ) && ------------------ | Branch (1629:9): [True: 737, False: 0] ------------------ 1630| 737| ( p2 = is_in_the_list( at[i2].neighbor, nCumulene[len - 1], at[i2].valence ) )) ------------------ | Branch (1630:9): [True: 737, False: 0] ------------------ 1631| 737| { 1632| 737| sb_ord_m1 = (int) ( p1 - at[i1].neighbor ); /* indes of stereobond in the atom's adjacency list */ 1633| 737| sb_ord_m2 = (int) ( p2 - at[i2].neighbor ); 1634| 737| } 1635| 0| else 1636| 0| { 1637| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1638| 0| } 1639| 737| num_neigh1 = at[i1].valence + at[i1].num_H; 1640| 737| num_neigh2 = at[i2].valence + at[i2].num_H; 1641| | 1642| 737| if (num_neigh1 < MIN_NUM_STEREO_BOND_NEIGH || num_neigh1 > MAX_NUM_STEREO_BOND_NEIGH || ------------------ | | 875| 1.47k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ if (num_neigh1 < MIN_NUM_STEREO_BOND_NEIGH || num_neigh1 > MAX_NUM_STEREO_BOND_NEIGH || ------------------ | | 874| 1.47k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (1642:9): [True: 3, False: 734] | Branch (1642:51): [True: 1, False: 733] ------------------ 1643| 733| num_neigh2 < MIN_NUM_STEREO_BOND_NEIGH || num_neigh2 > MAX_NUM_STEREO_BOND_NEIGH) ------------------ | | 875| 1.47k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ num_neigh2 < MIN_NUM_STEREO_BOND_NEIGH || num_neigh2 > MAX_NUM_STEREO_BOND_NEIGH) ------------------ | | 874| 730|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (1643:10): [True: 3, False: 730] | Branch (1643:52): [True: 1, False: 729] ------------------ 1644| 8| { 1645| 8| return RI_ERR_SYNTAX; ------------------ | | 16| 8|#define RI_ERR_SYNTAX (-2) ------------------ 1646| 8| } 1647| | 1648| | 1649| 729| sb_ord1 = st ? st[i1].sb_ord : at[i1].sb_ord; ------------------ | Branch (1649:15): [True: 77, False: 652] ------------------ 1650| 729| sb_ord2 = st ? st[i2].sb_ord : at[i2].sb_ord; ------------------ | Branch (1650:15): [True: 77, False: 652] ------------------ 1651| 729| sb_parity1 = st ? st[i1].sb_parity : at[i1].sb_parity; ------------------ | Branch (1651:18): [True: 77, False: 652] ------------------ 1652| 729| sb_parity2 = st ? st[i2].sb_parity : at[i2].sb_parity; ------------------ | Branch (1652:18): [True: 77, False: 652] ------------------ 1653| | 1654| | /* find the first unoccupied locations in the stereobond 0D descriptor lists; check whether the stereo has already been set */ 1655| 802| for (m1 = k1 = 0; m1 < MAX_NUM_STEREO_BONDS && sb_parity1[m1] && !( k1 = sb_ord1[m1] == sb_ord_m1 ); m1++) ------------------ | | 873| 1.60k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1655:23): [True: 802, False: 0] | Branch (1655:52): [True: 84, False: 718] | Branch (1655:70): [True: 73, False: 11] ------------------ 1656| 73| ; 1657| 873| for (m2 = k2 = 0; m2 < MAX_NUM_STEREO_BONDS && sb_parity2[m2] && !( k2 = sb_ord2[m2] == sb_ord_m2 ); m2++) ------------------ | | 873| 1.74k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1657:23): [True: 873, False: 0] | Branch (1657:52): [True: 156, False: 717] | Branch (1657:70): [True: 144, False: 12] ------------------ 1658| 144| ; 1659| 729| if (m1 == MAX_NUM_STEREO_BONDS || m2 == MAX_NUM_STEREO_BONDS) ------------------ | | 873| 1.45k|#define MAX_NUM_STEREO_BONDS 3 ------------------ if (m1 == MAX_NUM_STEREO_BONDS || m2 == MAX_NUM_STEREO_BONDS) ------------------ | | 873| 729|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1659:9): [True: 0, False: 729] | Branch (1659:39): [True: 0, False: 729] ------------------ 1660| 0| { 1661| 0| return RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1662| 0| } 1663| 729| if (k1 && k2) ------------------ | Branch (1663:9): [True: 11, False: 718] | Branch (1663:15): [True: 10, False: 1] ------------------ 1664| 10| { 1665| 10| return 0; /* the stereo descriptor of this bond/allene/cumulene has already been set */ 1666| 10| } 1667| 719| if (k1 || k2) ------------------ | Branch (1667:9): [True: 1, False: 718] | Branch (1667:15): [True: 2, False: 716] ------------------ 1668| 3| { 1669| 3| return RI_ERR_SYNTAX; /* only half of a bond was set */ ------------------ | | 16| 3|#define RI_ERR_SYNTAX (-2) ------------------ 1670| 3| } 1671| | 1672| 716| sn_ord1 = st ? st[i1].sn_ord : at[i1].sn_ord; ------------------ | Branch (1672:15): [True: 67, False: 649] ------------------ 1673| 716| sn_ord2 = st ? st[i2].sn_ord : at[i2].sn_ord; ------------------ | Branch (1673:15): [True: 67, False: 649] ------------------ 1674| 716| sn_orig_at_num1 = st ? st[i1].sn_orig_at_num : at[i1].sn_orig_at_num; ------------------ | Branch (1674:23): [True: 67, False: 649] ------------------ 1675| 716| sn_orig_at_num2 = st ? st[i2].sn_orig_at_num : at[i2].sn_orig_at_num; ------------------ | Branch (1675:23): [True: 67, False: 649] ------------------ 1676| | 1677| | /* stereo bond neighbors connection index */ 1678| 716| sb_ord1[m1] = sb_ord_m1; 1679| 716| sb_ord2[m2] = sb_ord_m2; 1680| | /* stereo bond end atom neighbors */ 1681| 716| sn_orig_at_num1[m1] = at[idelH1].orig_at_number; 1682| 716| if (idelH1 < num_at) ------------------ | Branch (1682:9): [True: 673, False: 43] ------------------ 1683| 673| { 1684| 673| if ((p1 = is_in_the_list( at[i1].neighbor, (AT_NUMB) idelH1, at[i1].valence ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1684:13): [True: 673, False: 0] ------------------ 1685| 673| { 1686| 673| sn_ord1[m1] = (int) ( p1 - at[i1].neighbor ); 1687| 673| } 1688| 0| else 1689| 0| { 1690| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1691| 0| } 1692| 673| } 1693| 43| else 1694| 43| { 1695| 43| sn_ord1[m1] = -1; 1696| 43| } 1697| | 1698| 716| sn_orig_at_num2[m2] = at[idelH2].orig_at_number; 1699| 716| if (idelH2 < num_at) ------------------ | Branch (1699:9): [True: 688, False: 28] ------------------ 1700| 688| { 1701| 688| if ((p2 = is_in_the_list( at[i2].neighbor, (AT_NUMB) idelH2, at[i2].valence ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1701:13): [True: 688, False: 0] ------------------ 1702| 688| { 1703| 688| sn_ord2[m2] = (int) ( p2 - at[i2].neighbor ); 1704| 688| } 1705| 0| else 1706| 0| { 1707| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1708| 0| } 1709| 688| } 1710| 28| else 1711| 28| { 1712| 28| sn_ord2[m2] = -1; 1713| 28| } 1714| 716| if (ATOM_PARITY_WELL_DEF( parity )) ------------------ | | 259| 716|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 716|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 716|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 716, False: 0] | | | Branch (259:75): [True: 481, False: 235] | | ------------------ ------------------ 1715| 481| { 1716| | /* special case: 2 bonds to sb atom => inverse parity because */ 1717| | /* InChI parity refers to the lone pair as a neighbor */ 1718| 481| int num_inv = ( num_neigh1 == MIN_NUM_STEREO_BOND_NEIGH ) + ( num_neigh2 == MIN_NUM_STEREO_BOND_NEIGH ); ------------------ | | 875| 481|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ int num_inv = ( num_neigh1 == MIN_NUM_STEREO_BOND_NEIGH ) + ( num_neigh2 == MIN_NUM_STEREO_BOND_NEIGH ); ------------------ | | 875| 481|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ 1719| 481| if (num_inv % 2) ------------------ | Branch (1719:13): [True: 148, False: 333] ------------------ 1720| 148| { 1721| 148| parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : AB_PARITY_EVEN; ------------------ | | 220| 148|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : AB_PARITY_EVEN; ------------------ | | 219| 37|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : AB_PARITY_EVEN; ------------------ | | 220| 259|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (1721:22): [True: 37, False: 111] ------------------ 1722| 148| } 1723| 481| parity1 = AB_PARITY_EVEN; ------------------ | | 220| 481|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ 1724| 481| parity2 = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_EVEN : AB_PARITY_ODD; ------------------ | | 220| 481|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ parity2 = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_EVEN : AB_PARITY_ODD; ------------------ | | 220| 227|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ parity2 = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_EVEN : AB_PARITY_ODD; ------------------ | | 219| 735|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (1724:19): [True: 227, False: 254] ------------------ 1725| 481| } 1726| 235| else 1727| 235| { 1728| 235| parity1 = parity2 = parity; 1729| 235| } 1730| 716| sb_parity1[m1] = parity1; 1731| 716| sb_parity2[m2] = parity2; 1732| | 1733| 716| return 0; 1734| 716|} set_atom_0D_parity: 1744| 712|{ 1745| 712| int m1 = 0, m2, i, j, tot_num_neigh; 1746| | /* the following types must exactly match types in inp_ATOM and inp_ATOM_STEREO */ 1747| | /* Given parity from InChI, the order of stereo center neighbors is: */ 1748| | /* 1. The stereocenter itself if the total number of neighbors is 3 (not 4) */ 1749| | /* 2. Explicit H: non-isotopic, isotopic in order ofascending atomic mass */ 1750| | /* Explicit H have already been sorted in this order */ 1751| | /* 3. Normal neighboring atoms, atom numbers (=canonical numbers from InChI - 1) in ascending order */ 1752| | /* Normal neighboring atoms have already been sorted in this order */ 1753| 712| S_CHAR *p_parity; 1754| 712| AT_NUMB *p_orig_at_num; 1755| | 1756| 712| if (!st || !at[i1].p_parity) ------------------ | Branch (1756:9): [True: 658, False: 54] | Branch (1756:16): [True: 54, False: 0] ------------------ 1757| 712| { 1758| 712| m1 = 0; 1759| 712| p_parity = st ? &st[i1].p_parity : &at[i1].p_parity; ------------------ | Branch (1759:20): [True: 54, False: 658] ------------------ 1760| 712| p_orig_at_num = st ? st[i1].p_orig_at_num : at[i1].p_orig_at_num; ------------------ | Branch (1760:25): [True: 54, False: 658] ------------------ 1761| | 1762| 712| tot_num_neigh = at[i1].valence + at[i1].num_H; 1763| 712| if (tot_num_neigh == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 877| 712|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1763:13): [True: 210, False: 502] ------------------ 1764| 210| { 1765| | /* only 3 neighbors: the atom itself is the first neighbor */ 1766| 210| p_orig_at_num[m1++] = at[i1].orig_at_number; 1767| 210| } 1768| 502| else 1769| 502| if (tot_num_neigh != MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 502|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1769:17): [True: 187, False: 315] ------------------ 1770| 187| { 1771| 187| return RI_ERR_PROGR; /* wrong number of members */ ------------------ | | 17| 187|#define RI_ERR_PROGR (-3) ------------------ 1772| 187| } 1773| 525| m2 = m1 + ( MAX_NUM_STEREO_ATOM_NEIGH - at[i1].valence ); ------------------ | | 877| 525|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ 1774| | /* stereoneighbors: deleted explicit atoms H first, in order of increasing isotopic mass */ 1775| 525| if (at[i1].num_H) ------------------ | Branch (1775:13): [True: 15, False: 510] ------------------ 1776| 15| { 1777| 38| for (j = 0; m1 < m2 && j < num_deleted_H; j++) ------------------ | Branch (1777:25): [True: 37, False: 1] | Branch (1777:36): [True: 23, False: 14] ------------------ 1778| 23| { 1779| 23| if (at[j + num_at].neighbor[0] == i1) ------------------ | Branch (1779:21): [True: 23, False: 0] ------------------ 1780| 23| { 1781| 23| p_orig_at_num[m1++] = at[j + num_at].orig_at_number; 1782| 23| } 1783| 23| } 1784| 15| } 1785| 525| if (m1 + at[i1].valence != MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 525|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1785:13): [True: 0, False: 525] ------------------ 1786| 0| { 1787| 0| return RI_ERR_PROGR; /* wrong number of members */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1788| 0| } 1789| | /* stereoneighbors: other than explicit H atoms */ 1790| 2.39k| for (i = 0; i < at[i1].valence; i++) ------------------ | Branch (1790:21): [True: 1.86k, False: 525] ------------------ 1791| 1.86k| { 1792| 1.86k| m2 = at[i1].neighbor[i]; 1793| 1.86k| p_orig_at_num[m1++] = at[m2].orig_at_number; 1794| 1.86k| } 1795| 525| *p_parity = parity; 1796| 525| } 1797| | 1798| 525| return 0; 1799| 712|} MoveRadToAtomsAddCharges: 1814| 87.8k|{ 1815| 87.8k| int nNumRad, ret = 0, ret2; 1816| 87.8k| int i, j, k, num_rad_not_atom, num_moved = 0, num_candidates = 0, extra_charge = 0, added_charge, delta; 1817| 87.8k| BNS_EDGE *pEdge; 1818| 87.8k| BNS_VERTEX *pv; 1819| 87.8k| Vertex v1, v2; 1820| 87.8k| S_SHORT *pnRad = NULL, *pnDelta = NULL; 1821| 87.8k| CC_CAND *pCand = NULL; 1822| 87.8k| int cnBits, bAtomRadRemoved = 0; 1823| | 1824| 87.8k| int num_at = pStruct->num_atoms; 1825| 87.8k| int num_deleted_H = pStruct->num_deleted_H; 1826| 87.8k| int len_at = num_at + num_deleted_H; 1827| 87.8k| int local_num_vertices = pBNS->num_vertices; /* djb-rwth: addressing LLVM warning */ 1828| | 1829| 632k| for (i = pBNS->num_atoms, num_rad_not_atom = 0; i < local_num_vertices; i++) ------------------ | Branch (1829:53): [True: 544k, False: 87.8k] ------------------ 1830| 544k| { 1831| 544k| num_rad_not_atom += pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow; 1832| 544k| } 1833| 87.8k| if (!num_rad_not_atom) ------------------ | Branch (1833:9): [True: 86.1k, False: 1.65k] ------------------ 1834| 86.1k| { 1835| 86.1k| goto exit_function; 1836| 86.1k| } 1837| | /****************************************************/ 1838| | /* */ 1839| | /* Move radicals from ChargeStruct to atoms */ 1840| | /* */ 1841| | /****************************************************/ 1842| | 1843| | /* allocate memory to keep track of moved radicals */ 1844| 1.65k| pnRad = (S_SHORT *) inchi_malloc(local_num_vertices * sizeof( pnRad[0] ) ); ------------------ | | 1143| 1.65k|#define inchi_malloc malloc ------------------ 1845| 1.65k| pnDelta = (S_SHORT *) inchi_calloc( pBNS->num_atoms, sizeof( pnDelta[0] ) ); ------------------ | | 1146| 1.65k|#define inchi_calloc calloc ------------------ 1846| 1.65k| if (!pnRad || !pnDelta) ------------------ | Branch (1846:9): [True: 0, False: 1.65k] | Branch (1846:19): [True: 0, False: 1.65k] ------------------ 1847| 0| { 1848| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1849| 0| goto exit_function; 1850| 0| } 1851| 35.2k| for (i = 0; i < local_num_vertices; i++) ------------------ | Branch (1851:17): [True: 33.5k, False: 1.65k] ------------------ 1852| 33.5k| { 1853| 33.5k| pnRad[i] = pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow; 1854| 33.5k| } 1855| 3.08k| while (1) ------------------ | Branch (1855:12): [True: 3.08k, Folded] ------------------ 1856| 3.08k| { 1857| | /* remove radicals from atoms */ 1858| 31.5k| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (1858:21): [True: 28.5k, False: 3.08k] ------------------ 1859| 28.5k| { 1860| 28.5k| pnDelta[i] = pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow; 1861| 28.5k| pBNS->vert[i].st_edge.cap -= pnDelta[i]; 1862| 28.5k| bAtomRadRemoved += ( 0 != pnDelta[i] ); 1863| 28.5k| } 1864| 3.08k| ret = SetRadEndpoints( pBNS, pBD, RAD_SRCH_FROM_FICT ); 1865| 3.08k| if (!ret) ------------------ | Branch (1865:13): [True: 1.65k, False: 1.43k] ------------------ 1866| 1.65k| { 1867| 1.65k| break; 1868| 1.65k| } 1869| 1.43k| if (ret < 0) ------------------ | Branch (1869:13): [True: 0, False: 1.43k] ------------------ 1870| 0| { 1871| 0| goto exit_function; 1872| 0| } 1873| 1.43k| nNumRad = ret; 1874| 2.89k| for (i = 0; i < nNumRad; i++) ------------------ | Branch (1874:21): [True: 1.45k, False: 1.43k] ------------------ 1875| 1.45k| { 1876| 1.45k| pEdge = pBNS->edge + pBD->RadEdges[i]; 1877| 1.45k| v1 = pEdge->neighbor1; 1878| 1.45k| v2 = pEdge->neighbor12 ^ v1; 1879| 1.45k| pBNS->vert[v1].st_edge.flow -= pEdge->flow; 1880| 1.45k| pBNS->vert[v2].st_edge.flow -= pEdge->flow; 1881| 1.45k| pBNS->tot_st_flow -= 2 * pEdge->flow; 1882| 1.45k| pEdge->flow = 0; 1883| 1.45k| pEdge->forbidden |= forbidden_mask; 1884| 1.45k| pBNS->edge_forbidden_mask |= forbidden_mask; 1885| 1.45k| } 1886| 1.43k| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1887| 1.43k| if (ret < 0) ------------------ | Branch (1887:13): [True: 0, False: 1.43k] ------------------ 1888| 0| { 1889| 0| goto exit_function; 1890| 0| } 1891| 1.43k| else 1892| 1.43k| { 1893| 1.43k| num_moved += ret; 1894| 1.43k| } 1895| 1.43k| RemoveRadEndpoints( pBNS, pBD, NULL ); 1896| 1.43k| if (ret == 0) ------------------ | Branch (1896:13): [True: 0, False: 1.43k] ------------------ 1897| 0| { 1898| 0| break; /* could not move more radicals */ 1899| 0| } 1900| 1.43k| if (bAtomRadRemoved) ------------------ | Branch (1900:13): [True: 407, False: 1.03k] ------------------ 1901| 407| { 1902| | /* restore radicals to atoms */ 1903| 5.58k| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (1903:25): [True: 5.17k, False: 407] ------------------ 1904| 5.17k| { 1905| 5.17k| pBNS->vert[i].st_edge.cap += pnDelta[i]; 1906| 5.17k| } 1907| 407| bAtomRadRemoved = 0; 1908| 407| } 1909| 1.43k| } 1910| 1.65k| if (bAtomRadRemoved) ------------------ | Branch (1910:9): [True: 1.32k, False: 329] ------------------ 1911| 1.32k| { 1912| | /* restore radicals to atoms */ 1913| 13.2k| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (1913:21): [True: 11.9k, False: 1.32k] ------------------ 1914| 11.9k| { 1915| 11.9k| pBNS->vert[i].st_edge.cap += pnDelta[i]; 1916| 11.9k| } 1917| | /* djb-rwth: removing redundant code */ 1918| 1.32k| } 1919| 1.65k| pBNS->edge_forbidden_mask &= ~forbidden_mask; 1920| | 1921| | 1922| | /****************************************************/ 1923| | /* */ 1924| | /* Fix the charges */ 1925| | /* */ 1926| | /****************************************************/ 1927| 1.65k| if (num_moved) ------------------ | Branch (1927:9): [True: 1.24k, False: 407] ------------------ 1928| 1.24k| { 1929| | /* find reqired charge */ 1930| 1.24k| extra_charge = 0; 1931| 14.6k| for (i = pBNS->num_atoms, pv = pBNS->vert + i; i < local_num_vertices; i++, pv++) ------------------ | Branch (1931:56): [True: 13.4k, False: 1.22k] ------------------ 1932| 13.4k| { 1933| 13.4k| if ((delta = pv->st_edge.cap - pv->st_edge.flow)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1933:17): [True: 377, False: 13.0k] ------------------ 1934| 377| { 1935| 377| if (IS_BNS_VT_C_OR_CSUPER_GR( pv->type )) ------------------ | | 77| 377|#define IS_BNS_VT_C_OR_CSUPER_GR(X) ((X) & BNS_VT_C_POS) | | ------------------ | | | | 63| 377|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 49| 377|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | | Branch (77:37): [True: 289, False: 88] | | ------------------ ------------------ 1936| 289| { 1937| 289| extra_charge -= delta; 1938| 289| } 1939| 88| else 1940| 88| if (BNS_VERT_TYPE__AUX == pv->type) ------------------ | | 53| 88|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ ------------------ | Branch (1940:25): [True: 72, False: 16] ------------------ 1941| 72| { 1942| 72| extra_charge += delta; 1943| 72| } 1944| 16| else 1945| 16| { 1946| 16| ret = RI_ERR_PROGR; ------------------ | | 17| 16|#define RI_ERR_PROGR (-3) ------------------ 1947| 16| goto exit_function; 1948| 16| } 1949| 377| } 1950| 13.4k| } 1951| 1.22k| if (!extra_charge) ------------------ | Branch (1951:13): [True: 871, False: 357] ------------------ 1952| 871| { 1953| 871| goto exit_function; 1954| 871| } 1955| | /* find differences */ 1956| 357| num_candidates = 0; 1957| 7.71k| for (i = 0; i < local_num_vertices; i++) ------------------ | Branch (1957:21): [True: 7.36k, False: 357] ------------------ 1958| 7.36k| { 1959| 7.36k| pnRad[i] = ( pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow ); /* djb-rwth: garbage values on the right side of - -- discussion required; pnRad[i] = ( pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow ) - pnRad[i]; */ 1960| 7.36k| if (pnRad[i] > 0 && i < pBNS->num_atoms && !pVA[i].nTautGroupEdge) ------------------ | Branch (1960:17): [True: 1.32k, False: 6.04k] | Branch (1960:33): [True: 962, False: 358] | Branch (1960:56): [True: 926, False: 36] ------------------ 1961| 926| { 1962| 926| num_candidates++; 1963| 926| } 1964| 7.36k| } 1965| 357| } 1966| 764| if (num_moved && num_candidates > 0) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (1966:9): [True: 357, False: 407] | Branch (1966:22): [True: 352, False: 5] ------------------ 1967| 352| { 1968| 352| pCand = (CC_CAND *) inchi_calloc( num_candidates, sizeof( pCand[0] ) ); ------------------ | | 1146| 352|#define inchi_calloc calloc ------------------ 1969| 352| if (!pCand) ------------------ | Branch (1969:13): [True: 0, False: 352] ------------------ 1970| 0| { 1971| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1972| 0| goto exit_function; 1973| 0| } 1974| | /* create atom */ 1975| 352| memcpy(at2, at, len_at * sizeof(at2[0])); 1976| 352| pStruct->at = at2; 1977| 352| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 1978| 352| pStruct->at = at; 1979| 352| if (ret2 < 0) ------------------ | Branch (1979:13): [True: 0, False: 352] ------------------ 1980| 0| { 1981| 0| ret = ret2; 1982| 0| goto exit_function; 1983| 0| } 1984| | 1985| 7.61k| for (i = 0, j = 0; i < local_num_vertices; i++) ------------------ | Branch (1985:28): [True: 7.26k, False: 352] ------------------ 1986| 7.26k| { 1987| 7.26k| if (pnRad[i] > 0 && i < pBNS->num_atoms && !pVA[i].nTautGroupEdge) ------------------ | Branch (1987:17): [True: 1.30k, False: 5.95k] | Branch (1987:33): [True: 954, False: 353] | Branch (1987:56): [True: 926, False: 28] ------------------ 1988| 926| { 1989| 926| pCand[j].iat = i; 1990| 926| pCand[j].num_bonds = at2[i].valence; 1991| 926| pCand[j].chem_valence = at2[i].chem_bonds_valence; 1992| 926| pCand[j].cMetal = pVA[i].cMetal; 1993| 926| pCand[j].cNumBondsToMetal = pVA[i].cNumBondsToMetal; 1994| 926| pCand[j].cNumValenceElectrons = pVA[i].cNumValenceElectrons; 1995| 926| pCand[j].cPeriodicRowNumber = pVA[i].cPeriodicRowNumber; 1996| 926| pCand[j].el_number = at2[i].el_number; 1997| 926| cnBits = ( pVA[i].cnListIndex > 0 ) ? cnList[pVA[i].cnListIndex - 1].bits : 0; ------------------ | Branch (1997:26): [True: 892, False: 34] ------------------ 1998| 2.54k| while (cnBits > 0) ------------------ | Branch (1998:24): [True: 1.62k, False: 926] ------------------ 1999| 1.62k| { 2000| 1.62k| pCand[j].cNumChargeStates++; 2001| 1.62k| cnBits >>= cn_bits_shift; ------------------ | | 419| 1.62k|#define cn_bits_shift 3 ------------------ 2002| 1.62k| } 2003| 926| j++; 2004| 926| } 2005| 7.26k| } 2006| 352| if (j > 1) ------------------ | Branch (2006:13): [True: 88, False: 264] ------------------ 2007| 88| { 2008| 88| qsort( pCand, j, sizeof( pCand[0] ), comp_cc_cand ); 2009| 88| } 2010| 352| added_charge = 0; 2011| | 2012| 1.27k| for (k = 0; k < j; k++) ------------------ | Branch (2012:21): [True: 926, False: 352] ------------------ 2013| 926| { 2014| 926| int rest_of_charge = extra_charge - added_charge; 2015| 926| int charge_per_left_atom = ( abs( rest_of_charge ) + j - k - 1 ) / ( j - k ); 2016| 926| int this_atom_add_charge = rest_of_charge > 0 ? charge_per_left_atom : -charge_per_left_atom; ------------------ | Branch (2016:40): [True: 263, False: 663] ------------------ 2017| 926| pVA[pCand[k].iat].cInitCharge += this_atom_add_charge; 2018| 926| added_charge += this_atom_add_charge; 2019| 926| if (this_atom_add_charge) ------------------ | Branch (2019:17): [True: 606, False: 320] ------------------ 2020| 606| { 2021| 3.67k| for (i = local_num_vertices - 1, pv = pBNS->vert + i; this_atom_add_charge && pBNS->num_atoms <= i; i--, pv--) ------------------ | Branch (2021:71): [True: 3.07k, False: 606] | Branch (2021:95): [True: 3.07k, False: 0] ------------------ 2022| 3.07k| { 2023| 3.07k| if ((delta = pv->st_edge.cap - pv->st_edge.flow)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2023:25): [True: 610, False: 2.46k] ------------------ 2024| 610| { 2025| 610| if (this_atom_add_charge < 0 && IS_BNS_VT_C_OR_CSUPER_GR( pv->type )) ------------------ | | 77| 347|#define IS_BNS_VT_C_OR_CSUPER_GR(X) ((X) & BNS_VT_C_POS) | | ------------------ | | | | 63| 347|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 49| 347|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | | Branch (77:37): [True: 347, False: 0] | | ------------------ ------------------ | Branch (2025:29): [True: 347, False: 263] ------------------ 2026| 347| { 2027| 347| if (delta + this_atom_add_charge > 0) ------------------ | Branch (2027:33): [True: 59, False: 288] ------------------ 2028| 59| { 2029| 59| delta = -this_atom_add_charge; 2030| 59| } 2031| 347| pv->st_edge.cap -= delta; 2032| 347| pBNS->tot_st_cap -= delta; 2033| 347| this_atom_add_charge += delta; 2034| 347| } 2035| 263| else 2036| 263| { 2037| 263| if (this_atom_add_charge > 0 && BNS_VERT_TYPE__AUX == pv->type) ------------------ | | 53| 263|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ ------------------ | Branch (2037:33): [True: 263, False: 0] | Branch (2037:61): [True: 263, False: 0] ------------------ 2038| 263| { 2039| 263| if (delta > this_atom_add_charge) ------------------ | Branch (2039:37): [True: 195, False: 68] ------------------ 2040| 195| { 2041| 195| delta = this_atom_add_charge; 2042| 195| } 2043| 263| pv->st_edge.cap -= delta; 2044| 263| pBNS->tot_st_cap -= delta; 2045| 263| this_atom_add_charge -= delta; 2046| 263| } 2047| 263| } 2048| 610| } 2049| 3.07k| } 2050| 606| } 2051| 926| } 2052| 352| } 2053| | 2054| 87.8k|exit_function: 2055| 87.8k| if (pnRad) ------------------ | Branch (2055:9): [True: 1.65k, False: 86.1k] ------------------ 2056| 1.65k| { 2057| 1.65k| inchi_free( pnRad ); ------------------ | | 1152| 1.65k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.65k, False: 0] | | | Branch (1152:50): [Folded, False: 1.65k] | | ------------------ ------------------ 2058| 1.65k| } 2059| 87.8k| if (pnDelta) ------------------ | Branch (2059:9): [True: 1.65k, False: 86.1k] ------------------ 2060| 1.65k| { 2061| 1.65k| inchi_free( pnDelta ); ------------------ | | 1152| 1.65k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.65k, False: 0] | | | Branch (1152:50): [Folded, False: 1.65k] | | ------------------ ------------------ 2062| 1.65k| } 2063| 87.8k| if (pCand) ------------------ | Branch (2063:9): [True: 352, False: 87.4k] ------------------ 2064| 352| { 2065| 352| inchi_free( pCand ); ------------------ | | 1152| 352|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 352, False: 0] | | | Branch (1152:50): [Folded, False: 352] | | ------------------ ------------------ 2066| 352| } 2067| | 2068| 87.8k| return ret; 2069| 764|} AdjustTgroupsToForbiddenEdges2: 2104| 486|{ 2105| 486| int i, j, k; 2106| 486| int centerpoint_type, neigh_type; 2107| 486| int num_changes; 2108| 486| int num_donors, num_acceptors, num_donor_endpoints, num_acceptor_endpoints; 2109| 486| int neigh, tg_number, num_eql_mobile_gr, num_dif_mobile_gr, bond_type, has_mobile_H; /* djb-rwth: removing redundant variables */ 2110| 486| int num_forbidden, ind_forbidden, forbidden, num_N, num_O, num_P, num_S, num_OSt; 2111| 486| int val, delta_val, delta_met, num_bonds_non_metal, bonds_valence_non_metal; 2112| | /* djb-rwth: removing redundant variables */ 2113| 486| int inv_forbidden_mask = ~forbidden_mask; 2114| 486| MOBILE_GR MobileGr[MAXVAL]; 2115| 486| int num_endpoints; 2116| 486| MGROUPS MGroups[MAXVAL]; 2117| 486| int num_mgroups, num_diff_t_groups; 2118| 486| BNS_EDGE *e, *e1, *e2, *ev, *ev1, *ev2; 2119| 486| BNS_VERTEX *pv1, *pv2; 2120| 486| num_changes = 0; 2121| | /* search for possible centerpoints */ 2122| 4.59k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (2122:17): [True: 4.10k, False: 486] ------------------ 2123| 4.10k| { 2124| | 2125| 4.10k| if (at[i].chem_bonds_valence == at[i].valence || at[i].num_H || ------------------ | Branch (2125:13): [True: 2.68k, False: 1.42k] | Branch (2125:58): [True: 44, False: 1.38k] ------------------ 2126| 1.38k| at[i].endpoint || at[i].charge || at[i].radical || ------------------ | Branch (2126:14): [True: 340, False: 1.04k] | Branch (2126:32): [True: 313, False: 729] | Branch (2126:48): [True: 37, False: 692] ------------------ 2127| 692| !is_centerpoint_elem( at[i].el_number ) || ------------------ | Branch (2127:14): [True: 121, False: 571] ------------------ 2128| 571| !( centerpoint_type = get_pVA_atom_type( pVA, at, i, 0 ) ) || ------------------ | Branch (2128:14): [True: 0, False: 571] ------------------ 2129| 571| 2 > ( delta_val = at[i].chem_bonds_valence - ( val = get_el_valence( at[i].el_number, 0, 0 ) ) ) || ------------------ | Branch (2129:14): [True: 299, False: 272] ------------------ 2130| 272| 2 > ( delta_met = ( bonds_valence_non_metal = nNoMetalBondsValence( at, i ) ) - val ) ------------------ | Branch (2130:14): [True: 4, False: 268] ------------------ 2131| 4.10k| ) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 2132| 3.83k| { 2133| 3.83k| continue; 2134| 3.83k| } 2135| | 2136| 268| num_donors = num_acceptors = num_donor_endpoints = num_acceptor_endpoints = 0; 2137| 268| num_mgroups = num_endpoints = num_diff_t_groups = 0; 2138| 268| has_mobile_H = num_eql_mobile_gr = num_dif_mobile_gr = tg_number = 0; /* djb-rwth: removing redundant code */ 2139| 268| ind_forbidden = -1; 2140| 268| num_forbidden = 0; 2141| 268| num_N = num_O = num_P = num_S = num_OSt = 0; 2142| 268| num_bonds_non_metal = nNoMetalNumBonds( at, i ); 2143| | /* djb-rwth: removing redundant code */ 2144| | /* djb-rwth: removing redundant code */ 2145| | 2146| 1.11k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (2146:21): [True: 850, False: 268] ------------------ 2147| 850| { 2148| | /* collect neighbors info */ 2149| 850| neigh = at[i].neighbor[j]; 2150| 850| val = get_endpoint_valence( at[neigh].el_number ); 2151| 850| forbidden = pBNS->edge[(int) pBNS->vert[i].iedge[j]].forbidden; 2152| 850| bond_type = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 189| 850|#define BOND_TYPE_MASK 0x0f ------------------ 2153| 850| neigh_type = get_pVA_atom_type( pVA, at, neigh, bond_type ); 2154| 850| if (!forbidden && !at[neigh].endpoint) ------------------ | Branch (2154:17): [True: 761, False: 89] | Branch (2154:31): [True: 481, False: 280] ------------------ 2155| 481| { 2156| | /* save forbidden bonds */ 2157| 481| if (is_el_a_metal( at[neigh].el_number )) ------------------ | Branch (2157:21): [True: 44, False: 437] ------------------ 2158| 44| { 2159| 44| continue; 2160| 44| } 2161| 437| switch (bond_type) 2162| 437| { 2163| 213| case BOND_TYPE_SINGLE: ------------------ | | 32| 213|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2163:21): [True: 213, False: 224] ------------------ 2164| 213| if (!at[neigh].num_H && at[neigh].charge != -1) ------------------ | Branch (2164:29): [True: 213, False: 0] | Branch (2164:49): [True: 179, False: 34] ------------------ 2165| 179| { 2166| 179| continue; /* not a donor */ 2167| 179| } 2168| 34| break; 2169| 186| case BOND_TYPE_DOUBLE: ------------------ | | 33| 186|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2169:21): [True: 186, False: 251] ------------------ 2170| 186| if (!neigh_type) ------------------ | Branch (2170:29): [True: 1, False: 185] ------------------ 2171| 1| { 2172| 1| continue; 2173| 1| } 2174| 185| break; 2175| 185| default: ------------------ | Branch (2175:21): [True: 38, False: 399] ------------------ 2176| 38| continue; 2177| 437| } 2178| 437| } 2179| | 2180| 588| MobileGr[num_endpoints].atom_number = neigh; 2181| 588| MobileGr[num_endpoints].ineigh = j; 2182| 588| MobileGr[num_endpoints].bond_type = bond_type; 2183| 588| MobileGr[num_endpoints].group_number = at[neigh].endpoint; 2184| 588| MobileGr[num_endpoints].endpoint_valence = val; 2185| 588| MobileGr[num_endpoints].forbidden = forbidden; 2186| 588| MobileGr[num_endpoints].atom_type_pVA = neigh_type; 2187| 588| MobileGr[num_endpoints].num_bonds = at[neigh].valence; 2188| 588| MobileGr[num_endpoints].bonds_valence = at[neigh].chem_bonds_valence; 2189| 588| MobileGr[num_endpoints].num_bonds_non_metal = nNoMetalNumBonds( at, neigh ); 2190| 588| MobileGr[num_endpoints].bonds_valence_non_metal = nNoMetalBondsValence( at, neigh ); 2191| | 2192| 588| if (forbidden & forbidden_mask) ------------------ | Branch (2192:17): [True: 87, False: 501] ------------------ 2193| 87| { 2194| 87| num_forbidden++; 2195| 87| ind_forbidden = num_endpoints; 2196| 87| } 2197| 588| num_O += 0 != ( neigh_type & EL_TYPE_O ) && at[neigh].valence == 1; /* ignore -O- */ ------------------ | | 386| 588|#define EL_TYPE_O 0x0001 ------------------ | Branch (2197:22): [True: 124, False: 464] | Branch (2197:57): [True: 109, False: 15] ------------------ 2198| 588| num_N += 0 != ( neigh_type & EL_TYPE_N ) && ------------------ | | 388| 588|#define EL_TYPE_N 0x0004 ------------------ | Branch (2198:22): [True: 229, False: 359] ------------------ 2199| 229| !( at[neigh].valence == 3 && at[neigh].chem_bonds_valence == 3 ); /* ignore -N< */ ------------------ | Branch (2199:20): [True: 24, False: 205] | Branch (2199:46): [True: 10, False: 14] ------------------ 2200| 588| num_S += 0 != ( neigh_type & EL_TYPE_S ) && at[neigh].valence == 1; /* ignore -S- */ ------------------ | | 387| 588|#define EL_TYPE_S 0x0002 ------------------ | Branch (2200:22): [True: 123, False: 465] | Branch (2200:57): [True: 78, False: 45] ------------------ 2201| 588| num_P += 0 != ( neigh_type & EL_TYPE_P ) && ------------------ | | 389| 588|#define EL_TYPE_P 0x0008 ------------------ | Branch (2201:22): [True: 41, False: 547] ------------------ 2202| 41| !( at[neigh].valence == 3 && at[neigh].chem_bonds_valence == 3 ); /* ignore -P< */ ------------------ | Branch (2202:20): [True: 12, False: 29] | Branch (2202:46): [True: 3, False: 9] ------------------ 2203| 588| num_OSt += 0 != ( neigh_type & EL_TYPE_OSt ); ------------------ | | 393| 588|#define EL_TYPE_OSt 0x0100 /* terminal -OH, -O(-), -SH, -S(-), ... from fix_special_bonds(...) */ ------------------ 2204| 588| num_acceptors += ( bond_type == BOND_TYPE_DOUBLE ) && ( neigh_type & EL_TYPE_PT ); ------------------ | | 33| 588|#define BOND_TYPE_DOUBLE 2 ------------------ num_acceptors += ( bond_type == BOND_TYPE_DOUBLE ) && ( neigh_type & EL_TYPE_PT ); ------------------ | | 394| 354|#define EL_TYPE_PT 0x0200 /* may be a tautomeric endpoint */ ------------------ | Branch (2204:30): [True: 354, False: 234] | Branch (2204:67): [True: 228, False: 126] ------------------ 2205| 588| num_donors += ( bond_type == BOND_TYPE_SINGLE ) && ( neigh_type & EL_TYPE_PT ) && ------------------ | | 32| 588|#define BOND_TYPE_SINGLE 1 ------------------ num_donors += ( bond_type == BOND_TYPE_SINGLE ) && ( neigh_type & EL_TYPE_PT ) && ------------------ | | 394| 227|#define EL_TYPE_PT 0x0200 /* may be a tautomeric endpoint */ ------------------ | Branch (2205:27): [True: 227, False: 361] | Branch (2205:64): [True: 128, False: 99] ------------------ 2206| 128| ( at[neigh].num_H || at[neigh].charge == -1 || at[neigh].endpoint ); ------------------ | Branch (2206:19): [True: 21, False: 107] | Branch (2206:38): [True: 59, False: 48] | Branch (2206:64): [True: 47, False: 1] ------------------ 2207| 588| if (at[neigh].endpoint) ------------------ | Branch (2207:17): [True: 315, False: 273] ------------------ 2208| 315| { 2209| 315| num_acceptor_endpoints += ( bond_type == BOND_TYPE_DOUBLE ); ------------------ | | 33| 315|#define BOND_TYPE_DOUBLE 2 ------------------ 2210| 315| num_donor_endpoints += ( bond_type == BOND_TYPE_SINGLE ); ------------------ | | 32| 315|#define BOND_TYPE_SINGLE 1 ------------------ 2211| 315| if (!tg_number) ------------------ | Branch (2211:21): [True: 207, False: 108] ------------------ 2212| 207| { 2213| 207| tg_number = at[neigh].endpoint; 2214| 207| num_eql_mobile_gr = 1; 2215| 207| } 2216| 108| else 2217| 108| { 2218| 108| if (tg_number == at[neigh].endpoint) ------------------ | Branch (2218:25): [True: 101, False: 7] ------------------ 2219| 101| { 2220| 101| num_eql_mobile_gr++; 2221| 101| } 2222| 7| else 2223| 7| { 2224| 7| num_dif_mobile_gr++; 2225| 7| } 2226| 108| } 2227| 315| } 2228| 273| else 2229| 273| { 2230| 273| if (bond_type == BOND_TYPE_SINGLE && val) ------------------ | | 32| 546|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2230:21): [True: 61, False: 212] | Branch (2230:54): [True: 49, False: 12] ------------------ 2231| 49| { 2232| 49| if (at[neigh].endpoint) ------------------ | Branch (2232:25): [True: 0, False: 49] ------------------ 2233| 0| { 2234| 0| has_mobile_H |= 1; 2235| | /* djb-rwth: removing redundant code */ 2236| 0| } 2237| 49| else 2238| 49| { 2239| 49| has_mobile_H |= ( 0 != at[neigh].num_H ); 2240| | /* djb-rwth: removing redundant code */ 2241| 49| } 2242| 49| } 2243| 273| } 2244| 588| num_endpoints++; 2245| | 2246| 588| if (at[neigh].endpoint || ( neigh_type & EL_TYPE_PT )) ------------------ | | 394| 273|#define EL_TYPE_PT 0x0200 /* may be a tautomeric endpoint */ ------------------ | Branch (2246:17): [True: 315, False: 273] | Branch (2246:39): [True: 138, False: 135] ------------------ 2247| 453| { 2248| 563| for (k = 0; k < num_mgroups; k++) ------------------ | Branch (2248:29): [True: 237, False: 326] ------------------ 2249| 237| { 2250| 237| if (MGroups[k].group_number == at[neigh].endpoint) ------------------ | Branch (2250:25): [True: 127, False: 110] ------------------ 2251| 127| { 2252| 127| MGroups[k].num++; 2253| 127| break; 2254| 127| } 2255| 237| } 2256| 453| if (k == num_mgroups) ------------------ | Branch (2256:21): [True: 326, False: 127] ------------------ 2257| 326| { 2258| 326| MGroups[k].group_number = at[neigh].endpoint; 2259| 326| MGroups[k].num = 1; 2260| 326| num_mgroups++; 2261| 326| num_diff_t_groups += ( 0 != at[neigh].endpoint ); 2262| 326| } 2263| 453| } 2264| 588| } 2265| 268| if (!num_acceptors || !num_donors || /* num_acceptors > 2 ||*/ ------------------ | Branch (2265:13): [True: 108, False: 160] | Branch (2265:31): [True: 79, False: 81] ------------------ 2266| 81| (num_eql_mobile_gr == num_endpoints && !num_forbidden) || ------------------ | Branch (2266:15): [True: 16, False: 65] | Branch (2266:53): [True: 4, False: 12] ------------------ 2267| 77| (!tg_number && !has_mobile_H)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2267:15): [True: 5, False: 72] | Branch (2267:29): [True: 5, False: 0] ------------------ 2268| 196| { 2269| 196| continue; /* nothing to do */ 2270| 196| } 2271| | 2272| | /* case_5_1: */ 2273| | /***************** determine the case ************************/ 2274| 72| if (3 == num_bonds_non_metal && ------------------ | Branch (2274:13): [True: 35, False: 37] ------------------ 2275| 35| 4 == bonds_valence_non_metal && ------------------ | Branch (2275:14): [True: 23, False: 12] ------------------ 2276| 23| ( centerpoint_type == EL_TYPE_C ) && ------------------ | | 390| 23|#define EL_TYPE_C 0x0010 ------------------ | Branch (2276:14): [True: 0, False: 23] ------------------ 2277| 0| 2 == num_O && 1 == num_N + num_S && num_OSt && ------------------ | Branch (2277:14): [True: 0, False: 0] | Branch (2277:28): [True: 0, False: 0] | Branch (2277:50): [True: 0, False: 0] ------------------ 2278| 0| 1 == num_forbidden && 3 == num_eql_mobile_gr) ------------------ | Branch (2278:14): [True: 0, False: 0] | Branch (2278:36): [True: 0, False: 0] ------------------ 2279| 0| { 2280| | /******************************************************** 2281| | *** InChI Tech. Man., Table 5, case 1 *** 2282| | ******************************************************** 2283| | 2 2284| | OH OH X = N, S, Se, Te 2285| | / / f = fixed bond 2286| | e / / tg = Mobile-H vertex 2287| | HX---C --> X===C 2288| | ev2|| f \\ ev1 f \ 2289| | || \\ \ 2290| | tg------O OH 2291| | 1 2292| | Problem: 2293| | XH, O, and O belong to the same Mobile-H group. 2294| | Fixed bond prevents the correct structure restoration: 2295| | H cannot migrate from X to O because HX-N bond is fixed 2296| | Solution: 2297| | Move H from X to allow XH-C bond change 2298| | (this unfixes the bond, see SetForbiddenEdges(...) ) 2299| | *********************************************************/ 2300| 0| int jXH = -1, jO1 = -1, jO2 = -1, n = 0; 2301| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2301:25): [True: 0, False: 0] ------------------ 2302| 0| { 2303| 0| if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_S ) ) && ------------------ | | 388| 0|#define EL_TYPE_N 0x0004 ------------------ if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_S ) ) && ------------------ | | 387| 0|#define EL_TYPE_S 0x0002 ------------------ | Branch (2303:21): [True: 0, False: 0] ------------------ 2304| 0| ( MobileGr[j].forbidden == forbidden_mask ) && ------------------ | Branch (2304:21): [True: 0, False: 0] ------------------ 2305| 0| MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2305:22): [True: 0, False: 0] ------------------ 2306| 0| jXH < 0) ------------------ | Branch (2306:22): [True: 0, False: 0] ------------------ 2307| 0| { 2308| 0| jXH = j; 2309| 0| n++; 2310| 0| } 2311| 0| else 2312| 0| { 2313| 0| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_O && ------------------ | | 392| 0|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_O && ------------------ | | 386| 0|#define EL_TYPE_O 0x0001 ------------------ | Branch (2313:25): [True: 0, False: 0] ------------------ 2314| 0| MobileGr[j].num_bonds_non_metal == 1 && ------------------ | Branch (2314:29): [True: 0, False: 0] ------------------ 2315| 0| !MobileGr[j].forbidden) ------------------ | Branch (2315:29): [True: 0, False: 0] ------------------ 2316| 0| { 2317| 0| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && jO1 < 0) ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2317:29): [True: 0, False: 0] | Branch (2317:74): [True: 0, False: 0] ------------------ 2318| 0| { 2319| 0| jO1 = j; 2320| 0| n++; 2321| 0| } 2322| 0| else 2323| 0| { 2324| 0| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && jO2 < 0) ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2324:33): [True: 0, False: 0] | Branch (2324:78): [True: 0, False: 0] ------------------ 2325| 0| { 2326| 0| jO2 = j; 2327| 0| n++; 2328| 0| } 2329| 0| } 2330| 0| } 2331| 0| } 2332| 0| } 2333| 0| if (n != 3) ------------------ | Branch (2333:17): [True: 0, False: 0] ------------------ 2334| 0| { 2335| 0| goto case_5_2; 2336| 0| } 2337| | /* XH-C edge */ 2338| 0| e = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jXH].ineigh]; 2339| | /* C=O edge */ 2340| 0| ev1 = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jO1].ineigh]; 2341| | /* XH-tg edge */ 2342| 0| ev2 = pBNS->edge + pVA[MobileGr[jXH].atom_number].nTautGroupEdge - 1; 2343| | 2344| 0| if (!ev1->flow || !ev2->flow) ------------------ | Branch (2344:17): [True: 0, False: 0] | Branch (2344:31): [True: 0, False: 0] ------------------ 2345| 0| { 2346| 0| goto case_5_2; 2347| 0| } 2348| | 2349| | /* do not remove forbidden edge bit */ 2350| 0| e->flow++; 2351| 0| ev1->flow--; 2352| 0| ev2->flow--; 2353| 0| pBNS->vert[ev1->neighbor12 ^ i].st_edge.flow--; 2354| 0| pBNS->vert[ev2->neighbor12 ^ ev2->neighbor1].st_edge.flow--; 2355| 0| pBNS->tot_st_flow -= 2; 2356| 0| num_changes++; 2357| 0| continue; 2358| 0| } 2359| 72| case_5_2: 2360| | /*********************************************************************/ 2361| 72| if (3 == num_bonds_non_metal && ------------------ | Branch (2361:13): [True: 35, False: 37] ------------------ 2362| 35| 5 == bonds_valence_non_metal && ------------------ | Branch (2362:14): [True: 12, False: 23] ------------------ 2363| 12| ( centerpoint_type == EL_TYPE_N ) && ------------------ | | 388| 12|#define EL_TYPE_N 0x0004 ------------------ | Branch (2363:14): [True: 8, False: 4] ------------------ 2364| 8| 2 == num_O && 1 == num_N + num_S && ------------------ | Branch (2364:14): [True: 2, False: 6] | Branch (2364:28): [True: 2, False: 0] ------------------ 2365| 2| 1 == num_forbidden && 3 == num_eql_mobile_gr) ------------------ | Branch (2365:14): [True: 2, False: 0] | Branch (2365:36): [True: 1, False: 1] ------------------ 2366| 1| { 2367| | /******************************************************** 2368| | *** InChI Tech. Man., Table 5, case 2 *** 2369| | ******************************************************** 2370| | 2371| | O OH X = N, S, Se, Te 2372| | // / f = fixed bond 2373| | e // / tg = Mobile-H vertex 2374| | HX---N --> X===N 2375| | ev2|| f \\ ev1 f \\ 2376| | || \\ \\ 2377| | tg------O O 2378| | 2379| | Problem: 2380| | XH, O, and O belong to the same Mobile-H group. 2381| | Fixed bond prevents the correct structure restoration: 2382| | H cannot migrate from X to O because HX-N bond is fixed 2383| | Solution: 2384| | Move H from X to allow XH-N bond change 2385| | (this unfixes the bond, see SetForbiddenEdges(...) ) 2386| | *********************************************************/ 2387| 1| int jXH = -1, jO1 = -1, jO2 = -1, n = 0; 2388| 4| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2388:25): [True: 3, False: 1] ------------------ 2389| 3| { 2390| 3| if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_S ) ) && ------------------ | | 388| 3|#define EL_TYPE_N 0x0004 ------------------ if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_S ) ) && ------------------ | | 387| 3|#define EL_TYPE_S 0x0002 ------------------ | Branch (2390:21): [True: 1, False: 2] ------------------ 2391| 1| ( MobileGr[j].forbidden == forbidden_mask ) && ------------------ | Branch (2391:21): [True: 1, False: 0] ------------------ 2392| 1| MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 4|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2392:22): [True: 1, False: 0] ------------------ 2393| 1| jXH < 0) ------------------ | Branch (2393:22): [True: 1, False: 0] ------------------ 2394| 1| { 2395| 1| jXH = j; 2396| 1| n++; 2397| 1| } 2398| 2| else 2399| 2| { 2400| 2| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_O && ------------------ | | 392| 2|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_O && ------------------ | | 386| 4|#define EL_TYPE_O 0x0001 ------------------ | Branch (2400:25): [True: 2, False: 0] ------------------ 2401| 2| MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 4|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2401:29): [True: 2, False: 0] ------------------ 2402| 2| MobileGr[j].num_bonds_non_metal == 1 && ------------------ | Branch (2402:29): [True: 2, False: 0] ------------------ 2403| 2| !MobileGr[j].forbidden) ------------------ | Branch (2403:29): [True: 2, False: 0] ------------------ 2404| 2| { 2405| 2| if (jO1 < 0) ------------------ | Branch (2405:29): [True: 1, False: 1] ------------------ 2406| 1| { 2407| 1| jO1 = j; 2408| 1| n++; 2409| 1| } 2410| 1| else 2411| 1| { 2412| 1| if (jO2 < 0) ------------------ | Branch (2412:33): [True: 1, False: 0] ------------------ 2413| 1| { 2414| 1| jO2 = j; 2415| 1| n++; 2416| 1| } 2417| 1| } 2418| 2| } 2419| 2| } 2420| 3| } 2421| 1| if (n != 3) ------------------ | Branch (2421:17): [True: 0, False: 1] ------------------ 2422| 0| { 2423| 0| goto case_5_4; 2424| 0| } 2425| | /* XH-N edge */ 2426| 1| e = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jXH].ineigh]; 2427| | /* N=O edge */ 2428| 1| ev1 = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jO1].ineigh]; 2429| | /* XH-tg edge */ 2430| 1| ev2 = pBNS->edge + pVA[MobileGr[jXH].atom_number].nTautGroupEdge - 1; 2431| | 2432| 1| if (!ev1->flow || !ev2->flow) ------------------ | Branch (2432:17): [True: 0, False: 1] | Branch (2432:31): [True: 1, False: 0] ------------------ 2433| 1| { 2434| 1| goto case_5_4; 2435| 1| } 2436| | /* do not remove forbidden edge bit */ 2437| 0| e->flow++; 2438| 0| ev1->flow--; 2439| 0| ev2->flow--; 2440| 0| pBNS->vert[ev1->neighbor12 ^ i].st_edge.flow--; /* first =O vertex */ 2441| 0| pBNS->vert[ev2->neighbor12 ^ ev2->neighbor1].st_edge.flow--; /* taut group vertex tg */ 2442| 0| pBNS->tot_st_flow -= 2; 2443| 0| num_changes++; 2444| 0| continue; 2445| 1| } 2446| | 2447| 72| case_5_4: 2448| | /*********************************************************************/ 2449| 72| if (3 == num_bonds_non_metal && ------------------ | Branch (2449:13): [True: 35, False: 37] ------------------ 2450| 35| 5 == bonds_valence_non_metal && ------------------ | Branch (2450:14): [True: 12, False: 23] ------------------ 2451| 12| ( centerpoint_type & ( EL_TYPE_N | EL_TYPE_P ) ) && ------------------ | | 388| 12|#define EL_TYPE_N 0x0004 ------------------ ( centerpoint_type & ( EL_TYPE_N | EL_TYPE_P ) ) && ------------------ | | 389| 12|#define EL_TYPE_P 0x0008 ------------------ | Branch (2451:14): [True: 11, False: 1] ------------------ 2452| 11| 1 == num_O + num_S && 0 < num_N && 2 == ( num_N + num_P ) && ------------------ | Branch (2452:14): [True: 4, False: 7] | Branch (2452:36): [True: 4, False: 0] | Branch (2452:49): [True: 2, False: 2] ------------------ 2453| 2| 1 == num_forbidden && num_O + num_S + num_N == num_eql_mobile_gr) ------------------ | Branch (2453:14): [True: 2, False: 0] | Branch (2453:36): [True: 1, False: 1] ------------------ 2454| 1| { 2455| | /******************************************************** 2456| | *** InChI Tech. Man., Table 5, case 4 *** 2457| | ******************************************************** 2458| | O = O, S, Se, Te 2459| | X X X = N, P, As 2460| | // // f = fixed bond 2461| | e // ev2 // tg = Mobile-H vertex 2462| | O===N --> HO---N 2463| | || f \ ev1 f \\ 2464| | || \ \\ 2465| | tg------NH N 2466| | 2467| | Problem: 2468| | O, NH, and possibly X belong to the same Mobile-H group. 2469| | Fixed bond prevents the correct structure restoration: 2470| | H cannot migrate from NH to O because O=N bond is fixed 2471| | Solution: 2472| | Move H from NH to O to allow O=N bond change 2473| | (this unfixes the bond, see fix_special_bonds(...) ) 2474| | *********************************************************/ 2475| 1| int jO = -1, jNH = -1, jX = -1, n = 0; 2476| 4| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2476:25): [True: 3, False: 1] ------------------ 2477| 3| { 2478| 3| if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 386| 3|#define EL_TYPE_O 0x0001 ------------------ if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 387| 3|#define EL_TYPE_S 0x0002 ------------------ | Branch (2478:21): [True: 1, False: 2] ------------------ 2479| 1| MobileGr[j].forbidden == forbidden_mask && ------------------ | Branch (2479:22): [True: 1, False: 0] ------------------ 2480| 1| MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 4|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2480:22): [True: 1, False: 0] ------------------ 2481| 1| MobileGr[j].num_bonds_non_metal == 1 && ------------------ | Branch (2481:22): [True: 1, False: 0] ------------------ 2482| 1| jO < 0) ------------------ | Branch (2482:22): [True: 1, False: 0] ------------------ 2483| 1| { 2484| 1| jO = j; 2485| 1| n++; 2486| 1| } 2487| 2| else 2488| 2| { 2489| 2| if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_P ) ) && ------------------ | | 388| 2|#define EL_TYPE_N 0x0004 ------------------ if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_P ) ) && ------------------ | | 389| 2|#define EL_TYPE_P 0x0008 ------------------ | Branch (2489:25): [True: 2, False: 0] ------------------ 2490| 2| !MobileGr[j].forbidden) ------------------ | Branch (2490:29): [True: 2, False: 0] ------------------ 2491| 2| { 2492| 2| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 4|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2492:29): [True: 1, False: 1] ------------------ 2493| 1| ( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && jNH < 0) ------------------ | | 392| 1|#define EL_TYPE_MASK 0x003f ------------------ ( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && jNH < 0) ------------------ | | 388| 3|#define EL_TYPE_N 0x0004 ------------------ | Branch (2493:29): [True: 1, False: 0] | Branch (2493:90): [True: 1, False: 0] ------------------ 2494| 1| { 2495| 1| jNH = j; 2496| 1| n++; 2497| 1| } 2498| 1| else 2499| 1| { 2500| 1| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && jX < 0) ------------------ | | 33| 2|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2500:33): [True: 1, False: 0] | Branch (2500:78): [True: 1, False: 0] ------------------ 2501| 1| { 2502| 1| jX = j; 2503| 1| n++; 2504| 1| } 2505| 1| } 2506| 2| } 2507| 2| } 2508| 3| } 2509| 1| if (n != 3) ------------------ | Branch (2509:17): [True: 0, False: 1] ------------------ 2510| 0| { 2511| 0| goto case_5_6; 2512| 0| } 2513| | /* O=N edge */ 2514| 1| e = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jO].ineigh]; 2515| | /* N-NH edge */ 2516| 1| ev1 = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jNH].ineigh]; 2517| | /* N=X edge */ 2518| 1| ev2 = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jX].ineigh]; 2519| | 2520| 1| if (!e->flow) ------------------ | Branch (2520:17): [True: 0, False: 1] ------------------ 2521| 0| { 2522| 0| goto case_5_6; 2523| 0| } 2524| | /* do not remove forbidden edge bit */ 2525| 1| e->flow--; 2526| 1| ev1->flow++; 2527| 1| pBNS->vert[e->neighbor12 ^ i].st_edge.flow--; 2528| 1| pBNS->vert[ev1->neighbor12 ^ i].st_edge.flow--; 2529| 1| pBNS->tot_st_flow -= 2; 2530| 1| num_changes++; 2531| 1| continue; 2532| 1| } 2533| 71| case_5_6: 2534| | /********* InChI Tech.Man. Table 5, case 6 **************/ 2535| 71| if (2 == delta_met && 4 == num_bonds_non_metal && ------------------ | Branch (2535:13): [True: 57, False: 14] | Branch (2535:31): [True: 22, False: 35] ------------------ 2536| 22| 5 == bonds_valence_non_metal && ------------------ | Branch (2536:14): [True: 22, False: 0] ------------------ 2537| 22| 1 == num_forbidden && 1 < num_eql_mobile_gr && ------------------ | Branch (2537:14): [True: 9, False: 13] | Branch (2537:36): [True: 8, False: 1] ------------------ 2538| 8| !num_dif_mobile_gr && ------------------ | Branch (2538:14): [True: 8, False: 0] ------------------ 2539| 8| ( centerpoint_type & ( EL_TYPE_N | EL_TYPE_P ) ) && ------------------ | | 388| 8|#define EL_TYPE_N 0x0004 ------------------ ( centerpoint_type & ( EL_TYPE_N | EL_TYPE_P ) ) && ------------------ | | 389| 8|#define EL_TYPE_P 0x0008 ------------------ | Branch (2539:14): [True: 8, False: 0] ------------------ 2540| 8| 1 <= num_N && 2 <= num_N + num_O + num_S && ------------------ | Branch (2540:14): [True: 8, False: 0] | Branch (2540:28): [True: 8, False: 0] ------------------ 2541| 8| 1 == num_acceptor_endpoints && 0 < num_donor_endpoints) ------------------ | Branch (2541:14): [True: 7, False: 1] | Branch (2541:45): [True: 7, False: 0] ------------------ 2542| 7| { 2543| 7| int jN = -1, njFix = 0, jFix[4], n = 0; 2544| | /* centerpoint is N, P, As, Sb 2545| | 2546| | input output 2547| | ----- ------ 2548| | end 2549| | po- 2550| | int 2551| | 2 2552| | 2553| | X ZH X Z Z=N,O,S,Se,Te [terminal endpoint] 2554| | \ | \ || 2555| | \| f f \|| 2556| | Y---N===N--- Y---N---NH--- 2557| | e f 2558| | cen end no bond 2559| | ter po- fixed 2560| | po- int 2561| | int 1 tautomerism O==N--NH is allowed 2562| | 2563| | Problem: OH and =N- belong to a Mobile-H group, but 2564| | forbidden edge e does not allow them to be 2565| | tautomeric in the restored structure. 2566| | 2567| | Solution: 2568| | 2569| | 1. Decrement flow in edge e 2570| | 2. Decrement st_edge flow in N and N connected by e 2571| | 3. Fix all single order bonds to not terminal tautomeric N around N(centerpoint) 2572| | 4. Run BNS to establist new flow distribution 2573| | */ 2574| | 2575| | /* fixed bond */ 2576| 30| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2576:25): [True: 23, False: 7] ------------------ 2577| 23| { 2578| 23| neigh = MobileGr[j].atom_number; 2579| 23| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 46|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2579:21): [True: 7, False: 16] ------------------ 2580| 7| ( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 392| 7|#define EL_TYPE_MASK 0x003f ------------------ ( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 388| 30|#define EL_TYPE_N 0x0004 ------------------ | Branch (2580:21): [True: 6, False: 1] ------------------ 2581| 6| MobileGr[j].num_bonds_non_metal == 2 && ------------------ | Branch (2581:22): [True: 6, False: 0] ------------------ 2582| 6| MobileGr[j].bonds_valence_non_metal == 3 && ------------------ | Branch (2582:22): [True: 6, False: 0] ------------------ 2583| 6| at[neigh].endpoint && ------------------ | Branch (2583:22): [True: 6, False: 0] ------------------ 2584| 6| !at[neigh].num_H && !at[neigh].charge && ------------------ | Branch (2584:22): [True: 6, False: 0] | Branch (2584:42): [True: 6, False: 0] ------------------ 2585| 6| !at[neigh].radical && ------------------ | Branch (2585:22): [True: 6, False: 0] ------------------ 2586| 6| ( MobileGr[j].forbidden & forbidden_mask ) && jN < 0) ------------------ | Branch (2586:22): [True: 6, False: 0] | Branch (2586:68): [True: 6, False: 0] ------------------ 2587| 6| { 2588| 6| jN = j; 2589| 6| n++; 2590| 6| } 2591| 17| else 2592| 17| { 2593| 17| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 34|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2593:25): [True: 16, False: 1] ------------------ 2594| 16| at[neigh].endpoint) ------------------ | Branch (2594:29): [True: 13, False: 3] ------------------ 2595| 13| { 2596| 13| if (MobileGr[j].num_bonds > 1) ------------------ | Branch (2596:29): [True: 11, False: 2] ------------------ 2597| 11| { 2598| 11| jFix[njFix++] = j; 2599| 11| } 2600| 13| n++; 2601| 13| } 2602| 17| } 2603| 23| } 2604| | 2605| 7| if (jN < 0 || n < 2 || 1 + njFix == n) ------------------ | Branch (2605:17): [True: 1, False: 6] | Branch (2605:27): [True: 0, False: 6] | Branch (2605:36): [True: 4, False: 2] ------------------ 2606| 5| { 2607| 5| goto case_5_7; /* nothing to do */ 2608| 5| } 2609| | 2610| 2| e = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jN].ineigh]; /* fixed edge */ 2611| 2| if (!e->flow) ------------------ | Branch (2611:17): [True: 0, False: 2] ------------------ 2612| 0| { 2613| 0| goto case_5_7; 2614| 0| } 2615| 2| e->flow--; 2616| 2| pBNS->vert[i].st_edge.flow--; 2617| 2| pBNS->vert[e->neighbor12 ^ i].st_edge.flow--; 2618| 2| pBNS->tot_st_flow -= 2; 2619| | 2620| 4| for (j = 0; j < njFix; j++) ------------------ | Branch (2620:25): [True: 2, False: 2] ------------------ 2621| 2| { 2622| |/* edges to fix */ 2623| 2| ev = pBNS->edge + pBNS->vert[i].iedge[(int) MobileGr[jFix[j]].ineigh]; 2624| 2| ev->forbidden |= forbidden_mask; 2625| 2| } 2626| 2| num_changes++; 2627| 2| continue; 2628| 2| } 2629| 69| case_5_7: 2630| | /*********************************************************************/ 2631| 69| if (3 == num_bonds_non_metal && ------------------ | Branch (2631:13): [True: 34, False: 35] ------------------ 2632| 34| 4 == bonds_valence_non_metal && ------------------ | Branch (2632:14): [True: 23, False: 11] ------------------ 2633| 23| ( centerpoint_type == EL_TYPE_S ) && ------------------ | | 387| 23|#define EL_TYPE_S 0x0002 ------------------ | Branch (2633:14): [True: 23, False: 0] ------------------ 2634| 23| 2 == num_O + num_S && 1 == num_OSt && 1 == num_N && ------------------ | Branch (2634:14): [True: 1, False: 22] | Branch (2634:36): [True: 1, False: 0] | Branch (2634:52): [True: 1, False: 0] ------------------ 2635| 1| 1 == num_forbidden && 3 == num_eql_mobile_gr && ------------------ | Branch (2635:14): [True: 1, False: 0] | Branch (2635:36): [True: 0, False: 1] ------------------ 2636| 0| MobileGr[ind_forbidden].bond_type == BOND_TYPE_SINGLE) ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2636:14): [True: 0, False: 0] ------------------ 2637| 0| { 2638| | /******************************************************** 2639| | *** InChI Tech. Man., Table 5, case 7 *** 2640| | ******************************************************** 2641| | O = O, S, Se, Te 2642| | OH OH S = S, Se, Te 2643| | / / f = fixed bond 2644| | e /ev2 f / tg = Mobile-H vertex 2645| | HN---S --> N===S X = N or non-endpoint; 2646| | || f \\ \ 2647| | ev2|| \\ev1 \ 2648| | tg------O OH 2649| | N, O, O 2650| | Problem: ======= 2651| | O, NH, OH belong to the same Mobile-H group. 2652| | Fixed bond prevents the correct structure restoration: 2653| | H cannot migrate from NH to O because HN-S bond is fixed 2654| | Solution: 2655| | Move H from NH to =O to allow HN=S bond change by making a 2nd terminal -OH 2656| | (this unfixes the bond, see fix_special_bonds(...) ) 2657| | *********************************************************/ 2658| 0| int jO = -1, jNH = -1, jOH = -1, n = 0; 2659| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2659:25): [True: 0, False: 0] ------------------ 2660| 0| { 2661| 0| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 392| 0|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 388| 0|#define EL_TYPE_N 0x0004 ------------------ | Branch (2661:21): [True: 0, False: 0] ------------------ 2662| 0| MobileGr[j].forbidden == forbidden_mask && ------------------ | Branch (2662:22): [True: 0, False: 0] ------------------ 2663| 0| MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2663:22): [True: 0, False: 0] ------------------ 2664| 0| MobileGr[j].num_bonds_non_metal <= 2 && ------------------ | Branch (2664:22): [True: 0, False: 0] ------------------ 2665| 0| jNH < 0) ------------------ | Branch (2665:22): [True: 0, False: 0] ------------------ 2666| 0| { 2667| 0| jNH = j; 2668| 0| n++; 2669| 0| } 2670| 0| else 2671| 0| { 2672| 0| if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 386| 0|#define EL_TYPE_O 0x0001 ------------------ if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 387| 0|#define EL_TYPE_S 0x0002 ------------------ | Branch (2672:25): [True: 0, False: 0] ------------------ 2673| 0| !MobileGr[j].forbidden && ------------------ | Branch (2673:29): [True: 0, False: 0] ------------------ 2674| 0| MobileGr[j].num_bonds_non_metal == 1) ------------------ | Branch (2674:29): [True: 0, False: 0] ------------------ 2675| 0| { 2676| 0| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2676:29): [True: 0, False: 0] ------------------ 2677| 0| jO < 0) ------------------ | Branch (2677:30): [True: 0, False: 0] ------------------ 2678| 0| { 2679| 0| jO = j; 2680| 0| n++; 2681| 0| } 2682| 0| else 2683| 0| { 2684| 0| if (jOH < 0) ------------------ | Branch (2684:33): [True: 0, False: 0] ------------------ 2685| 0| { 2686| 0| jOH = j; 2687| 0| n++; 2688| 0| } 2689| 0| } 2690| 0| } 2691| 0| } 2692| 0| } 2693| 0| if (n != 3) ------------------ | Branch (2693:17): [True: 0, False: 0] ------------------ 2694| 0| { 2695| 0| goto case_5_9a; 2696| 0| } 2697| | /* NH-S edge */ 2698| 0| e = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jNH].ineigh]; 2699| | /* S=O edge */ 2700| 0| ev1 = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jO].ineigh]; 2701| | /* XH-tg edge */ 2702| 0| ev2 = pBNS->edge + pVA[MobileGr[jNH].atom_number].nTautGroupEdge - 1; 2703| | 2704| 0| if (!ev1->flow || !ev2->flow) ------------------ | Branch (2704:17): [True: 0, False: 0] | Branch (2704:31): [True: 0, False: 0] ------------------ 2705| 0| { 2706| 0| goto case_5_9a; 2707| 0| } 2708| | 2709| | /* do not remove forbidden edge bit */ 2710| 0| e->flow++; 2711| 0| ev1->flow--; 2712| 0| ev2->flow--; 2713| 0| pBNS->vert[ev1->neighbor12 ^ i].st_edge.flow--; /* first =O vertex */ 2714| 0| pBNS->vert[ev2->neighbor12 ^ ev2->neighbor1].st_edge.flow--; /* taut group vertex tg */ 2715| 0| pBNS->tot_st_flow -= 2; 2716| 0| num_changes++; 2717| 0| continue; 2718| 0| } 2719| 69| case_5_9a: 2720| | /*********************************************************************/ 2721| 69| if (3 == num_bonds_non_metal && ------------------ | Branch (2721:13): [True: 34, False: 35] ------------------ 2722| 34| 4 == bonds_valence_non_metal && ------------------ | Branch (2722:14): [True: 23, False: 11] ------------------ 2723| 23| ( centerpoint_type == EL_TYPE_S ) && ------------------ | | 387| 23|#define EL_TYPE_S 0x0002 ------------------ | Branch (2723:14): [True: 23, False: 0] ------------------ 2724| 23| 1 == num_O + num_S && !num_OSt && 1 <= num_N && ------------------ | Branch (2724:14): [True: 1, False: 22] | Branch (2724:36): [True: 1, False: 0] | Branch (2724:48): [True: 1, False: 0] ------------------ 2725| 1| 1 == num_forbidden && ------------------ | Branch (2725:14): [True: 1, False: 0] ------------------ 2726| 1| num_O + num_S + num_N == num_eql_mobile_gr && ------------------ | Branch (2726:14): [True: 1, False: 0] ------------------ 2727| 1| MobileGr[ind_forbidden].bond_type == BOND_TYPE_SINGLE) ------------------ | | 32| 1|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2727:14): [True: 0, False: 1] ------------------ 2728| 0| { 2729| | /******************************************************** 2730| | *** InChI Tech. Man., Table 5, case 9a *** 2731| | ******************************************************** 2732| | O = O, S, Se, Te 2733| | X X S = S, Se, Te 2734| | / / f = fixed bond 2735| | / / tg = Mobile-H vertex 2736| | HN---S --> N===S X = N or non-endpoint; 2737| | || \\ e \ -X is not -O(terminal) 2738| | || f\\ f\ 2739| | tg------O OH 2740| | N, N, O or N, O 2741| | Problem: ================ 2742| | O, NH belong to the same Mobile-H group. 2743| | Fixed bond prevents the correct structure restoration: 2744| | H cannot migrate from NH to O because O=S bond is fixed 2745| | Solution: 2746| | Move H from NH to =O to allow O=S bond change by making a terminal -OH 2747| | (this unfixes the bond, see fix_special_bonds(...) ) 2748| | *********************************************************/ 2749| 0| int jO = -1, jNH = -1, jX = -1, n = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 2750| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2750:25): [True: 0, False: 0] ------------------ 2751| 0| { 2752| 0| if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 386| 0|#define EL_TYPE_O 0x0001 ------------------ if (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 387| 0|#define EL_TYPE_S 0x0002 ------------------ | Branch (2752:21): [True: 0, False: 0] ------------------ 2753| 0| MobileGr[j].forbidden == forbidden_mask && ------------------ | Branch (2753:22): [True: 0, False: 0] ------------------ 2754| 0| MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2754:22): [True: 0, False: 0] ------------------ 2755| 0| MobileGr[j].num_bonds_non_metal == 1 && ------------------ | Branch (2755:22): [True: 0, False: 0] ------------------ 2756| 0| jO < 0) ------------------ | Branch (2756:22): [True: 0, False: 0] ------------------ 2757| 0| { 2758| 0| jO = j; 2759| 0| n++; 2760| 0| } 2761| 0| else 2762| 0| { 2763| 0| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 392| 0|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 388| 0|#define EL_TYPE_N 0x0004 ------------------ | Branch (2763:25): [True: 0, False: 0] ------------------ 2764| 0| !MobileGr[j].forbidden && ------------------ | Branch (2764:29): [True: 0, False: 0] ------------------ 2765| 0| MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2765:29): [True: 0, False: 0] ------------------ 2766| 0| jNH < 0) ------------------ | Branch (2766:29): [True: 0, False: 0] ------------------ 2767| 0| { 2768| 0| jNH = j; 2769| 0| n++; 2770| 0| } 2771| 0| else 2772| 0| { 2773| 0| if (jX < 0) ------------------ | Branch (2773:29): [True: 0, False: 0] ------------------ 2774| 0| { 2775| 0| jX = j; 2776| 0| n++; 2777| 0| } 2778| 0| } 2779| 0| } 2780| 0| } 2781| 0| if (jO < 0 || jNH < 0) ------------------ | Branch (2781:17): [True: 0, False: 0] | Branch (2781:27): [True: 0, False: 0] ------------------ 2782| 0| { 2783| 0| goto case_5_8b_to_9b; 2784| 0| } 2785| | 2786| 0| e = pBNS->edge + pBNS->vert[i].iedge[MobileGr[ind_forbidden].ineigh]; 2787| 0| if (!e->flow) ------------------ | Branch (2787:17): [True: 0, False: 0] ------------------ 2788| 0| { 2789| 0| goto case_5_8b_to_9b; 2790| 0| } 2791| 0| e->flow--; 2792| 0| pBNS->vert[e->neighbor1].st_edge.flow--; 2793| 0| pBNS->vert[e->neighbor1 ^ e->neighbor12].st_edge.flow--; 2794| 0| pBNS->tot_st_flow -= 2; 2795| 0| num_changes++; 2796| 0| continue; 2797| 0| } 2798| 69| case_5_8b_to_9b: /* #1 */ 2799| | /*********************************************************************/ 2800| 69| if (3 == num_bonds_non_metal && ------------------ | Branch (2800:13): [True: 34, False: 35] ------------------ 2801| 34| 4 == bonds_valence_non_metal && ------------------ | Branch (2801:14): [True: 23, False: 11] ------------------ 2802| 23| ( centerpoint_type == EL_TYPE_S ) && ------------------ | | 387| 23|#define EL_TYPE_S 0x0002 ------------------ | Branch (2802:14): [True: 23, False: 0] ------------------ 2803| 23| 0 == num_O + num_S && 2 == num_N && 0 == num_P && !num_OSt && ------------------ | Branch (2803:14): [True: 21, False: 2] | Branch (2803:36): [True: 20, False: 1] | Branch (2803:50): [True: 20, False: 0] | Branch (2803:64): [True: 20, False: 0] ------------------ 2804| 20| 1 == num_forbidden && ------------------ | Branch (2804:14): [True: 14, False: 6] ------------------ 2805| 14| 1 == num_eql_mobile_gr && 0 == num_dif_mobile_gr && ------------------ | Branch (2805:14): [True: 12, False: 2] | Branch (2805:40): [True: 12, False: 0] ------------------ 2806| 12| 1 == num_donor_endpoints && 0 == num_acceptor_endpoints && ------------------ | Branch (2806:14): [True: 12, False: 0] | Branch (2806:42): [True: 12, False: 0] ------------------ 2807| 12| 1 == num_donors && 1 == num_acceptors && ------------------ | Branch (2807:14): [True: 12, False: 0] | Branch (2807:33): [True: 12, False: 0] ------------------ 2808| 12| MobileGr[ind_forbidden].bond_type == BOND_TYPE_SINGLE) ------------------ | | 32| 12|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2808:14): [True: 11, False: 1] ------------------ 2809| 11| { 2810| | /******************************************************** 2811| | *** InChI Tech. Man., Table 5, case 8b->9b *** 2812| | ******************************************************** 2813| | ---> O = O, S, Se, Te 2814| | X X S = S, Se, Te 2815| | \ f/ \ f/ f = fixed bond 2816| | \ ev / C=====Z \ / C-----ZH tg = Mobile-H vertex 2817| | N===S | | N===S || || X = is N not an endpoint; 2818| | not \ | | \ || || -X is not terminal -O,-S,-Se,-Te or 2819| | an \ | e | \|| e || any N, P, As 2820| | endpoint NH=====tg N------tg 2821| | is an f N, N, X, fixed single 2822| | endpoint ===================== 2823| | 2824| | Problem: 2825| | N is not a Mobile-H endpoint, NH is a Mobile-H endpoint 2826| | Unfixed bond N==S prevents the correct structure restoration: 2827| | H can migrate from NH to N because N=S bond is not fixed 2828| | Solution: 2829| | Move H from NH to =Z to make N=S bond fixed (Table 5, case 9) 2830| | (this unfixes the bond, see fix_special_bonds(...) ) 2831| | *********************************************************/ 2832| 11| int jN = -1, jNH = -1, jX = -1, n = 0; 2833| 44| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2833:25): [True: 33, False: 11] ------------------ 2834| 33| { 2835| 33| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 392| 33|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 388| 66|#define EL_TYPE_N 0x0004 ------------------ | Branch (2835:21): [True: 23, False: 10] ------------------ 2836| 23| !( MobileGr[j].forbidden & forbidden_mask )) ------------------ | Branch (2836:22): [True: 22, False: 1] ------------------ 2837| 22| { 2838| 22| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 44|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2838:25): [True: 11, False: 11] ------------------ 2839| 11| !at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (2839:26): [True: 11, False: 0] ------------------ 2840| 11| jN < 0) ------------------ | Branch (2840:26): [True: 11, False: 0] ------------------ 2841| 11| { 2842| 11| jN = j; 2843| 11| n++; 2844| 11| } 2845| 11| else 2846| 11| { 2847| 11| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 22|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2847:29): [True: 11, False: 0] ------------------ 2848| 11| MobileGr[j].num_bonds == 2 && ------------------ | Branch (2848:31): [True: 11, False: 0] ------------------ 2849| 11| MobileGr[j].bonds_valence == 2 && ------------------ | Branch (2849:31): [True: 11, False: 0] ------------------ 2850| 11| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (2850:31): [True: 11, False: 0] ------------------ 2851| 11| jNH < 0) ------------------ | Branch (2851:31): [True: 11, False: 0] ------------------ 2852| 11| { 2853| 11| jNH = j; 2854| 11| n++; 2855| 11| } 2856| 11| } 2857| 22| } 2858| 11| else 2859| 11| { 2860| 11| if (!( ( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_P ) ) || ------------------ | | 388| 11|#define EL_TYPE_N 0x0004 ------------------ if (!( ( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_P ) ) || ------------------ | | 389| 11|#define EL_TYPE_P 0x0008 ------------------ | Branch (2860:28): [True: 1, False: 10] ------------------ 2861| 10| (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 386| 10|#define EL_TYPE_O 0x0001 ------------------ (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 387| 10|#define EL_TYPE_S 0x0002 ------------------ | Branch (2861:26): [True: 6, False: 4] ------------------ 2862| 6| MobileGr[j].num_bonds > 1 )) && ------------------ | Branch (2862:28): [True: 6, False: 0] ------------------ 2863| 4| ( MobileGr[j].forbidden & forbidden_mask ) && ------------------ | Branch (2863:28): [True: 4, False: 0] ------------------ 2864| 4| MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 15|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2864:29): [True: 4, False: 0] ------------------ 2865| 4| jX < 0) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2865:29): [True: 4, False: 0] ------------------ 2866| 4| { 2867| 4| jX = j; 2868| 4| n++; 2869| 4| } 2870| 11| } 2871| 33| } 2872| 11| if (n != 3) ------------------ | Branch (2872:17): [True: 7, False: 4] ------------------ 2873| 7| { 2874| 7| goto case_5_8c_to_9c; 2875| 7| } 2876| | 2877| 4| e = pBNS->edge + pVA[MobileGr[jNH].atom_number].nTautGroupEdge - 1; 2878| 4| if (!e->flow) ------------------ | Branch (2878:17): [True: 1, False: 3] ------------------ 2879| 1| { 2880| 1| goto case_5_8c_to_9c; /* should not happen ??? */ 2881| 1| } 2882| 3| e->flow--; 2883| 3| pBNS->vert[e->neighbor1].st_edge.flow--; 2884| 3| pBNS->vert[e->neighbor1 ^ e->neighbor12].st_edge.flow--; 2885| 3| pBNS->tot_st_flow -= 2; 2886| 3| e->forbidden |= forbidden_mask; 2887| 3| num_changes++; 2888| 3| continue; 2889| 4| } 2890| 66| case_5_8c_to_9c: /* #2 */ 2891| | /*********************************************************************/ 2892| 66| if (3 == num_bonds_non_metal && ------------------ | Branch (2892:13): [True: 31, False: 35] ------------------ 2893| 31| 4 == bonds_valence_non_metal && ------------------ | Branch (2893:14): [True: 20, False: 11] ------------------ 2894| 20| ( centerpoint_type == EL_TYPE_S ) && ------------------ | | 387| 20|#define EL_TYPE_S 0x0002 ------------------ | Branch (2894:14): [True: 20, False: 0] ------------------ 2895| 20| 0 == num_O + num_S && 3 == num_N && 0 == num_P && ------------------ | Branch (2895:14): [True: 18, False: 2] | Branch (2895:36): [True: 1, False: 17] | Branch (2895:50): [True: 1, False: 0] ------------------ 2896| 1| 1 == num_forbidden && ------------------ | Branch (2896:14): [True: 1, False: 0] ------------------ 2897| 1| 3 == num_eql_mobile_gr && 0 == num_dif_mobile_gr && ------------------ | Branch (2897:14): [True: 0, False: 1] | Branch (2897:40): [True: 0, False: 0] ------------------ 2898| 0| 2 == num_donor_endpoints && 1 == num_acceptor_endpoints && ------------------ | Branch (2898:14): [True: 0, False: 0] | Branch (2898:42): [True: 0, False: 0] ------------------ 2899| 0| 2 == num_donors && 1 == num_acceptors && ------------------ | Branch (2899:14): [True: 0, False: 0] | Branch (2899:33): [True: 0, False: 0] ------------------ 2900| 0| MobileGr[ind_forbidden].bond_type == BOND_TYPE_SINGLE) ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2900:14): [True: 0, False: 0] ------------------ 2901| 0| { 2902| | /******************************************************** 2903| | *** InChI Tech. Man., Table 5, case 8c->9c *** 2904| | ******************************************************** 2905| | is an endpoint ---> O = O, S, Se, Te 2906| | NH2(X) NH2(X) S = S, Se, Te 2907| | \ / pv1 pv2 \ / f = fixed bond 2908| | \ 1 / C-----ZH \ / C=====Z tg = Mobile-H vertex 2909| | N===S || || N===S | | X = is N not an endpoint; 2910| | is an \f||ev1 ||ev2 \f | | -X is not terminal -O,-S,-Se,-Te or 2911| | endpoint \|| e || \ | e | any N, P, As 2912| | 2 N------tg NH=====tg C is a centerpoint of a t-group 2913| | is an f N, N, X, fixed single 2914| | endpoint ===================== 2915| | 2916| | Problem: 2917| | N is not a Mobile-H endpoint, NH is a Mobile-H endpoint 2918| | Unfixed bond N==S prevents the correct structure restoration: 2919| | H can migrate from NH to N because N=S bond is not fixed 2920| | Solution: 2921| | Move H from NH to =Z to make N=S bond fixed (Table 5, case 9) 2922| | (this unfixes the bond, see fix_special_bonds(...) ) 2923| | *********************************************************/ 2924| 0| int jN1 = -1, jN2 = -1, jX = -1, n = 0; 2925| 0| EdgeIndex ie1, ie2; /* djb-rwth: removing redundant variables */ 2926| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (2926:25): [True: 0, False: 0] ------------------ 2927| 0| { 2928| 0| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 392| 0|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N && ------------------ | | 388| 0|#define EL_TYPE_N 0x0004 ------------------ | Branch (2928:21): [True: 0, False: 0] ------------------ 2929| 0| !( MobileGr[j].forbidden & forbidden_mask )) ------------------ | Branch (2929:22): [True: 0, False: 0] ------------------ 2930| 0| { 2931| 0| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2931:25): [True: 0, False: 0] ------------------ 2932| 0| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (2932:26): [True: 0, False: 0] ------------------ 2933| 0| jN1 < 0) ------------------ | Branch (2933:26): [True: 0, False: 0] ------------------ 2934| 0| { 2935| 0| jN1 = j; 2936| 0| n++; 2937| 0| } 2938| 0| else 2939| 0| { 2940| 0| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2940:29): [True: 0, False: 0] ------------------ 2941| 0| MobileGr[j].num_bonds == 2 && ------------------ | Branch (2941:33): [True: 0, False: 0] ------------------ 2942| 0| MobileGr[j].bonds_valence == 3 && ------------------ | Branch (2942:33): [True: 0, False: 0] ------------------ 2943| 0| MobileGr[j].forbidden == forbidden_mask && ------------------ | Branch (2943:33): [True: 0, False: 0] ------------------ 2944| 0| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (2944:33): [True: 0, False: 0] ------------------ 2945| 0| jN2 < 0) ------------------ | Branch (2945:33): [True: 0, False: 0] ------------------ 2946| 0| { 2947| 0| jN2 = j; 2948| 0| n++; 2949| 0| } 2950| 0| else 2951| 0| { 2952| 0| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2952:33): [True: 0, False: 0] ------------------ 2953| 0| MobileGr[j].num_bonds <= 2 && ------------------ | Branch (2953:35): [True: 0, False: 0] ------------------ 2954| 0| MobileGr[j].bonds_valence <= 3 && ------------------ | Branch (2954:35): [True: 0, False: 0] ------------------ 2955| 0| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (2955:35): [True: 0, False: 0] ------------------ 2956| 0| jX < 0) ------------------ | Branch (2956:35): [True: 0, False: 0] ------------------ 2957| 0| { 2958| 0| jX = j; 2959| 0| n++; 2960| 0| } 2961| 0| } 2962| 0| } 2963| 0| } 2964| 0| } 2965| 0| if (n != 3) ------------------ | Branch (2965:17): [True: 0, False: 0] ------------------ 2966| 0| { 2967| 0| goto case_5_9b_to_8b; 2968| 0| } 2969| | 2970| 0| e = pBNS->edge + pVA[MobileGr[jN2].atom_number].nTautGroupEdge - 1; 2971| 0| if (e->flow) ------------------ | Branch (2971:17): [True: 0, False: 0] ------------------ 2972| 0| { 2973| 0| goto case_5_9b_to_8b; /* should not happen ??? */ 2974| 0| } 2975| 0| pv1 = pBNS->vert + e->neighbor1; /* must be jN2 */ 2976| 0| pv2 = pBNS->vert + ( e->neighbor1 ^ e->neighbor12 ); 2977| | /* djb-rwth: removing redundant code */ 2978| 0| ie1 = ie2 = -1; 2979| 0| for (j = 0; j < pv1->num_adj_edges; j++) ------------------ | Branch (2979:25): [True: 0, False: 0] ------------------ 2980| 0| { 2981| 0| ev1 = pBNS->edge + pv1->iedge[j]; 2982| 0| if (ev1->flow && !ev1->forbidden) ------------------ | Branch (2982:21): [True: 0, False: 0] | Branch (2982:34): [True: 0, False: 0] ------------------ 2983| 0| { 2984| 0| ie1 = (int) ( ev1 - pBNS->edge ); 2985| 0| pv1 = pBNS->vert + ( ev1->neighbor12 ^ ( pv1 - pBNS->vert ) ); 2986| 0| break; 2987| 0| } 2988| 0| } 2989| 0| for (j = 0; j < pv2->num_adj_edges; j++) ------------------ | Branch (2989:25): [True: 0, False: 0] ------------------ 2990| 0| { 2991| 0| ev2 = pBNS->edge + pv2->iedge[j]; 2992| 0| if (ev2->flow && !ev2->forbidden) ------------------ | Branch (2992:21): [True: 0, False: 0] | Branch (2992:34): [True: 0, False: 0] ------------------ 2993| 0| { 2994| 0| ie2 = (int) ( ev2 - pBNS->edge ); 2995| 0| pv2 = pBNS->vert + ( ev2->neighbor12 ^ ( pv2 - pBNS->vert ) ); 2996| 0| break; 2997| 0| } 2998| 0| } 2999| 0| if (ie1 < 0 || ie2 < 0) ------------------ | Branch (2999:17): [True: 0, False: 0] | Branch (2999:28): [True: 0, False: 0] ------------------ 3000| 0| { 3001| 0| goto case_5_9b_to_8b; 3002| 0| } 3003| 0| e->flow++; 3004| 0| e->forbidden |= forbidden_mask; 3005| 0| ev1->flow--; 3006| 0| ev2->flow--; 3007| 0| pv1->st_edge.flow--; 3008| 0| pv2->st_edge.flow--; 3009| 0| pBNS->tot_st_flow -= 2; 3010| 0| num_changes++; 3011| 0| continue; 3012| 0| } 3013| 66| case_5_9b_to_8b: /* #3 */ 3014| | /*********************************************************************/ 3015| 66| if (3 == num_bonds_non_metal && ------------------ | Branch (3015:13): [True: 31, False: 35] ------------------ 3016| 31| 4 == bonds_valence_non_metal && ------------------ | Branch (3016:14): [True: 20, False: 11] ------------------ 3017| 20| ( centerpoint_type == EL_TYPE_S ) && ------------------ | | 387| 20|#define EL_TYPE_S 0x0002 ------------------ | Branch (3017:14): [True: 20, False: 0] ------------------ 3018| 20| 0 == num_O + num_S && 2 == num_N && 0 == num_P && ------------------ | Branch (3018:14): [True: 18, False: 2] | Branch (3018:36): [True: 17, False: 1] | Branch (3018:50): [True: 17, False: 0] ------------------ 3019| 17| 1 == num_forbidden && ------------------ | Branch (3019:14): [True: 11, False: 6] ------------------ 3020| 11| 2 == num_eql_mobile_gr && 0 == num_dif_mobile_gr && ------------------ | Branch (3020:14): [True: 2, False: 9] | Branch (3020:40): [True: 2, False: 0] ------------------ 3021| 2| 1 == num_donor_endpoints && 1 == num_acceptor_endpoints && ------------------ | Branch (3021:14): [True: 2, False: 0] | Branch (3021:42): [True: 2, False: 0] ------------------ 3022| 2| 1 == num_donors && 1 == num_acceptors && ------------------ | Branch (3022:14): [True: 2, False: 0] | Branch (3022:33): [True: 2, False: 0] ------------------ 3023| 2| MobileGr[ind_forbidden].bond_type == BOND_TYPE_DOUBLE) ------------------ | | 33| 2|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (3023:14): [True: 2, False: 0] ------------------ 3024| 2| { 3025| | /******************************************************** 3026| | *** InChI Tech. Man., Table 5, case 9b->8b *** 3027| | ******************************************************** 3028| | ---> O = O, S, Se, Te 3029| | X is an X S = S, Se, Te 3030| | \ / endpoint \ / f = fixed bond 3031| | \ 1ev / C-----ZH \ / C=====Z tg = Mobile-H vertex 3032| | N===S || || N===S | | X = is N not an endpoint; 3033| | is an f \ || || f \ | | -X is not terminal -O,-S,-Se,-Te or 3034| | endpoint 2\|| e || \ | e | any N, P, As 3035| | N------tg NH=====tg 3036| | is an f N, N, X, fixed double 3037| | endpoint ===================== 3038| | 3039| | Problem: 3040| | N1 and N2 are Mobile-H endpoints and belong to the same Mobile-H group. 3041| | Fixed bond N1==S prevents the correct structure restoration: 3042| | H cannot migrate ZH->N2->N1 because N1=S bond is fixed 3043| | Solution: 3044| | Move H from ZH to N2 to make N1=S bond unfixed and fix S-X bond (Table 5, case 8) 3045| | (see fix_special_bonds(...) for details ) 3046| | *********************************************************/ 3047| 2| int jN1 = -1, jN2 = -1, jX = -1, n = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 3048| 2| EdgeIndex ie1, ie2; /* djb-rwth: removing redundant variables */ 3049| 6| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (3049:25): [True: 4, False: 2] ------------------ 3050| 4| { 3051| 4| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N) ------------------ | | 392| 4|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N) ------------------ | | 388| 4|#define EL_TYPE_N 0x0004 ------------------ | Branch (3051:21): [True: 4, False: 0] ------------------ 3052| 4| { 3053| 4| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 8|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (3053:25): [True: 2, False: 2] ------------------ 3054| 2| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (3054:26): [True: 2, False: 0] ------------------ 3055| 2| ( MobileGr[j].forbidden == forbidden_mask ) && ------------------ | Branch (3055:26): [True: 2, False: 0] ------------------ 3056| 2| jN1 < 0) ------------------ | Branch (3056:26): [True: 2, False: 0] ------------------ 3057| 2| { 3058| 2| jN1 = j; 3059| 2| n++; 3060| 2| } 3061| 2| else 3062| 2| { 3063| 2| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 4|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (3063:29): [True: 2, False: 0] ------------------ 3064| 2| MobileGr[j].num_bonds == 2 && ------------------ | Branch (3064:31): [True: 2, False: 0] ------------------ 3065| 2| MobileGr[j].bonds_valence == 3 && ------------------ | Branch (3065:31): [True: 2, False: 0] ------------------ 3066| 2| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (3066:31): [True: 2, False: 0] ------------------ 3067| 2| !( MobileGr[j].forbidden & forbidden_mask ) && ------------------ | Branch (3067:31): [True: 2, False: 0] ------------------ 3068| 2| jN2 < 0) ------------------ | Branch (3068:31): [True: 2, False: 0] ------------------ 3069| 2| { 3070| 2| jN2 = j; 3071| 2| n++; 3072| 2| } 3073| 2| } 3074| 4| } 3075| 0| else 3076| 0| { 3077| 0| if (!( ( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_P ) ) || ------------------ | | 388| 0|#define EL_TYPE_N 0x0004 ------------------ if (!( ( MobileGr[j].atom_type_pVA & ( EL_TYPE_N | EL_TYPE_P ) ) || ------------------ | | 389| 0|#define EL_TYPE_P 0x0008 ------------------ | Branch (3077:28): [True: 0, False: 0] ------------------ 3078| 0| (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 386| 0|#define EL_TYPE_O 0x0001 ------------------ (( MobileGr[j].atom_type_pVA & ( EL_TYPE_O | EL_TYPE_S ) ) && ------------------ | | 387| 0|#define EL_TYPE_S 0x0002 ------------------ | Branch (3078:26): [True: 0, False: 0] ------------------ 3079| 0| MobileGr[j].num_bonds > 1 )) && ------------------ | Branch (3079:28): [True: 0, False: 0] ------------------ 3080| 0| !( MobileGr[j].forbidden & forbidden_mask ) && ------------------ | Branch (3080:29): [True: 0, False: 0] ------------------ 3081| 0| MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (3081:29): [True: 0, False: 0] ------------------ 3082| 0| jX < 0) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3082:29): [True: 0, False: 0] ------------------ 3083| 0| { 3084| 0| jX = j; 3085| 0| n++; 3086| 0| } 3087| 0| } 3088| 4| } 3089| 2| if (jN1 < 0 || jN2 < 0) ------------------ | Branch (3089:17): [True: 0, False: 2] | Branch (3089:28): [True: 0, False: 2] ------------------ 3090| 0| { 3091| 0| goto case_5_9c_to_8c; 3092| 0| } 3093| | 3094| 2| ev = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jN1].ineigh]; 3095| 2| e = pBNS->edge + pVA[MobileGr[jN2].atom_number].nTautGroupEdge - 1; 3096| 2| if (e->flow) ------------------ | Branch (3096:17): [True: 0, False: 2] ------------------ 3097| 0| { 3098| 0| goto case_5_9c_to_8c; /* should not happen ??? */ 3099| 0| } 3100| 2| pv1 = pBNS->vert + e->neighbor1; /* must be jN2 */ 3101| 2| pv2 = pBNS->vert + ( e->neighbor1 ^ e->neighbor12 ); 3102| | /* djb-rwth: removing redundant code */ 3103| 2| ie1 = ie2 = -1; 3104| 2| ev->forbidden &= inv_forbidden_mask; 3105| 4| for (j = 0; j < pv1->num_adj_edges; j++) ------------------ | Branch (3105:25): [True: 4, False: 0] ------------------ 3106| 4| { 3107| 4| ev1 = pBNS->edge + pv1->iedge[j]; 3108| 4| if (ev1->flow && !ev1->forbidden) ------------------ | Branch (3108:21): [True: 2, False: 2] | Branch (3108:34): [True: 2, False: 0] ------------------ 3109| 2| { 3110| 2| ie1 = (int) ( ev1 - pBNS->edge ); 3111| 2| pv1 = pBNS->vert + ( ev1->neighbor12 ^ ( pv1 - pBNS->vert ) ); 3112| 2| break; 3113| 2| } 3114| 4| } 3115| 5| for (j = 0; j < pv2->num_adj_edges; j++) ------------------ | Branch (3115:25): [True: 5, False: 0] ------------------ 3116| 5| { 3117| 5| ev2 = pBNS->edge + pv2->iedge[j]; 3118| 5| if (ev2->flow && !ev2->forbidden) ------------------ | Branch (3118:21): [True: 2, False: 3] | Branch (3118:34): [True: 2, False: 0] ------------------ 3119| 2| { 3120| 2| ie2 = (int) ( ev2 - pBNS->edge ); 3121| 2| pv2 = pBNS->vert + ( ev2->neighbor12 ^ ( pv2 - pBNS->vert ) ); 3122| 2| break; 3123| 2| } 3124| 5| } 3125| 2| if (ie1 < 0 || ie2 < 0) ------------------ | Branch (3125:17): [True: 0, False: 2] | Branch (3125:28): [True: 0, False: 2] ------------------ 3126| 0| { 3127| 0| ev->forbidden |= forbidden_mask; /* failed; restore the forbidden bit */ 3128| 0| goto case_5_9c_to_8c; 3129| 0| } 3130| 2| e->flow++; 3131| 2| e->forbidden |= forbidden_mask; 3132| 2| ev1->flow--; 3133| 2| ev2->flow--; 3134| 2| pv1->st_edge.flow--; 3135| 2| pv2->st_edge.flow--; 3136| 2| pBNS->tot_st_flow -= 2; 3137| 2| num_changes++; 3138| 2| continue; 3139| 2| } 3140| 64| case_5_9c_to_8c: /* #4 */ 3141| | /*********************************************************************/ 3142| 64| if (3 == num_bonds_non_metal && ------------------ | Branch (3142:13): [True: 29, False: 35] ------------------ 3143| 29| 4 == bonds_valence_non_metal && ------------------ | Branch (3143:14): [True: 18, False: 11] ------------------ 3144| 18| ( centerpoint_type == EL_TYPE_S ) && ------------------ | | 387| 18|#define EL_TYPE_S 0x0002 ------------------ | Branch (3144:14): [True: 18, False: 0] ------------------ 3145| 18| 0 == num_O + num_S && 3 == num_N && 0 == num_P && ------------------ | Branch (3145:14): [True: 16, False: 2] | Branch (3145:36): [True: 1, False: 15] | Branch (3145:50): [True: 1, False: 0] ------------------ 3146| 1| 0 == num_forbidden && ------------------ | Branch (3146:14): [True: 0, False: 1] ------------------ 3147| 0| 2 == num_diff_t_groups && 2 == num_mgroups && /* all neighbors belong to 2 t-groups */ ------------------ | Branch (3147:14): [True: 0, False: 0] | Branch (3147:40): [True: 0, False: 0] ------------------ 3148| 0| 3 == num_eql_mobile_gr + num_dif_mobile_gr && /* all 3 neighbors belong to t-groups */ ------------------ | Branch (3148:14): [True: 0, False: 0] ------------------ 3149| 0| 2 == num_donor_endpoints && 1 == num_acceptor_endpoints && ------------------ | Branch (3149:14): [True: 0, False: 0] | Branch (3149:42): [True: 0, False: 0] ------------------ 3150| 0| 2 == num_donors && 1 == num_acceptors) ------------------ | Branch (3150:14): [True: 0, False: 0] | Branch (3150:33): [True: 0, False: 0] ------------------ 3151| 0| { 3152| | /******************************************************** 3153| | *** InChI Tech. Man., Table 5, case 8c->9c *** 3154| | ******************************************************** 3155| | is an endpoint ---> O = O, S, Se, Te 3156| | tg1 NH2(X) NH2(X) S = S, Se, Te 3157| | \ / pv1 pv2 \ / f = fixed bond 3158| | \(1) / C=====Z \ / C-----ZH tg = Mobile-H vertex 3159| | N===S | | N===S || || X = is N not an endpoint; 3160| | is an \ |ev1 | ev2 \ || || -X is not terminal -O,-S,-Se,-Te or 3161| | endpoint \ | e | \|| e || any N, P, As 3162| | tg1 (2)NH=====tg N------tg C is a centerpoint of a t-group 3163| | is an f N, N, X, fixed single 3164| | endpoint ===================== 3165| | tg2 3166| | Problem: 3167| | N (1) and NH2 are Mobile-H group 1 endpoiints, NH (2) is a Mobile-H group 2 endpoint 3168| | Unfixed bonds N==S--NH(2) allows the two Mobile H groups to merge 3169| | hence prevents the correct structure restoration: 3170| | H can migrate from NH (2) to N (1) because S-NH(1) bond is not fixed 3171| | Solution: 3172| | Move H from NH(2) to =Z to make S-NH(2) bond fixed (Table 5, case 8c) 3173| | (this unfixes the bond, see fix_special_bonds(...) ) 3174| | *********************************************************/ 3175| 0| int jN1 = -1, jN2 = -1, jX = -1, n = 0; 3176| | /* find t-group that is represented by only one neighbor */ 3177| 0| for (j = 0, k = 0; j < num_mgroups; j++) ------------------ | Branch (3177:32): [True: 0, False: 0] ------------------ 3178| 0| { 3179| 0| if (1 == MGroups[k].num && MGroups[k].group_number) ------------------ | Branch (3179:21): [True: 0, False: 0] | Branch (3179:44): [True: 0, False: 0] ------------------ 3180| 0| { 3181| 0| k = MGroups[k].group_number; 3182| 0| break; 3183| 0| } 3184| 0| } 3185| 0| if (!k) ------------------ | Branch (3185:17): [True: 0, False: 0] ------------------ 3186| 0| { 3187| 0| goto case_5_9c_to_9d; 3188| 0| } 3189| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (3189:25): [True: 0, False: 0] ------------------ 3190| 0| { 3191| 0| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N) ------------------ | | 392| 0|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N) ------------------ | | 388| 0|#define EL_TYPE_N 0x0004 ------------------ | Branch (3191:21): [True: 0, False: 0] ------------------ 3192| 0| { 3193| 0| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (3193:25): [True: 0, False: 0] ------------------ 3194| 0| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (3194:26): [True: 0, False: 0] ------------------ 3195| 0| at[MobileGr[j].atom_number].endpoint != k && ------------------ | Branch (3195:26): [True: 0, False: 0] ------------------ 3196| 0| jN1 < 0) ------------------ | Branch (3196:26): [True: 0, False: 0] ------------------ 3197| 0| { 3198| 0| jN1 = j; 3199| 0| n++; 3200| 0| } 3201| 0| else 3202| 0| { 3203| 0| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (3203:29): [True: 0, False: 0] ------------------ 3204| 0| MobileGr[j].num_bonds == 2 && ------------------ | Branch (3204:33): [True: 0, False: 0] ------------------ 3205| 0| MobileGr[j].bonds_valence == 2 && ------------------ | Branch (3205:33): [True: 0, False: 0] ------------------ 3206| 0| at[MobileGr[j].atom_number].endpoint == k && ------------------ | Branch (3206:33): [True: 0, False: 0] ------------------ 3207| 0| jN2 < 0) ------------------ | Branch (3207:33): [True: 0, False: 0] ------------------ 3208| 0| { 3209| 0| jN2 = j; 3210| 0| n++; 3211| 0| } 3212| 0| else 3213| 0| { 3214| 0| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (3214:33): [True: 0, False: 0] ------------------ 3215| 0| MobileGr[j].num_bonds <= 2 && ------------------ | Branch (3215:35): [True: 0, False: 0] ------------------ 3216| 0| MobileGr[j].bonds_valence <= 3 && ------------------ | Branch (3216:35): [True: 0, False: 0] ------------------ 3217| 0| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (3217:35): [True: 0, False: 0] ------------------ 3218| 0| at[MobileGr[j].atom_number].endpoint != k && ------------------ | Branch (3218:35): [True: 0, False: 0] ------------------ 3219| 0| jX < 0) ------------------ | Branch (3219:35): [True: 0, False: 0] ------------------ 3220| 0| { 3221| 0| jX = j; 3222| 0| n++; 3223| 0| } 3224| 0| } 3225| 0| } 3226| 0| } 3227| 0| } 3228| 0| if (n != 3) ------------------ | Branch (3228:17): [True: 0, False: 0] ------------------ 3229| 0| { 3230| 0| goto case_5_9c_to_9d; 3231| 0| } 3232| | 3233| 0| e = pBNS->edge + pVA[MobileGr[jN2].atom_number].nTautGroupEdge - 1; 3234| 0| if (!e->flow) ------------------ | Branch (3234:17): [True: 0, False: 0] ------------------ 3235| 0| { 3236| 0| goto case_5_9c_to_9d; /* should not happen ??? */ 3237| 0| } 3238| 0| e->flow--; 3239| 0| pBNS->vert[e->neighbor1].st_edge.flow--; 3240| 0| pBNS->vert[e->neighbor1 ^ e->neighbor12].st_edge.flow--; 3241| 0| pBNS->tot_st_flow -= 2; 3242| 0| e->forbidden |= forbidden_mask; 3243| 0| num_changes++; 3244| 0| continue; 3245| 0| } 3246| 64| case_5_9c_to_9d: /* #6 */ 3247| | /*********************************************************************/ 3248| 64| if (3 == num_bonds_non_metal && ------------------ | Branch (3248:13): [True: 29, False: 35] ------------------ 3249| 29| 4 == bonds_valence_non_metal && ------------------ | Branch (3249:14): [True: 18, False: 11] ------------------ 3250| 18| ( centerpoint_type == EL_TYPE_S ) && ------------------ | | 387| 18|#define EL_TYPE_S 0x0002 ------------------ | Branch (3250:14): [True: 18, False: 0] ------------------ 3251| 18| 0 == num_O + num_S && 3 == num_N && 0 == num_P && ------------------ | Branch (3251:14): [True: 16, False: 2] | Branch (3251:36): [True: 1, False: 15] | Branch (3251:50): [True: 1, False: 0] ------------------ 3252| 1| 0 == num_forbidden && ------------------ | Branch (3252:14): [True: 0, False: 1] ------------------ 3253| 0| 3 == num_mgroups && 2 == num_diff_t_groups && ------------------ | Branch (3253:14): [True: 0, False: 0] | Branch (3253:34): [True: 0, False: 0] ------------------ 3254| 0| 2 == num_donor_endpoints && 0 == num_acceptor_endpoints && ------------------ | Branch (3254:14): [True: 0, False: 0] | Branch (3254:42): [True: 0, False: 0] ------------------ 3255| 0| 2 == num_donors && 1 == num_acceptors) ------------------ | Branch (3255:14): [True: 0, False: 0] | Branch (3255:33): [True: 0, False: 0] ------------------ 3256| 0| { 3257| | /******************************************************** 3258| | *** InChI Tech. Man., Table 5, case 9b->8b *** 3259| | ******************************************************** 3260| | 3(X) ---> e2| O = O, S, Se, Te 3261| | NH---is an N====== S = S, Se, Te 3262| | \ / endpoint \ / f = fixed bond 3263| | \ 1 / C=====Z \ f / C-----Z tg = Mobile-H vertex 3264| | N===S | | N===S || || X = is N not an endpoint; 3265| | is an ev \ | | ev \ || || -X is not terminal -O,-S,-Se,-Te or 3266| | endpoint 2\ | e1 | \|| e1 || any N, P, As 3267| | NH=====tg N------tg 3268| | is an f N, N, X, fixed double 3269| | endpoint ===================== 3270| | 3271| | Problem: 3272| | N1, N2, and N3 are Mobile-H endpoints and belong to the same Mobile-H group. 3273| | Fixed bond N1==S prevents the correct structure restoration: 3274| | H cannot migrate N3->N2->N1 because N1=S bond is fixed 3275| | Solution: 3276| | Move mobile H to N2 and N3 to make N1=S bond unfixed (Table 5, case 9c) 3277| | (see fix_special_bonds(...) for details ) 3278| | *********************************************************/ 3279| 0| int jN1 = -1, jN2 = -1, jX = -1, n = 0; 3280| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (3280:25): [True: 0, False: 0] ------------------ 3281| 0| { 3282| 0| if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N) ------------------ | | 392| 0|#define EL_TYPE_MASK 0x003f ------------------ if (( MobileGr[j].atom_type_pVA & EL_TYPE_MASK ) == EL_TYPE_N) ------------------ | | 388| 0|#define EL_TYPE_N 0x0004 ------------------ | Branch (3282:21): [True: 0, False: 0] ------------------ 3283| 0| { 3284| 0| if (MobileGr[j].bond_type == BOND_TYPE_DOUBLE && ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (3284:25): [True: 0, False: 0] ------------------ 3285| 0| !at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (3285:26): [True: 0, False: 0] ------------------ 3286| 0| !( MobileGr[j].forbidden & forbidden_mask ) && ------------------ | Branch (3286:26): [True: 0, False: 0] ------------------ 3287| 0| jN1 < 0) ------------------ | Branch (3287:26): [True: 0, False: 0] ------------------ 3288| 0| { 3289| 0| jN1 = j; 3290| 0| n++; 3291| 0| } 3292| 0| else 3293| 0| { 3294| 0| if (MobileGr[j].bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (3294:29): [True: 0, False: 0] ------------------ 3295| 0| MobileGr[j].num_bonds == 2 && ------------------ | Branch (3295:33): [True: 0, False: 0] ------------------ 3296| 0| MobileGr[j].bonds_valence <= 3 && ------------------ | Branch (3296:33): [True: 0, False: 0] ------------------ 3297| 0| at[MobileGr[j].atom_number].endpoint && ------------------ | Branch (3297:33): [True: 0, False: 0] ------------------ 3298| 0| !( MobileGr[j].forbidden & forbidden_mask )) ------------------ | Branch (3298:33): [True: 0, False: 0] ------------------ 3299| 0| { 3300| 0| if (jN2 < 0) ------------------ | Branch (3300:33): [True: 0, False: 0] ------------------ 3301| 0| { 3302| 0| jN2 = j; 3303| 0| n++; 3304| 0| } 3305| 0| else 3306| 0| { 3307| 0| if (jX < 0) ------------------ | Branch (3307:37): [True: 0, False: 0] ------------------ 3308| 0| { 3309| 0| jX = j; 3310| 0| n++; 3311| 0| } 3312| 0| } 3313| 0| } 3314| 0| } 3315| 0| } 3316| 0| } 3317| 0| if (n != 3) ------------------ | Branch (3317:17): [True: 0, False: 0] ------------------ 3318| 0| { 3319| 0| goto case_end; 3320| 0| } 3321| 0| ev = pBNS->edge + pBNS->vert[i].iedge[MobileGr[jN1].ineigh]; 3322| 0| if (!ev->flow) /* 2017-02-15 Fixed typo ("!e->flow") which has been here since v. 1.01 */ ------------------ | Branch (3322:17): [True: 0, False: 0] ------------------ 3323| 0| { 3324| 0| goto case_end; 3325| 0| } 3326| 0| e1 = pBNS->edge + pVA[MobileGr[jN2].atom_number].nTautGroupEdge - 1; 3327| 0| if (!e1->flow) ------------------ | Branch (3327:17): [True: 0, False: 0] ------------------ 3328| 0| { 3329| 0| goto case_end; /* should not happen ??? */ 3330| 0| } 3331| 0| e2 = pBNS->edge + pVA[MobileGr[jX].atom_number].nTautGroupEdge - 1; 3332| 0| if (!e2->flow) ------------------ | Branch (3332:17): [True: 0, False: 0] ------------------ 3333| 0| { 3334| 0| goto case_end; /* should not happen ??? */ 3335| 0| } 3336| | /* take care of edge e1 */ 3337| 0| e = e1; 3338| 0| e->flow--; 3339| 0| pBNS->vert[e->neighbor1].st_edge.flow--; 3340| 0| pBNS->vert[e->neighbor1 ^ e->neighbor12].st_edge.flow--; 3341| 0| pBNS->tot_st_flow -= 2; 3342| 0| e->forbidden |= forbidden_mask; 3343| 0| num_changes++; 3344| | /* take care of edge e2 */ 3345| 0| e = e2; 3346| 0| e->flow--; 3347| 0| pBNS->vert[e->neighbor1].st_edge.flow--; 3348| 0| pBNS->vert[e->neighbor1 ^ e->neighbor12].st_edge.flow--; 3349| 0| pBNS->tot_st_flow -= 2; 3350| 0| e->forbidden |= forbidden_mask; 3351| 0| num_changes++; 3352| | /* take care of edge ev: do not let it change */ 3353| 0| ev->forbidden |= forbidden_mask; 3354| 0| continue; 3355| 0| } 3356| 64| case_end:; 3357| 64| } 3358| | 3359| |/*exit_function:*/ 3360| 486| return num_changes; 3361| 486|} RearrangePlusMinusEdgesFlow: 3373| 87.8k|{ 3374| 87.8k| int ret, ePlus, eMinus; 3375| 87.8k| EDGE_LIST NewlyFixedEdges; 3376| 87.8k| BNS_EDGE *pPlus, *pMinus; 3377| 87.8k| int i, k1, k2, num_found, num_tot, delta, v1, v2; 3378| | 3379| 87.8k| ret = 0; 3380| | 3381| 87.8k| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.8k|#define EDGE_LIST_CLEAR (-1) ------------------ 3382| 920k| for (i = 0, num_found = num_tot = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (3382:42): [True: 832k, False: 87.8k] ------------------ 3383| 832k| { 3384| 832k| eMinus = pVA[i].nCMinusGroupEdge - 1; 3385| 832k| ePlus = pVA[i].nCPlusGroupEdge - 1; 3386| 832k| num_tot += ( eMinus >= 0 ) + ( ePlus >= 0 ); 3387| 832k| if (eMinus >= 0 && ePlus >= 0) ------------------ | Branch (3387:13): [True: 119k, False: 712k] | Branch (3387:28): [True: 102k, False: 17.6k] ------------------ 3388| 102k| { 3389| 102k| pPlus = pBNS->edge + ePlus; 3390| 102k| pMinus = pBNS->edge + eMinus; 3391| 102k| if (( pMinus->flow ) > 0 && ( pPlus->cap - pPlus->flow ) > 0) /* djb-rwth: removing redundant code */ ------------------ | Branch (3391:17): [True: 19.4k, False: 82.8k] | Branch (3391:41): [True: 14, False: 19.4k] ------------------ 3392| 14| { 3393| 14| num_found++; 3394| 14| } 3395| 102k| } 3396| 832k| } 3397| 87.8k| if (!num_found) ------------------ | Branch (3397:9): [True: 87.7k, False: 14] ------------------ 3398| 87.7k| { 3399| 87.7k| goto exit_function; 3400| 87.7k| } 3401| 14| if ((ret = AllocEdgeList( &NewlyFixedEdges, num_tot + pBNS->num_bonds ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3401:9): [True: 0, False: 14] ------------------ 3402| 0| { 3403| 0| goto exit_function; 3404| 0| } 3405| | 3406| 117| for (i = 0, num_tot = 0; i < pBNS->num_atoms; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (3406:30): [True: 103, False: 14] ------------------ 3407| 103| { 3408| 103| eMinus = pVA[i].nCMinusGroupEdge - 1; 3409| 103| ePlus = pVA[i].nCPlusGroupEdge - 1; 3410| 103| num_tot += ( eMinus >= 0 ) + ( ePlus >= 0 ); 3411| 103| if (eMinus >= 0 && ePlus >= 0) ------------------ | Branch (3411:13): [True: 74, False: 29] | Branch (3411:28): [True: 65, False: 9] ------------------ 3412| 65| { 3413| 65| pPlus = pBNS->edge + ePlus; 3414| 65| pMinus = pBNS->edge + eMinus; 3415| 65| if (( k1 = pMinus->flow ) > 0 && ( k2 = pPlus->cap - pPlus->flow ) > 0) ------------------ | Branch (3415:17): [True: 26, False: 39] | Branch (3415:46): [True: 14, False: 12] ------------------ 3416| 14| { 3417| | /* rearrange */ 3418| 14| v1 = pMinus->neighbor1; 3419| 14| v2 = pMinus->neighbor12 ^ v1; 3420| 14| delta = inchi_min( k1, k2 ); ------------------ | | 139| 14|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 14] | | ------------------ ------------------ 3421| 14| pMinus->flow -= delta; 3422| 14| pBNS->vert[v1].st_edge.flow -= delta; 3423| 14| pBNS->vert[v2].st_edge.flow -= delta; 3424| 14| pBNS->tot_st_flow -= 2 * delta; 3425| 14| } 3426| | /* fix charges */ 3427| 65| pPlus->forbidden |= forbidden_edge_mask; 3428| 65| pMinus->forbidden |= forbidden_edge_mask; 3429| 65| if (( ret = AddToEdgeList( &NewlyFixedEdges, eMinus, 0 ) ) || ------------------ | Branch (3429:17): [True: 0, False: 65] ------------------ 3430| 65| ( ret = AddToEdgeList( &NewlyFixedEdges, ePlus, 0 ) )) ------------------ | Branch (3430:17): [True: 0, False: 65] ------------------ 3431| 0| { 3432| 0| goto exit_function; 3433| 0| } 3434| 65| } 3435| 38| else 3436| 38| { 3437| 38| if (eMinus >= 0) ------------------ | Branch (3437:17): [True: 9, False: 29] ------------------ 3438| 9| { 3439| | /* fix charges */ 3440| 9| pMinus = pBNS->edge + eMinus; 3441| 9| pMinus->forbidden |= forbidden_edge_mask; 3442| 9| if ((ret = AddToEdgeList( &NewlyFixedEdges, eMinus, 0 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3442:21): [True: 0, False: 9] ------------------ 3443| 0| { 3444| 0| goto exit_function; 3445| 0| } 3446| 9| } 3447| 29| else 3448| 29| { 3449| 29| if (ePlus >= 0) ------------------ | Branch (3449:21): [True: 10, False: 19] ------------------ 3450| 10| { 3451| | /* fix charges */ 3452| 10| pPlus = pBNS->edge + ePlus; 3453| 10| pPlus->forbidden |= forbidden_edge_mask; 3454| 10| if ((ret = AddToEdgeList( &NewlyFixedEdges, ePlus, 0 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3454:25): [True: 0, False: 10] ------------------ 3455| 0| { 3456| 0| goto exit_function; 3457| 0| } 3458| 10| } 3459| 29| } 3460| 38| } 3461| 103| } 3462| 114| for (i = 0; i < pBNS->num_bonds; i++) ------------------ | Branch (3462:17): [True: 100, False: 14] ------------------ 3463| 100| { 3464| 100| pBNS->edge[i].forbidden |= forbidden_edge_mask; 3465| 100| if ((ret = AddToEdgeList( &NewlyFixedEdges, i, 0 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3465:13): [True: 0, False: 100] ------------------ 3466| 0| { 3467| 0| goto exit_function; 3468| 0| } 3469| 100| } 3470| 14| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3471| 14| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 3472| 14| if (ret < 0) ------------------ | Branch (3472:9): [True: 0, False: 14] ------------------ 3473| 0| { 3474| 0| goto exit_function; 3475| 0| } 3476| | 3477| 87.8k|exit_function: 3478| 87.8k| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.8k|#define EDGE_LIST_FREE (-2) ------------------ 3479| | 3480| 87.8k| return ret; 3481| 14|} IncrementZeroOrderBondsToHeteroat: 3495| 87.8k|{ 3496| 87.8k|#define FIX_BOND_ADD_ALLOC 128 3497| 87.8k| Vertex vPathStart, vPathEnd; 3498| 87.8k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 3499| 87.8k| BNS_EDGE *pe, *peZero, *peNeighMeigh = NULL, *peMeFlower; 3500| 87.8k| BNS_VERTEX *pMeFlower = NULL, *pNeigh = NULL, *pNeighNeigh = NULL; 3501| | 3502| 87.8k| int i, j, k, ret2, ret, bFixedCarbonCharges, num_changes, bSuccess; 3503| 87.8k| int num_at = pStruct->num_atoms; 3504| 87.8k| int num_deleted_H = pStruct->num_deleted_H; 3505| 87.8k| int len_at = num_at + num_deleted_H; 3506| 87.8k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 3507| 87.8k| Vertex vMeFlower0, vNeigh, vNeighMeigh = NO_VERTEX; ------------------ | | 118| 87.8k|#define NO_VERTEX -2 ------------------ 3508| | 3509| 87.8k| EDGE_LIST CarbonChargeEdges; 3510| 87.8k| EDGE_LIST NewlyFixedEdges; 3511| | 3512| 87.8k| ret = 0; 3513| 87.8k| num_changes = 0; 3514| | 3515| 87.8k| bFixedCarbonCharges = 0; 3516| 87.8k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.8k|#define EDGE_LIST_CLEAR (-1) ------------------ 3517| 87.8k| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.8k|#define EDGE_LIST_CLEAR (-1) ------------------ 3518| | 3519| 87.8k| if (!pTCGroups->num_metal_atoms || ------------------ | Branch (3519:9): [True: 22.3k, False: 65.4k] ------------------ 3520| 65.4k| 0 > ( k = pTCGroups->nGroup[TCG_MeFlower0] ) || ------------------ | Branch (3520:10): [True: 48.3k, False: 17.0k] ------------------ 3521| 17.0k| 0 > ( vMeFlower0 = pTCGroups->pTCG[k].nVertexNumber )) ------------------ | Branch (3521:10): [True: 0, False: 17.0k] ------------------ 3522| 70.7k| { 3523| 70.7k| goto exit_function; 3524| 70.7k| } 3525| | 3526| 17.0k| memcpy(at2, at, len_at * sizeof(at2[0])); 3527| 17.0k| pStruct->at = at2; 3528| 17.0k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3529| 17.0k| pStruct->at = at; 3530| 17.0k| if (ret2 < 0) ------------------ | Branch (3530:9): [True: 9, False: 17.0k] ------------------ 3531| 9| { 3532| 9| ret = ret2; 3533| 9| goto exit_function; 3534| 9| } 3535| 110k| for (i = 0; i < num_at; i++) ------------------ | Branch (3535:17): [True: 93.7k, False: 17.0k] ------------------ 3536| 93.7k| { 3537| 93.7k| if (!pVA[i].cMetal || pVA[i].nMetalGroupEdge <= 0) ------------------ | Branch (3537:13): [True: 69.4k, False: 24.3k] | Branch (3537:31): [True: 0, False: 24.3k] ------------------ 3538| 69.4k| { 3539| 69.4k| continue; 3540| 69.4k| } 3541| 24.3k| peMeFlower = pBNS->edge + pVA[i].nMetalGroupEdge - 1; 3542| 24.3k| if (vMeFlower0 != ( peMeFlower->neighbor12 ^ i )) ------------------ | Branch (3542:13): [True: 0, False: 24.3k] ------------------ 3543| 0| { 3544| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3545| 0| goto exit_function; 3546| 0| } 3547| 24.3k| pMeFlower = pBNS->vert + vMeFlower0; 3548| | 3549| 67.4k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (3549:21): [True: 43.1k, False: 24.2k] ------------------ 3550| 43.1k| { 3551| 43.1k| if (!peMeFlower->flow) ------------------ | Branch (3551:17): [True: 17, False: 43.1k] ------------------ 3552| 17| { 3553| 17| break; /* cannot do anything */ 3554| 17| } 3555| 43.1k| if (!( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 189| 43.1k|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (3555:17): [True: 13.9k, False: 29.2k] ------------------ 3556| 13.9k| { 3557| | /* found a zero order bond */ 3558| 13.9k| if (!bFixedCarbonCharges) ------------------ | Branch (3558:21): [True: 9.80k, False: 4.10k] ------------------ 3559| 9.80k| { 3560| | /* do not let carbon atoms get charged */ 3561| 9.80k| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (3561:25): [True: 0, False: 9.80k] ------------------ 3562| 0| { 3563| 0| goto exit_function; 3564| 0| } 3565| 9.80k| bFixedCarbonCharges++; 3566| 9.80k| } 3567| 13.9k| peZero = pBNS->edge + pBNS->vert[i].iedge[j]; 3568| 13.9k| if (peZero->flow) ------------------ | Branch (3568:21): [True: 0, False: 13.9k] ------------------ 3569| 0| { 3570| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3571| 0| goto exit_function; 3572| 0| } 3573| | /* fix other edges */ 3574| 43.0k| for (k = 0; k < at2[i].valence; k++) ------------------ | Branch (3574:29): [True: 29.1k, False: 13.9k] ------------------ 3575| 29.1k| { 3576| 29.1k| pe = pBNS->edge + pBNS->vert[i].iedge[k]; 3577| 29.1k| if (pe->flow == 1 && !( pe->forbidden & forbidden_edge_mask )) ------------------ | Branch (3577:25): [True: 6.61k, False: 22.5k] | Branch (3577:42): [True: 6.31k, False: 298] ------------------ 3578| 6.31k| { 3579| 6.31k| if ((ret = AddToEdgeList( &NewlyFixedEdges, (int) ( pe - pBNS->edge ), FIX_BOND_ADD_ALLOC ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 3496| 6.31k|#define FIX_BOND_ADD_ALLOC 128 ------------------ | Branch (3579:29): [True: 0, False: 6.31k] ------------------ 3580| 0| { 3581| 0| goto exit_function; 3582| 0| } 3583| 6.31k| pe->forbidden |= forbidden_edge_mask; 3584| 6.31k| } 3585| 29.1k| } 3586| | /* do not create =N(+)= in a ring or #O(+) terminal */ 3587| 93.5k| for (k = 0; k < num_at; k++) ------------------ | Branch (3587:29): [True: 79.6k, False: 13.9k] ------------------ 3588| 79.6k| { 3589| 79.6k| if (!pVA[k].cMetal && pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (3589:25): [True: 51.7k, False: 27.9k] | Branch (3589:43): [True: 15.7k, False: 36.0k] ------------------ 3590| 15.7k| at2[k].valence == 2 && !at2[k].num_H && pVA[k].cMinRingSize <= 6 && ------------------ | Branch (3590:26): [True: 6.87k, False: 8.87k] | Branch (3590:49): [True: 6.75k, False: 122] | Branch (3590:66): [True: 6.62k, False: 128] ------------------ 3591| 6.62k| pVA[k].nCPlusGroupEdge > 0 && ------------------ | Branch (3591:26): [True: 6.58k, False: 36] ------------------ 3592| 6.58k| ( pe = pBNS->edge + pVA[k].nCPlusGroupEdge - 1 )->flow == 1 && ------------------ | Branch (3592:26): [True: 5.05k, False: 1.53k] ------------------ 3593| 5.05k| !( pe->forbidden & forbidden_edge_mask )) ------------------ | Branch (3593:26): [True: 4.74k, False: 309] ------------------ 3594| 4.74k| { 3595| | 3596| 4.74k| if ((ret = AddToEdgeList( &NewlyFixedEdges, (int) ( pe - pBNS->edge ), FIX_BOND_ADD_ALLOC ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 3496| 4.74k|#define FIX_BOND_ADD_ALLOC 128 ------------------ | Branch (3596:29): [True: 0, False: 4.74k] ------------------ 3597| 0| { 3598| 0| goto exit_function; 3599| 0| } 3600| 4.74k| pe->forbidden |= forbidden_edge_mask; 3601| 4.74k| } 3602| 79.6k| } 3603| | 3604| | /* metal's neighbor connected by a zero-order bond */ 3605| 13.9k| pNeigh = pBNS->vert + ( vNeigh = at2[i].neighbor[j] ); 3606| | /*for ( k = 0; k < pNeigh->num_adj_edges; k ++ )*/ 3607| 36.1k| for (k = pNeigh->num_adj_edges - 1; 0 <= k; k--) ------------------ | Branch (3607:53): [True: 35.0k, False: 1.15k] ------------------ 3608| 35.0k| { 3609| 35.0k| peNeighMeigh = pBNS->edge + pNeigh->iedge[k]; 3610| 35.0k| if (!peNeighMeigh->flow) ------------------ | Branch (3610:25): [True: 18.6k, False: 16.4k] ------------------ 3611| 18.6k| { 3612| 18.6k| continue; 3613| 18.6k| } 3614| 16.4k| vNeighMeigh = peNeighMeigh->neighbor12 ^ vNeigh; 3615| 16.4k| if (vNeighMeigh != i && vNeighMeigh != vMeFlower0) ------------------ | Branch (3615:25): [True: 16.4k, False: 0] | Branch (3615:45): [True: 12.7k, False: 3.65k] ------------------ 3616| 12.7k| { 3617| | /* metal neighbor's neighbor connected by a not-zero-order bond */ 3618| 12.7k| pNeighNeigh = pBNS->vert + vNeighMeigh; 3619| 12.7k| break; /* found */ 3620| 12.7k| } 3621| 16.4k| } 3622| 13.9k| if (k < 0) ------------------ | Branch (3622:21): [True: 1.15k, False: 12.7k] ------------------ 3623| 1.15k| { 3624| 1.15k| continue; /* neighbor not found */ 3625| 1.15k| } 3626| 12.7k| peZero->flow++; 3627| 12.7k| peZero->forbidden |= forbidden_edge_mask; 3628| 12.7k| peMeFlower->flow--; 3629| 12.7k| peNeighMeigh->flow--; 3630| 12.7k| pMeFlower->st_edge.flow--; 3631| 12.7k| pNeighNeigh->st_edge.flow--; 3632| 12.7k| pBNS->tot_st_flow -= 2; 3633| | /* test */ 3634| 12.7k| bSuccess = 0; 3635| 12.7k| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3636| 12.7k| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3637| | 3638| 12.7k| if (ret == 1 && ( (vPathEnd == vMeFlower0 && vPathStart == vNeighMeigh) || ------------------ | Branch (3638:21): [True: 11.0k, False: 1.72k] | Branch (3638:36): [True: 5.01k, False: 6.01k] | Branch (3638:62): [True: 4.72k, False: 288] ------------------ 3639| 10.5k| (vPathEnd == vNeighMeigh && vPathStart == vMeFlower0) ) && abs( nDeltaCharge ) <= 2) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3639:22): [True: 5.92k, False: 373] | Branch (3639:49): [True: 5.86k, False: 63] | Branch (3639:80): [True: 10.5k, False: 88] ------------------ 3640| 10.5k| { 3641| 10.5k| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3642| 10.5k| if (ret > 0) ------------------ | Branch (3642:25): [True: 10.5k, False: 0] ------------------ 3643| 10.5k| { 3644| 10.5k| ( *pnNumRunBNS )++; 3645| 10.5k| *pnTotalDelta += ret; 3646| 10.5k| num_changes++; 3647| 10.5k| bSuccess = ret; 3648| 10.5k| } 3649| 10.5k| if ((ret = AddToEdgeList( &NewlyFixedEdges, (int) ( peZero - pBNS->edge ), FIX_BOND_ADD_ALLOC ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 3496| 10.5k|#define FIX_BOND_ADD_ALLOC 128 ------------------ | Branch (3649:25): [True: 0, False: 10.5k] ------------------ 3650| 0| { 3651| 0| goto exit_function; 3652| 0| } 3653| 10.5k| } 3654| 2.24k| else 3655| 2.24k| { 3656| 2.24k| peZero->flow--; 3657| 2.24k| peZero->forbidden &= inv_forbidden_edge_mask; 3658| 2.24k| peMeFlower->flow++; 3659| 2.24k| peNeighMeigh->flow++; 3660| 2.24k| pMeFlower->st_edge.flow++; 3661| 2.24k| pNeighNeigh->st_edge.flow++; 3662| 2.24k| pBNS->tot_st_flow += 2; 3663| 2.24k| } 3664| 12.7k| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 3665| 12.7k| NewlyFixedEdges.num_edges = 0; 3666| 12.7k| if (bSuccess) ------------------ | Branch (3666:21): [True: 10.5k, False: 2.24k] ------------------ 3667| 10.5k| { 3668| | /* update at2[] */ 3669| 10.5k| memcpy(at2, at, len_at * sizeof(at2[0])); 3670| 10.5k| pStruct->at = at2; 3671| 10.5k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3672| 10.5k| pStruct->at = at; 3673| 10.5k| if (ret2 < 0) ------------------ | Branch (3673:25): [True: 0, False: 10.5k] ------------------ 3674| 0| { 3675| 0| ret = ret2; 3676| 0| goto exit_function; 3677| 0| } 3678| 10.5k| } 3679| 12.7k| } 3680| 43.1k| } 3681| 24.3k| } 3682| 17.0k| ret = num_changes; 3683| | 3684| 87.8k|exit_function: 3685| 87.8k| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 3686| 87.8k| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 3687| 87.8k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.8k|#define EDGE_LIST_FREE (-2) ------------------ 3688| 87.8k| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.8k|#define EDGE_LIST_FREE (-2) ------------------ 3689| | 3690| 87.8k| return ret; 3691| 17.0k|} MovePlusFromS2DiaminoCarbon: 3711| 87.7k|{ 3712| 87.7k| int i, j, k, ret, ret2; /* djb-rwth: removing redundant variables */ 3713| 87.7k| int delta; 3714| 87.7k| EdgeIndex ePlusS, ePlusC, eMinusC, e; 3715| 87.7k| BNS_VERTEX *pvS, *pvC, *pv1, *pv2; 3716| 87.7k| BNS_EDGE *pePlusS, *pePlusC, *pe1, *pe2, *peCN[3], *peSC, *pe; 3717| 87.7k| Vertex vC, vN; 3718| | 3719| 87.7k| int num_at = pStruct->num_atoms; 3720| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 3721| 87.7k| int len_at = num_at + num_deleted_H; 3722| | 3723| 87.7k| Vertex vPathStart, vPathEnd, v1, v2; 3724| 87.7k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 3725| | 3726| 87.7k| EDGE_LIST AllChargeEdges; 3727| | 3728| 87.7k| ret = 0; 3729| | /* djb-rwth: removing redundant code */ 3730| | 3731| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 3732| | 3733| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 3734| 87.7k| pStruct->at = at2; 3735| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3736| 87.7k| pStruct->at = at; 3737| 87.7k| if (ret2 < 0) ------------------ | Branch (3737:9): [True: 12, False: 87.7k] ------------------ 3738| 12| { 3739| 12| ret = ret2; 3740| 12| goto exit_function; 3741| 12| } 3742| | /* find (NH2)C=S(+) */ 3743| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (3743:17): [True: 832k, False: 87.7k] ------------------ 3744| 832k| { 3745| 832k| pvS = pBNS->vert + i; /* djb-rwth: avoiding unsequenced modification and access */ 3746| 832k| if (!pVA[i].cMetal && pVA[i].cNumValenceElectrons == 6 && ------------------ | Branch (3746:13): [True: 513k, False: 318k] | Branch (3746:31): [True: 215k, False: 298k] ------------------ 3747| 215k| at2[i].valence == 2 && ------------------ | Branch (3747:14): [True: 9.54k, False: 205k] ------------------ 3748| 9.54k| pvS->st_edge.cap == pvS->st_edge.flow && ------------------ | Branch (3748:14): [True: 9.50k, False: 41] ------------------ 3749| 9.50k| 0 <= ( ePlusS = pVA[i].nCPlusGroupEdge - 1 ) && !( pePlusS = pBNS->edge + ePlusS )->flow && /* S(+) */ ------------------ | Branch (3749:14): [True: 9.44k, False: 61] | Branch (3749:62): [True: 3.88k, False: 5.55k] ------------------ 3750| 3.88k| ( pe1 = pBNS->edge + pvS->iedge[0] )->flow + ------------------ | Branch (3750:14): [True: 2.97k, False: 905] ------------------ 3751| 3.88k| ( pe2 = pBNS->edge + pvS->iedge[1] )->flow == 1 /* -S(+)= */ && 3752| 2.97k| pVA[vC = ( peSC = pe1->flow ? pe1 : pe2 )->neighbor12 ^ i].cNumValenceElectrons == 4 && ------------------ | Branch (3752:14): [True: 1.62k, False: 1.35k] | Branch (3752:32): [True: 2.05k, False: 920] ------------------ 3753| 1.62k| at2[vC].valence == 3 && ------------------ | Branch (3753:14): [True: 174, False: 1.45k] ------------------ 3754| 174| 0 <= ( ePlusC = pVA[vC].nCPlusGroupEdge - 1 ) && ( pePlusC = pBNS->edge + ePlusC )->flow && ------------------ | Branch (3754:14): [True: 172, False: 2] | Branch (3754:63): [True: 171, False: 1] ------------------ 3755| 171| !( 0 <= ( eMinusC = pVA[vC].nCMinusGroupEdge - 1 ) && pBNS->edge[eMinusC].flow )) ------------------ | Branch (3755:17): [True: 171, False: 0] | Branch (3755:68): [True: 1, False: 170] ------------------ 3756| 170| { 3757| | /* found >C=S(+)- */ 3758| 170| pvC = pBNS->vert + vC; 3759| 680| for (j = k = 0; j < at[vC].valence; j++) ------------------ | Branch (3759:29): [True: 510, False: 170] ------------------ 3760| 510| { 3761| 510| if (peSC != ( peCN[k] = pBNS->edge + pvC->iedge[j] ) && !peCN[k]->flow) ------------------ | Branch (3761:21): [True: 340, False: 170] | Branch (3761:73): [True: 329, False: 11] ------------------ 3762| 329| { 3763| 329| k++; /* a single bond from C */ 3764| 329| } 3765| 510| } 3766| 170| if (k != 2) ------------------ | Branch (3766:17): [True: 10, False: 160] ------------------ 3767| 10| { 3768| 10| continue; 3769| 10| } 3770| 160| for (j = 0; j < k; j++) ------------------ | Branch (3770:25): [True: 160, False: 0] ------------------ 3771| 160| { 3772| 160| vN = peCN[j]->neighbor12 ^ vC; 3773| 160| if (pVA[vN].cNumValenceElectrons != 5 || ------------------ | Branch (3773:21): [True: 156, False: 4] ------------------ 3774| 4| pBNS->vert[vN].st_edge.cap != pBNS->vert[vN].st_edge.flow || ------------------ | Branch (3774:22): [True: 0, False: 4] ------------------ 3775| 4| at2[vN].num_H != 2 || ------------------ | Branch (3775:22): [True: 4, False: 0] ------------------ 3776| 0| at2[vN].endpoint || ( pStruct->endpoint && pStruct->endpoint[vN] )) ------------------ | Branch (3776:22): [True: 0, False: 0] | Branch (3776:44): [True: 0, False: 0] | Branch (3776:65): [True: 0, False: 0] ------------------ 3777| 160| { 3778| 160| break; /* does not fit the pattern */ 3779| 160| } 3780| 160| } 3781| 160| if (j != k) ------------------ | Branch (3781:17): [True: 160, False: 0] ------------------ 3782| 160| { 3783| 160| continue; 3784| 160| } 3785| | /* fix all charges */ 3786| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (3786:17): [True: 0, False: 0] ------------------ 3787| 0| { 3788| 0| for (j = 0; j < num_at; j++) ------------------ | Branch (3788:29): [True: 0, False: 0] ------------------ 3789| 0| { 3790| 0| if (0 <= ( e = pVA[j].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (3790:25): [True: 0, False: 0] | Branch (3790:68): [True: 0, False: 0] ------------------ 3791| 0| ( ret = AddToEdgeList( &AllChargeEdges, e, 2 * num_at ) )) ------------------ | Branch (3791:25): [True: 0, False: 0] ------------------ 3792| 0| { 3793| 0| goto exit_function; 3794| 0| } 3795| 0| if (0 <= ( e = pVA[j].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (3795:25): [True: 0, False: 0] | Branch (3795:69): [True: 0, False: 0] ------------------ 3796| 0| ( ret = AddToEdgeList( &AllChargeEdges, e, 2 * num_at ) )) ------------------ | Branch (3796:25): [True: 0, False: 0] ------------------ 3797| 0| { 3798| 0| goto exit_function; 3799| 0| } 3800| 0| } 3801| 0| } 3802| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3803| 0| pePlusS->forbidden &= ~forbidden_edge_mask; 3804| 0| pe = pePlusC; 3805| 0| if (!pe->flow) ------------------ | Branch (3805:17): [True: 0, False: 0] ------------------ 3806| 0| continue; 3807| 0| delta = 1; 3808| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 3809| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 3810| | 3811| 0| pe->flow -= delta; 3812| 0| pv1->st_edge.flow -= delta; 3813| 0| pv2->st_edge.flow -= delta; 3814| 0| pBNS->tot_st_flow -= 2 * delta; 3815| | 3816| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3817| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3818| | 3819| 0| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (3819:17): [True: 0, False: 0] | Branch (3819:32): [True: 0, False: 0] | Branch (3819:50): [True: 0, False: 0] ------------------ 3820| 0| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3820:18): [True: 0, False: 0] | Branch (3820:36): [True: 0, False: 0] | Branch (3820:59): [True: 0, False: 0] ------------------ 3821| 0| { 3822| | /* Remover (+)charge from S => nDeltaCharge == -1 */ 3823| | /* Flow change on pe (+)charge edge (atom S) is not known to RunBnsTestOnce()) */ 3824| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3825| 0| if (ret > 0) ------------------ | Branch (3825:21): [True: 0, False: 0] ------------------ 3826| 0| { 3827| 0| ( *pnNumRunBNS )++; 3828| | /* djb-rwth: removing redundant code */ 3829| 0| } 3830| 0| } 3831| 0| else 3832| 0| { 3833| 0| pe->flow += delta; 3834| 0| pv1->st_edge.flow += delta; 3835| 0| pv2->st_edge.flow += delta; 3836| 0| pBNS->tot_st_flow += 2 * delta; 3837| 0| } 3838| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3839| 0| } 3840| 832k| } 3841| 87.7k|exit_function: 3842| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 3843| | 3844| 87.7k| return ret; 3845| 87.7k|} EliminateChargeSeparationOnHeteroatoms: 3861| 100k|{ 3862| 100k| int i, j, k, ret, ret2, num_pos, num_neg, num_min = 0, bFixedCarbonCharges; 3863| 100k| int vPlusSuper; /* (+)super vertex */ 3864| 100k| int ePlusSuper; /* edge from vPlusSuper to (+/-) */ 3865| 100k| int vPlusMinus; /* (+/-) vertex */ 3866| 100k| int nDeltaPlus1, nDeltaMinus1, delta; 3867| 100k| BNS_VERTEX *pvPlusSuper, *pvPlusMinus; 3868| 100k| BNS_EDGE *pEdge; 3869| | 3870| 100k| int num_at = pStruct->num_atoms; 3871| 100k| int num_deleted_H = pStruct->num_deleted_H; 3872| 100k| int len_at = num_at + num_deleted_H; 3873| 100k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 3874| | 3875| 100k| Vertex vPathStart, vPathEnd; 3876| 100k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 3877| | 3878| 100k| EDGE_LIST FixedLargeRingStereoEdges, CarbonChargeEdges; 3879| | 3880| 100k| ret = 0; 3881| | 3882| 100k| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 100k|#define EDGE_LIST_CLEAR (-1) ------------------ 3883| 100k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 100k|#define EDGE_LIST_CLEAR (-1) ------------------ 3884| 100k| bFixedCarbonCharges = 0; 3885| | 3886| 100k| if (forbidden_stereo_edge_mask) ------------------ | Branch (3886:9): [True: 13.1k, False: 87.7k] ------------------ 3887| 13.1k| { 3888| 86.6k| for (i = 0; i < num_at; i++) ------------------ | Branch (3888:21): [True: 73.4k, False: 13.1k] ------------------ 3889| 73.4k| { 3890| 203k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (3890:25): [True: 130k, False: 73.4k] ------------------ 3891| 130k| { 3892| 130k| if (pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask) ------------------ | Branch (3892:21): [True: 186, False: 130k] ------------------ 3893| 186| { 3894| 186| int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q, 3895| 186| pStruct->pbfsq->nAtomLevel, 3896| 186| pStruct->pbfsq->cSource, 99 /* max ring size */ ); 3897| 186| if (0 < nMinRingSize && ( ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, 64 ) )) ------------------ | Branch (3897:25): [True: 128, False: 58] | Branch (3897:45): [True: 0, False: 128] ------------------ 3898| 0| { 3899| 0| goto exit_function; 3900| 0| } 3901| 186| } 3902| 130k| } 3903| 73.4k| } 3904| 13.1k| if (!FixedLargeRingStereoEdges.num_edges) ------------------ | Branch (3904:13): [True: 13.0k, False: 52] ------------------ 3905| 13.0k| { 3906| 13.0k| goto exit_function; 3907| 13.0k| } 3908| 52| else 3909| 52| { 3910| | /* allow stereobonds in rings change */ 3911| 52| RemoveForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 3912| 52| } 3913| 13.1k| } 3914| | 3915| 87.8k| memcpy(at2, at, len_at * sizeof(at2[0])); 3916| 87.8k| pStruct->at = at2; 3917| 87.8k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3918| 87.8k| pStruct->at = at; 3919| 87.8k| if (ret2 < 0) ------------------ | Branch (3919:9): [True: 0, False: 87.8k] ------------------ 3920| 0| { 3921| 0| ret = ret2; 3922| 0| goto exit_function; 3923| 0| } 3924| | /* count charges */ 3925| 87.8k| num_pos = num_neg = 0; 3926| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (3926:17): [True: 833k, False: 87.8k] ------------------ 3927| 833k| { 3928| 833k| if (!pVA[i].cMetal && !at2[i].radical) ------------------ | Branch (3928:13): [True: 514k, False: 318k] | Branch (3928:31): [True: 495k, False: 18.6k] ------------------ 3929| 495k| { 3930| 495k| num_pos += ( at2[i].charge > 0 ); 3931| 495k| num_neg += ( at2[i].charge < 0 ); 3932| 495k| } 3933| 833k| } 3934| 87.8k| num_min = inchi_min( num_pos, num_neg ); ------------------ | | 139| 87.8k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 7.00k, False: 80.8k] | | ------------------ ------------------ 3935| | 3936| | 3937| 87.8k| if (num_min && ------------------ | Branch (3937:9): [True: 15.1k, False: 72.6k] ------------------ 3938| 15.1k| ( k = pTCGroups->nGroup[TCG_Plus] ) >= 0 && ------------------ | Branch (3938:9): [True: 15.1k, False: 0] ------------------ 3939| 15.1k| ( ePlusSuper = pTCGroups->pTCG[k].nForwardEdge ) > 0 && ------------------ | Branch (3939:9): [True: 15.1k, False: 0] ------------------ 3940| 15.1k| ( vPlusSuper = pTCGroups->pTCG[k].nVertexNumber ) >= num_at && ------------------ | Branch (3940:9): [True: 15.1k, False: 0] ------------------ 3941| 15.1k| !( pEdge = pBNS->edge + ePlusSuper )->forbidden) ------------------ | Branch (3941:10): [True: 15.1k, False: 0] ------------------ 3942| 15.1k| { 3943| | 3944| 15.1k| vPlusMinus = pEdge->neighbor12 ^ vPlusSuper; 3945| 15.1k| pvPlusSuper = pBNS->vert + vPlusSuper; 3946| 15.1k| pvPlusMinus = pBNS->vert + vPlusMinus; 3947| 15.1k| num_min = inchi_min( num_min, pEdge->flow ); ------------------ | | 139| 15.1k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 7.99k, False: 7.17k] | | ------------------ ------------------ 3948| 15.1k| nDeltaPlus1 = pvPlusSuper->st_edge.cap - pvPlusSuper->st_edge.flow; 3949| 15.1k| nDeltaMinus1 = pvPlusMinus->st_edge.cap - pvPlusMinus->st_edge.flow; 3950| 15.1k| if (num_min && ( !nDeltaPlus1 && !nDeltaMinus1 )) ------------------ | Branch (3950:13): [True: 15.1k, False: 0] | Branch (3950:26): [True: 15.1k, False: 4] | Branch (3950:42): [True: 15.1k, False: 27] ------------------ 3951| 15.1k| { 3952| 15.1k| if (!bFixedCarbonCharges) ------------------ | Branch (3952:17): [True: 15.1k, False: 0] ------------------ 3953| 15.1k| { /* 02-02-2006 */ 3954| | /* do not let carbon atoms get charged */ 3955| 15.1k| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (3955:21): [True: 0, False: 15.1k] ------------------ 3956| 0| { 3957| 0| goto exit_function; 3958| 0| } 3959| 15.1k| bFixedCarbonCharges++; 3960| 15.1k| } 3961| 15.1k| delta = 1; 3962| 15.1k| pEdge->forbidden |= forbidden_edge_mask; 3963| 15.1k| pBNS->edge_forbidden_mask |= forbidden_edge_mask; 3964| 17.9k| for (i = 0; i < num_min; i += delta) ------------------ | Branch (3964:25): [True: 15.9k, False: 1.98k] ------------------ 3965| 15.9k| { 3966| | /* cancel 1 pair of charges at a time */ 3967| | /* an attempt to cancel all at once may */ 3968| | /* convert a pair of N(IV)(+) into a pair of N(V) neutral with total charge reduced by 2 */ 3969| 15.9k| pEdge->flow -= delta; 3970| 15.9k| pvPlusSuper->st_edge.flow -= delta; 3971| 15.9k| pvPlusMinus->st_edge.flow -= delta; 3972| 15.9k| pBNS->tot_st_flow -= 2 * delta; 3973| | /* test for charhe cancellation */ 3974| 15.9k| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3975| 15.9k| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3976| 15.9k| if (ret < 0) ------------------ | Branch (3976:21): [True: 0, False: 15.9k] ------------------ 3977| 0| { 3978| 0| goto exit_function; 3979| 0| } 3980| 15.9k| if (ret == 1 && ( (vPathEnd == vPlusSuper && vPathStart == vPlusMinus) || ------------------ | Branch (3980:21): [True: 3.35k, False: 12.6k] | Branch (3980:36): [True: 468, False: 2.89k] | Branch (3980:62): [True: 202, False: 266] ------------------ 3981| 3.15k| (vPathEnd == vPlusMinus && vPathStart == vPlusSuper) ) && nDeltaCharge < 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3981:22): [True: 2.87k, False: 282] | Branch (3981:48): [True: 2.63k, False: 244] | Branch (3981:79): [True: 2.81k, False: 19] ------------------ 3982| 2.81k| { 3983| 2.81k| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3984| 2.81k| ( *pnNumRunBNS )++; 3985| 2.81k| if (ret < 0) ------------------ | Branch (3985:25): [True: 0, False: 2.81k] ------------------ 3986| 0| { 3987| 0| goto exit_function; 3988| 0| } 3989| 2.81k| else 3990| 2.81k| if (ret == 1) ------------------ | Branch (3990:29): [True: 2.81k, False: 0] ------------------ 3991| 2.81k| { 3992| 2.81k| *pnTotalDelta += ret; 3993| 2.81k| } 3994| 0| else 3995| 0| { 3996| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3997| 0| goto exit_function; 3998| 0| } 3999| 2.81k| } 4000| 13.1k| else 4001| 13.1k| { 4002| 13.1k| pEdge->flow += delta; 4003| 13.1k| pvPlusSuper->st_edge.flow += delta; 4004| 13.1k| pvPlusMinus->st_edge.flow += delta; 4005| 13.1k| pBNS->tot_st_flow += 2 * delta; 4006| 13.1k| break; 4007| 13.1k| } 4008| 15.9k| } 4009| 15.1k| num_min -= i; /* how many pairs of charges left */ 4010| 15.1k| pEdge->forbidden &= inv_forbidden_edge_mask; 4011| 15.1k| } 4012| 15.1k| nDeltaPlus1 = pvPlusSuper->st_edge.cap - pvPlusSuper->st_edge.flow; 4013| 15.1k| nDeltaMinus1 = pvPlusMinus->st_edge.cap - pvPlusMinus->st_edge.flow; 4014| 15.1k| if (num_min > 1 && ( !nDeltaPlus1 && !nDeltaMinus1 )) ------------------ | Branch (4014:13): [True: 2.51k, False: 12.6k] | Branch (4014:30): [True: 2.51k, False: 2] | Branch (4014:46): [True: 2.50k, False: 8] ------------------ 4015| 2.50k| { 4016| 2.50k| delta = 2; 4017| 2.50k| pEdge->forbidden |= forbidden_edge_mask; 4018| 2.50k| pBNS->edge_forbidden_mask |= forbidden_edge_mask; 4019| 2.50k| for (i = 0; i < num_min; i += delta) ------------------ | Branch (4019:25): [True: 2.50k, False: 0] ------------------ 4020| 2.50k| { 4021| | /* cancel 2 pairs of opposite charges at a time */ 4022| | /* 1. test cancellation of a pair of (+) charges */ 4023| 2.50k| pvPlusSuper->st_edge.cap += delta; 4024| 2.50k| pBNS->tot_st_cap += delta; 4025| 2.50k| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4026| 2.50k| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4027| 2.50k| if (ret < 0) ------------------ | Branch (4027:21): [True: 0, False: 2.50k] ------------------ 4028| 0| { 4029| 0| goto exit_function; 4030| 0| } 4031| 2.50k| pvPlusSuper->st_edge.cap -= delta; 4032| 2.50k| pBNS->tot_st_cap -= delta; 4033| 2.50k| if (ret != 1 || ( vPathEnd != vPlusSuper || vPathStart != vPlusSuper ) || nDeltaCharge >= 0) ------------------ | Branch (4033:21): [True: 2.24k, False: 260] | Branch (4033:35): [True: 4, False: 256] | Branch (4033:61): [True: 26, False: 230] | Branch (4033:91): [True: 1, False: 229] ------------------ 4034| 2.27k| { 4035| 2.27k| break; 4036| 2.27k| } 4037| | /* 2. test cancellation of a pair of (-) charges */ 4038| 229| pvPlusMinus->st_edge.cap += delta; 4039| 229| pBNS->tot_st_cap += delta; 4040| 229| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4041| 229| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4042| 229| if (ret < 0) ------------------ | Branch (4042:21): [True: 0, False: 229] ------------------ 4043| 0| { 4044| 0| goto exit_function; 4045| 0| } 4046| 229| pvPlusMinus->st_edge.cap -= delta; 4047| 229| pBNS->tot_st_cap -= delta; 4048| 229| if (ret != 1 || ( vPathEnd != vPlusMinus || vPathStart != vPlusMinus ) || nDeltaCharge >= 0) ------------------ | Branch (4048:21): [True: 228, False: 1] | Branch (4048:35): [True: 0, False: 1] | Branch (4048:61): [True: 1, False: 0] | Branch (4048:91): [True: 0, False: 0] ------------------ 4049| 229| { 4050| 229| break; 4051| 229| } 4052| | /* 3. Actually cancel the pair of charges */ 4053| 0| pEdge->flow -= delta; 4054| 0| pvPlusSuper->st_edge.flow -= delta; 4055| 0| pvPlusMinus->st_edge.flow -= delta; 4056| 0| pBNS->tot_st_flow -= 2 * delta; 4057| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4058| 0| ( *pnNumRunBNS )++; 4059| 0| if (ret < 0) ------------------ | Branch (4059:21): [True: 0, False: 0] ------------------ 4060| 0| { 4061| 0| goto exit_function; 4062| 0| } 4063| 0| else 4064| 0| { 4065| 0| if (ret == 2) ------------------ | Branch (4065:25): [True: 0, False: 0] ------------------ 4066| 0| { 4067| 0| *pnTotalDelta += ret; 4068| 0| } 4069| 0| else 4070| 0| { 4071| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 4072| 0| goto exit_function; 4073| 0| } 4074| 0| } 4075| 0| } 4076| 2.50k| num_min -= i; /* how many pairs of charges left */ 4077| 2.50k| pEdge->forbidden &= inv_forbidden_edge_mask; 4078| 2.50k| } 4079| 15.1k| } 4080| 87.8k| memcpy(at2, at, len_at * sizeof(at2[0])); 4081| 87.8k| pStruct->at = at; 4082| | 4083| 100k|exit_function: 4084| 100k| if (bFixedCarbonCharges) ------------------ | Branch (4084:9): [True: 15.1k, False: 85.7k] ------------------ 4085| 15.1k| { 4086| 15.1k| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4087| 15.1k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 15.1k|#define EDGE_LIST_FREE (-2) ------------------ 4088| 15.1k| } 4089| 100k| if (forbidden_stereo_edge_mask && FixedLargeRingStereoEdges.num_edges) ------------------ | Branch (4089:9): [True: 13.1k, False: 87.7k] | Branch (4089:39): [True: 52, False: 13.0k] ------------------ 4090| 52| { 4091| 52| SetForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 4092| 52| } 4093| 100k| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE ); ------------------ | | 243| 100k|#define EDGE_LIST_FREE (-2) ------------------ 4094| | 4095| 100k| return ret < 0 ? ret : num_min; ------------------ | Branch (4095:12): [True: 0, False: 100k] ------------------ 4096| 87.8k|} RestoreCyanoGroup: 4529| 87.7k|{ 4530| 87.7k| Vertex vPathStart, vPathEnd; 4531| 87.7k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 4532| 87.7k| BNS_EDGE *pe; 4533| | 4534| 87.7k| int i, j, ret2, ret; 4535| 87.7k| int num_at = pStruct->num_atoms; 4536| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 4537| 87.7k| int len_at = num_at + num_deleted_H; 4538| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 4539| 87.7k| Vertex v1, v2; 4540| | 4541| 87.7k| EDGE_LIST CarbonChargeEdges; 4542| | 4543| 87.7k| ret = 0; 4544| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 4545| | 4546| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 4547| 87.7k| pStruct->at = at2; 4548| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 4549| 87.7k| pStruct->at = at; 4550| 87.7k| if (ret2 < 0) ------------------ | Branch (4550:9): [True: 0, False: 87.7k] ------------------ 4551| 0| { 4552| 0| ret = ret2; 4553| 0| goto exit_function; 4554| 0| } 4555| | 4556| 920k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (4556:17): [True: 832k, False: 87.7k] | Branch (4556:31): [True: 832k, False: 0] ------------------ 4557| 832k| { 4558| 832k| if (at2[i].valence == 1 && ------------------ | Branch (4558:13): [True: 79.1k, False: 753k] ------------------ 4559| 79.1k| at2[i].num_H == 0 && ------------------ | Branch (4559:14): [True: 78.4k, False: 744] ------------------ 4560| 78.4k| at2[i].chem_bonds_valence == 2 && ------------------ | Branch (4560:14): [True: 20.9k, False: 57.4k] ------------------ 4561| 20.9k| at2[i].charge == -1 && ------------------ | Branch (4561:14): [True: 7.80k, False: 13.1k] ------------------ 4562| 7.80k| at2[i].radical == 0 && ------------------ | Branch (4562:14): [True: 7.13k, False: 671] ------------------ 4563| 7.13k| pVA[i].cNumValenceElectrons == 5 && /* terminal N(-)=, P, As, Sb, Bi */ ------------------ | Branch (4563:14): [True: 7.02k, False: 106] ------------------ 4564| 7.02k| pVA[i].nCMinusGroupEdge > 0 && ------------------ | Branch (4564:14): [True: 7.02k, False: 0] ------------------ 4565| 7.02k| pVA[i].nTautGroupEdge == 0 && ------------------ | Branch (4565:14): [True: 7.02k, False: 0] ------------------ 4566| 7.02k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (4566:14): [True: 2.88k, False: 4.13k] ------------------ 4567| 2.88k| at2[j].num_H == 0 && ------------------ | Branch (4567:14): [True: 2.87k, False: 10] ------------------ 4568| 2.87k| at2[j].chem_bonds_valence == 4 && ------------------ | Branch (4568:14): [True: 1.26k, False: 1.61k] ------------------ 4569| 1.26k| at2[j].charge == 0 && ------------------ | Branch (4569:14): [True: 25, False: 1.23k] ------------------ 4570| 25| at2[j].radical == 0 && ------------------ | Branch (4570:14): [True: 24, False: 1] ------------------ 4571| 24| pVA[j].cNumValenceElectrons == 4 && /* C or Si or Ge or Sn or Pb */ ------------------ | Branch (4571:14): [True: 18, False: 6] ------------------ 4572| 18| pVA[i].cnListIndex > 0 && ------------------ | Branch (4572:14): [True: 18, False: 0] ------------------ 4573| 18| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 436| 18|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 421| 18|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 18|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 18|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 18|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (4573:14): [True: 17, False: 1] ------------------ 4574| 17| { 4575| | /* found N(-)=C= */ 4576| 17| pe = pBNS->edge + ( (long long)pVA[i].nCMinusGroupEdge - 1 ); /* N#N(+) triple bond edge */ /* djb-rwth: cast operator added */ 4577| | 4578| 17| if (!pe->flow) ------------------ | Branch (4578:17): [True: 0, False: 17] ------------------ 4579| 0| { 4580| 0| continue; /* wrong atom ??? Strange... */ 4581| 0| } 4582| 17| v1 = pe->neighbor1; 4583| 17| v2 = pe->neighbor12 ^ v1; 4584| 17| pe->flow--; 4585| 17| pBNS->vert[v1].st_edge.flow--; 4586| 17| pBNS->vert[v2].st_edge.flow--; 4587| 17| pBNS->tot_st_flow -= 2; 4588| 17| pe->forbidden |= forbidden_edge_mask; 4589| | 4590| | /* do not let carbon atoms get charged */ 4591| 17| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (4591:17): [True: 0, False: 17] ------------------ 4592| 0| { 4593| 0| goto exit_function; 4594| 0| } 4595| | 4596| 17| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4597| 17| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4598| | 4599| 17| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (4599:17): [True: 15, False: 2] | Branch (4599:32): [True: 1, False: 14] | Branch (4599:50): [True: 1, False: 0] ------------------ 4600| 14| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4600:18): [True: 14, False: 0] | Branch (4600:36): [True: 9, False: 5] | Branch (4600:59): [True: 6, False: 4] ------------------ 4601| 6| { 4602| 6| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4603| 6| ( *pnNumRunBNS )++; 4604| 6| *pnTotalDelta += ret; 4605| 6| } 4606| 11| else 4607| 11| { 4608| 11| pe->flow++; 4609| 11| pBNS->vert[v1].st_edge.flow++; 4610| 11| pBNS->vert[v2].st_edge.flow++; 4611| 11| pBNS->tot_st_flow += 2; 4612| 11| } 4613| 17| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4614| | 4615| 17| pe->forbidden &= inv_forbidden_edge_mask; /* unmask the edges */ 4616| 17| } 4617| 832k| } 4618| | 4619| 87.7k|exit_function: 4620| | 4621| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 4622| | 4623| 87.7k| return ret; 4624| 87.7k|} RestoreIsoCyanoGroup: 4638| 87.7k|{ 4639| 87.7k|#define INC_EDGE_LIST 16 4640| 87.7k| Vertex vPathStart, vPathEnd; 4641| 87.7k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms, num_failed, num_success; 4642| 87.7k| BNS_EDGE *pe; 4643| 87.7k| Vertex v1, v2; 4644| | 4645| 87.7k| int i, j, ret2, ret, bIsCarbon; 4646| 87.7k| int num_at = pStruct->num_atoms; 4647| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 4648| 87.7k| int len_at = num_at + num_deleted_H; 4649| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 4650| 87.7k| EdgeIndex eNMinusEdge, eNPlusEdge, eNPlusEdge1, eN34Edge; 4651| 87.7k| EdgeIndex eNFlowerEdge1; 4652| | 4653| 87.7k| EDGE_LIST CarbonChargeEdges, AllChargeEdges, IsoCyanoCarbonChargeEdges; 4654| | 4655| 87.7k| ret = 0; 4656| 87.7k| num_failed = num_success = 0; 4657| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); /* carbon charge edges */ ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 4658| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); /* heteroatom charge edges */ ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 4659| 87.7k| AllocEdgeList( &IsoCyanoCarbonChargeEdges, EDGE_LIST_CLEAR ); /* C in C(+)#N(+) charge edges */ ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 4660| | 4661| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 4662| 87.7k| pStruct->at = at2; 4663| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 4664| 87.7k| pStruct->at = at; 4665| 87.7k| if (ret2 < 0) ------------------ | Branch (4665:9): [True: 0, False: 87.7k] ------------------ 4666| 0| { 4667| 0| ret = ret2; 4668| 0| goto exit_function; 4669| 0| } 4670| | /* 1st attempt: take care of C(+)#N(+)- => C(-)#N(+)- and remove 2 negative charges */ 4671| | /* This would produce nDeltaCharge = 2 */ 4672| 87.7k| AllocEdgeList( &CarbonChargeEdges, 2 * num_at ); 4673| 920k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (4673:17): [True: 832k, False: 87.7k] | Branch (4673:31): [True: 832k, False: 0] ------------------ 4674| 832k| { 4675| | /* accumulate edges for subsequent fixing them */ 4676| 832k| bIsCarbon = ( pVA[i].cNumValenceElectrons == 4 && pVA[i].cPeriodicRowNumber == 1 ); ------------------ | Branch (4676:23): [True: 92.9k, False: 739k] | Branch (4676:59): [True: 88.2k, False: 4.73k] ------------------ 4677| | /* djb-rwth: removing redundant variables/code */ 4678| 832k| if (( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4678:13): [True: 119k, False: 712k] ------------------ 4679| 119k| !pBNS->edge[eNMinusEdge].forbidden) ------------------ | Branch (4679:14): [True: 119k, False: 0] ------------------ 4680| 119k| { 4681| 119k| if (bIsCarbon) ------------------ | Branch (4681:17): [True: 25.6k, False: 94.2k] ------------------ 4682| 25.6k| { 4683| 25.6k| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 25.6k|#define INC_EDGE_LIST 16 ------------------ | Branch (4683:21): [True: 0, False: 25.6k] ------------------ 4684| 0| { 4685| 0| goto exit_function; 4686| 0| } 4687| 25.6k| } 4688| 94.2k| else 4689| 94.2k| { 4690| 94.2k| if (!pVA[i].cMetal && !at2[i].endpoint && at2[i].charge != -1) ------------------ | Branch (4690:21): [True: 70.0k, False: 24.2k] | Branch (4690:39): [True: 70.0k, False: 0] | Branch (4690:59): [True: 46.6k, False: 23.4k] ------------------ 4691| 46.6k| { 4692| 46.6k| if ((ret = AddToEdgeList( &AllChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 46.6k|#define INC_EDGE_LIST 16 ------------------ | Branch (4692:25): [True: 0, False: 46.6k] ------------------ 4693| 0| { 4694| 0| goto exit_function; 4695| 0| } 4696| 46.6k| } 4697| 94.2k| } 4698| 119k| } 4699| 832k| if (( eNPlusEdge = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4699:13): [True: 138k, False: 694k] ------------------ 4700| 138k| !pBNS->edge[eNPlusEdge].forbidden) ------------------ | Branch (4700:14): [True: 133k, False: 5.04k] ------------------ 4701| 133k| { 4702| 133k| if (bIsCarbon) ------------------ | Branch (4702:17): [True: 25.6k, False: 107k] ------------------ 4703| 25.6k| { 4704| 25.6k| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 25.6k|#define INC_EDGE_LIST 16 ------------------ | Branch (4704:21): [True: 0, False: 25.6k] ------------------ 4705| 0| { 4706| 0| goto exit_function; 4707| 0| } 4708| 25.6k| } 4709| 107k| else 4710| 107k| { 4711| 107k| if (!pVA[i].cMetal && !at2[i].endpoint) ------------------ | Branch (4711:21): [True: 83.1k, False: 24.2k] | Branch (4711:39): [True: 83.1k, False: 0] ------------------ 4712| 83.1k| { 4713| 83.1k| if ((ret = AddToEdgeList( &AllChargeEdges, eNPlusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 83.1k|#define INC_EDGE_LIST 16 ------------------ | Branch (4713:25): [True: 0, False: 83.1k] ------------------ 4714| 0| { 4715| 0| goto exit_function; 4716| 0| } 4717| 83.1k| if (pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (4717:25): [True: 40.3k, False: 42.7k] ------------------ 4718| 40.3k| NO_VERTEX != ( eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge ) ) && ------------------ | | 118| 40.3k|#define NO_VERTEX -2 ------------------ | Branch (4718:26): [True: 8.37k, False: 32.0k] ------------------ 4719| 8.37k| !pBNS->edge[eNFlowerEdge1].flow) ------------------ | Branch (4719:26): [True: 4.67k, False: 3.70k] ------------------ 4720| 4.67k| { 4721| 4.67k| if ((ret = AddToEdgeList( &AllChargeEdges, eNFlowerEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 4.67k|#define INC_EDGE_LIST 16 ------------------ | Branch (4721:29): [True: 0, False: 4.67k] ------------------ 4722| 0| { 4723| 0| goto exit_function; 4724| 0| } 4725| 4.67k| } 4726| 83.1k| } 4727| 107k| } 4728| 133k| } 4729| 832k| if (bIsCarbon && ------------------ | Branch (4729:13): [True: 88.2k, False: 744k] ------------------ 4730| 88.2k| 0 <= eNMinusEdge && ------------------ | Branch (4730:14): [True: 25.6k, False: 62.5k] ------------------ 4731| 25.6k| 0 <= eNPlusEdge && ------------------ | Branch (4731:14): [True: 25.6k, False: 0] ------------------ 4732| 25.6k| at2[i].valence == 1 && ------------------ | Branch (4732:14): [True: 11.9k, False: 13.6k] ------------------ 4733| 11.9k| at2[i].num_H == 0 && ------------------ | Branch (4733:14): [True: 11.9k, False: 12] ------------------ 4734| 11.9k| at2[i].radical == 0 && ------------------ | Branch (4734:14): [True: 6.61k, False: 5.35k] ------------------ 4735| 6.61k| !pBNS->edge[eNMinusEdge].forbidden && ------------------ | Branch (4735:14): [True: 6.61k, False: 0] ------------------ 4736| 6.61k| pBNS->edge[eNMinusEdge].flow == 0 && ------------------ | Branch (4736:14): [True: 2.87k, False: 3.74k] ------------------ 4737| 2.87k| !pBNS->edge[eNPlusEdge].forbidden && ------------------ | Branch (4737:14): [True: 2.87k, False: 0] ------------------ 4738| 2.87k| pBNS->edge[eNPlusEdge].flow == 0 && /* found terminal C(+) */ ------------------ | Branch (4738:14): [True: 2.87k, False: 0] ------------------ 4739| | 4740| 2.87k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (4740:14): [True: 1.28k, False: 1.59k] ------------------ 4741| 1.28k| at2[j].num_H == 0 && ------------------ | Branch (4741:14): [True: 1.28k, False: 1] ------------------ 4742| 1.28k| at2[j].radical == 0 && ------------------ | Branch (4742:14): [True: 1.28k, False: 0] ------------------ 4743| 1.28k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (4743:14): [True: 585, False: 703] ------------------ 4744| 585| ( eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4744:14): [True: 585, False: 0] ------------------ 4745| 585| pBNS->edge[eNPlusEdge].flow == 0) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | Branch (4745:14): [True: 585, False: 0] ------------------ 4746| 585| { /* -N(+)- */ 4747| | 4748| |#ifdef NEVER /* I have not found a good reason to do this yet */ 4749| | /* fix (+) charge on -N(+)- as much as C charges are fixed */ 4750| | if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) 4751| | { 4752| | goto exit_function; 4753| | } 4754| | /* fix floer edge to prevent N(V) ??? */ 4755| | if (NO_VERTEX != ( eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge1 ) ) && 4756| | !pBNS->edge[eNFlowerEdge1].flow) 4757| | { 4758| | if (ret = AddToEdgeList( &CarbonChargeEdges, eNFlowerEdge1, INC_EDGE_LIST )) 4759| | { 4760| | goto exit_function; 4761| | } 4762| | } 4763| |#endif 4764| | /* 4765| | Carbon(+) Carbon(-) 4766| | ChargeStruct: ChargeStruct: 4767| | 4768| | 5(+C) 5(+C) 4769| | / // 4770| | 6(-C) 4 6(-C) 4 4771| | \ // \\ / 4772| | 3 3 4773| | | | 4774| | 2 2 4775| | || || 4776| | -C1- -C1- 4777| | | | 4778| | 4779| | 3-6 is (-) Charge Edge; 4-5 is (+) Charge Edge 4780| | 4781| | To convert the left pattern to the right one: 4782| | 4783| | We need to release these charge edges and decrement 4784| | edge 3-4 flow to change charge from (+) to (-) 4785| | 4786| | */ 4787| | 4788| | /* find vertices 4 and 5 */ 4789| 585| v1 = pBNS->edge[eNPlusEdge].neighbor1; /* one of two vertices incident with edge 4-5 */ 4790| 585| v2 = pBNS->edge[eNPlusEdge].neighbor12 ^ v1; 4791| 585| if (IS_BNS_VT_C_GR( pBNS->vert[v1].type )) ------------------ | | 78| 585|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 585|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 585|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 585|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 585|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 585, False: 0] | | ------------------ ------------------ 4792| 585| { 4793| | /* v1 is 5(+C) */ 4794| | /* djb-rwth: removing redundant variables */ 4795| 585| v1 = v2; 4796| | /* djb-rwth: removing redundant code */ 4797| 585| } 4798| | /* v1 should be 4, v2 - 5(+C) */ 4799| 585| if (!IS_BNS_VT_CHRG_STRUCT( pBNS->vert[v1].type ) || pBNS->vert[v1].num_adj_edges != 2) ------------------ | | 82| 1.17k|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 53| 585|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ | | #define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 51| 585|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (82:38): [True: 585, False: 0] | | | Branch (82:69): [True: 585, False: 0] | | ------------------ ------------------ | Branch (4799:66): [True: 0, False: 585] ------------------ 4800| 0| { 4801| 0| continue; /* mismatch */ 4802| 0| } 4803| | /* find edge 3-4 */ 4804| 585| eN34Edge = pBNS->vert[v1].iedge[pBNS->vert[v1].iedge[0] == eNPlusEdge]; 4805| 585| if (pBNS->edge[eN34Edge].forbidden || !pBNS->edge[eN34Edge].flow) ------------------ | Branch (4805:17): [True: 0, False: 585] | Branch (4805:51): [True: 0, False: 585] ------------------ 4806| 0| { 4807| 0| continue; 4808| 0| } 4809| | /* save 3 edges: 6-3, 4-5, and 3-4 in this order */ 4810| 585| if ((ret = AddToEdgeList( &IsoCyanoCarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 585|#define INC_EDGE_LIST 16 ------------------ | Branch (4810:17): [True: 0, False: 585] ------------------ 4811| 0| { 4812| 0| goto exit_function; 4813| 0| } 4814| 585| if ((ret = AddToEdgeList( &IsoCyanoCarbonChargeEdges, eNPlusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 585|#define INC_EDGE_LIST 16 ------------------ | Branch (4814:17): [True: 0, False: 585] ------------------ 4815| 0| { 4816| 0| goto exit_function; 4817| 0| } 4818| 585| if ((ret = AddToEdgeList( &IsoCyanoCarbonChargeEdges, eN34Edge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 4639| 585|#define INC_EDGE_LIST 16 ------------------ | Branch (4818:17): [True: 0, False: 585] ------------------ 4819| 0| { 4820| 0| goto exit_function; 4821| 0| } 4822| 585| } 4823| 832k| } 4824| | /* 1st attempt: move (-) charges from heteroatoms to C(+) */ 4825| 87.7k| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4826| 87.7k| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4827| 87.7k| RemoveForbiddenEdgeMask( pBNS, &IsoCyanoCarbonChargeEdges, forbidden_edge_mask ); 4828| 88.3k| for (i = IsoCyanoCarbonChargeEdges.num_edges - 3; 0 <= i; i -= 3) ------------------ | Branch (4828:55): [True: 585, False: 87.7k] ------------------ 4829| 585| { 4830| | /* djb-rwth: removing redundant code */ 4831| 585| eN34Edge = IsoCyanoCarbonChargeEdges.pnEdges[i + 2]; 4832| | 4833| 585| pe = pBNS->edge + eN34Edge; 4834| 585| pe->forbidden |= forbidden_edge_mask; 4835| 585| if (!pe->flow) ------------------ | Branch (4835:13): [True: 0, False: 585] ------------------ 4836| 0| { 4837| 0| continue; /* already done */ 4838| 0| } 4839| | 4840| 585| v1 = pe->neighbor1; 4841| 585| v2 = pe->neighbor12 ^ v1; 4842| 585| pe->flow--; 4843| 585| pBNS->vert[v1].st_edge.flow--; 4844| 585| pBNS->vert[v2].st_edge.flow--; 4845| 585| pBNS->tot_st_flow -= 2; 4846| | 4847| 585| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4848| 585| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4849| | 4850| 585| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (4850:13): [True: 274, False: 311] | Branch (4850:28): [True: 3, False: 271] | Branch (4850:46): [True: 3, False: 0] ------------------ 4851| 274| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge <= -2) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4851:14): [True: 271, False: 0] | Branch (4851:32): [True: 271, False: 0] | Branch (4851:55): [True: 274, False: 0] ------------------ 4852| 274| { 4853| 274| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4854| 274| ( *pnNumRunBNS )++; 4855| 274| *pnTotalDelta += ret; 4856| 274| num_success++; 4857| 274| } 4858| 311| else 4859| 311| { 4860| 311| pe->flow++; 4861| 311| pBNS->vert[v1].st_edge.flow++; 4862| 311| pBNS->vert[v2].st_edge.flow++; 4863| 311| pBNS->tot_st_flow += 2; 4864| 311| pe->forbidden &= inv_forbidden_edge_mask; 4865| 311| num_failed++; 4866| 311| } 4867| 585| } 4868| 87.7k| if (num_failed) ------------------ | Branch (4868:9): [True: 311, False: 87.4k] ------------------ 4869| 311| { 4870| | /* relax conditions: allow all heteroatoms to change charge */ 4871| 311| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4872| 622| for (i = IsoCyanoCarbonChargeEdges.num_edges - 3; 0 <= i; i -= 3) ------------------ | Branch (4872:59): [True: 311, False: 311] ------------------ 4873| 311| { 4874| | /* djb-rwth: removing redundant code */ 4875| 311| eN34Edge = IsoCyanoCarbonChargeEdges.pnEdges[i + 2]; 4876| | 4877| 311| pe = pBNS->edge + eN34Edge; 4878| 311| pe->forbidden |= forbidden_edge_mask; 4879| 311| if (!pe->flow) ------------------ | Branch (4879:17): [True: 0, False: 311] ------------------ 4880| 0| { 4881| 0| continue; /* already done */ 4882| 0| } 4883| | 4884| 311| v1 = pe->neighbor1; 4885| 311| v2 = pe->neighbor12 ^ v1; 4886| 311| pe->flow--; 4887| 311| pBNS->vert[v1].st_edge.flow--; 4888| 311| pBNS->vert[v2].st_edge.flow--; 4889| 311| pBNS->tot_st_flow -= 2; 4890| | 4891| 311| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4892| 311| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4893| | 4894| 311| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (4894:17): [True: 15, False: 296] | Branch (4894:32): [True: 3, False: 12] | Branch (4894:50): [True: 3, False: 0] ------------------ 4895| 15| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge <= 2) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4895:18): [True: 12, False: 0] | Branch (4895:36): [True: 12, False: 0] | Branch (4895:59): [True: 15, False: 0] ------------------ 4896| 15| { 4897| 15| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4898| 15| ( *pnNumRunBNS )++; 4899| 15| *pnTotalDelta += ret; 4900| 15| num_success++; 4901| 15| } 4902| 296| else 4903| 296| { 4904| 296| pe->flow++; 4905| 296| pBNS->vert[v1].st_edge.flow++; 4906| 296| pBNS->vert[v2].st_edge.flow++; 4907| 296| pBNS->tot_st_flow += 2; 4908| 296| pe->forbidden &= inv_forbidden_edge_mask; /* let it change if it wants */ 4909| 296| num_failed++; 4910| 296| } 4911| 311| } 4912| 311| } 4913| 87.7k| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4914| 87.7k| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4915| 87.7k| RemoveForbiddenEdgeMask( pBNS, &IsoCyanoCarbonChargeEdges, forbidden_edge_mask ); 4916| | 4917| | 4918| 87.7k|exit_function: 4919| | 4920| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 4921| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 4922| 87.7k| AllocEdgeList( &IsoCyanoCarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 4923| | 4924| 87.7k| return ret; 4925| 87.7k|#undef INC_EDGE_LIST 4926| 87.7k|} FixMetal_Nminus_Ominus: 4940| 87.7k|{ 4941| 87.7k|#define INC_EDGE_LIST 16 4942| 87.7k| Vertex vPathStart, vPathEnd; 4943| 87.7k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 4944| 87.7k| int num_success, n; /* djb-rwth: removing redundant variables */ 4945| 87.7k| BNS_EDGE *pe; 4946| 87.7k| Vertex v1, v2; 4947| | 4948| 87.7k| int i, j, k, ret2, ret; 4949| 87.7k| int num_at = pStruct->num_atoms; 4950| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 4951| 87.7k| int len_at = num_at + num_deleted_H; 4952| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 4953| 87.7k| EdgeIndex e, eNMinusEdge, eNMinusEdge1, eNMinusEdge2, eNPlusEdge2; 4954| | 4955| 87.7k| EDGE_LIST AllChargeEdges; 4956| | 4957| 87.7k| ret = 0; 4958| 87.7k| num_success = 0; /* djb-rwth: removing redundant code */ 4959| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 4960| | 4961| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 4962| 87.7k| pStruct->at = at2; 4963| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 4964| 87.7k| pStruct->at = at; 4965| 87.7k| if (ret2 < 0) ------------------ | Branch (4965:9): [True: 0, False: 87.7k] ------------------ 4966| 0| { 4967| 0| ret = ret2; 4968| 0| goto exit_function; 4969| 0| } 4970| | /* attepmt #1 N#N(+)-N => N(-)=N(+)=N */ 4971| 920k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (4971:17): [True: 832k, False: 87.7k] | Branch (4971:31): [True: 832k, False: 0] ------------------ 4972| 832k| { 4973| 832k| if (at2[i].valence == 1 && ------------------ | Branch (4973:13): [True: 79.1k, False: 753k] ------------------ 4974| 79.1k| at2[i].num_H == 0 && ------------------ | Branch (4974:14): [True: 78.4k, False: 744] ------------------ 4975| 78.4k| at2[i].radical == 0 && ------------------ | Branch (4975:14): [True: 64.9k, False: 13.4k] ------------------ 4976| 64.9k| pVA[i].cNumValenceElectrons == 6 && /* terminal -O */ ------------------ | Branch (4976:14): [True: 18.6k, False: 46.3k] ------------------ 4977| 18.6k| ( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && pBNS->edge[eNMinusEdge].flow == 1 && ------------------ | Branch (4977:14): [True: 18.4k, False: 241] | Branch (4977:68): [True: 9.36k, False: 9.04k] ------------------ 4978| 9.36k| !pBNS->edge[eNMinusEdge].forbidden && /* terminal O(-) */ ------------------ | Branch (4978:14): [True: 9.36k, False: 0] ------------------ 4979| | 4980| 9.36k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (4980:14): [True: 2.10k, False: 7.26k] ------------------ 4981| 2.10k| at2[j].num_H == 0 && ------------------ | Branch (4981:14): [True: 2.09k, False: 11] ------------------ 4982| 2.09k| at2[j].radical == 0 && ------------------ | Branch (4982:14): [True: 2.05k, False: 37] ------------------ 4983| 2.05k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (4983:14): [True: 230, False: 1.82k] ------------------ 4984| 230| ( eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && pBNS->edge[eNMinusEdge1].flow == 1 && ------------------ | Branch (4984:14): [True: 224, False: 6] | Branch (4984:69): [True: 28, False: 196] ------------------ 4985| 28| !pBNS->edge[eNMinusEdge1].forbidden && ------------------ | Branch (4985:14): [True: 28, False: 0] ------------------ 4986| | 4987| 28| pVA[k = at2[j].neighbor[at2[j].neighbor[0] == i]].cMetal && ------------------ | Branch (4987:14): [True: 18, False: 10] ------------------ 4988| | 4989| 18| ( eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4989:14): [True: 18, False: 0] ------------------ 4990| 18| !pBNS->edge[eNMinusEdge2].forbidden && ------------------ | Branch (4990:14): [True: 18, False: 0] ------------------ 4991| 18| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4991:14): [True: 18, False: 0] ------------------ 4992| 18| !pBNS->edge[eNPlusEdge2].forbidden) ------------------ | Branch (4992:14): [True: 18, False: 0] ------------------ 4993| 18| { 4994| | /* found M(q)-N(-)-O(-); convert to M(q-2)-N=O */ 4995| | 4996| | /* find all charge edges to fix */ 4997| 18| if (0 == AllChargeEdges.num_edges) ------------------ | Branch (4997:17): [True: 16, False: 2] ------------------ 4998| 16| { 4999| 117| for (n = 0; n < num_at; n++) ------------------ | Branch (4999:29): [True: 101, False: 16] ------------------ 5000| 101| { 5001| 101| if (( e = pVA[n].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5001:25): [True: 68, False: 33] ------------------ 5002| 68| !pBNS->edge[e].forbidden) ------------------ | Branch (5002:26): [True: 68, False: 0] ------------------ 5003| 68| { 5004| 68| if ((ret = AddToEdgeList( &AllChargeEdges, e, num_at ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5004:29): [True: 0, False: 68] ------------------ 5005| 0| { 5006| 0| goto exit_function; 5007| 0| } 5008| 68| } 5009| 101| if (( e = pVA[n].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5009:25): [True: 84, False: 17] ------------------ 5010| 84| !pBNS->edge[e].forbidden) ------------------ | Branch (5010:26): [True: 77, False: 7] ------------------ 5011| 77| { 5012| 77| if ((ret = AddToEdgeList( &AllChargeEdges, e, num_at ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5012:29): [True: 0, False: 77] ------------------ 5013| 0| { 5014| 0| goto exit_function; 5015| 0| } 5016| 77| if (pVA[n].cNumValenceElectrons == 6 && ------------------ | Branch (5016:29): [True: 35, False: 42] ------------------ 5017| 35| NO_VERTEX != ( e = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ) && ------------------ | | 118| 35|#define NO_VERTEX -2 ------------------ | Branch (5017:30): [True: 14, False: 21] ------------------ 5018| 14| pBNS->edge[e].flow == 0) ------------------ | Branch (5018:30): [True: 3, False: 11] ------------------ 5019| 3| { 5020| 3| if ((ret = AddToEdgeList( &AllChargeEdges, e, num_at ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5020:33): [True: 0, False: 3] ------------------ 5021| 0| { 5022| 0| goto exit_function; 5023| 0| } 5024| 3| } 5025| 77| } 5026| 101| } 5027| 16| } 5028| | 5029| | /* djb-rwth: removing redundant code */ 5030| | /* djb-rwth: removing redundant code */ 5031| | 5032| 18| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5033| 18| pBNS->edge[eNMinusEdge1].forbidden &= inv_forbidden_edge_mask; 5034| 18| pBNS->edge[eNMinusEdge2].forbidden &= inv_forbidden_edge_mask; 5035| 18| pBNS->edge[eNPlusEdge2].forbidden &= inv_forbidden_edge_mask; 5036| | 5037| 18| pe = pBNS->edge + eNMinusEdge; /* must be already fixed as a charge edge */ 5038| | 5039| 18| v1 = pe->neighbor1; 5040| 18| v2 = pe->neighbor12 ^ v1; 5041| 18| pe->flow--; 5042| 18| pBNS->vert[v1].st_edge.flow--; 5043| 18| pBNS->vert[v2].st_edge.flow--; 5044| 18| pBNS->tot_st_flow -= 2; 5045| | 5046| 18| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5047| 18| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5048| | 5049| 18| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5049:17): [True: 9, False: 9] | Branch (5049:32): [True: 2, False: 7] | Branch (5049:50): [True: 0, False: 2] ------------------ 5050| 9| (vPathEnd == v2 && vPathStart == v1) ) /*&& nDeltaCharge == nDeltaChargeMax*/) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (5050:18): [True: 6, False: 3] | Branch (5050:36): [True: 6, False: 0] ------------------ 5051| 6| { 5052| 6| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5053| 6| ( *pnNumRunBNS )++; 5054| 6| *pnTotalDelta += ret; 5055| 6| num_success++; 5056| 6| } 5057| 12| else 5058| 12| { 5059| 12| pe->flow++; 5060| 12| pBNS->vert[v1].st_edge.flow++; 5061| 12| pBNS->vert[v2].st_edge.flow++; 5062| 12| pBNS->tot_st_flow += 2; 5063| | /* djb-rwth: removing redundant code */ 5064| 12| } 5065| 18| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5066| 18| } 5067| 832k| } 5068| 87.7k| ret = num_success; 5069| | 5070| 87.7k|exit_function: 5071| | 5072| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 5073| | 5074| 87.7k| return ret; 5075| 87.7k|#undef INC_EDGE_LIST 5076| 87.7k|} RestoreNNNgroup: 5090| 87.7k|{ 5091| 87.7k|#define INC_EDGE_LIST 16 5092| 87.7k| Vertex vPathStart, vPathEnd; 5093| 87.7k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms, num_failed, num_success, n, nDeltaChargeMax; 5094| 87.7k| BNS_EDGE *pe; 5095| 87.7k| Vertex v1, v2; 5096| | 5097| 87.7k| int i, j, k, ret2, ret; 5098| 87.7k| int num_at = pStruct->num_atoms; 5099| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 5100| 87.7k| int len_at = num_at + num_deleted_H; 5101| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 5102| 87.7k| EdgeIndex eNMinusEdge, eNPlusEdge, eNMinusEdge1, eNPlusEdge1, eNMinusEdge2, eNPlusEdge2; 5103| 87.7k| EdgeIndex eNFlowerEdge1, eNFlowerEdge2; 5104| | 5105| 87.7k| EDGE_LIST CarbonChargeEdges, AllChargeEdges, NNNChargeEdges, CurNNNChargeEdges, AllNNNTermAtoms, AllNIIIChargeEdges; 5106| | 5107| 87.7k| ret = 0; 5108| 87.7k| num_failed = num_success = 0; 5109| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 5110| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 5111| 87.7k| AllocEdgeList( &NNNChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 5112| 87.7k| AllocEdgeList( &CurNNNChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 5113| 87.7k| AllocEdgeList( &AllNNNTermAtoms, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 5114| 87.7k| AllocEdgeList( &AllNIIIChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 5115| | 5116| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 5117| 87.7k| pStruct->at = at2; 5118| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 5119| 87.7k| pStruct->at = at; 5120| 87.7k| if (ret2 < 0) ------------------ | Branch (5120:9): [True: 0, False: 87.7k] ------------------ 5121| 0| { 5122| 0| ret = ret2; 5123| 0| goto exit_function; 5124| 0| } 5125| | /* attepmt #1 N#N(+)-N => N(-)=N(+)=N: naive approach; expecting tp move (-) from some other atom */ 5126| 920k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (5126:17): [True: 832k, False: 87.7k] | Branch (5126:31): [True: 832k, False: 0] ------------------ 5127| 832k| { 5128| 832k| if (at2[i].valence == 1 && ------------------ | Branch (5128:13): [True: 79.1k, False: 753k] ------------------ 5129| 79.1k| at2[i].num_H == 0 && ------------------ | Branch (5129:14): [True: 78.4k, False: 744] ------------------ 5130| 78.4k| at2[i].chem_bonds_valence == 3 && ------------------ | Branch (5130:14): [True: 14.1k, False: 64.2k] ------------------ 5131| 14.1k| at2[i].charge == 0 && ------------------ | Branch (5131:14): [True: 6.71k, False: 7.46k] ------------------ 5132| 6.71k| at2[i].radical == 0 && ------------------ | Branch (5132:14): [True: 5.37k, False: 1.34k] ------------------ 5133| 5.37k| pVA[i].cNumValenceElectrons == 5 && /* terminal N# */ ------------------ | Branch (5133:14): [True: 4.07k, False: 1.30k] ------------------ 5134| 4.07k| ( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && pBNS->edge[eNMinusEdge].flow == 0 && ------------------ | Branch (5134:14): [True: 4.06k, False: 14] | Branch (5134:68): [True: 4.06k, False: 0] ------------------ 5135| 4.06k| !pBNS->edge[eNMinusEdge].forbidden && ------------------ | Branch (5135:14): [True: 4.06k, False: 0] ------------------ 5136| 4.06k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (5136:14): [True: 2.05k, False: 2.00k] ------------------ 5137| 2.05k| at2[j].num_H == 0 && ------------------ | Branch (5137:14): [True: 2.04k, False: 6] ------------------ 5138| 2.04k| at2[j].chem_bonds_valence == 4 && ------------------ | Branch (5138:14): [True: 1.88k, False: 164] ------------------ 5139| 1.88k| at2[j].charge == 1 && ------------------ | Branch (5139:14): [True: 1.27k, False: 612] ------------------ 5140| 1.27k| at2[j].radical == 0 && ------------------ | Branch (5140:14): [True: 1.27k, False: 0] ------------------ 5141| 1.27k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (5141:14): [True: 1.23k, False: 34] ------------------ 5142| 1.23k| ( eNPlusEdge = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && pBNS->edge[eNPlusEdge].flow == 0 && ------------------ | Branch (5142:14): [True: 1.23k, False: 0] | Branch (5142:66): [True: 1.23k, False: 0] ------------------ 5143| 1.23k| !pBNS->edge[eNPlusEdge].forbidden && ------------------ | Branch (5143:14): [True: 1.23k, False: 0] ------------------ 5144| 1.23k| at2[k = at2[j].neighbor[at2[j].neighbor[0] == i]].valence == 2 && ------------------ | Branch (5144:14): [True: 837, False: 401] ------------------ 5145| 837| at2[k].num_H == 0 && ------------------ | Branch (5145:14): [True: 819, False: 18] ------------------ 5146| 819| at2[k].chem_bonds_valence == 3 && ------------------ | Branch (5146:14): [True: 332, False: 487] ------------------ 5147| 332| pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (5147:14): [True: 299, False: 33] ------------------ 5148| 299| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && pBNS->edge[eNPlusEdge2].flow == 1 && ------------------ | Branch (5148:14): [True: 299, False: 0] | Branch (5148:67): [True: 292, False: 7] ------------------ 5149| 292| !pBNS->edge[eNPlusEdge2].forbidden && ------------------ | Branch (5149:14): [True: 292, False: 0] ------------------ 5150| 292| pVA[i].cnListIndex > 0 && ------------------ | Branch (5150:14): [True: 292, False: 0] ------------------ 5151| 292| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 436| 292|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 421| 292|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 292|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 292|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 292|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5151:14): [True: 292, False: 0] ------------------ 5152| 292| { 5153| | /* found N#N(+)-N~ where the last N (at2[k]) may be charged */ 5154| 292| pe = pBNS->edge + pBNS->vert[i].iedge[0]; /* N#N(+) triple bond edge */ 5155| | 5156| 292| v1 = pe->neighbor1; 5157| 292| v2 = pe->neighbor12 ^ v1; 5158| 292| pe->flow--; 5159| 292| pBNS->vert[v1].st_edge.flow--; 5160| 292| pBNS->vert[v2].st_edge.flow--; 5161| 292| pBNS->tot_st_flow -= 2; 5162| | 5163| 292| pe->forbidden |= forbidden_edge_mask; 5164| 292| pBNS->edge[eNPlusEdge].forbidden |= forbidden_edge_mask; 5165| 292| pBNS->edge[eNPlusEdge2].forbidden |= forbidden_edge_mask; 5166| | 5167| | 5168| 292| if (!CarbonChargeEdges.num_edges) ------------------ | Branch (5168:17): [True: 291, False: 1] ------------------ 5169| 291| { 5170| | /* do not let carbon atoms get charged */ 5171| 291| AllocEdgeList( &CarbonChargeEdges, INC_EDGE_LIST ); ------------------ | | 5091| 291|#define INC_EDGE_LIST 16 ------------------ 5172| 291| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (5172:21): [True: 0, False: 291] ------------------ 5173| 0| { 5174| 0| goto exit_function; 5175| 0| } 5176| 291| } 5177| 1| else 5178| 1| { 5179| 1| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5180| 1| } 5181| 292| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5182| 292| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5183| | 5184| 292| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5184:17): [True: 216, False: 76] | Branch (5184:32): [True: 9, False: 207] | Branch (5184:50): [True: 5, False: 4] ------------------ 5185| 211| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge <= 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (5185:18): [True: 206, False: 5] | Branch (5185:36): [True: 205, False: 1] | Branch (5185:59): [True: 115, False: 95] ------------------ 5186| 115| { 5187| 115| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5188| 115| ( *pnNumRunBNS )++; 5189| 115| *pnTotalDelta += ret; 5190| 115| num_success++; 5191| | /* fix charges on N(-)=N(+)=N- */ 5192| 115| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 115|#define INC_EDGE_LIST 16 ------------------ | Branch (5192:21): [True: 0, False: 115] ------------------ 5193| 0| { 5194| 0| goto exit_function; 5195| 0| } 5196| 115| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 115|#define INC_EDGE_LIST 16 ------------------ | Branch (5196:21): [True: 0, False: 115] ------------------ 5197| 0| { 5198| 0| goto exit_function; 5199| 0| } 5200| 115| } 5201| 177| else 5202| 177| { 5203| 177| pe->flow++; 5204| 177| pBNS->vert[v1].st_edge.flow++; 5205| 177| pBNS->vert[v2].st_edge.flow++; 5206| 177| pBNS->tot_st_flow += 2; 5207| 177| num_failed++; 5208| 177| } 5209| 292| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5210| | 5211| 292| pe->forbidden &= inv_forbidden_edge_mask; 5212| 292| pBNS->edge[eNPlusEdge].forbidden &= inv_forbidden_edge_mask; 5213| 292| pBNS->edge[eNPlusEdge2].forbidden &= inv_forbidden_edge_mask; 5214| 292| } 5215| 832k| } 5216| | 5217| | /* 2nd attempt: take care of N#N(+)-N=-...=N-N(-) */ 5218| | /* This would produce nDeltaCharge >= 2 */ 5219| | 5220| 87.7k| AllChargeEdges.num_edges = 0; 5221| 87.7k| AllNNNTermAtoms.num_edges = 0; 5222| 87.7k| NNNChargeEdges.num_edges = 0; 5223| 87.7k| AllNIIIChargeEdges.num_edges = 0; 5224| | 5225| 920k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (5225:17): [True: 832k, False: 87.7k] | Branch (5225:31): [True: 832k, False: 0] ------------------ 5226| 832k| { 5227| 832k| if (( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5227:13): [True: 119k, False: 712k] ------------------ 5228| 119k| !pBNS->edge[eNMinusEdge].forbidden) ------------------ | Branch (5228:14): [True: 119k, False: 0] ------------------ 5229| 119k| { 5230| 119k| if ((ret = AddToEdgeList( &AllChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 119k|#define INC_EDGE_LIST 16 ------------------ | Branch (5230:17): [True: 0, False: 119k] ------------------ 5231| 0| { 5232| 0| goto exit_function; 5233| 0| } 5234| 119k| } 5235| 712k| else 5236| 712k| { 5237| 712k| eNMinusEdge = -1; 5238| 712k| } 5239| 832k| if (( eNPlusEdge = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5239:13): [True: 138k, False: 694k] ------------------ 5240| 138k| !pBNS->edge[eNPlusEdge].forbidden) ------------------ | Branch (5240:14): [True: 133k, False: 5.04k] ------------------ 5241| 133k| { 5242| 133k| if ((ret = AddToEdgeList( &AllChargeEdges, eNPlusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 133k|#define INC_EDGE_LIST 16 ------------------ | Branch (5242:17): [True: 0, False: 133k] ------------------ 5243| 0| { 5244| 0| goto exit_function; 5245| 0| } 5246| 133k| if (pVA[i].cNumValenceElectrons == 5 && at2[i].valence == 3 && at2[i].chem_bonds_valence == 3) ------------------ | Branch (5246:17): [True: 42.2k, False: 90.8k] | Branch (5246:53): [True: 8.75k, False: 33.4k] | Branch (5246:76): [True: 2.30k, False: 6.45k] ------------------ 5247| 2.30k| { 5248| 2.30k| if ((ret = AddToEdgeList( &AllNIIIChargeEdges, eNPlusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 2.30k|#define INC_EDGE_LIST 16 ------------------ | Branch (5248:21): [True: 0, False: 2.30k] ------------------ 5249| 0| { 5250| 0| goto exit_function; 5251| 0| } 5252| 2.30k| } 5253| | /* N flower edge */ 5254| 133k| if (pVA[i].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (5254:17): [True: 42.2k, False: 90.8k] | Branch (5254:53): [True: 30.2k, False: 11.9k] ------------------ 5255| 30.2k| NO_VERTEX != ( eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge ) ) && ------------------ | | 118| 30.2k|#define NO_VERTEX -2 ------------------ | Branch (5255:18): [True: 6.38k, False: 23.8k] ------------------ 5256| 6.38k| pBNS->edge[eNFlowerEdge1].flow == 0 && ------------------ | Branch (5256:18): [True: 3.39k, False: 2.98k] ------------------ 5257| 3.39k| ( ret = AddToEdgeList( &AllChargeEdges, eNFlowerEdge1, INC_EDGE_LIST ) )) ------------------ | | 5091| 3.39k|#define INC_EDGE_LIST 16 ------------------ | Branch (5257:18): [True: 0, False: 3.39k] ------------------ 5258| 0| { 5259| 0| goto exit_function; 5260| 0| } 5261| 133k| } 5262| | /* djb-rwth: removing redundant code */ 5263| | 5264| 832k| if (0 <= eNMinusEdge && ------------------ | Branch (5264:13): [True: 119k, False: 712k] ------------------ 5265| 119k| at2[i].valence == 1 && ------------------ | Branch (5265:14): [True: 60.2k, False: 59.6k] ------------------ 5266| 60.2k| at2[i].num_H == 0 && ------------------ | Branch (5266:14): [True: 60.1k, False: 160] ------------------ 5267| 60.1k| at2[i].radical == 0 && ------------------ | Branch (5267:14): [True: 47.3k, False: 12.7k] ------------------ 5268| 47.3k| pVA[i].cNumValenceElectrons == 5 && /* terminal N# */ ------------------ | Branch (5268:14): [True: 11.3k, False: 36.0k] ------------------ 5269| | 5270| 11.3k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (5270:14): [True: 4.78k, False: 6.53k] ------------------ 5271| 4.78k| at2[j].num_H == 0 && ------------------ | Branch (5271:14): [True: 4.76k, False: 16] ------------------ 5272| 4.76k| at2[j].radical == 0 && ------------------ | Branch (5272:14): [True: 4.75k, False: 7] ------------------ 5273| 4.75k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (5273:14): [True: 3.41k, False: 1.33k] ------------------ 5274| 3.41k| ( eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5274:14): [True: 3.41k, False: 6] ------------------ 5275| 3.41k| ( eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5275:14): [True: 3.41k, False: 0] ------------------ 5276| 3.41k| !pBNS->edge[eNMinusEdge1].forbidden && ------------------ | Branch (5276:14): [True: 3.41k, False: 0] ------------------ 5277| 3.41k| !pBNS->edge[eNPlusEdge1].forbidden && ------------------ | Branch (5277:14): [True: 3.41k, False: 0] ------------------ 5278| | 5279| 3.41k| at2[k = at2[j].neighbor[at2[j].neighbor[0] == i]].valence == 2 && ------------------ | Branch (5279:14): [True: 2.38k, False: 1.02k] ------------------ 5280| 2.38k| at2[k].num_H == 0 && ------------------ | Branch (5280:14): [True: 2.36k, False: 23] ------------------ 5281| 2.36k| at2[k].radical == 0 && ------------------ | Branch (5281:14): [True: 2.20k, False: 163] ------------------ 5282| 2.20k| pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (5282:14): [True: 1.22k, False: 973] ------------------ 5283| 1.22k| ( eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5283:14): [True: 1.22k, False: 1] ------------------ 5284| 1.22k| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5284:14): [True: 1.22k, False: 0] ------------------ 5285| 1.22k| !pBNS->edge[eNMinusEdge2].forbidden && ------------------ | Branch (5285:14): [True: 1.22k, False: 0] ------------------ 5286| 1.22k| !pBNS->edge[eNPlusEdge2].forbidden && ------------------ | Branch (5286:14): [True: 1.22k, False: 0] ------------------ 5287| | 5288| 1.22k| pVA[i].cnListIndex > 0 && ------------------ | Branch (5288:14): [True: 1.22k, False: 0] ------------------ 5289| 1.22k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 436| 1.22k|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 421| 1.22k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 1.22k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 1.22k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 1.22k|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5289:14): [True: 1.21k, False: 10] ------------------ 5290| 1.21k| { 5291| | /* found N#N(+)-N~ or N(-)=N-N= where the last N (at2[k]) may be charged */ 5292| | 5293| | /* 1. N(-)=N(+)=N- */ 5294| 1.21k| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5294:17): [True: 896, False: 322] ------------------ 5295| 896| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5295:18): [True: 894, False: 2] | Branch (5295:56): [True: 308, False: 586] ------------------ 5296| 308| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5296:18): [True: 308, False: 0] | Branch (5296:56): [True: 308, False: 0] ------------------ 5297| 308| { 5298| 308| continue; /* already good */ 5299| 308| } 5300| | /* accumulate terminal atoms of all other NNN */ 5301| 910| if ((ret = AddToEdgeList( &AllNNNTermAtoms, i, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 910|#define INC_EDGE_LIST 16 ------------------ | Branch (5301:17): [True: 0, False: 910] ------------------ 5302| 0| { 5303| 0| goto exit_function; 5304| 0| } 5305| | /* 2. N#N(+)-N= */ 5306| 910| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5306:17): [True: 322, False: 588] ------------------ 5307| 322| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5307:18): [True: 321, False: 1] | Branch (5307:56): [True: 256, False: 65] ------------------ 5308| 256| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5308:18): [True: 183, False: 73] | Branch (5308:56): [True: 178, False: 5] ------------------ 5309| 178| { 5310| |/* unfix (-) edge on terminal N# */ 5311| 178| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 178|#define INC_EDGE_LIST 16 ------------------ | Branch (5311:21): [True: 0, False: 178] ------------------ 5312| 0| { 5313| 0| goto exit_function; 5314| 0| } 5315| 178| continue; 5316| 178| } 5317| | /* 3. N(-)=N-N= */ 5318| 732| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5318:17): [True: 588, False: 144] ------------------ 5319| 588| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 1 && /* N */ ------------------ | Branch (5319:18): [True: 586, False: 2] | Branch (5319:56): [True: 585, False: 1] ------------------ 5320| 585| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5320:18): [True: 574, False: 11] | Branch (5320:56): [True: 116, False: 458] ------------------ 5321| 116| { 5322| | /* unfix (+) edge on middle N */ 5323| 116| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 116|#define INC_EDGE_LIST 16 ------------------ | Branch (5323:21): [True: 0, False: 116] ------------------ 5324| 0| { 5325| 0| goto exit_function; 5326| 0| } 5327| 116| continue; 5328| 116| } 5329| | /* 4. N#N(+)-N(-)- */ 5330| 616| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5330:17): [True: 144, False: 472] ------------------ 5331| 144| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5331:18): [True: 143, False: 1] | Branch (5331:56): [True: 78, False: 65] ------------------ 5332| 78| pBNS->edge[eNMinusEdge2].flow == 1 && pBNS->edge[eNPlusEdge2].flow == 1 /* N(-) */) ------------------ | Branch (5332:18): [True: 73, False: 5] | Branch (5332:56): [True: 72, False: 1] ------------------ 5333| 72| { 5334| | /* unfix (-) edge on the 1st and 3rd N */ 5335| 72| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 72|#define INC_EDGE_LIST 16 ------------------ | Branch (5335:21): [True: 0, False: 72] ------------------ 5336| 0| { 5337| 0| goto exit_function; 5338| 0| } 5339| 72| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 72|#define INC_EDGE_LIST 16 ------------------ | Branch (5339:21): [True: 0, False: 72] ------------------ 5340| 0| { 5341| 0| goto exit_function; 5342| 0| } 5343| 72| continue; 5344| 72| } 5345| | /* 5. N#N(+)-N(+)# */ 5346| 544| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5346:17): [True: 72, False: 472] ------------------ 5347| 72| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5347:18): [True: 71, False: 1] | Branch (5347:56): [True: 6, False: 65] ------------------ 5348| 6| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 0 /* N(+) */) ------------------ | Branch (5348:18): [True: 5, False: 1] | Branch (5348:56): [True: 4, False: 1] ------------------ 5349| 4| { 5350| | /* unfix (-) edge on the 1st and (+) edge on the 3rd N */ 5351| 4| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 4|#define INC_EDGE_LIST 16 ------------------ | Branch (5351:21): [True: 0, False: 4] ------------------ 5352| 0| { 5353| 0| goto exit_function; 5354| 0| } 5355| 4| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 4|#define INC_EDGE_LIST 16 ------------------ | Branch (5355:21): [True: 0, False: 4] ------------------ 5356| 0| { 5357| 0| goto exit_function; 5358| 0| } 5359| 4| continue; 5360| 4| } 5361| 544| } 5362| 832k| } 5363| | /* try to fix each NNN */ 5364| 88.6k| for (n = AllNNNTermAtoms.num_edges - 1; 0 <= n; n--) ------------------ | Branch (5364:45): [True: 910, False: 87.7k] ------------------ 5365| 910| { 5366| 910| i = AllNNNTermAtoms.pnEdges[n]; 5367| 910| eNMinusEdge = pVA[i].nCMinusGroupEdge - 1; 5368| | /*eNPlusEdge = pVA[i].nCPlusGroupEdge - 1;*/ 5369| 910| j = at2[i].neighbor[0]; 5370| 910| eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1; 5371| 910| eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1; 5372| 910| k = at2[j].neighbor[at2[j].neighbor[0] == i]; 5373| 910| eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1; 5374| 910| eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1; 5375| | /*SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask );*/ 5376| | /* 1. N(-)=N(+)=N- */ 5377| 910| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5377:13): [True: 588, False: 322] ------------------ 5378| 588| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5378:14): [True: 586, False: 2] | Branch (5378:52): [True: 72, False: 514] ------------------ 5379| 72| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5379:14): [True: 72, False: 0] | Branch (5379:52): [True: 72, False: 0] ------------------ 5380| 72| { 5381| | 5382| 72| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge ); 5383| 72| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge1 ); 5384| 72| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge1 ); 5385| 72| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge2 ); 5386| 72| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge2 ); 5387| | 5388| 72| pe = NULL; 5389| 72| } 5390| | 5391| 838| else 5392| 838| { 5393| | /* 2. N#N(+)-N= */ 5394| 838| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5394:17): [True: 322, False: 516] ------------------ 5395| 322| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5395:18): [True: 321, False: 1] | Branch (5395:56): [True: 256, False: 65] ------------------ 5396| 256| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5396:18): [True: 183, False: 73] | Branch (5396:56): [True: 178, False: 5] ------------------ 5397| 178| { 5398| | /* decrement triple bond on terminal N# */ 5399| 178| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5400| 178| } 5401| 660| else 5402| 660| { 5403| | /* 3. N(-)=N-N= */ 5404| 660| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5404:21): [True: 516, False: 144] ------------------ 5405| 516| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 1 && /* N */ ------------------ | Branch (5405:22): [True: 514, False: 2] | Branch (5405:60): [True: 513, False: 1] ------------------ 5406| 513| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5406:22): [True: 502, False: 11] | Branch (5406:60): [True: 44, False: 458] ------------------ 5407| 44| { 5408| | /* decrement flow on (+) charge edge of the middle =N- */ 5409| 44| pe = pBNS->edge + eNPlusEdge1; 5410| 44| } 5411| 616| else 5412| 616| { 5413| | /* 4. N#N(+)-N(-)- */ 5414| 616| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5414:25): [True: 144, False: 472] ------------------ 5415| 144| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5415:26): [True: 143, False: 1] | Branch (5415:64): [True: 78, False: 65] ------------------ 5416| 78| pBNS->edge[eNMinusEdge2].flow == 1 && pBNS->edge[eNPlusEdge2].flow == 1 /* N(-) */) ------------------ | Branch (5416:26): [True: 73, False: 5] | Branch (5416:64): [True: 72, False: 1] ------------------ 5417| 72| { 5418| | /* decrement triple bond on terminal N# */ 5419| 72| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5420| 72| } 5421| 544| else 5422| 544| {/* 5. N#N(+)-N(+)# */ 5423| 544| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5423:29): [True: 72, False: 472] ------------------ 5424| 72| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5424:30): [True: 71, False: 1] | Branch (5424:68): [True: 6, False: 65] ------------------ 5425| 6| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 0 /* N(+) */) ------------------ | Branch (5425:30): [True: 5, False: 1] | Branch (5425:68): [True: 4, False: 1] ------------------ 5426| 4| { 5427| | /* decrement triple bond on terminal N# */ 5428| 4| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5429| 4| } 5430| 540| else 5431| 540| { 5432| 540| pe = NULL; /* unknown case */ 5433| 540| } 5434| 544| } 5435| 616| } 5436| 660| } 5437| 838| } 5438| | 5439| 910| if (pe) ------------------ | Branch (5439:13): [True: 298, False: 612] ------------------ 5440| 298| { 5441| 298| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5442| 298| RemoveForbiddenEdgeMask( pBNS, &NNNChargeEdges, forbidden_edge_mask ); 5443| | 5444| 298| v1 = pe->neighbor1; 5445| 298| v2 = pe->neighbor12 ^ v1; 5446| 298| pe->flow--; 5447| 298| pBNS->vert[v1].st_edge.flow--; 5448| 298| pBNS->vert[v2].st_edge.flow--; 5449| 298| pBNS->tot_st_flow -= 2; 5450| | 5451| 298| pe->forbidden |= forbidden_edge_mask; 5452| | 5453| 298| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5454| 298| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5455| | 5456| 298| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5456:17): [True: 150, False: 148] | Branch (5456:32): [True: 3, False: 147] | Branch (5456:50): [True: 0, False: 3] ------------------ 5457| 150| (vPathEnd == v2 && vPathStart == v1) ) /*&& nDeltaCharge <= 2*/) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (5457:18): [True: 146, False: 4] | Branch (5457:36): [True: 144, False: 2] ------------------ 5458| 144| { 5459| 144| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5460| 144| ( *pnNumRunBNS )++; 5461| 144| *pnTotalDelta += ret; 5462| 144| num_success++; 5463| | /* fix charges on N(-)=N(+)=N- */ 5464| 144| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge ); 5465| 144| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge1 ); 5466| 144| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge1 ); 5467| 144| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge2 ); 5468| 144| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge2 ); 5469| 144| } 5470| 154| else 5471| 154| { 5472| 154| pe->flow++; 5473| 154| pBNS->vert[v1].st_edge.flow++; 5474| 154| pBNS->vert[v2].st_edge.flow++; 5475| 154| pBNS->tot_st_flow += 2; 5476| 154| num_failed++; 5477| 154| } 5478| 298| pe->forbidden &= inv_forbidden_edge_mask; 5479| 298| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5480| 298| } 5481| 910| } 5482| | 5483| | /* 3rd attempt */ 5484| | 5485| | /* 5486| | AllChargeEdges.num_edges = 0; 5487| | AllNNNTermAtoms.num_edges = 0; 5488| | NNNChargeEdges.num_edges = 0; 5489| | */ 5490| 920k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (5490:17): [True: 832k, False: 87.7k] | Branch (5490:31): [True: 832k, False: 0] ------------------ 5491| 832k| { 5492| | 5493| 832k| eNMinusEdge = pVA[i].nCMinusGroupEdge - 1; 5494| | /*eNPlusEdge = pVA[i].nCPlusGroupEdge - 1;*/ 5495| | 5496| 832k| if (0 <= eNMinusEdge && ------------------ | Branch (5496:13): [True: 119k, False: 712k] ------------------ 5497| 119k| at2[i].valence == 1 && ------------------ | Branch (5497:14): [True: 60.2k, False: 59.6k] ------------------ 5498| 60.2k| at2[i].num_H == 0 && ------------------ | Branch (5498:14): [True: 60.1k, False: 160] ------------------ 5499| 60.1k| at2[i].radical == 0 && ------------------ | Branch (5499:14): [True: 47.3k, False: 12.7k] ------------------ 5500| 47.3k| pVA[i].cNumValenceElectrons == 5 && /* terminal N# */ ------------------ | Branch (5500:14): [True: 11.3k, False: 36.0k] ------------------ 5501| | 5502| 11.3k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (5502:14): [True: 4.78k, False: 6.53k] ------------------ 5503| 4.78k| at2[j].num_H == 0 && ------------------ | Branch (5503:14): [True: 4.76k, False: 16] ------------------ 5504| 4.76k| at2[j].radical == 0 && ------------------ | Branch (5504:14): [True: 4.75k, False: 7] ------------------ 5505| 4.75k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (5505:14): [True: 3.41k, False: 1.33k] ------------------ 5506| 3.41k| ( eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5506:14): [True: 3.41k, False: 6] ------------------ 5507| 3.41k| ( eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5507:14): [True: 3.41k, False: 0] ------------------ 5508| 3.41k| !pBNS->edge[eNMinusEdge1].forbidden && ------------------ | Branch (5508:14): [True: 3.41k, False: 0] ------------------ 5509| 3.41k| !pBNS->edge[eNPlusEdge1].forbidden && ------------------ | Branch (5509:14): [True: 3.41k, False: 0] ------------------ 5510| | 5511| 3.41k| at2[k = at2[j].neighbor[at2[j].neighbor[0] == i]].valence == 2 && ------------------ | Branch (5511:14): [True: 2.38k, False: 1.02k] ------------------ 5512| 2.38k| at2[k].num_H == 0 && ------------------ | Branch (5512:14): [True: 2.36k, False: 23] ------------------ 5513| 2.36k| at2[k].radical == 0 && ------------------ | Branch (5513:14): [True: 2.20k, False: 163] ------------------ 5514| 2.20k| pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (5514:14): [True: 1.22k, False: 973] ------------------ 5515| 1.22k| ( eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5515:14): [True: 1.22k, False: 1] ------------------ 5516| 1.22k| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5516:14): [True: 1.22k, False: 0] ------------------ 5517| 1.22k| !pBNS->edge[eNMinusEdge2].forbidden && ------------------ | Branch (5517:14): [True: 1.22k, False: 0] ------------------ 5518| 1.22k| !pBNS->edge[eNPlusEdge2].forbidden && ------------------ | Branch (5518:14): [True: 1.22k, False: 0] ------------------ 5519| | 5520| 1.22k| pVA[i].cnListIndex > 0 && ------------------ | Branch (5520:14): [True: 1.22k, False: 0] ------------------ 5521| 1.22k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 436| 1.22k|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 421| 1.22k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 1.22k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 1.22k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 1.22k|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5521:14): [True: 1.21k, False: 10] ------------------ 5522| 1.21k| { 5523| | /* found N#N(+)-N~ or N(-)=N-N= where the last N (at2[k]) may be charged */ 5524| 1.21k| NNNChargeEdges.num_edges = 0; 5525| | 5526| 1.21k| eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge1 ); 5527| 1.21k| eNFlowerEdge2 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge2 ); 5528| | 5529| | /* 1. N(-)=N(+)=N- */ 5530| 1.21k| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5530:17): [True: 1.04k, False: 177] ------------------ 5531| 1.04k| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5531:18): [True: 1.03k, False: 2] | Branch (5531:56): [True: 524, False: 515] ------------------ 5532| 524| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5532:18): [True: 524, False: 0] | Branch (5532:56): [True: 524, False: 0] ------------------ 5533| 524| { 5534| | /* fix charges on N(-)=N(+)=N- */ 5535| 524| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 524|#define INC_EDGE_LIST 16 ------------------ | Branch (5535:21): [True: 0, False: 524] ------------------ 5536| 0| { 5537| 0| goto exit_function; 5538| 0| } 5539| 524| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 524|#define INC_EDGE_LIST 16 ------------------ | Branch (5539:21): [True: 0, False: 524] ------------------ 5540| 0| { 5541| 0| goto exit_function; 5542| 0| } 5543| 524| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 524|#define INC_EDGE_LIST 16 ------------------ | Branch (5543:21): [True: 0, False: 524] ------------------ 5544| 0| { 5545| 0| goto exit_function; 5546| 0| } 5547| 524| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 524|#define INC_EDGE_LIST 16 ------------------ | Branch (5547:21): [True: 0, False: 524] ------------------ 5548| 0| { 5549| 0| goto exit_function; 5550| 0| } 5551| 524| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 524|#define INC_EDGE_LIST 16 ------------------ | Branch (5551:21): [True: 0, False: 524] ------------------ 5552| 0| { 5553| 0| goto exit_function; 5554| 0| } 5555| 524| continue; /* already good */ 5556| 524| } 5557| | /* 2. N#N(+)-N= */ 5558| 694| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5558:17): [True: 177, False: 517] ------------------ 5559| 177| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5559:18): [True: 176, False: 1] | Branch (5559:56): [True: 111, False: 65] ------------------ 5560| 111| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5560:18): [True: 110, False: 1] | Branch (5560:56): [True: 105, False: 5] ------------------ 5561| 105| { 5562| | /* unfix (-) edge on terminal N# */ 5563| 105| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 105|#define INC_EDGE_LIST 16 ------------------ | Branch (5563:21): [True: 0, False: 105] ------------------ 5564| 0| { 5565| 0| goto exit_function; 5566| 0| } 5567| 105| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 105|#define INC_EDGE_LIST 16 ------------------ | Branch (5567:21): [True: 0, False: 105] ------------------ 5568| 0| { 5569| 0| goto exit_function; 5570| 0| } 5571| 105| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 105|#define INC_EDGE_LIST 16 ------------------ | Branch (5571:21): [True: 0, False: 105] ------------------ 5572| 0| { 5573| 0| goto exit_function; 5574| 0| } 5575| 105| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 105|#define INC_EDGE_LIST 16 ------------------ | Branch (5575:21): [True: 0, False: 105] ------------------ 5576| 0| { 5577| 0| goto exit_function; 5578| 0| } 5579| 105| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5580| | /* djb-rwth: removing redundant code */ 5581| 105| nDeltaChargeMax = ( num_failed && !num_success && pStruct->nNumRemovedProtonsMobHInChI > 0 ) ? 2 : 0; ------------------ | Branch (5581:37): [True: 105, False: 0] | Branch (5581:51): [True: 104, False: 1] | Branch (5581:67): [True: 0, False: 104] ------------------ 5582| 105| } 5583| 589| else 5584| 589| { 5585| | /* 3. N(-)=N-N= */ 5586| 589| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5586:21): [True: 517, False: 72] ------------------ 5587| 517| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 1 && /* N */ ------------------ | Branch (5587:22): [True: 515, False: 2] | Branch (5587:60): [True: 514, False: 1] ------------------ 5588| 514| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5588:22): [True: 503, False: 11] | Branch (5588:60): [True: 45, False: 458] ------------------ 5589| 45| { 5590| | /* unfix (+) edge on middle N */ 5591| 45| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 45|#define INC_EDGE_LIST 16 ------------------ | Branch (5591:25): [True: 0, False: 45] ------------------ 5592| 0| { 5593| 0| goto exit_function; 5594| 0| } 5595| 45| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 45|#define INC_EDGE_LIST 16 ------------------ | Branch (5595:25): [True: 0, False: 45] ------------------ 5596| 0| { 5597| 0| goto exit_function; 5598| 0| } 5599| 45| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 45|#define INC_EDGE_LIST 16 ------------------ | Branch (5599:25): [True: 0, False: 45] ------------------ 5600| 0| { 5601| 0| goto exit_function; 5602| 0| } 5603| 45| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 45|#define INC_EDGE_LIST 16 ------------------ | Branch (5603:25): [True: 0, False: 45] ------------------ 5604| 0| { 5605| 0| goto exit_function; 5606| 0| } 5607| 45| if (NO_VERTEX != eNFlowerEdge1 && ------------------ | | 118| 45|#define NO_VERTEX -2 ------------------ | Branch (5607:25): [True: 0, False: 45] ------------------ 5608| 0| ( ret = AddToEdgeList( &NNNChargeEdges, eNFlowerEdge1, INC_EDGE_LIST ) )) ------------------ | | 5091| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5608:25): [True: 0, False: 0] ------------------ 5609| 0| { 5610| 0| goto exit_function; 5611| 0| } 5612| | /* decrement flow on (+) charge edge of the middle =N- */ 5613| 45| pe = pBNS->edge + eNPlusEdge1; 5614| 45| nDeltaChargeMax = 2; 5615| 45| } 5616| 544| else 5617| 544| { 5618| | /* 4. N#N(+)-N(-)- */ 5619| 544| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5619:25): [True: 72, False: 472] ------------------ 5620| 72| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5620:26): [True: 71, False: 1] | Branch (5620:64): [True: 6, False: 65] ------------------ 5621| 6| pBNS->edge[eNMinusEdge2].flow == 1 && pBNS->edge[eNPlusEdge2].flow == 1 /* N(-) */) ------------------ | Branch (5621:26): [True: 1, False: 5] | Branch (5621:64): [True: 0, False: 1] ------------------ 5622| 0| { 5623| | /* unfix (-) edge on the 1st and 3rd N */ 5624| 0| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5624:29): [True: 0, False: 0] ------------------ 5625| 0| { 5626| 0| goto exit_function; 5627| 0| } 5628| 0| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5628:29): [True: 0, False: 0] ------------------ 5629| 0| { 5630| 0| goto exit_function; 5631| 0| } 5632| 0| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5632:29): [True: 0, False: 0] ------------------ 5633| 0| { 5634| 0| goto exit_function; 5635| 0| } 5636| | /* decrement triple bond on terminal N# */ 5637| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5638| 0| nDeltaChargeMax = 0; 5639| 0| } 5640| 544| else 5641| 544| { 5642| | /* 5. N#N(+)-N(+)# */ 5643| 544| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5643:29): [True: 72, False: 472] ------------------ 5644| 72| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5644:30): [True: 71, False: 1] | Branch (5644:68): [True: 6, False: 65] ------------------ 5645| 6| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 0 /* N(+) */) ------------------ | Branch (5645:30): [True: 5, False: 1] | Branch (5645:68): [True: 4, False: 1] ------------------ 5646| 4| { 5647| | /* unfix (-) edge on the 1st and (+) edge on the 3rd N */ 5648| 4| if ((ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 4|#define INC_EDGE_LIST 16 ------------------ | Branch (5648:33): [True: 0, False: 4] ------------------ 5649| 0| { 5650| 0| goto exit_function; 5651| 0| } 5652| 4| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 4|#define INC_EDGE_LIST 16 ------------------ | Branch (5652:33): [True: 0, False: 4] ------------------ 5653| 0| { 5654| 0| goto exit_function; 5655| 0| } 5656| 4| if ((ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 4|#define INC_EDGE_LIST 16 ------------------ | Branch (5656:33): [True: 0, False: 4] ------------------ 5657| 0| { 5658| 0| goto exit_function; 5659| 0| } 5660| | /* decrement triple bond on terminal N# */ 5661| 4| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5662| 4| nDeltaChargeMax = 0; 5663| 4| } 5664| 540| else 5665| 540| { 5666| 540| continue; 5667| 540| } 5668| 544| } 5669| 544| } 5670| 589| } 5671| | 5672| 154| if (NO_VERTEX != eNFlowerEdge1 && !pBNS->edge[eNFlowerEdge1].flow) ------------------ | | 118| 154|#define NO_VERTEX -2 ------------------ | Branch (5672:17): [True: 0, False: 154] | Branch (5672:47): [True: 0, False: 0] ------------------ 5673| 0| { 5674| 0| if ((ret = AddToEdgeList( &NNNChargeEdges, eNFlowerEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5674:21): [True: 0, False: 0] ------------------ 5675| 0| { 5676| 0| goto exit_function; 5677| 0| } 5678| 0| } 5679| 154| if (NO_VERTEX != eNFlowerEdge2 && !pBNS->edge[eNFlowerEdge2].flow) ------------------ | | 118| 154|#define NO_VERTEX -2 ------------------ | Branch (5679:17): [True: 0, False: 154] | Branch (5679:47): [True: 0, False: 0] ------------------ 5680| 0| { 5681| 0| if ((ret = AddToEdgeList( &NNNChargeEdges, eNFlowerEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5681:21): [True: 0, False: 0] ------------------ 5682| 0| { 5683| 0| goto exit_function; 5684| 0| } 5685| 0| } 5686| | 5687| 154| v1 = pe->neighbor1; 5688| 154| v2 = pe->neighbor12 ^ v1; 5689| 154| pe->flow--; 5690| 154| pBNS->vert[v1].st_edge.flow--; 5691| 154| pBNS->vert[v2].st_edge.flow--; 5692| 154| pBNS->tot_st_flow -= 2; 5693| | 5694| 154| pe->forbidden |= forbidden_edge_mask; 5695| | 5696| 154| if (!CarbonChargeEdges.num_edges) ------------------ | Branch (5696:17): [True: 141, False: 13] ------------------ 5697| 141| { 5698| | /* do not let carbon atoms get charged */ 5699| 141| AllocEdgeList( &CarbonChargeEdges, INC_EDGE_LIST ); ------------------ | | 5091| 141|#define INC_EDGE_LIST 16 ------------------ 5700| 141| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (5700:21): [True: 0, False: 141] ------------------ 5701| 0| { 5702| 0| goto exit_function; 5703| 0| } 5704| 141| } 5705| 13| else 5706| 13| { 5707| 13| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5708| 13| } 5709| 154| SetForbiddenEdgeMask( pBNS, &NNNChargeEdges, forbidden_edge_mask ); 5710| | 5711| 154| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5712| 154| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5713| | 5714| 154| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5714:17): [True: 78, False: 76] | Branch (5714:32): [True: 9, False: 69] | Branch (5714:50): [True: 4, False: 5] ------------------ 5715| 74| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge <= nDeltaChargeMax) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (5715:18): [True: 67, False: 7] | Branch (5715:36): [True: 65, False: 2] | Branch (5715:59): [True: 44, False: 25] ------------------ 5716| 44| { 5717| 44| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5718| 44| ( *pnNumRunBNS )++; 5719| 44| *pnTotalDelta += ret; 5720| 44| num_success++; 5721| | /* fix charges on N(-)=N(+)=N- */ 5722| 44| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 44|#define INC_EDGE_LIST 16 ------------------ | Branch (5722:21): [True: 0, False: 44] ------------------ 5723| 0| { 5724| 0| goto exit_function; 5725| 0| } 5726| 44| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 44|#define INC_EDGE_LIST 16 ------------------ | Branch (5726:21): [True: 0, False: 44] ------------------ 5727| 0| { 5728| 0| goto exit_function; 5729| 0| } 5730| 44| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge1, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 44|#define INC_EDGE_LIST 16 ------------------ | Branch (5730:21): [True: 0, False: 44] ------------------ 5731| 0| { 5732| 0| goto exit_function; 5733| 0| } 5734| 44| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 44|#define INC_EDGE_LIST 16 ------------------ | Branch (5734:21): [True: 0, False: 44] ------------------ 5735| 0| { 5736| 0| goto exit_function; 5737| 0| } 5738| 44| if ((ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge2, INC_EDGE_LIST ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5091| 44|#define INC_EDGE_LIST 16 ------------------ | Branch (5738:21): [True: 0, False: 44] ------------------ 5739| 0| { 5740| 0| goto exit_function; 5741| 0| } 5742| 44| } 5743| 110| else 5744| 110| { 5745| 110| pe->flow++; 5746| 110| pBNS->vert[v1].st_edge.flow++; 5747| 110| pBNS->vert[v2].st_edge.flow++; 5748| 110| pBNS->tot_st_flow += 2; 5749| 110| num_failed++; 5750| 110| } 5751| 154| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5752| 154| RemoveForbiddenEdgeMask( pBNS, &NNNChargeEdges, forbidden_edge_mask ); 5753| 154| pe->forbidden &= inv_forbidden_edge_mask; 5754| | /*pBNS->edge[eNPlusEdge].forbidden &= inv_forbidden_edge_mask;*/ /* BC: array index out of range */ 5755| 154| } 5756| 832k| } 5757| 87.7k| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5758| | 5759| | 5760| 87.7k|exit_function: 5761| | 5762| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 5763| 87.7k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 5764| 87.7k| AllocEdgeList( &NNNChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 5765| 87.7k| AllocEdgeList( &CurNNNChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 5766| 87.7k| AllocEdgeList( &AllNNNTermAtoms, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 5767| 87.7k| AllocEdgeList( &AllNIIIChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 5768| | 5769| 87.7k| return ret; 5770| 87.7k|#undef INC_EDGE_LIST 5771| 87.7k|} EliminateNitrogen5Val3Bonds: 5785| 87.7k|{ 5786| 87.7k| int i, j, k, bForbiddenCarbonCharges, ret2, ret; 5787| 87.7k| int num_at = pStruct->num_atoms; 5788| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 5789| 87.7k| int len_at = num_at + num_deleted_H; 5790| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 5791| 87.7k| EDGE_LIST CarbonChargeEdges; 5792| | 5793| 87.7k| ret = 0; 5794| 87.7k| bForbiddenCarbonCharges = 0; 5795| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 5796| | 5797| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 5798| 87.7k| pStruct->at = at2; 5799| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 5800| 87.7k| if (ret2 < 0) ------------------ | Branch (5800:9): [True: 0, False: 87.7k] ------------------ 5801| 0| { 5802| 0| ret = ret2; 5803| 0| goto exit_function; 5804| 0| } 5805| | 5806| | /* forbid creation of other N(V) atoms */ 5807| | /* fix single bonds to metals */ 5808| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (5808:17): [True: 832k, False: 87.7k] ------------------ 5809| 832k| { 5810| 832k| if (pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (5810:13): [True: 104k, False: 728k] ------------------ 5811| 104k| 0 <= ( k = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (5811:14): [True: 8.37k, False: 96.1k] ------------------ 5812| 8.37k| 1 == pBNS->edge[k].flow) ------------------ | Branch (5812:14): [True: 3.69k, False: 4.67k] ------------------ 5813| 3.69k| { 5814| 3.69k| pBNS->edge[k].forbidden |= forbidden_edge_mask; 5815| 3.69k| } 5816| 829k| else 5817| 829k| if (pVA[i].cMetal) ------------------ | Branch (5817:17): [True: 318k, False: 510k] ------------------ 5818| 318k| { 5819| 362k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (5819:29): [True: 43.1k, False: 318k] ------------------ 5820| 43.1k| { 5821| 43.1k| if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 32| 43.1k|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 189| 43.1k|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (5821:25): [True: 24.6k, False: 18.4k] ------------------ 5822| 24.6k| { 5823| 24.6k| pBNS->edge[pBNS->vert[i].iedge[j]].forbidden |= forbidden_edge_mask; 5824| 24.6k| } 5825| 43.1k| } 5826| 318k| } 5827| 832k| } 5828| | 5829| | /*------------------------------------------------------------------------------ 5830| | (+) single line => flow = 0 (+)-(Y)=(+)super 5831| | 01 // double line => flow = 1 fix-> 01 // <-- fix 5832| | 1 --- 0 1 === 0 5833| | \\ // edge eij connects vertices i < j: \ / 02 5834| | 12 2 02 <--- edge number: e02 connects vertices v0 12 2(..) <- double 'radical' 5835| | | v0 and v2 | 5836| | =N= vertex N has number i =N= 5837| | | | 5838| | --------------------------------------------------------------------------------*/ 5839| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (5839:17): [True: 832k, False: 87.7k] ------------------ 5840| 832k| { 5841| 832k| if (pVA[i].cNumValenceElectrons == 5 && at2[i].valence == 3 && ------------------ | Branch (5841:13): [True: 104k, False: 728k] | Branch (5841:49): [True: 8.79k, False: 95.7k] ------------------ 5842| 8.79k| at2[i].chem_bonds_valence == 5 && !at2[i].charge && !at2[i].radical && ------------------ | Branch (5842:14): [True: 4.85k, False: 3.94k] | Branch (5842:48): [True: 4.78k, False: 65] | Branch (5842:66): [True: 4.78k, False: 0] ------------------ 5843| 4.78k| !( at2[i].endpoint || (pStruct->endpoint && pStruct->endpoint[i]) ) && pVA[i].cnListIndex > 0 && ------------------ | Branch (5843:17): [True: 3, False: 4.78k] | Branch (5843:37): [True: 293, False: 4.49k] | Branch (5843:58): [True: 52, False: 241] | Branch (5843:85): [True: 4.73k, False: 0] ------------------ 5844| 832k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_NPN && ------------------ | | 425| 4.73k|#define cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0) | | ------------------ | | | | 421| 837k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 4.73k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 4.73k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 4.73k|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5844:14): [True: 4.61k, False: 116] ------------------ 5845| 4.61k| pVA[i].nCPlusGroupEdge > 0) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5845:14): [True: 4.61k, False: 0] ------------------ 5846| 4.61k| { 5847| | 5848| 4.61k| Vertex v, v0 = NO_VERTEX, v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ Vertex v, v0 = NO_VERTEX, v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ Vertex v, v0 = NO_VERTEX, v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ 5849| 4.61k| EdgeIndex iePlus, ie, ie12 = NO_VERTEX; /* djb-rwth: removing redundant variables */ ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ 5850| 4.61k| BNS_VERTEX *pv0, *pv2 = NULL; /* djb-rwth: removing redundant variables */ 5851| 4.61k| BNS_EDGE *pePlus, *pe, *pe12 = NULL, *pe02 = NULL, *pe01 = NULL; 5852| 4.61k| Vertex vPathStart, vPathEnd; 5853| 4.61k| int nPathLen; 5854| 4.61k| int nDeltaH, nDeltaCharge, nNumVisitedAtoms; 5855| | 5856| 4.61k| iePlus = pVA[i].nCPlusGroupEdge - 1; 5857| 4.61k| pePlus = pBNS->edge + iePlus; 5858| | 5859| 4.61k| v0 = IS_BNS_VT_C_GR( pBNS->vert[pePlus->neighbor1].type ) ? ------------------ | | 78| 4.61k|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 4.61k|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 4.61k|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 4.61k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 4.61k|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 4.61k, False: 0] | | ------------------ ------------------ 5860| 4.61k| ( pePlus->neighbor1 ^ pePlus->neighbor12 ) : pePlus->neighbor1; 5861| 4.61k| pv0 = pBNS->vert + v0; 5862| 18.4k| for (j = 0; j < pv0->num_adj_edges; j++) ------------------ | Branch (5862:25): [True: 13.8k, False: 4.61k] ------------------ 5863| 13.8k| { 5864| 13.8k| ie = pv0->iedge[j]; 5865| 13.8k| if (ie == iePlus) ------------------ | Branch (5865:21): [True: 4.61k, False: 9.23k] ------------------ 5866| 4.61k| { 5867| 4.61k| continue; 5868| 4.61k| } 5869| 9.23k| pe = pBNS->edge + ie; 5870| 9.23k| if (pe->flow == 1 && v2 == NO_VERTEX) ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ | Branch (5870:21): [True: 4.61k, False: 4.61k] | Branch (5870:38): [True: 4.61k, False: 0] ------------------ 5871| 4.61k| { 5872| | /* 0 - 2, edge 02 */ 5873| 4.61k| v2 = pe->neighbor12 ^ v0; 5874| 4.61k| pv2 = pBNS->vert + v2; 5875| | /* djb-rwth: removing redundant code */ 5876| 4.61k| pe02 = pe; 5877| 4.61k| } 5878| 4.61k| else 5879| 4.61k| { 5880| 4.61k| if (pe->flow == 0 && v1 == NO_VERTEX) ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ | Branch (5880:25): [True: 4.61k, False: 0] | Branch (5880:42): [True: 4.61k, False: 0] ------------------ 5881| 4.61k| { 5882| | /* 0 - 1, edge 01 */ 5883| 4.61k| v1 = pe->neighbor12 ^ v0; 5884| | /* djb-rwth: removing redundant code */ 5885| | /* djb-rwth: removing redundant code */ 5886| 4.61k| pe01 = pe; 5887| 4.61k| } 5888| 0| else 5889| 0| { 5890| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5891| 0| goto exit_function; 5892| 0| } 5893| 4.61k| } 5894| 9.23k| } 5895| 4.61k| if (v1 == NO_VERTEX || v2 == NO_VERTEX) ------------------ | | 118| 9.23k|#define NO_VERTEX -2 ------------------ if (v1 == NO_VERTEX || v2 == NO_VERTEX) ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ | Branch (5895:17): [True: 0, False: 4.61k] | Branch (5895:36): [True: 0, False: 4.61k] ------------------ 5896| 0| { 5897| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5898| 0| goto exit_function; 5899| 0| } 5900| 18.4k| for (j = 0; j < pv2->num_adj_edges; j++) ------------------ | Branch (5900:25): [True: 13.8k, False: 4.61k] ------------------ 5901| 13.8k| { 5902| 13.8k| ie = pv2->iedge[j]; 5903| 13.8k| pe = pBNS->edge + ie; 5904| 13.8k| v = pe->neighbor12 ^ v2; 5905| 13.8k| if (v == v0 || v == i) ------------------ | Branch (5905:21): [True: 4.61k, False: 9.23k] | Branch (5905:32): [True: 4.61k, False: 4.61k] ------------------ 5906| 9.23k| { 5907| 9.23k| continue; 5908| 9.23k| } 5909| 4.61k| else 5910| 4.61k| { 5911| 4.61k| if (v == v1 && pe->flow == 1) ------------------ | Branch (5911:25): [True: 4.61k, False: 0] | Branch (5911:36): [True: 4.61k, False: 0] ------------------ 5912| 4.61k| { 5913| | /* 1 - 2, edge 12 */ 5914| 4.61k| ie12 = ie; 5915| 4.61k| pe12 = pe; 5916| 4.61k| } 5917| 0| else 5918| 0| { 5919| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5920| 0| goto exit_function; 5921| 0| } 5922| 4.61k| } 5923| 13.8k| } 5924| 4.61k| if (ie12 == NO_VERTEX) ------------------ | | 118| 4.61k|#define NO_VERTEX -2 ------------------ | Branch (5924:17): [True: 0, False: 4.61k] ------------------ 5925| 0| { 5926| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 5927| 0| goto exit_function; 5928| 0| } 5929| | /* rearrange cap and flow, forbid 2 edges */ 5930| 4.61k| pe01->flow = 1; 5931| 4.61k| pe12->flow = 0; 5932| 4.61k| pe02->flow = 0; 5933| 4.61k| pv2->st_edge.flow -= 2; 5934| 4.61k| pBNS->tot_st_flow -= 2; 5935| 4.61k| pePlus->forbidden |= forbidden_edge_mask; 5936| 4.61k| pe01->forbidden |= forbidden_edge_mask; 5937| | 5938| 4.61k| if (!bForbiddenCarbonCharges) ------------------ | Branch (5938:17): [True: 4.12k, False: 489] ------------------ 5939| 4.12k| { 5940| 4.12k| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (5940:21): [True: 0, False: 4.12k] ------------------ 5941| 0| { 5942| 0| goto exit_function; 5943| 0| } 5944| 4.12k| bForbiddenCarbonCharges = 1; 5945| 4.12k| } 5946| | 5947| | 5948| 4.61k| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5949| 4.61k| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5950| 4.61k| if (ret == 1 && vPathEnd == v2 && vPathStart == v2 && nDeltaCharge <= ( pVA[i].cNumBondsToMetal ? 2 : 0 )) ------------------ | Branch (5950:17): [True: 1.79k, False: 2.82k] | Branch (5950:29): [True: 1.72k, False: 70] | Branch (5950:47): [True: 856, False: 867] | Branch (5950:67): [True: 473, False: 383] | Branch (5950:85): [True: 159, False: 697] ------------------ 5951| 473| { 5952| 473| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5953| 473| } 5954| 4.14k| else 5955| 4.14k| { 5956| 4.14k| pe01->flow = 0; 5957| 4.14k| pe12->flow = 1; 5958| 4.14k| pe02->flow = 1; 5959| 4.14k| pv2->st_edge.flow += 2; 5960| 4.14k| pBNS->tot_st_flow += 2; 5961| 4.14k| } 5962| 4.61k| pePlus->forbidden &= inv_forbidden_edge_mask; 5963| 4.61k| pe01->forbidden &= inv_forbidden_edge_mask; 5964| | 5965| 4.61k| if (ret < 0) ------------------ | Branch (5965:17): [True: 0, False: 4.61k] ------------------ 5966| 0| { 5967| 0| goto exit_function; 5968| 0| } 5969| 4.61k| else 5970| 4.61k| { 5971| 4.61k| if (ret) ------------------ | Branch (5971:21): [True: 1.79k, False: 2.82k] ------------------ 5972| 1.79k| { 5973| 1.79k| memcpy(at2, at, len_at * sizeof(at2[0])); 5974| 1.79k| pStruct->at = at2; 5975| 1.79k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 5976| 1.79k| if (ret2 < 0) ------------------ | Branch (5976:25): [True: 0, False: 1.79k] ------------------ 5977| 0| { 5978| 0| ret = ret2; 5979| 0| goto exit_function; 5980| 0| } 5981| 1.79k| } 5982| 4.61k| } 5983| 4.61k| } 5984| 832k| } 5985| | 5986| 87.7k|exit_function: 5987| | 5988| | /* allow creation of other N(V) atoms */ 5989| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (5989:17): [True: 832k, False: 87.7k] ------------------ 5990| 832k| { 5991| 832k| if (pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (5991:13): [True: 104k, False: 728k] ------------------ 5992| 104k| 0 <= ( k = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (5992:14): [True: 8.37k, False: 96.1k] ------------------ 5993| 8.37k| 1 == pBNS->edge[k].flow && ( pBNS->edge[k].forbidden & forbidden_edge_mask )) ------------------ | Branch (5993:14): [True: 4.17k, False: 4.20k] | Branch (5993:41): [True: 3.69k, False: 473] ------------------ 5994| 3.69k| { 5995| 3.69k| pBNS->edge[k].forbidden &= inv_forbidden_edge_mask; 5996| 3.69k| } 5997| 829k| else 5998| 829k| { 5999| 829k| if (pVA[i].cMetal) ------------------ | Branch (5999:17): [True: 318k, False: 510k] ------------------ 6000| 318k| { 6001| 362k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (6001:29): [True: 43.1k, False: 318k] ------------------ 6002| 43.1k| { 6003| 43.1k| if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 32| 43.1k|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 189| 43.1k|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (6003:25): [True: 24.6k, False: 18.4k] ------------------ 6004| 24.6k| { 6005| 24.6k| pBNS->edge[pBNS->vert[i].iedge[j]].forbidden &= inv_forbidden_edge_mask; 6006| 24.6k| } 6007| 43.1k| } 6008| 318k| } 6009| 829k| } 6010| 832k| } 6011| 87.7k| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6012| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 6013| | 6014| 87.7k| return ret; 6015| 87.7k|} Convert_SIV_to_SVI: 6029| 87.7k|{ 6030| 87.7k| int i, j, k, neigh, bForbiddenCarbonCharges, nFlowerEdge, delta, ret2, ret; 6031| 87.7k| int num_at = pStruct->num_atoms; 6032| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 6033| 87.7k| int len_at = num_at + num_deleted_H; 6034| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 6035| 87.7k| EDGE_LIST CarbonChargeEdges, FlowerEdgesList; 6036| | 6037| 87.7k| ret = 0; 6038| 87.7k| bForbiddenCarbonCharges = 0; 6039| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 6040| 87.7k| AllocEdgeList( &FlowerEdgesList, EDGE_LIST_CLEAR ); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 6041| | 6042| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 6043| 87.7k| pStruct->at = at2; 6044| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6045| 87.7k| if (ret2 < 0) ------------------ | Branch (6045:9): [True: 0, False: 87.7k] ------------------ 6046| 0| { 6047| 0| ret = ret2; 6048| 0| goto exit_function; 6049| 0| } 6050| | 6051| | /* forbid creation of other S(IV) atoms */ 6052| | /* fix single bonds to metals and (N(IV), flow=1), (S(IV), flow=0) */ 6053| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (6053:17): [True: 832k, False: 87.7k] ------------------ 6054| 832k| { 6055| 832k| if (( pVA[i].cNumValenceElectrons == 5 /* N(IV)*/ || pVA[i].cNumValenceElectrons == 6 /* S(VI)*/ ) && ------------------ | Branch (6055:15): [True: 104k, False: 728k] | Branch (6055:62): [True: 215k, False: 512k] ------------------ 6056| 320k| 0 <= ( k = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (6056:14): [True: 15.2k, False: 304k] ------------------ 6057| 15.2k| !pBNS->edge[k].forbidden && ------------------ | Branch (6057:14): [True: 15.2k, False: 0] ------------------ 6058| 15.2k| 6 == pVA[i].cNumValenceElectrons + pBNS->edge[k].flow) ------------------ | Branch (6058:14): [True: 6.14k, False: 9.15k] ------------------ 6059| 6.14k| { 6060| | 6061| 6.14k| pBNS->edge[k].forbidden |= forbidden_edge_mask; 6062| 6.14k| if ((ret = AddToEdgeList( &FlowerEdgesList, k, 64 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6062:17): [True: 0, False: 6.14k] ------------------ 6063| 0| { 6064| 0| goto exit_function; 6065| 0| } 6066| 6.14k| } 6067| 826k| else 6068| 826k| { 6069| 826k| if (pVA[i].cMetal) ------------------ | Branch (6069:17): [True: 318k, False: 507k] ------------------ 6070| 318k| { 6071| 362k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (6071:29): [True: 43.1k, False: 318k] ------------------ 6072| 43.1k| { 6073| 43.1k| if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 32| 43.1k|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 189| 43.1k|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (6073:25): [True: 24.6k, False: 18.4k] ------------------ 6074| 24.6k| { 6075| | 6076| 24.6k| pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden |= forbidden_edge_mask; 6077| 24.6k| if ((ret = AddToEdgeList( &FlowerEdgesList, k, 64 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6077:29): [True: 0, False: 24.6k] ------------------ 6078| 0| { 6079| 0| goto exit_function; 6080| 0| } 6081| 24.6k| } 6082| 43.1k| } 6083| 318k| } 6084| 507k| else 6085| 507k| { 6086| | /* fix bonds to neighbors of S(IV) if they are not O,S,Se,Te with 2 or more bonds */ 6087| | /* exactly same if(..) as below */ 6088| 507k| if (pVA[i].cNumValenceElectrons == 6 && at2[i].valence == 4 && ------------------ | Branch (6088:21): [True: 213k, False: 294k] | Branch (6088:57): [True: 1.59k, False: 211k] ------------------ 6089| 1.59k| at2[i].chem_bonds_valence == 4 && !at2[i].charge && !at2[i].radical && ------------------ | Branch (6089:22): [True: 571, False: 1.02k] | Branch (6089:56): [True: 487, False: 84] | Branch (6089:74): [True: 477, False: 10] ------------------ 6090| 477| !at2[i].endpoint && pVA[i].cnListIndex > 0 && ------------------ | Branch (6090:22): [True: 476, False: 1] | Branch (6090:42): [True: 476, False: 0] ------------------ 6091| 507k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_NPN && ------------------ | | 425| 476|#define cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0) | | ------------------ | | | | 421| 508k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 476|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 476|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 476|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (6091:22): [True: 475, False: 1] ------------------ 6092| 475| 0 <= ( nFlowerEdge = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (6092:22): [True: 475, False: 0] ------------------ 6093| 475| pBNS->edge[nFlowerEdge].flow > 0) ------------------ | Branch (6093:22): [True: 475, False: 0] ------------------ 6094| 475| { 6095| | 6096| 2.37k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (6096:33): [True: 1.90k, False: 475] ------------------ 6097| 1.90k| { 6098| 1.90k| neigh = at2[i].neighbor[j]; 6099| 1.90k| if (pVA[neigh].cNumValenceElectrons != 6 && at2[neigh].valence > 1) ------------------ | Branch (6099:29): [True: 1.25k, False: 641] | Branch (6099:69): [True: 767, False: 492] ------------------ 6100| 767| { 6101| 767| k = pBNS->vert[i].iedge[j]; 6102| 767| if (!pBNS->edge[k].forbidden) ------------------ | Branch (6102:33): [True: 675, False: 92] ------------------ 6103| 675| { 6104| 675| if ((ret = AddToEdgeList( &FlowerEdgesList, k, 64 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6104:37): [True: 0, False: 675] ------------------ 6105| 0| { 6106| 0| goto exit_function; 6107| 0| } 6108| 675| pBNS->edge[k].forbidden |= forbidden_edge_mask; 6109| 675| } 6110| 767| } 6111| 1.90k| } 6112| 475| } 6113| 507k| } 6114| 826k| } 6115| 832k| } 6116| | 6117| | /*------------------------------------------------------------------------------ 6118| | example: struct #301, 6119| | | | disconnected porphyrin with four -SO3(-) 6120| | -S- => =S= 6121| | | | 6122| | 6123| | -------------------------------------------------------------------------------*/ 6124| | 6125| | /*------------------------------------------------------------------------------- 6126| | found: super(+)=(Y) super(+)=(Y) 6127| | \ \ 6128| | (+) single line => flow = 0 (+) (+) 6129| | 01 // double line => flow = 1 fix-> 01 // 01 // 6130| | 1 === 0 triple line => flow = 2 (.)1 --- 0(.) ---> 1 --- 0 6131| | \ / edge eij connects vertices i 0 && ------------------ | Branch (6141:14): [True: 476, False: 1] | Branch (6141:34): [True: 476, False: 0] ------------------ 6142| 832k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_NPN && ------------------ | | 425| 476|#define cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0) | | ------------------ | | | | 421| 833k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 476|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 476|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 476|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (6142:14): [True: 469, False: 7] ------------------ 6143| | /* 01 is nFlowerEdge */ 6144| 469| 0 <= ( nFlowerEdge = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (6144:14): [True: 469, False: 0] ------------------ 6145| 469| pBNS->edge[nFlowerEdge].flow > 0) ------------------ | Branch (6145:14): [True: 469, False: 0] ------------------ 6146| 469| { 6147| | 6148| 469| Vertex v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 118| 469|#define NO_VERTEX -2 ------------------ Vertex v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 118| 469|#define NO_VERTEX -2 ------------------ 6149| 469| BNS_VERTEX *pv1, *pv2; 6150| 469| BNS_EDGE *pe; 6151| 469| Vertex vPathStart, vPathEnd; 6152| 469| int nPathLen; 6153| 469| int nDeltaH, nDeltaCharge, nNumVisitedAtoms; 6154| | 6155| 469| if (!bForbiddenCarbonCharges) ------------------ | Branch (6155:17): [True: 445, False: 24] ------------------ 6156| 445| { 6157| 445| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (6157:21): [True: 0, False: 445] ------------------ 6158| 0| { 6159| 0| goto exit_function; 6160| 0| } 6161| 445| bForbiddenCarbonCharges = 1; 6162| 445| } 6163| | 6164| 469| delta = 1; 6165| 469| pe = pBNS->edge + nFlowerEdge; /* edge 01 */ 6166| 469| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); /* vertex 0 */ 6167| 469| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); /* vertex 1 */ 6168| | 6169| 469| pe->forbidden |= forbidden_edge_mask; 6170| 469| pe->flow -= delta; 6171| 469| pv1->st_edge.flow -= delta; 6172| 469| pv2->st_edge.flow -= delta; 6173| 469| pBNS->tot_st_flow -= 2 * delta; 6174| | 6175| 469| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6176| 469| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6177| 469| if (ret == 1 && ------------------ | Branch (6177:17): [True: 312, False: 157] ------------------ 6178| 312| ( (vPathEnd == v1 && vPathStart == v2) || (vPathEnd == v2 && vPathStart == v1) ) && ------------------ | Branch (6178:20): [True: 161, False: 151] | Branch (6178:38): [True: 0, False: 161] | Branch (6178:60): [True: 151, False: 161] | Branch (6178:78): [True: 151, False: 0] ------------------ 6179| 151| nDeltaCharge <= ( pVA[i].cNumBondsToMetal ? 2 : 0 )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6179:18): [True: 137, False: 14] | Branch (6179:36): [True: 93, False: 58] ------------------ 6180| 137| { 6181| 137| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6182| 137| } 6183| 332| else 6184| 332| { 6185| 332| pe->forbidden &= inv_forbidden_edge_mask; 6186| 332| pe->flow += delta; 6187| 332| pv1->st_edge.flow += delta; 6188| 332| pv2->st_edge.flow += delta; 6189| 332| pBNS->tot_st_flow += 2 * delta; 6190| 332| } 6191| 469| if (ret < 0) ------------------ | Branch (6191:17): [True: 0, False: 469] ------------------ 6192| 0| { 6193| 0| goto exit_function; 6194| 0| } 6195| 469| else 6196| 469| { 6197| 469| if (ret) ------------------ | Branch (6197:21): [True: 312, False: 157] ------------------ 6198| 312| { 6199| 312| memcpy(at2, at, len_at * sizeof(at2[0])); 6200| 312| pStruct->at = at2; 6201| 312| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6202| 312| if (ret2 < 0) ------------------ | Branch (6202:25): [True: 0, False: 312] ------------------ 6203| 0| { 6204| 0| ret = ret2; 6205| 0| goto exit_function; 6206| 0| } 6207| | /* store the fixed edge to unfix it upon exit */ 6208| 312| if ((ret = AddToEdgeList( &FlowerEdgesList, nFlowerEdge, 64 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6208:25): [True: 0, False: 312] ------------------ 6209| 0| { 6210| 0| goto exit_function; 6211| 0| } 6212| 312| } 6213| 469| } 6214| 469| } 6215| 832k| } 6216| | 6217| 87.7k|exit_function: 6218| | 6219| 87.7k| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6220| 87.7k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 6221| 87.7k| RemoveForbiddenEdgeMask( pBNS, &FlowerEdgesList, forbidden_edge_mask ); 6222| 87.7k| AllocEdgeList( &FlowerEdgesList, EDGE_LIST_FREE ); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 6223| | 6224| 87.7k| return ret; 6225| 87.7k|} PlusFromDB_N_DB_O_to_Metal: 6245| 87.7k|{ 6246| 87.7k| int i, j, k, n, delta, ret2, ret, num_NO, num_M; /* djb-rwth: removing redundant variables */ 6247| 87.7k| int num_at = pStruct->num_atoms; 6248| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 6249| 87.7k| int len_at = num_at + num_deleted_H; 6250| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 6251| 87.7k| EDGE_LIST CarbonChargeEdges, NO_ChargeEdgeList, NO_EdgeList; 6252| | 6253| 87.7k| Vertex v1, v2; 6254| 87.7k| BNS_VERTEX *pv1, *pv2; 6255| 87.7k| BNS_EDGE *pe; 6256| 87.7k| Vertex vPathStart, vPathEnd; 6257| 87.7k| int nPathLen; 6258| 87.7k| int nDeltaH, nDeltaCharge, nNumVisitedAtoms; 6259| | 6260| | 6261| 87.7k| if (!pTCGroups->num_metal_atoms) ------------------ | Branch (6261:9): [True: 22.3k, False: 65.4k] ------------------ 6262| 22.3k| { 6263| 22.3k| return 0; 6264| 22.3k| } 6265| | 6266| 65.4k| ret = 0; 6267| | /* djb-rwth: removing redundant code */ 6268| 65.4k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); /* all charges */ ------------------ | | 242| 65.4k|#define EDGE_LIST_CLEAR (-1) ------------------ 6269| 65.4k| AllocEdgeList( &NO_ChargeEdgeList, EDGE_LIST_CLEAR ); /* charges to be changed */ ------------------ | | 242| 65.4k|#define EDGE_LIST_CLEAR (-1) ------------------ 6270| 65.4k| AllocEdgeList( &NO_EdgeList, EDGE_LIST_CLEAR ); /* N(+)=O edges */ ------------------ | | 242| 65.4k|#define EDGE_LIST_CLEAR (-1) ------------------ 6271| | 6272| 65.4k| memcpy(at2, at, len_at * sizeof(at2[0])); 6273| 65.4k| pStruct->at = at2; 6274| 65.4k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6275| 65.4k| if (ret2 < 0) ------------------ | Branch (6275:9): [True: 0, False: 65.4k] ------------------ 6276| 0| { 6277| 0| ret = ret2; 6278| 0| goto exit_function; 6279| 0| } 6280| | 6281| 65.4k| num_NO = num_M = 0; 6282| | 6283| | /* forbid creation of other S(IV) atoms */ 6284| | /* fix single bonds to metals and (N(IV), flow=1), (S(IV), flow=0) */ 6285| 787k| for (i = 0; i < num_at; i++) ------------------ | Branch (6285:17): [True: 722k, False: 65.4k] ------------------ 6286| 722k| { 6287| 722k| if (!pVA[i].cMetal) ------------------ | Branch (6287:13): [True: 403k, False: 318k] ------------------ 6288| 403k| { 6289| 403k| if (( k = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (6289:17): [True: 49.1k, False: 354k] | Branch (6289:60): [True: 47.0k, False: 2.17k] ------------------ 6290| 47.0k| { 6291| 47.0k| if ((ret = AddToEdgeList( &CarbonChargeEdges, k, 64 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6291:21): [True: 0, False: 47.0k] ------------------ 6292| 0| { 6293| 0| goto exit_function; 6294| 0| } 6295| 47.0k| } 6296| 403k| if (( k = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (6296:17): [True: 39.7k, False: 363k] | Branch (6296:61): [True: 39.7k, False: 0] ------------------ 6297| 39.7k| { 6298| 39.7k| if ((ret = AddToEdgeList( &CarbonChargeEdges, k, 64 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6298:21): [True: 0, False: 39.7k] ------------------ 6299| 0| { 6300| 0| goto exit_function; 6301| 0| } 6302| 39.7k| } 6303| 403k| } 6304| 318k| else 6305| 318k| { 6306| 318k| num_M++; 6307| 318k| } 6308| | /* 6309| | if ( pVA[i].cMetal ) 6310| | { 6311| | if ( (k = pVA[i].nCPlusGroupEdge-1) >= 0 && !pBNS->edge[k].forbidden ) 6312| | { 6313| | if ( ret = AddToEdgeList( &NO_ChargeEdgeList, k, 64 ) ) 6314| | { 6315| | goto exit_function; 6316| | } 6317| | } 6318| | if ( (k = pVA[i].nCMinusGroupEdge-1) >= 0 && !pBNS->edge[k].forbidden ) 6319| | { 6320| | if ( ret = AddToEdgeList( &NO_ChargeEdgeList, k, 64 ) ) 6321| | { 6322| | goto exit_function; 6323| | } 6324| | } 6325| | } 6326| | else 6327| | */ 6328| 722k| if (!pVA[i].cMetal && ------------------ | Branch (6328:13): [True: 403k, False: 318k] ------------------ 6329| 403k| pVA[i].cNumValenceElectrons == 6 && ------------------ | Branch (6329:14): [True: 188k, False: 214k] ------------------ 6330| 188k| at2[i].charge == 0 && !at2[i].num_H && ------------------ | Branch (6330:14): [True: 180k, False: 8.27k] | Branch (6330:36): [True: 180k, False: 416] ------------------ 6331| 180k| 1 == at2[i].valence && 2 == at2[i].chem_bonds_valence && ------------------ | Branch (6331:14): [True: 5.83k, False: 174k] | Branch (6331:37): [True: 5.79k, False: 35] ------------------ 6332| 5.79k| pVA[j = at2[i].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (6332:14): [True: 1.65k, False: 4.14k] ------------------ 6333| 1.65k| at2[j].charge == 1 && !at2[j].num_H && ------------------ | Branch (6333:14): [True: 188, False: 1.47k] | Branch (6333:36): [True: 178, False: 10] ------------------ 6334| 178| 2 == at2[j].valence && 4 == at2[j].chem_bonds_valence) ------------------ | Branch (6334:14): [True: 45, False: 133] | Branch (6334:37): [True: 45, False: 0] ------------------ 6335| 45| { 6336| | /* found =N(+)=O */ 6337| 45| if (( k = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden /* O */ && ------------------ | Branch (6337:17): [True: 44, False: 1] | Branch (6337:61): [True: 44, False: 0] ------------------ 6338| 44| ( n = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[j].forbidden /* N */) ------------------ | Branch (6338:17): [True: 44, False: 0] | Branch (6338:60): [True: 43, False: 1] ------------------ 6339| 43| { 6340| 43| if (( ret = AddToEdgeList( &NO_ChargeEdgeList, k, 64 ) ) || ------------------ | Branch (6340:21): [True: 0, False: 43] ------------------ 6341| 43| ( ret = AddToEdgeList( &NO_ChargeEdgeList, n, 64 ) )) ------------------ | Branch (6341:21): [True: 0, False: 43] ------------------ 6342| 0| { 6343| 0| goto exit_function; 6344| 0| } 6345| 43| k = pBNS->vert[i].iedge[0]; /* N(+)=O bond */ 6346| 43| if (!pBNS->edge[k].forbidden) ------------------ | Branch (6346:21): [True: 43, False: 0] ------------------ 6347| 43| { 6348| 43| if ((ret = AddToEdgeList( &NO_EdgeList, k, 64 ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6348:25): [True: 0, False: 43] ------------------ 6349| 0| { 6350| 0| goto exit_function; 6351| 0| } 6352| 43| num_NO++; 6353| 43| } 6354| 43| } 6355| 45| } 6356| 722k| } 6357| 65.4k| if (num_M && num_NO) ------------------ | Branch (6357:9): [True: 65.4k, False: 0] | Branch (6357:18): [True: 43, False: 65.3k] ------------------ 6358| 43| { 6359| 43| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6360| 43| SetForbiddenEdgeMask( pBNS, &NO_EdgeList, forbidden_edge_mask ); 6361| 43| RemoveForbiddenEdgeMask( pBNS, &NO_ChargeEdgeList, forbidden_edge_mask ); 6362| | /* now only N(+), O(-) and metal charges are allowed to change */ 6363| 86| for (i = 0; i < NO_EdgeList.num_edges; i++) ------------------ | Branch (6363:21): [True: 43, False: 43] ------------------ 6364| 43| { 6365| 43| k = NO_EdgeList.pnEdges[i]; 6366| 43| delta = 1; 6367| 43| pe = pBNS->edge + k; /* edge N(+)=O */ 6368| 43| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); /* vertex 0 */ 6369| 43| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); /* vertex 1 */ 6370| | 6371| 43| pe->flow -= delta; 6372| 43| pv1->st_edge.flow -= delta; 6373| 43| pv2->st_edge.flow -= delta; 6374| 43| pBNS->tot_st_flow -= 2 * delta; 6375| | 6376| 43| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6377| 43| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6378| 43| if (ret == 1 && ------------------ | Branch (6378:17): [True: 43, False: 0] ------------------ 6379| 43| ( (vPathEnd == v1 && vPathStart == v2) || (vPathEnd == v2 && vPathStart == v1) ) && ------------------ | Branch (6379:20): [True: 1, False: 42] | Branch (6379:38): [True: 0, False: 1] | Branch (6379:60): [True: 41, False: 2] | Branch (6379:78): [True: 41, False: 0] ------------------ 6380| 41| nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6380:18): [True: 8, False: 33] ------------------ 6381| 8| { 6382| 8| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6383| 8| } 6384| 35| else 6385| 35| { 6386| 35| pe->forbidden &= inv_forbidden_edge_mask; 6387| 35| pe->flow += delta; 6388| 35| pv1->st_edge.flow += delta; 6389| 35| pv2->st_edge.flow += delta; 6390| 35| pBNS->tot_st_flow += 2 * delta; 6391| 35| } 6392| 43| if (ret < 0) ------------------ | Branch (6392:17): [True: 0, False: 43] ------------------ 6393| 0| { 6394| 0| goto exit_function; 6395| 0| } 6396| 43| } 6397| 43| } 6398| | 6399| 65.4k|exit_function: 6400| 65.4k| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6401| 65.4k| RemoveForbiddenEdgeMask( pBNS, &NO_EdgeList, forbidden_edge_mask ); 6402| 65.4k| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 65.4k|#define EDGE_LIST_FREE (-2) ------------------ 6403| 65.4k| AllocEdgeList( &NO_EdgeList, EDGE_LIST_FREE ); ------------------ | | 243| 65.4k|#define EDGE_LIST_FREE (-2) ------------------ 6404| 65.4k| AllocEdgeList( &NO_ChargeEdgeList, EDGE_LIST_FREE ); ------------------ | | 243| 65.4k|#define EDGE_LIST_FREE (-2) ------------------ 6405| | 6406| 65.4k| return ret; 6407| 65.4k|} MoveMobileHToAvoidFixedBonds: 6421| 87.7k|{ 6422| 87.7k| int ret2, ret; 6423| 87.7k| int num_at = pStruct->num_atoms; 6424| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 6425| 87.7k| int len_at = num_at + num_deleted_H; 6426| 87.7k| int nNumFixedEdges, nNumAdjEdges; 6427| | 6428| 87.7k| ret = 0; 6429| | 6430| 87.7k| if (pTCGroups->num_tgroups) ------------------ | Branch (6430:9): [True: 486, False: 87.2k] ------------------ 6431| 486| { 6432| 486| memcpy(at2, at, len_at * sizeof(at2[0])); 6433| 486| pStruct->at = at2; 6434| 486| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6435| 486| pStruct->at = at; 6436| 486| if (ret2 < 0) ------------------ | Branch (6436:13): [True: 0, False: 486] ------------------ 6437| 0| { 6438| 0| ret = ret2; 6439| 0| goto exit_function; 6440| 0| } 6441| 486|#if ( FIND_RING_SYSTEMS == 1 ) 6442| 486| ret2 = MarkRingSystemsInp( at2, num_at, 0 ); 6443| 486| if (ret2 < 0) ------------------ | Branch (6443:13): [True: 0, False: 486] ------------------ 6444| 0| { 6445| 0| ret = ret2; 6446| 0| goto exit_function; 6447| 0| } 6448| 486|#endif 6449| | /* --- forbidden edges --- */ 6450| 486| ret2 = SetForbiddenEdges( pBNS, at2, num_at, forbidden_edge_mask, 0, NULL ); 6451| | 6452| 486| if (ret2 < 0) ------------------ | Branch (6452:13): [True: 0, False: 486] ------------------ 6453| 0| { 6454| 0| ret2 = -( ret + 1 ); 6455| 0| } 6456| 486| nNumFixedEdges = ret2; 6457| 486| ret = AdjustTgroupsToForbiddenEdges2( pBNS, at2, pVA, num_at, forbidden_edge_mask ); 6458| 486| nNumAdjEdges = ret; 6459| 486| if (ret) ------------------ | Branch (6459:13): [True: 8, False: 478] ------------------ 6460| 8| { 6461| 8| pBNS->edge_forbidden_mask |= forbidden_edge_mask; 6462| 8| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6463| 8| ( *pnNumRunBNS )++; 6464| 8| if (ret < 0) ------------------ | Branch (6464:17): [True: 0, False: 8] ------------------ 6465| 0| { 6466| 0| goto exit_function; 6467| 0| } 6468| 8| else 6469| 8| { 6470| 8| *pnTotalDelta += ret; 6471| 8| } 6472| 8| } 6473| 486| if (nNumFixedEdges || nNumAdjEdges) ------------------ | Branch (6473:13): [True: 69, False: 417] | Branch (6473:31): [True: 0, False: 417] ------------------ 6474| 69| { 6475| | /* removes this edge mask from ALL edges */ 6476| 69| RemoveForbiddenBondFlowBits( pBNS, forbidden_edge_mask ); 6477| 69| } 6478| 486| } 6479| | 6480| 87.7k|exit_function: 6481| | 6482| 87.7k| return ret; 6483| 87.7k|} RemoveRadFromMobileHEndpoint: 6500| 86.6k|{ 6501| 86.6k| int i, num_fixes, tot_num_fixes = 0; 6502| | 6503| 86.6k| int ret2, ret; 6504| 86.6k| int num_at = pStruct->num_atoms; 6505| 86.6k| int num_deleted_H = pStruct->num_deleted_H; 6506| 86.6k| int len_at = num_at + num_deleted_H; 6507| | 6508| 86.6k| int itg, j, k, n, m; 6509| 86.6k| Vertex vtg1, endpoint0 = NO_VERTEX, endpoint1, endpoint2, centerpoint; ------------------ | | 118| 86.6k|#define NO_VERTEX -2 ------------------ 6510| 86.6k| Vertex centerpoint_found = NO_VERTEX; ------------------ | | 118| 86.6k|#define NO_VERTEX -2 ------------------ 6511| 86.6k| BNS_VERTEX *ptg1, *pEndp0 = NULL, *pEndp1, *pEndp2, *pCentp, *pCentp_found, *pEndp2_found = NULL; 6512| 86.6k| BNS_EDGE *etg0 = NULL, *etg1, *etg2, *ecp0, *ecp1, *ecp2; 6513| 86.6k| BNS_EDGE *etg1_found = NULL, *ecp0_found = NULL, *ecp1_found = NULL, *ecp2_found = NULL; 6514| 86.6k| int num_endpoints, max_vertices, nMaxAddAtoms = 2; /* djb-rwth: removing redundant variables; fixing oss-fuzz issue #25732 */ 6515| | 6516| | /* djb-rwth: removing redundant code */ 6517| 86.6k| memcpy(at2, at, len_at * sizeof(at2[0])); 6518| 86.6k| pStruct->at = at2; 6519| 86.6k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6520| 86.6k| if (ret2 < 0) ------------------ | Branch (6520:9): [True: 0, False: 86.6k] ------------------ 6521| 0| { 6522| 0| ret = ret2; 6523| 0| goto exit_function; 6524| 0| } 6525| 86.7k| while (pBNS->tot_st_cap > pBNS->tot_st_flow && pTCGroups->num_tgroups) ------------------ | Branch (6525:12): [True: 13.3k, False: 73.3k] | Branch (6525:52): [True: 335, False: 13.0k] ------------------ 6526| 335| { 6527| 335| num_fixes = 0; 6528| 700| for (itg = 0; itg < pTCGroups->num_tgroups; itg++) ------------------ | Branch (6528:23): [True: 365, False: 335] ------------------ 6529| 365| { 6530| 365| pCentp_found = NULL; 6531| | /* djb-rwth: removing redundant code */ 6532| 365| vtg1 = pTCGroups->pTCG[itg].nVertexNumber; /* taut group vertex index */ 6533| 365| ptg1 = pBNS->vert + vtg1; /* taut group vertex */ 6534| 365| num_endpoints = pTCGroups->pTCG[itg].num_edges; 6535| 966| for (i = 0; i < num_endpoints; i++) ------------------ | Branch (6535:25): [True: 765, False: 201] ------------------ 6536| 765| { 6537| 765| etg0 = pBNS->edge + ptg1->iedge[i]; /* edge from t-group to endpoint */ 6538| 765| endpoint0 = etg0->neighbor12 ^ vtg1; /* taut endpoint vertex index */ 6539| | /* djb-rwth: fixing oss-fuzz issues #68494, #25732 */ 6540| 765| max_vertices = pTCGroups->nVertices + nMaxAddAtoms; 6541| 765| if (endpoint0 < max_vertices) ------------------ | Branch (6541:21): [True: 762, False: 3] ------------------ 6542| 762| { 6543| 762| pEndp0 = pBNS->vert + endpoint0; /* taut endpoint vertex (possible location of mobile H */ 6544| 762| if (pEndp0->st_edge.cap > pEndp0->st_edge.flow) ------------------ | Branch (6544:25): [True: 164, False: 598] ------------------ 6545| 164| { 6546| | /* radical endpoint1 has been detected */ 6547| | /* find a 1-3 centerpoint that has two or more endpoints */ 6548| | /* connected to the t-group vertex by edges with flow>0 and */ 6549| | /* to the centerpoint by edges with flow = 0 */ 6550| | /* after that: (1) increment etg1 flow to eliminate radical */ 6551| | /* (2) increment flow on one of the two other edges to the t-group */ 6552| | /* (3) increment st_cap on the found centerpoint */ 6553| | /* (4) rerun the BNS and re-create the structure */ 6554| 164| break; 6555| 164| } 6556| 762| } 6557| 765| } 6558| 365| if (i == num_endpoints) ------------------ | Branch (6558:17): [True: 201, False: 164] ------------------ 6559| 201| { 6560| 201| continue; 6561| 201| } 6562| 164| if (i < num_endpoints) ------------------ | Branch (6562:17): [True: 164, False: 0] ------------------ 6563| 164| { 6564| | /* tautomeric endpoint found; traverse its t-group edges */ 6565| 650| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (6565:29): [True: 486, False: 164] ------------------ 6566| 486| { 6567| 486| if (i == j) ------------------ | Branch (6567:25): [True: 164, False: 322] ------------------ 6568| 164| { 6569| 164| continue; /* avoid the already found radical endpoint */ 6570| 164| } 6571| 322| etg1 = pBNS->edge + ptg1->iedge[j]; /* another edge from t-group to another endpoinr */ 6572| 322| endpoint1 = etg1->neighbor12 ^ vtg1; /* another endpoint vertex index */ 6573| 322| pEndp1 = pBNS->vert + endpoint1; /* another endpoint vertex */ 6574| 322| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (6574:25): [True: 47, False: 275] ------------------ 6575| 47| { 6576| 47| continue; /* one more radical-endpoint! What is going on here??? */ 6577| 47| } 6578| 275| if (!etg1->flow) ------------------ | Branch (6578:25): [True: 107, False: 168] ------------------ 6579| 107| { 6580| 107| continue; /* avoid enpoints that do not have an attachment */ 6581| 107| } 6582| 168| if (!( pEndp1->type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 46| 168|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6582:25): [True: 1, False: 167] ------------------ 6583| 1| { 6584| 1| continue; /* should not happen */ 6585| 1| } 6586| | /* traverse endpoint1 edges to find a single bond connecting it to the centerpoint */ 6587| 414| for (k = 0; k < at2[endpoint1].valence; k++) ------------------ | Branch (6587:33): [True: 247, False: 167] ------------------ 6588| 247| { 6589| 247| ecp1 = pBNS->edge + pEndp1->iedge[k]; 6590| 247| if (ecp1->flow) ------------------ | Branch (6590:29): [True: 30, False: 217] ------------------ 6591| 30| { 6592| 30| continue; 6593| 30| } 6594| 217| centerpoint = ecp1->neighbor12 ^ endpoint1; 6595| 217| pCentp = pBNS->vert + centerpoint; 6596| | /* traverse centerpoint edges to find a single bond to the 2nd endpoint */ 6597| 861| for (n = 0; n < at2[centerpoint].valence; n++) ------------------ | Branch (6597:37): [True: 688, False: 173] ------------------ 6598| 688| { 6599| 688| ecp2 = pBNS->edge + pCentp->iedge[n]; 6600| 688| if (ecp2->flow) ------------------ | Branch (6600:33): [True: 97, False: 591] ------------------ 6601| 97| { 6602| 97| continue; 6603| 97| } 6604| 591| endpoint2 = ecp2->neighbor12 ^ centerpoint; 6605| 591| if (endpoint2 <= endpoint1 || !pVA[endpoint2].nTautGroupEdge) ------------------ | Branch (6605:33): [True: 346, False: 245] | Branch (6605:59): [True: 91, False: 154] ------------------ 6606| 437| { 6607| 437| continue; /* don't go back: neighbors are in order of ascending ord. numbers */ 6608| 437| } 6609| 154| pEndp2 = pBNS->vert + endpoint2; 6610| 154| if (!( pEndp2->type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 46| 154|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6610:33): [True: 0, False: 154] ------------------ 6611| 0| { 6612| 0| continue; 6613| 0| } 6614| 154| etg2 = pBNS->edge + pVA[endpoint2].nTautGroupEdge - 1; 6615| 154| if (!etg2->flow || ( etg2->neighbor12 ^ endpoint2 ) != vtg1) ------------------ | Branch (6615:33): [True: 92, False: 62] | Branch (6615:48): [True: 0, False: 62] ------------------ 6616| 92| { 6617| 92| continue; 6618| 92| } 6619| | /* we have found the path: 6620| | Endp1 Endp1 6621| | etg1 // \ ecp1 etg1 / \\ ecp1 6622| | etg0 // \ etg0 / \\ 6623| | Endp0-----tg1 Centp --> Endp0=====tg1 Centp 6624| | ^ \\ / \\ / 6625| | radical | etg2 \\ / ecp2 etg2 \\ / ecp2 6626| | Endp2 Endp2 6627| | */ 6628| | 6629| | /* compare centerpoints */ 6630| 62| if (!pCentp_found || ------------------ | Branch (6630:33): [True: 33, False: 29] ------------------ 6631| | /* try to avoid carbons */ 6632| 29| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6632:36): [True: 23, False: 6] ------------------ 6633| 6| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6633:37): [True: 0, False: 6] ------------------ 6634| 23| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (6634:34): [True: 3, False: 20] ------------------ 6635| 3| pVA[centerpoint_found].cPeriodicRowNumber == 1) || ------------------ | Branch (6635:34): [True: 3, False: 0] ------------------ 6636| | /* try a better non-carbon */ 6637| 26| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6637:37): [True: 20, False: 6] ------------------ 6638| 6| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6638:38): [True: 0, False: 6] ------------------ 6639| 20| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (6639:40): [True: 3, False: 17] ------------------ 6640| 17| (at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (6640:43): [True: 16, False: 1] ------------------ 6641| 16| at[centerpoint].el_number > at[centerpoint_found].el_number) ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6641:42): [True: 5, False: 11] ------------------ 6642| 44| { 6643| | 6644| 44| pCentp_found = pCentp; 6645| 44| etg1_found = etg1; 6646| 44| ecp1_found = ecp1; 6647| 44| centerpoint_found = centerpoint; 6648| 44| break; 6649| 44| } 6650| 62| } 6651| 217| } 6652| 167| } 6653| 164| } 6654| 164| if (pCentp_found) ------------------ | Branch (6654:17): [True: 33, False: 131] ------------------ 6655| 33| { 6656| | /* ---- (1) */ 6657| 33| etg0->flow++; 6658| 33| pEndp0->st_edge.flow++; 6659| | /* ---- (2) */ 6660| 33| etg1_found->flow--; 6661| | /* ---- (3) */ 6662| 33| ecp1_found->flow++; 6663| | /* ---- (4) */ 6664| 33| pCentp_found->st_edge.flow++; 6665| 33| pCentp_found->st_edge.cap++; 6666| | 6667| 33| pBNS->tot_st_flow += 2; 6668| 33| pBNS->tot_st_cap += 1; 6669| 33| pCentp_found = NULL; 6670| 33| num_fixes++; 6671| 33| tot_num_fixes++; /* #1 Mob-H */ 6672| 33| continue; 6673| 33| } 6674| | 6675| | /* 2nd attempt: increment flow in centerpoint---radical_endpint edge */ 6676| 131| if (i < num_endpoints) ------------------ | Branch (6676:17): [True: 131, False: 0] ------------------ 6677| 131| { 6678| | /* tautomeric endpoint found; traverse its t-group edges */ 6679| 487| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (6679:29): [True: 356, False: 131] ------------------ 6680| 356| { 6681| 356| if (i == j) ------------------ | Branch (6681:25): [True: 131, False: 225] ------------------ 6682| 131| { 6683| 131| continue; /* avoid the found radical endpoint */ 6684| 131| } 6685| 225| etg1 = pBNS->edge + ptg1->iedge[j]; 6686| 225| endpoint1 = etg1->neighbor12 ^ vtg1; 6687| 225| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 6688| 225| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (6688:25): [True: 34, False: 191] ------------------ 6689| 34| { 6690| 34| continue; /* one more radical-endpoint! What is going on here??? */ 6691| 34| } 6692| 191| if (!etg1->flow) ------------------ | Branch (6692:25): [True: 101, False: 90] ------------------ 6693| 101| { 6694| 101| continue; /* avoid enpoints that do not have an attachment */ 6695| 101| } 6696| 90| if (!( pEndp1->type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 46| 90|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6696:25): [True: 1, False: 89] ------------------ 6697| 1| { 6698| 1| continue; /* should not happen */ 6699| 1| } 6700| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 6701| 215| for (k = 0; k < at2[endpoint1].valence; k++) ------------------ | Branch (6701:33): [True: 126, False: 89] ------------------ 6702| 126| { 6703| 126| ecp1 = pBNS->edge + pEndp1->iedge[k]; 6704| 126| if (ecp1->flow) ------------------ | Branch (6704:29): [True: 13, False: 113] ------------------ 6705| 13| { 6706| 13| continue; 6707| 13| } 6708| 113| centerpoint = ecp1->neighbor12 ^ endpoint1; 6709| 113| pCentp = pBNS->vert + centerpoint; 6710| 113| if (pCentp->type & BNS_VERT_TYPE_ENDPOINT) ------------------ | | 46| 113|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6710:29): [True: 13, False: 100] ------------------ 6711| 13| { 6712| 13| continue; /* do not set another endpoint's valence = an unusual value */ 6713| 13| } 6714| | 6715| | /* traverse centerpoint edges to find edge connecting it to the endpoint0 */ 6716| 100| ecp2 = NULL; 6717| 100| pEndp2 = NULL; 6718| 389| for (n = 0; n < at2[centerpoint].valence; n++) ------------------ | Branch (6718:37): [True: 303, False: 86] ------------------ 6719| 303| { 6720| 303| ecp0 = pBNS->edge + pCentp->iedge[n]; 6721| 303| if (ecp0->flow) ------------------ | Branch (6721:33): [True: 57, False: 246] ------------------ 6722| 57| { 6723| 57| endpoint2 = ecp0->neighbor12 ^ centerpoint; 6724| 57| if (( pBNS->vert[endpoint2].type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 46| 57|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6724:37): [True: 42, False: 15] ------------------ 6725| 42| { 6726| 42| continue; /* ignore endpoint2 if it is tautomeric endpoint */ 6727| 42| } 6728| | /* check whether ecp0 is stereogenic: if it is then we cannot decrement its flow */ 6729| 16| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[centerpoint].sb_parity[m]; m++) ------------------ | | 873| 32|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (6729:45): [True: 16, False: 0] | Branch (6729:73): [True: 2, False: 14] ------------------ 6730| 2| { 6731| 2| if (at[centerpoint].sb_ord[m] == n) ------------------ | Branch (6731:41): [True: 1, False: 1] ------------------ 6732| 1| { 6733| 1| endpoint2 = NO_VERTEX; ------------------ | | 118| 1|#define NO_VERTEX -2 ------------------ 6734| 1| break; 6735| 1| } 6736| 2| } 6737| 15| if (endpoint2 == NO_VERTEX) ------------------ | | 118| 15|#define NO_VERTEX -2 ------------------ | Branch (6737:37): [True: 1, False: 14] ------------------ 6738| 1| { 6739| 1| continue; 6740| 1| } 6741| 14| pEndp2 = pBNS->vert + endpoint2; /* found */ 6742| 14| ecp2 = ecp0; 6743| 14| break; 6744| 15| } 6745| 303| } 6746| 349| for (n = 0; n < at[centerpoint].valence; n++) ------------------ | Branch (6746:37): [True: 288, False: 61] ------------------ 6747| 288| { 6748| 288| ecp0 = pBNS->edge + pCentp->iedge[n]; 6749| 288| if (ecp0->flow) ------------------ | Branch (6749:33): [True: 59, False: 229] ------------------ 6750| 59| { 6751| 59| continue; 6752| 59| } 6753| 229| if (endpoint0 != ( ecp0->neighbor12 ^ centerpoint )) ------------------ | Branch (6753:33): [True: 185, False: 44] ------------------ 6754| 185| { 6755| 185| continue; 6756| 185| } 6757| | /* Found: 6758| | Endp2(not endpoint) Endp2(not radical) 6759| | || | 6760| | ||ecp2 |ecp2 6761| | ecp0 || ecp1 ecp0 | ecp1 6762| | Endp0----Centp----Endp1 Endp0====Centp----Endp1 6763| | ^ \ / --> \ / 6764| | radical | \ / \ / 6765| | \ / \ / 6766| | etg0 \ / etg1 etg0 \ / etg1 6767| | \ / \ / 6768| | tg1 tg1 6769| | 6770| | */ 6771| | 6772| | /* compare centerpoints */ 6773| 44| if (!pCentp_found || ------------------ | Branch (6773:33): [True: 35, False: 9] ------------------ 6774| | /* try to avoid carbons */ 6775| 9| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6775:36): [True: 8, False: 1] ------------------ 6776| 1| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6776:37): [True: 0, False: 1] ------------------ 6777| 8| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (6777:34): [True: 2, False: 6] ------------------ 6778| 2| pVA[centerpoint_found].cPeriodicRowNumber == 1) || ------------------ | Branch (6778:34): [True: 2, False: 0] ------------------ 6779| | /* try a better non-carbon */ 6780| 7| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6780:37): [True: 6, False: 1] ------------------ 6781| 1| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6781:38): [True: 0, False: 1] ------------------ 6782| 6| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (6782:40): [True: 1, False: 5] ------------------ 6783| 5| (at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (6783:43): [True: 4, False: 1] ------------------ 6784| 4| at[centerpoint].el_number > at[centerpoint_found].el_number)) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6784:42): [True: 1, False: 3] ------------------ 6785| 39| { 6786| | 6787| 39| pCentp_found = pCentp; 6788| 39| etg1_found = etg1; 6789| 39| ecp0_found = ecp0; 6790| 39| centerpoint_found = centerpoint; 6791| 39| pEndp2_found = pEndp2; 6792| 39| ecp2_found = ecp2; 6793| 39| break; 6794| 39| } 6795| 44| } 6796| 100| } 6797| 89| } 6798| 131| } 6799| 131| if (pCentp_found) ------------------ | Branch (6799:17): [True: 35, False: 96] ------------------ 6800| 35| { 6801| 35| ecp0_found->flow++; 6802| 35| if (ecp0_found->cap < ecp0_found->flow) ------------------ | Branch (6802:21): [True: 11, False: 24] ------------------ 6803| 11| { 6804| 11| ecp0_found->cap = ecp0_found->flow; 6805| 11| } 6806| 35| pEndp0->st_edge.flow++; 6807| 35| if (pEndp2_found && ecp2_found) ------------------ | Branch (6807:21): [True: 1, False: 34] | Branch (6807:37): [True: 1, False: 0] ------------------ 6808| 1| { 6809| 1| ecp2_found->flow--; 6810| 1| pEndp2_found->st_edge.flow--; 6811| 1| } 6812| 34| else 6813| 34| { 6814| | /* Endp2 not found */ 6815| 34| pCentp_found->st_edge.flow++; 6816| 34| pCentp_found->st_edge.cap++; 6817| 34| pBNS->tot_st_flow += 2; /* radical elimination */ 6818| 34| pBNS->tot_st_cap += 1; 6819| 34| } 6820| | 6821| 35| pCentp_found = NULL; 6822| 35| num_fixes++; 6823| 35| tot_num_fixes++; /* #2 Mob-H */ 6824| 35| continue; 6825| 35| } 6826| | /* 3rd attempt: find =C= and move radical to it */ 6827| 96| if (i < num_endpoints) ------------------ | Branch (6827:17): [True: 96, False: 0] ------------------ 6828| 96| { 6829| 96| int jj, delta, bNotFixed = 1; 6830| 96| Vertex vPathStart, vPathEnd, v1, v2; 6831| 96| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 6832| 683| for (jj = 0; jj < num_at && bNotFixed; jj++) ------------------ | Branch (6832:30): [True: 592, False: 91] | Branch (6832:45): [True: 592, False: 0] ------------------ 6833| 592| { 6834| 592| if (at2[i].endpoint) ------------------ | Branch (6834:25): [True: 188, False: 404] ------------------ 6835| 188| { 6836| 188| continue; 6837| 188| } 6838| 404| if (2 == at2[jj].valence && pBNS->vert[jj].st_edge.cap == pBNS->vert[jj].st_edge.flow && ------------------ | Branch (6838:25): [True: 142, False: 262] | Branch (6838:49): [True: 113, False: 29] ------------------ 6839| 113| 4 == pVA[jj].cNumValenceElectrons && ------------------ | Branch (6839:26): [True: 36, False: 77] ------------------ 6840| 36| !( ecp0 = pBNS->edge + pBNS->vert[jj].iedge[0] )->forbidden && ------------------ | Branch (6840:26): [True: 32, False: 4] ------------------ 6841| 32| !( ecp1 = pBNS->edge + pBNS->vert[jj].iedge[1] )->forbidden && ------------------ | Branch (6841:26): [True: 31, False: 1] ------------------ 6842| 31| 1 == ecp0->flow && 1 == ecp1->flow && ------------------ | Branch (6842:26): [True: 19, False: 12] | Branch (6842:45): [True: 15, False: 4] ------------------ 6843| 15| !at2[(int) at2[i].neighbor[0]].sb_parity[0] && ------------------ | Branch (6843:26): [True: 12, False: 3] ------------------ 6844| 12| !at2[(int) at2[i].neighbor[1]].sb_parity[0]) ------------------ | Branch (6844:26): [True: 9, False: 3] ------------------ 6845| 9| { 6846| | /* found =C=; make a radical and try to cancel the two radicals */ 6847| 9| k = ecp0->neighbor12 ^ jj; 6848| 9| if (at2[k].endpoint) ------------------ | Branch (6848:29): [True: 2, False: 7] ------------------ 6849| 2| { 6850| 2| ecp0 = ecp1; 6851| 2| k = ecp0->neighbor12 ^ jj; 6852| 2| if (at2[k].endpoint) ------------------ | Branch (6852:33): [True: 1, False: 1] ------------------ 6853| 1| { 6854| 1| continue; 6855| 1| } 6856| 2| } 6857| 8| delta = 1; 6858| | /* decrement C valence */ 6859| 8| pBNS->vert[jj].st_edge.flow -= delta; 6860| 8| pBNS->vert[jj].st_edge.cap -= delta; 6861| | /* decrement bond order */ 6862| 8| ecp0->flow -= delta; 6863| | /* reflect the changes in at2[k] to make it a radical */ 6864| 8| pBNS->vert[k].st_edge.flow -= delta; 6865| 8| pBNS->tot_st_cap -= delta; 6866| 8| pBNS->tot_st_flow -= 2 * delta; 6867| | 6868| 8| v1 = endpoint0; 6869| 8| v2 = k; 6870| | 6871| 8| ret2 = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6872| 8| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6873| | 6874| 8| if (ret2 == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (6874:29): [True: 7, False: 1] | Branch (6874:45): [True: 4, False: 3] | Branch (6874:63): [True: 4, False: 0] ------------------ 6875| 5| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6875:30): [True: 2, False: 1] | Branch (6875:48): [True: 1, False: 1] | Branch (6875:71): [True: 5, False: 0] ------------------ 6876| 5| { 6877| 5| ret2 = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6878| 5| if (ret2 > 0) ------------------ | Branch (6878:33): [True: 5, False: 0] ------------------ 6879| 5| { 6880| 5| num_fixes++; 6881| 5| tot_num_fixes++; /* #3 Mob-H */ 6882| 5| pBNS->vert[jj].st_edge.cap += delta; /* create radical on =C- */ 6883| 5| pBNS->tot_st_cap += delta; 6884| 5| pCentp_found = NULL; 6885| | /* djb-rwth: removing redundant code */ 6886| 5| break; 6887| 5| } 6888| 5| } 6889| 3| else 6890| 3| { 6891| | /* failed */ 6892| 3| pBNS->vert[jj].st_edge.flow += delta; 6893| 3| pBNS->vert[jj].st_edge.cap += delta; 6894| | /* decrement bond order */ 6895| 3| ecp0->flow += delta; 6896| | /* reflect the changes in at2[k] to make it a radical */ 6897| 3| pBNS->vert[k].st_edge.flow += delta; 6898| 3| pBNS->tot_st_cap += delta; 6899| 3| pBNS->tot_st_flow += 2 * delta; 6900| 3| } 6901| 3| if (ret2 < 0) ------------------ | Branch (6901:29): [True: 0, False: 3] ------------------ 6902| 0| { 6903| 0| ret = ret2; 6904| 0| goto exit_function; 6905| 0| } 6906| 3| } 6907| 404| } 6908| 96| } 6909| 96| } 6910| 335| if (!num_fixes) ------------------ | Branch (6910:13): [True: 262, False: 73] ------------------ 6911| 262| { 6912| 262| break; 6913| 262| } 6914| 335| } 6915| 86.6k| ret = tot_num_fixes; 6916| | 6917| 86.6k|exit_function: 6918| 86.6k| pStruct->at = at; 6919| 86.6k| memcpy(at2, at, len_at * sizeof(at2[0])); 6920| 86.6k| return ret; 6921| 86.6k|} RemoveRadFromMobileHEndpointFixH: 6938| 1.13k|{ 6939| 1.13k|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) 6940| 1.13k| int i, num_fixes, tot_num_fixes = 0; 6941| | 6942| 1.13k| int ret2, ret; 6943| 1.13k| int num_at = pStruct->num_atoms; 6944| 1.13k| int num_deleted_H = pStruct->num_deleted_H; 6945| 1.13k| int len_at = num_at + num_deleted_H; 6946| 1.13k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 6947| 1.13k| EDGE_LIST ChargeEdgeList, BondEdgeList; 6948| 1.13k| int itg, j, k, n, m; /* djb-rwth: removing redundant variables */ 6949| 1.13k| Vertex endpoint0 = NO_VERTEX, endpoint1, endpoint2 = NO_VERTEX, centerpoint; ------------------ | | 118| 1.13k|#define NO_VERTEX -2 ------------------ Vertex endpoint0 = NO_VERTEX, endpoint1, endpoint2 = NO_VERTEX, centerpoint; ------------------ | | 118| 1.13k|#define NO_VERTEX -2 ------------------ 6950| 1.13k| Vertex centerpoint_found = NO_VERTEX, endpoint2_found = NO_VERTEX; ------------------ | | 118| 1.13k|#define NO_VERTEX -2 ------------------ Vertex centerpoint_found = NO_VERTEX, endpoint2_found = NO_VERTEX; ------------------ | | 118| 1.13k|#define NO_VERTEX -2 ------------------ 6951| 1.13k| BNS_VERTEX *pEndp0 = NULL, *pEndp1, *pEndp2, *pCentp, *pCentp_found, *pEndp2_found = NULL; 6952| 1.13k| BNS_EDGE *ecp0, *ecp1, *ecp2, *ecp0_found = NULL, *ecp1_found = NULL, *ecp2_found = NULL; 6953| 1.13k| int num_endpoints; /* djb-rwth: removing redundant variables */ 6954| | 6955| 1.13k| ret = 0; 6956| | 6957| 1.13k| if (pStruct->iMobileH != TAUT_NON) ------------------ | | 574| 1.13k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (6957:9): [True: 0, False: 1.13k] ------------------ 6958| 0| return ret; 6959| | 6960| 1.13k| AllocEdgeList( &ChargeEdgeList, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.13k|#define EDGE_LIST_CLEAR (-1) ------------------ 6961| 1.13k| AllocEdgeList( &BondEdgeList, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.13k|#define EDGE_LIST_CLEAR (-1) ------------------ 6962| | 6963| 1.13k| memcpy(at2, at, len_at * sizeof(at2[0])); 6964| 1.13k| pStruct->at = at2; 6965| 1.13k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6966| 1.13k| if (ret2 < 0) ------------------ | Branch (6966:9): [True: 0, False: 1.13k] ------------------ 6967| 0| { 6968| 0| ret = ret2; 6969| 0| goto exit_function; 6970| 0| } 6971| 1.26k| while (pBNS->tot_st_cap > pBNS->tot_st_flow && pStruct->ti.num_t_groups) ------------------ | Branch (6971:12): [True: 521, False: 747] | Branch (6971:52): [True: 361, False: 160] ------------------ 6972| 361| { 6973| 361| int iEndpoint = 0; 6974| 361| num_fixes = 0; 6975| 768| for (itg = 0; itg < pStruct->ti.num_t_groups; iEndpoint += num_endpoints, itg++) ------------------ | Branch (6975:23): [True: 407, False: 361] ------------------ 6976| 407| { 6977| 407| pCentp_found = NULL; 6978| | /* djb-rwth: removing redundant code */ 6979| 407| num_endpoints = pStruct->ti.t_group[itg].nNumEndpoints; 6980| 1.02k| for (i = 0; i < num_endpoints; i++) ------------------ | Branch (6980:25): [True: 940, False: 80] ------------------ 6981| 940| { 6982| 940| endpoint0 = pStruct->ti.nEndpointAtomNumber[iEndpoint + i]; 6983| 940| pEndp0 = pBNS->vert + endpoint0; /* taut endpoint vertex (possible location of mobile H */ 6984| 940| if (pEndp0->st_edge.cap > pEndp0->st_edge.flow) ------------------ | Branch (6984:21): [True: 327, False: 613] ------------------ 6985| 327| { 6986| | /* radical endpoint1 has been detected */ 6987| | /* find a 1-3 centerpoint that has two or more endpoints */ 6988| | /* connected to the t-group vertex by edges with flow>0 and */ 6989| | /* to the centerpoint by edges with flow = 0 */ 6990| | /* after that: (1) increment etg1 flow to eliminate radical */ 6991| | /* (2) increment flow on one of the two other edges to the t-group */ 6992| | /* (3) increment st_cap on the found centerpoint */ 6993| | /* (4) rerun the BNS and re-create the structure */ 6994| 327| break; 6995| 327| } 6996| 940| } 6997| | 6998| | /* 2nd attempt: increment flow in centerpoint---radical_endpoint edge */ 6999| 407| pCentp_found = NULL; 7000| 407| if (i < num_endpoints) ------------------ | Branch (7000:17): [True: 327, False: 80] ------------------ 7001| 327| { 7002| | /* tautomeric endpoint found; traverse its t-group edges */ 7003| 2.03k| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (7003:29): [True: 1.70k, False: 327] ------------------ 7004| 1.70k| { 7005| 1.70k| if (i == j) ------------------ | Branch (7005:25): [True: 327, False: 1.37k] ------------------ 7006| 327| { 7007| 327| continue; /* avoid the found radical endpoint */ 7008| 327| } 7009| 1.37k| endpoint1 = pStruct->ti.nEndpointAtomNumber[iEndpoint + j]; 7010| 1.37k| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 7011| | 7012| 1.37k| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (7012:25): [True: 195, False: 1.18k] ------------------ 7013| 195| { 7014| 195| continue; /* one more radical-endpoint! What is going on here??? */ 7015| 195| } 7016| 1.18k| if (!at2[endpoint1].num_H && at2[endpoint1].charge != -1) ------------------ | Branch (7016:25): [True: 875, False: 308] | Branch (7016:50): [True: 313, False: 562] ------------------ 7017| 313| { 7018| 313| continue; /* avoid enpoints that do not have an attachment */ 7019| 313| } 7020| 870| if (!pStruct->endpoint[endpoint1]) ------------------ | Branch (7020:25): [True: 0, False: 870] ------------------ 7021| 0| { 7022| 0| continue; /* should not happen */ 7023| 0| } 7024| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 7025| 4.09k| for (k = 0; k < pEndp1->num_adj_edges; k++) ------------------ | Branch (7025:33): [True: 3.75k, False: 341] ------------------ 7026| 3.75k| { 7027| 3.75k| ecp1 = pBNS->edge + pEndp1->iedge[k]; 7028| 3.75k| if (ecp1->flow) ------------------ | Branch (7028:29): [True: 1.17k, False: 2.57k] ------------------ 7029| 1.17k| { 7030| 1.17k| continue; 7031| 1.17k| } 7032| 2.57k| centerpoint = ecp1->neighbor12 ^ endpoint1; 7033| 2.57k| if (centerpoint >= pBNS->num_atoms) ------------------ | Branch (7033:29): [True: 529, False: 2.04k] ------------------ 7034| 529| { 7035| 529| break; /* no more edges to atoms */ 7036| 529| } 7037| 2.04k| pCentp = pBNS->vert + centerpoint; 7038| 2.04k| if (pStruct->endpoint[centerpoint]) ------------------ | Branch (7038:29): [True: 797, False: 1.25k] ------------------ 7039| 797| { 7040| 797| continue; /* do not set another endpoint's valence = an unusual value */ 7041| 797| } 7042| | /* traverse centerpoint edges to find edge connecting it to the endpoint0 */ 7043| | /* 1. Find a double bond to an endpoint */ 7044| 1.25k| ecp2 = NULL; 7045| 1.25k| pEndp2 = NULL; 7046| 2.91k| for (n = 0; n < at2[centerpoint].valence; n++) /* djb-rwth: removing redundant code */ ------------------ | Branch (7046:37): [True: 2.22k, False: 688] ------------------ 7047| 2.22k| { 7048| 2.22k| ecp0 = pBNS->edge + pCentp->iedge[n]; 7049| 2.22k| if (ecp0->flow) ------------------ | Branch (7049:33): [True: 768, False: 1.45k] ------------------ 7050| 768| { 7051| 768| endpoint2 = ecp0->neighbor12 ^ centerpoint; 7052| 768| if (pStruct->endpoint[endpoint2] /* ??? */) ------------------ | Branch (7052:37): [True: 195, False: 573] ------------------ 7053| 195| { 7054| 195| continue; 7055| 195| } 7056| | /* check whether ecp0 is stereogenic: if it is then we cannot decrement its flow */ 7057| 583| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[centerpoint].sb_parity[m]; m++) ------------------ | | 873| 1.16k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (7057:45): [True: 583, False: 0] | Branch (7057:73): [True: 20, False: 563] ------------------ 7058| 20| { 7059| 20| if (at[centerpoint].sb_ord[m] == n) ------------------ | Branch (7059:41): [True: 10, False: 10] ------------------ 7060| 10| { 7061| 10| endpoint2 = NO_VERTEX; ------------------ | | 118| 10|#define NO_VERTEX -2 ------------------ 7062| 10| break; 7063| 10| } 7064| 20| } 7065| 573| if (endpoint2 == NO_VERTEX) ------------------ | | 118| 573|#define NO_VERTEX -2 ------------------ | Branch (7065:37): [True: 10, False: 563] ------------------ 7066| 10| { 7067| 10| continue; 7068| 10| } 7069| 563| pEndp2 = pBNS->vert + endpoint2; 7070| 563| ecp2 = ecp0; 7071| 563| break; 7072| 573| } 7073| 2.22k| } 7074| 1.25k| if (!ecp2) ------------------ | Branch (7074:29): [True: 688, False: 563] ------------------ 7075| 688| { 7076| 688| continue; 7077| 688| } 7078| | /* 2. Find a single bond to an endpoint0 */ 7079| 2.01k| for (n = 0; n < at2[centerpoint].valence; n++) /* djb-rwth: removing redundant code */ ------------------ | Branch (7079:37): [True: 1.48k, False: 531] ------------------ 7080| 1.48k| { 7081| 1.48k| ecp0 = pBNS->edge + pCentp->iedge[n]; 7082| 1.48k| if (ecp0->flow) ------------------ | Branch (7082:33): [True: 673, False: 810] ------------------ 7083| 673| { 7084| 673| continue; 7085| 673| } 7086| 810| if (endpoint0 != ( ecp0->neighbor12 ^ centerpoint )) ------------------ | Branch (7086:33): [True: 668, False: 142] ------------------ 7087| 668| { 7088| 668| continue; 7089| 668| } 7090| | /* Found: 7091| | Endp2 Endp2(not radical) 7092| | || | 7093| | ||ecp2 |ecp2 7094| | ecp0 || ecp1 ecp0 | ecp1 7095| | Endp0----Centp----Endp1 Endp0====Centp----Endp1 7096| | ^ \ / --> \ / 7097| | radical | \ / \ / 7098| | \ / \ / 7099| | etg0 \ / etg1 etg0 \ / etg1 7100| | \ / \ / 7101| | tg1 tg1 7102| | 7103| | */ 7104| | 7105| | /* compare centerpoints */ 7106| 142| if (!pCentp_found || ------------------ | Branch (7106:33): [True: 32, False: 110] ------------------ 7107| | /* try to avoid carbons */ 7108| 110| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7108:36): [True: 79, False: 31] ------------------ 7109| 31| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7109:37): [True: 11, False: 20] ------------------ 7110| 90| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (7110:34): [True: 11, False: 79] ------------------ 7111| 11| pVA[centerpoint_found].cPeriodicRowNumber == 1) || ------------------ | Branch (7111:34): [True: 0, False: 11] ------------------ 7112| | /* try a better non-carbon */ 7113| 110| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7113:37): [True: 79, False: 31] ------------------ 7114| 31| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7114:38): [True: 11, False: 20] ------------------ 7115| 90| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (7115:40): [True: 0, False: 90] ------------------ 7116| 90| (at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (7116:43): [True: 90, False: 0] ------------------ 7117| 90| at[centerpoint].el_number > at[centerpoint_found].el_number)) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (7117:42): [True: 0, False: 90] ------------------ 7118| 32| { 7119| | 7120| 32| pCentp_found = pCentp; 7121| 32| ecp0_found = ecp0; 7122| 32| centerpoint_found = centerpoint; 7123| 32| pEndp2_found = pEndp2; 7124| 32| ecp2_found = ecp2; 7125| 32| break; 7126| 32| } 7127| 142| } 7128| 563| } 7129| 870| } 7130| 327| } 7131| | /* decrement st_flow, st_cap on Endp2; decrement flow on ecp2; decrement st_flow on Centp */ 7132| | /* result: radicals on Endp0 and Centp => run BNS */ 7133| 407| if (pCentp_found) ------------------ | Branch (7133:17): [True: 32, False: 375] ------------------ 7134| 32| { 7135| | /* make ecp0 a double bond, make ecp2 a single bond, remove radical */ 7136| 32| ecp0_found->flow++; 7137| 32| if (ecp0_found->cap < ecp0_found->flow) ------------------ | Branch (7137:21): [True: 0, False: 32] ------------------ 7138| 0| { 7139| 0| ecp0_found->cap = ecp0_found->flow; 7140| 0| } 7141| 32| pEndp0->st_edge.flow++; 7142| 32| if (pEndp2_found && ecp2_found) ------------------ | Branch (7142:21): [True: 32, False: 0] | Branch (7142:37): [True: 32, False: 0] ------------------ 7143| 32| { 7144| 32| ecp2_found->flow--; 7145| 32| pEndp2_found->st_edge.flow--; 7146| 32| } 7147| 0| else 7148| 0| { 7149| | /* Endp2 not found: only make ecp0 a double bond */ 7150| 0| pCentp_found->st_edge.flow++; 7151| 0| pCentp_found->st_edge.cap++; 7152| 0| pBNS->tot_st_flow += 2; /* radical elimination */ 7153| 0| pBNS->tot_st_cap += 1; 7154| 0| } 7155| | 7156| 32| pCentp_found = NULL; 7157| 32| num_fixes++; /* #2 */ 7158| 32| tot_num_fixes++; 7159| 32| continue; 7160| 32| } 7161| | /* 1st attempt */ 7162| 375| pCentp_found = NULL; 7163| 375| if (i < num_endpoints) ------------------ | Branch (7163:17): [True: 295, False: 80] ------------------ 7164| 295| { 7165| | /* tautomeric endpoint found; traverse its t-group edges */ 7166| 1.80k| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (7166:29): [True: 1.50k, False: 295] ------------------ 7167| 1.50k| { 7168| 1.50k| if (i == j) ------------------ | Branch (7168:25): [True: 295, False: 1.21k] ------------------ 7169| 295| { 7170| 295| continue; /* avoid the found radical endpoint */ 7171| 295| } 7172| 1.21k| endpoint1 = pStruct->ti.nEndpointAtomNumber[iEndpoint + j]; 7173| 1.21k| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 7174| 1.21k| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (7174:25): [True: 185, False: 1.02k] ------------------ 7175| 185| { 7176| 185| continue; /* one more radical-endpoint! What is going on here??? */ 7177| 185| } 7178| 1.02k| if (!at2[endpoint1].num_H && at2[endpoint1].charge != -1) ------------------ | Branch (7178:25): [True: 727, False: 299] | Branch (7178:50): [True: 300, False: 427] ------------------ 7179| 300| { 7180| 300| continue; /* avoid enpoints that do not have an attachment */ 7181| 300| } 7182| 726| if (!pStruct->endpoint[endpoint1]) ------------------ | Branch (7182:25): [True: 0, False: 726] ------------------ 7183| 0| { 7184| 0| continue; /* should not happen */ 7185| 0| } 7186| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 7187| 3.37k| for (k = 0; k < pEndp1->num_adj_edges; k++) ------------------ | Branch (7187:33): [True: 3.06k, False: 311] ------------------ 7188| 3.06k| { 7189| 3.06k| ecp1 = pBNS->edge + pEndp1->iedge[k]; 7190| 3.06k| if (ecp1->flow) ------------------ | Branch (7190:29): [True: 1.01k, False: 2.04k] ------------------ 7191| 1.01k| { 7192| 1.01k| continue; 7193| 1.01k| } 7194| 2.04k| centerpoint = ecp1->neighbor12 ^ endpoint1; 7195| 2.04k| if (centerpoint >= pBNS->num_atoms) ------------------ | Branch (7195:29): [True: 415, False: 1.63k] ------------------ 7196| 415| { 7197| 415| break; 7198| 415| } 7199| 1.63k| pCentp = pBNS->vert + centerpoint; 7200| | /* traverse centerpoint edges to find the 2nd endpoint */ 7201| 5.58k| for (n = 0; n < pCentp->num_adj_edges; n++) /* djb-rwth: removing redundant code */ ------------------ | Branch (7201:37): [True: 4.87k, False: 709] ------------------ 7202| 4.87k| { 7203| 4.87k| ecp2 = pBNS->edge + pCentp->iedge[n]; 7204| 4.87k| if (ecp2->flow) ------------------ | Branch (7204:33): [True: 1.72k, False: 3.15k] ------------------ 7205| 1.72k| { 7206| 1.72k| continue; 7207| 1.72k| } 7208| 3.15k| endpoint2 = ecp2->neighbor12 ^ centerpoint; 7209| 3.15k| if (endpoint2 >= pBNS->num_atoms) ------------------ | Branch (7209:33): [True: 777, False: 2.37k] ------------------ 7210| 777| { 7211| 777| break; 7212| 777| } 7213| 2.37k| if (!pStruct->endpoint[endpoint2]) ------------------ | Branch (7213:33): [True: 277, False: 2.09k] ------------------ 7214| 277| { 7215| 277| continue; 7216| 277| } 7217| | /* djb-rwth: removing redundant code */ 7218| | 7219| 2.09k| if (at2[endpoint2].num_H || at2[endpoint1].charge == -1) ------------------ | Branch (7219:33): [True: 738, False: 1.35k] | Branch (7219:57): [True: 1.01k, False: 342] ------------------ 7220| 1.75k| { 7221| 1.75k| continue; 7222| 1.75k| } 7223| | 7224| | /* we have found the path: 7225| | 7226| | Endp1 has no attachments, Endp2 has. 7227| | 7228| | Endp1 Endp1 7229| | etg1 // \ ecp1 etg1 / \\ ecp1 7230| | etg0 // \ etg0 / \\ 7231| | Endp0-----tg1 Centp --> Endp0=====tg1 Centp 7232| | ^ \\ / \\ / 7233| | radical | etg2 \\ / ecp2 etg2 \\ / ecp2 7234| | Endp2 Endp2 7235| | */ 7236| | 7237| | /* compare centerpoints */ 7238| 342| if (!pCentp_found || ------------------ | Branch (7238:33): [True: 113, False: 229] ------------------ 7239| | /* try to avoid carbons */ 7240| 229| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7240:36): [True: 75, False: 154] ------------------ 7241| 154| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7241:37): [True: 137, False: 17] ------------------ 7242| 212| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (7242:34): [True: 67, False: 145] ------------------ 7243| 67| pVA[centerpoint_found].cPeriodicRowNumber == 1) || ------------------ | Branch (7243:34): [True: 10, False: 57] ------------------ 7244| | /* try a better non-carbon */ 7245| 219| (( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7245:37): [True: 65, False: 154] ------------------ 7246| 154| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7246:38): [True: 137, False: 17] ------------------ 7247| 202| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (7247:40): [True: 19, False: 183] ------------------ 7248| 183| (at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (7248:43): [True: 72, False: 111] ------------------ 7249| 72| at[centerpoint].el_number > at[centerpoint_found].el_number)) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (7249:42): [True: 6, False: 66] ------------------ 7250| 148| { 7251| | 7252| 148| pCentp_found = pCentp; 7253| 148| ecp1_found = ecp1; 7254| 148| centerpoint_found = centerpoint; 7255| 148| break; 7256| 148| } 7257| 342| } 7258| 1.63k| } 7259| 726| } 7260| 295| } 7261| 375| if (pCentp_found) ------------------ | Branch (7261:17): [True: 113, False: 262] ------------------ 7262| 113| { 7263| | /* create a new radical at the centerpoint and try to cancel them */ 7264| 113| int delta = 1, ret3; 7265| 113| Vertex vPathStart, vPathEnd, v1, v2; 7266| 113| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 7267| | 7268| 113| pCentp_found->st_edge.cap += delta; 7269| 113| pBNS->tot_st_cap += delta; 7270| | 7271| 113| v1 = (int) ( pCentp_found - pBNS->vert ); 7272| 113| v2 = (int) ( pEndp0 - pBNS->vert ); 7273| | 7274| 113| ret3 = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7275| 113| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7276| | 7277| 113| if (ret3 == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (7277:21): [True: 104, False: 9] | Branch (7277:37): [True: 10, False: 94] | Branch (7277:55): [True: 6, False: 4] ------------------ 7278| 98| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge % 2 == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (7278:22): [True: 88, False: 10] | Branch (7278:40): [True: 88, False: 0] | Branch (7278:63): [True: 91, False: 3] ------------------ 7279| 91| { 7280| 91| ret3 = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7281| 91| if (ret3 > 0) ------------------ | Branch (7281:25): [True: 91, False: 0] ------------------ 7282| 91| { 7283| 91| num_fixes++; 7284| 91| tot_num_fixes++; /* #1 */ 7285| 91| pCentp_found = NULL; 7286| 91| continue; 7287| 91| } 7288| 91| } 7289| 22| else 7290| 22| { 7291| 22| pCentp_found->st_edge.cap -= delta; 7292| 22| pBNS->tot_st_cap -= delta; 7293| 22| } 7294| 22| if (ret3 < 0) ------------------ | Branch (7294:21): [True: 0, False: 22] ------------------ 7295| 0| { 7296| 0| ret = ret3; 7297| 0| goto exit_function; 7298| 0| } 7299| 22| } 7300| | /*---------------------------------------------------------------------------------------- 7301| | 3rd attempt: add radical to keep 7302| | ============== u,f=>unfixed, fixed edges (N electrons)%2 7303| | (-) (-) (-) | 7304| | e0/ \\ e1 => u/ \\u => // \ v 7305| | / \\ ecp1 ecp2 / \\ u f // \ 7306| | C--X* Y(-)--C==Z C--X* Y(-)--C*--Z --X(-) Y===C---Z* 7307| | rad. endp not rad. endp rad not rad. endp not 7308| | Endp0 Endp1 endp endp to endp endp endp 7309| | Endp2 cancel 7310| | 7311| | Note: endpoints X and Y may belong to different t-groups 7312| | ----------------------------------------------------------------------------------------*/ 7313| 284| pCentp_found = NULL; 7314| 284| if (i < num_endpoints) ------------------ | Branch (7314:17): [True: 204, False: 80] ------------------ 7315| 204| { 7316| 204| int e0, e1; 7317| 204| if (( e0 = pVA[endpoint0].nCMinusGroupEdge - 1 ) < 0 || pBNS->edge[e0].forbidden) ------------------ | Branch (7317:21): [True: 7, False: 197] | Branch (7317:73): [True: 0, False: 197] ------------------ 7318| 7| { 7319| 7| continue; /* no negative charge on Endp0 is possible */ 7320| 7| } 7321| | /* a radical-tautomeric endpoint found; traverse all endpoints */ 7322| 1.17k| for (j = 0; j < pStruct->ti.nNumEndpoints; j++) ------------------ | Branch (7322:29): [True: 973, False: 197] ------------------ 7323| 973| { 7324| 973| if (iEndpoint + i == j) ------------------ | Branch (7324:25): [True: 197, False: 776] ------------------ 7325| 197| { 7326| 197| continue; /* avoid the found radical endpoint */ 7327| 197| } 7328| | 7329| 776| endpoint1 = pStruct->ti.nEndpointAtomNumber[j]; 7330| 776| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 7331| | 7332| 776| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (7332:25): [True: 111, False: 665] ------------------ 7333| 111| { 7334| 111| continue; /* one more radical-endpoint! What is going on here??? */ 7335| 111| } 7336| 665| if (( ( e1 = pVA[endpoint1].nCMinusGroupEdge - 1 ) < 0 || !pBNS->edge[e1].flow ) || pBNS->edge[e1].forbidden) ------------------ | Branch (7336:27): [True: 120, False: 545] | Branch (7336:79): [True: 138, False: 407] | Branch (7336:105): [True: 0, False: 407] ------------------ 7337| 258| { 7338| 258| continue; /* no negative charge on Endp1 */ 7339| 258| } 7340| 407| if (!pStruct->endpoint[endpoint1]) ------------------ | Branch (7340:25): [True: 0, False: 407] ------------------ 7341| 0| { 7342| 0| continue; /* should not happen */ 7343| 0| } 7344| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 7345| 1.65k| for (k = 0; k < pEndp1->num_adj_edges; k++) ------------------ | Branch (7345:33): [True: 1.55k, False: 91] ------------------ 7346| 1.55k| { 7347| 1.55k| ecp1 = pBNS->edge + pEndp1->iedge[k]; /* e1C */ 7348| 1.55k| if (ecp1->flow || ecp1->forbidden) ------------------ | Branch (7348:29): [True: 445, False: 1.11k] | Branch (7348:43): [True: 0, False: 1.11k] ------------------ 7349| 445| { 7350| 445| continue; 7351| 445| } 7352| 1.11k| centerpoint = ecp1->neighbor12 ^ endpoint1; 7353| 1.11k| if (centerpoint >= pBNS->num_atoms) ------------------ | Branch (7353:29): [True: 234, False: 880] ------------------ 7354| 234| { 7355| 234| break; /* no more edges to atoms */ 7356| 234| } 7357| 880| pCentp = pBNS->vert + centerpoint; 7358| 880| if (pStruct->endpoint[centerpoint]) ------------------ | Branch (7358:29): [True: 155, False: 725] ------------------ 7359| 155| { 7360| 155| continue; /* do not set another endpoint's valence = an unusual value */ 7361| 155| } 7362| | /* traverse centerpoint edges to find edge connecting it to the endpoint0 */ 7363| | /* 1. Find a double bond to a not endpoint */ 7364| 725| ecp2 = NULL; 7365| 725| pEndp2 = NULL; 7366| 2.21k| for (n = 0; n < pCentp->num_adj_edges; n++) /* djb-rwth: removing redundant variables/code */ ------------------ | Branch (7366:37): [True: 1.84k, False: 377] ------------------ 7367| 1.84k| { 7368| 1.84k| ecp0 = pBNS->edge + pCentp->iedge[n]; 7369| 1.84k| if (ecp0->flow && !ecp0->forbidden) ------------------ | Branch (7369:33): [True: 822, False: 1.01k] | Branch (7369:47): [True: 812, False: 10] ------------------ 7370| 812| { 7371| 812| endpoint2 = ecp0->neighbor12 ^ centerpoint; 7372| 812| if (endpoint2 >= pBNS->num_atoms || pStruct->endpoint[endpoint2]) ------------------ | Branch (7372:37): [True: 315, False: 497] | Branch (7372:69): [True: 149, False: 348] ------------------ 7373| 464| { 7374| 464| continue; 7375| 464| } 7376| | /* check whether ecp0 is stereogenic: if it is then we cannot decrement its flow */ 7377| 358| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[centerpoint].sb_parity[m]; m++) ------------------ | | 873| 716|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (7377:45): [True: 358, False: 0] | Branch (7377:73): [True: 10, False: 348] ------------------ 7378| 10| { 7379| 10| if (at[centerpoint].sb_ord[m] == n) ------------------ | Branch (7379:41): [True: 0, False: 10] ------------------ 7380| 0| { 7381| 0| endpoint2 = NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 7382| 0| break; 7383| 0| } 7384| 10| } 7385| 348| if (endpoint2 == NO_VERTEX) ------------------ | | 118| 348|#define NO_VERTEX -2 ------------------ | Branch (7385:37): [True: 0, False: 348] ------------------ 7386| 0| { 7387| 0| continue; 7388| 0| } 7389| | /* djb-rwth: removing redundant code */ 7390| 348| ecp2 = ecp0; /* e2C */ 7391| 348| break; 7392| 348| } 7393| 1.84k| } 7394| 725| if (!ecp2) ------------------ | Branch (7394:29): [True: 377, False: 348] ------------------ 7395| 377| { 7396| 377| continue; 7397| 377| } 7398| | /* compare centerpoints */ 7399| 348| if (!pCentp_found || ------------------ | Branch (7399:29): [True: 65, False: 283] ------------------ 7400| | /* try to find carbons */ 7401| 283| (!IS_C( endpoint2_found ) && IS_C( endpoint2 )) || ------------------ | | 6939| 566|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 283|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 283, False: 0] | | | Branch (6939:36): [True: 212, False: 71] | | | Branch (6939:72): [True: 185, False: 27] | | ------------------ ------------------ (!IS_C( endpoint2_found ) && IS_C( endpoint2 )) || ------------------ | | 6939| 98|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 98|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 98, False: 0] | | | Branch (6939:36): [True: 30, False: 68] | | | Branch (6939:72): [True: 16, False: 14] | | ------------------ ------------------ 7402| 267| (IS_C( endpoint2_found ) && IS_C( endpoint2 ) && ------------------ | | 6939| 534|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 267|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 267, False: 0] | | | Branch (6939:36): [True: 209, False: 58] | | | Branch (6939:72): [True: 185, False: 24] | | ------------------ ------------------ (IS_C( endpoint2_found ) && IS_C( endpoint2 ) && ------------------ | | 6939| 452|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 185|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 185, False: 0] | | | Branch (6939:36): [True: 138, False: 47] | | | Branch (6939:72): [True: 130, False: 8] | | ------------------ ------------------ 7403| 130| !IS_C( centerpoint_found ) && IS_C( centerpoint ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 6939| 397|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 130|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 130, False: 0] | | | Branch (6939:36): [True: 45, False: 85] | | | Branch (6939:72): [True: 34, False: 11] | | ------------------ ------------------ !IS_C( centerpoint_found ) && IS_C( centerpoint ))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 6939| 96|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 96|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 96, False: 0] | | | Branch (6939:36): [True: 12, False: 84] | | | Branch (6939:72): [True: 1, False: 11] | | ------------------ ------------------ 7404| 82| { 7405| | 7406| 82| pCentp_found = pCentp; 7407| 82| centerpoint_found = centerpoint; 7408| 82| endpoint2_found = endpoint2; 7409| 82| ecp2_found = ecp2; 7410| 82| ecp1_found = ecp1; 7411| 82| ecp0_found = pBNS->edge + e0; 7412| 82| break; 7413| 82| } 7414| 348| } 7415| 407| } 7416| 197| } 7417| | /* decrement st_flow, st_cap on Endp2; decrement flow on ecp2; decrement st_flow on Centp */ 7418| | /* result: radicals on Endp0 and Centp => run BNS */ 7419| 277| if (pCentp_found) ------------------ | Branch (7419:17): [True: 65, False: 212] ------------------ 7420| 65| { 7421| 65| Vertex vPathStart, vPathEnd, v1, v2; 7422| 65| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 7423| 65| int delta; 7424| | 7425| 65| Vertex vEndp0 = ecp0_found->neighbor1; 7426| 65| Vertex vEndp1 = ecp1_found->neighbor12 ^ centerpoint_found; 7427| 65| Vertex vEndp2 = ecp2_found->neighbor12 ^ centerpoint_found; 7428| 65| BNS_EDGE *pe0 = ecp0_found; 7429| 65| BNS_EDGE *pe1 = pBNS->edge + ( (long long)pVA[vEndp1].nCMinusGroupEdge - 1 ); /* djb-rwth: cast operator added */ 7430| | /* djb-rwth: removing redundant code */ 7431| 65| pEndp2 = pBNS->vert + vEndp2; 7432| 65| pCentp = pCentp_found; 7433| 65| if (!ChargeEdgeList.num_alloc) ------------------ | Branch (7433:21): [True: 56, False: 9] ------------------ 7434| 56| { 7435| 429| for (n = 0; n < pStruct->num_atoms; n++) ------------------ | Branch (7435:33): [True: 373, False: 56] ------------------ 7436| 373| { 7437| 373| if (( k = pVA[n].nCMinusGroupEdge ) >= 0 && !pBNS->edge[k].forbidden && ------------------ | Branch (7437:29): [True: 373, False: 0] | Branch (7437:69): [True: 372, False: 1] ------------------ 7438| 372| ( ret = AddToEdgeList( &ChargeEdgeList, k, pStruct->num_atoms ) )) ------------------ | Branch (7438:29): [True: 0, False: 372] ------------------ 7439| 0| { 7440| 0| goto exit_function; 7441| 0| } 7442| 373| if (( k = pVA[n].nCPlusGroupEdge ) >= 0 && !pBNS->edge[k].forbidden && ------------------ | Branch (7442:29): [True: 373, False: 0] | Branch (7442:68): [True: 370, False: 3] ------------------ 7443| 370| ( ret = AddToEdgeList( &ChargeEdgeList, k, pStruct->num_atoms ) )) ------------------ | Branch (7443:29): [True: 0, False: 370] ------------------ 7444| 0| { 7445| 0| goto exit_function; 7446| 0| } 7447| 373| } 7448| 56| } 7449| 65| if (!BondEdgeList.num_alloc) ------------------ | Branch (7449:21): [True: 56, False: 9] ------------------ 7450| 56| { 7451| 397| for (n = 0; n < pBNS->num_bonds; n++) ------------------ | Branch (7451:33): [True: 341, False: 56] ------------------ 7452| 341| { 7453| 341| if (( ret = AddToEdgeList( &BondEdgeList, n, pBNS->num_bonds ) )) ------------------ | Branch (7453:29): [True: 0, False: 341] ------------------ 7454| 0| { 7455| 0| goto exit_function; 7456| 0| } 7457| 341| } 7458| 56| } 7459| | /* fix all bonds and charges */ 7460| 65| SetForbiddenEdgeMask( pBNS, &ChargeEdgeList, forbidden_edge_mask ); 7461| 65| SetForbiddenEdgeMask( pBNS, &BondEdgeList, forbidden_edge_mask ); 7462| | /* prepare flow for testing */ 7463| 65| delta = 1; 7464| 65| ecp2_found->flow -= delta; 7465| 65| pCentp->st_edge.flow -= delta; 7466| 65| pEndp2->st_edge.flow -= delta; 7467| 65| pBNS->tot_st_flow -= 2 * delta; 7468| | /* unfix edges to be changed */ 7469| 65| pe0->forbidden &= inv_forbidden_edge_mask; 7470| 65| pe1->forbidden &= inv_forbidden_edge_mask; 7471| 65| ecp1_found->forbidden &= inv_forbidden_edge_mask; 7472| | 7473| 65| pBNS->tot_st_cap += delta; 7474| | 7475| 65| v1 = vEndp0; 7476| 65| v2 = centerpoint_found; 7477| 65| ret2 = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7478| 65| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7479| | 7480| 65| if (ret2 == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (7480:21): [True: 10, False: 55] | Branch (7480:37): [True: 5, False: 5] | Branch (7480:55): [True: 5, False: 0] ------------------ 7481| 7| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (7481:22): [True: 4, False: 1] | Branch (7481:40): [True: 2, False: 2] | Branch (7481:63): [True: 7, False: 0] ------------------ 7482| 7| { 7483| 7| ret2 = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7484| 7| if (ret2 > 0) ------------------ | Branch (7484:25): [True: 7, False: 0] ------------------ 7485| 7| { 7486| 7| num_fixes++; 7487| 7| tot_num_fixes++; /* #3 */ 7488| 7| pCentp_found = NULL; 7489| 7| } 7490| 7| } 7491| 58| else 7492| 58| { 7493| | /* roll back */ 7494| 58| ecp2_found->flow += delta; 7495| 58| pCentp->st_edge.flow += delta; 7496| 58| pEndp2->st_edge.flow += delta; 7497| 58| pBNS->tot_st_flow += 2 * delta; 7498| 58| } 7499| 65| RemoveForbiddenEdgeMask( pBNS, &ChargeEdgeList, forbidden_edge_mask ); 7500| 65| RemoveForbiddenEdgeMask( pBNS, &BondEdgeList, forbidden_edge_mask ); 7501| 65| if (ret2 < 0) ------------------ | Branch (7501:21): [True: 0, False: 65] ------------------ 7502| 0| { 7503| 0| ret = ret2; 7504| 0| goto exit_function; 7505| 0| } 7506| 65| if (!pCentp_found) ------------------ | Branch (7506:21): [True: 7, False: 58] ------------------ 7507| 7| continue; 7508| 65| } 7509| 277| } 7510| 361| if (!num_fixes) ------------------ | Branch (7510:13): [True: 231, False: 130] ------------------ 7511| 231| { 7512| 231| break; 7513| 231| } 7514| 361| } 7515| | 7516| | /************ again ***********************************************************/ 7517| 1.18k| while (pBNS->tot_st_cap > pBNS->tot_st_flow && pStruct->ti.num_t_groups) ------------------ | Branch (7517:12): [True: 433, False: 747] | Branch (7517:52): [True: 273, False: 160] ------------------ 7518| 273| { 7519| 273| int iEndpoint = 0; 7520| 273| num_fixes = 0; 7521| 584| for (itg = 0; itg < pStruct->ti.num_t_groups; iEndpoint += num_endpoints, itg++) ------------------ | Branch (7521:23): [True: 311, False: 273] ------------------ 7522| 311| { 7523| 311| pCentp_found = NULL; 7524| | /* djb-rwth: removing redundant code */ 7525| 311| num_endpoints = pStruct->ti.t_group[itg].nNumEndpoints; 7526| 751| for (i = 0; i < num_endpoints; i++) ------------------ | Branch (7526:25): [True: 642, False: 109] ------------------ 7527| 642| { 7528| 642| endpoint0 = pStruct->ti.nEndpointAtomNumber[iEndpoint + i]; 7529| 642| pEndp0 = pBNS->vert + endpoint0; /* taut endpoint vertex (possible location of mobile H */ 7530| 642| if (pEndp0->st_edge.cap > pEndp0->st_edge.flow) ------------------ | Branch (7530:21): [True: 202, False: 440] ------------------ 7531| 202| { 7532| | /* radical endpoint1 has been detected */ 7533| | /* find a 1-3 centerpoint that has two or more endpoints */ 7534| | /* connected to the t-group vertex by edges with flow>0 and */ 7535| | /* to the centerpoint by edges with flow = 0 */ 7536| | /* after that: (1) increment etg1 flow to eliminate radical */ 7537| | /* (2) increment flow on one of the two other edges to the t-group */ 7538| | /* (3) increment st_cap on the found centerpoint */ 7539| | /* (4) rerun the BNS and re-create the structure */ 7540| 202| break; 7541| 202| } 7542| 642| } 7543| | /* 4th attempt */ 7544| 311| if (i < num_endpoints) ------------------ | Branch (7544:17): [True: 202, False: 109] ------------------ 7545| 202| { 7546| | /* tautomeric endpoint found; traverse its t-group edges */ 7547| 202| pEndp2_found = NULL; 7548| 635| for (j = 0; j < pEndp0->num_adj_edges; j++) ------------------ | Branch (7548:29): [True: 433, False: 202] ------------------ 7549| 433| { 7550| 433| ecp0 = pBNS->edge + pEndp0->iedge[j]; 7551| 433| centerpoint = ecp0->neighbor12 ^ endpoint0; 7552| 433| if (centerpoint >= pBNS->num_atoms || ecp0->flow || pStruct->endpoint[centerpoint]) ------------------ | Branch (7552:25): [True: 199, False: 234] | Branch (7552:59): [True: 77, False: 157] | Branch (7552:73): [True: 47, False: 110] ------------------ 7553| 323| { 7554| 323| continue; /* ignore non-single bonds, orig. InChI endpoints, and fictitious atoms */ 7555| 323| } 7556| 110| pCentp = pBNS->vert + centerpoint; 7557| 537| for (k = 0; k < pCentp->num_adj_edges; k++) ------------------ | Branch (7557:33): [True: 427, False: 110] ------------------ 7558| 427| { 7559| 427| ecp1 = pBNS->edge + pCentp->iedge[k]; 7560| 427| endpoint1 = ecp1->neighbor12 ^ centerpoint; 7561| 427| if (endpoint1 >= pBNS->num_atoms || !ecp1->flow || pStruct->endpoint[endpoint1]) ------------------ | Branch (7561:29): [True: 105, False: 322] | Branch (7561:61): [True: 233, False: 89] | Branch (7561:76): [True: 26, False: 63] ------------------ 7562| 364| { 7563| 364| continue; /* ignore single bonds, orig. InChI endpoints, and fictitious atoms */ 7564| 364| } 7565| 63| pEndp1 = pBNS->vert + endpoint1; 7566| 63| if (endpoint1 == endpoint0 || pEndp1->st_edge.cap != pEndp1->st_edge.flow) ------------------ | Branch (7566:29): [True: 0, False: 63] | Branch (7566:55): [True: 7, False: 56] ------------------ 7567| 7| { 7568| 7| continue; /* ignore radicals */ 7569| 7| } 7570| 56| if (!pEndp2_found || ------------------ | Branch (7570:29): [True: 42, False: 14] ------------------ 7571| | /* try to find carbons */ 7572| 14| (!IS_C( endpoint2_found ) && IS_C( endpoint1 )) || ------------------ | | 6939| 28|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 14|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 14, False: 0] | | | Branch (6939:36): [True: 7, False: 7] | | | Branch (6939:72): [True: 6, False: 1] | | ------------------ ------------------ (!IS_C( endpoint2_found ) && IS_C( endpoint1 )) || ------------------ | | 6939| 8|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 8|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 8, False: 0] | | | Branch (6939:36): [True: 3, False: 5] | | | Branch (6939:72): [True: 1, False: 2] | | ------------------ ------------------ 7573| 13| (IS_C( endpoint2_found ) && IS_C( endpoint1 ) && ------------------ | | 6939| 26|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 13|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 13, False: 0] | | | Branch (6939:36): [True: 7, False: 6] | | | Branch (6939:72): [True: 6, False: 1] | | ------------------ ------------------ (IS_C( endpoint2_found ) && IS_C( endpoint1 ) && ------------------ | | 6939| 19|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 6|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 6, False: 0] | | | Branch (6939:36): [True: 5, False: 1] | | | Branch (6939:72): [True: 4, False: 1] | | ------------------ ------------------ 7574| 4| !IS_C( centerpoint_found ) && IS_C( centerpoint ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 6939| 17|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 4|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 4, False: 0] | | | Branch (6939:36): [True: 1, False: 3] | | | Branch (6939:72): [True: 1, False: 0] | | ------------------ ------------------ !IS_C( centerpoint_found ) && IS_C( centerpoint ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 6939| 3|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 118| 3|#define NO_VERTEX -2 | | ------------------ | | | Branch (6939:18): [True: 3, False: 0] | | | Branch (6939:36): [True: 2, False: 1] | | | Branch (6939:72): [True: 1, False: 1] | | ------------------ ------------------ 7575| 44| { 7576| 44| pEndp2_found = pEndp1; 7577| | /* djb-rwth: removing redundant code */ 7578| 44| endpoint2_found = endpoint1; 7579| 44| centerpoint_found = centerpoint; 7580| 44| ecp1_found = ecp0; 7581| 44| ecp2_found = ecp1; 7582| 44| } 7583| 56| } 7584| 110| } 7585| 202| if (pEndp2_found) ------------------ | Branch (7585:21): [True: 42, False: 160] ------------------ 7586| 42| { 7587| | /* move radical from pEndp0 to pEndp2 */ 7588| 42| pEndp0->st_edge.flow++; 7589| 42| ecp1_found->flow++; 7590| 42| ecp2_found->flow--; 7591| 42| pEndp2_found->st_edge.flow--; 7592| 42| pEndp2_found = NULL; 7593| 42| pCentp_found = NULL; 7594| 42| num_fixes++; /* #4 */ 7595| 42| tot_num_fixes++; 7596| 42| continue; 7597| 42| } 7598| 202| } 7599| 311| } 7600| 273| if (!num_fixes) ------------------ | Branch (7600:13): [True: 231, False: 42] ------------------ 7601| 231| { 7602| 231| break; 7603| 231| } 7604| 273| } 7605| | 7606| 1.13k| ret = tot_num_fixes; 7607| | 7608| 1.13k|exit_function: 7609| 1.13k| AllocEdgeList( &ChargeEdgeList, EDGE_LIST_FREE ); ------------------ | | 243| 1.13k|#define EDGE_LIST_FREE (-2) ------------------ 7610| 1.13k| AllocEdgeList( &BondEdgeList, EDGE_LIST_FREE ); ------------------ | | 243| 1.13k|#define EDGE_LIST_FREE (-2) ------------------ 7611| | 7612| 1.13k| pStruct->at = at; 7613| 1.13k| memcpy(at2, at, len_at * sizeof(at2[0])); 7614| | 7615| 1.13k| return ret; 7616| 1.13k|#undef IS_C 7617| 1.13k|} MoveChargeToMakeCenerpoints: 7633| 87.7k|{ 7634| 87.7k| int i, j, neigh, num_endpoints, tg_group = 0, num_success; 7635| 87.7k| int ret2, ret, delta; 7636| 87.7k| int num_at = pStruct->num_atoms; 7637| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 7638| 87.7k| int len_at = num_at + num_deleted_H; 7639| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 7640| | 7641| | /* for RunBnsTestOnce */ 7642| 87.7k| Vertex vPathStart, vPathEnd; 7643| 87.7k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 7644| | 7645| 87.7k| BNS_EDGE *pEdgePlus, *pEdgeMinus; 7646| 87.7k| Vertex v1p, v2p, v1m, v2m; 7647| 87.7k| BNS_VERTEX *pv1p, *pv2p, *pv1m, *pv2m; 7648| | 7649| | /* djb-rwth: removing redundant code */ 7650| 87.7k| num_success = 0; 7651| | 7652| | /* to simplify, prepare new at[] from pBNS */ 7653| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 7654| 87.7k| pStruct->at = at2; 7655| 87.7k| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 7656| 87.7k| pStruct->at = at; 7657| 87.7k| if (ret2 < 0) ------------------ | Branch (7657:9): [True: 0, False: 87.7k] ------------------ 7658| 0| { 7659| 0| ret = ret2; 7660| 0| goto exit_function; 7661| 0| } 7662| | 7663| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (7663:17): [True: 832k, False: 87.7k] ------------------ 7664| 832k| { 7665| 832k| if (pVA[i].cNumValenceElectrons != 4 && /* not C, Si, Ge */ ------------------ | Branch (7665:13): [True: 739k, False: 92.9k] ------------------ 7666| 739k| !pVA[i].cMetal && !pVA[i].nTautGroupEdge && ------------------ | Branch (7666:14): [True: 423k, False: 316k] | Branch (7666:32): [True: 422k, False: 947] ------------------ 7667| 422k| !at2[i].num_H && at2[i].valence >= 3 && ------------------ | Branch (7667:14): [True: 419k, False: 3.12k] | Branch (7667:31): [True: 25.5k, False: 393k] ------------------ 7668| 25.5k| at2[i].valence == at2[i].chem_bonds_valence && ------------------ | Branch (7668:14): [True: 10.7k, False: 14.8k] ------------------ 7669| 10.7k| !at2[i].charge && pVA[i].nCPlusGroupEdge > 0 && ------------------ | Branch (7669:14): [True: 7.97k, False: 2.73k] | Branch (7669:32): [True: 3.08k, False: 4.89k] ------------------ 7670| 3.08k| is_centerpoint_elem( at2[i].el_number )) ------------------ | Branch (7670:14): [True: 3.06k, False: 12] ------------------ 7671| 3.06k| { 7672| 12.6k| for (j = 0, num_endpoints = 0; j < at2[i].valence; j++) ------------------ | Branch (7672:44): [True: 9.58k, False: 3.06k] ------------------ 7673| 9.58k| { 7674| 9.58k| neigh = at2[i].neighbor[j]; 7675| 9.58k| if (at2[neigh].endpoint) ------------------ | Branch (7675:21): [True: 86, False: 9.50k] ------------------ 7676| 86| { 7677| 86| if (!num_endpoints) ------------------ | Branch (7677:25): [True: 53, False: 33] ------------------ 7678| 53| { 7679| 53| tg_group = at2[neigh].endpoint; 7680| 53| } 7681| 33| else if (tg_group != at2[neigh].endpoint) ------------------ | Branch (7681:30): [True: 2, False: 31] ------------------ 7682| 2| { 7683| 2| break; /* not a centerpoint */ 7684| 2| } 7685| 84| num_endpoints++; 7686| 84| } 7687| 9.58k| } 7688| | 7689| 3.06k| if (j == at2[i].valence && num_endpoints > 1) ------------------ | Branch (7689:17): [True: 3.06k, False: 2] | Branch (7689:40): [True: 26, False: 3.04k] ------------------ 7690| 26| { 7691| | /* found possible centerpoint */ 7692| 26| pEdgePlus = pBNS->edge + ( (long long)pVA[i].nCPlusGroupEdge - 1 ); /* djb-rwth: cast operator added */ 7693| 26| pEdgeMinus = ( pVA[i].nCMinusGroupEdge > 0 ) ? pBNS->edge + ((long long) pVA[i].nCMinusGroupEdge - 1 ) : NULL; /* djb-rwth: cast operator added */ ------------------ | Branch (7693:30): [True: 1, False: 25] ------------------ 7694| 26| if (pEdgePlus->flow + ( pEdgeMinus ? pEdgeMinus->flow : 0 ) != 1) ------------------ | Branch (7694:21): [True: 0, False: 26] | Branch (7694:41): [True: 1, False: 25] ------------------ 7695| 0| { 7696| 0| continue; 7697| 0| } 7698| 26| v1p = pEdgePlus->neighbor1; 7699| 26| v2p = pEdgePlus->neighbor12 ^ v1p; 7700| 26| pv1p = pBNS->vert + v1p; 7701| 26| pv2p = pBNS->vert + v2p; 7702| 26| if (pEdgeMinus) ------------------ | Branch (7702:21): [True: 1, False: 25] ------------------ 7703| 1| { 7704| 1| v1m = pEdgeMinus->neighbor1; 7705| 1| v2m = pEdgeMinus->neighbor12 ^ v1m; 7706| 1| pv1m = pBNS->vert + v1m; 7707| 1| pv2m = pBNS->vert + v2m; 7708| 1| } 7709| 25| else 7710| 25| { 7711| 25| v1m = NO_VERTEX; ------------------ | | 118| 25|#define NO_VERTEX -2 ------------------ 7712| 25| v2m = NO_VERTEX; ------------------ | | 118| 25|#define NO_VERTEX -2 ------------------ 7713| 25| pv1m = NULL; 7714| 25| pv2m = NULL; 7715| 25| } 7716| 26| ret = 0; 7717| | 7718| | /* set new flow to run BNS Search */ 7719| 26| if ((delta = pEdgePlus->flow)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7719:21): [True: 26, False: 0] ------------------ 7720| 26| { 7721| | /* positive charge <=> flow=0 on (=) edge */ 7722| 26| pEdgePlus->flow -= delta; 7723| 26| pv1p->st_edge.flow -= delta; 7724| 26| pv2p->st_edge.flow -= delta; 7725| 26| pBNS->tot_st_flow -= 2 * delta; 7726| 26| pEdgePlus->forbidden |= forbidden_edge_mask; 7727| 26| if (pEdgeMinus) ------------------ | Branch (7727:25): [True: 1, False: 25] ------------------ 7728| 1| { 7729| 1| pEdgeMinus->forbidden |= forbidden_edge_mask; 7730| 1| } 7731| | 7732| 26| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7733| 26| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7734| | 7735| 26| if (ret < 0) ------------------ | Branch (7735:25): [True: 0, False: 26] ------------------ 7736| 0| { 7737| 0| goto exit_function; 7738| 0| } 7739| | 7740| 26| if (ret == 1 && ( (vPathEnd == v1p && vPathStart == v2p) || ------------------ | Branch (7740:25): [True: 22, False: 4] | Branch (7740:40): [True: 8, False: 14] | Branch (7740:59): [True: 4, False: 4] ------------------ 7741| 18| (vPathEnd == v2p && vPathStart == v1p) ) && ------------------ | Branch (7741:26): [True: 14, False: 4] | Branch (7741:45): [True: 8, False: 6] ------------------ 7742| 12| nDeltaCharge == -1 /* charge moving to this atom disappers*/) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7742:39): [True: 4, False: 8] ------------------ 7743| 4| { 7744| 4| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7745| 4| ( *pnNumRunBNS )++; 7746| 4| if (ret < 0) ------------------ | Branch (7746:29): [True: 0, False: 4] ------------------ 7747| 0| { 7748| 0| goto exit_function; 7749| 0| } 7750| 4| else if (ret == 1) ------------------ | Branch (7750:34): [True: 4, False: 0] ------------------ 7751| 4| { 7752| 4| *pnTotalDelta += ret; 7753| 4| } 7754| 0| else 7755| 0| { 7756| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 7757| 0| goto exit_function; 7758| 0| } 7759| 4| } 7760| 22| else 7761| 22| { 7762| 22| ret = 0; 7763| 22| pEdgePlus->flow += delta; 7764| 22| pv1p->st_edge.flow += delta; 7765| 22| pv2p->st_edge.flow += delta; 7766| 22| pBNS->tot_st_flow += 2 * delta; 7767| 22| } 7768| 26| pEdgePlus->forbidden &= inv_forbidden_edge_mask; 7769| 26| if (pEdgeMinus) ------------------ | Branch (7769:25): [True: 1, False: 25] ------------------ 7770| 1| { 7771| 1| pEdgeMinus->forbidden &= inv_forbidden_edge_mask; 7772| 1| } 7773| 26| } 7774| 0| else 7775| 0| { 7776| 0| if (pEdgeMinus && ( delta == pEdgeMinus->flow ) && pEdgePlus->flow == 0) ------------------ | Branch (7776:25): [True: 0, False: 0] | Branch (7776:39): [True: 0, False: 0] | Branch (7776:72): [True: 0, False: 0] ------------------ 7777| 0| { 7778| | /* positive charge <=> flow=0 on (=) edge and flow=0 on (-) edge */ 7779| 0| pEdgeMinus->flow -= delta; 7780| 0| pv1m->st_edge.flow -= delta; 7781| 0| pv2m->st_edge.flow -= delta; 7782| 0| pBNS->tot_st_flow -= 2 * delta; 7783| 0| pEdgePlus->forbidden |= forbidden_edge_mask; 7784| 0| pEdgeMinus->forbidden |= forbidden_edge_mask; 7785| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7786| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7787| 0| if (ret < 0) ------------------ | Branch (7787:29): [True: 0, False: 0] ------------------ 7788| 0| { 7789| 0| goto exit_function; 7790| 0| } 7791| 0| if (ret == 1 && ( (vPathEnd == v1m && vPathStart == v2m) || ------------------ | Branch (7791:29): [True: 0, False: 0] | Branch (7791:44): [True: 0, False: 0] | Branch (7791:63): [True: 0, False: 0] ------------------ 7792| 0| (vPathEnd == v2m && vPathStart == v1m) ) && ------------------ | Branch (7792:44): [True: 0, False: 0] | Branch (7792:63): [True: 0, False: 0] ------------------ 7793| 0| nDeltaCharge == -1 /* charge moving to this atom disappers*/) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (7793:43): [True: 0, False: 0] ------------------ 7794| 0| { 7795| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7796| 0| ( *pnNumRunBNS )++; 7797| 0| if (ret < 0) ------------------ | Branch (7797:33): [True: 0, False: 0] ------------------ 7798| 0| { 7799| 0| goto exit_function; 7800| 0| } 7801| 0| else if (ret == 1) ------------------ | Branch (7801:38): [True: 0, False: 0] ------------------ 7802| 0| { 7803| 0| *pnTotalDelta += ret; 7804| 0| } 7805| 0| else 7806| 0| { 7807| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 7808| 0| goto exit_function; 7809| 0| } 7810| 0| } 7811| 0| else 7812| 0| { 7813| 0| ret = 0; 7814| 0| pEdgeMinus->flow += delta; 7815| 0| pv1m->st_edge.flow += delta; 7816| 0| pv2m->st_edge.flow += delta; 7817| 0| pBNS->tot_st_flow += 2 * delta; 7818| 0| } 7819| 0| pEdgePlus->forbidden &= inv_forbidden_edge_mask; 7820| 0| pEdgeMinus->forbidden &= inv_forbidden_edge_mask; 7821| 0| } 7822| 0| } 7823| 26| if (ret) ------------------ | Branch (7823:21): [True: 4, False: 22] ------------------ 7824| 4| { 7825| 4| num_success++; 7826| 4| memcpy(at2, at, len_at * sizeof(at2[0])); 7827| 4| pStruct->at = at2; 7828| 4| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 7829| 4| pStruct->at = at; 7830| 4| if (ret2 < 0) ------------------ | Branch (7830:25): [True: 0, False: 4] ------------------ 7831| 0| { 7832| 0| ret = ret2; 7833| 0| goto exit_function; 7834| 0| } 7835| 4| } 7836| 26| } 7837| 3.06k| } 7838| 832k| } 7839| | 7840| | 7841| 87.7k| ret = num_success; 7842| | 7843| 87.7k|exit_function: 7844| | 7845| 87.7k| return ret; 7846| 87.7k|} bHas_N_V: 58| 1.13k|{ 59| 1.13k| int i, num_found = 0; 60| 9.48k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (60:17): [True: 8.35k, False: 1.13k] ------------------ 61| 8.35k| { 62| 8.35k| if (at2[i].el_number == EL_NUMBER_N && ------------------ | | 14| 16.7k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (62:13): [True: 2.23k, False: 6.11k] ------------------ 63| 2.23k| !at2[i].charge && ------------------ | Branch (63:14): [True: 1.36k, False: 871] ------------------ 64| 1.36k| !at2[i].num_H && ------------------ | Branch (64:14): [True: 1.09k, False: 273] ------------------ 65| 1.09k| !at2[i].radical && ------------------ | Branch (65:14): [True: 1.06k, False: 30] ------------------ 66| 1.06k| at2[i].chem_bonds_valence == 5 && ------------------ | Branch (66:14): [True: 241, False: 820] ------------------ 67| 241| ( at2[i].valence == 3 )) ------------------ | Branch (67:14): [True: 151, False: 90] ------------------ 68| 151| { 69| 151| num_found++; 70| 151| } 71| 8.35k| } 72| | 73| 1.13k| return num_found; 74| 1.13k|} FixFixedHRestoredStructure: 320| 1.21k|{ 321| | /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/ 322| | /* at2 should be the most recently restored atom, Fixed-H */ 323| 1.21k| int i, j, k, delta, num_try, tot_succes, cur_success, ret = 0, bAllowedNFlowerEdges = 0, num_zero_ret; 324| 1.21k| CMP2FHINCHI c2i; 325| 1.21k| CMP2FHINCHI *pc2i = &c2i; 326| | 327| 1.21k| EDGE_LIST AllChargeEdges, CurrEdges, SFlowerEdges, NFlowerEdges, OtherNFlowerEdges, FixedLargeRingStereoEdges; 328| 1.21k| EDGE_LIST AllBondEdges; 329| | 330| 1.21k| EdgeIndex e; 331| 1.21k| BNS_EDGE *pe; 332| 1.21k| Vertex v1, v2; 333| 1.21k| BNS_VERTEX *pv1, *pv2; 334| | 335| 1.21k| Vertex vPathStart, vPathEnd; 336| 1.21k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 337| | 338| 1.21k| int nNumRunBNS = 0, forbidden_edge_mask_inv = ~forbidden_edge_mask; /* djb-rwth: ignoring LLVM warning: variable used */ 339| | 340| | INCHI_HEAPCHK 341| | 342| 1.21k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.21k|#define EDGE_LIST_CLEAR (-1) ------------------ 343| 1.21k| AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.21k|#define EDGE_LIST_CLEAR (-1) ------------------ 344| 1.21k| AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.21k|#define EDGE_LIST_CLEAR (-1) ------------------ 345| 1.21k| AllocEdgeList( &SFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.21k|#define EDGE_LIST_CLEAR (-1) ------------------ 346| 1.21k| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.21k|#define EDGE_LIST_CLEAR (-1) ------------------ 347| 1.21k| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.21k|#define EDGE_LIST_CLEAR (-1) ------------------ 348| 1.21k| AllocEdgeList( &AllBondEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.21k|#define EDGE_LIST_CLEAR (-1) ------------------ 349| | 350| 1.21k| tot_succes = 0; 351| | 352| 1.21k| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (352:9): [True: 457, False: 756] | Branch (352:37): [True: 0, False: 457] ------------------ 353| 0| { 354| 0| goto exit_function; /* no fixed-H found */ 355| 0| } 356| | 357| 10.0k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (357:17): [True: 8.80k, False: 1.21k] ------------------ 358| 8.80k| { 359| 8.80k| if (( e = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (359:13): [True: 5.36k, False: 3.44k] | Branch (359:57): [True: 5.36k, False: 0] ------------------ 360| 5.36k| ( ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 18| 5.36k|#define INC_ADD_EDGE 64 ------------------ | Branch (360:13): [True: 0, False: 5.36k] ------------------ 361| 0| { 362| 0| goto exit_function; 363| 0| } 364| 8.80k| if (( e = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (364:13): [True: 7.16k, False: 1.64k] | Branch (364:56): [True: 6.88k, False: 282] ------------------ 365| 6.88k| { 366| 6.88k| if ((ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 6.88k|#define INC_ADD_EDGE 64 ------------------ | Branch (366:17): [True: 0, False: 6.88k] ------------------ 367| 0| { 368| 0| goto exit_function; 369| 0| } 370| | 371| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 372| 6.88k| if (pVA[i].cNumValenceElectrons == 5 && !pVA[i].cMetal && /* N, P, As */ ------------------ | Branch (372:17): [True: 2.60k, False: 4.27k] | Branch (372:53): [True: 2.52k, False: 79] ------------------ 373| 2.52k| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) )) ------------------ | | 118| 2.52k|#define NO_VERTEX -2 ------------------ | Branch (373:18): [True: 813, False: 1.71k] ------------------ 374| 813| { 375| | 376| 813| if (pBNS->edge[j].forbidden) ------------------ | Branch (376:21): [True: 0, False: 813] ------------------ 377| 0| { 378| 0| continue; 379| 0| } 380| | 381| 813| if (pBNS->edge[j].flow) ------------------ | Branch (381:21): [True: 543, False: 270] ------------------ 382| 543| { 383| 543| if ((ret = AddToEdgeList( &AllChargeEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 543|#define INC_ADD_EDGE 64 ------------------ | Branch (383:25): [True: 0, False: 543] ------------------ 384| 0| { 385| 0| goto exit_function; 386| 0| } 387| 543| if ((ret = AddToEdgeList( &NFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 543|#define INC_ADD_EDGE 64 ------------------ | Branch (387:25): [True: 0, False: 543] ------------------ 388| 0| { 389| 0| goto exit_function; 390| 0| } 391| 543| } 392| 270| else 393| 270| { 394| 270| if ((ret = AddToEdgeList( &OtherNFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 270|#define INC_ADD_EDGE 64 ------------------ | Branch (394:25): [True: 0, False: 270] ------------------ 395| 0| { 396| 0| goto exit_function; 397| 0| } 398| 270| } 399| 813| } 400| 6.07k| else 401| 6.07k| { 402| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 403| 6.07k| if (pVA[i].cNumValenceElectrons == 6 && !pVA[i].cMetal && /* N, P, As */ ------------------ | Branch (403:21): [True: 2.33k, False: 3.73k] | Branch (403:57): [True: 2.29k, False: 38] ------------------ 404| 2.29k| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) )) ------------------ | | 118| 2.29k|#define NO_VERTEX -2 ------------------ | Branch (404:22): [True: 483, False: 1.81k] ------------------ 405| 483| { 406| | 407| 483| if (pBNS->edge[j].forbidden) ------------------ | Branch (407:25): [True: 0, False: 483] ------------------ 408| 0| { 409| 0| continue; 410| 0| } 411| | 412| 483| if (pBNS->edge[j].flow) ------------------ | Branch (412:25): [True: 360, False: 123] ------------------ 413| 360| { 414| 360| if ((ret = AddToEdgeList( &SFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 360|#define INC_ADD_EDGE 64 ------------------ | Branch (414:29): [True: 0, False: 360] ------------------ 415| 0| { 416| 0| goto exit_function; 417| 0| } 418| 360| } 419| 483| } 420| 6.07k| } 421| 6.88k| } 422| 25.3k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (422:21): [True: 16.5k, False: 8.80k] ------------------ 423| 16.5k| { 424| 16.5k| k = at2[i].neighbor[j]; 425| 16.5k| if (k < i && !pBNS->edge[e = pBNS->vert[i].iedge[j]].forbidden) ------------------ | Branch (425:17): [True: 8.28k, False: 8.28k] | Branch (425:26): [True: 8.22k, False: 63] ------------------ 426| 8.22k| { 427| 8.22k| if ((ret = AddToEdgeList( &AllBondEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 8.22k|#define INC_ADD_EDGE 64 ------------------ | Branch (427:21): [True: 0, False: 8.22k] ------------------ 428| 0| { 429| 0| goto exit_function; 430| 0| } 431| 8.22k| } 432| 16.5k| } 433| 8.80k| } 434| 1.21k| if (forbidden_stereo_edge_mask) ------------------ | Branch (434:9): [True: 1.21k, False: 0] ------------------ 435| 1.21k| { 436| 10.0k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (436:21): [True: 8.80k, False: 1.21k] ------------------ 437| 8.80k| { 438| 25.3k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (438:25): [True: 16.5k, False: 8.80k] ------------------ 439| 16.5k| { 440| 16.5k| if (pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask) ------------------ | Branch (440:21): [True: 126, False: 16.4k] ------------------ 441| 126| { 442| 126| int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q, 443| 126| pStruct->pbfsq->nAtomLevel, 444| 126| pStruct->pbfsq->cSource, 99 /* max ring size */ ); 445| 126| if (0 < nMinRingSize && ( ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, INC_ADD_EDGE ) )) ------------------ | | 18| 88|#define INC_ADD_EDGE 64 ------------------ | Branch (445:25): [True: 88, False: 38] | Branch (445:45): [True: 0, False: 88] ------------------ 446| 0| { 447| 0| goto exit_function; 448| 0| } 449| 126| } 450| 16.5k| } 451| 8.80k| } 452| 1.21k| } 453| | 454| 1.21k| INCHI_HEAPCHK 455| 1.21k| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (455:13): [True: 0, False: 1.21k] ------------------ 456| 0| { 457| 0| goto exit_function; 458| 0| } 459| 1.21k| INCHI_HEAPCHK 460| 1.21k| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (460:13): [True: 0, False: 1.21k] ------------------ 461| 0| { 462| 0| goto exit_function; 463| 0| } 464| | 465| | INCHI_HEAPCHK 466| | 467| 1.21k| if (!pc2i->bHasDifference || ------------------ | Branch (467:13): [True: 66, False: 1.14k] ------------------ 468| 1.14k| (!pc2i->len_c2at && pc2i->nNumTgRevrs == pc2i->nNumTgInChI && ------------------ | Branch (468:15): [True: 10, False: 1.13k] | Branch (468:34): [True: 10, False: 0] ------------------ 469| 10| pc2i->nNumEndpRevrs == pc2i->nNumRemHInChI && ------------------ | Branch (469:14): [True: 7, False: 3] ------------------ 470| 7| pc2i->nNumEndpRevrs == pc2i->nNumEndpInChI && ------------------ | Branch (470:14): [True: 7, False: 0] ------------------ 471| 7| !pc2i->nNumTgDiffMinus && !pc2i->nNumTgDiffH)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (471:14): [True: 7, False: 0] | Branch (471:40): [True: 7, False: 0] ------------------ 472| 73| { 473| 73| goto exit_function; /* nothing to do */ 474| 73| } 475| | 476| | /*goto exit_function;*/ /* debug only*/ 477| | 478| 1.14k| if (pc2i->len_c2at >= 2) ------------------ | Branch (478:9): [True: 1.03k, False: 106] ------------------ 479| 1.03k| { 480| | /*----------------------------------------------------*/ 481| | /* case 01: restored: O=AB-O(-) original: (-)O-AB=O */ 482| | /* FixH: 0 -1 -1 0 */ 483| | /* MobH: 0 1 1 0 */ 484| | /* non-taut non-taut */ 485| | /* O = O, S, Se; charged atoms O are not tautomeric */ 486| | /* Solution: move (-) from B-O(-) to O=A */ 487| | /*----------------------------------------------------*/ 488| 1.03k| int num_DB_O = 0, num_SB_O_Minus = 0, iat; 489| 1.03k| cur_success = 0; 490| | 491| 4.52k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (491:21): [True: 3.48k, False: 1.03k] ------------------ 492| 3.48k| { 493| 3.48k| iat = pc2i->c2at[i].atomNumber; 494| 3.48k| if (pc2i->c2at[i].nValElectr == 6 /* && !pc2i->c2at[i].endptInChI -- mod#1*/ && ------------------ | Branch (494:17): [True: 1.76k, False: 1.72k] ------------------ 495| 1.76k| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (495:17): [True: 1.12k, False: 641] | Branch (495:61): [True: 1.12k, False: 0] ------------------ 496| 1.12k| { 497| 1.12k| if ( /* orig. InChI info: */ 498| 1.12k| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 2.24k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (498:21): [True: 1.12k, False: 0] ------------------ 499| 1.12k| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (499:21): [True: 1.02k, False: 94] | Branch (499:54): [True: 1.02k, False: 0] ------------------ 500| | /* reversed structure info: */ 501| 1.02k| pc2i->c2at[i].nFixHRevrs == -1 && pc2i->c2at[i].nMobHRevrs == 1 && ------------------ | Branch (501:21): [True: 46, False: 982] | Branch (501:55): [True: 46, False: 0] ------------------ 502| 46| pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H && /* at2 is Fixed-H */ ------------------ | Branch (502:21): [True: 46, False: 0] | Branch (502:59): [True: 46, False: 0] ------------------ 503| 46| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1) ------------------ | Branch (503:21): [True: 46, False: 0] | Branch (503:46): [True: 46, False: 0] ------------------ 504| 46| { 505| 46| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 506| 46| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 46|#define INC_ADD_EDGE 64 ------------------ | Branch (506:25): [True: 0, False: 46] ------------------ 507| 0| { 508| 0| goto exit_function; 509| 0| } 510| 46| } 511| 1.07k| else 512| 1.07k| { 513| 1.07k| if ( /* orig. InChI info: */ 514| 1.07k| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 2.15k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (514:25): [True: 1.07k, False: 0] ------------------ 515| 1.07k| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (515:25): [True: 56, False: 1.02k] | Branch (515:59): [True: 25, False: 31] ------------------ 516| | /* reversed structure info: */ 517| 25| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (517:25): [True: 25, False: 0] | Branch (517:58): [True: 25, False: 0] ------------------ 518| 25| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (518:25): [True: 16, False: 9] | Branch (518:62): [True: 16, False: 0] ------------------ 519| 16| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (519:25): [True: 16, False: 0] | Branch (519:50): [True: 14, False: 2] ------------------ 520| 14| { 521| 14| iat_DB_O[num_DB_O++] = iat; 522| 14| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 14|#define INC_ADD_EDGE 64 ------------------ | Branch (522:29): [True: 0, False: 14] ------------------ 523| 0| { 524| 0| goto exit_function; 525| 0| } 526| 14| } 527| 1.07k| } 528| 1.12k| } 529| 3.48k| } 530| 1.03k| if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.03k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 14, False: 1.02k] | | ------------------ ------------------ | Branch (530:13): [True: 0, False: 1.03k] ------------------ 531| 0| { 532| | /* detected; attempt to fix */ 533| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 534| 0| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 535| 0| delta = 1; 536| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (536:25): [True: 0, False: 0] | Branch (536:47): [True: 0, False: 0] ------------------ 537| 0| { 538| 0| iat = iat_SB_O_Minus[i]; 539| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 540| 0| if (!pe->flow) ------------------ | Branch (540:21): [True: 0, False: 0] ------------------ 541| 0| continue; 542| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 543| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 544| | 545| 0| pe->forbidden |= forbidden_edge_mask; 546| 0| pe->flow -= delta; /* remove (-) from AB-O(-) */ 547| 0| pv1->st_edge.flow -= delta; 548| 0| pv2->st_edge.flow -= delta; 549| 0| pBNS->tot_st_flow -= 2 * delta; 550| | 551| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 552| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 553| | 554| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (554:21): [True: 0, False: 0] | Branch (554:35): [True: 0, False: 0] | Branch (554:53): [True: 0, False: 0] ------------------ 555| 0| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (555:22): [True: 0, False: 0] | Branch (555:40): [True: 0, False: 0] | Branch (555:62): [True: 0, False: 0] ------------------ 556| 0| { 557| | /* Added (-)charge to O=AB => nDeltaCharge == -1 */ 558| | /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */ 559| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 560| 0| if (ret > 0) ------------------ | Branch (560:25): [True: 0, False: 0] ------------------ 561| 0| { 562| 0| nNumRunBNS++; 563| 0| cur_success++; /* 01 */ 564| 0| } 565| 0| } 566| 0| else 567| 0| { 568| 0| pe->forbidden &= forbidden_edge_mask_inv; 569| 0| pe->flow += delta; 570| 0| pv1->st_edge.flow += delta; 571| 0| pv2->st_edge.flow += delta; 572| 0| pBNS->tot_st_flow += 2 * delta; 573| 0| } 574| 0| INCHI_HEAPCHK 575| 0| } 576| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 577| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 578| 0| } 579| 1.03k| if (cur_success) ------------------ | Branch (579:13): [True: 0, False: 1.03k] ------------------ 580| 0| { 581| 0| tot_succes += cur_success; 582| | /* recalculate InChI from the structure */ 583| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ------------------ | Branch (583:17): [True: 0, False: 0] ------------------ 584| 0| ip, sd, pBNS, pStruct, 585| 0| at, at2, at3, pVA, 586| 0| pTCGroups, 587| 0| ppt_group_info, ppat_norm, 588| 0| ppat_prep))) 589| 0| { 590| 0| goto exit_function; 591| 0| } 592| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (592:17): [True: 0, False: 0] ------------------ 593| 0| { 594| 0| goto exit_function; 595| 0| } 596| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (596:17): [True: 0, False: 0] | Branch (596:45): [True: 0, False: 0] ------------------ 597| 0| { 598| 0| goto exit_function; /* no fixed-H found */ 599| 0| } 600| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (600:17): [True: 0, False: 0] ------------------ 601| 0| { 602| 0| goto exit_function; 603| 0| } 604| 0| if (!pc2i->bHasDifference) ------------------ | Branch (604:17): [True: 0, False: 0] ------------------ 605| 0| { 606| 0| goto exit_function; /* nothing to do */ 607| 0| } 608| 0| } 609| 1.03k| } 610| | 611| 1.14k| if (pc2i->len_c2at >= 1) ------------------ | Branch (611:9): [True: 1.13k, False: 3] ------------------ 612| 1.13k| { 613| | /*--------------------------------------------------------------*/ 614| | /* case 02: restored: -O(+)=AB-NH2 original: -O-AB=NH2(+) */ 615| | /* FixH: 0 0 0 1 */ 616| | /* MobH: 0 2 0 1 */ 617| | /* O = P, As, Sb, O, S, Se, F, Cl, Br, I; not taut. in InChI */ 618| | /* N = N, O, S, Se, Te; has H; tautomeric or not tautomeric */ 619| | /* Solution: move (+) from O(+) to NH2 */ 620| | /*--------------------------------------------------------------*/ 621| 1.13k| int num_DB_O_Plus = 0, num_SB_NH = 0, iat; 622| 1.13k| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 623| 1.13k| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (623:32): [True: 1.13k, False: 0] | Branch (623:45): [True: 1.13k, False: 0] ------------------ 624| 1.13k| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (624:13): [True: 0, False: 0] | Branch (624:26): [True: 0, False: 0] ------------------ 625| 1.13k| cur_success = 0; 626| 1.13k| num_zero_ret = 0; 627| | 628| 4.72k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (628:21): [True: 3.59k, False: 1.13k] ------------------ 629| 3.59k| { 630| 3.59k| iat = pc2i->c2at[i].atomNumber; 631| 3.59k| if ( /* orig. InChI info: =NH2(+), =OH(+) */ 632| 3.59k| num_SB_NH < MAX_DIFF_FIXH && ------------------ | | 456| 7.18k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (632:17): [True: 3.59k, False: 0] ------------------ 633| 3.59k| ((pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) || ------------------ | Branch (633:19): [True: 1.25k, False: 2.33k] | Branch (633:52): [True: 1.07k, False: 180] ------------------ 634| 2.51k| pc2i->c2at[i].nValElectr == 6) /* N, O, S, Se, Te */ && ------------------ | Branch (634:21): [True: 1.83k, False: 685] ------------------ 635| | /*!pc2i->c2at[i].endptInChI &&*/ /* <=== relaxation */ 636| 2.90k| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (636:17): [True: 2.13k, False: 771] | Branch (636:60): [True: 2.06k, False: 76] ------------------ 637| 2.06k| pc2i->c2at[i].nFixHInChI>0 /*== 1 --modification#2*/ && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (637:17): [True: 593, False: 1.46k] ------------------ 638| | /* reversed structure info: */ 639| 593| pc2i->c2at[i].nFixHRevrs == 0 && /* pc2i->c2at[i].nMobHRevrs == 0 &&*/ ------------------ | Branch (639:17): [True: 400, False: 193] ------------------ 640| 400| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && ------------------ | Branch (640:17): [True: 274, False: 126] | Branch (640:54): [True: 274, False: 0] ------------------ 641| 274| at2[iat].valence == at2[iat].chem_bonds_valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (641:17): [True: 254, False: 20] ------------------ 642| 254| { 643| 254| iat_SB_NH[num_SB_NH++] = iat; 644| 254| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 254|#define INC_ADD_EDGE 64 ------------------ | Branch (644:21): [True: 0, False: 254] ------------------ 645| 0| { 646| 0| goto exit_function; 647| 0| } 648| 254| } 649| 3.59k| } 650| 9.53k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (650:21): [True: 8.39k, False: 1.13k] ------------------ 651| 8.39k| { 652| | /* i = canonical number - 1 */ 653| 8.39k| iat = nCanon2AtnoRevrs[i]; 654| 8.39k| if ( /* in restored atom: charge=+1, no H, has double bond, P, As, O, S, Se, Te, F, Cl, Br, I */ 655| 8.39k| num_DB_O_Plus < MAX_DIFF_FIXH && ------------------ | | 456| 16.7k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (655:17): [True: 8.39k, False: 0] ------------------ 656| 8.39k| at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (656:17): [True: 1.28k, False: 7.11k] | Branch (656:41): [True: 914, False: 369] ------------------ 657| 914| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (657:17): [True: 601, False: 313] | Branch (657:67): [True: 548, False: 53] ------------------ 658| 548| (pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cNumValenceElectrons == 7 || ------------------ | Branch (658:18): [True: 210, False: 338] | Branch (658:56): [True: 40, False: 298] ------------------ 659| 298| (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber > 1)) && ------------------ | Branch (659:22): [True: 258, False: 40] | Branch (659:60): [True: 37, False: 221] ------------------ 660| | /* in orig.InChI: not an endpoint, has no H */ 661| 287| !pStruct->endpoint[i] && ------------------ | Branch (661:17): [True: 263, False: 24] ------------------ 662| 263| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (662:19): [True: 263, False: 0] | Branch (662:39): [True: 5, False: 258] ------------------ 663| 258| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (663:19): [True: 258, False: 0] | Branch (663:33): [True: 1, False: 257] ------------------ 664| | /* has (+) edge */ 665| 257| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (665:17): [True: 257, False: 0] | Branch (665:60): [True: 221, False: 36] ------------------ 666| 221| { 667| 221| iat_DB_O_Plus[num_DB_O_Plus++] = iat; 668| 221| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 221|#define INC_ADD_EDGE 64 ------------------ | Branch (668:21): [True: 0, False: 221] ------------------ 669| 0| { 670| 0| goto exit_function; 671| 0| } 672| 221| } 673| 8.39k| } 674| 1.13k| if ((num_try = inchi_min(num_DB_O_Plus, num_SB_NH))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.13k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 156, False: 981] | | ------------------ ------------------ | Branch (674:13): [True: 83, False: 1.05k] ------------------ 675| 83| { 676| | /* detected; attempt to fix */ 677| 83| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 678| 83| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 679| 83| delta = 1; 680| 93| repeat_02_allow_NV: 681| 191| for (i = 0; i < num_SB_NH && cur_success < num_try; i++) ------------------ | Branch (681:25): [True: 100, False: 91] | Branch (681:42): [True: 98, False: 2] ------------------ 682| 98| { 683| 98| iat = iat_SB_NH[i]; 684| 98| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 685| 98| if (!pe->flow) ------------------ | Branch (685:21): [True: 0, False: 98] ------------------ 686| 0| continue; 687| 98| pv1 = pBNS->vert + (v1 = pe->neighbor1); 688| 98| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 689| | 690| 98| pe->forbidden |= forbidden_edge_mask; 691| 98| pe->flow -= delta; 692| 98| pv1->st_edge.flow -= delta; 693| 98| pv2->st_edge.flow -= delta; 694| 98| pBNS->tot_st_flow -= 2 * delta; 695| | 696| 98| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 697| 98| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 698| | 699| 98| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (699:21): [True: 74, False: 24] | Branch (699:35): [True: 5, False: 69] | Branch (699:53): [True: 2, False: 3] ------------------ 700| 72| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (700:22): [True: 67, False: 5] | Branch (700:40): [True: 66, False: 1] | Branch (700:62): [True: 67, False: 1] ------------------ 701| 67| { 702| | /* Removed charge from O(+) => nDeltaCharge == -1 */ 703| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 704| 67| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 705| 67| if (ret > 0) ------------------ | Branch (705:25): [True: 67, False: 0] ------------------ 706| 67| { 707| 67| nNumRunBNS++; 708| 67| cur_success++; /* 02 */ 709| 67| } 710| 67| } 711| 31| else 712| 31| { 713| 31| num_zero_ret += !ret; 714| 31| pe->forbidden &= forbidden_edge_mask_inv; 715| 31| pe->flow += delta; 716| 31| pv1->st_edge.flow += delta; 717| 31| pv2->st_edge.flow += delta; 718| 31| pBNS->tot_st_flow += 2 * delta; 719| 31| } 720| 98| INCHI_HEAPCHK 721| 98| } 722| 93| if (num_zero_ret == num_try && !bAllowedNFlowerEdges && NFlowerEdges.num_edges) ------------------ | Branch (722:17): [True: 26, False: 67] | Branch (722:44): [True: 19, False: 7] | Branch (722:69): [True: 10, False: 9] ------------------ 723| 10| { 724| 10| RemoveForbiddenEdgeMask(pBNS, &NFlowerEdges, forbidden_edge_mask); 725| 10| bAllowedNFlowerEdges = 1; 726| 10| goto repeat_02_allow_NV; 727| 10| } 728| 83| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 729| | /* djb-rwth: removing redundant code */ 730| 83| } 731| 1.13k| CurrEdges.num_edges = 0; /* clear current edge list */ 732| 1.13k| if (cur_success) ------------------ | Branch (732:13): [True: 67, False: 1.07k] ------------------ 733| 67| { 734| 67| tot_succes += cur_success; 735| | /* recalculate InChI from the structure */ 736| 67| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (736:17): [True: 1, False: 66] ------------------ 737| 67| ppt_group_info, ppat_norm, ppat_prep))) 738| 1| { 739| 1| goto exit_function; 740| 1| } 741| 66| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (741:17): [True: 0, False: 66] ------------------ 742| 0| { 743| 0| goto exit_function; 744| 0| } 745| 66| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (745:17): [True: 0, False: 66] | Branch (745:45): [True: 0, False: 0] ------------------ 746| 0| { 747| 0| goto exit_function; /* no fixed-H found */ 748| 0| } 749| 66| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (749:17): [True: 0, False: 66] ------------------ 750| 0| { 751| 0| goto exit_function; 752| 0| } 753| 66| if (!pc2i->bHasDifference) ------------------ | Branch (753:17): [True: 1, False: 65] ------------------ 754| 1| { 755| 1| goto exit_function; /* nothing to do */ 756| 1| } 757| 66| } 758| 1.13k| } 759| | 760| 1.13k| if (pc2i->len_c2at >= 1 && pc2i->nNumTgRevrs == 1 && ------------------ | Branch (760:9): [True: 1.13k, False: 3] | Branch (760:32): [True: 405, False: 730] ------------------ 761| 405| ( pc2i->nNumEndpRevrs > pc2i->nNumEndpInChI || pc2i->nNumTgInChI > 1 ) /* ADP in Revrs */) ------------------ | Branch (761:11): [True: 200, False: 205] | Branch (761:56): [True: 23, False: 182] ------------------ 762| 223| { 763| | /*--------------------------------------------------------------*/ 764| | /* case 03: restored: -N(-)-AB=O original: -N=AB-O(-) */ 765| | /* FixH: 0 0 0 -1 */ 766| | /* MobH: 0 0 0 1 */ 767| | /* O = O, S, Se; N = N; */ 768| | /* restored atoms are tautomeric; original atoms are not taut. */ 769| | /* restored struct has 1 t-group; original has less endpoints */ 770| | /* and possibly >1 t-groups */ 771| | /* Solution: move (-) from N(-) to =O */ 772| | /* these atoms are tautomeric in restored structure */ 773| | /*--------------------------------------------------------------*/ 774| 223| int num_SB_N_Minus = 0, num_DB_O = 0, iat; 775| 223| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 776| 223| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (776:41): [True: 223, False: 0] ------------------ 777| 223| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (777:41): [True: 223, False: 0] ------------------ 778| | /* 779| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 780| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 781| | */ 782| 223| cur_success = 0; 783| | 784| 1.04k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (784:21): [True: 817, False: 223] ------------------ 785| 817| { 786| 817| iat = pc2i->c2at[i].atomNumber; 787| 817| if ( /* orig. InChI info: -O(-) */ 788| 817| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 1.63k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (788:17): [True: 817, False: 0] ------------------ 789| 817| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (789:17): [True: 336, False: 481] ------------------ 790| 336| !pc2i->c2at[i].endptInChI && ------------------ | Branch (790:17): [True: 308, False: 28] ------------------ 791| 308| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (791:17): [True: 231, False: 77] | Branch (791:61): [True: 231, False: 0] ------------------ 792| 231| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (792:17): [True: 10, False: 221] | Branch (792:51): [True: 5, False: 5] ------------------ 793| | /* reversed structure info: */ 794| 5| pc2i->c2at[i].endptRevrs && ------------------ | Branch (794:17): [True: 3, False: 2] ------------------ 795| 3| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (795:17): [True: 3, False: 0] | Branch (795:50): [True: 3, False: 0] ------------------ 796| 3| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (796:17): [True: 1, False: 2] | Branch (796:54): [True: 1, False: 0] ------------------ 797| 1| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (797:17): [True: 1, False: 0] | Branch (797:42): [True: 1, False: 0] ------------------ 798| 1| { 799| 1| iat_DB_O[num_DB_O++] = iat; 800| 1| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 1|#define INC_ADD_EDGE 64 ------------------ | Branch (800:21): [True: 0, False: 1] ------------------ 801| 0| { 802| 0| goto exit_function; 803| 0| } 804| 1| } 805| 817| } 806| 1.88k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (806:21): [True: 1.65k, False: 223] ------------------ 807| 1.65k| { 808| | /* i = canonical number - 1 */ 809| 1.65k| iat = nCanon2AtnoRevrs[i]; 810| 1.65k| if ( /* in restored atom N: charge=-1, no H, has no double bond, endpoint */ 811| 1.65k| num_SB_N_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 3.31k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (811:17): [True: 1.65k, False: 0] ------------------ 812| 1.65k| at2[iat].charge == -1 && /*!at2[iat].num_H &&*/ ------------------ | Branch (812:17): [True: 323, False: 1.33k] ------------------ 813| 323| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (813:17): [True: 242, False: 81] | Branch (813:68): [True: 235, False: 7] ------------------ 814| 235| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (814:17): [True: 71, False: 164] | Branch (814:55): [True: 64, False: 7] ------------------ 815| 64| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && ------------------ | Branch (815:17): [True: 64, False: 0] | Branch (815:38): [True: 51, False: 13] ------------------ 816| | /* in orig.InChI: not an endpoint, has no H */ 817| | /* !pStruct->endpoint[i] && */ 818| | /* 819| | !(pStruct->fixed_H && pStruct->fixed_H[i]) && 820| | !(nMobHInChI && nMobHInChI[i] ) && 821| | */ 822| | /* has (-) edge */ 823| 51| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (823:17): [True: 51, False: 0] | Branch (823:61): [True: 51, False: 0] ------------------ 824| 51| { 825| 51| iat_SB_N_Minus[num_SB_N_Minus++] = iat; 826| 51| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 51|#define INC_ADD_EDGE 64 ------------------ | Branch (826:21): [True: 0, False: 51] ------------------ 827| 0| { 828| 0| goto exit_function; 829| 0| } 830| 51| } 831| 1.65k| } 832| 223| if ((num_try = inchi_min(num_SB_N_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 223|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 1, False: 222] | | ------------------ ------------------ | Branch (832:13): [True: 0, False: 223] ------------------ 833| 0| { 834| | /* detected; attempt to fix */ 835| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 836| 0| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 837| 0| delta = 1; 838| 0| for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++) ------------------ | Branch (838:25): [True: 0, False: 0] | Branch (838:47): [True: 0, False: 0] ------------------ 839| 0| { 840| 0| iat = iat_SB_N_Minus[i]; 841| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; /* 2006-03-03: changed from CPlusGroupEdge */ 842| 0| if (!pe->flow) ------------------ | Branch (842:21): [True: 0, False: 0] ------------------ 843| 0| continue; 844| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 845| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 846| | 847| 0| pe->forbidden |= forbidden_edge_mask; 848| 0| pe->flow -= delta; 849| 0| pv1->st_edge.flow -= delta; 850| 0| pv2->st_edge.flow -= delta; 851| 0| pBNS->tot_st_flow -= 2 * delta; 852| | 853| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 854| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 855| | 856| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (856:21): [True: 0, False: 0] | Branch (856:35): [True: 0, False: 0] | Branch (856:53): [True: 0, False: 0] ------------------ 857| 0| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (857:22): [True: 0, False: 0] | Branch (857:40): [True: 0, False: 0] | Branch (857:62): [True: 0, False: 0] ------------------ 858| 0| { 859| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 860| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 861| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 862| 0| if (ret > 0) ------------------ | Branch (862:25): [True: 0, False: 0] ------------------ 863| 0| { 864| 0| nNumRunBNS++; 865| 0| cur_success++; /* 03 */ 866| 0| } 867| 0| } 868| 0| else 869| 0| { 870| 0| pe->forbidden &= forbidden_edge_mask_inv; 871| 0| pe->flow += delta; 872| 0| pv1->st_edge.flow += delta; 873| 0| pv2->st_edge.flow += delta; 874| 0| pBNS->tot_st_flow += 2 * delta; 875| 0| } 876| 0| INCHI_HEAPCHK 877| 0| } 878| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 879| 0| } 880| 223| CurrEdges.num_edges = 0; /* clear current edge list */ 881| 223| if (cur_success) ------------------ | Branch (881:13): [True: 0, False: 223] ------------------ 882| 0| { 883| 0| tot_succes += cur_success; 884| | /* recalculate InChI from the structure */ 885| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (885:17): [True: 0, False: 0] ------------------ 886| 0| ppt_group_info, ppat_norm, ppat_prep))) 887| 0| { 888| 0| goto exit_function; 889| 0| } 890| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (890:17): [True: 0, False: 0] ------------------ 891| 0| { 892| 0| goto exit_function; 893| 0| } 894| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (894:17): [True: 0, False: 0] | Branch (894:45): [True: 0, False: 0] ------------------ 895| 0| { 896| 0| goto exit_function; /* no fixed-H found */ 897| 0| } 898| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (898:17): [True: 0, False: 0] ------------------ 899| 0| { 900| 0| goto exit_function; 901| 0| } 902| 0| if (!pc2i->bHasDifference) ------------------ | Branch (902:17): [True: 0, False: 0] ------------------ 903| 0| { 904| 0| goto exit_function; /* nothing to do */ 905| 0| } 906| 0| } 907| 223| } 908| | 909| 1.13k| if (pc2i->nNumTgRevrs == 1 && /* pc2i->nNumRemHInChI < 0 &&*/ ------------------ | Branch (909:9): [True: 408, False: 730] ------------------ 910| 408| ( pc2i->nNumEndpRevrs > pc2i->nNumEndpInChI || pc2i->nNumTgInChI > 1 ) /* ADP in Revrs */) ------------------ | Branch (910:11): [True: 200, False: 208] | Branch (910:56): [True: 23, False: 185] ------------------ 911| 223| { 912| | /*--------------------------------------------------------------*/ 913| | /* case 03a:restored: -N(-)-AB=O original: -N=AB-O(-) */ 914| | /* FixH: 0 0 0 0 */ 915| | /* MobH: 0 0 0 0 */ 916| | /* O = O, S, Se; N = N; taut */ 917| | /* restored atoms are tautomeric; original atom is; N may be. */ 918| | /* restored struct has 1 t-group; original has less endpoints */ 919| | /* and possibly >1 t-groups */ 920| | /* Solution: move (-) from N(-) to =O */ 921| | /* these atoms are tautomeric in restored structure */ 922| | /*--------------------------------------------------------------*/ 923| 223| int num_SB_N_Minus = 0, num_DB_O = 0, iat; 924| 223| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 925| 223| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (925:41): [True: 223, False: 0] ------------------ 926| 223| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (926:41): [True: 223, False: 0] ------------------ 927| 223| S_CHAR *pnMobHInChI = ( pInChI[1] && pInChI[1]->nNum_H ) ? pInChI[1]->nNum_H : ------------------ | Branch (927:35): [True: 223, False: 0] | Branch (927:48): [True: 223, False: 0] ------------------ 928| 223| ( pInChI[0] && pInChI[0]->nNum_H ) ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (928:15): [True: 0, False: 0] | Branch (928:28): [True: 0, False: 0] ------------------ 929| 223| S_CHAR *pnFixHInChI = pStruct->fixed_H; 930| | 931| 223| cur_success = 0; 932| 223| CurrEdges.num_edges = 0; 933| | 934| 1.88k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (934:21): [True: 1.65k, False: 223] ------------------ 935| 1.65k| { /* i = canonical number - 1 */ 936| 1.65k| iat = nCanon2AtnoRevrs[i]; 937| 1.65k| if ( /* in restored atom N: charge=-1, no H, has no double bond, endpoint */ 938| 1.65k| num_SB_N_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 3.31k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (938:17): [True: 1.65k, False: 0] ------------------ 939| 1.65k| at2[iat].charge == -1 && /*!at2[iat].num_H &&*/ ------------------ | Branch (939:17): [True: 323, False: 1.33k] ------------------ 940| 323| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (940:17): [True: 242, False: 81] | Branch (940:68): [True: 235, False: 7] ------------------ 941| 235| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (941:17): [True: 71, False: 164] | Branch (941:55): [True: 64, False: 7] ------------------ 942| 64| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && ------------------ | Branch (942:17): [True: 64, False: 0] | Branch (942:38): [True: 51, False: 13] ------------------ 943| | /* in orig.InChI: may be an endpoint, has no H */ 944| | /* has (-) edge */ 945| 51| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (945:17): [True: 51, False: 0] | Branch (945:61): [True: 51, False: 0] ------------------ 946| 51| { 947| 51| iat_SB_N_Minus[num_SB_N_Minus++] = iat; 948| 51| } 949| 1.60k| else 950| 1.60k| if (num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 3.21k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (950:21): [True: 1.60k, False: 0] ------------------ 951| 1.60k| at2[iat].charge == 0 && /*!at2[iat].num_H &&*/ ------------------ | Branch (951:21): [True: 1.06k, False: 538] ------------------ 952| 1.06k| at2[iat].valence + 1 == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (952:21): [True: 596, False: 473] | Branch (952:76): [True: 576, False: 20] ------------------ 953| 576| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (953:21): [True: 206, False: 370] ------------------ 954| 206| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && /* endpoint in Reconstructed */ ------------------ | Branch (954:21): [True: 206, False: 0] | Branch (954:42): [True: 140, False: 66] ------------------ 955| 140| (pStruct->endpoint[i] || /* endpoint or H(+) acceptor in original */ ------------------ | Branch (955:22): [True: 34, False: 106] ------------------ 956| 106| (pnMobHInChI && pnMobHInChI[i] == 1 && pnFixHInChI && pnFixHInChI[i] == -1)) && ------------------ | Branch (956:26): [True: 106, False: 0] | Branch (956:41): [True: 5, False: 101] | Branch (956:64): [True: 5, False: 0] | Branch (956:79): [True: 2, False: 3] ------------------ 957| | /* has (-) edge */ 958| 36| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (958:21): [True: 36, False: 0] | Branch (958:65): [True: 36, False: 0] ------------------ 959| 36| { 960| 36| iat_DB_O[num_DB_O++] = iat; 961| 36| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 36|#define INC_ADD_EDGE 64 ------------------ | Branch (961:25): [True: 0, False: 36] ------------------ 962| 0| { 963| 0| goto exit_function; 964| 0| } 965| 36| } 966| 1.65k| } 967| 223| if ((num_try = inchi_min(num_SB_N_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 223|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 14, False: 209] | | ------------------ ------------------ | Branch (967:13): [True: 22, False: 201] ------------------ 968| 22| { 969| | /* detected; attempt to fix */ 970| 22| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 971| | /* allow charge transfer to all found =O */ 972| 22| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 973| 22| delta = 1; 974| 44| for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++) ------------------ | Branch (974:25): [True: 22, False: 22] | Branch (974:47): [True: 22, False: 0] ------------------ 975| 22| { 976| 22| iat = iat_SB_N_Minus[i]; 977| 22| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 978| 22| if (!pe->flow) ------------------ | Branch (978:21): [True: 0, False: 22] ------------------ 979| 0| continue; 980| 22| pv1 = pBNS->vert + (v1 = pe->neighbor1); 981| 22| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 982| | 983| 22| pe->forbidden |= forbidden_edge_mask; 984| 22| pe->flow -= delta; 985| 22| pv1->st_edge.flow -= delta; 986| 22| pv2->st_edge.flow -= delta; 987| 22| pBNS->tot_st_flow -= 2 * delta; 988| | 989| 22| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 990| 22| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 991| | 992| 22| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (992:21): [True: 21, False: 1] | Branch (992:35): [True: 7, False: 14] | Branch (992:53): [True: 7, False: 0] ------------------ 993| 20| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (993:22): [True: 14, False: 0] | Branch (993:40): [True: 13, False: 1] | Branch (993:62): [True: 20, False: 0] ------------------ 994| 20| { 995| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 996| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 997| 20| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 998| 20| if (ret > 0) ------------------ | Branch (998:25): [True: 20, False: 0] ------------------ 999| 20| { 1000| 20| nNumRunBNS++; 1001| 20| cur_success++; /* 03a */ 1002| 20| } 1003| 20| } 1004| 2| else 1005| 2| { 1006| 2| pe->forbidden &= forbidden_edge_mask_inv; 1007| 2| pe->flow += delta; 1008| 2| pv1->st_edge.flow += delta; 1009| 2| pv2->st_edge.flow += delta; 1010| 2| pBNS->tot_st_flow += 2 * delta; 1011| 2| } 1012| 22| INCHI_HEAPCHK 1013| 22| } 1014| 22| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 1015| 22| } 1016| 223| CurrEdges.num_edges = 0; /* clear current edge list */ 1017| 223| if (cur_success) ------------------ | Branch (1017:13): [True: 20, False: 203] ------------------ 1018| 20| { 1019| 20| tot_succes += cur_success; 1020| | /* recalculate InChI from the structure */ 1021| 20| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1021:17): [True: 1, False: 19] ------------------ 1022| 20| ppt_group_info, ppat_norm, ppat_prep))) 1023| 1| { 1024| 1| goto exit_function; 1025| 1| } 1026| 19| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1026:17): [True: 0, False: 19] ------------------ 1027| 0| { 1028| 0| goto exit_function; 1029| 0| } 1030| 19| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1030:17): [True: 10, False: 9] | Branch (1030:45): [True: 0, False: 10] ------------------ 1031| 0| { 1032| 0| goto exit_function; /* no fixed-H found */ 1033| 0| } 1034| 19| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1034:17): [True: 0, False: 19] ------------------ 1035| 0| { 1036| 0| goto exit_function; 1037| 0| } 1038| 19| if (!pc2i->bHasDifference) ------------------ | Branch (1038:17): [True: 0, False: 19] ------------------ 1039| 0| { 1040| 0| goto exit_function; /* nothing to do */ 1041| 0| } 1042| 19| } 1043| 223| } 1044| | 1045| 1.13k| if (pc2i->len_c2at >= 1 && pc2i->nNumTgInChI == 1 && /* ADP in InChI */ ------------------ | Branch (1045:9): [True: 1.13k, False: 3] | Branch (1045:32): [True: 734, False: 400] ------------------ 1046| 734| ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 )) ------------------ | Branch (1046:11): [True: 620, False: 114] | Branch (1046:56): [True: 12, False: 102] ------------------ 1047| 632| { 1048| | /*--------------------------------------------------------------*/ 1049| | /* case 04: restored: OH(+)=AB-O- OH- orig. HO-AB=O(+)- OH- */ 1050| | /* FixH: 1 0 0 1 0 1 */ 1051| | /* MobH: 0 0 1 0 0 0 */ 1052| | /* non-taut. taut taut */ 1053| | /* ADP: one t-group or more endpoints */ 1054| | /* O(+) = N, P, As, As, O, S, Se; OH = N, O, S, Se, Te */ 1055| | /* Solution: move (+) from O(+) to NH2 */ 1056| | /*--------------------------------------------------------------*/ 1057| 632| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 1058| 632| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1059| 632| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (1059:32): [True: 632, False: 0] | Branch (1059:45): [True: 632, False: 0] ------------------ 1060| 632| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (1060:13): [True: 0, False: 0] | Branch (1060:26): [True: 0, False: 0] ------------------ 1061| 632| cur_success = 0; 1062| | 1063| 5.50k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1063:21): [True: 4.87k, False: 632] ------------------ 1064| 4.87k| { /* i = canonical number - 1 */ 1065| 4.87k| iat = nCanon2AtnoRevrs[i]; 1066| 4.87k| if ( /* in restored atom: charge=+1, has H, has double bond, N, O, S, Se, Te */ 1067| 4.87k| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 456| 9.74k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1067:17): [True: 4.87k, False: 0] ------------------ 1068| 4.87k| at2[iat].charge == 1 && at2[iat].num_H && ------------------ | Branch (1068:17): [True: 778, False: 4.09k] | Branch (1068:41): [True: 209, False: 569] ------------------ 1069| 209| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (1069:17): [True: 186, False: 23] | Branch (1069:67): [True: 183, False: 3] ------------------ 1070| 183| (pVA[iat].cNumValenceElectrons == 6 || ------------------ | Branch (1070:18): [True: 122, False: 61] ------------------ 1071| 61| (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1)) && ------------------ | Branch (1071:22): [True: 50, False: 11] | Branch (1071:60): [True: 49, False: 1] ------------------ 1072| | /* in orig.InChI: an endpoint, has fixed-H */ 1073| 171| pStruct->endpoint[i] && ------------------ | Branch (1073:17): [True: 79, False: 92] ------------------ 1074| 79| (pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (1074:18): [True: 79, False: 0] | Branch (1074:38): [True: 74, False: 5] ------------------ 1075| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 1076| | /* has (+) edge */ 1077| 74| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1077:17): [True: 74, False: 0] | Branch (1077:60): [True: 70, False: 4] ------------------ 1078| 70| { 1079| | 1080| 70| iat_DB_Charged[num_DB_Charged++] = iat; 1081| | 1082| 70| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 70|#define INC_ADD_EDGE 64 ------------------ | Branch (1082:21): [True: 0, False: 70] ------------------ 1083| 0| { 1084| 0| goto exit_function; 1085| 0| } 1086| 70| } 1087| 4.80k| else 1088| 4.80k| { 1089| 4.80k| if ( /* in restored atom: charge=0, has no H, has no double bond, N, P, O, S, Se, Te */ 1090| 4.80k| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 9.60k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1090:21): [True: 4.80k, False: 0] ------------------ 1091| 4.80k| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (1091:21): [True: 3.24k, False: 1.55k] | Branch (1091:45): [True: 2.87k, False: 373] ------------------ 1092| 2.87k| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (1092:21): [True: 860, False: 2.01k] | Branch (1092:72): [True: 665, False: 195] ------------------ 1093| 665| (pVA[iat].cNumValenceElectrons == 6 || ------------------ | Branch (1093:22): [True: 231, False: 434] ------------------ 1094| 434| pVA[iat].cNumValenceElectrons == 5) && ------------------ | Branch (1094:25): [True: 191, False: 243] ------------------ 1095| | /* in orig.InChI: an endpoint, has fixed-H */ 1096| | /* pStruct->endpoint[i] && */ 1097| 422| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (1097:23): [True: 422, False: 0] | Branch (1097:43): [True: 4, False: 418] ------------------ 1098| 418| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (1098:23): [True: 418, False: 0] | Branch (1098:37): [True: 0, False: 418] ------------------ 1099| | /* has (+) edge */ 1100| 418| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && ------------------ | Branch (1100:21): [True: 369, False: 49] ------------------ 1101| 369| 0 == pBNS->edge[e].forbidden) ------------------ | Branch (1101:21): [True: 369, False: 0] ------------------ 1102| 369| { 1103| | 1104| 369| iat_SB_Neutr[num_SB_Neutr++] = iat; 1105| | 1106| 369| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 369|#define INC_ADD_EDGE 64 ------------------ | Branch (1106:25): [True: 0, False: 369] ------------------ 1107| 0| { 1108| 0| goto exit_function; 1109| 0| } 1110| 369| } 1111| 4.80k| } 1112| 4.87k| } 1113| 632| if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 632|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 19, False: 613] | | ------------------ ------------------ | Branch (1113:13): [True: 50, False: 582] ------------------ 1114| 50| { 1115| | /* detected; attempt to fix */ 1116| 50| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 1117| 50| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 1118| 50| delta = 1; 1119| 112| for (i = 0; i < num_SB_Neutr && cur_success < num_try; i++) ------------------ | Branch (1119:25): [True: 68, False: 44] | Branch (1119:45): [True: 62, False: 6] ------------------ 1120| 62| { 1121| 62| iat = iat_SB_Neutr[i]; 1122| 62| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 1123| 62| if (!pe->flow) ------------------ | Branch (1123:21): [True: 0, False: 62] ------------------ 1124| 0| continue; 1125| 62| pv1 = pBNS->vert + (v1 = pe->neighbor1); 1126| 62| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 1127| | 1128| 62| pe->forbidden |= forbidden_edge_mask; 1129| 62| pe->flow -= delta; 1130| 62| pv1->st_edge.flow -= delta; 1131| 62| pv2->st_edge.flow -= delta; 1132| 62| pBNS->tot_st_flow -= 2 * delta; 1133| | 1134| 62| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1135| 62| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 1136| | 1137| 62| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1137:21): [True: 48, False: 14] | Branch (1137:35): [True: 3, False: 45] | Branch (1137:53): [True: 1, False: 2] ------------------ 1138| 47| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1138:22): [True: 43, False: 4] | Branch (1138:40): [True: 36, False: 7] | Branch (1138:62): [True: 37, False: 0] ------------------ 1139| 37| { 1140| | /* Removed charge from O(+) => nDeltaCharge == -1 */ 1141| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 1142| 37| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 1143| 37| if (ret > 0) ------------------ | Branch (1143:25): [True: 37, False: 0] ------------------ 1144| 37| { 1145| 37| nNumRunBNS++; 1146| 37| cur_success++; /* 04 */ 1147| 37| } 1148| 37| } 1149| 25| else 1150| 25| { 1151| 25| pe->forbidden &= forbidden_edge_mask_inv; 1152| 25| pe->flow += delta; 1153| 25| pv1->st_edge.flow += delta; 1154| 25| pv2->st_edge.flow += delta; 1155| 25| pBNS->tot_st_flow += 2 * delta; 1156| 25| } 1157| 62| INCHI_HEAPCHK 1158| 62| } 1159| 50| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 1160| 50| } 1161| 632| CurrEdges.num_edges = 0; /* clear current edge list */ 1162| 632| if (cur_success) ------------------ | Branch (1162:13): [True: 37, False: 595] ------------------ 1163| 37| { 1164| 37| tot_succes += cur_success; 1165| | /* recalculate InChI from the structure */ 1166| 37| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1166:17): [True: 0, False: 37] ------------------ 1167| 37| ppt_group_info, ppat_norm, ppat_prep))) 1168| 0| { 1169| 0| goto exit_function; 1170| 0| } 1171| 37| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1171:17): [True: 0, False: 37] ------------------ 1172| 0| { 1173| 0| goto exit_function; 1174| 0| } 1175| 37| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1175:17): [True: 0, False: 37] | Branch (1175:45): [True: 0, False: 0] ------------------ 1176| 0| { 1177| 0| goto exit_function; /* no fixed-H found */ 1178| 0| } 1179| 37| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1179:17): [True: 0, False: 37] ------------------ 1180| 0| { 1181| 0| goto exit_function; 1182| 0| } 1183| 37| if (!pc2i->bHasDifference) ------------------ | Branch (1183:17): [True: 0, False: 37] ------------------ 1184| 0| { 1185| 0| goto exit_function; /* nothing to do */ 1186| 0| } 1187| 37| } 1188| 632| } 1189| | 1190| 1.13k| if (pc2i->len_c2at > 1) ------------------ | Branch (1190:9): [True: 1.01k, False: 121] ------------------ 1191| 1.01k| { 1192| | /*--------------------------------------------------------------*/ 1193| | /* case 05: restored: O=AB-NH original:(-)O-AB=NH(+) */ 1194| | /* FixH: 0 0 -1 1 */ 1195| | /* MobH: 0 1 1 0 */ 1196| | /* O = O, S, Se; N = N, O, S, Se, Te; all atoms not tautomeric */ 1197| | /* Solution: Separate charges */ 1198| | /*--------------------------------------------------------------*/ 1199| 1.01k| int num_DB_O = 0, num_SB_NH = 0, iat; 1200| 1.01k| cur_success = 0; 1201| | 1202| 4.49k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1202:21): [True: 3.47k, False: 1.01k] ------------------ 1203| 3.47k| { 1204| 3.47k| iat = pc2i->c2at[i].atomNumber; 1205| 3.47k| if ( /* orig. InChI info: =NH2(+), =OH(+) */ 1206| 3.47k| num_SB_NH < MAX_DIFF_FIXH && ------------------ | | 456| 6.95k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1206:17): [True: 3.47k, False: 0] ------------------ 1207| 3.47k| ((pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) || ------------------ | Branch (1207:19): [True: 1.24k, False: 2.23k] | Branch (1207:52): [True: 1.07k, False: 169] ------------------ 1208| 2.40k| pc2i->c2at[i].nValElectr == 6) /* N, O, S, Se, Te */ && ------------------ | Branch (1208:21): [True: 1.74k, False: 661] ------------------ 1209| 2.81k| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1209:17): [True: 1.61k, False: 1.20k] ------------------ 1210| 1.61k| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (1210:17): [True: 1.46k, False: 148] | Branch (1210:60): [True: 1.41k, False: 44] ------------------ 1211| 1.41k| pc2i->c2at[i].nFixHInChI == 1 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (1211:17): [True: 433, False: 985] ------------------ 1212| | /* reversed structure info: */ 1213| 433| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs && ------------------ | Branch (1213:17): [True: 246, False: 187] | Branch (1213:50): [True: 240, False: 6] ------------------ 1214| 240| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && ------------------ | Branch (1214:17): [True: 151, False: 89] | Branch (1214:54): [True: 151, False: 0] ------------------ 1215| 151| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1215:17): [True: 151, False: 0] ------------------ 1216| 151| at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (1216:17): [True: 131, False: 20] ------------------ 1217| 131| { 1218| 131| iat_SB_NH[num_SB_NH++] = iat; 1219| 131| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 131|#define INC_ADD_EDGE 64 ------------------ | Branch (1219:21): [True: 0, False: 131] ------------------ 1220| 0| { 1221| 0| goto exit_function; 1222| 0| } 1223| 131| } 1224| 3.34k| else 1225| 3.34k| { 1226| 3.34k| if ( /* orig. InChI info: -O(-) */ 1227| 3.34k| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 6.69k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1227:21): [True: 3.34k, False: 0] ------------------ 1228| 3.34k| (pc2i->c2at[i].nValElectr == 6) /* O, S, Se, Te */ && ------------------ | Branch (1228:21): [True: 1.65k, False: 1.69k] ------------------ 1229| 1.65k| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1229:21): [True: 911, False: 742] ------------------ 1230| 911| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (1230:21): [True: 569, False: 342] | Branch (1230:65): [True: 569, False: 0] ------------------ 1231| 569| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (1231:21): [True: 47, False: 522] | Branch (1231:55): [True: 23, False: 24] ------------------ 1232| | /* reversed structure info: */ 1233| 23| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (1233:21): [True: 23, False: 0] | Branch (1233:54): [True: 23, False: 0] ------------------ 1234| 23| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (1234:21): [True: 16, False: 7] | Branch (1234:58): [True: 16, False: 0] ------------------ 1235| 16| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1235:21): [True: 15, False: 1] ------------------ 1236| 15| at2[iat].valence + 1 == at2[iat].chem_bonds_valence) ------------------ | Branch (1236:21): [True: 13, False: 2] ------------------ 1237| 13| { 1238| 13| iat_DB_O[num_DB_O++] = iat; 1239| 13| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 13|#define INC_ADD_EDGE 64 ------------------ | Branch (1239:25): [True: 0, False: 13] ------------------ 1240| 0| { 1241| 0| goto exit_function; 1242| 0| } 1243| 13| } 1244| 3.34k| } 1245| 3.47k| } 1246| 1.01k| if ((num_try = inchi_min(num_DB_O, num_SB_NH))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.01k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 114, False: 902] | | ------------------ ------------------ | Branch (1246:13): [True: 9, False: 1.00k] ------------------ 1247| 9| { 1248| | /* detected; attempt to fix */ 1249| 9| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 1250| 9| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 1251| 9| delta = 1; 1252| 18| for (i = 0; i < num_SB_NH && cur_success < num_try; i++) ------------------ | Branch (1252:25): [True: 9, False: 9] | Branch (1252:42): [True: 9, False: 0] ------------------ 1253| 9| { 1254| 9| iat = iat_SB_NH[i]; 1255| 9| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 1256| 9| if (!pe->flow) ------------------ | Branch (1256:21): [True: 0, False: 9] ------------------ 1257| 0| continue; 1258| 9| pv1 = pBNS->vert + (v1 = pe->neighbor1); 1259| 9| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 1260| | 1261| 9| pe->forbidden |= forbidden_edge_mask; 1262| 9| pe->flow -= delta; 1263| 9| pv1->st_edge.flow -= delta; 1264| 9| pv2->st_edge.flow -= delta; 1265| 9| pBNS->tot_st_flow -= 2 * delta; 1266| | 1267| 9| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1268| 9| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 1269| | 1270| 9| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1270:21): [True: 8, False: 1] | Branch (1270:35): [True: 2, False: 6] | Branch (1270:53): [True: 1, False: 1] ------------------ 1271| 7| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1271:22): [True: 6, False: 1] | Branch (1271:40): [True: 5, False: 1] | Branch (1271:62): [True: 6, False: 0] ------------------ 1272| 6| { 1273| | /* Added charge to =O => nDeltaCharge == 1 */ 1274| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 1275| 6| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 1276| 6| if (ret > 0) ------------------ | Branch (1276:25): [True: 6, False: 0] ------------------ 1277| 6| { 1278| 6| nNumRunBNS++; 1279| 6| cur_success++; /* 05 */ 1280| 6| } 1281| 6| } 1282| 3| else 1283| 3| { 1284| 3| pe->forbidden &= forbidden_edge_mask_inv; 1285| 3| pe->flow += delta; 1286| 3| pv1->st_edge.flow += delta; 1287| 3| pv2->st_edge.flow += delta; 1288| 3| pBNS->tot_st_flow += 2 * delta; 1289| 3| } 1290| 9| INCHI_HEAPCHK 1291| 9| } 1292| 9| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 1293| 9| } 1294| 1.01k| CurrEdges.num_edges = 0; /* clear current edge list */ 1295| 1.01k| if (cur_success) ------------------ | Branch (1295:13): [True: 6, False: 1.01k] ------------------ 1296| 6| { 1297| 6| tot_succes += cur_success; 1298| | /* recalculate InChI from the structure */ 1299| 6| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1299:17): [True: 0, False: 6] ------------------ 1300| 6| ppt_group_info, ppat_norm, ppat_prep))) 1301| 0| { 1302| 0| goto exit_function; 1303| 0| } 1304| 6| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1304:17): [True: 0, False: 6] ------------------ 1305| 0| { 1306| 0| goto exit_function; 1307| 0| } 1308| 6| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1308:17): [True: 0, False: 6] | Branch (1308:45): [True: 0, False: 0] ------------------ 1309| 0| { 1310| 0| goto exit_function; /* no fixed-H found */ 1311| 0| } 1312| 6| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1312:17): [True: 0, False: 6] ------------------ 1313| 0| { 1314| 0| goto exit_function; 1315| 0| } 1316| 6| if (!pc2i->bHasDifference) ------------------ | Branch (1316:17): [True: 1, False: 5] ------------------ 1317| 1| { 1318| 1| goto exit_function; /* nothing to do */ 1319| 1| } 1320| 6| } 1321| 1.01k| } 1322| | 1323| 1.13k| if (pStruct->fixed_H && pStruct->endpoint && pc2i->nChargeFixHInChI > 0 && pc2i->nChargeFixHInChI > pc2i->nChargeMobHInChI) ------------------ | Branch (1323:9): [True: 1.13k, False: 0] | Branch (1323:29): [True: 1.13k, False: 0] | Branch (1323:50): [True: 1, False: 1.13k] | Branch (1323:80): [True: 0, False: 1] ------------------ 1324| 0| { 1325| | /*----------------------------------------------------------*/ 1326| | /* case 06c: restored -NH- or -NH(+) orig: -NH- */ 1327| | /* Fixed-H 1 1 0 */ 1328| | /* Mobile-H 0 0 1 */ 1329| | /* not tautomeric not tautomeric */ 1330| | /* has adjacent (+) */ 1331| | /* charges */ 1332| | /* Solution: move (+) charges to the -NH- unless it already*/ 1333| | /* N = N, O, S, Se, Te */ 1334| | /* has (+) charge blocked by adjacent (+) */ 1335| | /*----------------------------------------------------------*/ 1336| 0| int iat; 1337| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1338| | /* 1339| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1340| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1341| | inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && 1342| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds? 1343| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL; 1344| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 1345| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : NULL; 1346| | */ 1347| 0| EDGE_LIST CurChargeEdges; 1348| 0| EdgeIndex e2; 1349| 0| cur_success = 0; 1350| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 1351| 0| CurrEdges.num_edges = 0; 1352| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1352:21): [True: 0, False: 0] ------------------ 1353| 0| { 1354| | /* atoms -NH- from which H(+) were removed by the Normalization in orig. InChI */ 1355| 0| iat = pc2i->c2at[i].atomNumber; 1356| 0| if (( pc2i->c2at[i].nValElectr == 6 || ------------------ | Branch (1356:19): [True: 0, False: 0] ------------------ 1357| 0| (pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) ) && ------------------ | Branch (1357:20): [True: 0, False: 0] | Branch (1357:53): [True: 0, False: 0] ------------------ 1358| 0| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1358:18): [True: 0, False: 0] ------------------ 1359| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1359:18): [True: 0, False: 0] | Branch (1359:63): [True: 0, False: 0] ------------------ 1360| 0| { 1361| 0| if ( /* orig. InChI info: -NH- */ 1362| 0| pc2i->c2at[i].nFixHInChI == 1 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (1362:22): [True: 0, False: 0] | Branch (1362:55): [True: 0, False: 0] ------------------ 1363| | /* reversed structure info: */ 1364| 0| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 1 && /* was not removed */ ------------------ | Branch (1364:22): [True: 0, False: 0] | Branch (1364:55): [True: 0, False: 0] ------------------ 1365| 0| /*pc2i->c2at[i].nAtChargeRevrs == 0 &&*/ at2[iat].num_H && /* at2 is Fixed-H */ ------------------ | Branch (1365:63): [True: 0, False: 0] ------------------ 1366| 0| at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (1366:22): [True: 0, False: 0] ------------------ 1367| 0| { 1368| 0| if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1368:25): [True: 0, False: 0] ------------------ 1369| 0| { 1370| 0| goto exit_function; 1371| 0| } 1372| 0| } 1373| 0| } 1374| 0| } 1375| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1375:21): [True: 0, False: 0] ------------------ 1376| 0| { 1377| | /* find adjacent charged atoms */ 1378| 0| iat = nCanon2AtnoRevrs[i]; 1379| 0| if (pStruct->endpoint[i] || at2[iat].charge != 1 || at2[iat].radical || pVA[iat].cMetal) ------------------ | Branch (1379:17): [True: 0, False: 0] | Branch (1379:41): [True: 0, False: 0] | Branch (1379:65): [True: 0, False: 0] | Branch (1379:85): [True: 0, False: 0] ------------------ 1380| 0| { 1381| 0| continue; 1382| 0| } 1383| 0| if (0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow && pVA[iat].cNumValenceElectrons >= 5) ------------------ | Branch (1383:17): [True: 0, False: 0] | Branch (1383:62): [True: 0, False: 0] | Branch (1383:90): [True: 0, False: 0] | Branch (1383:113): [True: 0, False: 0] ------------------ 1384| 0| { 1385| | /* positively charged atom */ 1386| 0| for (j = 0; j < at2[iat].valence; j++) ------------------ | Branch (1386:29): [True: 0, False: 0] ------------------ 1387| 0| { 1388| 0| if (at2[k = (int) at2[iat].neighbor[j]].charge == 1 && !pVA[k].cMetal && ------------------ | Branch (1388:25): [True: 0, False: 0] | Branch (1388:76): [True: 0, False: 0] ------------------ 1389| 0| 0 <= ( e2 = pVA[k].nCPlusGroupEdge - 1 ) && !pBNS->edge[e2].forbidden && !pBNS->edge[e2].flow) ------------------ | Branch (1389:26): [True: 0, False: 0] | Branch (1389:70): [True: 0, False: 0] | Branch (1389:99): [True: 0, False: 0] ------------------ 1390| 0| { 1391| 0| if (0 > FindInEdgeList( &CurrEdges, e ) && ------------------ | Branch (1391:29): [True: 0, False: 0] ------------------ 1392| 0| 0 > FindInEdgeList( &CurChargeEdges, e ) && ------------------ | Branch (1392:30): [True: 0, False: 0] ------------------ 1393| 0| ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1393:30): [True: 0, False: 0] ------------------ 1394| 0| { 1395| 0| goto exit_case_06c; 1396| 0| } 1397| 0| if (0 > FindInEdgeList( &CurrEdges, e2 ) && ------------------ | Branch (1397:29): [True: 0, False: 0] ------------------ 1398| 0| 0 > FindInEdgeList( &CurChargeEdges, e2 ) && ------------------ | Branch (1398:30): [True: 0, False: 0] ------------------ 1399| 0| ( ret = AddToEdgeList( &CurChargeEdges, e2, INC_ADD_EDGE ) )) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1399:30): [True: 0, False: 0] ------------------ 1400| 0| { 1401| 0| goto exit_case_06c; 1402| 0| } 1403| 0| } 1404| 0| } 1405| 0| } 1406| 0| } 1407| 0| if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1407:13): [True: 0, False: 0] ------------------ 1408| 0| { 1409| | /* detected; attempt to fix */ 1410| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1411| 0| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1412| 0| delta = 1; 1413| 0| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1413:25): [True: 0, False: 0] | Branch (1413:52): [True: 0, False: 0] ------------------ 1414| 0| { 1415| 0| e = CurrEdges.pnEdges[i]; 1416| 0| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 1417| 0| if (!pe->flow) ------------------ | Branch (1417:21): [True: 0, False: 0] ------------------ 1418| 0| continue; 1419| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1420| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1421| | 1422| 0| pe->flow -= delta; /* add (+) to -NHm */ 1423| 0| pv1->st_edge.flow -= delta; 1424| 0| pv2->st_edge.flow -= delta; 1425| 0| pBNS->tot_st_flow -= 2 * delta; 1426| | 1427| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1428| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1429| | 1430| 0| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1430:21): [True: 0, False: 0] | Branch (1430:36): [True: 0, False: 0] | Branch (1430:54): [True: 0, False: 0] ------------------ 1431| 0| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1431:36): [True: 0, False: 0] | Branch (1431:54): [True: 0, False: 0] | Branch (1431:77): [True: 0, False: 0] ------------------ 1432| 0| { 1433| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 1434| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1435| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1436| 0| if (ret > 0) ------------------ | Branch (1436:25): [True: 0, False: 0] ------------------ 1437| 0| { 1438| 0| nNumRunBNS++; 1439| 0| cur_success++; /* 06c */ 1440| 0| } 1441| 0| } 1442| 0| else 1443| 0| { 1444| 0| pe->flow += delta; 1445| 0| pv1->st_edge.flow += delta; 1446| 0| pv2->st_edge.flow += delta; 1447| 0| pBNS->tot_st_flow += 2 * delta; 1448| 0| } 1449| 0| INCHI_HEAPCHK 1450| 0| } 1451| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1452| 0| } 1453| 0| exit_case_06c: 1454| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 1455| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 0|#define EDGE_LIST_FREE (-2) ------------------ 1456| 0| if (ret < 0) ------------------ | Branch (1456:13): [True: 0, False: 0] ------------------ 1457| 0| { 1458| 0| goto exit_function; 1459| 0| } 1460| 0| if (cur_success) ------------------ | Branch (1460:13): [True: 0, False: 0] ------------------ 1461| 0| { 1462| 0| tot_succes += cur_success; 1463| | /* recalculate InChI from the structure */ 1464| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1464:17): [True: 0, False: 0] ------------------ 1465| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1466| 0| { 1467| 0| goto exit_function; 1468| 0| } 1469| 0| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1469:17): [True: 0, False: 0] ------------------ 1470| 0| { 1471| 0| goto exit_function; 1472| 0| } 1473| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1473:17): [True: 0, False: 0] | Branch (1473:45): [True: 0, False: 0] ------------------ 1474| 0| { 1475| 0| goto exit_function; /* no fixed-H found */ 1476| 0| } 1477| 0| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1477:17): [True: 0, False: 0] ------------------ 1478| 0| { 1479| 0| goto exit_function; 1480| 0| } 1481| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1481:17): [True: 0, False: 0] ------------------ 1482| 0| { 1483| 0| goto exit_function; /* nothing to do */ 1484| 0| } 1485| 0| } 1486| 0| } 1487| | 1488| 1.13k| if (pc2i->len_c2at >= 2) ------------------ | Branch (1488:9): [True: 1.01k, False: 123] ------------------ 1489| 1.01k| { 1490| | /*------------------------------------------------------------*/ 1491| | /* case 06d: restored: XH(+)=-AB-NH orig.: XH-=AB=NH(+) */ 1492| | /* FixH: 1 1 0 0 1 1 */ 1493| | /* MobH: 0 taut 1 1 taut 0 */ 1494| | /* */ 1495| | /* */ 1496| | /* N = N, O, S, Se; atoms N are not tautomeric in orig InChI */ 1497| | /* X = N, O, S, Se, Te, F, Cl, Br, I; atom X is non-taut */ 1498| | /* Solution: move (+) from X to NH */ 1499| | /*------------------------------------------------------------*/ 1500| 1.01k| int iat; 1501| | /* 1502| | AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1503| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1504| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1505| | inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && 1506| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds? 1507| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : 1508| | pStruct->pOne_norm_data[TAUT_NON]->at; 1509| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 1510| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 1511| | */ 1512| 1.01k| EDGE_LIST CurChargeEdges; 1513| 1.01k| cur_success = 0; 1514| 1.01k| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 1.01k|#define EDGE_LIST_CLEAR (-1) ------------------ 1515| 1.01k| CurrEdges.num_edges = 0; 1516| 4.48k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1516:21): [True: 3.47k, False: 1.01k] ------------------ 1517| 3.47k| { 1518| 3.47k| iat = pc2i->c2at[i].atomNumber; 1519| | /* XH(+) */ 1520| 3.47k| if ( /* reconstructed: non-taut and (+) */ 1521| 3.47k| ( pc2i->c2at[i].nMobHRevrs + 1 == pc2i->c2at[i].nFixHRevrs && ------------------ | Branch (1521:19): [True: 676, False: 2.79k] ------------------ 1522| 676| pc2i->c2at[i].nFixHRevrs > 0 && !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1522:19): [True: 286, False: 390] | Branch (1522:51): [True: 41, False: 245] ------------------ 1523| 41| pc2i->c2at[i].nAtChargeRevrs == 1 && ------------------ | Branch (1523:19): [True: 37, False: 4] ------------------ 1524| | /* original InChI: non-taut & has H or an endpoint, has Fixed H */ 1525| 37| ( (!pc2i->c2at[i].nFixHInChI && pc2i->c2at[i].nMobHInChI == pc2i->c2at[i].nFixHRevrs) || ------------------ | Branch (1525:22): [True: 19, False: 18] | Branch (1525:51): [True: 19, False: 0] ------------------ 1526| 18| (pc2i->c2at[i].nFixHInChI == pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].endptInChI) ) ) && ------------------ | Branch (1526:22): [True: 18, False: 0] | Branch (1526:78): [True: 18, False: 0] ------------------ 1527| 37| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1527:18): [True: 37, False: 0] | Branch (1527:63): [True: 28, False: 9] | Branch (1527:91): [True: 28, False: 0] ------------------ 1528| 28| { 1529| | 1530| 28| if ((ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 28|#define INC_ADD_EDGE 64 ------------------ | Branch (1530:21): [True: 0, False: 28] ------------------ 1531| 0| { 1532| 0| goto exit_case_06d; 1533| 0| } 1534| 28| } 1535| 3.44k| else 1536| 3.44k| { 1537| | /* -NH- */ 1538| 3.44k| if ( /* original InChI: has H and is not an endpoint */ 1539| 3.44k| ( pc2i->c2at[i].nMobHInChI + 1 == pc2i->c2at[i].nFixHInChI && ------------------ | Branch (1539:23): [True: 660, False: 2.78k] ------------------ 1540| 660| pc2i->c2at[i].nFixHInChI > 0 && !pc2i->c2at[i].endptInChI && ------------------ | Branch (1540:23): [True: 660, False: 0] | Branch (1540:55): [True: 513, False: 147] ------------------ 1541| 513| pc2i->c2at[i].nAtChargeRevrs == 0 && ------------------ | Branch (1541:23): [True: 367, False: 146] ------------------ 1542| | /* reconstructed InChI: non-taut & has H or an endpoint, has Fixed H */ 1543| 367| ( (!pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].nMobHRevrs == pc2i->c2at[i].nFixHInChI) || ------------------ | Branch (1543:26): [True: 204, False: 163] | Branch (1543:55): [True: 198, False: 6] ------------------ 1544| 169| (pc2i->c2at[i].nFixHRevrs == pc2i->c2at[i].nFixHInChI && pc2i->c2at[i].endptRevrs) ) ) && ------------------ | Branch (1544:26): [True: 163, False: 6] | Branch (1544:82): [True: 163, False: 0] ------------------ 1545| 361| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (1545:22): [True: 352, False: 9] | Branch (1545:67): [True: 351, False: 1] ------------------ 1546| 351| pBNS->edge[e].flow) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1546:22): [True: 351, False: 0] ------------------ 1547| 351| { 1548| | 1549| 351| if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 351|#define INC_ADD_EDGE 64 ------------------ | Branch (1549:25): [True: 0, False: 351] ------------------ 1550| 0| { 1551| 0| goto exit_case_06d; 1552| 0| } 1553| 351| } 1554| 3.44k| } 1555| 3.47k| } 1556| 1.01k| if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.01k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 14, False: 999] | | ------------------ ------------------ | Branch (1556:13): [True: 14, False: 999] ------------------ 1557| 14| { 1558| | /* detected; attempt to fix */ 1559| 14| int bSFlowerEdgesMayBeForbidden = ( SFlowerEdges.num_edges > 0 ); 1560| 14| int bSFlowerEdgesIsForbidden; 1561| 14| for (bSFlowerEdgesIsForbidden = bSFlowerEdgesMayBeForbidden; 1562| 41| 0 <= bSFlowerEdgesIsForbidden; bSFlowerEdgesIsForbidden--) ------------------ | Branch (1562:19): [True: 27, False: 14] ------------------ 1563| 27| { 1564| 27| if (bSFlowerEdgesIsForbidden) ------------------ | Branch (1564:21): [True: 13, False: 14] ------------------ 1565| 13| { 1566| | /* on the 1st pass disallow -S(+)= => =S=, allow only -S(+)= => -S- */ 1567| 13| SetForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 1568| 13| } 1569| 27| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1570| 27| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1571| 27| delta = 1; 1572| 57| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1572:29): [True: 32, False: 25] | Branch (1572:56): [True: 30, False: 2] ------------------ 1573| 30| { 1574| 30| e = CurrEdges.pnEdges[i]; 1575| 30| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 1576| 30| if (!pe->flow) ------------------ | Branch (1576:25): [True: 0, False: 30] ------------------ 1577| 0| continue; 1578| 30| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1579| 30| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1580| | 1581| 30| pe->flow -= delta; /* add (+) to -NHm */ 1582| 30| pv1->st_edge.flow -= delta; 1583| 30| pv2->st_edge.flow -= delta; 1584| 30| pBNS->tot_st_flow -= 2 * delta; 1585| | 1586| 30| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1587| 30| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1588| | 1589| 30| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1589:25): [True: 15, False: 15] | Branch (1589:40): [True: 3, False: 12] | Branch (1589:58): [True: 1, False: 2] ------------------ 1590| 14| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1590:40): [True: 10, False: 4] | Branch (1590:58): [True: 5, False: 5] | Branch (1590:81): [True: 6, False: 0] ------------------ 1591| 6| { 1592| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 1593| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1594| 6| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1595| 6| if (ret > 0) ------------------ | Branch (1595:29): [True: 6, False: 0] ------------------ 1596| 6| { 1597| 6| nNumRunBNS++; 1598| 6| cur_success++; /* 06d */ 1599| 6| } 1600| 6| } 1601| 24| else 1602| 24| { 1603| 24| pe->flow += delta; 1604| 24| pv1->st_edge.flow += delta; 1605| 24| pv2->st_edge.flow += delta; 1606| 24| pBNS->tot_st_flow += 2 * delta; 1607| 24| } 1608| 30| INCHI_HEAPCHK 1609| 30| } 1610| 27| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1611| 27| RemoveForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 1612| 27| } 1613| 14| } 1614| 1.01k| exit_case_06d: 1615| 1.01k| CurrEdges.num_edges = 0; /* clear current edge list */ 1616| 1.01k| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.01k|#define EDGE_LIST_FREE (-2) ------------------ 1617| 1.01k| if (cur_success) ------------------ | Branch (1617:13): [True: 6, False: 1.00k] ------------------ 1618| 6| { 1619| 6| tot_succes += cur_success; 1620| | /* recalculate InChI from the structure */ 1621| 6| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1621:17): [True: 0, False: 6] ------------------ 1622| 6| ppt_group_info, ppat_norm, ppat_prep ) )) 1623| 0| { 1624| 0| goto exit_function; 1625| 0| } 1626| 6| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1626:17): [True: 0, False: 6] ------------------ 1627| 0| { 1628| 0| goto exit_function; 1629| 0| } 1630| 6| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1630:17): [True: 0, False: 6] | Branch (1630:45): [True: 0, False: 0] ------------------ 1631| 0| { 1632| 0| goto exit_function; /* no fixed-H found */ 1633| 0| } 1634| 6| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1634:17): [True: 0, False: 6] ------------------ 1635| 0| { 1636| 0| goto exit_function; 1637| 0| } 1638| 6| if (!pc2i->bHasDifference) ------------------ | Branch (1638:17): [True: 2, False: 4] ------------------ 1639| 2| { 1640| 2| goto exit_function; /* nothing to do */ 1641| 2| } 1642| 6| } 1643| 1.01k| } 1644| | 1645| 1.13k| if (pc2i->len_c2at >= 2) ------------------ | Branch (1645:9): [True: 1.00k, False: 125] ------------------ 1646| 1.00k| { 1647| | /*--------------------------------------------------------*/ 1648| | /* case 06: restored: NHn(+)=AB-NHm orig.: NHn-AB=NHm(+) */ 1649| | /* FixH: 1 0 0 1 */ 1650| | /* MobH: n-1 m n m-1 */ 1651| | /* N = N, O, S, Se; atoms N are not tautomeric */ 1652| | /* Solution: move (+) from NHn(+) to NHn */ 1653| | /*--------------------------------------------------------*/ 1654| 1.00k| int num_DB_NHn_Plus = 0, num_SB_NHm_Neutr = 0, iat; 1655| 1.00k| cur_success = 0; 1656| | 1657| 4.47k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1657:21): [True: 3.46k, False: 1.00k] ------------------ 1658| 3.46k| { 1659| 3.46k| iat = pc2i->c2at[i].atomNumber; 1660| 3.46k| if ((pc2i->c2at[i].nValElectr == 6 || ------------------ | Branch (1660:18): [True: 1.73k, False: 1.73k] ------------------ 1661| 1.73k| (pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1)) && ------------------ | Branch (1661:18): [True: 1.23k, False: 492] | Branch (1661:51): [True: 1.07k, False: 169] ------------------ 1662| 2.80k| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1662:17): [True: 1.59k, False: 1.20k] ------------------ 1663| 1.59k| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1663:17): [True: 1.44k, False: 146] | Branch (1663:60): [True: 1.40k, False: 44] ------------------ 1664| 1.40k| { 1665| 1.40k| if ( /* orig. InChI info: NHm */ 1666| 1.40k| num_SB_NHm_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 2.80k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1666:21): [True: 1.40k, False: 0] ------------------ 1667| 1.40k| pc2i->c2at[i].nFixHInChI == 1 && /*pc2i->c2at[i].nMobHInChI == 0 &&*/ ------------------ | Branch (1667:21): [True: 424, False: 978] ------------------ 1668| | /* reversed structure info: */ 1669| 424| pc2i->c2at[i].nFixHRevrs == 0 && /*pc2i->c2at[i].nMobHRevrs == 1 &&*/ ------------------ | Branch (1669:21): [True: 236, False: 188] ------------------ 1670| 236| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && /* at2 is Fixed-H */ ------------------ | Branch (1670:21): [True: 145, False: 91] | Branch (1670:58): [True: 145, False: 0] ------------------ 1671| 145| at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (1671:21): [True: 126, False: 19] ------------------ 1672| 126| { 1673| 126| iat_SB_NHm_Neutr[num_SB_NHm_Neutr++] = iat; 1674| 126| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 126|#define INC_ADD_EDGE 64 ------------------ | Branch (1674:25): [True: 0, False: 126] ------------------ 1675| 0| { 1676| 0| goto exit_function; 1677| 0| } 1678| 126| } 1679| 1.27k| else 1680| 1.27k| { 1681| 1.27k| if ( /* orig. InChI info: */ 1682| 1.27k| num_DB_NHn_Plus < MAX_DIFF_FIXH && ------------------ | | 456| 2.55k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1682:25): [True: 1.27k, False: 0] ------------------ 1683| 1.27k| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI &&*/ ------------------ | Branch (1683:25): [True: 772, False: 504] ------------------ 1684| | /* reversed structure info: */ 1685| 772| pc2i->c2at[i].nFixHRevrs == 1 && /*pc2i->c2at[i].nMobHRevrs == 0 &&*/ ------------------ | Branch (1685:25): [True: 69, False: 703] ------------------ 1686| 69| pc2i->c2at[i].nAtChargeRevrs == 1 && at2[iat].num_H && ------------------ | Branch (1686:25): [True: 11, False: 58] | Branch (1686:62): [True: 11, False: 0] ------------------ 1687| 11| at2[iat].valence < at2[iat].chem_bonds_valence) ------------------ | Branch (1687:25): [True: 7, False: 4] ------------------ 1688| 7| { 1689| 7| iat_DB_NHn_Plus[num_DB_NHn_Plus++] = iat; 1690| 7| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 7|#define INC_ADD_EDGE 64 ------------------ | Branch (1690:29): [True: 0, False: 7] ------------------ 1691| 0| { 1692| 0| goto exit_function; 1693| 0| } 1694| 7| } 1695| 1.27k| } 1696| 1.40k| } 1697| 3.46k| } 1698| 1.00k| if ((num_try = inchi_min(num_SB_NHm_Neutr, num_DB_NHn_Plus))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.00k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 4, False: 1.00k] | | ------------------ ------------------ | Branch (1698:13): [True: 3, False: 1.00k] ------------------ 1699| 3| { 1700| | /* detected; attempt to fix */ 1701| 3| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 1702| 3| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 1703| 3| delta = 1; 1704| 7| for (i = 0; i < num_SB_NHm_Neutr && cur_success < num_try; i++) ------------------ | Branch (1704:25): [True: 4, False: 3] | Branch (1704:49): [True: 4, False: 0] ------------------ 1705| 4| { 1706| 4| iat = iat_SB_NHm_Neutr[i]; 1707| 4| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 1708| 4| if (!pe->flow) ------------------ | Branch (1708:21): [True: 0, False: 4] ------------------ 1709| 0| continue; 1710| 4| pv1 = pBNS->vert + (v1 = pe->neighbor1); 1711| 4| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 1712| | 1713| 4| pe->forbidden |= forbidden_edge_mask; 1714| 4| pe->flow -= delta; /* add (+) to -NHm */ 1715| 4| pv1->st_edge.flow -= delta; 1716| 4| pv2->st_edge.flow -= delta; 1717| 4| pBNS->tot_st_flow -= 2 * delta; 1718| | 1719| 4| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1720| 4| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 1721| | 1722| 4| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1722:21): [True: 1, False: 3] | Branch (1722:35): [True: 1, False: 0] | Branch (1722:53): [True: 0, False: 1] ------------------ 1723| 1| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1723:22): [True: 0, False: 1] | Branch (1723:40): [True: 0, False: 0] | Branch (1723:62): [True: 0, False: 0] ------------------ 1724| 0| { 1725| | /* Removed (+)charge from -NHn => nDeltaCharge == -1 */ 1726| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1727| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 1728| 0| if (ret > 0) ------------------ | Branch (1728:25): [True: 0, False: 0] ------------------ 1729| 0| { 1730| 0| nNumRunBNS++; 1731| 0| cur_success++; /* 06 */ 1732| 0| } 1733| 0| } 1734| 4| else 1735| 4| { 1736| 4| pe->forbidden &= forbidden_edge_mask_inv; 1737| 4| pe->flow += delta; 1738| 4| pv1->st_edge.flow += delta; 1739| 4| pv2->st_edge.flow += delta; 1740| 4| pBNS->tot_st_flow += 2 * delta; 1741| 4| } 1742| 4| INCHI_HEAPCHK 1743| 4| } 1744| 3| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 1745| 3| } 1746| 1.00k| CurrEdges.num_edges = 0; /* clear current edge list */ 1747| 1.00k| if (cur_success) ------------------ | Branch (1747:13): [True: 0, False: 1.00k] ------------------ 1748| 0| { 1749| 0| tot_succes += cur_success; 1750| | /* recalculate InChI from the structure */ 1751| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1751:17): [True: 0, False: 0] ------------------ 1752| 0| ppt_group_info, ppat_norm, ppat_prep))) 1753| 0| { 1754| 0| goto exit_function; 1755| 0| } 1756| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1756:17): [True: 0, False: 0] ------------------ 1757| 0| { 1758| 0| goto exit_function; 1759| 0| } 1760| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1760:17): [True: 0, False: 0] | Branch (1760:45): [True: 0, False: 0] ------------------ 1761| 0| { 1762| 0| goto exit_function; /* no fixed-H found */ 1763| 0| } 1764| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1764:17): [True: 0, False: 0] ------------------ 1765| 0| { 1766| 0| goto exit_function; 1767| 0| } 1768| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1768:17): [True: 0, False: 0] ------------------ 1769| 0| { 1770| 0| goto exit_function; /* nothing to do */ 1771| 0| } 1772| 0| } 1773| 1.00k| } 1774| | 1775| 1.13k| if (( (pc2i->nNumTgInChI > pc2i->nNumTgRevrs && pc2i->nNumTgRevrs == 1) || ------------------ | Branch (1775:12): [True: 529, False: 605] | Branch (1775:53): [True: 26, False: 503] ------------------ 1776| 1.10k| pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs ) && ------------------ | Branch (1776:11): [True: 239, False: 869] ------------------ 1777| 265| pStruct->nNumRemovedProtonsMobHInChI == pStruct->One_ti.tni.nNumRemovedProtons && ------------------ | Branch (1777:10): [True: 156, False: 109] ------------------ 1778| 156| pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */ ------------------ | | 575| 156|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */ ------------------ | | 575| 156|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1778:10): [True: 156, False: 0] | Branch (1778:30): [True: 156, False: 0] | Branch (1778:51): [True: 156, False: 0] | Branch (1778:88): [True: 156, False: 0] ------------------ 1779| 156| { 1780| | /*----------------------------------------------------------*/ 1781| | /* case 06a: restored: N'(+)=-AB-NH orig.: N'-=AB=NH(+) */ 1782| | /* FixH: 0 1 0 1 */ 1783| | /* MobH: 0 0 0 0 */ 1784| | /* single t-group multiple t-groups */ 1785| | /* N = N, O, S, Se; atoms N are not tautomeric */ 1786| | /* N' = N atom N' is not tautomeric */ 1787| | /* Solution: move (+) from N' to NH */ 1788| | /*----------------------------------------------------------*/ 1789| 156| int iat; 1790| 156| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1791| | /* 1792| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1793| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1794| | */ 1795| 156| inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 575| 156|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1795:39): [True: 156, False: 0] ------------------ 1796| 156| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ? ------------------ | | 575| 156|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1796:13): [True: 156, False: 0] ------------------ 1797| 156| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL; ------------------ | | 575| 156|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1798| 156| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (1798:32): [True: 156, False: 0] | Branch (1798:45): [True: 156, False: 0] ------------------ 1799| 156| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (1799:13): [True: 0, False: 0] | Branch (1799:26): [True: 0, False: 0] ------------------ 1800| 156| EDGE_LIST CurChargeEdges; 1801| 156| cur_success = 0; 1802| 156| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 156|#define EDGE_LIST_CLEAR (-1) ------------------ 1803| 156| CurrEdges.num_edges = 0; 1804| 1.33k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1804:21): [True: 1.18k, False: 156] ------------------ 1805| 1.18k| { 1806| 1.18k| iat = nCanon2AtnoRevrs[i]; 1807| 1.18k| if (pStruct->endpoint[i]) ------------------ | Branch (1807:17): [True: 96, False: 1.08k] ------------------ 1808| 96| { 1809| 96| continue; 1810| 96| } 1811| | /* -NH-, -OH */ 1812| 1.08k| if (pStruct->fixed_H[i] && nMobHInChI && !nMobHInChI[i] && ------------------ | Branch (1812:17): [True: 307, False: 779] | Branch (1812:40): [True: 307, False: 0] | Branch (1812:54): [True: 289, False: 18] ------------------ 1813| 289| at2[iat].charge == 0 && at2[iat].radical == 0 && ------------------ | Branch (1813:18): [True: 220, False: 69] | Branch (1813:42): [True: 214, False: 6] ------------------ 1814| 214| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (1814:18): [True: 184, False: 30] | Branch (1814:63): [True: 184, False: 0] | Branch (1814:91): [True: 184, False: 0] ------------------ 1815| 184| ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) )) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 18| 184|#define INC_ADD_EDGE 64 ------------------ | Branch (1815:18): [True: 0, False: 184] ------------------ 1816| 0| { 1817| 0| goto exit_case_06a; 1818| 0| } 1819| 1.08k| else 1820| 1.08k| { 1821| | /* >N(+)= */ 1822| 1.08k| if (at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (1822:21): [True: 155, False: 931] | Branch (1822:45): [True: 121, False: 34] ------------------ 1823| 121| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (1823:22): [True: 21, False: 100] | Branch (1823:60): [True: 18, False: 3] ------------------ 1824| 18| atfMobile_H_Revrs && atfMobile_H_Revrs[iat].charge == 0 && ------------------ | Branch (1824:22): [True: 18, False: 0] | Branch (1824:43): [True: 10, False: 8] ------------------ 1825| 10| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow && ------------------ | Branch (1825:22): [True: 10, False: 0] | Branch (1825:67): [True: 10, False: 0] | Branch (1825:95): [True: 10, False: 0] ------------------ 1826| 10| ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 18| 10|#define INC_ADD_EDGE 64 ------------------ | Branch (1826:22): [True: 0, False: 10] ------------------ 1827| 0| { 1828| 0| goto exit_case_06a; 1829| 0| } 1830| 1.08k| } 1831| 1.08k| } 1832| 156| if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 156|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 156] | | ------------------ ------------------ | Branch (1832:13): [True: 10, False: 146] ------------------ 1833| 10| { 1834| | /* detected; attempt to fix */ 1835| 10| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1836| 10| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1837| 10| delta = 1; 1838| 20| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1838:25): [True: 14, False: 6] | Branch (1838:52): [True: 10, False: 4] ------------------ 1839| 10| { 1840| 10| e = CurrEdges.pnEdges[i]; 1841| 10| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 1842| 10| if (!pe->flow) ------------------ | Branch (1842:21): [True: 0, False: 10] ------------------ 1843| 0| continue; 1844| 10| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1845| 10| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1846| | 1847| 10| pe->flow -= delta; /* add (+) to -NHm */ 1848| 10| pv1->st_edge.flow -= delta; 1849| 10| pv2->st_edge.flow -= delta; 1850| 10| pBNS->tot_st_flow -= 2 * delta; 1851| | 1852| 10| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1853| 10| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1854| | 1855| 10| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1855:21): [True: 10, False: 0] | Branch (1855:36): [True: 1, False: 9] | Branch (1855:54): [True: 1, False: 0] ------------------ 1856| 10| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1856:36): [True: 9, False: 0] | Branch (1856:54): [True: 9, False: 0] | Branch (1856:77): [True: 10, False: 0] ------------------ 1857| 10| { 1858| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 1859| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1860| 10| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1861| 10| if (ret > 0) ------------------ | Branch (1861:25): [True: 10, False: 0] ------------------ 1862| 10| { 1863| 10| nNumRunBNS++; 1864| 10| cur_success++; /* 06a */ 1865| 10| } 1866| 10| } 1867| 0| else 1868| 0| { 1869| 0| pe->flow += delta; 1870| 0| pv1->st_edge.flow += delta; 1871| 0| pv2->st_edge.flow += delta; 1872| 0| pBNS->tot_st_flow += 2 * delta; 1873| 0| } 1874| 10| INCHI_HEAPCHK 1875| 10| } 1876| 10| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1877| 10| } 1878| 156| exit_case_06a: 1879| 156| CurrEdges.num_edges = 0; /* clear current edge list */ 1880| 156| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 156|#define EDGE_LIST_FREE (-2) ------------------ 1881| 156| if (cur_success) ------------------ | Branch (1881:13): [True: 10, False: 146] ------------------ 1882| 10| { 1883| 10| tot_succes += cur_success; 1884| | /* recalculate InChI from the structure */ 1885| 10| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1885:17): [True: 1, False: 9] ------------------ 1886| 10| ppt_group_info, ppat_norm, ppat_prep ) )) 1887| 1| { 1888| 1| goto exit_function; 1889| 1| } 1890| 9| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1890:17): [True: 0, False: 9] ------------------ 1891| 0| { 1892| 0| goto exit_function; 1893| 0| } 1894| 9| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1894:17): [True: 0, False: 9] | Branch (1894:45): [True: 0, False: 0] ------------------ 1895| 0| { 1896| 0| goto exit_function; /* no fixed-H found */ 1897| 0| } 1898| 9| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1898:17): [True: 0, False: 9] ------------------ 1899| 0| { 1900| 0| goto exit_function; 1901| 0| } 1902| 9| if (!pc2i->bHasDifference) ------------------ | Branch (1902:17): [True: 0, False: 9] ------------------ 1903| 0| { 1904| 0| goto exit_function; /* nothing to do */ 1905| 0| } 1906| 9| } 1907| 156| } 1908| 1.13k| if (( (pc2i->nNumTgInChI > pc2i->nNumTgRevrs && pc2i->nNumTgRevrs == 1) || ------------------ | Branch (1908:12): [True: 533, False: 600] | Branch (1908:53): [True: 26, False: 507] ------------------ 1909| 1.10k| pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs ) && ------------------ | Branch (1909:11): [True: 233, False: 874] ------------------ 1910| 259| ( pStruct->nNumRemovedProtonsMobHInChI == pStruct->One_ti.tni.nNumRemovedProtons || ------------------ | Branch (1910:13): [True: 148, False: 111] ------------------ 1911| 111| pStruct->nNumRemovedProtonsMobHInChI > pStruct->One_ti.tni.nNumRemovedProtons ) && ------------------ | Branch (1911:13): [True: 76, False: 35] ------------------ 1912| 224| pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */ ------------------ | | 575| 224|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */ ------------------ | | 575| 224|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1912:10): [True: 224, False: 0] | Branch (1912:30): [True: 224, False: 0] | Branch (1912:51): [True: 224, False: 0] | Branch (1912:88): [True: 224, False: 0] ------------------ 1913| 224| { 1914| | /*----------------------------------------------------------*/ 1915| | /* case 06b: restored: X(+)=-AB-NH orig.: X-=AB=NH(+) */ 1916| | /* FixH: 0 1 1 0 1 */ 1917| | /* MobH: 0 0 t 0 0 */ 1918| | /* single t-group multiple t-groups */ 1919| | /* or no t-groupd */ 1920| | /* N = N, O, S, Se; atoms N are not tautomeric */ 1921| | /* X = O, S, Se, Te, F, Cl, Br, I; atom X is not tautomeric*/ 1922| | /* Solution: move (+) from X to NH */ 1923| | /*----------------------------------------------------------*/ 1924| 224| int iat; 1925| 224| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1926| | /* 1927| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1928| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1929| | */ 1930| 224| inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 575| 224|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1930:39): [True: 224, False: 0] ------------------ 1931| 224| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ? ------------------ | | 575| 224|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1931:13): [True: 224, False: 0] ------------------ 1932| 224| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL; ------------------ | | 575| 224|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1933| 224| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (1933:32): [True: 224, False: 0] | Branch (1933:45): [True: 224, False: 0] ------------------ 1934| 224| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (1934:13): [True: 0, False: 0] | Branch (1934:26): [True: 0, False: 0] ------------------ 1935| 224| EDGE_LIST CurChargeEdges; 1936| 224| cur_success = 0; 1937| 224| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 224|#define EDGE_LIST_CLEAR (-1) ------------------ 1938| 224| CurrEdges.num_edges = 0; 1939| 1.90k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1939:21): [True: 1.67k, False: 224] ------------------ 1940| 1.67k| { 1941| 1.67k| iat = nCanon2AtnoRevrs[i]; 1942| 1.67k| if (pStruct->endpoint[i]) ------------------ | Branch (1942:17): [True: 190, False: 1.48k] ------------------ 1943| 190| { 1944| 190| continue; 1945| 190| } 1946| | /* -NH-, -OH */ 1947| 1.48k| if (pStruct->fixed_H[i] && nMobHInChI && !nMobHInChI[i] && ------------------ | Branch (1947:17): [True: 306, False: 1.18k] | Branch (1947:40): [True: 306, False: 0] | Branch (1947:54): [True: 287, False: 19] ------------------ 1948| 287| at2[iat].charge == 0 && at2[iat].radical == 0 && ------------------ | Branch (1948:18): [True: 211, False: 76] | Branch (1948:42): [True: 205, False: 6] ------------------ 1949| 205| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (1949:18): [True: 175, False: 30] | Branch (1949:63): [True: 175, False: 0] | Branch (1949:91): [True: 175, False: 0] ------------------ 1950| 175| ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) )) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 18| 175|#define INC_ADD_EDGE 64 ------------------ | Branch (1950:18): [True: 0, False: 175] ------------------ 1951| 0| { 1952| 0| goto exit_case_06b; 1953| 0| } 1954| 1.48k| else 1955| 1.48k| { 1956| | /* X(+)= */ 1957| 1.48k| if (at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (1957:21): [True: 176, False: 1.31k] | Branch (1957:45): [True: 138, False: 38] ------------------ 1958| 138| ( pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cPeriodicRowNumber == 7 ) && ------------------ | Branch (1958:23): [True: 60, False: 78] | Branch (1958:61): [True: 0, False: 78] ------------------ 1959| 60| atfMobile_H_Revrs && atfMobile_H_Revrs[iat].charge == 1 && ------------------ | Branch (1959:22): [True: 60, False: 0] | Branch (1959:43): [True: 58, False: 2] ------------------ 1960| 58| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow && ------------------ | Branch (1960:22): [True: 58, False: 0] | Branch (1960:67): [True: 50, False: 8] | Branch (1960:95): [True: 49, False: 1] ------------------ 1961| 49| ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 18| 49|#define INC_ADD_EDGE 64 ------------------ | Branch (1961:22): [True: 0, False: 49] ------------------ 1962| 0| { 1963| 0| goto exit_case_06b; 1964| 0| } 1965| 1.48k| } 1966| 1.48k| } 1967| 224| if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 224|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 2, False: 222] | | ------------------ ------------------ | Branch (1967:13): [True: 47, False: 177] ------------------ 1968| 47| { 1969| | /* detected; attempt to fix */ 1970| 47| int bSFlowerEdgesMayBeForbidden = ( SFlowerEdges.num_edges > 0 ); 1971| 47| int bSFlowerEdgesIsForbidden; 1972| 47| for (bSFlowerEdgesIsForbidden = bSFlowerEdgesMayBeForbidden; 1973| 114| 0 <= bSFlowerEdgesIsForbidden; bSFlowerEdgesIsForbidden--) ------------------ | Branch (1973:19): [True: 67, False: 47] ------------------ 1974| 67| { 1975| 67| if (bSFlowerEdgesIsForbidden) ------------------ | Branch (1975:21): [True: 20, False: 47] ------------------ 1976| 20| { 1977| | /* on the 1st pass disallow -S(+)= => =S=, allow only -S(+)= => -S- */ 1978| 20| SetForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 1979| 20| } 1980| 67| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1981| 67| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1982| 67| delta = 1; 1983| 132| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1983:29): [True: 95, False: 37] | Branch (1983:56): [True: 65, False: 30] ------------------ 1984| 65| { 1985| 65| e = CurrEdges.pnEdges[i]; 1986| 65| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 1987| 65| if (!pe->flow) ------------------ | Branch (1987:25): [True: 0, False: 65] ------------------ 1988| 0| continue; 1989| 65| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1990| 65| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1991| | 1992| 65| pe->flow -= delta; /* add (+) to -NHm */ 1993| 65| pv1->st_edge.flow -= delta; 1994| 65| pv2->st_edge.flow -= delta; 1995| 65| pBNS->tot_st_flow -= 2 * delta; 1996| | 1997| 65| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1998| 65| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1999| | 2000| 65| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2000:25): [True: 43, False: 22] | Branch (2000:40): [True: 5, False: 38] | Branch (2000:58): [True: 4, False: 1] ------------------ 2001| 42| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2001:40): [True: 38, False: 1] | Branch (2001:58): [True: 38, False: 0] | Branch (2001:81): [True: 42, False: 0] ------------------ 2002| 42| { 2003| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 2004| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 2005| 42| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2006| 42| if (ret > 0) ------------------ | Branch (2006:29): [True: 42, False: 0] ------------------ 2007| 42| { 2008| 42| nNumRunBNS++; 2009| 42| cur_success++; /* 06b */ 2010| 42| } 2011| 42| } 2012| 23| else 2013| 23| { 2014| 23| pe->flow += delta; 2015| 23| pv1->st_edge.flow += delta; 2016| 23| pv2->st_edge.flow += delta; 2017| 23| pBNS->tot_st_flow += 2 * delta; 2018| 23| } 2019| 65| INCHI_HEAPCHK 2020| 65| } 2021| 67| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2022| 67| RemoveForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 2023| 67| } 2024| 47| } 2025| 224| exit_case_06b: 2026| 224| CurrEdges.num_edges = 0; /* clear current edge list */ 2027| 224| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 224|#define EDGE_LIST_FREE (-2) ------------------ 2028| 224| if (cur_success) ------------------ | Branch (2028:13): [True: 42, False: 182] ------------------ 2029| 42| { 2030| 42| tot_succes += cur_success; 2031| | /* recalculate InChI from the structure */ 2032| 42| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2032:17): [True: 1, False: 41] ------------------ 2033| 42| ppt_group_info, ppat_norm, ppat_prep ) )) 2034| 1| { 2035| 1| goto exit_function; 2036| 1| } 2037| 41| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2037:17): [True: 0, False: 41] ------------------ 2038| 0| { 2039| 0| goto exit_function; 2040| 0| } 2041| 41| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2041:17): [True: 0, False: 41] | Branch (2041:45): [True: 0, False: 0] ------------------ 2042| 0| { 2043| 0| goto exit_function; /* no fixed-H found */ 2044| 0| } 2045| 41| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2045:17): [True: 0, False: 41] ------------------ 2046| 0| { 2047| 0| goto exit_function; 2048| 0| } 2049| 41| if (!pc2i->bHasDifference) ------------------ | Branch (2049:17): [True: 0, False: 41] ------------------ 2050| 0| { 2051| 0| goto exit_function; /* nothing to do */ 2052| 0| } 2053| 41| } 2054| 224| } 2055| | 2056| 1.13k| if (pc2i->nNumTgInChI > 1 && ------------------ | Branch (2056:9): [True: 47, False: 1.08k] ------------------ 2057| 47| ( pStruct->nNumRemovedProtonsMobHInChI > 0 || pStruct->ti.tni.nNumRemovedProtons > 0 ) && ------------------ | Branch (2057:11): [True: 0, False: 47] | Branch (2057:55): [True: 0, False: 47] ------------------ 2058| 0| pStruct->fixed_H && pStruct->endpoint && ------------------ | Branch (2058:10): [True: 0, False: 0] | Branch (2058:30): [True: 0, False: 0] ------------------ 2059| 0| pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2059:10): [True: 0, False: 0] | Branch (2059:47): [True: 0, False: 0] ------------------ 2060| 0| { 2061| | /*----------------------------------------------------------*/ 2062| | /* case 06e:restored: XHn(+)=-AB-YHm orig.: XHn-=AB=YHm(+) */ 2063| | /* FixH: 1 0 1 1 */ 2064| | /* MobH: 0 1 t t */ 2065| | /* non-taut atoms multiple t-groups */ 2066| | /* */ 2067| | /* 1. orig. t-group has more H on its endpoints counted */ 2068| | /* in atf and has no (+) on endpoint that has H */ 2069| | /* 2. orig. t-group has less H on its endpoints counted */ 2070| | /* in atf and has (+) on endpoint that has H */ 2071| | /* in reconstructed struct and less H in atf */ 2072| | /* Solution: move (+) from (2) to atom in (1) that has H */ 2073| | /* */ 2074| | /* tg1 reconstr: XHn and more H than in orig t-group */ 2075| | /* atf: XHn */ 2076| | /* tg2 reconstr: XHm(+) and less H than in */ 2077| | /* atf: XH(m-1) orig in t-group */ 2078| | /* */ 2079| | /* N = N, O, S, Se; atoms N are not tautomeric */ 2080| | /* X = O, S, Se, Te, F, Cl, Br, I; atom X is not tautomeric*/ 2081| | /* Solution: move (+) from X to NH */ 2082| | /*----------------------------------------------------------*/ 2083| | 2084| 0| int iat, nNumWrongTg, jjoffs, jj, nNum2RemovePlus, nNum2AddPlus, nNum2MovePlus; 2085| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2086| | /* 2087| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 2088| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 2089| | */ 2090| 0| inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2090:39): [True: 0, False: 0] ------------------ 2091| 0| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ? ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2091:13): [True: 0, False: 0] ------------------ 2092| 0| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2093| 0| pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2093:13): [True: 0, False: 0] ------------------ 2094| 0| pStruct->pOne_norm_data[TAUT_YES]->at ? ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2094:13): [True: 0, False: 0] ------------------ 2095| 0| pStruct->pOne_norm_data[TAUT_YES]->at : NULL; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2096| | /* 2097| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 2098| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 2099| | */ 2100| 0| EDGE_LIST CurChargeEdges /* source of (+)*/, EndpList; 2101| 0| BNS_VERTEX *pv1n, *pv2n; 2102| 0| BNS_EDGE *pe1n, *pe2n; 2103| 0| Vertex v1n, v2n; 2104| | 2105| 0| cur_success = 0; 2106| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 2107| 0| AllocEdgeList( &EndpList, EDGE_LIST_CLEAR ); ------------------ | | 242| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 2108| 0| CurrEdges.num_edges = 0; /* receptors of (+) */ 2109| | 2110| 0| if (!atfMobile_H_Revrs) ------------------ | Branch (2110:13): [True: 0, False: 0] ------------------ 2111| 0| { 2112| 0| goto exit_case_06e; 2113| 0| } 2114| 0| nNumWrongTg = FillTgDiffHChgFH(tdhc, MAX_DIFF_FIXH, at2, atfMobile_H_Revrs, ------------------ | | 456| 0|#define MAX_DIFF_FIXH 256 ------------------ 2115| 0| nCanon2AtnoRevrs, pVA, &pStruct->ti, &EndpList); 2116| 0| if (nNumWrongTg < 1) ------------------ | Branch (2116:13): [True: 0, False: 0] ------------------ 2117| 0| { 2118| 0| goto exit_case_06e; /* for now only transfer (+) from one Mobile-H group to another */ 2119| 0| } 2120| 0| nNum2RemovePlus = nNum2AddPlus = 0; /* djb-rwth: removing redundant code */ 2121| 0| for (i = 0; i < nNumWrongTg; i++) ------------------ | Branch (2121:21): [True: 0, False: 0] ------------------ 2122| 0| { 2123| | /* detect t-group that has extra (+) on H */ 2124| 0| if (tdhc[i].nNumHInchi > tdhc[i].nNumHNorml && ------------------ | Branch (2124:17): [True: 0, False: 0] ------------------ 2125| 0| tdhc[i].nNumPRevrs > tdhc[i].nNumPNorml && tdhc[i].n[fNumRPosChgH]) ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2125:17): [True: 0, False: 0] | Branch (2125:60): [True: 0, False: 0] ------------------ 2126| 0| { 2127| | /* count how many (+) to remove */ 2128| | /* store XH(+) atom numbers */ 2129| 0| int nNumNeeded = inchi_min(tdhc[i].nNumHInchi - tdhc[i].nNumHNorml, tdhc[i].n[fNumRPosChgH]); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2130| 0| nNum2RemovePlus += nNumNeeded; 2131| 0| jjoffs = tdhc[i].i[fNumRPosChgH]; ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ 2132| 0| for (jj = 0; jj < tdhc[i].n[fNumRPosChgH]; jj++) ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2132:30): [True: 0, False: 0] ------------------ 2133| 0| { 2134| 0| iat = EndpList.pnEdges[jjoffs + jj]; 2135| 0| e = pVA[iat].nCPlusGroupEdge - 1; 2136| 0| if ((ret = AddToEdgeList(&CurChargeEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2136:25): [True: 0, False: 0] ------------------ 2137| 0| { 2138| 0| goto exit_case_06e; 2139| 0| } 2140| 0| } 2141| 0| } 2142| 0| else 2143| 0| { 2144| | /* detect t-group that needs (+) on XH to reduce number of H */ 2145| 0| if (tdhc[i].nNumHInchi < tdhc[i].nNumHNorml && tdhc[i].n[fNumRNeutrlH]) ------------------ | | 27| 0|#define fNumRNeutrlH 4 /* number of neutral endp that have H in at2[] */ ------------------ | Branch (2145:21): [True: 0, False: 0] | Branch (2145:64): [True: 0, False: 0] ------------------ 2146| 0| { 2147| | /* store XH atom numbers */ 2148| 0| int nNumNeeded = inchi_min(tdhc[i].nNumHNorml - tdhc[i].nNumHInchi, tdhc[i].n[fNumRNeutrlH]); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2149| 0| nNum2AddPlus += nNumNeeded; 2150| 0| jjoffs = tdhc[i].i[fNumRNeutrlH]; ------------------ | | 27| 0|#define fNumRNeutrlH 4 /* number of neutral endp that have H in at2[] */ ------------------ 2151| 0| for (jj = 0; jj < tdhc[i].n[fNumRNeutrlH]; jj++) ------------------ | | 27| 0|#define fNumRNeutrlH 4 /* number of neutral endp that have H in at2[] */ ------------------ | Branch (2151:34): [True: 0, False: 0] ------------------ 2152| 0| { 2153| 0| iat = EndpList.pnEdges[jjoffs + jj]; 2154| 0| e = pVA[iat].nCPlusGroupEdge - 1; 2155| 0| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2155:29): [True: 0, False: 0] ------------------ 2156| 0| { 2157| 0| goto exit_case_06e; 2158| 0| } 2159| 0| } 2160| 0| } 2161| 0| } 2162| 0| } 2163| 0| nNum2MovePlus = inchi_min(nNum2RemovePlus, nNum2AddPlus); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2164| 0| if (CurrEdges.num_edges > 0 && CurChargeEdges.num_edges > 0) ------------------ | Branch (2164:13): [True: 0, False: 0] | Branch (2164:40): [True: 0, False: 0] ------------------ 2165| 0| { 2166| 0| for (i = 0; 0 < nNum2MovePlus && i < nNumWrongTg; i++) ------------------ | Branch (2166:25): [True: 0, False: 0] | Branch (2166:46): [True: 0, False: 0] ------------------ 2167| 0| { 2168| | /* detect t-group that has extra (+) on H */ 2169| 0| if (tdhc[i].nNumHInchi > tdhc[i].nNumHNorml && ------------------ | Branch (2169:21): [True: 0, False: 0] ------------------ 2170| 0| tdhc[i].nNumPRevrs > tdhc[i].nNumPNorml && tdhc[i].n[fNumRPosChgH]) ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2170:21): [True: 0, False: 0] | Branch (2170:64): [True: 0, False: 0] ------------------ 2171| 0| { 2172| 0| int nNum2Remove = tdhc[i].nNumHInchi - tdhc[i].nNumHNorml; 2173| 0| if (nNum2Remove < tdhc[i].n[fNumRPosChgH]) ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2173:25): [True: 0, False: 0] ------------------ 2174| 0| { 2175| 0| nNum2Remove = tdhc[i].n[fNumRPosChgH]; ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ 2176| 0| } 2177| | /* store XH(+) atom numbers */ 2178| 0| jjoffs = tdhc[i].i[fNumRPosChgH]; ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ 2179| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2180| 0| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 2181| 0| for (jj = 0; 0 < nNum2MovePlus && 0 < nNum2Remove && jj < tdhc[i].n[fNumRPosChgH]; jj++) ------------------ | | 23| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2181:34): [True: 0, False: 0] | Branch (2181:55): [True: 0, False: 0] | Branch (2181:74): [True: 0, False: 0] ------------------ 2182| 0| { 2183| 0| iat = EndpList.pnEdges[jjoffs + jj]; 2184| 0| e = pVA[iat].nCPlusGroupEdge - 1; 2185| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 2186| 0| if (pe->flow) ------------------ | Branch (2186:29): [True: 0, False: 0] ------------------ 2187| 0| continue; 2188| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 2189| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 2190| | 2191| 0| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (2191:58): [True: 0, False: 0] ------------------ 2192| 0| { 2193| 0| pe1n = pBNS->edge + pv1->iedge[j]; 2194| 0| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (2194:33): [True: 0, False: 0] | Branch (2194:47): [True: 0, False: 0] ------------------ 2195| 0| { 2196| 0| pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1); 2197| 0| break; 2198| 0| } 2199| 0| } 2200| 0| if (j < 0) ------------------ | Branch (2200:29): [True: 0, False: 0] ------------------ 2201| 0| { 2202| 0| continue; /* not found */ 2203| 0| } 2204| 0| for (j = pv2->num_adj_edges - 2; 0 <= j; j--) ------------------ | Branch (2204:58): [True: 0, False: 0] ------------------ 2205| 0| { 2206| 0| pe2n = pBNS->edge + pv2->iedge[j]; 2207| 0| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (2207:33): [True: 0, False: 0] | Branch (2207:47): [True: 0, False: 0] ------------------ 2208| 0| { 2209| 0| pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2); 2210| 0| break; 2211| 0| } 2212| 0| } 2213| 0| if (j < 0) ------------------ | Branch (2213:29): [True: 0, False: 0] ------------------ 2214| 0| { 2215| 0| continue; /* not found */ 2216| 0| } 2217| 0| delta = 1; 2218| 0| pe->flow += delta; 2219| 0| pe1n->flow -= delta; 2220| 0| pe2n->flow -= delta; 2221| 0| pv1n->st_edge.flow -= delta; 2222| 0| pv2n->st_edge.flow -= delta; 2223| 0| pBNS->tot_st_flow -= 2 * delta; 2224| | 2225| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2226| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 2227| | 2228| 0| if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) || ------------------ | Branch (2228:29): [True: 0, False: 0] | Branch (2228:43): [True: 0, False: 0] | Branch (2228:62): [True: 0, False: 0] ------------------ 2229| 0| (vPathEnd == v2n && vPathStart == v1n)) && ------------------ | Branch (2229:30): [True: 0, False: 0] | Branch (2229:49): [True: 0, False: 0] ------------------ 2230| 0| (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2230:30): [True: 0, False: 0] | Branch (2230:51): [True: 0, False: 0] ------------------ 2231| 0| { 2232| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2233| 0| if (ret > 0) ------------------ | Branch (2233:33): [True: 0, False: 0] ------------------ 2234| 0| { 2235| 0| nNumRunBNS++; 2236| 0| nNum2Remove--; 2237| 0| nNum2MovePlus--; 2238| 0| cur_success++; /* 06e */ 2239| 0| } 2240| 0| } 2241| 0| else 2242| 0| { 2243| 0| pe->flow -= delta; 2244| 0| pe1n->flow += delta; 2245| 0| pe2n->flow += delta; 2246| 0| pv1n->st_edge.flow += delta; 2247| 0| pv2n->st_edge.flow += delta; 2248| 0| pBNS->tot_st_flow += 2 * delta; 2249| 0| } 2250| 0| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2250:29): [True: 0, False: 0] ------------------ 2251| 0| { 2252| 0| goto exit_case_06e; 2253| 0| } 2254| 0| } 2255| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2256| 0| } 2257| 0| } 2258| 0| } 2259| 0| exit_case_06e: 2260| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 2261| 0| AllocEdgeList(&CurChargeEdges, EDGE_LIST_FREE); ------------------ | | 243| 0|#define EDGE_LIST_FREE (-2) ------------------ 2262| 0| AllocEdgeList(&EndpList, EDGE_LIST_FREE); ------------------ | | 243| 0|#define EDGE_LIST_FREE (-2) ------------------ 2263| 0| if (cur_success) ------------------ | Branch (2263:13): [True: 0, False: 0] ------------------ 2264| 0| { 2265| 0| tot_succes += cur_success; 2266| | /* recalculate InChI from the structure */ 2267| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2267:17): [True: 0, False: 0] ------------------ 2268| 0| ppt_group_info, ppat_norm, ppat_prep))) 2269| 0| { 2270| 0| goto exit_function; 2271| 0| } 2272| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2272:17): [True: 0, False: 0] ------------------ 2273| 0| { 2274| 0| goto exit_function; 2275| 0| } 2276| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2276:17): [True: 0, False: 0] | Branch (2276:45): [True: 0, False: 0] ------------------ 2277| 0| { 2278| 0| goto exit_function; /* no fixed-H found */ 2279| 0| } 2280| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2280:17): [True: 0, False: 0] ------------------ 2281| 0| { 2282| 0| goto exit_function; 2283| 0| } 2284| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2284:17): [True: 0, False: 0] ------------------ 2285| 0| { 2286| 0| goto exit_function; /* nothing to do */ 2287| 0| } 2288| 0| } 2289| 0| } 2290| | 2291| 1.13k| if (pc2i->len_c2at >= 1) ------------------ | Branch (2291:9): [True: 1.12k, False: 3] ------------------ 2292| 1.12k| { 2293| | /*--------------------------------------------------------------*/ 2294| | /* case 07: restored: O(-)-AB=O original: O=AB-O(-) */ 2295| | /* FixH: 0 0 0 -1 */ 2296| | /* MobH: 0 0 0 1 */ 2297| | /* taut (non-taut) (taut) non-taut */ 2298| | /* taut (taut) (non-taut) non-taut */ 2299| | /* O = O, S, Se, Te */ 2300| | /* Solution: move (-) from O(-)-AB to AB=O */ 2301| | /*--------------------------------------------------------------*/ 2302| 1.12k| int num_SB_O_Minus = 0, num_DB_O_Neutr = 0, iat; 2303| 1.12k| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2304| 1.12k| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (2304:41): [True: 600, False: 529] ------------------ 2305| 1.12k| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (2305:41): [True: 600, False: 0] ------------------ 2306| 1.12k| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (2306:32): [True: 1.12k, False: 0] | Branch (2306:45): [True: 1.12k, False: 0] ------------------ 2307| 1.12k| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (2307:13): [True: 0, False: 0] | Branch (2307:26): [True: 0, False: 0] ------------------ 2308| 1.12k| cur_success = 0; 2309| | 2310| 4.65k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2310:21): [True: 3.52k, False: 1.12k] ------------------ 2311| 3.52k| { 2312| 3.52k| iat = pc2i->c2at[i].atomNumber; 2313| 3.52k| if ( /* orig. InChI info: -O(-), non-taut */ 2314| 3.52k| num_DB_O_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 7.04k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2314:17): [True: 3.52k, False: 0] ------------------ 2315| 3.52k| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (2315:17): [True: 1.78k, False: 1.73k] ------------------ 2316| 1.78k| !pc2i->c2at[i].endptInChI && ------------------ | Branch (2316:17): [True: 1.02k, False: 766] ------------------ 2317| 1.02k| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (2317:17): [True: 571, False: 450] | Branch (2317:61): [True: 571, False: 0] ------------------ 2318| 571| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (2318:17): [True: 50, False: 521] | Branch (2318:51): [True: 25, False: 25] ------------------ 2319| | /* reversed structure info: */ 2320| 25| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (2320:17): [True: 25, False: 0] | Branch (2320:50): [True: 25, False: 0] ------------------ 2321| 25| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (2321:17): [True: 10, False: 15] | Branch (2321:54): [True: 10, False: 0] ------------------ 2322| 10| at2[iat].valence < at2[iat].chem_bonds_valence) ------------------ | Branch (2322:17): [True: 8, False: 2] ------------------ 2323| 8| { 2324| 8| iat_DB_O_Neutr[num_DB_O_Neutr++] = iat; 2325| 8| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 8|#define INC_ADD_EDGE 64 ------------------ | Branch (2325:21): [True: 0, False: 8] ------------------ 2326| 0| { 2327| 0| goto exit_function; 2328| 0| } 2329| 8| } 2330| 3.52k| } 2331| 9.47k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (2331:21): [True: 8.34k, False: 1.12k] ------------------ 2332| 8.34k| { 2333| | /* i = canonical number - 1 */ 2334| 8.34k| iat = nCanon2AtnoRevrs[i]; 2335| 8.34k| if ( /* in restored atom: charge=-1, no H, has single bond, O, S, Se, Te */ 2336| 8.34k| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 16.6k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2336:17): [True: 8.34k, False: 0] ------------------ 2337| 8.34k| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (2337:17): [True: 1.40k, False: 6.93k] | Branch (2337:42): [True: 1.19k, False: 216] ------------------ 2338| 1.19k| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2338:17): [True: 947, False: 243] | Branch (2338:68): [True: 913, False: 34] ------------------ 2339| 913| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (2339:17): [True: 764, False: 149] ------------------ 2340| 764| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && ------------------ | Branch (2340:17): [True: 471, False: 293] | Branch (2340:38): [True: 347, False: 124] ------------------ 2341| | /* in orig.InChI: not an endpoint, has no H */ 2342| | /*pStruct->endpoint[i] && -- modificatuion#1 */ 2343| 347| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (2343:19): [True: 347, False: 0] | Branch (2343:39): [True: 7, False: 340] ------------------ 2344| 340| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (2344:19): [True: 340, False: 0] | Branch (2344:33): [True: 1, False: 339] ------------------ 2345| | /* has (-) edge */ 2346| 339| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2346:17): [True: 339, False: 0] | Branch (2346:61): [True: 339, False: 0] ------------------ 2347| 339| { 2348| 339| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 2349| 339| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 339|#define INC_ADD_EDGE 64 ------------------ | Branch (2349:21): [True: 0, False: 339] ------------------ 2350| 0| { 2351| 0| goto exit_function; 2352| 0| } 2353| 339| } 2354| 8.34k| } 2355| 1.12k| if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O_Neutr))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.12k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 7, False: 1.12k] | | ------------------ ------------------ | Branch (2355:13): [True: 1, False: 1.12k] ------------------ 2356| 1| { 2357| | /* detected; attempt to fix */ 2358| 1| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2359| 1| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 2360| 1| delta = 1; 2361| 2| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (2361:25): [True: 1, False: 1] | Branch (2361:47): [True: 1, False: 0] ------------------ 2362| 1| { 2363| 1| iat = iat_SB_O_Minus[i]; 2364| 1| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 2365| 1| if (!pe->flow) ------------------ | Branch (2365:21): [True: 0, False: 1] ------------------ 2366| 0| continue; 2367| 1| pv1 = pBNS->vert + (v1 = pe->neighbor1); 2368| 1| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 2369| | 2370| 1| pe->forbidden |= forbidden_edge_mask; 2371| 1| pe->flow -= delta; 2372| 1| pv1->st_edge.flow -= delta; 2373| 1| pv2->st_edge.flow -= delta; 2374| 1| pBNS->tot_st_flow -= 2 * delta; 2375| | 2376| 1| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2377| 1| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 2378| | 2379| 1| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2379:21): [True: 1, False: 0] | Branch (2379:35): [True: 0, False: 1] | Branch (2379:53): [True: 0, False: 0] ------------------ 2380| 1| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2380:22): [True: 1, False: 0] | Branch (2380:40): [True: 1, False: 0] | Branch (2380:62): [True: 1, False: 0] ------------------ 2381| 1| { 2382| | /* Moved (-) charge to AB=O => nDeltaCharge == 1 */ 2383| | /* Flow change on pe (-)charge edge (O(-)-AB) is not known to RunBnsTestOnce()) */ 2384| 1| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2385| 1| if (ret > 0) ------------------ | Branch (2385:25): [True: 1, False: 0] ------------------ 2386| 1| { 2387| 1| nNumRunBNS++; 2388| 1| cur_success++; /* 07 */ 2389| 1| } 2390| 1| } 2391| 0| else 2392| 0| { 2393| 0| pe->forbidden &= forbidden_edge_mask_inv; 2394| 0| pe->flow += delta; 2395| 0| pv1->st_edge.flow += delta; 2396| 0| pv2->st_edge.flow += delta; 2397| 0| pBNS->tot_st_flow += 2 * delta; 2398| 0| } 2399| 1| INCHI_HEAPCHK 2400| 1| } 2401| 1| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2402| 1| } 2403| 1.12k| CurrEdges.num_edges = 0; /* clear current edge list */ 2404| 1.12k| if (cur_success) ------------------ | Branch (2404:13): [True: 1, False: 1.12k] ------------------ 2405| 1| { 2406| 1| tot_succes += cur_success; 2407| | /* recalculate InChI from the structure */ 2408| 1| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2408:17): [True: 0, False: 1] ------------------ 2409| 1| ppt_group_info, ppat_norm, ppat_prep))) 2410| 0| { 2411| 0| goto exit_function; 2412| 0| } 2413| 1| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2413:17): [True: 0, False: 1] ------------------ 2414| 0| { 2415| 0| goto exit_function; 2416| 0| } 2417| 1| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2417:17): [True: 0, False: 1] | Branch (2417:45): [True: 0, False: 0] ------------------ 2418| 0| { 2419| 0| goto exit_function; /* no fixed-H found */ 2420| 0| } 2421| 1| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2421:17): [True: 0, False: 1] ------------------ 2422| 0| { 2423| 0| goto exit_function; 2424| 0| } 2425| 1| if (!pc2i->bHasDifference) ------------------ | Branch (2425:17): [True: 0, False: 1] ------------------ 2426| 0| { 2427| 0| goto exit_function; /* nothing to do */ 2428| 0| } 2429| 1| } 2430| 1.12k| } 2431| | 2432| 1.13k| if (pc2i->len_c2at >= 1) ------------------ | Branch (2432:9): [True: 1.12k, False: 3] ------------------ 2433| 1.12k| { 2434| | /*--------------------------------------------------------------*/ 2435| | /* case 07a: restored: O(-)-N(V)B=O original: O=N(V)B-O(-) */ 2436| | /* FixH: 0 0 0 -1 */ 2437| | /* MobH: 0 0 0 1 */ 2438| | /* non-taut (non-taut) non-taut non-taut */ 2439| | /* non-taut (taut) non-taut non-taut */ 2440| | /* O = O, S, Se, Te */ 2441| | /* Solution: move (-) from O(-)-AB to AB=O */ 2442| | /*--------------------------------------------------------------*/ 2443| 1.12k| int num_SB_O_Minus = 0, num_DB_O_Neutr = 0, iat, iN; 2444| 1.12k| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2445| 1.12k| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (2445:32): [True: 1.12k, False: 0] | Branch (2445:45): [True: 1.12k, False: 0] ------------------ 2446| 1.12k| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (2446:13): [True: 0, False: 0] | Branch (2446:26): [True: 0, False: 0] ------------------ 2447| 1.12k| cur_success = 0; 2448| | 2449| 4.65k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2449:21): [True: 3.52k, False: 1.12k] ------------------ 2450| 3.52k| { 2451| 3.52k| iat = pc2i->c2at[i].atomNumber; 2452| 3.52k| if ( /* orig. InChI info: -O(-), non-taut */ 2453| 3.52k| num_DB_O_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 7.04k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2453:17): [True: 3.52k, False: 0] ------------------ 2454| 3.52k| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (2454:17): [True: 1.78k, False: 1.73k] ------------------ 2455| 1.78k| !pc2i->c2at[i].endptInChI && ------------------ | Branch (2455:17): [True: 1.02k, False: 766] ------------------ 2456| 1.02k| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (2456:17): [True: 571, False: 450] | Branch (2456:61): [True: 571, False: 0] ------------------ 2457| 571| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (2457:17): [True: 50, False: 521] | Branch (2457:51): [True: 25, False: 25] ------------------ 2458| | /* reversed structure info: */ 2459| 25| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (2459:17): [True: 25, False: 0] | Branch (2459:50): [True: 25, False: 0] ------------------ 2460| 25| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (2460:17): [True: 9, False: 16] | Branch (2460:54): [True: 9, False: 0] ------------------ 2461| 9| at2[iat].valence < at2[iat].chem_bonds_valence) ------------------ | Branch (2461:17): [True: 7, False: 2] ------------------ 2462| 7| { 2463| 7| iat_DB_O_Neutr[num_DB_O_Neutr++] = iat; 2464| 7| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 7|#define INC_ADD_EDGE 64 ------------------ | Branch (2464:21): [True: 0, False: 7] ------------------ 2465| 0| { 2466| 0| goto exit_function; 2467| 0| } 2468| 7| } 2469| 3.52k| } 2470| 9.47k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (2470:21): [True: 8.34k, False: 1.12k] ------------------ 2471| 8.34k| { 2472| | /* i = canonical number - 1 */ 2473| 8.34k| iat = nCanon2AtnoRevrs[i]; 2474| 8.34k| if ( /* in restored atom: charge=-1, no H, has single bond, O, S, Se, Te */ 2475| 8.34k| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 16.6k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2475:17): [True: 8.34k, False: 0] ------------------ 2476| 8.34k| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (2476:17): [True: 1.40k, False: 6.93k] | Branch (2476:42): [True: 1.19k, False: 216] ------------------ 2477| 1.19k| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2477:17): [True: 947, False: 243] | Branch (2477:68): [True: 913, False: 34] ------------------ 2478| 913| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (2478:17): [True: 764, False: 149] ------------------ 2479| | /*at_Mobile_H_Revrs && !at_Mobile_H_Revrs[iat].endpoint &&*/ 2480| | /* in orig.InChI: not an endpoint, has no H */ 2481| 764| !pStruct->endpoint[i] && ------------------ | Branch (2481:17): [True: 448, False: 316] ------------------ 2482| 448| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (2482:19): [True: 448, False: 0] | Branch (2482:39): [True: 21, False: 427] ------------------ 2483| 427| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (2483:19): [True: 427, False: 0] | Branch (2483:33): [True: 1, False: 426] ------------------ 2484| | /* has N(V) neighbor */ 2485| 426| 1 == at2[iat].valence && at2[iN = at2[iat].neighbor[0]].chem_bonds_valence == 5 && ------------------ | Branch (2485:17): [True: 426, False: 0] | Branch (2485:42): [True: 96, False: 330] ------------------ 2486| 96| !at2[iN].charge && pVA[iN].cNumValenceElectrons == 5 && ------------------ | Branch (2486:17): [True: 70, False: 26] | Branch (2486:36): [True: 62, False: 8] ------------------ 2487| | /* has (-) edge */ 2488| 62| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2488:17): [True: 62, False: 0] | Branch (2488:61): [True: 62, False: 0] ------------------ 2489| 62| { 2490| 62| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 2491| 62| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 62|#define INC_ADD_EDGE 64 ------------------ | Branch (2491:21): [True: 0, False: 62] ------------------ 2492| 0| { 2493| 0| goto exit_function; 2494| 0| } 2495| 62| } 2496| 8.34k| } 2497| 1.12k| if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O_Neutr))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.12k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 7, False: 1.12k] | | ------------------ ------------------ | Branch (2497:13): [True: 0, False: 1.12k] ------------------ 2498| 0| { 2499| | /* detected; attempt to fix */ 2500| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2501| 0| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 2502| 0| delta = 1; 2503| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (2503:25): [True: 0, False: 0] | Branch (2503:47): [True: 0, False: 0] ------------------ 2504| 0| { 2505| 0| iat = iat_SB_O_Minus[i]; 2506| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 2507| 0| if (!pe->flow) ------------------ | Branch (2507:21): [True: 0, False: 0] ------------------ 2508| 0| continue; 2509| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 2510| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 2511| | 2512| 0| pe->forbidden |= forbidden_edge_mask; 2513| 0| pe->flow -= delta; 2514| 0| pv1->st_edge.flow -= delta; 2515| 0| pv2->st_edge.flow -= delta; 2516| 0| pBNS->tot_st_flow -= 2 * delta; 2517| | 2518| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2519| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 2520| | 2521| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2521:21): [True: 0, False: 0] | Branch (2521:35): [True: 0, False: 0] | Branch (2521:53): [True: 0, False: 0] ------------------ 2522| 0| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2522:22): [True: 0, False: 0] | Branch (2522:40): [True: 0, False: 0] | Branch (2522:62): [True: 0, False: 0] ------------------ 2523| 0| { 2524| | /* Moved (-) charge to AB=O => nDeltaCharge == 1 */ 2525| | /* Flow change on pe (-)charge edge (O(-)-AB) is not known to RunBnsTestOnce()) */ 2526| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2527| 0| if (ret > 0) ------------------ | Branch (2527:25): [True: 0, False: 0] ------------------ 2528| 0| { 2529| 0| nNumRunBNS++; 2530| 0| cur_success++; /* 07 */ 2531| 0| } 2532| 0| } 2533| 0| else 2534| 0| { 2535| 0| pe->forbidden &= forbidden_edge_mask_inv; 2536| 0| pe->flow += delta; 2537| 0| pv1->st_edge.flow += delta; 2538| 0| pv2->st_edge.flow += delta; 2539| 0| pBNS->tot_st_flow += 2 * delta; 2540| 0| } 2541| 0| INCHI_HEAPCHK 2542| 0| } 2543| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2544| 0| } 2545| 1.12k| CurrEdges.num_edges = 0; /* clear current edge list */ 2546| 1.12k| if (cur_success) ------------------ | Branch (2546:13): [True: 0, False: 1.12k] ------------------ 2547| 0| { 2548| 0| tot_succes += cur_success; 2549| | /* recalculate InChI from the structure */ 2550| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2550:17): [True: 0, False: 0] ------------------ 2551| 0| ppt_group_info, ppat_norm, ppat_prep))) 2552| 0| { 2553| 0| goto exit_function; 2554| 0| } 2555| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2555:17): [True: 0, False: 0] ------------------ 2556| 0| { 2557| 0| goto exit_function; 2558| 0| } 2559| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2559:17): [True: 0, False: 0] | Branch (2559:45): [True: 0, False: 0] ------------------ 2560| 0| { 2561| 0| goto exit_function; /* no fixed-H found */ 2562| 0| } 2563| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2563:17): [True: 0, False: 0] ------------------ 2564| 0| { 2565| 0| goto exit_function; 2566| 0| } 2567| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2567:17): [True: 0, False: 0] ------------------ 2568| 0| { 2569| 0| goto exit_function; /* nothing to do */ 2570| 0| } 2571| 0| } 2572| 1.12k| } 2573| | 2574| 1.13k| if ( /*(pc2i->len_c2at >= 1 || pc2i->nNumRemHRevrs) &&*/ pc2i->nNumTgInChI == 1 && /* ADP in InChI */ ------------------ | Branch (2574:62): [True: 737, False: 395] ------------------ 2575| 737| (pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1)) ------------------ | Branch (2575:10): [True: 624, False: 113] | Branch (2575:55): [True: 12, False: 101] ------------------ 2576| 636| { 2577| | /*----------------------------------------------------------------*/ 2578| | /* case 08: restored: O(-)-AB=N- OH- orig. O=AB-N(-)- OH- */ 2579| | /* FixH: 1 0 0 0 0 1 */ 2580| | /* MobH: 0 0 1 0 0 0 */ 2581| | /* may be taut or not non-taut taut taut taut */ 2582| | /* ADP: one t-group or more endpoints */ 2583| | /* O(-) = S, Se, Te; N = N; */ 2584| | /* Solution: move (-) from O(-) to =N-; avoid stereogenic DB on N */ 2585| | /*----------------------------------------------------------------*/ 2586| 636| int num_DB_N_Neutr = 0, num_SB_O_Minus = 0, iat; 2587| | 2588| 636| AT_NUMB* nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2589| 636| S_CHAR* nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (2589:30): [True: 636, False: 0] | Branch (2589:43): [True: 636, False: 0] ------------------ 2590| 636| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (2590:13): [True: 0, False: 0] | Branch (2590:26): [True: 0, False: 0] ------------------ 2591| 636| cur_success = 0; 2592| | 2593| 5.54k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (2593:21): [True: 4.90k, False: 636] ------------------ 2594| 4.90k| { 2595| | /* i = canonical number - 1 */ 2596| 4.90k| iat = nCanon2AtnoRevrs[i]; 2597| 4.90k| if ( /* in restored atom: charge=-1, has no H, has single bond, O, S, Se, Te */ 2598| 4.90k| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 9.81k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2598:17): [True: 4.90k, False: 0] ------------------ 2599| 4.90k| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (2599:17): [True: 793, False: 4.11k] | Branch (2599:42): [True: 728, False: 65] ------------------ 2600| 728| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2600:17): [True: 575, False: 153] | Branch (2600:68): [True: 551, False: 24] ------------------ 2601| 551| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (2601:17): [True: 460, False: 91] ------------------ 2602| | /* in orig.InChI: an endpoint, may have fixed-H */ 2603| 460| pStruct->endpoint[i] && ------------------ | Branch (2603:17): [True: 230, False: 230] ------------------ 2604| | /*!(pStruct->fixed_H && pStruct->fixed_H[i]) &&*/ 2605| 230| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (2605:19): [True: 230, False: 0] | Branch (2605:33): [True: 0, False: 230] ------------------ 2606| | /* has (-) edge */ 2607| 230| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2607:17): [True: 230, False: 0] | Branch (2607:61): [True: 230, False: 0] ------------------ 2608| 230| { 2609| | 2610| 230| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 2611| | 2612| 230| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 230|#define INC_ADD_EDGE 64 ------------------ | Branch (2612:21): [True: 0, False: 230] ------------------ 2613| 0| { 2614| 0| goto exit_function; 2615| 0| } 2616| 230| } 2617| 4.67k| else 2618| 4.67k| { 2619| 4.67k| if ( /* in restored atom: charge=0, has no H, has double non-stereogenic bond, N */ 2620| 4.67k| num_DB_N_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 9.35k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2620:21): [True: 4.67k, False: 0] ------------------ 2621| 4.67k| at2[iat].charge == 0 && !at2[iat].num_H && !at2[iat].sb_parity[0] && ------------------ | Branch (2621:21): [True: 3.25k, False: 1.41k] | Branch (2621:45): [True: 2.84k, False: 414] | Branch (2621:64): [True: 2.82k, False: 16] ------------------ 2622| 2.82k| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2622:21): [True: 1.87k, False: 957] | Branch (2622:71): [True: 1.75k, False: 120] ------------------ 2623| 1.75k| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (2623:21): [True: 689, False: 1.06k] | Branch (2623:59): [True: 534, False: 155] ------------------ 2624| | /* in orig.InChI: an endpoint, has no fixed-H */ 2625| 534| pStruct->endpoint[i] && ------------------ | Branch (2625:21): [True: 276, False: 258] ------------------ 2626| 276| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (2626:23): [True: 276, False: 0] | Branch (2626:43): [True: 3, False: 273] ------------------ 2627| 273| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (2627:23): [True: 273, False: 0] | Branch (2627:37): [True: 0, False: 273] ------------------ 2628| | /* has (-) edge */ 2629| 273| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && ------------------ | Branch (2629:21): [True: 234, False: 39] ------------------ 2630| 234| 0 == pBNS->edge[e].forbidden) ------------------ | Branch (2630:21): [True: 234, False: 0] ------------------ 2631| 234| { 2632| | 2633| 234| iat_DB_N_Neutr[num_DB_N_Neutr++] = iat; 2634| | 2635| 234| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 234|#define INC_ADD_EDGE 64 ------------------ | Branch (2635:25): [True: 0, False: 234] ------------------ 2636| 0| { 2637| 0| goto exit_function; 2638| 0| } 2639| 234| } 2640| 4.67k| } 2641| 4.90k| } 2642| 636| if ((num_try = inchi_min(num_DB_N_Neutr, num_SB_O_Minus))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 636|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 112, False: 524] | | ------------------ ------------------ | Branch (2642:13): [True: 97, False: 539] ------------------ 2643| 97| { 2644| | /* detected; attempt to fix */ 2645| 97| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2646| 97| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 2647| | /* allow stereobonds in rings change */ 2648| 97| if (forbidden_stereo_edge_mask) ------------------ | Branch (2648:17): [True: 97, False: 0] ------------------ 2649| 97| RemoveForbiddenEdgeMask(pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask); 2650| | 2651| 97| delta = 1; 2652| 198| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (2652:25): [True: 116, False: 82] | Branch (2652:47): [True: 101, False: 15] ------------------ 2653| 101| { 2654| 101| iat = iat_SB_O_Minus[i]; 2655| 101| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 2656| 101| if (!pe->flow) ------------------ | Branch (2656:21): [True: 0, False: 101] ------------------ 2657| 0| continue; 2658| 101| pv1 = pBNS->vert + (v1 = pe->neighbor1); 2659| 101| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 2660| | 2661| 101| pe->forbidden |= forbidden_edge_mask; 2662| 101| pe->flow -= delta; 2663| 101| pv1->st_edge.flow -= delta; 2664| 101| pv2->st_edge.flow -= delta; 2665| 101| pBNS->tot_st_flow -= 2 * delta; 2666| | 2667| 101| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2668| 101| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 2669| | 2670| 101| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2670:21): [True: 80, False: 21] | Branch (2670:35): [True: 3, False: 77] | Branch (2670:53): [True: 2, False: 1] ------------------ 2671| 78| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2671:22): [True: 77, False: 1] | Branch (2671:40): [True: 72, False: 5] | Branch (2671:62): [True: 74, False: 0] ------------------ 2672| 74| { 2673| | /* Moved (-) charge to =N- => nDeltaCharge == 1 */ 2674| | /* Flow change on pe (-)charge edge (atom (-)O-) is not known to RunBnsTestOnce()) */ 2675| 74| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2676| 74| if (ret > 0) ------------------ | Branch (2676:25): [True: 74, False: 0] ------------------ 2677| 74| { 2678| 74| nNumRunBNS++; 2679| 74| cur_success++; /* 08 */ 2680| 74| } 2681| 74| } 2682| 27| else 2683| 27| { 2684| 27| pe->forbidden &= forbidden_edge_mask_inv; 2685| 27| pe->flow += delta; 2686| 27| pv1->st_edge.flow += delta; 2687| 27| pv2->st_edge.flow += delta; 2688| 27| pBNS->tot_st_flow += 2 * delta; 2689| 27| } 2690| 101| INCHI_HEAPCHK 2691| 101| } 2692| 97| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2693| 97| if (forbidden_stereo_edge_mask) ------------------ | Branch (2693:17): [True: 97, False: 0] ------------------ 2694| 97| SetForbiddenEdgeMask(pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask); 2695| 97| } 2696| 636| CurrEdges.num_edges = 0; /* clear current edge list */ 2697| 636| if (cur_success) ------------------ | Branch (2697:13): [True: 74, False: 562] ------------------ 2698| 74| { 2699| 74| tot_succes += cur_success; 2700| | /* recalculate InChI from the structure */ 2701| 74| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2701:17): [True: 0, False: 74] ------------------ 2702| 74| ppt_group_info, ppat_norm, ppat_prep))) 2703| 0| { 2704| 0| goto exit_function; 2705| 0| } 2706| 74| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2706:17): [True: 0, False: 74] ------------------ 2707| 0| { 2708| 0| goto exit_function; 2709| 0| } 2710| 74| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2710:17): [True: 44, False: 30] | Branch (2710:45): [True: 0, False: 44] ------------------ 2711| 0| { 2712| 0| goto exit_function; /* no fixed-H found */ 2713| 0| } 2714| 74| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2714:17): [True: 0, False: 74] ------------------ 2715| 0| { 2716| 0| goto exit_function; 2717| 0| } 2718| 74| if (!pc2i->bHasDifference) ------------------ | Branch (2718:17): [True: 0, False: 74] ------------------ 2719| 0| { 2720| 0| goto exit_function; /* nothing to do */ 2721| 0| } 2722| 74| } 2723| 636| } 2724| | 2725| 1.13k| if (pc2i->len_c2at >= 2) ------------------ | Branch (2725:9): [True: 993, False: 139] ------------------ 2726| 993| { 2727| | /*--------------------------------------------------------*/ 2728| | /* case 09: restored: NH2(+)=C--NH2 orig.: NH2-C(+)-NH2 */ 2729| | /* FixH: 2 | 2 0 | 0 */ 2730| | /* MobH: 0 0 2 2 */ 2731| | /* N = N, taut taut non-taut non-taut*/ 2732| | /* Solution: move (+) from NH2(+) to C */ 2733| | /*--------------------------------------------------------*/ 2734| 993| int iat; 2735| 993| cur_success = 0; 2736| 4.36k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2736:21): [True: 3.36k, False: 993] ------------------ 2737| 3.36k| { 2738| 3.36k| iat = pc2i->c2at[i].atomNumber; 2739| 3.36k| if (( pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 ) && ------------------ | Branch (2739:19): [True: 1.18k, False: 2.18k] | Branch (2739:52): [True: 1.02k, False: 162] ------------------ 2740| | /* orig. InChI info: */ 2741| 1.02k| !pc2i->c2at[i].endptInChI && ------------------ | Branch (2741:18): [True: 563, False: 459] ------------------ 2742| 563| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI && ------------------ | Branch (2742:18): [True: 256, False: 307] | Branch (2742:51): [True: 54, False: 202] ------------------ 2743| | /* reversed structure info: */ 2744| 54| pc2i->c2at[i].endptRevrs && ------------------ | Branch (2744:18): [True: 49, False: 5] ------------------ 2745| 49| pc2i->c2at[i].nFixHRevrs && !pc2i->c2at[i].nMobHRevrs && ------------------ | Branch (2745:18): [True: 49, False: 0] | Branch (2745:46): [True: 49, False: 0] ------------------ 2746| 49| pc2i->c2at[i].nAtChargeRevrs == 1 && ------------------ | Branch (2746:18): [True: 4, False: 45] ------------------ 2747| 4| at2[iat].valence + 1 == at2[iat].chem_bonds_valence && ------------------ | Branch (2747:18): [True: 4, False: 0] ------------------ 2748| 4| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2748:18): [True: 4, False: 0] | Branch (2748:63): [True: 2, False: 2] ------------------ 2749| 2| { 2750| 2| EdgeIndex eNC = NO_VERTEX, eCPlusC; ------------------ | | 118| 2|#define NO_VERTEX -2 ------------------ 2751| 2| int iNH2, iatC, iatNH2; /* djb-rwth: removing redundant variables */ 2752| | /* found NH2(+)=; locate =C< and find whether it has -NH2 neighbor */ 2753| 3| for (j = 0; j < at2[iat].valence; j++) ------------------ | Branch (2753:29): [True: 3, False: 0] ------------------ 2754| 3| { 2755| 3| if (at2[iat].bond_type[j] == BOND_TYPE_DOUBLE) ------------------ | | 33| 3|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2755:25): [True: 2, False: 1] ------------------ 2756| 2| break; 2757| 3| } 2758| 2| if (j == at2[iat].valence) ------------------ | Branch (2758:21): [True: 0, False: 2] ------------------ 2759| 0| { 2760| 0| continue; 2761| 0| } 2762| 2| eNC = pBNS->vert[iat].iedge[j]; /* edge NH2(+)=C */ 2763| 2| iatC = at2[iat].neighbor[j]; 2764| 2| if (pVA[iatC].cNumValenceElectrons != 4 || pVA[iatC].cMetal || at2[iatC].charge || ------------------ | Branch (2764:21): [True: 2, False: 0] | Branch (2764:60): [True: 0, False: 0] | Branch (2764:80): [True: 0, False: 0] ------------------ 2765| 0| at2[iatC].valence != 3 || at2[iatC].valence + 1 != at2[iatC].chem_bonds_valence || ------------------ | Branch (2765:22): [True: 0, False: 0] | Branch (2765:48): [True: 0, False: 0] ------------------ 2766| 0| ( eCPlusC = pVA[iatC].nCPlusGroupEdge - 1 ) < 0 || pBNS->edge[eCPlusC].forbidden) ------------------ | Branch (2766:22): [True: 0, False: 0] | Branch (2766:73): [True: 0, False: 0] ------------------ 2767| 2| { 2768| 2| continue; 2769| 2| } 2770| 0| for (j = 0; j < at2[iatC].valence; j++) ------------------ | Branch (2770:29): [True: 0, False: 0] ------------------ 2771| 0| { 2772| 0| iatNH2 = at2[iatC].neighbor[j]; 2773| 0| if (iatNH2 == iat || pVA[iatNH2].cNumValenceElectrons != 5 || ------------------ | Branch (2773:25): [True: 0, False: 0] | Branch (2773:42): [True: 0, False: 0] ------------------ 2774| 0| pVA[iatNH2].cPeriodicRowNumber != 1 || !at2[iatNH2].num_H || at2[iatNH2].charge) ------------------ | Branch (2774:26): [True: 0, False: 0] | Branch (2774:65): [True: 0, False: 0] | Branch (2774:87): [True: 0, False: 0] ------------------ 2775| 0| continue; 2776| | /* djb-rwth: removing redundant code */ 2777| 0| for (iNH2 = 0; iNH2 < pc2i->len_c2at; iNH2++) ------------------ | Branch (2777:36): [True: 0, False: 0] ------------------ 2778| 0| { 2779| 0| if (iatNH2 == pc2i->c2at[iNH2].atomNumber) ------------------ | Branch (2779:29): [True: 0, False: 0] ------------------ 2780| 0| break; 2781| 0| } 2782| 0| if (iNH2 == pc2i->len_c2at) ------------------ | Branch (2782:25): [True: 0, False: 0] ------------------ 2783| 0| { 2784| 0| continue; 2785| 0| } 2786| | 2787| 0| if (( pc2i->c2at[iNH2].nValElectr == 5 && pc2i->c2at[iNH2].nPeriodNum == 1 ) && ------------------ | Branch (2787:27): [True: 0, False: 0] | Branch (2787:63): [True: 0, False: 0] ------------------ 2788| | /* orig. InChI info: */ 2789| 0| !pc2i->c2at[iNH2].endptInChI && ------------------ | Branch (2789:26): [True: 0, False: 0] ------------------ 2790| 0| pc2i->c2at[iNH2].nFixHInChI == 0 && pc2i->c2at[iNH2].nMobHInChI && ------------------ | Branch (2790:26): [True: 0, False: 0] | Branch (2790:62): [True: 0, False: 0] ------------------ 2791| | /* reversed structure info: */ 2792| 0| pc2i->c2at[iNH2].endptRevrs && ------------------ | Branch (2792:26): [True: 0, False: 0] ------------------ 2793| 0| pc2i->c2at[iNH2].nFixHRevrs && !pc2i->c2at[iNH2].nMobHRevrs && ------------------ | Branch (2793:26): [True: 0, False: 0] | Branch (2793:57): [True: 0, False: 0] ------------------ 2794| 0| pc2i->c2at[iNH2].nAtChargeRevrs == 0 && ------------------ | Branch (2794:26): [True: 0, False: 0] ------------------ 2795| 0| at2[iatNH2].valence == at2[iatNH2].chem_bonds_valence) ------------------ | Branch (2795:26): [True: 0, False: 0] ------------------ 2796| 0| { 2797| | /* we have found NH2(+)=, =C<, and bond between them */ 2798| | 2799| 0| if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2799:29): [True: 0, False: 0] ------------------ 2800| 0| { 2801| 0| goto exit_function; 2802| 0| } 2803| 0| if ((ret = AddToEdgeList( &CurrEdges, eCPlusC, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2803:29): [True: 0, False: 0] ------------------ 2804| 0| { 2805| 0| goto exit_function; 2806| 0| } 2807| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2808| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2809| 0| delta = 1; 2810| | 2811| 0| pe = pBNS->edge + eNC; 2812| 0| if (!pe->flow) ------------------ | Branch (2812:29): [True: 0, False: 0] ------------------ 2813| 0| continue; 2814| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2815| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2816| | 2817| 0| pe->forbidden |= forbidden_edge_mask; 2818| 0| pe->flow -= delta; /* add (+) to -NHm */ 2819| 0| pv1->st_edge.flow -= delta; 2820| 0| pv2->st_edge.flow -= delta; 2821| 0| pBNS->tot_st_flow -= 2 * delta; 2822| | 2823| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2824| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2825| | 2826| 0| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2826:29): [True: 0, False: 0] | Branch (2826:44): [True: 0, False: 0] | Branch (2826:62): [True: 0, False: 0] ------------------ 2827| 0| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2827:44): [True: 0, False: 0] | Branch (2827:62): [True: 0, False: 0] | Branch (2827:85): [True: 0, False: 0] ------------------ 2828| 0| { 2829| | /* Removed (+)charge from -NHn => nDeltaCharge == -1 */ 2830| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 2831| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2832| 0| if (ret > 0) ------------------ | Branch (2832:33): [True: 0, False: 0] ------------------ 2833| 0| { 2834| 0| nNumRunBNS++; 2835| 0| cur_success++; /* 09 */ 2836| 0| } 2837| 0| } 2838| 0| else 2839| 0| { 2840| 0| pe->flow += delta; 2841| 0| pv1->st_edge.flow += delta; 2842| 0| pv2->st_edge.flow += delta; 2843| 0| pBNS->tot_st_flow += 2 * delta; 2844| 0| } 2845| 0| INCHI_HEAPCHK 2846| 0| pe->forbidden &= forbidden_edge_mask_inv; 2847| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2848| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 2849| 0| break; 2850| 0| } 2851| 0| } 2852| 0| } 2853| 3.36k| } 2854| 993| if (cur_success) ------------------ | Branch (2854:13): [True: 0, False: 993] ------------------ 2855| 0| { 2856| 0| tot_succes += cur_success; 2857| | /* recalculate InChI from the structure */ 2858| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2858:17): [True: 0, False: 0] ------------------ 2859| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 2860| 0| { 2861| 0| goto exit_function; 2862| 0| } 2863| 0| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2863:17): [True: 0, False: 0] ------------------ 2864| 0| { 2865| 0| goto exit_function; 2866| 0| } 2867| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2867:17): [True: 0, False: 0] | Branch (2867:45): [True: 0, False: 0] ------------------ 2868| 0| { 2869| 0| goto exit_function; /* no fixed-H found */ 2870| 0| } 2871| 0| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2871:17): [True: 0, False: 0] ------------------ 2872| 0| { 2873| 0| goto exit_function; 2874| 0| } 2875| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2875:17): [True: 0, False: 0] ------------------ 2876| 0| { 2877| 0| goto exit_function; /* nothing to do */ 2878| 0| } 2879| 0| } 2880| 993| } 2881| | 2882| 1.13k| if (pc2i->len_c2at >= 2) ------------------ | Branch (2882:9): [True: 993, False: 139] ------------------ 2883| 993| { 2884| | /*--------------------------------------------------------*/ 2885| | /* case 10: restored: NH2-X(+)-NH- orig.: NH2(+)=X-NH- */ 2886| | /* FixH: 0 0 2 1 */ 2887| | /* MobH: 2 1 0 0 */ 2888| | /* N = N,O,S,Se,Te non-taut non-taut taut taut */ 2889| | /* Solution: move (+) from X(+) to NH2 or NH */ 2890| | /*--------------------------------------------------------*/ 2891| 993| int iat; 2892| 993| cur_success = 0; 2893| 4.36k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2893:21): [True: 3.36k, False: 993] ------------------ 2894| 3.36k| { 2895| 3.36k| if (pc2i->c2at[i].nValue) ------------------ | Branch (2895:17): [True: 3, False: 3.36k] ------------------ 2896| 3| continue; 2897| 3.36k| iat = pc2i->c2at[i].atomNumber; 2898| 3.36k| if (( pc2i->c2at[i].nValElectr == 6 || ------------------ | Branch (2898:19): [True: 1.68k, False: 1.67k] ------------------ 2899| 1.67k| (pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) ) && ------------------ | Branch (2899:20): [True: 1.18k, False: 492] | Branch (2899:53): [True: 1.02k, False: 162] ------------------ 2900| | /* orig. InChI info: */ 2901| 2.71k| pc2i->c2at[i].endptInChI && ------------------ | Branch (2901:18): [True: 1.17k, False: 1.53k] ------------------ 2902| 1.17k| pc2i->c2at[i].nFixHInChI && !pc2i->c2at[i].nMobHInChI && ------------------ | Branch (2902:18): [True: 194, False: 981] | Branch (2902:46): [True: 194, False: 0] ------------------ 2903| | /* reversed structure info: */ 2904| 194| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (2904:18): [True: 194, False: 0] ------------------ 2905| 194| !pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].nMobHRevrs && ------------------ | Branch (2905:18): [True: 175, False: 19] | Branch (2905:47): [True: 166, False: 9] ------------------ 2906| 166| pc2i->c2at[i].nAtChargeRevrs == 0 && ------------------ | Branch (2906:18): [True: 113, False: 53] ------------------ 2907| 113| at2[iat].valence == at2[iat].chem_bonds_valence && ------------------ | Branch (2907:18): [True: 96, False: 17] ------------------ 2908| 96| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2908:18): [True: 95, False: 1] | Branch (2908:63): [True: 95, False: 0] ------------------ 2909| 95| { 2910| | 2911| 95| EdgeIndex eCPlusC, eCPlusNH2, bContinue = 1; 2912| 95| int iNH2, iatC, iatNH2, j1, j2; /* djb-rwth: removing redundant variables */ 2913| 95| BNS_EDGE *pe_iat, *pe_iNH2; 2914| | /* found NH2- locate -X(+) and find whether it has another -NH2 neighbor */ 2915| 255| for (j1 = 0; j1 < at2[iat].valence && bContinue; j1++) ------------------ | Branch (2915:30): [True: 160, False: 95] | Branch (2915:55): [True: 160, False: 0] ------------------ 2916| 160| { 2917| 160| if (at2[iat].bond_type[j1] == BOND_TYPE_SINGLE && ------------------ | | 32| 320|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2917:25): [True: 139, False: 21] ------------------ 2918| 139| at2[iatC = at2[iat].neighbor[j1]].charge == 1 && ------------------ | Branch (2918:26): [True: 39, False: 100] ------------------ 2919| 39| ( 4 <= pVA[iatC].cNumValenceElectrons && pVA[iatC].cNumValenceElectrons <= 6 ) && ------------------ | Branch (2919:28): [True: 36, False: 3] | Branch (2919:67): [True: 32, False: 4] ------------------ 2920| 32| at2[iatC].valence == at2[iatC].chem_bonds_valence && ------------------ | Branch (2920:26): [True: 21, False: 11] ------------------ 2921| 21| ( eCPlusC = pVA[iatC].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eCPlusC].forbidden) ------------------ | Branch (2921:26): [True: 21, False: 0] | Branch (2921:78): [True: 14, False: 7] ------------------ 2922| 14| { 2923| | /* found a candidate for X; find another NH2 */ 2924| 65| for (j2 = 0; j2 < at2[iatC].valence && bContinue; j2++) ------------------ | Branch (2924:38): [True: 55, False: 10] | Branch (2924:64): [True: 51, False: 4] ------------------ 2925| 51| { 2926| 51| if (at2[iatC].bond_type[j2] == BOND_TYPE_SINGLE && ------------------ | | 32| 102|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2926:33): [True: 51, False: 0] ------------------ 2927| 51| iat != ( iatNH2 = at2[iatC].neighbor[j2] ) && ------------------ | Branch (2927:34): [True: 38, False: 13] ------------------ 2928| 38| at2[iatNH2].charge == 0 && at2[iatNH2].num_H && ------------------ | Branch (2928:34): [True: 35, False: 3] | Branch (2928:61): [True: 16, False: 19] ------------------ 2929| 16| ( pVA[iatNH2].cNumValenceElectrons == 5 || pVA[iatNH2].cNumValenceElectrons == 6 ) && ------------------ | Branch (2929:36): [True: 2, False: 14] | Branch (2929:77): [True: 5, False: 9] ------------------ 2930| 7| at2[iatNH2].valence == at2[iatNH2].chem_bonds_valence && ------------------ | Branch (2930:34): [True: 7, False: 0] ------------------ 2931| 7| ( eCPlusNH2 = pVA[iatNH2].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eCPlusNH2].forbidden) ------------------ | Branch (2931:34): [True: 7, False: 0] | Branch (2931:90): [True: 7, False: 0] ------------------ 2932| 7| { 2933| 23| for (iNH2 = 0; iNH2 < pc2i->len_c2at; iNH2++) ------------------ | Branch (2933:48): [True: 21, False: 2] ------------------ 2934| 21| { 2935| 21| if (iatNH2 != pc2i->c2at[iNH2].atomNumber || pc2i->c2at[iNH2].nValue) ------------------ | Branch (2935:41): [True: 14, False: 7] | Branch (2935:82): [True: 0, False: 7] ------------------ 2936| 14| continue; 2937| | /* check the second -NH */ 2938| | /* djb-rwth: removing redundant code */ 2939| 7| if ( /* orig. InChI info: */ 2940| 7| pc2i->c2at[iNH2].endptInChI && ------------------ | Branch (2940:42): [True: 5, False: 2] ------------------ 2941| 5| pc2i->c2at[iNH2].nFixHInChI && !pc2i->c2at[iNH2].nMobHInChI && ------------------ | Branch (2941:42): [True: 5, False: 0] | Branch (2941:73): [True: 5, False: 0] ------------------ 2942| | /* reversed structure info: */ 2943| 5| !pc2i->c2at[iNH2].endptRevrs && ------------------ | Branch (2943:42): [True: 5, False: 0] ------------------ 2944| 5| !pc2i->c2at[iNH2].nFixHRevrs && pc2i->c2at[iNH2].nMobHRevrs && ------------------ | Branch (2944:42): [True: 5, False: 0] | Branch (2944:74): [True: 5, False: 0] ------------------ 2945| 5| pc2i->c2at[iNH2].nAtChargeRevrs == 0) ------------------ | Branch (2945:42): [True: 5, False: 0] ------------------ 2946| 5| { 2947| | /* we have found NH-X(+)-NH; remove charge from X(+) */ 2948| 5| pe_iat = pBNS->edge + pBNS->vert[iat].iedge[j1]; 2949| 5| pe_iNH2 = pBNS->edge + pBNS->vert[iatC].iedge[j2]; 2950| | /* pick up one of -NH to move (+) to it */ 2951| 5| if (!pe_iat->forbidden && pBNS->edge[e].flow) ------------------ | Branch (2951:45): [True: 5, False: 0] | Branch (2951:67): [True: 5, False: 0] ------------------ 2952| 5| { 2953| 5| pe = pBNS->edge + e; 2954| 5| } 2955| 0| else 2956| 0| if (!pe_iNH2->forbidden && pBNS->edge[eCPlusNH2].flow) ------------------ | Branch (2956:49): [True: 0, False: 0] | Branch (2956:72): [True: 0, False: 0] ------------------ 2957| 0| { 2958| 0| pe = pBNS->edge + eCPlusNH2; 2959| 0| } 2960| 0| else 2961| 0| { 2962| 0| continue; /* none of the two -X(+)- bonds may be changed */ 2963| 0| } 2964| 5| if ((ret = AddToEdgeList( &CurrEdges, eCPlusC, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 5|#define INC_ADD_EDGE 64 ------------------ | Branch (2964:45): [True: 0, False: 5] ------------------ 2965| 0| { 2966| 0| goto exit_function; 2967| 0| } 2968| 5| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2969| 5| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2970| 5| delta = 1; 2971| | 2972| 5| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2973| 5| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2974| | 2975| | /*pe->forbidden |= forbidden_edge_mask;*/ 2976| 5| pe->flow -= delta; /* add (+) to -NHm */ 2977| 5| pv1->st_edge.flow -= delta; 2978| 5| pv2->st_edge.flow -= delta; 2979| 5| pBNS->tot_st_flow -= 2 * delta; 2980| | 2981| 5| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2982| 5| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2983| | 2984| 5| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2984:45): [True: 5, False: 0] | Branch (2984:60): [True: 1, False: 4] | Branch (2984:78): [True: 0, False: 1] ------------------ 2985| 5| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2985:60): [True: 4, False: 1] | Branch (2985:78): [True: 4, False: 0] | Branch (2985:101): [True: 4, False: 0] ------------------ 2986| 4| { 2987| | /* Removed (+)charge from -NHn => nDeltaCharge == -1 */ 2988| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 2989| 4| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2990| 4| if (ret > 0) ------------------ | Branch (2990:49): [True: 4, False: 0] ------------------ 2991| 4| { 2992| 4| nNumRunBNS++; 2993| 4| cur_success++; /* 10 */ 2994| 4| bContinue = 0; 2995| 4| pc2i->c2at[i].nValue = 1; /* mark as used */ 2996| 4| pc2i->c2at[iNH2].nValue = 1; /* mark as used */ 2997| 4| } 2998| 4| } 2999| 1| else 3000| 1| { 3001| 1| pe->flow += delta; 3002| 1| pv1->st_edge.flow += delta; 3003| 1| pv2->st_edge.flow += delta; 3004| 1| pBNS->tot_st_flow += 2 * delta; 3005| 1| } 3006| 5| INCHI_HEAPCHK 3007| | 3008| | /*pe->forbidden &= forbidden_edge_mask_inv;*/ 3009| 5| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3010| 5| CurrEdges.num_edges = 0; /* clear current edge list */ 3011| 5| break; 3012| 5| } 3013| 7| } /* iNH2: pc2i->c2at[iNH2] cycle */ 3014| 7| } 3015| 51| } /* j2: iatC neighbors cycle */ 3016| 14| } 3017| 160| } /* j1: iat neighbors cycle */ 3018| 95| } 3019| 3.36k| } /* i: pc2i->c2at[i] cycle */ 3020| | 3021| 993| if (cur_success) ------------------ | Branch (3021:13): [True: 4, False: 989] ------------------ 3022| 4| { 3023| | /* 3024| | for ( i = 0; i < pc2i->len_c2at; i ++ ) { 3025| | pc2i->c2at[i].nValue = 0; 3026| | } 3027| | */ 3028| 4| tot_succes += cur_success; 3029| | /* recalculate InChI from the structure */ 3030| 4| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3030:17): [True: 0, False: 4] ------------------ 3031| 4| ppt_group_info, ppat_norm, ppat_prep ) )) 3032| 0| { 3033| 0| goto exit_function; 3034| 0| } 3035| 4| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3035:17): [True: 0, False: 4] ------------------ 3036| 0| { 3037| 0| goto exit_function; 3038| 0| } 3039| 4| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3039:17): [True: 0, False: 4] | Branch (3039:45): [True: 0, False: 0] ------------------ 3040| 0| { 3041| 0| goto exit_function; /* no fixed-H found */ 3042| 0| } 3043| 4| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3043:17): [True: 0, False: 4] ------------------ 3044| 0| { 3045| 0| goto exit_function; 3046| 0| } 3047| 4| if (!pc2i->bHasDifference) ------------------ | Branch (3047:17): [True: 0, False: 4] ------------------ 3048| 0| { 3049| 0| goto exit_function; /* nothing to do */ 3050| 0| } 3051| 4| } 3052| 993| } 3053| | 3054| 1.13k| if ( /*pc2i->len_c2at >= 1 &&*/ pc2i->nNumTgInChI == 1 && /* ADP in InChI */ ------------------ | Branch (3054:37): [True: 737, False: 395] ------------------ 3055| 737| ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 )) ------------------ | Branch (3055:11): [True: 609, False: 128] | Branch (3055:56): [True: 12, False: 116] ------------------ 3056| 621| { 3057| | /*--------------------------------------------------------------*/ 3058| | /* case 11: restored: NH(+)=AB-N< OH- orig. NH-AB=N(+)< OH- */ 3059| | /* FixH: 0 0 0 1 0 1 */ 3060| | /* MobH: 1 0 1 0 0 0 */ 3061| | /* non-taut. taut taut */ 3062| | /* ADP: one t-group or more endpoints */ 3063| | /* NH(+)= => N, O, S, Se; -N< => N */ 3064| | /* Solution: move (+) from NH(+) to -N< */ 3065| | /*--------------------------------------------------------------*/ 3066| 621| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 3067| 621| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3068| 621| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3068:32): [True: 621, False: 0] | Branch (3068:45): [True: 621, False: 0] ------------------ 3069| 621| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3069:13): [True: 0, False: 0] | Branch (3069:26): [True: 0, False: 0] ------------------ 3070| 621| cur_success = 0; 3071| | 3072| | /* search for NH(+)= */ 3073| |/* search for -N< */ 3074| 5.40k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3074:21): [True: 4.78k, False: 621] ------------------ 3075| 4.78k| { /* i = canonical number - 1 */ 3076| 4.78k| iat = nCanon2AtnoRevrs[i]; 3077| 4.78k| if ( /* in restored atom: charge=0, has no H, has no double bond, N only */ 3078| 4.78k| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 456| 9.57k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3078:17): [True: 4.78k, False: 0] ------------------ 3079| 4.78k| at2[iat].charge == 1 && at2[iat].num_H && ------------------ | Branch (3079:17): [True: 760, False: 4.02k] | Branch (3079:41): [True: 175, False: 585] ------------------ 3080| 175| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (3080:17): [True: 154, False: 21] | Branch (3080:67): [True: 151, False: 3] ------------------ 3081| 151| ((pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1) || ------------------ | Branch (3081:19): [True: 43, False: 108] | Branch (3081:57): [True: 42, False: 1] ------------------ 3082| 109| pVA[iat].cNumValenceElectrons == 6) && ------------------ | Branch (3082:21): [True: 94, False: 15] ------------------ 3083| | /* in orig.InChI: an endpoint, has fixed-H */ 3084| | /*pStruct->endpoint[i] &&*/ 3085| 136| (pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (3085:18): [True: 136, False: 0] | Branch (3085:38): [True: 126, False: 10] ------------------ 3086| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 3087| | /* has (+) edge */ 3088| 126| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3088:17): [True: 126, False: 0] | Branch (3088:60): [True: 120, False: 6] ------------------ 3089| 120| { 3090| | 3091| 120| iat_DB_Charged[num_DB_Charged++] = iat; 3092| | /* 3093| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 3094| | goto exit_function; 3095| | } 3096| | */ 3097| 120| } 3098| 4.66k| else 3099| 4.66k| { 3100| 4.66k| if ( /* in restored atom: charge=0, has no H, has no double bond, N only */ 3101| 4.66k| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 9.33k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3101:21): [True: 4.66k, False: 0] ------------------ 3102| 4.66k| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (3102:21): [True: 3.19k, False: 1.47k] | Branch (3102:45): [True: 2.79k, False: 396] ------------------ 3103| 2.79k| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (3103:21): [True: 804, False: 1.99k] | Branch (3103:72): [True: 607, False: 197] ------------------ 3104| 607| (pVA[iat].cNumValenceElectrons == 5 && ------------------ | Branch (3104:22): [True: 188, False: 419] ------------------ 3105| 188| pVA[iat].cPeriodicRowNumber == 1) && ------------------ | Branch (3105:25): [True: 149, False: 39] ------------------ 3106| | /* in orig.InChI: an endpoint, has fixed-H */ 3107| | /*pStruct->endpoint[i] &&*/ 3108| 149| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (3108:23): [True: 149, False: 0] | Branch (3108:43): [True: 0, False: 149] ------------------ 3109| 149| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (3109:23): [True: 149, False: 0] | Branch (3109:37): [True: 0, False: 149] ------------------ 3110| | /* has (+) edge */ 3111| 149| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden) ------------------ | Branch (3111:21): [True: 139, False: 10] | Branch (3111:64): [True: 139, False: 0] ------------------ 3112| 139| { 3113| | 3114| 139| iat_SB_Neutr[num_SB_Neutr++] = iat; 3115| 139| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 139|#define INC_ADD_EDGE 64 ------------------ | Branch (3115:25): [True: 0, False: 139] ------------------ 3116| 0| { 3117| 0| goto exit_function; 3118| 0| } 3119| 139| } 3120| 4.66k| } 3121| 4.78k| } 3122| 621| if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 621|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 78, False: 543] | | ------------------ ------------------ | Branch (3122:13): [True: 32, False: 589] ------------------ 3123| 32| { 3124| | /* detected; attempt to fix */ 3125| 32| BNS_VERTEX* pv1n, * pv2n; 3126| 32| BNS_EDGE* pe1n, * pe2n; 3127| 32| Vertex v1n, v2n; 3128| 32| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3129| 32| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 3130| 32| delta = 1; 3131| 64| for (i = 0; i < num_DB_Charged && cur_success < num_try; i++) ------------------ | Branch (3131:25): [True: 37, False: 27] | Branch (3131:47): [True: 32, False: 5] ------------------ 3132| 32| { 3133| 32| iat = iat_DB_Charged[i]; 3134| 32| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 3135| 32| if (pe->flow) ------------------ | Branch (3135:21): [True: 0, False: 32] ------------------ 3136| 0| continue; 3137| 32| pv1 = pBNS->vert + (v1 = pe->neighbor1); 3138| 32| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 3139| | 3140| 75| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (3140:50): [True: 75, False: 0] ------------------ 3141| 75| { 3142| 75| pe1n = pBNS->edge + pv1->iedge[j]; 3143| 75| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (3143:25): [True: 32, False: 43] | Branch (3143:39): [True: 32, False: 0] ------------------ 3144| 32| { 3145| 32| pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1); 3146| 32| break; 3147| 32| } 3148| 75| } 3149| 32| if (j < 0) ------------------ | Branch (3149:21): [True: 0, False: 32] ------------------ 3150| 0| { 3151| 0| continue; /* not found */ 3152| 0| } 3153| | 3154| 125| for (j = pv2->num_adj_edges - 2; 0 <= j; j--) ------------------ | Branch (3154:50): [True: 125, False: 0] ------------------ 3155| 125| { 3156| 125| pe2n = pBNS->edge + pv2->iedge[j]; 3157| 125| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (3157:25): [True: 83, False: 42] | Branch (3157:39): [True: 32, False: 51] ------------------ 3158| 32| { 3159| 32| pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2); 3160| 32| break; 3161| 32| } 3162| 125| } 3163| 32| if (j < 0) ------------------ | Branch (3163:21): [True: 0, False: 32] ------------------ 3164| 0| { 3165| 0| continue; /* not found */ 3166| 0| } 3167| | 3168| 32| pe->flow += delta; 3169| 32| pe1n->flow -= delta; 3170| 32| pe2n->flow -= delta; 3171| 32| pv1n->st_edge.flow -= delta; 3172| 32| pv2n->st_edge.flow -= delta; 3173| 32| pBNS->tot_st_flow -= 2 * delta; 3174| | 3175| 32| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3176| 32| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 3177| | 3178| 32| if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) || ------------------ | Branch (3178:21): [True: 24, False: 8] | Branch (3178:35): [True: 3, False: 21] | Branch (3178:54): [True: 3, False: 0] ------------------ 3179| 21| (vPathEnd == v2n && vPathStart == v1n)) && ------------------ | Branch (3179:22): [True: 19, False: 2] | Branch (3179:41): [True: 18, False: 1] ------------------ 3180| 21| (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3180:22): [True: 18, False: 3] | Branch (3180:43): [True: 3, False: 0] ------------------ 3181| 21| { 3182| | /* before setting flows the structure could be: 3183| | [NH+ neigh, v1n]=e1n=[NH+,v1]-pe-[+,v2]=e2n=[another at or its chargeStruct] 3184| | or 3185| | 3186| | [NH+ or ChStr, v1n]=pe1n=[NH+ or ChStr, v1]-pe-[+,v2]=pe2n=[at2 or ChStr, v2n] 3187| | ^ ^ ^ 3188| | NH+(+)edge | N (+) edge: only 3189| | | these are not forbidden 3190| | | 3191| | hetero (+) vertex 3192| | 3193| | After setting flows (* mark radicals, =pe= is forbidden): 3194| | 3195| | *[NH+ or ChStr, v1n]-pe1n-[NH+ or ChStr, v1]=pe=[+,v2]-pe2n-[at2 or ChStr, v2n]* 3196| | ^ ^ ^ 3197| | NH+(+)edge | N (+) edge: only 3198| | | these are not forbidden 3199| | | 3200| | hetero (+) vertex 3201| | 3202| | Flow in 3203| | pe1n and pe2n will or will not change, depending on the structure. 3204| | 3205| | Consider what happens if pe2n changes. It may only increment. 3206| | If pe2n flow increments then another (+)edge flow dectrements. If 3207| | [at2 or ChStr, v2n] is at2 then at2 charge would change from (+) to 0, 3208| | and another N charge would change from 0 to (+), giving tot. change of 3209| | number of charges (-1)+(+1)=0. However, if [at2 or ChStr, v2n] is 3210| | ChargeStruct then at2 will not be on the alt path and only the creation 3211| | of another (+) will be detected. 3212| | */ 3213| | /* Removed charge from O(+) => nDeltaCharge == -1 */ 3214| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 3215| 21| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 3216| 21| if (ret > 0) ------------------ | Branch (3216:25): [True: 21, False: 0] ------------------ 3217| 21| { 3218| 21| nNumRunBNS++; 3219| 21| cur_success++; /* 11 */ 3220| 21| } 3221| 21| } 3222| 11| else 3223| 11| { 3224| 11| pe->flow -= delta; 3225| 11| pe1n->flow += delta; 3226| 11| pe2n->flow += delta; 3227| 11| pv1n->st_edge.flow += delta; 3228| 11| pv2n->st_edge.flow += delta; 3229| 11| pBNS->tot_st_flow += 2 * delta; 3230| 11| } 3231| 32| INCHI_HEAPCHK 3232| 32| } 3233| 32| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3234| 32| } 3235| 621| CurrEdges.num_edges = 0; /* clear current edge list */ 3236| 621| if (cur_success) ------------------ | Branch (3236:13): [True: 21, False: 600] ------------------ 3237| 21| { 3238| 21| tot_succes += cur_success; 3239| | /* recalculate InChI from the structure */ 3240| 21| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3240:17): [True: 0, False: 21] ------------------ 3241| 21| ppt_group_info, ppat_norm, ppat_prep))) 3242| 0| { 3243| 0| goto exit_function; 3244| 0| } 3245| 21| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3245:17): [True: 0, False: 21] ------------------ 3246| 0| { 3247| 0| goto exit_function; 3248| 0| } 3249| 21| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3249:17): [True: 0, False: 21] | Branch (3249:45): [True: 0, False: 0] ------------------ 3250| 0| { 3251| 0| goto exit_function; /* no fixed-H found */ 3252| 0| } 3253| 21| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3253:17): [True: 0, False: 21] ------------------ 3254| 0| { 3255| 0| goto exit_function; 3256| 0| } 3257| 21| if (!pc2i->bHasDifference) ------------------ | Branch (3257:17): [True: 0, False: 21] ------------------ 3258| 0| { 3259| 0| goto exit_function; /* nothing to do */ 3260| 0| } 3261| 21| } 3262| 621| } 3263| | 3264| 1.13k| if (pc2i->len_c2at >= 1 && pc2i->nNumTgInChI == 1 && ------------------ | Branch (3264:9): [True: 1.12k, False: 3] | Branch (3264:32): [True: 734, False: 395] ------------------ 3265| 734| pc2i->nNumRemHInChI >= -1 && /* 2006-03-03 */ ------------------ | Branch (3265:10): [True: 734, False: 0] ------------------ 3266| 734| ( pc2i->nNumEndpInChI > pc2i->nNumEndpRevrs || pc2i->nNumTgRevrs > 1 ) /* ADP in InChI */) ------------------ | Branch (3266:12): [True: 605, False: 129] | Branch (3266:57): [True: 12, False: 117] ------------------ 3267| 617| { 3268| | /*--------------------------------------------------------------*/ 3269| | /* case 12: restored: O=AB-N< original: (-)O-AB=N(+)< */ 3270| | /* FixH: 0 0 0 0 */ 3271| | /* MobH: 0 0 0 0 */ 3272| | /* non-taut taut */ 3273| | /* O = O, S, Se, N; N = N; */ 3274| | /* restored atom O is not tautomeric; original atom O is taut. */ 3275| | /* original struct has 1 t-group; restored has less endpoints */ 3276| | /* and/or possibly >1 t-groups */ 3277| | /* Solution: separate charges between O= and -N< */ 3278| | /* allow moving charge to N(V) to make it N(IV)(+) */ 3279| | /*--------------------------------------------------------------*/ 3280| 617| int bOnly_N_V = 1; 3281| | /* djb-rwth: removing redundant code */ 3282| 1.14k| while (1) ------------------ | Branch (3282:16): [True: 1.14k, Folded] ------------------ 3283| 1.14k| { 3284| 1.14k| int num_SB_N_Neutr = 0, num_DB_O = 0, iat, num_N_V = 0, bN_V; 3285| 1.14k| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3286| 1.14k| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (3286:45): [True: 355, False: 788] ------------------ 3287| 1.14k| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (3287:45): [True: 355, False: 0] ------------------ 3288| 1.14k| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3288:36): [True: 1.14k, False: 0] | Branch (3288:49): [True: 1.14k, False: 0] ------------------ 3289| 1.14k| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3289:17): [True: 0, False: 0] | Branch (3289:30): [True: 0, False: 0] ------------------ 3290| 1.14k| cur_success = 0; 3291| | 3292| 4.89k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (3292:25): [True: 3.75k, False: 1.14k] ------------------ 3293| 3.75k| { 3294| 3.75k| iat = pc2i->c2at[i].atomNumber; 3295| 3.75k| if ( /* orig. InChI info: -O(-) */ 3296| 3.75k| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 7.50k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3296:21): [True: 3.75k, False: 0] ------------------ 3297| 3.75k| (pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ || ------------------ | Branch (3297:22): [True: 2.02k, False: 1.73k] ------------------ 3298| 1.73k| (pc2i->c2at[i].nValElectr == 5 && ------------------ | Branch (3298:26): [True: 1.11k, False: 619] ------------------ 3299| 1.11k| pc2i->c2at[i].nPeriodNum == 1) /* N */) && /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3299:25): [True: 912, False: 200] ------------------ 3300| 2.93k| pc2i->c2at[i].endptInChI && ------------------ | Branch (3300:21): [True: 2.01k, False: 917] ------------------ 3301| 2.01k| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3301:21): [True: 1.49k, False: 519] | Branch (3301:65): [True: 1.49k, False: 0] ------------------ 3302| 1.49k| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (3302:21): [True: 1.45k, False: 45] | Branch (3302:54): [True: 1.45k, False: 0] ------------------ 3303| | /* reversed structure info: */ 3304| 1.45k| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (3304:21): [True: 1.45k, False: 0] ------------------ 3305| 1.45k| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (3305:21): [True: 1.42k, False: 27] | Branch (3305:54): [True: 1.42k, False: 0] ------------------ 3306| 1.42k| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (3306:21): [True: 992, False: 432] | Branch (3306:58): [True: 992, False: 0] ------------------ 3307| 992| ((pc2i->c2at[i].nValElectr == 6) ? ------------------ | Branch (3307:21): [True: 923, False: 69] | Branch (3307:22): [True: 700, False: 292] ------------------ 3308| 700| (at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) : ------------------ | Branch (3308:26): [True: 695, False: 5] | Branch (3308:51): [True: 650, False: 45] ------------------ 3309| 992| (pc2i->c2at[i].nValElectr == 5) ? ------------------ | Branch (3309:25): [True: 292, False: 0] ------------------ 3310| 292| (at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 3) : ------------------ | Branch (3310:26): [True: 278, False: 14] | Branch (3310:51): [True: 273, False: 5] ------------------ 3311| 292| 0)) 3312| 923| { 3313| | 3314| 923| iat_DB_O[num_DB_O++] = iat; 3315| | /* 3316| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 3317| | goto exit_function; 3318| | } 3319| | */ 3320| 923| } 3321| 3.75k| } 3322| 9.93k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3322:25): [True: 8.79k, False: 1.14k] ------------------ 3323| 8.79k| { 3324| | /* i = canonical number - 1 */ 3325| 8.79k| iat = nCanon2AtnoRevrs[i]; 3326| 8.79k| bN_V = 0; 3327| 8.79k| if ( /* in restored atom N: charge=0, no H, has no double bond, not an endpoint */ 3328| 8.79k| num_SB_N_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 17.5k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3328:21): [True: 8.79k, False: 0] ------------------ 3329| 8.79k| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (3329:21): [True: 5.79k, False: 2.99k] | Branch (3329:45): [True: 5.01k, False: 784] ------------------ 3330| 5.01k| (at2[iat].valence == at2[iat].chem_bonds_valence || ------------------ | Branch (3330:22): [True: 1.42k, False: 3.58k] ------------------ 3331| 3.58k| (bN_V = at2[iat].valence + 2 == at2[iat].chem_bonds_valence)) && ------------------ | Branch (3331:25): [True: 702, False: 2.88k] ------------------ 3332| 2.12k| !pVA[iat].cMetal && ------------------ | Branch (3332:21): [True: 1.68k, False: 438] ------------------ 3333| 1.68k| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (3333:21): [True: 680, False: 1.00k] | Branch (3333:59): [True: 499, False: 181] ------------------ 3334| 499| !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) && ------------------ | Branch (3334:23): [True: 129, False: 370] | Branch (3334:44): [True: 0, False: 129] ------------------ 3335| | /* in orig.InChI: not an endpoint, has no H */ 3336| 499| !pStruct->endpoint[i] && ------------------ | Branch (3336:21): [True: 379, False: 120] ------------------ 3337| 379| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (3337:23): [True: 379, False: 0] | Branch (3337:43): [True: 8, False: 371] ------------------ 3338| 371| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (3338:23): [True: 371, False: 0] | Branch (3338:37): [True: 0, False: 371] ------------------ 3339| | /* has (+) edge */ 3340| 371| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (3340:21): [True: 309, False: 62] | Branch (3340:64): [True: 309, False: 0] ------------------ 3341| 309| { 3342| | 3343| 309| if (bOnly_N_V && bN_V && ------------------ | Branch (3343:25): [True: 204, False: 105] | Branch (3343:38): [True: 100, False: 104] ------------------ 3344| 100| NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) && ------------------ | | 118| 100|#define NO_VERTEX -2 ------------------ | Branch (3344:25): [True: 97, False: 3] ------------------ 3345| 97| !pBNS->edge[j].forbidden && !pBNS->edge[j].flow) ------------------ | Branch (3345:25): [True: 97, False: 0] | Branch (3345:53): [True: 97, False: 0] ------------------ 3346| 97| { 3347| 97| if (!num_N_V) ------------------ | Branch (3347:29): [True: 95, False: 2] ------------------ 3348| 95| { 3349| | /* switch to N(V) only mode */ 3350| 95| CurrEdges.num_edges = 0; 3351| 95| num_SB_N_Neutr = 0; 3352| 95| } 3353| 97| iat_SB_N_Neutr[num_SB_N_Neutr++] = iat; 3354| 97| num_N_V++; 3355| 97| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 97|#define INC_ADD_EDGE 64 ------------------ | Branch (3355:29): [True: 0, False: 97] ------------------ 3356| 0| { 3357| 0| goto exit_function; 3358| 0| } 3359| 97| if ((ret = AddToEdgeList(&CurrEdges, j, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 97|#define INC_ADD_EDGE 64 ------------------ | Branch (3359:29): [True: 0, False: 97] ------------------ 3360| 0| { 3361| 0| goto exit_function; 3362| 0| } 3363| 97| } 3364| 212| else 3365| 212| { 3366| 212| if (!num_N_V) ------------------ | Branch (3366:29): [True: 209, False: 3] ------------------ 3367| 209| { 3368| 209| iat_SB_N_Neutr[num_SB_N_Neutr++] = iat; 3369| 209| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 209|#define INC_ADD_EDGE 64 ------------------ | Branch (3369:33): [True: 0, False: 209] ------------------ 3370| 0| { 3371| 0| goto exit_function; 3372| 0| } 3373| | /* in addition, permit N(V)=>N(IV)(+) change by allowing charge flower edge change flow */ 3374| 209| if (bN_V && NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) && ------------------ | | 118| 41|#define NO_VERTEX -2 ------------------ | Branch (3374:33): [True: 41, False: 168] | Branch (3374:41): [True: 36, False: 5] ------------------ 3375| 36| !pBNS->edge[j].forbidden && !pBNS->edge[j].flow) ------------------ | Branch (3375:33): [True: 36, False: 0] | Branch (3375:61): [True: 36, False: 0] ------------------ 3376| 36| { 3377| 36| if ((ret = AddToEdgeList(&CurrEdges, j, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 36|#define INC_ADD_EDGE 64 ------------------ | Branch (3377:37): [True: 0, False: 36] ------------------ 3378| 0| { 3379| 0| goto exit_function; 3380| 0| } 3381| 36| } 3382| 209| } 3383| 212| } 3384| 309| } 3385| 8.79k| } 3386| 1.14k| if ((num_try = inchi_min(num_SB_N_Neutr, num_DB_O))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.14k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 482, False: 661] | | ------------------ ------------------ | Branch (3386:17): [True: 173, False: 970] ------------------ 3387| 173| { 3388| | /* detected; attempt to fix */ 3389| 173| BNS_EDGE* pe_CMinus; 3390| 173| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3391| 173| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 3392| 173| delta = 1; 3393| 401| for (i = 0; i < num_DB_O && cur_success < num_try; i++) ------------------ | Branch (3393:29): [True: 273, False: 128] | Branch (3393:45): [True: 228, False: 45] ------------------ 3394| 228| { 3395| 228| iat = iat_DB_O[i]; 3396| 228| pe_CMinus = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 3397| 228| pe_CMinus->forbidden &= forbidden_edge_mask_inv; 3398| | 3399| 228| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; /* double bond O=...*/ 3400| 228| if (!pe->flow) ------------------ | Branch (3400:25): [True: 38, False: 190] ------------------ 3401| 38| continue; 3402| 190| pv1 = pBNS->vert + (v1 = pe->neighbor1); 3403| 190| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 3404| | 3405| 190| pe->forbidden |= forbidden_edge_mask; /* change bond O=X to O(rad)-X(rad) */ 3406| 190| pe->flow -= delta; 3407| 190| pv1->st_edge.flow -= delta; 3408| 190| pv2->st_edge.flow -= delta; 3409| 190| pBNS->tot_st_flow -= 2 * delta; 3410| | 3411| 190| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3412| 190| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 3413| | 3414| 190| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (3414:25): [True: 168, False: 22] | Branch (3414:39): [True: 21, False: 147] | Branch (3414:57): [True: 5, False: 16] ------------------ 3415| 163| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 2) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3415:26): [True: 131, False: 32] | Branch (3415:44): [True: 120, False: 11] | Branch (3415:66): [True: 91, False: 34] ------------------ 3416| 91| { 3417| | /* Added (-) charge to =O and (+) charge to N => nDeltaCharge == 2 */ 3418| 91| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 3419| 91| if (ret > 0) ------------------ | Branch (3419:29): [True: 91, False: 0] ------------------ 3420| 91| { 3421| 91| nNumRunBNS++; 3422| 91| cur_success++; /* 12 */ 3423| 91| } 3424| 91| } 3425| 99| else 3426| 99| { 3427| 99| pe->flow += delta; 3428| 99| pv1->st_edge.flow += delta; 3429| 99| pv2->st_edge.flow += delta; 3430| 99| pBNS->tot_st_flow += 2 * delta; 3431| 99| } 3432| 190| pe->forbidden &= forbidden_edge_mask_inv; /* allow changes to O=X bond */ 3433| 190| INCHI_HEAPCHK 3434| 190| } 3435| 173| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3436| 173| } 3437| 1.14k| CurrEdges.num_edges = 0; /* clear current edge list */ 3438| 1.14k| if (cur_success) ------------------ | Branch (3438:17): [True: 91, False: 1.05k] ------------------ 3439| 91| { 3440| 91| tot_succes += cur_success; 3441| | /* recalculate InChI from the structure */ 3442| 91| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3442:21): [True: 1, False: 90] ------------------ 3443| 91| ppt_group_info, ppat_norm, ppat_prep))) 3444| 1| { 3445| 1| goto exit_function; 3446| 1| } 3447| 90| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3447:21): [True: 0, False: 90] ------------------ 3448| 0| { 3449| 0| goto exit_function; 3450| 0| } 3451| 90| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3451:21): [True: 58, False: 32] | Branch (3451:49): [True: 0, False: 58] ------------------ 3452| 0| { 3453| 0| goto exit_function; /* no fixed-H found */ 3454| 0| } 3455| 90| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3455:21): [True: 0, False: 90] ------------------ 3456| 0| { 3457| 0| goto exit_function; 3458| 0| } 3459| 90| if (!pc2i->bHasDifference) ------------------ | Branch (3459:21): [True: 0, False: 90] ------------------ 3460| 0| { 3461| 0| goto exit_function; /* nothing to do */ 3462| 0| } 3463| 90| break; 3464| 90| } 3465| 1.05k| else 3466| 1.05k| { 3467| 1.05k| if (bOnly_N_V) ------------------ | Branch (3467:21): [True: 526, False: 526] ------------------ 3468| 526| { 3469| 526| bOnly_N_V = 0; 3470| 526| } 3471| 526| else 3472| 526| { 3473| 526| break; 3474| 526| } 3475| 1.05k| } 3476| 1.14k| } 3477| 617| } 3478| | 3479| | 3480| 1.13k| if (pc2i->nNumTgDiffMinus /*|| pc2i->nNumTgDiffH */ /* no ADP in InChI needed */) ------------------ | Branch (3480:9): [True: 66, False: 1.06k] ------------------ 3481| 66| { 3482| | /*--------------------------------------------------------------*/ 3483| | /* | | */ 3484| | /* case 13: restored: O=AB=N= original: (-)O-AB-N(+)= */ 3485| | /* FixH: 0 0 0 0 */ 3486| | /* MobH: 0 0 0 0 */ 3487| | /* non-taut taut non-taut */ 3488| | /* O = O, S, Se, N; N = N, P, ... */ 3489| | /* t-group in original has same num. endpoints */ 3490| | /* same num_H and less (-) than in the restored structure */ 3491| | /* original atom O is tautomeric, N is not taut in both */ 3492| | /* original struct has 1 t-group; restored has less endpoints */ 3493| | /* and/or possibly >1 t-groups */ 3494| | /* Solution: separate charges between O= and -N< */ 3495| | /* allow moving charge to N(V) to make it N(IV)(+) */ 3496| | /*--------------------------------------------------------------*/ 3497| 66| int itg; 3498| 66| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3499| 66| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (3499:41): [True: 66, False: 0] ------------------ 3500| 66| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (3500:41): [True: 66, False: 0] ------------------ 3501| | 3502| 66| S_CHAR *num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL; ------------------ | Branch (3502:39): [True: 66, False: 0] ------------------ 3503| 66| S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ? ------------------ | Branch (3503:35): [True: 66, False: 0] | Branch (3503:60): [True: 66, False: 0] ------------------ 3504| 66| pStruct->pOneINChI[1]->nNum_H : 3505| 66| ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (3505:15): [True: 0, False: 0] | Branch (3505:40): [True: 0, False: 0] ------------------ 3506| 0| pStruct->pOneINChI[0]->nNum_H : NULL; 3507| 66| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3507:32): [True: 66, False: 0] | Branch (3507:45): [True: 66, False: 0] ------------------ 3508| 66| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3508:13): [True: 0, False: 0] | Branch (3508:26): [True: 0, False: 0] ------------------ 3509| | /* djb-rwth: removing redundant code */ 3510| | /* find whether this may help */ 3511| 139| for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++) ------------------ | Branch (3511:23): [True: 78, False: 61] | Branch (3511:57): [True: 73, False: 5] ------------------ 3512| 73| { 3513| 73| if (pStruct->ti.t_group[itg].nNumEndpoints == pStruct->One_ti.t_group[itg].nNumEndpoints && ------------------ | Branch (3513:17): [True: 68, False: 5] ------------------ 3514| 68| pStruct->ti.t_group[itg].num[0] - pStruct->ti.t_group[itg].num[1] == ------------------ | Branch (3514:18): [True: 0, False: 68] ------------------ 3515| 68| pStruct->One_ti.t_group[itg].num[0] - pStruct->One_ti.t_group[itg].num[1] && 3516| 0| pStruct->ti.t_group[itg].num[1] > pStruct->One_ti.t_group[itg].num[1]) ------------------ | Branch (3516:18): [True: 0, False: 0] ------------------ 3517| 0| { 3518| | /* restored InChI t-group has more (-) and same number of H */ 3519| 0| int num_SB_N_Neutr = 0, num_DB_O = 0, iat; 3520| 0| cur_success = 0; 3521| | 3522| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3522:29): [True: 0, False: 0] ------------------ 3523| 0| { /* i = canonical number - 1 */ 3524| 0| iat = nCanon2AtnoRevrs[i]; 3525| 0| if ( /* orig. InChI info: -O(-) */ 3526| 0| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3526:25): [True: 0, False: 0] ------------------ 3527| 0| (pVA[i].cNumValenceElectrons == 6 /* O, S, Se, Te */) && ------------------ | Branch (3527:25): [True: 0, False: 0] ------------------ 3528| 0| pStruct->endpoint[i] == itg + 1 && ------------------ | Branch (3528:25): [True: 0, False: 0] ------------------ 3529| 0| (e = pVA[i].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3529:25): [True: 0, False: 0] | Branch (3529:67): [True: 0, False: 0] ------------------ 3530| 0| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (3530:27): [True: 0, False: 0] | Branch (3530:47): [True: 0, False: 0] ------------------ 3531| 0| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (3531:27): [True: 0, False: 0] | Branch (3531:41): [True: 0, False: 0] ------------------ 3532| | /* reversed structure info: */ 3533| | /*!pc2i->c2at[i].endptRevrs &&*/ 3534| 0| !(num_Fixed_H_Revrs && num_Fixed_H_Revrs[iat]) && ------------------ | Branch (3534:27): [True: 0, False: 0] | Branch (3534:48): [True: 0, False: 0] ------------------ 3535| 0| !(pnMobHRevrs && pnMobHRevrs[iat]) && ------------------ | Branch (3535:27): [True: 0, False: 0] | Branch (3535:42): [True: 0, False: 0] ------------------ 3536| 0| at2[iat].charge == 0 && at2[iat].num_H == 0 && ------------------ | Branch (3536:25): [True: 0, False: 0] | Branch (3536:49): [True: 0, False: 0] ------------------ 3537| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (3537:25): [True: 0, False: 0] | Branch (3537:50): [True: 0, False: 0] ------------------ 3538| 0| { 3539| | 3540| 0| iat_DB_O[num_DB_O++] = iat; 3541| | /* 3542| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 3543| | goto exit_function; 3544| | } 3545| | */ 3546| 0| } 3547| 0| else 3548| 0| { 3549| 0| if ( /* in restored atom N: charge=0, no H, has no double bond, not an endpoint */ 3550| 0| num_SB_N_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3550:29): [True: 0, False: 0] ------------------ 3551| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (3551:29): [True: 0, False: 0] | Branch (3551:53): [True: 0, False: 0] ------------------ 3552| | /*at2[iat].valence == at2[iat].chem_bonds_valence ||*/ 3553| 0| (at2[iat].valence == 4 && at2[iat].chem_bonds_valence == 5) && ------------------ | Branch (3553:30): [True: 0, False: 0] | Branch (3553:55): [True: 0, False: 0] ------------------ 3554| 0| !pVA[iat].cMetal && ------------------ | Branch (3554:29): [True: 0, False: 0] ------------------ 3555| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber >= 1 && ------------------ | Branch (3555:29): [True: 0, False: 0] | Branch (3555:67): [True: 0, False: 0] ------------------ 3556| 0| !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) && ------------------ | Branch (3556:31): [True: 0, False: 0] | Branch (3556:52): [True: 0, False: 0] ------------------ 3557| | /* in orig.InChI: not an endpoint, has no H */ 3558| 0| !pStruct->endpoint[i] && ------------------ | Branch (3558:29): [True: 0, False: 0] ------------------ 3559| 0| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (3559:31): [True: 0, False: 0] | Branch (3559:51): [True: 0, False: 0] ------------------ 3560| 0| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (3560:31): [True: 0, False: 0] | Branch (3560:45): [True: 0, False: 0] ------------------ 3561| | /* has (+) edge */ 3562| 0| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (3562:29): [True: 0, False: 0] | Branch (3562:72): [True: 0, False: 0] ------------------ 3563| 0| { 3564| | 3565| 0| iat_SB_N_Neutr[num_SB_N_Neutr++] = iat; 3566| 0| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (3566:33): [True: 0, False: 0] ------------------ 3567| 0| { 3568| 0| goto exit_function; 3569| 0| } 3570| 0| } 3571| 0| } 3572| 0| } 3573| 0| if ((num_try = inchi_min(num_SB_N_Neutr, num_DB_O))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3573:21): [True: 0, False: 0] ------------------ 3574| 0| { 3575| | /* detected; attempt to fix */ 3576| 0| BNS_EDGE* pe_CMinus; 3577| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3578| 0| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 3579| 0| delta = 1; 3580| 0| for (i = 0; i < num_DB_O && cur_success < num_try; i++) ------------------ | Branch (3580:33): [True: 0, False: 0] | Branch (3580:49): [True: 0, False: 0] ------------------ 3581| 0| { 3582| 0| iat = iat_DB_O[i]; 3583| 0| pe_CMinus = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 3584| 0| pe_CMinus->forbidden &= forbidden_edge_mask_inv; 3585| | 3586| 0| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; /* double bond O=...*/ 3587| 0| if (!pe->flow) ------------------ | Branch (3587:29): [True: 0, False: 0] ------------------ 3588| 0| continue; 3589| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 3590| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 3591| | 3592| 0| pe->forbidden |= forbidden_edge_mask; /* change bond O=X to O(rad)-X(rad) */ 3593| 0| pe->flow -= delta; 3594| 0| pv1->st_edge.flow -= delta; 3595| 0| pv2->st_edge.flow -= delta; 3596| 0| pBNS->tot_st_flow -= 2 * delta; 3597| | 3598| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3599| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 3600| | 3601| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (3601:29): [True: 0, False: 0] | Branch (3601:43): [True: 0, False: 0] | Branch (3601:61): [True: 0, False: 0] ------------------ 3602| 0| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 2) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3602:30): [True: 0, False: 0] | Branch (3602:48): [True: 0, False: 0] | Branch (3602:70): [True: 0, False: 0] ------------------ 3603| 0| { 3604| | /* Added (-) charge to =O and (+) charge to N => nDeltaCharge == 2 */ 3605| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 3606| 0| if (ret > 0) ------------------ | Branch (3606:33): [True: 0, False: 0] ------------------ 3607| 0| { 3608| 0| nNumRunBNS++; 3609| 0| cur_success++; /* 13 */ 3610| 0| } 3611| 0| } 3612| 0| else 3613| 0| { 3614| 0| pe->flow += delta; 3615| 0| pv1->st_edge.flow += delta; 3616| 0| pv2->st_edge.flow += delta; 3617| 0| pBNS->tot_st_flow += 2 * delta; 3618| 0| } 3619| 0| pe->forbidden &= forbidden_edge_mask_inv; /* allow changes to O=X bond */ 3620| 0| INCHI_HEAPCHK 3621| 0| } 3622| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3623| 0| } 3624| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 3625| 0| if (cur_success) ------------------ | Branch (3625:21): [True: 0, False: 0] ------------------ 3626| 0| { 3627| 0| tot_succes += cur_success; 3628| | /* recalculate InChI from the structure */ 3629| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3629:25): [True: 0, False: 0] ------------------ 3630| 0| ppt_group_info, ppat_norm, ppat_prep))) 3631| 0| { 3632| 0| goto exit_function; 3633| 0| } 3634| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3634:25): [True: 0, False: 0] ------------------ 3635| 0| { 3636| 0| goto exit_function; 3637| 0| } 3638| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3638:25): [True: 0, False: 0] | Branch (3638:53): [True: 0, False: 0] ------------------ 3639| 0| { 3640| 0| goto exit_function; /* no fixed-H found */ 3641| 0| } 3642| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3642:25): [True: 0, False: 0] ------------------ 3643| 0| { 3644| 0| goto exit_function; 3645| 0| } 3646| 0| if (!pc2i->bHasDifference) ------------------ | Branch (3646:25): [True: 0, False: 0] ------------------ 3647| 0| { 3648| 0| goto exit_function; /* nothing to do */ 3649| 0| } 3650| 0| break; 3651| 0| }/* else 3652| | if ( bOnly_N_V ) { 3653| | bOnly_N_V = 0; 3654| | } 3655| | */ 3656| 0| } 3657| 73| } 3658| 66| } 3659| | 3660| 1.13k| if (( (pc2i->nNumTgInChI <= 1 && ------------------ | Branch (3660:12): [True: 1.08k, False: 47] ------------------ 3661| 1.08k| pc2i->nNumRemHInChI > pc2i->nNumRemHRevrs) || pc2i->len_c2at ) && ------------------ | Branch (3661:11): [True: 231, False: 853] | Branch (3661:57): [True: 900, False: 0] ------------------ 3662| 1.13k| bHas_N_V( at2, pStruct->num_atoms )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3662:10): [True: 148, False: 983] ------------------ 3663| 148| { 3664| | /*-----------------------------------------------------------------*/ 3665| | /* | | */ 3666| | /* case 14: restored:-N=AB=N=CD-XH original: (-)N-AB-N(+)=CD-XH */ 3667| | /* FixH: 0 0 0/1 0 1 */ 3668| | /* MobH: 0 0 1/0 0 0 */ 3669| | /* non-taut n/t any non any */ 3670| | /* taut */ 3671| | /* X = O, S, Se, N; N = N */ 3672| | /* t-group in original may have more (-) than in restored */ 3673| | /* same num_H and less (-) than in the restored structure */ 3674| | /* atom N(V)/N(IV)(+) is not taut in both */ 3675| | /* The following transformation should be possible: */ 3676| | /* | | */ 3677| | /* N=AB=N=CD-XH -> (-)N-AB-N-CD=XH(+) */ 3678| | /* This allows ADP to remove H(+) from -XH */ 3679| | /* As the result, the original structure has 0 or 1 t-group */ 3680| | /* Solution: separate charges between -N(III)= and N(V) */ 3681| | /*-----------------------------------------------------------------*/ 3682| 148| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3683| 148| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (3683:41): [True: 66, False: 82] ------------------ 3684| 148| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (3684:41): [True: 66, False: 0] ------------------ 3685| | 3686| 148| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3686:32): [True: 148, False: 0] | Branch (3686:45): [True: 148, False: 0] ------------------ 3687| 148| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3687:13): [True: 0, False: 0] | Branch (3687:26): [True: 0, False: 0] ------------------ 3688| 148| int num_N_V = 0, iat, i1, i2, i3, e1Flower, e1Plus, e2Plus, e2Minus, e3Plus; 3689| 148| int max_success = pc2i->nNumRemHInChI - pc2i->nNumRemHRevrs; 3690| 148| EDGE_LIST iat_X_List, iat_N_III_List; 3691| 148| AllocEdgeList( &iat_X_List, EDGE_LIST_CLEAR ); ------------------ | | 242| 148|#define EDGE_LIST_CLEAR (-1) ------------------ 3692| 148| AllocEdgeList( &iat_N_III_List, EDGE_LIST_CLEAR ); ------------------ | | 242| 148|#define EDGE_LIST_CLEAR (-1) ------------------ 3693| 148| cur_success = 0; 3694| 148| ret = 0; 3695| | 3696| 1.31k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3696:21): [True: 1.16k, False: 148] ------------------ 3697| 1.16k| { 3698| 1.16k| iat = nCanon2AtnoRevrs[i]; 3699| | /* search for N(V), 3 bonds */ 3700| 1.16k| if ( /* restored structure */ 3701| 1.16k| num_N_V < MAX_DIFF_FIXH && ------------------ | | 456| 2.32k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3701:17): [True: 1.16k, False: 0] ------------------ 3702| 1.16k| at2[iat].chem_bonds_valence == 5 && at2[iat].valence == 3 && ------------------ | Branch (3702:17): [True: 204, False: 960] | Branch (3702:53): [True: 190, False: 14] ------------------ 3703| 190| !at2[iat].charge && !at2[iat].radical && ------------------ | Branch (3703:17): [True: 186, False: 4] | Branch (3703:37): [True: 185, False: 1] ------------------ 3704| 185| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (3704:17): [True: 170, False: 15] | Branch (3704:55): [True: 152, False: 18] ------------------ 3705| 152| !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) && ------------------ | Branch (3705:19): [True: 70, False: 82] | Branch (3705:40): [True: 0, False: 70] ------------------ 3706| 152| !at2[iat].num_H && ------------------ | Branch (3706:17): [True: 151, False: 1] ------------------ 3707| 151| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3707:17): [True: 151, False: 0] | Branch (3707:60): [True: 151, False: 0] ------------------ 3708| 151| pBNS->edge[e].flow /* no charge */ && ------------------ | Branch (3708:17): [True: 151, False: 0] ------------------ 3709| 151| NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) && !pBNS->edge[j].forbidden && ------------------ | | 118| 151|#define NO_VERTEX -2 ------------------ | Branch (3709:17): [True: 148, False: 3] | Branch (3709:78): [True: 148, False: 0] ------------------ 3710| 148| !pBNS->edge[j].flow /* neutral, valence=5 */ && ------------------ | Branch (3710:17): [True: 148, False: 0] ------------------ 3711| | /* orig. InChI */ 3712| 148| !pStruct->endpoint[i] && ------------------ | Branch (3712:17): [True: 107, False: 41] ------------------ 3713| 107| !(nMobHInChI && nMobHInChI[i]) && pStruct->fixed_H && !pStruct->fixed_H[i]) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (3713:19): [True: 107, False: 0] | Branch (3713:33): [True: 4, False: 103] | Branch (3713:51): [True: 103, False: 0] | Branch (3713:71): [True: 102, False: 1] ------------------ 3714| 102| { 3715| 102| iat_N_V_Array[num_N_V++] = iat; 3716| 102| } 3717| 1.06k| else 3718| 1.06k| { 3719| | /* search for -N= */ 3720| 1.06k| if ( /* restored structure */ 3721| 1.06k| at2[iat].chem_bonds_valence == 3 && at2[iat].valence == 2 && ------------------ | Branch (3721:21): [True: 297, False: 765] | Branch (3721:57): [True: 223, False: 74] ------------------ 3722| 223| !at2[iat].charge && !at2[iat].radical && ------------------ | Branch (3722:21): [True: 185, False: 38] | Branch (3722:41): [True: 180, False: 5] ------------------ 3723| 180| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (3723:21): [True: 163, False: 17] | Branch (3723:59): [True: 138, False: 25] ------------------ 3724| 138| !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) && ------------------ | Branch (3724:23): [True: 85, False: 53] | Branch (3724:44): [True: 28, False: 57] ------------------ 3725| 110| !at2[iat].num_H && ------------------ | Branch (3725:21): [True: 107, False: 3] ------------------ 3726| 107| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3726:21): [True: 107, False: 0] | Branch (3726:65): [True: 107, False: 0] ------------------ 3727| 107| !pBNS->edge[e].flow /* no charge */ && ------------------ | Branch (3727:21): [True: 107, False: 0] ------------------ 3728| | /* orig. InChI */ 3729| | /*!pStruct->endpoint[i] &&*/ 3730| 107| !(nMobHInChI && nMobHInChI[i]) && pStruct->fixed_H && !pStruct->fixed_H[i]) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (3730:23): [True: 107, False: 0] | Branch (3730:37): [True: 3, False: 104] | Branch (3730:55): [True: 104, False: 0] | Branch (3730:75): [True: 99, False: 5] ------------------ 3731| 99| { 3732| | 3733| 99| if ((ret = AddToEdgeList(&iat_N_III_List, iat, 32))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3733:25): [True: 0, False: 99] ------------------ 3734| 0| { 3735| 0| goto exit_case_14; 3736| 0| } 3737| 99| } 3738| 963| else 3739| 963| { 3740| | /* search for -OH -NH-, -NH2 */ 3741| 963| if ( /* restored structure */ 3742| 963| at2[iat].chem_bonds_valence == at2[iat].valence && ------------------ | Branch (3742:25): [True: 324, False: 639] ------------------ 3743| 324| !at2[iat].charge && !at2[iat].radical && ------------------ | Branch (3743:25): [True: 222, False: 102] | Branch (3743:45): [True: 210, False: 12] ------------------ 3744| 210| ((pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1) || ------------------ | Branch (3744:27): [True: 45, False: 165] | Branch (3744:65): [True: 33, False: 12] ------------------ 3745| 177| pVA[iat].cNumValenceElectrons == 6) && ------------------ | Branch (3745:29): [True: 66, False: 111] ------------------ 3746| 99| at2[iat].num_H && ------------------ | Branch (3746:25): [True: 71, False: 28] ------------------ 3747| 71| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3747:25): [True: 71, False: 0] | Branch (3747:68): [True: 71, False: 0] ------------------ 3748| 71| pBNS->edge[e].flow /* no charge */ && ------------------ | Branch (3748:25): [True: 71, False: 0] ------------------ 3749| | /* orig. InChI */ 3750| 71| !(nMobHInChI && nMobHInChI[i]) && pStruct->fixed_H && pStruct->fixed_H[i]) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */ ------------------ | Branch (3750:27): [True: 71, False: 0] | Branch (3750:41): [True: 4, False: 67] | Branch (3750:59): [True: 67, False: 0] | Branch (3750:79): [True: 57, False: 10] ------------------ 3751| 57| { 3752| | 3753| 57| if ((ret = AddToEdgeList(&iat_X_List, iat, 32))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3753:29): [True: 0, False: 57] ------------------ 3754| 0| { 3755| 0| goto exit_case_14; 3756| 0| } 3757| 57| } 3758| 963| } 3759| 1.06k| } 3760| 1.16k| } 3761| 148| if (!max_success) ------------------ | Branch (3761:13): [True: 112, False: 36] ------------------ 3762| 112| { 3763| 112| max_success = inchi_min(num_N_V, iat_N_III_List.num_edges); ------------------ | | 139| 112|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 30, False: 82] | | ------------------ ------------------ 3764| 112| max_success = inchi_min(max_success, iat_X_List.num_edges); ------------------ | | 139| 112|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 21, False: 91] | | ------------------ ------------------ 3765| 112| } 3766| 148| if (num_N_V && iat_N_III_List.num_edges && iat_X_List.num_edges) ------------------ | Branch (3766:13): [True: 102, False: 46] | Branch (3766:24): [True: 51, False: 51] | Branch (3766:52): [True: 28, False: 23] ------------------ 3767| 28| { 3768| 56| for (i1 = 0; i1 < num_N_V && cur_success < max_success; i1++) ------------------ | Branch (3768:26): [True: 28, False: 28] | Branch (3768:42): [True: 28, False: 0] ------------------ 3769| 28| { 3770| 28| int iat_N_V = iat_N_V_Array[i1]; 3771| 28| if (NO_VERTEX == iat_N_V || ------------------ | | 118| 28|#define NO_VERTEX -2 ------------------ | Branch (3771:21): [True: 0, False: 28] ------------------ 3772| 28| 0 >= (e1Plus = pVA[iat_N_V].nCPlusGroupEdge - 1) || ------------------ | Branch (3772:21): [True: 0, False: 28] ------------------ 3773| 28| NO_VERTEX == (e1Flower = GetChargeFlowerUpperEdge(pBNS, pVA, e1Plus)) || ------------------ | | 118| 28|#define NO_VERTEX -2 ------------------ | Branch (3773:21): [True: 0, False: 28] ------------------ 3774| 28| 1 != pBNS->edge[e1Plus].flow || ------------------ | Branch (3774:21): [True: 0, False: 28] ------------------ 3775| 28| 0 != pBNS->edge[e1Flower].flow) ------------------ | Branch (3775:21): [True: 0, False: 28] ------------------ 3776| 0| { 3777| 0| continue; 3778| 0| } 3779| 56| for (i2 = iat_N_III_List.num_edges - 1; 0 <= i2 && cur_success < max_success; i2--) ------------------ | Branch (3779:57): [True: 33, False: 23] | Branch (3779:68): [True: 33, False: 0] ------------------ 3780| 33| { 3781| 33| int iat_N_III = iat_N_III_List.pnEdges[i2]; 3782| 33| if (NO_VERTEX == iat_N_III || ------------------ | | 118| 33|#define NO_VERTEX -2 ------------------ | Branch (3782:25): [True: 0, False: 33] ------------------ 3783| 33| 0 >= (e2Minus = pVA[iat_N_III].nCMinusGroupEdge - 1) || ------------------ | Branch (3783:25): [True: 0, False: 33] ------------------ 3784| 33| 0 >= (e2Plus = pVA[iat_N_III].nCPlusGroupEdge - 1) || ------------------ | Branch (3784:25): [True: 0, False: 33] ------------------ 3785| 33| 0 != pBNS->edge[e2Minus].flow || ------------------ | Branch (3785:25): [True: 0, False: 33] ------------------ 3786| 33| 1 != pBNS->edge[e2Plus].flow) ------------------ | Branch (3786:25): [True: 0, False: 33] ------------------ 3787| 0| { 3788| | /* do not consider this atom anymore */ 3789| 0| iat_N_III_List.pnEdges[i2] = NO_VERTEX; ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ 3790| 0| continue; 3791| 0| } 3792| 66| for (i3 = iat_X_List.num_edges - 1; 0 <= i3 && cur_success < max_success; i3--) ------------------ | Branch (3792:57): [True: 38, False: 28] | Branch (3792:68): [True: 38, False: 0] ------------------ 3793| 38| { 3794| 38| int iat_X = iat_X_List.pnEdges[i3]; 3795| 38| BNS_VERTEX* pv1n, * pv2n; 3796| 38| BNS_EDGE* pe1n, * pe2n, * pe1Plus, * pe2Minus, * pe3Plus; 3797| 38| Vertex v1n, v2n; 3798| 38| ret = 0; 3799| 38| if (NO_VERTEX == iat_X || ------------------ | | 118| 38|#define NO_VERTEX -2 ------------------ | Branch (3799:29): [True: 0, False: 38] ------------------ 3800| 38| 0 >= (e3Plus = pVA[iat_X].nCPlusGroupEdge - 1) || ------------------ | Branch (3800:29): [True: 0, False: 38] ------------------ 3801| 38| 1 != pBNS->edge[e3Plus].flow) ------------------ | Branch (3801:29): [True: 3, False: 35] ------------------ 3802| 3| { 3803| | /* do not consider this atom anymore */ 3804| 3| iat_X_List.pnEdges[i3] = NO_VERTEX; ------------------ | | 118| 3|#define NO_VERTEX -2 ------------------ 3805| 3| continue; 3806| 3| } 3807| | /* all is ready to check whether the following applies: 3808| | forbid changes of all charges and N,P,... flowers 3809| | allow to change edges: e2Minus, e3Plus 3810| | Increment flow in e1Flower 3811| | The result should be: increase in number of charges by 2 3812| | */ 3813| 35| pe1Plus = pBNS->edge + e1Plus; /* N(V) positive charge edge */ 3814| 35| pe2Minus = pBNS->edge + e2Minus; /* =N- negative charge edge */ 3815| 35| pe3Plus = pBNS->edge + e3Plus; /* -XH positive charge edge */ 3816| 35| pe = pBNS->edge + e1Flower; /* N(V) flower edge */ 3817| 35| pv1 = pBNS->vert + (v1 = pe->neighbor1); 3818| 35| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 3819| 105| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (3819:58): [True: 105, False: 0] ------------------ 3820| 105| { 3821| 105| pe1n = pBNS->edge + pv1->iedge[j]; 3822| 105| if (pe1n->flow && !pe1n->forbidden && pe1n != pe1Plus) ------------------ | Branch (3822:33): [True: 70, False: 35] | Branch (3822:47): [True: 70, False: 0] | Branch (3822:67): [True: 35, False: 35] ------------------ 3823| 35| { 3824| 35| pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1); 3825| 35| break; 3826| 35| } 3827| 105| } 3828| 35| if (j < 0) ------------------ | Branch (3828:29): [True: 0, False: 35] ------------------ 3829| 0| { 3830| 0| continue; /* not found -- should not happen */ 3831| 0| } 3832| 70| for (j = pv2->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (3832:58): [True: 70, False: 0] ------------------ 3833| 70| { /* was -2; changed 2006-2-28 12:35pm*/ 3834| 70| pe2n = pBNS->edge + pv2->iedge[j]; 3835| 70| if (pe2n->flow && !pe2n->forbidden && pe2n != pe1Plus) ------------------ | Branch (3835:33): [True: 35, False: 35] | Branch (3835:47): [True: 35, False: 0] | Branch (3835:67): [True: 35, False: 0] ------------------ 3836| 35| { 3837| 35| pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2); 3838| 35| break; 3839| 35| } 3840| 70| } 3841| 35| if (j < 0) ------------------ | Branch (3841:29): [True: 0, False: 35] ------------------ 3842| 0| { 3843| 0| continue; /* not found -- should not happen */ 3844| 0| } 3845| 35| delta = 1; 3846| 35| pe->flow += delta; 3847| 35| pe1n->flow -= delta; 3848| 35| pe2n->flow -= delta; 3849| 35| pv1n->st_edge.flow -= delta; 3850| 35| pv2n->st_edge.flow -= delta; 3851| 35| pBNS->tot_st_flow -= 2 * delta; 3852| | 3853| 35| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3854| 35| SetForbiddenEdgeMask(pBNS, &OtherNFlowerEdges, forbidden_edge_mask); 3855| | 3856| | /* allow two charges to change */ 3857| 35| pe2Minus->forbidden &= forbidden_edge_mask_inv; 3858| 35| pe3Plus->forbidden &= forbidden_edge_mask_inv; 3859| | /* test #1 */ 3860| 35| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3861| 35| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 3862| 35| INCHI_HEAPCHK 3863| 35| if (ret < 0) ------------------ | Branch (3863:33): [True: 0, False: 35] ------------------ 3864| 0| { 3865| 0| goto exit_case_14; 3866| 0| } 3867| 35| else 3868| 35| { 3869| 35| if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) || ------------------ | Branch (3869:37): [True: 22, False: 13] | Branch (3869:51): [True: 20, False: 2] | Branch (3869:70): [True: 11, False: 9] ------------------ 3870| 11| (vPathEnd == v2n && vPathStart == v1n)) && ------------------ | Branch (3870:38): [True: 9, False: 2] | Branch (3870:57): [True: 0, False: 9] ------------------ 3871| 11| nDeltaCharge == 2) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3871:37): [True: 5, False: 6] ------------------ 3872| 5| { 3873| 5| ; /* success */ 3874| 5| } 3875| 30| else 3876| 30| { 3877| 30| ret = 0; 3878| 30| } 3879| 35| } 3880| | /* restore BNS */ 3881| 35| pe2Minus->forbidden |= forbidden_edge_mask; 3882| 35| pe3Plus->forbidden |= forbidden_edge_mask; 3883| 35| pe->flow -= delta; 3884| 35| pe1n->flow += delta; 3885| 35| pe2n->flow += delta; 3886| 35| pv1n->st_edge.flow += delta; 3887| 35| pv2n->st_edge.flow += delta; 3888| 35| pBNS->tot_st_flow += 2 * delta; 3889| 35| if (ret == 1) ------------------ | Branch (3889:29): [True: 5, False: 30] ------------------ 3890| 5| { 3891| | /* test #2: check if charge separation is possible */ 3892| 5| pe->flow += delta; 3893| 5| pe1n->flow -= delta; 3894| 5| pe2n->flow -= delta; 3895| 5| pv1n->st_edge.flow -= delta; 3896| 5| pv2n->st_edge.flow -= delta; 3897| 5| pBNS->tot_st_flow -= 2 * delta; 3898| | 3899| | /* allow two charges (N(V) and N(III)) to change */ 3900| 5| pe2Minus->forbidden &= forbidden_edge_mask_inv; 3901| 5| pe1Plus->forbidden &= forbidden_edge_mask_inv; 3902| | /* test #2 */ 3903| 5| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3904| 5| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 3905| 5| if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) || ------------------ | Branch (3905:33): [True: 5, False: 0] | Branch (3905:47): [True: 5, False: 0] | Branch (3905:66): [True: 5, False: 0] ------------------ 3906| 0| (vPathEnd == v2n && vPathStart == v1n)) && ------------------ | Branch (3906:34): [True: 0, False: 0] | Branch (3906:53): [True: 0, False: 0] ------------------ 3907| 5| nDeltaCharge == 2) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3907:33): [True: 5, False: 0] ------------------ 3908| 5| { 3909| | /* success; actually change charges */ 3910| 5| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 3911| 5| if (ret > 0) ------------------ | Branch (3911:37): [True: 5, False: 0] ------------------ 3912| 5| { 3913| 5| nNumRunBNS++; 3914| 5| cur_success++; /* 14 */ 3915| 5| } 3916| 5| } 3917| 5| if (ret <= 0) ------------------ | Branch (3917:33): [True: 0, False: 5] ------------------ 3918| 0| { 3919| | /* failed: restore BNS flow */ 3920| 0| pe->flow -= delta; 3921| 0| pe1n->flow += delta; 3922| 0| pe2n->flow += delta; 3923| 0| pv1n->st_edge.flow += delta; 3924| 0| pv2n->st_edge.flow += delta; 3925| 0| pBNS->tot_st_flow += 2 * delta; 3926| 0| } 3927| 5| INCHI_HEAPCHK 3928| 5| } 3929| 35| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3930| 35| RemoveForbiddenEdgeMask(pBNS, &OtherNFlowerEdges, forbidden_edge_mask); 3931| 35| if (ret > 0) ------------------ | Branch (3931:29): [True: 5, False: 30] ------------------ 3932| 5| { 3933| | /* do not repeat for the same atoms */ 3934| 5| iat_N_V_Array[i1] = NO_VERTEX; ------------------ | | 118| 5|#define NO_VERTEX -2 ------------------ 3935| 5| iat_N_III_List.pnEdges[i2] = NO_VERTEX; ------------------ | | 118| 5|#define NO_VERTEX -2 ------------------ 3936| 5| iat_X_List.pnEdges[i3] = NO_VERTEX; ------------------ | | 118| 5|#define NO_VERTEX -2 ------------------ 3937| 5| } 3938| 35| if (ret < 0) ------------------ | Branch (3938:29): [True: 0, False: 35] ------------------ 3939| 0| { 3940| 0| goto exit_case_14; 3941| 0| } 3942| 35| if (ret > 0) ------------------ | Branch (3942:29): [True: 5, False: 30] ------------------ 3943| 5| { 3944| 5| break; 3945| 5| } 3946| 35| } /* i3 cycle */ 3947| 33| if (ret > 0) ------------------ | Branch (3947:25): [True: 5, False: 28] ------------------ 3948| 5| { 3949| 5| break; 3950| 5| } 3951| 33| } /* i2 cycle */ 3952| 28| } 3953| 28| } 3954| 148| exit_case_14: 3955| 148| AllocEdgeList(&iat_X_List, EDGE_LIST_FREE); ------------------ | | 243| 148|#define EDGE_LIST_FREE (-2) ------------------ 3956| 148| AllocEdgeList(&iat_N_III_List, EDGE_LIST_FREE); ------------------ | | 243| 148|#define EDGE_LIST_FREE (-2) ------------------ 3957| 148| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 3958| 148| RemoveForbiddenEdgeMask(pBNS, &OtherNFlowerEdges, forbidden_edge_mask); 3959| 148| CurrEdges.num_edges = 0; /* clear current edge list */ 3960| 148| if (ret < 0) ------------------ | Branch (3960:13): [True: 0, False: 148] ------------------ 3961| 0| { 3962| 0| goto exit_function; 3963| 0| } 3964| 148| if (cur_success) ------------------ | Branch (3964:13): [True: 5, False: 143] ------------------ 3965| 5| { 3966| 5| tot_succes += cur_success; 3967| | /* recalculate InChI from the structure */ 3968| 5| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3968:17): [True: 0, False: 5] ------------------ 3969| 5| ppt_group_info, ppat_norm, ppat_prep))) 3970| 0| { 3971| 0| goto exit_function; 3972| 0| } 3973| 5| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3973:17): [True: 0, False: 5] ------------------ 3974| 0| { 3975| 0| goto exit_function; 3976| 0| } 3977| 5| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3977:17): [True: 0, False: 5] | Branch (3977:45): [True: 0, False: 0] ------------------ 3978| 0| { 3979| 0| goto exit_function; /* no fixed-H found */ 3980| 0| } 3981| 5| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3981:17): [True: 0, False: 5] ------------------ 3982| 0| { 3983| 0| goto exit_function; 3984| 0| } 3985| 5| if (!pc2i->bHasDifference) ------------------ | Branch (3985:17): [True: 0, False: 5] ------------------ 3986| 0| { 3987| 0| goto exit_function; /* nothing to do */ 3988| 0| } 3989| 5| } 3990| 148| } 3991| | 3992| 1.13k| if (pc2i->nNumTgMRevrs > pc2i->nNumTgMInChI || ------------------ | Branch (3992:9): [True: 114, False: 1.01k] ------------------ 3993| 1.01k| pc2i->nNumRemHRevrs < pc2i->nNumRemHInChI || ------------------ | Branch (3993:10): [True: 230, False: 787] ------------------ 3994| 787| pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || ------------------ | Branch (3994:10): [True: 496, False: 291] ------------------ 3995| 291| (pc2i->nNumTgInChI <= 1 && pc2i->nNumTgRevrs > pc2i->nNumTgInChI)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3995:11): [True: 287, False: 4] | Branch (3995:37): [True: 73, False: 214] ------------------ 3996| 913| { 3997| | /*--------------------------------------------------------------*/ 3998| | /* case 15: restored: -(+)O=AB-N< orig: -O-AB=N(+)< */ 3999| | /* (a) restored t-groups have more (-) than in original InChI */ 4000| | /* (b) Mobile-H charge: restored > original InChI *and* */ 4001| | /* removed H: restored < original InChI */ 4002| | /* (c) restored t-groups have less endpnoits than in orig InChI */ 4003| | /* O = O, S, Se, Te; N = N */ 4004| | /* Solution: move (+) from -O(+)= to -N< */ 4005| | /*--------------------------------------------------------------*/ 4006| 913| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 4007| 913| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4008| 913| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (4008:32): [True: 913, False: 0] | Branch (4008:45): [True: 913, False: 0] ------------------ 4009| 913| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (4009:13): [True: 0, False: 0] | Branch (4009:26): [True: 0, False: 0] ------------------ 4010| 913| cur_success = 0; 4011| | 4012| | /* search for -O(+)= */ 4013| | /* search for -N< */ 4014| 7.85k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (4014:21): [True: 6.94k, False: 913] ------------------ 4015| 6.94k| { /* i = canonical number - 1 */ 4016| 6.94k| iat = nCanon2AtnoRevrs[i]; 4017| 6.94k| if ( /* -O(+)= in restored atom: charge=1, has no H, a double bond */ 4018| 6.94k| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 456| 13.8k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4018:17): [True: 6.94k, False: 0] ------------------ 4019| 6.94k| at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (4019:17): [True: 1.13k, False: 5.80k] | Branch (4019:41): [True: 879, False: 256] ------------------ 4020| 879| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4020:17): [True: 590, False: 289] | Branch (4020:67): [True: 537, False: 53] ------------------ 4021| 537| (pVA[iat].cNumValenceElectrons == 6) && ------------------ | Branch (4021:17): [True: 133, False: 404] ------------------ 4022| | /* in orig.InChI: an endpoint, has fixed-H */ 4023| | /*pStruct->endpoint[i] &&*/ 4024| 133| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (4024:19): [True: 133, False: 0] | Branch (4024:39): [True: 3, False: 130] ------------------ 4025| 130| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (4025:19): [True: 130, False: 0] | Branch (4025:33): [True: 0, False: 130] ------------------ 4026| | /* has (+) edge */ 4027| 130| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden) ------------------ | Branch (4027:17): [True: 130, False: 0] | Branch (4027:60): [True: 92, False: 38] ------------------ 4028| 92| { 4029| | 4030| 92| iat_DB_Charged[num_DB_Charged++] = iat; 4031| | /* 4032| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 4033| | goto exit_function; 4034| | } 4035| | */ 4036| 92| } 4037| 6.85k| else 4038| 6.85k| { 4039| 6.85k| if ( /* -N< in restored atom: charge=0, has no H, has no double bond, N only */ 4040| 6.85k| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 13.7k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4040:21): [True: 6.85k, False: 0] ------------------ 4041| 6.85k| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4041:21): [True: 4.40k, False: 2.44k] | Branch (4041:45): [True: 3.72k, False: 676] ------------------ 4042| 3.72k| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4042:21): [True: 983, False: 2.74k] | Branch (4042:72): [True: 766, False: 217] ------------------ 4043| 766| (pVA[iat].cNumValenceElectrons == 5 && ------------------ | Branch (4043:22): [True: 174, False: 592] ------------------ 4044| 174| pVA[iat].cPeriodicRowNumber == 1) && ------------------ | Branch (4044:25): [True: 123, False: 51] ------------------ 4045| | /* in orig.InChI: an endpoint, has fixed-H */ 4046| | /*pStruct->endpoint[i] &&*/ 4047| 123| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (4047:23): [True: 123, False: 0] | Branch (4047:43): [True: 2, False: 121] ------------------ 4048| 121| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (4048:23): [True: 121, False: 0] | Branch (4048:37): [True: 1, False: 120] ------------------ 4049| | /* has (+) edge */ 4050| 120| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden) ------------------ | Branch (4050:21): [True: 105, False: 15] | Branch (4050:64): [True: 105, False: 0] ------------------ 4051| 105| { 4052| | 4053| 105| iat_SB_Neutr[num_SB_Neutr++] = iat; 4054| 105| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 105|#define INC_ADD_EDGE 64 ------------------ | Branch (4054:25): [True: 0, False: 105] ------------------ 4055| 0| { 4056| 0| goto exit_function; 4057| 0| } 4058| 105| } 4059| 6.85k| } 4060| 6.94k| } 4061| 913| if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 913|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 76, False: 837] | | ------------------ ------------------ | Branch (4061:13): [True: 14, False: 899] ------------------ 4062| 14| { 4063| | /* detected; attempt to fix */ 4064| 14| BNS_VERTEX* pv1n, * pv2n; 4065| 14| BNS_EDGE* pe1n, * pe2n; 4066| 14| Vertex v1n, v2n; 4067| 14| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4068| 14| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 4069| 14| delta = 1; 4070| 28| for (i = 0; i < num_DB_Charged && cur_success < num_try; i++) ------------------ | Branch (4070:25): [True: 15, False: 13] | Branch (4070:47): [True: 14, False: 1] ------------------ 4071| 14| { 4072| 14| iat = iat_DB_Charged[i]; 4073| 14| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 4074| 14| if (pe->flow) ------------------ | Branch (4074:21): [True: 0, False: 14] ------------------ 4075| 0| continue; 4076| 14| pv1 = pBNS->vert + (v1 = pe->neighbor1); 4077| 14| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 4078| | 4079| 31| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4079:50): [True: 31, False: 0] ------------------ 4080| 31| { 4081| 31| pe1n = pBNS->edge + pv1->iedge[j]; 4082| 31| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (4082:25): [True: 14, False: 17] | Branch (4082:39): [True: 14, False: 0] ------------------ 4083| 14| { 4084| 14| pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1); 4085| 14| break; 4086| 14| } 4087| 31| } 4088| 14| if (j < 0) ------------------ | Branch (4088:21): [True: 0, False: 14] ------------------ 4089| 0| { 4090| 0| continue; /* not found */ 4091| 0| } 4092| | 4093| 14| for (j = pv2->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4093:50): [True: 14, False: 0] ------------------ 4094| 14| { /* was -2; changed 2006-2-28 12:35pm*/ 4095| 14| pe2n = pBNS->edge + pv2->iedge[j]; 4096| 14| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (4096:25): [True: 14, False: 0] | Branch (4096:39): [True: 14, False: 0] ------------------ 4097| 14| { 4098| 14| pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2); 4099| 14| break; 4100| 14| } 4101| 14| } 4102| 14| if (j < 0) ------------------ | Branch (4102:21): [True: 0, False: 14] ------------------ 4103| 0| { 4104| 0| continue; /* not found */ 4105| 0| } 4106| | 4107| 14| pe->flow += delta; 4108| 14| pe1n->flow -= delta; 4109| 14| pe2n->flow -= delta; 4110| 14| pv1n->st_edge.flow -= delta; 4111| 14| pv2n->st_edge.flow -= delta; 4112| 14| pBNS->tot_st_flow -= 2 * delta; 4113| | 4114| 14| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4115| 14| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 4116| | 4117| 14| if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) || ------------------ | Branch (4117:21): [True: 7, False: 7] | Branch (4117:35): [True: 2, False: 5] | Branch (4117:54): [True: 2, False: 0] ------------------ 4118| 5| (vPathEnd == v2n && vPathStart == v1n)) && ------------------ | Branch (4118:22): [True: 3, False: 2] | Branch (4118:41): [True: 2, False: 1] ------------------ 4119| 4| (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4119:22): [True: 0, False: 4] | Branch (4119:43): [True: 4, False: 0] ------------------ 4120| 4| { 4121| | /* Moved charge from O(+) to -N< => nDeltaCharge == 1 or 0 if pe2n = -N< charge edge */ 4122| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 4123| 4| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 4124| 4| if (ret > 0) ------------------ | Branch (4124:25): [True: 4, False: 0] ------------------ 4125| 4| { 4126| 4| nNumRunBNS++; 4127| 4| cur_success++; /* 15 */ 4128| 4| } 4129| 4| } 4130| 10| else 4131| 10| { 4132| 10| pe->flow -= delta; 4133| 10| pe1n->flow += delta; 4134| 10| pe2n->flow += delta; 4135| 10| pv1n->st_edge.flow += delta; 4136| 10| pv2n->st_edge.flow += delta; 4137| 10| pBNS->tot_st_flow += 2 * delta; 4138| 10| } 4139| 14| INCHI_HEAPCHK 4140| 14| } 4141| 14| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4142| 14| } 4143| 913| CurrEdges.num_edges = 0; /* clear current edge list */ 4144| 913| if (cur_success) ------------------ | Branch (4144:13): [True: 4, False: 909] ------------------ 4145| 4| { 4146| 4| tot_succes += cur_success; 4147| | /* recalculate InChI from the structure */ 4148| 4| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4148:17): [True: 0, False: 4] ------------------ 4149| 4| ppt_group_info, ppat_norm, ppat_prep))) 4150| 0| { 4151| 0| goto exit_function; 4152| 0| } 4153| 4| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4153:17): [True: 0, False: 4] ------------------ 4154| 0| { 4155| 0| goto exit_function; 4156| 0| } 4157| 4| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4157:17): [True: 2, False: 2] | Branch (4157:45): [True: 0, False: 2] ------------------ 4158| 0| { 4159| 0| goto exit_function; /* no fixed-H found */ 4160| 0| } 4161| 4| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4161:17): [True: 0, False: 4] ------------------ 4162| 0| { 4163| 0| goto exit_function; 4164| 0| } 4165| 4| if (!pc2i->bHasDifference) ------------------ | Branch (4165:17): [True: 0, False: 4] ------------------ 4166| 0| { 4167| 0| goto exit_function; /* nothing to do */ 4168| 0| } 4169| 4| } 4170| 913| } 4171| | 4172| 1.13k| if (pc2i->nNumTgDiffMinus) ------------------ | Branch (4172:9): [True: 65, False: 1.06k] ------------------ 4173| 65| { 4174| | /*----------------------------------------------------------------*/ 4175| | /* case 16: restored: O=X-NH(-) orig.: O(-)-X=NH */ 4176| | /* t-group: (H,-) (2H) */ 4177| | /* O(-) = S, Se, Te; N = N; */ 4178| | /* Solution: move (-) from O(-) to -NH(-) */ 4179| | /*----------------------------------------------------------------*/ 4180| 65| int num_SB_N_Minus = 0, num_DB_O_Neutr = 0, iat, itg; 4181| 65| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4182| 65| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (4182:32): [True: 65, False: 0] | Branch (4182:45): [True: 65, False: 0] ------------------ 4183| 65| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (4183:13): [True: 0, False: 0] | Branch (4183:26): [True: 0, False: 0] ------------------ 4184| 65| cur_success = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 4185| | 4186| 136| for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++) ------------------ | Branch (4186:23): [True: 77, False: 59] | Branch (4186:57): [True: 72, False: 5] ------------------ 4187| 72| { 4188| 72| if (pStruct->ti.t_group[itg].nNumEndpoints != pStruct->One_ti.t_group[itg].nNumEndpoints || ------------------ | Branch (4188:17): [True: 5, False: 67] ------------------ 4189| 67| pStruct->ti.t_group[itg].num[1] >= pStruct->One_ti.t_group[itg].num[1]) ------------------ | Branch (4189:17): [True: 29, False: 38] ------------------ 4190| 34| { 4191| 34| continue; 4192| 34| } 4193| 38| CurrEdges.num_edges = num_SB_N_Minus = num_DB_O_Neutr = 0; 4194| 38| cur_success = 0; 4195| 38| for (j = 0, k = pStruct->One_ti.t_group[itg].nFirstEndpointAtNoPos; 4196| 146| j < pStruct->One_ti.t_group[itg].nNumEndpoints; j++) ------------------ | Branch (4196:17): [True: 108, False: 38] ------------------ 4197| 108| { 4198| 108| i = pStruct->One_ti.nEndpointAtomNumber[k + j]; /* canonical number in restored struct. */ 4199| 108| iat = nCanon2AtnoRevrs[i]; 4200| 108| if ( /* in restored atom: charge=0, has no H, has double bond, O, S, Se, Te */ 4201| 108| num_DB_O_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 216|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4201:21): [True: 108, False: 0] ------------------ 4202| 108| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4202:21): [True: 50, False: 58] | Branch (4202:45): [True: 34, False: 16] ------------------ 4203| 34| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4203:21): [True: 34, False: 0] | Branch (4203:71): [True: 34, False: 0] ------------------ 4204| 34| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (4204:21): [True: 31, False: 3] ------------------ 4205| | /* in orig.InChI: an endpoint, may have fixed-H */ 4206| 31| pStruct->endpoint[i] && ------------------ | Branch (4206:21): [True: 20, False: 11] ------------------ 4207| | /*!(pStruct->fixed_H && pStruct->fixed_H[i]) &&*/ 4208| 20| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (4208:23): [True: 20, False: 0] | Branch (4208:37): [True: 0, False: 20] ------------------ 4209| | /* has (-) edge */ 4210| 20| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (4210:21): [True: 20, False: 0] | Branch (4210:65): [True: 20, False: 0] ------------------ 4211| 20| { 4212| | 4213| 20| iat_DB_O_Neutr[num_DB_O_Neutr++] = iat; 4214| | 4215| 20| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 20|#define INC_ADD_EDGE 64 ------------------ | Branch (4215:25): [True: 0, False: 20] ------------------ 4216| 0| { 4217| 0| goto exit_function; 4218| 0| } 4219| 20| } 4220| 88| else 4221| 88| { 4222| 88| if ( /* in restored atom: charge=-1, has H, has double bond, N */ 4223| 88| num_SB_N_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 176|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4223:25): [True: 88, False: 0] ------------------ 4224| 88| at2[iat].charge == -1 && at2[iat].num_H && ------------------ | Branch (4224:25): [True: 58, False: 30] | Branch (4224:50): [True: 13, False: 45] ------------------ 4225| 13| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4225:25): [True: 8, False: 5] | Branch (4225:76): [True: 8, False: 0] ------------------ 4226| 8| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (4226:25): [True: 8, False: 0] | Branch (4226:63): [True: 8, False: 0] ------------------ 4227| | /* in orig.InChI: an endpoint, has no fixed-H */ 4228| 8| pStruct->endpoint[i] && ------------------ | Branch (4228:25): [True: 4, False: 4] ------------------ 4229| 4| (pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (4229:26): [True: 4, False: 0] | Branch (4229:46): [True: 4, False: 0] ------------------ 4230| 4| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (4230:27): [True: 4, False: 0] | Branch (4230:41): [True: 0, False: 4] ------------------ 4231| | /* has (-) edge */ 4232| 4| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && ------------------ | Branch (4232:25): [True: 4, False: 0] ------------------ 4233| 4| 0 == pBNS->edge[e].forbidden) ------------------ | Branch (4233:25): [True: 4, False: 0] ------------------ 4234| 4| { 4235| | 4236| 4| iat_SB_N_Minus[num_SB_N_Minus++] = iat; 4237| | /* 4238| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 4239| | goto exit_function; 4240| | } 4241| | */ 4242| 4| } 4243| 88| } 4244| 108| } 4245| 38| if ((num_try = inchi_min(num_SB_N_Minus, num_DB_O_Neutr))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 38|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 15, False: 23] | | ------------------ ------------------ | Branch (4245:17): [True: 3, False: 35] ------------------ 4246| 3| { 4247| | /* detected; attempt to fix */ 4248| 3| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4249| 3| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 4250| | /* allow stereobonds in rings change */ 4251| | /* 4252| | if ( forbidden_stereo_edge_mask ) 4253| | RemoveForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 4254| | */ 4255| 3| delta = 1; 4256| 6| for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++) ------------------ | Branch (4256:29): [True: 3, False: 3] | Branch (4256:51): [True: 3, False: 0] ------------------ 4257| 3| { 4258| 3| iat = iat_SB_N_Minus[i]; 4259| 3| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 4260| 3| if (!pe->flow) ------------------ | Branch (4260:25): [True: 0, False: 3] ------------------ 4261| 0| continue; 4262| 3| pv1 = pBNS->vert + (v1 = pe->neighbor1); 4263| 3| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 4264| | 4265| | /*pe->forbidden |= forbidden_edge_mask;*/ 4266| 3| pe->flow -= delta; 4267| 3| pv1->st_edge.flow -= delta; 4268| 3| pv2->st_edge.flow -= delta; 4269| 3| pBNS->tot_st_flow -= 2 * delta; 4270| | 4271| 3| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4272| 3| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 4273| | 4274| 3| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (4274:25): [True: 3, False: 0] | Branch (4274:39): [True: 0, False: 3] | Branch (4274:57): [True: 0, False: 0] ------------------ 4275| 3| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4275:26): [True: 3, False: 0] | Branch (4275:44): [True: 2, False: 1] | Branch (4275:66): [True: 2, False: 0] ------------------ 4276| 2| { 4277| | /* Moved (-) charge to =O => nDeltaCharge == 1 */ 4278| | /* Flow change on pe (-)charge edge (atom -NH(-)) is not known to RunBnsTestOnce()) */ 4279| 2| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 4280| 2| if (ret > 0) ------------------ | Branch (4280:29): [True: 2, False: 0] ------------------ 4281| 2| { 4282| 2| nNumRunBNS++; 4283| 2| cur_success++; /* 16 */ 4284| 2| } 4285| 2| } 4286| 1| else 4287| 1| { 4288| 1| pe->forbidden &= forbidden_edge_mask_inv; 4289| 1| pe->flow += delta; 4290| 1| pv1->st_edge.flow += delta; 4291| 1| pv2->st_edge.flow += delta; 4292| 1| pBNS->tot_st_flow += 2 * delta; 4293| 1| } 4294| 3| INCHI_HEAPCHK 4295| 3| } 4296| 3| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4297| | /* 4298| | if ( forbidden_stereo_edge_mask ) 4299| | SetForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 4300| | */ 4301| 3| } 4302| 38| CurrEdges.num_edges = 0; /* clear current edge list */ 4303| 38| if (cur_success) ------------------ | Branch (4303:17): [True: 2, False: 36] ------------------ 4304| 2| { 4305| 2| tot_succes += cur_success; 4306| | /* recalculate InChI from the structure */ 4307| 2| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4307:21): [True: 1, False: 1] ------------------ 4308| 2| ppt_group_info, ppat_norm, ppat_prep))) 4309| 1| { 4310| 1| goto exit_function; 4311| 1| } 4312| 1| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4312:21): [True: 0, False: 1] ------------------ 4313| 0| { 4314| 0| goto exit_function; 4315| 0| } 4316| 1| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4316:21): [True: 0, False: 1] | Branch (4316:49): [True: 0, False: 0] ------------------ 4317| 0| { 4318| 0| goto exit_function; /* no fixed-H found */ 4319| 0| } 4320| 1| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4320:21): [True: 0, False: 1] ------------------ 4321| 0| { 4322| 0| goto exit_function; 4323| 0| } 4324| 1| if (!pc2i->bHasDifference) ------------------ | Branch (4324:21): [True: 0, False: 1] ------------------ 4325| 0| { 4326| 0| goto exit_function; /* nothing to do */ 4327| 0| } 4328| 1| } 4329| 38| } 4330| 65| } 4331| | 4332| 1.13k| if (pc2i->nNumRemHInChI < pc2i->nNumRemHRevrs) ------------------ | Branch (4332:9): [True: 173, False: 957] ------------------ 4333| 173| { 4334| | /*--------------------------------------------------------------*/ 4335| | /* case 17: restored: OH(+)=AB-O- orig. HO-AB=O(+)- */ 4336| | /* number of removed H: n+m n */ 4337| | /* OH(+) = N, O, S, Se; -O- = P,As,O,S,Se,Te,F,Cl,Br,I */ 4338| | /* Solution: move (+) from OH(+) to -O- */ 4339| | /*--------------------------------------------------------------*/ 4340| 173| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 4341| 173| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4342| 173| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (4342:32): [True: 173, False: 0] | Branch (4342:45): [True: 173, False: 0] ------------------ 4343| 173| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (4343:13): [True: 0, False: 0] | Branch (4343:26): [True: 0, False: 0] ------------------ 4344| 173| cur_success = 0; 4345| | 4346| 1.36k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (4346:21): [True: 1.19k, False: 173] ------------------ 4347| 1.19k| { /* i = canonical number - 1 */ 4348| 1.19k| iat = nCanon2AtnoRevrs[i]; 4349| 1.19k| if ( /* in restored atom: charge=+1, has H, has double bond, N, O, S, Se, Te */ 4350| 1.19k| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 456| 2.38k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4350:17): [True: 1.19k, False: 0] ------------------ 4351| 1.19k| at2[iat].charge == 1 && at2[iat].num_H && ------------------ | Branch (4351:17): [True: 199, False: 993] | Branch (4351:41): [True: 173, False: 26] ------------------ 4352| 173| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4352:17): [True: 146, False: 27] | Branch (4352:67): [True: 146, False: 0] ------------------ 4353| 146| (pVA[iat].cNumValenceElectrons == 6 || ------------------ | Branch (4353:18): [True: 53, False: 93] ------------------ 4354| 93| (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1)) && ------------------ | Branch (4354:22): [True: 93, False: 0] | Branch (4354:60): [True: 91, False: 2] ------------------ 4355| | /* has (+) edge */ 4356| 144| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4356:17): [True: 144, False: 0] | Branch (4356:60): [True: 137, False: 7] ------------------ 4357| 137| { 4358| | 4359| 137| iat_DB_Charged[num_DB_Charged++] = iat; 4360| | /* 4361| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 4362| | goto exit_function; 4363| | } 4364| | */ 4365| 137| } 4366| 1.05k| else 4367| 1.05k| { 4368| 1.05k| if ( /* in restored atom: charge=0, has no H, has no double bond, N, P, O, S, Se, Te */ 4369| 1.05k| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 456| 2.11k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4369:21): [True: 1.05k, False: 0] ------------------ 4370| 1.05k| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4370:21): [True: 807, False: 248] | Branch (4370:45): [True: 658, False: 149] ------------------ 4371| 658| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4371:21): [True: 280, False: 378] | Branch (4371:72): [True: 259, False: 21] ------------------ 4372| 259| (pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cNumValenceElectrons == 7 || ------------------ | Branch (4372:22): [True: 131, False: 128] | Branch (4372:60): [True: 32, False: 96] ------------------ 4373| 96| (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber > 1)) && ------------------ | Branch (4373:26): [True: 30, False: 66] | Branch (4373:64): [True: 15, False: 15] ------------------ 4374| | /* in orig.InChI: not an endpoint */ 4375| 178| !pStruct->endpoint[i] && ------------------ | Branch (4375:21): [True: 171, False: 7] ------------------ 4376| 171| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (4376:23): [True: 171, False: 0] | Branch (4376:43): [True: 7, False: 164] ------------------ 4377| 164| !(nMobHInChI && nMobHInChI[i]) && ------------------ | Branch (4377:23): [True: 164, False: 0] | Branch (4377:37): [True: 3, False: 161] ------------------ 4378| | /* has (+) edge */ 4379| 161| (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && ------------------ | Branch (4379:21): [True: 159, False: 2] ------------------ 4380| 159| 0 == pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4380:21): [True: 159, False: 0] ------------------ 4381| 159| { 4382| | 4383| 159| iat_SB_Neutr[num_SB_Neutr++] = iat; 4384| | 4385| 159| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 159|#define INC_ADD_EDGE 64 ------------------ | Branch (4385:25): [True: 0, False: 159] ------------------ 4386| 0| { 4387| 0| goto exit_function; 4388| 0| } 4389| 159| } 4390| 1.05k| } 4391| 1.19k| } 4392| 173| if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 173|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 25, False: 148] | | ------------------ ------------------ | Branch (4392:13): [True: 110, False: 63] ------------------ 4393| 110| { 4394| 110| BNS_VERTEX* pv1n, * pv2n; 4395| 110| BNS_EDGE* pe1n, * pe2n; 4396| 110| Vertex v1n, v2n; 4397| | 4398| 110| num_try = inchi_min(num_try, pc2i->nNumRemHRevrs - pc2i->nNumRemHInChI); ------------------ | | 139| 110|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 110] | | ------------------ ------------------ 4399| | /* detected; attempt to fix */ 4400| 110| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4401| 110| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 4402| 110| delta = 1; 4403| 221| for (i = 0; i < num_DB_Charged && cur_success < num_try; i++) ------------------ | Branch (4403:25): [True: 112, False: 109] | Branch (4403:47): [True: 111, False: 1] ------------------ 4404| 111| { 4405| 111| iat = iat_DB_Charged[i]; 4406| 111| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 4407| 111| if (pe->flow) ------------------ | Branch (4407:21): [True: 0, False: 111] ------------------ 4408| 0| { 4409| 0| continue; 4410| 0| } 4411| 111| pv1 = pBNS->vert + (v1 = pe->neighbor1); 4412| 111| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 4413| | 4414| 220| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4414:50): [True: 220, False: 0] ------------------ 4415| 220| { 4416| 220| pe1n = pBNS->edge + pv1->iedge[j]; 4417| 220| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (4417:25): [True: 111, False: 109] | Branch (4417:39): [True: 111, False: 0] ------------------ 4418| 111| { 4419| 111| pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1); 4420| 111| break; 4421| 111| } 4422| 220| } 4423| 111| if (j < 0) ------------------ | Branch (4423:21): [True: 0, False: 111] ------------------ 4424| 0| { 4425| 0| continue; /* not found */ 4426| 0| } 4427| | 4428| 115| for (j = pv2->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4428:50): [True: 115, False: 0] ------------------ 4429| 115| { /* was -2; changed 2006-2-28 12:35pm*/ 4430| 115| pe2n = pBNS->edge + pv2->iedge[j]; 4431| 115| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (4431:25): [True: 111, False: 4] | Branch (4431:39): [True: 111, False: 0] ------------------ 4432| 111| { 4433| 111| pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2); 4434| 111| break; 4435| 111| } 4436| 115| } 4437| 111| if (j < 0) ------------------ | Branch (4437:21): [True: 0, False: 111] ------------------ 4438| 0| continue; /* not found */ 4439| | 4440| 111| pe->flow += delta; 4441| 111| pe1n->flow -= delta; 4442| 111| pe2n->flow -= delta; 4443| 111| pv1n->st_edge.flow -= delta; 4444| 111| pv2n->st_edge.flow -= delta; 4445| 111| pBNS->tot_st_flow -= 2 * delta; 4446| | 4447| 111| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4448| 111| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 4449| | 4450| 111| if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) || ------------------ | Branch (4450:21): [True: 97, False: 14] | Branch (4450:35): [True: 32, False: 65] | Branch (4450:54): [True: 28, False: 4] ------------------ 4451| 69| (vPathEnd == v2n && vPathStart == v1n)) && ------------------ | Branch (4451:22): [True: 61, False: 8] | Branch (4451:41): [True: 59, False: 2] ------------------ 4452| 87| (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4452:22): [True: 0, False: 87] | Branch (4452:43): [True: 87, False: 0] ------------------ 4453| 87| { 4454| | /* Moved charge from OH(+) to -O- => nDeltaCharge == 1 or 0 if pe2n = -O- charge edge */ 4455| | /* Flow change on pe (+)charge edge (atom OH(+)) is not known to RunBnsTestOnce()) */ 4456| 87| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 4457| 87| if (ret > 0) ------------------ | Branch (4457:25): [True: 87, False: 0] ------------------ 4458| 87| { 4459| 87| nNumRunBNS++; 4460| 87| cur_success++; /* 17 */ 4461| 87| } 4462| 87| } 4463| 24| else 4464| 24| { 4465| 24| pe->flow -= delta; 4466| 24| pe1n->flow += delta; 4467| 24| pe2n->flow += delta; 4468| 24| pv1n->st_edge.flow += delta; 4469| 24| pv2n->st_edge.flow += delta; 4470| 24| pBNS->tot_st_flow += 2 * delta; 4471| 24| } 4472| 111| INCHI_HEAPCHK 4473| 111| } 4474| 110| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4475| 110| } 4476| 173| CurrEdges.num_edges = 0; /* clear current edge list */ 4477| 173| if (cur_success) ------------------ | Branch (4477:13): [True: 87, False: 86] ------------------ 4478| 87| { 4479| 87| tot_succes += cur_success; 4480| | /* recalculate InChI from the structure */ 4481| 87| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4481:17): [True: 0, False: 87] ------------------ 4482| 87| ppt_group_info, ppat_norm, ppat_prep))) 4483| 0| { 4484| 0| goto exit_function; 4485| 0| } 4486| 87| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4486:17): [True: 0, False: 87] ------------------ 4487| 0| { 4488| 0| goto exit_function; 4489| 0| } 4490| 87| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4490:17): [True: 0, False: 87] | Branch (4490:45): [True: 0, False: 0] ------------------ 4491| 0| { 4492| 0| goto exit_function; /* no fixed-H found */ 4493| 0| } 4494| 87| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4494:17): [True: 0, False: 87] ------------------ 4495| 0| { 4496| 0| goto exit_function; 4497| 0| } 4498| 87| if (!pc2i->bHasDifference) ------------------ | Branch (4498:17): [True: 0, False: 87] ------------------ 4499| 0| { 4500| 0| goto exit_function; /* nothing to do */ 4501| 0| } 4502| 87| } 4503| 173| } 4504| | 4505| 1.13k| if (( pc2i->nNumTgInChI && pStruct->endpoint && ------------------ | Branch (4505:11): [True: 782, False: 348] | Branch (4505:32): [True: 782, False: 0] ------------------ 4506| 782| pc2i->nNumTgMInChI > pc2i->nNumTgMRevrs && pc2i->nNumEndpInChI > pc2i->nNumEndpRevrs )) ------------------ | Branch (4506:11): [True: 250, False: 532] | Branch (4506:54): [True: 210, False: 40] ------------------ 4507| 210| { 4508| | /*-----------------------------------------------------------------*/ 4509| | /* */ 4510| | /* case 18: restored:-N=AB-X -(-)N-AB-X(+) */ 4511| | /* FixH: 0 0 0 0 */ 4512| | /* MobH: 0 0 0 0 */ 4513| | /* non non taut non */ 4514| | /* taut taut taut */ 4515| | /* X = any heteroatom N=N */ 4516| | /* t-group in original has (Hn,-m) in the restored: (Hn,-m+1) */ 4517| | /* same num_H and more (-) than in the restored structure */ 4518| | /* atom X is not taut in both */ 4519| | /* Solution: separate charges between -N(III)= and X */ 4520| | /*-----------------------------------------------------------------*/ 4521| 210| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4522| 210| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (4522:41): [True: 134, False: 76] ------------------ 4523| 210| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (4523:41): [True: 134, False: 0] ------------------ 4524| 210| int iat, e1, itg, max_success; 4525| 210| CurrEdges.num_edges = 0; 4526| 210| cur_success = 0; 4527| 210| ret = 0; 4528| | /* search for -N= */ 4529| 331| for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++) ------------------ | Branch (4529:23): [True: 234, False: 97] | Branch (4529:57): [True: 121, False: 113] ------------------ 4530| 121| { 4531| 121| if (pStruct->ti.t_group[itg].nNumEndpoints <= pStruct->One_ti.t_group[itg].nNumEndpoints || ------------------ | Branch (4531:17): [True: 14, False: 107] ------------------ 4532| 107| pStruct->ti.t_group[itg].num[1] <= pStruct->One_ti.t_group[itg].num[1]) ------------------ | Branch (4532:18): [True: 4, False: 103] ------------------ 4533| 18| { 4534| 18| continue; 4535| 18| } 4536| 103| CurrEdges.num_edges = 0; 4537| 103| cur_success = 0; 4538| 103| for (j = 0, k = pStruct->ti.t_group[itg].nFirstEndpointAtNoPos; 4539| 480| j < pStruct->ti.t_group[itg].nNumEndpoints; j++) ------------------ | Branch (4539:19): [True: 377, False: 103] ------------------ 4540| 377| { 4541| 377| i = pStruct->ti.nEndpointAtomNumber[k + j]; /* canonical number in restored struct. */ 4542| 377| iat = nCanon2AtnoRevrs[i]; 4543| 377| if (!pStruct->endpoint[i] || !at_Mobile_H_Revrs || at_Mobile_H_Revrs[iat].endpoint || ------------------ | Branch (4543:21): [True: 0, False: 377] | Branch (4543:46): [True: 0, False: 377] | Branch (4543:68): [True: 65, False: 312] ------------------ 4544| 312| pVA[i].cNumValenceElectrons != 5 || pVA[i].cPeriodicRowNumber != 1 || ------------------ | Branch (4544:22): [True: 133, False: 179] | Branch (4544:58): [True: 14, False: 165] ------------------ 4545| 165| 2 != at2[iat].valence || at2[iat].num_H || at2[iat].radical || ------------------ | Branch (4545:22): [True: 46, False: 119] | Branch (4545:47): [True: 3, False: 116] | Branch (4545:65): [True: 1, False: 115] ------------------ 4546| 115| (0 <= ( e1 = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e1].flow) || ------------------ | Branch (4546:23): [True: 115, False: 0] | Branch (4546:69): [True: 3, False: 112] ------------------ 4547| 112| 0 >( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4547:22): [True: 0, False: 112] | Branch (4547:66): [True: 0, False: 112] | Branch (4547:93): [True: 55, False: 57] ------------------ 4548| 320| { 4549| 320| continue; 4550| 320| } 4551| | /* found -N= */ 4552| 57| if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 57|#define INC_ADD_EDGE 64 ------------------ | Branch (4552:21): [True: 0, False: 57] ------------------ 4553| 0| { 4554| 0| goto exit_function; 4555| 0| } 4556| 57| } 4557| 103| } 4558| 210| if (!( max_success = CurrEdges.num_edges )) ------------------ | Branch (4558:13): [True: 169, False: 41] ------------------ 4559| 169| { 4560| 169| goto exit_case_18; 4561| 169| } 4562| | /* search for X */ 4563| 315| for (i = 0; i < pStruct->num_atoms && cur_success < max_success; i++) ------------------ | Branch (4563:21): [True: 290, False: 25] | Branch (4563:47): [True: 274, False: 16] ------------------ 4564| 274| { 4565| 274| iat = nCanon2AtnoRevrs[i]; 4566| 274| if (pStruct->endpoint[i] || !pVA[i].cNumValenceElectrons || pVA[i].cNumValenceElectrons == 4 || ------------------ | Branch (4566:17): [True: 117, False: 157] | Branch (4566:41): [True: 1, False: 156] | Branch (4566:73): [True: 24, False: 132] ------------------ 4567| 132| at2[iat].num_H || at2[iat].radical || ------------------ | Branch (4567:18): [True: 23, False: 109] | Branch (4567:36): [True: 1, False: 108] ------------------ 4568| 108| (0 <= ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e1].flow) || ------------------ | Branch (4568:19): [True: 65, False: 43] | Branch (4568:66): [True: 51, False: 14] ------------------ 4569| 57| 0 >( e = pVA[iat].nCPlusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow != 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4569:18): [True: 1, False: 56] | Branch (4569:61): [True: 16, False: 40] | Branch (4569:88): [True: 7, False: 33] ------------------ 4570| 241| { 4571| 241| continue; 4572| 241| } 4573| | /* try to move the charge */ 4574| 33| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4575| 33| SetForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask ); 4576| 33| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 4577| | 4578| 33| pe = pBNS->edge + e; 4579| 33| if (!pe->flow) ------------------ | Branch (4579:17): [True: 0, False: 33] ------------------ 4580| 0| continue; 4581| 33| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4582| 33| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4583| | 4584| 33| delta = 1; 4585| 33| pe->flow -= delta; 4586| 33| pv1->st_edge.flow -= delta; 4587| 33| pv2->st_edge.flow -= delta; 4588| 33| pBNS->tot_st_flow -= 2 * delta; 4589| | 4590| 33| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4591| 33| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4592| | 4593| 33| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (4593:17): [True: 22, False: 11] | Branch (4593:32): [True: 8, False: 14] | Branch (4593:50): [True: 7, False: 1] ------------------ 4594| 20| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4594:32): [True: 14, False: 1] | Branch (4594:50): [True: 13, False: 1] | Branch (4594:73): [True: 20, False: 0] ------------------ 4595| 20| { 4596| | /* Created (-) charge on -N= => nDeltaCharge == 1 */ 4597| | /* Flow change on pe (+)charge edge (atom X) is not known to RunBnsTestOnce()) */ 4598| 20| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4599| 20| if (ret > 0) ------------------ | Branch (4599:21): [True: 20, False: 0] ------------------ 4600| 20| { 4601| 20| nNumRunBNS++; 4602| 20| cur_success++; /* 18 */ 4603| 20| } 4604| 20| } 4605| 13| else 4606| 13| { 4607| 13| pe->flow += delta; 4608| 13| pv1->st_edge.flow += delta; 4609| 13| pv2->st_edge.flow += delta; 4610| 13| pBNS->tot_st_flow += 2 * delta; 4611| 13| } 4612| 33| INCHI_HEAPCHK 4613| 33| } 4614| 210| exit_case_18: 4615| 210| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4616| 210| RemoveForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask ); 4617| 210| CurrEdges.num_edges = 0; /* clear current edge list */ 4618| 210| if (ret < 0) ------------------ | Branch (4618:13): [True: 0, False: 210] ------------------ 4619| 0| { 4620| 0| goto exit_function; 4621| 0| } 4622| 210| if (cur_success) ------------------ | Branch (4622:13): [True: 20, False: 190] ------------------ 4623| 20| { 4624| 20| tot_succes += cur_success; 4625| | /* recalculate InChI from the structure */ 4626| 20| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4626:17): [True: 1, False: 19] ------------------ 4627| 20| ppt_group_info, ppat_norm, ppat_prep ) )) 4628| 1| { 4629| 1| goto exit_function; 4630| 1| } 4631| 19| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4631:17): [True: 0, False: 19] ------------------ 4632| 0| { 4633| 0| goto exit_function; 4634| 0| } 4635| 19| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4635:17): [True: 8, False: 11] | Branch (4635:45): [True: 0, False: 8] ------------------ 4636| 0| { 4637| 0| goto exit_function; /* no fixed-H found */ 4638| 0| } 4639| 19| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4639:17): [True: 0, False: 19] ------------------ 4640| 0| { 4641| 0| goto exit_function; 4642| 0| } 4643| 19| if (!pc2i->bHasDifference) ------------------ | Branch (4643:17): [True: 0, False: 19] ------------------ 4644| 0| { 4645| 0| goto exit_function; /* nothing to do */ 4646| 0| } 4647| 19| } 4648| 210| } 4649| | 4650| 1.12k| if (pc2i->len_c2at >= 1) ------------------ | Branch (4650:9): [True: 1.12k, False: 4] ------------------ 4651| 1.12k| { 4652| | /*--------------------------------------------------------------*/ 4653| | /* case 19 restored: M--OH original: M(-)==OH(+) */ 4654| | /* FixH: metal 0 1 */ 4655| | /* MobH: 1 0 */ 4656| | /* O = O, S, Se, Te; not taut. in InChI */ 4657| | /* In restored structure has H; tautomeric or not tautomeric */ 4658| | /* Solution: move (+) from -OH to M; charhe on M may vary */ 4659| | /*--------------------------------------------------------------*/ 4660| 1.12k| int iat; 4661| 1.12k| EdgeIndex eMPlus, eMMinus; /* djb-rwth: removing redundant variables/code */ 4662| 1.12k| BNS_EDGE *peOHPlus, *peMPlus, *peMMinus, *peOMBond; 4663| 1.12k| int iatMetal, ChargeOnMetal, DeltaChargeExpected; 4664| 1.12k| cur_success = 0; 4665| | /* djb-rwth: removing redundant code */ 4666| 4.66k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (4666:21): [True: 3.53k, False: 1.12k] ------------------ 4667| 3.53k| { 4668| 3.53k| iat = pc2i->c2at[i].atomNumber; 4669| 3.53k| if ( /* orig. InChI info: =NH2(+), =OH(+) */ 4670| 3.53k| ( pc2i->c2at[i].nValElectr == 6 ) /* N, O, S, Se, Te */ && ------------------ | Branch (4670:17): [True: 1.78k, False: 1.74k] ------------------ 4671| | /*!pc2i->c2at[i].endptInChI &&*/ /* <=== relaxation */ 4672| 1.78k| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (4672:18): [True: 1.15k, False: 637] | Branch (4672:63): [True: 1.09k, False: 56] | Branch (4672:91): [True: 969, False: 126] ------------------ 4673| 969| pc2i->c2at[i].nFixHInChI == 1 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (4673:18): [True: 278, False: 691] | Branch (4673:51): [True: 272, False: 6] ------------------ 4674| | /* reversed structure info: */ 4675| 272| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 1 && ------------------ | Branch (4675:18): [True: 188, False: 84] | Branch (4675:51): [True: 173, False: 15] ------------------ 4676| 173| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && ------------------ | Branch (4676:18): [True: 172, False: 1] | Branch (4676:55): [True: 172, False: 0] ------------------ 4677| 172| at2[iat].valence == 1 && ------------------ | Branch (4677:18): [True: 161, False: 11] ------------------ 4678| 161| at2[iat].valence == at2[iat].chem_bonds_valence && ------------------ | Branch (4678:18): [True: 156, False: 5] ------------------ 4679| | /* metal atom */ 4680| 156| pVA[iatMetal = at2[iat].neighbor[0]].cMetal && ------------------ | Branch (4680:18): [True: 109, False: 47] ------------------ 4681| 109| ( eMPlus = pVA[iatMetal].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eMPlus].forbidden && ------------------ | Branch (4681:18): [True: 109, False: 0] | Branch (4681:73): [True: 109, False: 0] ------------------ 4682| 109| ( eMMinus = pVA[iatMetal].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[eMMinus].forbidden && ------------------ | Branch (4682:18): [True: 109, False: 0] | Branch (4682:75): [True: 109, False: 0] ------------------ 4683| 109| !pBNS->edge[pBNS->vert[iat].iedge[0]].forbidden ------------------ | Branch (4683:18): [True: 109, False: 0] ------------------ 4684| 3.53k| ) /* djb-rwth: removing redundant code */ 4685| 109| { 4686| | /* -OH charge edges */ 4687| 109| if ((ret = AddToEdgeList( &CurrEdges, iat, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 109|#define INC_ADD_EDGE 64 ------------------ | Branch (4687:21): [True: 0, False: 109] ------------------ 4688| 0| { 4689| 0| goto exit_function; 4690| 0| } 4691| 109| } 4692| 3.53k| } 4693| 1.12k| if (CurrEdges.num_edges) ------------------ | Branch (4693:13): [True: 108, False: 1.01k] ------------------ 4694| 108| { 4695| | /* detected; fix */ 4696| 108| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4697| 108| SetForbiddenEdgeMask( pBNS, &NFlowerEdges, forbidden_edge_mask ); 4698| 108| SetForbiddenEdgeMask( pBNS, &AllBondEdges, forbidden_edge_mask ); 4699| 217| for (i = 0; i < CurrEdges.num_edges; i++) ------------------ | Branch (4699:25): [True: 109, False: 108] ------------------ 4700| 109| { 4701| | /* v1 is -OH, v2 is adjacent to it Metal */ 4702| 109| iat = CurrEdges.pnEdges[i]; 4703| 109| iatMetal = at2[iat].neighbor[0]; 4704| 109| peOHPlus = pBNS->edge + ( (long long)pVA[iat].nCPlusGroupEdge - 1 ); /* djb-rwth: removing redundant variables/code */ 4705| 109| peMPlus = pBNS->edge + ( (long long)pVA[iatMetal].nCPlusGroupEdge - 1 ); /* djb-rwth: removing redundant variables/code */ 4706| 109| peMMinus = pBNS->edge + ( (long long)pVA[iatMetal].nCMinusGroupEdge - 1 ); /* djb-rwth: removing redundant variables/code */ 4707| 109| peOMBond = pBNS->edge + ( pBNS->vert[iat].iedge[0] ); /* djb-rwth: removing redundant variables/code */ 4708| | /* remove forbidden edge masks */ 4709| 109| peMPlus->forbidden &= forbidden_edge_mask_inv; 4710| 109| peMMinus->forbidden &= forbidden_edge_mask_inv; 4711| 109| peOMBond->forbidden &= forbidden_edge_mask_inv; 4712| | 4713| 109| ChargeOnMetal = ( peMPlus->cap - peMPlus->flow ) - peMMinus->flow; 4714| 109| if (1 == ChargeOnMetal) ------------------ | Branch (4714:21): [True: 4, False: 105] ------------------ 4715| 4| { 4716| | /* We are going to subtract 1 from the charge on Metal */ 4717| | /* Added (+)charge to -OH is not known to RunBnsTestOnce() */ 4718| 4| DeltaChargeExpected = -1; /* charge will become = 0 */ 4719| 4| } 4720| 105| else 4721| 105| { 4722| 105| if (0 == ChargeOnMetal) ------------------ | Branch (4722:25): [True: 63, False: 42] ------------------ 4723| 63| { 4724| 63| DeltaChargeExpected = 1; /* charge on Metal will be created */ 4725| 63| } 4726| 42| else 4727| 42| { 4728| 42| DeltaChargeExpected = 0; 4729| 42| } 4730| 105| } 4731| | 4732| 109| delta = 1; 4733| 109| pe = peOHPlus; 4734| 109| if (!pe->flow) ------------------ | Branch (4734:21): [True: 0, False: 109] ------------------ 4735| 0| continue; 4736| 109| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4737| 109| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4738| | 4739| 109| pe->flow -= delta; /* remove (-) from AB-O(-) */ 4740| 109| pv1->st_edge.flow -= delta; 4741| 109| pv2->st_edge.flow -= delta; 4742| 109| pBNS->tot_st_flow -= 2 * delta; 4743| | 4744| 109| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4745| 109| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4746| | 4747| 109| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (4747:21): [True: 109, False: 0] | Branch (4747:36): [True: 9, False: 100] | Branch (4747:54): [True: 7, False: 2] ------------------ 4748| 107| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == DeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (4748:36): [True: 100, False: 2] | Branch (4748:54): [True: 100, False: 0] | Branch (4748:77): [True: 107, False: 0] ------------------ 4749| 107| { 4750| 107| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4751| 107| if (ret > 0) ------------------ | Branch (4751:25): [True: 107, False: 0] ------------------ 4752| 107| { 4753| 107| nNumRunBNS++; 4754| 107| cur_success++; /* 19 */ 4755| 107| } 4756| 107| } 4757| 2| else 4758| 2| { 4759| 2| pe->flow += delta; 4760| 2| pv1->st_edge.flow += delta; 4761| 2| pv2->st_edge.flow += delta; 4762| 2| pBNS->tot_st_flow += 2 * delta; 4763| 2| } 4764| 109| INCHI_HEAPCHK 4765| | /* set forbidden edge masks back */ 4766| 109| peMPlus->forbidden |= forbidden_edge_mask; 4767| 109| peMMinus->forbidden |= forbidden_edge_mask; 4768| 109| peOMBond->forbidden |= forbidden_edge_mask; 4769| 109| } 4770| 108| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4771| 108| RemoveForbiddenEdgeMask( pBNS, &NFlowerEdges, forbidden_edge_mask ); 4772| 108| RemoveForbiddenEdgeMask( pBNS, &AllBondEdges, forbidden_edge_mask ); 4773| | 4774| 108| CurrEdges.num_edges = 0; /* clear current edge list */ 4775| 108| if (cur_success) ------------------ | Branch (4775:17): [True: 106, False: 2] ------------------ 4776| 106| { 4777| 106| tot_succes += cur_success; 4778| | /* recalculate InChI from the structure */ 4779| 106| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4779:21): [True: 0, False: 106] ------------------ 4780| 106| ppt_group_info, ppat_norm, ppat_prep ) )) 4781| 0| { 4782| 0| goto exit_function; 4783| 0| } 4784| 106| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4784:21): [True: 0, False: 106] ------------------ 4785| 0| { 4786| 0| goto exit_function; 4787| 0| } 4788| 106| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4788:21): [True: 0, False: 106] | Branch (4788:49): [True: 0, False: 0] ------------------ 4789| 0| { 4790| 0| goto exit_function; /* no fixed-H found */ 4791| 0| } 4792| 106| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4792:21): [True: 0, False: 106] ------------------ 4793| 0| { 4794| 0| goto exit_function; 4795| 0| } 4796| 106| if (!pc2i->bHasDifference) ------------------ | Branch (4796:21): [True: 1, False: 105] ------------------ 4797| 1| { 4798| 1| goto exit_function; /* nothing to do */ 4799| 1| } 4800| 106| } 4801| 108| } 4802| 1.12k| } 4803| | 4804| 1.12k| if (pc2i->len_c2at > 1 && pc2i->nNumTgRevrs && pc2i->nNumTgInChI) ------------------ | Branch (4804:9): [True: 1.01k, False: 115] | Branch (4804:31): [True: 436, False: 577] | Branch (4804:52): [True: 290, False: 146] ------------------ 4805| 290| { 4806| | /*--------------------------------------------------------------*/ 4807| | /* case 20: restored: O(-)-AB=N- original: O=AB-N(-)- */ 4808| | /* FixH: 0 0 0 -1 */ 4809| | /* MobH: 0 0 0 1 */ 4810| | /* taut non-taut non-taut taut */ 4811| | /* or taut no H */ 4812| | /* no H */ 4813| | /* O = O, S, Se; N = N, O, S, Se, Te; */ 4814| | /* restored atoms are taut/non-taut; original are opposite. */ 4815| | /* Solution: move (-) from O(-) to =N- */ 4816| | /*--------------------------------------------------------------*/ 4817| 290| int num_SB_O_Minus = 0, num_DB_N = 0, iat; 4818| | 4819| 290| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4820| | /* 4821| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 4822| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 4823| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 4824| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 4825| | */ 4826| 290| cur_success = 0; 4827| | 4828| 290| CurrEdges.num_edges = 0; /* clear current edge list */ 4829| 1.40k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (4829:21): [True: 1.11k, False: 290] ------------------ 4830| 1.11k| { 4831| 1.11k| iat = pc2i->c2at[i].atomNumber; 4832| 1.11k| if ( /* orig. InChI info: =O or -N= */ 4833| 1.11k| num_DB_N < MAX_DIFF_FIXH && ------------------ | | 456| 2.22k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4833:17): [True: 1.11k, False: 0] ------------------ 4834| 1.11k| pc2i->c2at[i].endptInChI && ------------------ | Branch (4834:17): [True: 540, False: 574] ------------------ 4835| 540| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (4835:17): [True: 378, False: 162] | Branch (4835:61): [True: 378, False: 0] ------------------ 4836| 378| pBNS->edge[e].flow == 0 && ------------------ | Branch (4836:17): [True: 284, False: 94] ------------------ 4837| 284| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (4837:17): [True: 259, False: 25] | Branch (4837:50): [True: 259, False: 0] ------------------ 4838| | /* if more than 1 t-group are in orig. InChI then do not move (-) to N */ 4839| 259| (pc2i->nNumTgInChI == 1 || pc2i->c2at[i].nValElectr == 6) && ------------------ | Branch (4839:18): [True: 193, False: 66] | Branch (4839:44): [True: 14, False: 52] ------------------ 4840| | /* reversed structure info: */ 4841| 207| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (4841:17): [True: 207, False: 0] ------------------ 4842| 207| pc2i->c2at[i].nFixHRevrs == 0 && /*pc2i->c2at[i].nMobHRevrs == 0 &&*/ ------------------ | Branch (4842:17): [True: 207, False: 0] ------------------ 4843| 207| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (4843:17): [True: 181, False: 26] | Branch (4843:54): [True: 181, False: 0] ------------------ 4844| 181| at2[iat].valence + 1 == at2[iat].chem_bonds_valence) ------------------ | Branch (4844:17): [True: 154, False: 27] ------------------ 4845| 154| { 4846| 154| iat_DB_N[num_DB_N++] = iat; 4847| 154| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 154|#define INC_ADD_EDGE 64 ------------------ | Branch (4847:21): [True: 0, False: 154] ------------------ 4848| 0| { 4849| 0| goto exit_function; 4850| 0| } 4851| 154| } 4852| 960| else 4853| 960| { 4854| 960| if ( /* orig. InChI info: -O(-) */ 4855| 960| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 1.92k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4855:21): [True: 960, False: 0] ------------------ 4856| 960| !pc2i->c2at[i].endptInChI && ------------------ | Branch (4856:21): [True: 574, False: 386] ------------------ 4857| 574| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (4857:21): [True: 444, False: 130] | Branch (4857:65): [True: 444, False: 0] ------------------ 4858| 444| pBNS->edge[e].flow == 1 && ------------------ | Branch (4858:21): [True: 173, False: 271] ------------------ 4859| 173| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (4859:21): [True: 165, False: 8] | Branch (4859:54): [True: 165, False: 0] ------------------ 4860| 165| pc2i->c2at[i].nValElectr == 6 && ------------------ | Branch (4860:21): [True: 159, False: 6] ------------------ 4861| | /* reversed structure info: */ 4862| 159| pc2i->c2at[i].endptRevrs && ------------------ | Branch (4862:21): [True: 154, False: 5] ------------------ 4863| 154| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (4863:21): [True: 154, False: 0] | Branch (4863:54): [True: 154, False: 0] ------------------ 4864| 154| pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H && ------------------ | Branch (4864:21): [True: 154, False: 0] | Branch (4864:59): [True: 154, False: 0] ------------------ 4865| 154| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1) ------------------ | Branch (4865:21): [True: 154, False: 0] | Branch (4865:46): [True: 154, False: 0] ------------------ 4866| 154| { 4867| 154| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 4868| 154| } 4869| 960| } 4870| 1.11k| } 4871| 290| if (!num_DB_N) ------------------ | Branch (4871:13): [True: 181, False: 109] ------------------ 4872| 181| { 4873| | /* search among N that are tautomeric in both cases */ 4874| 1.57k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (4874:25): [True: 1.39k, False: 181] ------------------ 4875| 1.39k| { /* i = canonical number - 1 */ 4876| 1.39k| if (!pStruct->endpoint[i]) ------------------ | Branch (4876:21): [True: 925, False: 470] ------------------ 4877| 925| { 4878| 925| continue; 4879| 925| } 4880| 470| iat = nCanon2AtnoRevrs[i]; 4881| 470| if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */ 4882| 470| num_DB_N < MAX_DIFF_FIXH && ------------------ | | 456| 940|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4882:21): [True: 470, False: 0] ------------------ 4883| 470| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4883:21): [True: 246, False: 224] | Branch (4883:45): [True: 194, False: 52] ------------------ 4884| 194| at2[iat].valence + 1 == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4884:21): [True: 119, False: 75] | Branch (4884:76): [True: 119, False: 0] ------------------ 4885| | /* in orig.InChI: an endpoint, has no H */ 4886| 119| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (4886:23): [True: 119, False: 0] | Branch (4886:43): [True: 12, False: 107] ------------------ 4887| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 4888| | /* has (-) edge */ 4889| 107| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (4889:21): [True: 99, False: 8] | Branch (4889:65): [True: 99, False: 0] ------------------ 4890| 99| !pBNS->edge[e].flow) ------------------ | Branch (4890:21): [True: 99, False: 0] ------------------ 4891| 99| { 4892| | 4893| 99| iat_DB_N[num_DB_N++] = iat; 4894| 99| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 99|#define INC_ADD_EDGE 64 ------------------ | Branch (4894:25): [True: 0, False: 99] ------------------ 4895| 0| { 4896| 0| goto exit_function; 4897| 0| } 4898| 99| } 4899| 470| } 4900| 181| } 4901| 290| if ((num_try = inchi_min(num_SB_O_Minus, num_DB_N))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 290|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 101, False: 189] | | ------------------ ------------------ | Branch (4901:13): [True: 102, False: 188] ------------------ 4902| 102| { 4903| | /* detected; attempt to fix */ 4904| 102| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4905| 102| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 4906| 102| delta = 1; 4907| 218| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (4907:25): [True: 119, False: 99] | Branch (4907:47): [True: 116, False: 3] ------------------ 4908| 116| { 4909| 116| iat = iat_SB_O_Minus[i]; 4910| 116| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 4911| 116| if (!pe->flow) ------------------ | Branch (4911:21): [True: 0, False: 116] ------------------ 4912| 0| continue; 4913| 116| pv1 = pBNS->vert + (v1 = pe->neighbor1); 4914| 116| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 4915| | 4916| 116| pe->flow -= delta; 4917| 116| pv1->st_edge.flow -= delta; 4918| 116| pv2->st_edge.flow -= delta; 4919| 116| pBNS->tot_st_flow -= 2 * delta; 4920| | 4921| 116| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4922| 116| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 4923| | 4924| 116| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (4924:21): [True: 53, False: 63] | Branch (4924:35): [True: 2, False: 51] | Branch (4924:53): [True: 2, False: 0] ------------------ 4925| 51| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4925:22): [True: 51, False: 0] | Branch (4925:40): [True: 48, False: 3] | Branch (4925:62): [True: 50, False: 0] ------------------ 4926| 50| { 4927| | /* Added (-) charge to =N- => nDeltaCharge == 1 */ 4928| | /* Flow change on pe (-)charge edge (atom -O(-)) is not known to RunBnsTestOnce()) */ 4929| 50| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 4930| 50| if (ret > 0) ------------------ | Branch (4930:25): [True: 50, False: 0] ------------------ 4931| 50| { 4932| 50| nNumRunBNS++; 4933| 50| cur_success++; /* 20 */ 4934| 50| } 4935| 50| } 4936| 66| else 4937| 66| { 4938| 66| pe->flow += delta; 4939| 66| pv1->st_edge.flow += delta; 4940| 66| pv2->st_edge.flow += delta; 4941| 66| pBNS->tot_st_flow += 2 * delta; 4942| 66| } 4943| 116| INCHI_HEAPCHK 4944| 116| } 4945| 102| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 4946| 102| } 4947| 290| CurrEdges.num_edges = 0; /* clear current edge list */ 4948| 290| if (cur_success) ------------------ | Branch (4948:13): [True: 49, False: 241] ------------------ 4949| 49| { 4950| 49| tot_succes += cur_success; 4951| | /* recalculate InChI from the structure */ 4952| 49| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4952:17): [True: 1, False: 48] ------------------ 4953| 49| ppt_group_info, ppat_norm, ppat_prep))) 4954| 1| { 4955| 1| goto exit_function; 4956| 1| } 4957| 48| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4957:17): [True: 0, False: 48] ------------------ 4958| 0| { 4959| 0| goto exit_function; 4960| 0| } 4961| 48| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4961:17): [True: 32, False: 16] | Branch (4961:45): [True: 0, False: 32] ------------------ 4962| 0| { 4963| 0| goto exit_function; /* no fixed-H found */ 4964| 0| } 4965| 48| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4965:17): [True: 0, False: 48] ------------------ 4966| 0| { 4967| 0| goto exit_function; 4968| 0| } 4969| 48| if (!pc2i->bHasDifference) ------------------ | Branch (4969:17): [True: 0, False: 48] ------------------ 4970| 0| { 4971| 0| goto exit_function; /* nothing to do */ 4972| 0| } 4973| 48| } 4974| 290| } 4975| | 4976| 1.12k| if (pc2i->len_c2at && pc2i->nNumTgRevrs && pc2i->nNumTgHInChI && pStruct->endpoint) ------------------ | Branch (4976:9): [True: 1.12k, False: 4] | Branch (4976:27): [True: 450, False: 673] | Branch (4976:48): [True: 0, False: 450] | Branch (4976:70): [True: 0, False: 0] ------------------ 4977| 0| { 4978| | /*--------------------------------------------------------------*/ 4979| | /* O(-) O */ 4980| | /* | || */ 4981| | /* case 21: restored: R=S=O original: R-S=O */ 4982| | /* | | */ 4983| | /* O(-) O(-) */ 4984| | /* All O are taut R is not taut */ 4985| | /* */ 4986| | /* In addition, another atom O that should have been tautomeric */ 4987| | /* or has H(+) added in Mobile-H layer is not like that */ 4988| | /* O = O, S, Se; S=S, Se, Te */ 4989| | /* Solution: move (-) from O(-) to =O */ 4990| | /* these atoms are tautomeric in restored structure */ 4991| | /*--------------------------------------------------------------*/ 4992| 0| int num_SB_O_Minus = 0, num_DB_O = 0, iat, iS; 4993| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4994| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (4994:41): [True: 0, False: 0] ------------------ 4995| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (4995:41): [True: 0, False: 0] ------------------ 4996| | /* 4997| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 4998| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 4999| | */ 5000| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 5001| 0| cur_success = 0; 5002| | 5003| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5003:21): [True: 0, False: 0] ------------------ 5004| 0| { 5005| 0| iat = pc2i->c2at[i].atomNumber; 5006| 0| if ( /* orig. InChI info: =O */ 5007| 0| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5007:17): [True: 0, False: 0] ------------------ 5008| 0| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (5008:17): [True: 0, False: 0] ------------------ 5009| 0| (pc2i->c2at[i].endptInChI || pc2i->c2at[i].nMobHInChI) && ------------------ | Branch (5009:18): [True: 0, False: 0] | Branch (5009:46): [True: 0, False: 0] ------------------ 5010| 0| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5010:17): [True: 0, False: 0] | Branch (5010:61): [True: 0, False: 0] ------------------ 5011| 0| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5011:17): [True: 0, False: 0] ------------------ 5012| | /* reversed structure info: */ 5013| 0| !(pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs) && ------------------ | Branch (5013:19): [True: 0, False: 0] | Branch (5013:47): [True: 0, False: 0] ------------------ 5014| 0| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5014:17): [True: 0, False: 0] ------------------ 5015| 0| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (5015:17): [True: 0, False: 0] | Branch (5015:54): [True: 0, False: 0] ------------------ 5016| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (5016:17): [True: 0, False: 0] | Branch (5016:42): [True: 0, False: 0] ------------------ 5017| 0| { 5018| 0| iat_DB_O[num_DB_O++] = iat; 5019| 0| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5019:21): [True: 0, False: 0] ------------------ 5020| 0| { 5021| 0| goto exit_function; 5022| 0| } 5023| 0| } 5024| 0| } 5025| 0| for (i = 0; num_DB_O && i < pStruct->num_atoms; i++) ------------------ | Branch (5025:21): [True: 0, False: 0] | Branch (5025:33): [True: 0, False: 0] ------------------ 5026| 0| { 5027| | /* i = canonical number - 1 */ 5028| 0| if (!pStruct->endpoint[i]) ------------------ | Branch (5028:17): [True: 0, False: 0] ------------------ 5029| 0| { 5030| 0| continue; 5031| 0| } 5032| 0| iat = nCanon2AtnoRevrs[i]; 5033| 0| if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */ 5034| 0| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 456| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5034:17): [True: 0, False: 0] ------------------ 5035| 0| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (5035:17): [True: 0, False: 0] | Branch (5035:42): [True: 0, False: 0] ------------------ 5036| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (5036:17): [True: 0, False: 0] | Branch (5036:42): [True: 0, False: 0] | Branch (5036:73): [True: 0, False: 0] ------------------ 5037| 0| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (5037:17): [True: 0, False: 0] ------------------ 5038| 0| (at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) && ------------------ | Branch (5038:18): [True: 0, False: 0] | Branch (5038:39): [True: 0, False: 0] ------------------ 5039| | /* in orig.InChI: an endpoint, has no H */ 5040| 0| !(pStruct->fixed_H && pStruct->fixed_H[i]) && ------------------ | Branch (5040:19): [True: 0, False: 0] | Branch (5040:39): [True: 0, False: 0] ------------------ 5041| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 5042| | /* has (-) edge */ 5043| 0| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5043:17): [True: 0, False: 0] | Branch (5043:61): [True: 0, False: 0] ------------------ 5044| 0| pBNS->edge[e].flow) ------------------ | Branch (5044:17): [True: 0, False: 0] ------------------ 5045| 0| { 5046| 0| int nNumTautSB = 0, nNumTautDB = 0, nNumOtherDB = 0, nNumOtherSB = 0, nNumOthers = 0, nNumNegEndp = 0; /* djb-rwth: ignoring LLVM warning: variables used */ 5047| | /* traverse neighbors of the centerpoint iS */ 5048| 0| iS = at2[i].neighbor[0]; 5049| 0| for (j = 0; j < num_SB_O_Minus; j++) ------------------ | Branch (5049:29): [True: 0, False: 0] ------------------ 5050| 0| { 5051| 0| if (iat_Central[j] == iS) ------------------ | Branch (5051:25): [True: 0, False: 0] ------------------ 5052| 0| break; 5053| 0| } 5054| 0| if (j < num_SB_O_Minus) ------------------ | Branch (5054:21): [True: 0, False: 0] ------------------ 5055| 0| { 5056| 0| continue; /* have already been there */ 5057| 0| } 5058| 0| for (j = 0; j < at[iS].valence; j++) ------------------ | Branch (5058:29): [True: 0, False: 0] ------------------ 5059| 0| { 5060| 0| int bond_type = at2[iS].bond_type[j]; 5061| 0| k = at2[iS].neighbor[j]; 5062| 0| if (k == i) ------------------ | Branch (5062:25): [True: 0, False: 0] ------------------ 5063| 0| { 5064| 0| continue; 5065| 0| } 5066| 0| if (pStruct->endpoint[k] == pStruct->endpoint[i]) ------------------ | Branch (5066:25): [True: 0, False: 0] ------------------ 5067| 0| { 5068| 0| nNumTautSB += (bond_type == BOND_TYPE_SINGLE); ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ 5069| 0| nNumTautDB += (bond_type == BOND_TYPE_DOUBLE); ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 5070| 0| } 5071| 0| else 5072| 0| { 5073| 0| if (bond_type == BOND_TYPE_DOUBLE) ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5073:29): [True: 0, False: 0] ------------------ 5074| 0| { 5075| 0| nNumOtherDB++; 5076| 0| } 5077| 0| else 5078| 0| { 5079| 0| if (bond_type == BOND_TYPE_SINGLE) ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5079:33): [True: 0, False: 0] ------------------ 5080| 0| { 5081| 0| nNumOtherSB++; 5082| 0| } 5083| 0| else 5084| 0| { 5085| 0| nNumOthers++; 5086| 0| } 5087| 0| } 5088| 0| } 5089| 0| if (at2[k].endpoint == at2[i].endpoint && at2[k].valence == 1 && ------------------ | Branch (5089:25): [True: 0, False: 0] | Branch (5089:63): [True: 0, False: 0] ------------------ 5090| 0| at2[k].charge == -1 && pVA[k].cNumValenceElectrons == 6) ------------------ | Branch (5090:25): [True: 0, False: 0] | Branch (5090:48): [True: 0, False: 0] ------------------ 5091| 0| { 5092| 0| nNumNegEndp++; 5093| 0| } 5094| 0| } 5095| 0| if (!nNumTautSB) ------------------ | Branch (5095:21): [True: 0, False: 0] ------------------ 5096| 0| { 5097| 0| continue; 5098| 0| } 5099| 0| if (!(nNumOtherDB && nNumTautDB)) ------------------ | Branch (5099:23): [True: 0, False: 0] | Branch (5099:38): [True: 0, False: 0] ------------------ 5100| 0| { 5101| 0| continue; /* ignore */ 5102| 0| } 5103| | 5104| 0| iat_SB_O_Minus[num_SB_O_Minus] = iat; 5105| 0| iat_Central[num_SB_O_Minus++] = iS; 5106| 0| } 5107| 0| } 5108| 0| if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (5108:13): [True: 0, False: 0] ------------------ 5109| 0| { 5110| | /* detected; attempt to fix */ 5111| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 5112| 0| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 5113| 0| delta = 1; 5114| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (5114:25): [True: 0, False: 0] | Branch (5114:47): [True: 0, False: 0] ------------------ 5115| 0| { 5116| 0| iat = iat_SB_O_Minus[i]; 5117| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 5118| 0| if (!pe->flow) ------------------ | Branch (5118:21): [True: 0, False: 0] ------------------ 5119| 0| continue; 5120| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 5121| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 5122| | 5123| 0| pe->forbidden |= forbidden_edge_mask; 5124| 0| pe->flow -= delta; 5125| 0| pv1->st_edge.flow -= delta; 5126| 0| pv2->st_edge.flow -= delta; 5127| 0| pBNS->tot_st_flow -= 2 * delta; 5128| | 5129| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5130| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 5131| | 5132| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5132:21): [True: 0, False: 0] | Branch (5132:35): [True: 0, False: 0] | Branch (5132:53): [True: 0, False: 0] ------------------ 5133| 0| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5133:22): [True: 0, False: 0] | Branch (5133:40): [True: 0, False: 0] | Branch (5133:62): [True: 0, False: 0] ------------------ 5134| 0| { 5135| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 5136| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 5137| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 5138| 0| if (ret > 0) ------------------ | Branch (5138:25): [True: 0, False: 0] ------------------ 5139| 0| { 5140| 0| nNumRunBNS++; 5141| 0| cur_success++; /* 21 */ 5142| 0| } 5143| 0| } 5144| 0| else 5145| 0| { 5146| 0| pe->flow += delta; 5147| 0| pv1->st_edge.flow += delta; 5148| 0| pv2->st_edge.flow += delta; 5149| 0| pBNS->tot_st_flow += 2 * delta; 5150| 0| } 5151| 0| INCHI_HEAPCHK 5152| 0| } 5153| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 5154| 0| } 5155| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 5156| 0| if (cur_success) ------------------ | Branch (5156:13): [True: 0, False: 0] ------------------ 5157| 0| { 5158| 0| tot_succes += cur_success; 5159| | /* recalculate InChI from the structure */ 5160| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5160:17): [True: 0, False: 0] ------------------ 5161| 0| ppt_group_info, ppat_norm, ppat_prep))) 5162| 0| { 5163| 0| goto exit_function; 5164| 0| } 5165| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5165:17): [True: 0, False: 0] ------------------ 5166| 0| { 5167| 0| goto exit_function; 5168| 0| } 5169| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5169:17): [True: 0, False: 0] | Branch (5169:45): [True: 0, False: 0] ------------------ 5170| 0| { 5171| 0| goto exit_function; /* no fixed-H found */ 5172| 0| } 5173| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5173:17): [True: 0, False: 0] ------------------ 5174| 0| { 5175| 0| goto exit_function; 5176| 0| } 5177| 0| if (!pc2i->bHasDifference) ------------------ | Branch (5177:17): [True: 0, False: 0] ------------------ 5178| 0| { 5179| 0| goto exit_function; /* nothing to do */ 5180| 0| } 5181| 0| } 5182| 0| } 5183| | 5184| 1.12k| if (pc2i->len_c2at && pc2i->nNumTgRevrs && pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs) ------------------ | Branch (5184:9): [True: 1.12k, False: 4] | Branch (5184:27): [True: 450, False: 673] | Branch (5184:48): [True: 233, False: 217] ------------------ 5185| 233| { 5186| | /*--------------------------------------------------------------*/ 5187| | /* O O */ 5188| | /* || || */ 5189| | /* case 21a:restored: R=S-R' =X original: R-S-R' -X(-) */ 5190| | /* | || */ 5191| | /* O(-) O(-) */ 5192| | /* All O and X are taut O and X are not taut */ 5193| | /* it is possible that X is R */ 5194| | /* */ 5195| | /* O = O, S, Se; S=S, Se, Te; X = N, O, S, Se, Te */ 5196| | /* Solution: move (-) from O(-) to =X */ 5197| | /* these atoms are tautomeric in restored structure */ 5198| | /*--------------------------------------------------------------*/ 5199| 233| int iat, iS; 5200| | /* 5201| | AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5202| | */ 5203| 233| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5203:41): [True: 233, False: 0] ------------------ 5204| 233| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5204:41): [True: 233, False: 0] ------------------ 5205| | /* 5206| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5207| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5208| | */ 5209| 233| EDGE_LIST OtherSO, CentralS, SOMinus, MinusAcceptord; 5210| 233| CurrEdges.num_edges = 0; /* clear current edge list */ 5211| 233| AllocEdgeList( &OtherSO, EDGE_LIST_CLEAR ); ------------------ | | 242| 233|#define EDGE_LIST_CLEAR (-1) ------------------ 5212| 233| AllocEdgeList( &CentralS, EDGE_LIST_CLEAR ); ------------------ | | 242| 233|#define EDGE_LIST_CLEAR (-1) ------------------ 5213| 233| AllocEdgeList( &SOMinus, EDGE_LIST_CLEAR ); ------------------ | | 242| 233|#define EDGE_LIST_CLEAR (-1) ------------------ 5214| 233| AllocEdgeList( &MinusAcceptord, EDGE_LIST_CLEAR ); ------------------ | | 242| 233|#define EDGE_LIST_CLEAR (-1) ------------------ 5215| 233| cur_success = 0; 5216| 233| if (!at_Mobile_H_Revrs) ------------------ | Branch (5216:13): [True: 0, False: 233] ------------------ 5217| 0| { 5218| 0| goto exit_case_21a; 5219| 0| } 5220| 1.10k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5220:21): [True: 870, False: 233] ------------------ 5221| 870| { 5222| 870| iat = pc2i->c2at[i].atomNumber; 5223| 870| if ( /* orig. InChI info: -X(-) */ 5224| | /*num_DB_O < MAX_DIFF_FIXH &&*/ 5225| | /*pc2i->c2at[i].nValElectr == 6 */ /* O, S, Se, Te */ 5226| 870| !pc2i->c2at[i].endptInChI && ------------------ | Branch (5226:18): [True: 823, False: 47] ------------------ 5227| 823| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5227:18): [True: 594, False: 229] | Branch (5227:64): [True: 594, False: 0] ------------------ 5228| 594| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5228:18): [True: 443, False: 151] ------------------ 5229| | /* reversed structure info: */ 5230| 443| ( pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs ) && ------------------ | Branch (5230:20): [True: 436, False: 7] | Branch (5230:48): [True: 7, False: 0] ------------------ 5231| 443| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5231:18): [True: 436, False: 7] ------------------ 5232| 436| /*pc2i->c2at[i].nAtChargeRevrs == 0 &&*/ !at2[iat].num_H) ------------------ | Branch (5232:59): [True: 436, False: 0] ------------------ 5233| 436| { 5234| 436| if (pVA[iat].cNumValenceElectrons == 6 && at2[iat].charge == -1 && ------------------ | Branch (5234:21): [True: 257, False: 179] | Branch (5234:59): [True: 118, False: 139] ------------------ 5235| 118| pBNS->edge[e].flow && ------------------ | Branch (5235:22): [True: 118, False: 0] ------------------ 5236| 118| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1 && ------------------ | Branch (5236:22): [True: 118, False: 0] | Branch (5236:47): [True: 118, False: 0] ------------------ 5237| 118| pVA[iS = (int) at2[iat].neighbor[0]].cNumValenceElectrons == 6 && pVA[iS].cPeriodicRowNumber > 1 && ------------------ | Branch (5237:22): [True: 30, False: 88] | Branch (5237:88): [True: 28, False: 2] ------------------ 5238| 28| at2[iS].valence >= 4) ------------------ | Branch (5238:22): [True: 25, False: 3] ------------------ 5239| 25| { 5240| | /* a candidate for S in -SO2- */ 5241| 25| int nNumTautSB = 0, nNumTautDB = 0, nNumOtherDB = 0, nNumOtherSB = 0; /* djb-rwth: ignoring LLVM warning: variables used */ 5242| 25| int nNumOthers = 0, nNumNegEndp = 0, nNumEndpO = 0; 5243| | /* check whether we have already found it */ 5244| 25| if (0 <= FindInEdgeList( &CentralS, iS )) ------------------ | Branch (5244:25): [True: 4, False: 21] ------------------ 5245| 4| { 5246| 4| continue; 5247| 4| } 5248| 125| for (j = 0; j < at[iS].valence; j++) ------------------ | Branch (5248:33): [True: 104, False: 21] ------------------ 5249| 104| { 5250| 104| int bond_type = at2[iS].bond_type[j]; 5251| 104| k = at2[iS].neighbor[j]; 5252| 104| if (k == iat) ------------------ | Branch (5252:29): [True: 21, False: 83] ------------------ 5253| 21| { 5254| 21| continue; 5255| 21| } 5256| 83| if (pc2i->c2at[i].endptRevrs == at_Mobile_H_Revrs[k].endpoint && !at2[k].endpoint) ------------------ | Branch (5256:29): [True: 42, False: 41] | Branch (5256:90): [True: 42, False: 0] ------------------ 5257| 42| { 5258| 42| nNumTautSB += ( bond_type == BOND_TYPE_SINGLE ); ------------------ | | 32| 42|#define BOND_TYPE_SINGLE 1 ------------------ 5259| 42| nNumTautDB += ( bond_type == BOND_TYPE_DOUBLE ); ------------------ | | 33| 42|#define BOND_TYPE_DOUBLE 2 ------------------ 5260| 42| nNumEndpO += ( pVA[k].cNumValenceElectrons == 6 && at2[k].valence == 1 ); ------------------ | Branch (5260:44): [True: 32, False: 10] | Branch (5260:80): [True: 32, False: 0] ------------------ 5261| 42| } 5262| 41| else 5263| 41| { 5264| 41| if (bond_type == BOND_TYPE_DOUBLE) ------------------ | | 33| 41|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5264:33): [True: 8, False: 33] ------------------ 5265| 8| { 5266| 8| nNumOtherDB++; 5267| 8| } 5268| 33| else 5269| 33| { 5270| 33| if (bond_type == BOND_TYPE_SINGLE) ------------------ | | 32| 33|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5270:37): [True: 32, False: 1] ------------------ 5271| 32| { 5272| 32| nNumOtherSB++; 5273| 32| } 5274| 1| else 5275| 1| { 5276| 1| nNumOthers++; 5277| 1| } 5278| 33| } 5279| 41| } 5280| 83| if (at2[k].endpoint == at2[i].endpoint && at2[k].valence == 1 && ------------------ | Branch (5280:29): [True: 83, False: 0] | Branch (5280:67): [True: 51, False: 32] ------------------ 5281| 51| at2[k].charge == -1 && pVA[k].cNumValenceElectrons == 6) ------------------ | Branch (5281:30): [True: 24, False: 27] | Branch (5281:53): [True: 21, False: 3] ------------------ 5282| 21| { 5283| 21| nNumNegEndp++; 5284| 21| } 5285| 83| } 5286| 21| if (!nNumEndpO) ------------------ | Branch (5286:25): [True: 1, False: 20] ------------------ 5287| 1| { 5288| 1| continue; 5289| 1| } 5290| 20| if (nNumTautSB + nNumTautDB + nNumOtherDB <= nNumEndpO) ------------------ | Branch (5290:25): [True: 9, False: 11] ------------------ 5291| 9| { 5292| 9| continue; /* ignore */ 5293| 9| } 5294| | /* collect double bond taut =O */ 5295| 63| for (j = 0; j < at[iS].valence; j++) ------------------ | Branch (5295:33): [True: 52, False: 11] ------------------ 5296| 52| { 5297| 52| int bond_type = at2[iS].bond_type[j]; 5298| 52| k = at2[iS].neighbor[j]; 5299| 52| if (pc2i->c2at[i].endptRevrs == at_Mobile_H_Revrs[k].endpoint && ------------------ | Branch (5299:29): [True: 33, False: 19] ------------------ 5300| 33| !at2[k].endpoint && pVA[k].cNumValenceElectrons == 6 && at2[k].valence == 1 && ------------------ | Branch (5300:30): [True: 33, False: 0] | Branch (5300:50): [True: 25, False: 8] | Branch (5300:86): [True: 25, False: 0] ------------------ 5301| 25| 0 <= ( e = pVA[k].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden) ------------------ | Branch (5301:30): [True: 20, False: 5] | Branch (5301:74): [True: 20, False: 0] ------------------ 5302| 20| { 5303| 20| if (bond_type == BOND_TYPE_DOUBLE && !at2[k].charge && !pBNS->edge[e].flow) ------------------ | | 33| 40|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5303:33): [True: 5, False: 15] | Branch (5303:66): [True: 5, False: 0] | Branch (5303:84): [True: 5, False: 0] ------------------ 5304| 5| { 5305| | /* charges to be unchanged */ 5306| 5| if ((ret = AddToEdgeList( &OtherSO, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 5|#define INC_ADD_EDGE 64 ------------------ | Branch (5306:37): [True: 0, False: 5] ------------------ 5307| 0| { 5308| 0| goto exit_case_21a; 5309| 0| } 5310| 5| } 5311| 15| else 5312| 15| { 5313| 15| if (bond_type == BOND_TYPE_SINGLE && at2[k].charge == -1 && pBNS->edge[e].flow) ------------------ | | 32| 30|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5313:37): [True: 15, False: 0] | Branch (5313:70): [True: 15, False: 0] | Branch (5313:93): [True: 15, False: 0] ------------------ 5314| 15| { 5315| | /* charges to be removed */ 5316| 15| if ((ret = AddToEdgeList( &SOMinus, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 15|#define INC_ADD_EDGE 64 ------------------ | Branch (5316:41): [True: 0, False: 15] ------------------ 5317| 0| { 5318| 0| goto exit_case_21a; 5319| 0| } 5320| 15| } 5321| 15| } 5322| 20| } 5323| 52| } 5324| 11| if ((ret = AddToEdgeList( &CentralS, iS, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 11|#define INC_ADD_EDGE 64 ------------------ | Branch (5324:25): [True: 0, False: 11] ------------------ 5325| 0| { 5326| 0| goto exit_case_21a; 5327| 0| } 5328| 11| } 5329| 411| else 5330| 411| if (at2[iat].charge == 0 && !pBNS->edge[e].flow && ------------------ | Branch (5330:25): [True: 291, False: 120] | Branch (5330:49): [True: 291, False: 0] ------------------ 5331| 291| at2[iat].valence + 1 == at2[iat].chem_bonds_valence) ------------------ | Branch (5331:26): [True: 291, False: 0] ------------------ 5332| 291| { 5333| | /* changeable charges */ 5334| 291| if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 291|#define INC_ADD_EDGE 64 ------------------ | Branch (5334:29): [True: 0, False: 291] ------------------ 5335| 0| { 5336| 0| goto exit_function; 5337| 0| } 5338| 291| } 5339| 436| } 5340| 870| } 5341| | /* remove unchangeable from changeable */ 5342| 238| for (i = 0; i < OtherSO.num_edges; i++) ------------------ | Branch (5342:21): [True: 5, False: 233] ------------------ 5343| 5| { 5344| 5| RemoveFromEdgeListByValue( &CurrEdges, OtherSO.pnEdges[i] ); 5345| 5| } 5346| | 5347| 233| if ((num_try = inchi_min( SOMinus.num_edges, CurrEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 233|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 169, False: 64] | | ------------------ ------------------ | Branch (5347:13): [True: 2, False: 231] ------------------ 5348| 2| { 5349| | /* detected; attempt to fix */ 5350| 2| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5351| 2| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 5352| 2| delta = 1; 5353| 4| for (i = 0; i < SOMinus.num_edges && cur_success < num_try; i++) ------------------ | Branch (5353:25): [True: 2, False: 2] | Branch (5353:50): [True: 2, False: 0] ------------------ 5354| 2| { 5355| 2| pe = pBNS->edge + SOMinus.pnEdges[i]; 5356| 2| if (!pe->flow) ------------------ | Branch (5356:21): [True: 0, False: 2] ------------------ 5357| 0| continue; 5358| 2| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 5359| 2| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 5360| | 5361| | /*pe->forbidden |= forbidden_edge_mask;*/ 5362| 2| pe->flow -= delta; 5363| 2| pv1->st_edge.flow -= delta; 5364| 2| pv2->st_edge.flow -= delta; 5365| 2| pBNS->tot_st_flow -= 2 * delta; 5366| | 5367| 2| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5368| 2| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5369| | 5370| 2| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5370:21): [True: 2, False: 0] | Branch (5370:36): [True: 0, False: 2] | Branch (5370:54): [True: 0, False: 0] ------------------ 5371| 2| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (5371:36): [True: 2, False: 0] | Branch (5371:54): [True: 2, False: 0] | Branch (5371:77): [True: 2, False: 0] ------------------ 5372| 2| { 5373| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 5374| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 5375| 2| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5376| 2| if (ret > 0) ------------------ | Branch (5376:25): [True: 2, False: 0] ------------------ 5377| 2| { 5378| 2| nNumRunBNS++; 5379| 2| cur_success++; /* 21a */ 5380| 2| } 5381| 2| } 5382| 0| else 5383| 0| { 5384| 0| pe->flow += delta; 5385| 0| pv1->st_edge.flow += delta; 5386| 0| pv2->st_edge.flow += delta; 5387| 0| pBNS->tot_st_flow += 2 * delta; 5388| 0| } 5389| 2| INCHI_HEAPCHK 5390| 2| } 5391| 2| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5392| 2| } 5393| 233| exit_case_21a: 5394| 233| CurrEdges.num_edges = 0; /* clear current edge list */ 5395| 233| AllocEdgeList( &OtherSO, EDGE_LIST_FREE ); ------------------ | | 243| 233|#define EDGE_LIST_FREE (-2) ------------------ 5396| 233| AllocEdgeList( &CentralS, EDGE_LIST_FREE ); ------------------ | | 243| 233|#define EDGE_LIST_FREE (-2) ------------------ 5397| 233| AllocEdgeList( &SOMinus, EDGE_LIST_FREE ); ------------------ | | 243| 233|#define EDGE_LIST_FREE (-2) ------------------ 5398| 233| AllocEdgeList( &MinusAcceptord, EDGE_LIST_FREE ); ------------------ | | 243| 233|#define EDGE_LIST_FREE (-2) ------------------ 5399| 233| if (cur_success) ------------------ | Branch (5399:13): [True: 2, False: 231] ------------------ 5400| 2| { 5401| 2| tot_succes += cur_success; 5402| | /* recalculate InChI from the structure */ 5403| 2| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5403:17): [True: 0, False: 2] ------------------ 5404| 2| ppt_group_info, ppat_norm, ppat_prep ) )) 5405| 0| { 5406| 0| goto exit_function; 5407| 0| } 5408| 2| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5408:17): [True: 0, False: 2] ------------------ 5409| 0| { 5410| 0| goto exit_function; 5411| 0| } 5412| 2| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5412:17): [True: 0, False: 2] | Branch (5412:45): [True: 0, False: 0] ------------------ 5413| 0| { 5414| 0| goto exit_function; /* no fixed-H found */ 5415| 0| } 5416| 2| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5416:17): [True: 0, False: 2] ------------------ 5417| 0| { 5418| 0| goto exit_function; 5419| 0| } 5420| 2| if (!pc2i->bHasDifference) ------------------ | Branch (5420:17): [True: 0, False: 2] ------------------ 5421| 0| { 5422| 0| goto exit_function; /* nothing to do */ 5423| 0| } 5424| 2| } 5425| 233| } 5426| | 5427| 1.12k| if (pc2i->len_c2at) ------------------ | Branch (5427:9): [True: 1.12k, False: 4] ------------------ 5428| 1.12k| { 5429| | /*------------------------------------------------------------------*/ 5430| | /* case 22: restored: N(-)=N(+)=C...=O orig: N#N-N=...-O(-) */ 5431| | /* im InChI -O(-) may have H(+) added by Normalization */ 5432| | /* or may be tautomeric */ 5433| | /* Solution: move (-) from N(-) to =O */ 5434| | /* */ 5435| | /*------------------------------------------------------------------*/ 5436| 1.12k| int num_DB_O = 0, iat; 5437| 1.12k| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5438| 1.12k| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5438:41): [True: 573, False: 550] ------------------ 5439| 1.12k| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5439:41): [True: 573, False: 0] ------------------ 5440| 1.12k| int iN2, iC; 5441| 1.12k| BNS_EDGE *peDB_O_Minus; 5442| | /* 5443| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5444| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5445| | */ 5446| 1.12k| CurrEdges.num_edges = 0; /* clear current edge list */ 5447| 1.12k| cur_success = 0; 5448| | 5449| 4.63k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5449:21): [True: 3.50k, False: 1.12k] ------------------ 5450| 3.50k| { 5451| 3.50k| iat = pc2i->c2at[i].atomNumber; 5452| 3.50k| if ( /* orig. InChI info: =O */ 5453| 3.50k| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 7.01k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5453:17): [True: 3.50k, False: 0] ------------------ 5454| 3.50k| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (5454:17): [True: 1.76k, False: 1.74k] ------------------ 5455| 1.76k| (pc2i->c2at[i].endptInChI || pc2i->c2at[i].nMobHInChI) && ------------------ | Branch (5455:18): [True: 715, False: 1.04k] | Branch (5455:46): [True: 79, False: 969] ------------------ 5456| 794| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5456:17): [True: 567, False: 227] | Branch (5456:61): [True: 567, False: 0] ------------------ 5457| 567| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5457:17): [True: 530, False: 37] ------------------ 5458| | /* reversed structure info: */ 5459| 530| !(pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs) && ------------------ | Branch (5459:19): [True: 0, False: 530] | Branch (5459:47): [True: 18, False: 512] ------------------ 5460| 512| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5460:17): [True: 512, False: 0] ------------------ 5461| 512| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (5461:17): [True: 352, False: 160] | Branch (5461:54): [True: 352, False: 0] ------------------ 5462| 352| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (5462:17): [True: 349, False: 3] | Branch (5462:42): [True: 324, False: 25] ------------------ 5463| 324| { 5464| 324| iat_DB_O[num_DB_O++] = iat; 5465| 324| } 5466| 3.50k| } 5467| 2.84k| for (i = 0; num_DB_O && i < pStruct->num_atoms; i++) ------------------ | Branch (5467:21): [True: 1.93k, False: 905] | Branch (5467:33): [True: 1.71k, False: 218] ------------------ 5468| 1.71k| { 5469| | /* i = canonical number - 1 */ 5470| 1.71k| iat = nCanon2AtnoRevrs[i]; 5471| 1.71k| if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */ 5472| 1.71k| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (5472:17): [True: 294, False: 1.42k] | Branch (5472:42): [True: 282, False: 12] ------------------ 5473| 282| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && !pVA[iat].cMetal && ------------------ | Branch (5473:17): [True: 186, False: 96] | Branch (5473:42): [True: 36, False: 150] | Branch (5473:78): [True: 36, False: 0] ------------------ 5474| 36| pVA[iat].cNumValenceElectrons == 5 && ------------------ | Branch (5474:17): [True: 35, False: 1] ------------------ 5475| 35| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5475:17): [True: 35, False: 0] | Branch (5475:61): [True: 35, False: 0] ------------------ 5476| 35| pBNS->edge[e].flow && ------------------ | Branch (5476:17): [True: 35, False: 0] ------------------ 5477| 35| !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) && ------------------ | Branch (5477:19): [True: 9, False: 26] | Branch (5477:40): [True: 3, False: 6] ------------------ 5478| 32| pVA[iN2 = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (5478:17): [True: 23, False: 9] ------------------ 5479| 23| at2[iat].bond_type[0] == BOND_TYPE_DOUBLE && ------------------ | | 33| 1.74k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5479:17): [True: 23, False: 0] ------------------ 5480| 23| at2[iN2].charge == 1 && at2[iN2].valence == 2 && at2[iN2].chem_bonds_valence == 4 && ------------------ | Branch (5480:17): [True: 13, False: 10] | Branch (5480:41): [True: 3, False: 10] | Branch (5480:66): [True: 3, False: 0] ------------------ 5481| 3| pVA[iC = at2[iN2].neighbor[at2[iN2].neighbor[0] == iN2]].cNumValenceElectrons == 4) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | Branch (5481:17): [True: 0, False: 3] ------------------ 5482| 0| { 5483| | 5484| 0| if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5484:21): [True: 0, False: 0] ------------------ 5485| 0| { 5486| 0| goto exit_function; 5487| 0| } 5488| 0| } 5489| 1.71k| } 5490| 1.12k| if ((num_try = inchi_min(CurrEdges.num_edges, num_DB_O))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 139| 1.12k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 218, False: 905] | | ------------------ ------------------ | Branch (5490:13): [True: 0, False: 1.12k] ------------------ 5491| 0| { 5492| | /* detected; attempt to fix */ 5493| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 5494| 0| RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask); 5495| 0| delta = 1; 5496| 0| for (i = 0; i < num_DB_O && cur_success < num_try; i++) ------------------ | Branch (5496:25): [True: 0, False: 0] | Branch (5496:41): [True: 0, False: 0] ------------------ 5497| 0| { 5498| 0| iat = iat_DB_O[i]; 5499| | 5500| 0| peDB_O_Minus = pBNS->edge + ((long long)pVA[iat].nCMinusGroupEdge - 1); /* djb-rwth: cast operator added */ 5501| 0| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; 5502| 0| if (!pe->flow) ------------------ | Branch (5502:21): [True: 0, False: 0] ------------------ 5503| 0| continue; 5504| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 5505| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 5506| | 5507| 0| pe->forbidden |= forbidden_edge_mask; 5508| 0| peDB_O_Minus->forbidden &= forbidden_edge_mask_inv; 5509| | 5510| 0| pe->flow -= delta; 5511| 0| pv1->st_edge.flow -= delta; 5512| 0| pv2->st_edge.flow -= delta; 5513| 0| pBNS->tot_st_flow -= 2 * delta; 5514| | 5515| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5516| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 5517| | 5518| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5518:21): [True: 0, False: 0] | Branch (5518:35): [True: 0, False: 0] | Branch (5518:53): [True: 0, False: 0] ------------------ 5519| 0| (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (5519:22): [True: 0, False: 0] | Branch (5519:40): [True: 0, False: 0] | Branch (5519:62): [True: 0, False: 0] ------------------ 5520| 0| { 5521| | /* Added (-) charge to =O and removed from =N(-) => nDeltaCharge == 0 */ 5522| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 5523| 0| if (ret > 0) ------------------ | Branch (5523:25): [True: 0, False: 0] ------------------ 5524| 0| { 5525| 0| nNumRunBNS++; 5526| 0| cur_success++; /* 22 */ 5527| 0| } 5528| 0| } 5529| 0| else 5530| 0| { 5531| 0| pe->flow += delta; 5532| 0| pv1->st_edge.flow += delta; 5533| 0| pv2->st_edge.flow += delta; 5534| 0| pBNS->tot_st_flow += 2 * delta; 5535| 0| } 5536| 0| INCHI_HEAPCHK 5537| 0| pe->forbidden &= forbidden_edge_mask_inv; 5538| 0| peDB_O_Minus->forbidden |= forbidden_edge_mask; 5539| 0| } 5540| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 5541| 0| } 5542| 1.12k| CurrEdges.num_edges = 0; /* clear current edge list */ 5543| 1.12k| if (cur_success) ------------------ | Branch (5543:13): [True: 0, False: 1.12k] ------------------ 5544| 0| { 5545| 0| tot_succes += cur_success; 5546| | /* recalculate InChI from the structure */ 5547| 0| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5547:17): [True: 0, False: 0] ------------------ 5548| 0| ppt_group_info, ppat_norm, ppat_prep))) 5549| 0| { 5550| 0| goto exit_function; 5551| 0| } 5552| 0| if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5552:17): [True: 0, False: 0] ------------------ 5553| 0| { 5554| 0| goto exit_function; 5555| 0| } 5556| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5556:17): [True: 0, False: 0] | Branch (5556:45): [True: 0, False: 0] ------------------ 5557| 0| { 5558| 0| goto exit_function; /* no fixed-H found */ 5559| 0| } 5560| 0| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5560:17): [True: 0, False: 0] ------------------ 5561| 0| { 5562| 0| goto exit_function; 5563| 0| } 5564| 0| if (!pc2i->bHasDifference) ------------------ | Branch (5564:17): [True: 0, False: 0] ------------------ 5565| 0| { 5566| 0| goto exit_function; /* nothing to do */ 5567| 0| } 5568| 0| } 5569| 1.12k| } 5570| | 5571| 1.12k| if (pc2i->len_c2at && pc2i->nNumTgInChI == 1) ------------------ | Branch (5571:9): [True: 1.12k, False: 4] | Branch (5571:27): [True: 729, False: 394] ------------------ 5572| 729| { 5573| | /*------------------------------------------------------------------*/ 5574| | /* case 23: -NO2 are to be tautomeric but they are not AND */ 5575| | /* InChI has a SINGLE tautomeric group */ 5576| | /* */ 5577| | /* (-)O (-)O */ 5578| | /* Solution: convert \ \ */ 5579| | /* N-X=...-Z(-) => N(+)=X- ...=Z */ 5580| | /* // / */ 5581| | /* O (-)O */ 5582| | /* */ 5583| | /* O O */ 5584| | /* or \\ \\ */ 5585| | /* N-X=...-Z(-) => N=X- ...=Z */ 5586| | /* // / */ 5587| | /* O (-)O */ 5588| | /* */ 5589| | /* */ 5590| | /* (a) move (-) from other tautomeric atom to O in O=N-X */ 5591| | /* or from other atom that has to be tautomeric */ 5592| | /* but is not */ 5593| | /* (b) create (+) [ion pair creation] on N as in */ 5594| | /* */ 5595| | /* OH OH */ 5596| | /* / / */ 5597| | /* -C=N => =C-N(+) */ 5598| | /* \\ \\ */ 5599| | /* O O */ 5600| | /* */ 5601| | /*------------------------------------------------------------------*/ 5602| 729| int num_DB_O = 0, iat; 5603| 729| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5604| 729| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5604:41): [True: 303, False: 426] ------------------ 5605| 729| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5605:41): [True: 303, False: 0] ------------------ 5606| | /* 5607| | inp_ATOM *atfMobile_H_Revrs = (pStruct->pOne_norm_data[1] && 5608| | pStruct->pOne_norm_data[1]->at_fixed_bonds)? 5609| | pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL; 5610| | */ 5611| 729| S_CHAR *num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL; ------------------ | Branch (5611:39): [True: 729, False: 0] ------------------ 5612| 729| S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ? ------------------ | Branch (5612:35): [True: 303, False: 426] | Branch (5612:60): [True: 303, False: 0] ------------------ 5613| 303| pStruct->pOneINChI[1]->nNum_H : 5614| 729| ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (5614:15): [True: 426, False: 0] | Branch (5614:40): [True: 426, False: 0] ------------------ 5615| 426| pStruct->pOneINChI[0]->nNum_H : NULL; 5616| 729| int iN, one_success; 5617| 729| BNS_EDGE *peDB_O_Minus; 5618| 729| int neigh, nNumO, nNumOthers; 5619| 729|#define CHG_SET_NOOH 0 5620| 729|#define CHG_SET_WRONG_TAUT 1 5621| 729|#define CHG_SET_TAUT 2 5622| 729|#define CHG_LAST_SET 2 /* the last index in trying */ 5623| 729|#define CHG_SET_O_FIXED 3 5624| 729|#define CHG_SET_NUM 4 5625| 729| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 5626| 729| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5627| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 5628| | /* 5629| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5630| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5631| | */ 5632| 729| CurrEdges.num_edges = 0; /* clear current edge list */ 5633| 729| cur_success = 0; 5634| | 5635| 3.03k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5635:21): [True: 2.30k, False: 729] ------------------ 5636| 2.30k| { 5637| 2.30k| iat = pc2i->c2at[i].atomNumber; 5638| 2.30k| if ( /* orig. InChI info: taut in orig. InChI =O located in -NO2 that is not taut in Reconstructed InChI */ 5639| 2.30k| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 4.61k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5639:17): [True: 2.30k, False: 0] ------------------ 5640| 2.30k| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (5640:17): [True: 1.26k, False: 1.04k] ------------------ 5641| 1.26k| (pc2i->c2at[i].endptInChI /*|| pc2i->c2at[i].nMobHInChI*/) && ------------------ | Branch (5641:17): [True: 695, False: 566] ------------------ 5642| 695| (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5642:17): [True: 523, False: 172] | Branch (5642:61): [True: 523, False: 0] ------------------ 5643| 523| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5643:17): [True: 517, False: 6] ------------------ 5644| | /* reversed structure info: */ 5645| 517| !(pc2i->c2at[i].endptRevrs /*|| pc2i->c2at[i].nMobHRevrs*/) && ------------------ | Branch (5645:17): [True: 517, False: 0] ------------------ 5646| 517| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5646:17): [True: 499, False: 18] ------------------ 5647| 499| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (5647:17): [True: 339, False: 160] | Branch (5647:54): [True: 339, False: 0] ------------------ 5648| 339| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (5648:17): [True: 336, False: 3] | Branch (5648:42): [True: 311, False: 25] ------------------ 5649| | /* find whether it belongs to NO2 */ 5650| 311| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (5650:17): [True: 257, False: 54] ------------------ 5651| 257| at2[iN].valence == 3 && (at2[iN].charge == 0 || at2[iN].charge == 1) && ------------------ | Branch (5651:17): [True: 223, False: 34] | Branch (5651:42): [True: 103, False: 120] | Branch (5651:65): [True: 120, False: 0] ------------------ 5652| 223| at2[iN].chem_bonds_valence == 5 - at2[iN].charge) ------------------ | Branch (5652:17): [True: 217, False: 6] ------------------ 5653| 217| { 5654| | /* find the second O */ 5655| 217| nNumO = nNumOthers = 0; 5656| 868| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (5656:29): [True: 651, False: 217] ------------------ 5657| 651| { 5658| 651| neigh = at2[iN].neighbor[k]; 5659| 651| if (neigh == iat) ------------------ | Branch (5659:25): [True: 217, False: 434] ------------------ 5660| 217| { 5661| 217| continue; 5662| 217| } 5663| 434| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (5663:25): [True: 205, False: 229] ------------------ 5664| 205| pStruct->endpoint[neigh] && ------------------ | Branch (5664:25): [True: 167, False: 38] ------------------ 5665| 167| !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[neigh].endpoint) && ------------------ | Branch (5665:27): [True: 30, False: 137] | Branch (5665:48): [True: 0, False: 30] ------------------ 5666| 167| at2[neigh].valence == 1 && at2[neigh].num_H == 0 && ------------------ | Branch (5666:25): [True: 139, False: 28] | Branch (5666:52): [True: 139, False: 0] ------------------ 5667| 139| at2[neigh].radical == 0 && (at2[neigh].charge == 0 || at2[neigh].charge == -1) && ------------------ | Branch (5667:25): [True: 138, False: 1] | Branch (5667:53): [True: 86, False: 52] | Branch (5667:79): [True: 52, False: 0] ------------------ 5668| 138| at2[neigh].chem_bonds_valence - at2[neigh].charge == 2) ------------------ | Branch (5668:25): [True: 138, False: 0] ------------------ 5669| 138| { 5670| 138| nNumO++; 5671| 138| } 5672| 296| else 5673| 296| { 5674| 296| if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE && ------------------ | | 32| 592|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5674:29): [True: 219, False: 77] ------------------ 5675| 219| at2[neigh].valence > 1 && ------------------ | Branch (5675:29): [True: 213, False: 6] ------------------ 5676| 213| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (5676:29): [True: 129, False: 84] ------------------ 5677| 129| { 5678| 129| nNumOthers++; 5679| 129| } 5680| 296| } 5681| 434| } 5682| 217| if (nNumO != 1 || nNumOthers != 1) ------------------ | Branch (5682:21): [True: 79, False: 138] | Branch (5682:35): [True: 56, False: 82] ------------------ 5683| 135| { 5684| 135| continue; 5685| 135| } 5686| 84| for (k = 0; k < num_DB_O; k++) ------------------ | Branch (5686:29): [True: 21, False: 63] ------------------ 5687| 21| { 5688| 21| if (iat_NO2[k] == iN) ------------------ | Branch (5688:25): [True: 19, False: 2] ------------------ 5689| 19| { 5690| 19| break; 5691| 19| } 5692| 21| } 5693| 82| if (k == num_DB_O) ------------------ | Branch (5693:21): [True: 63, False: 19] ------------------ 5694| 63| { 5695| 63| iat_NO2[num_DB_O] = iN; 5696| 63| iat_DB_O[num_DB_O++] = iat; 5697| 63| } 5698| | /* save the edge to avoid interference */ 5699| 82| if ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 5623| 82|#define CHG_SET_O_FIXED 3 ------------------ if ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 82|#define INC_ADD_EDGE 64 ------------------ | Branch (5699:21): [True: 0, False: 82] ------------------ 5700| 0| { 5701| 0| goto exit_case_23; 5702| 0| } 5703| 82| } 5704| 2.30k| } 5705| 729| if (num_DB_O) ------------------ | Branch (5705:13): [True: 62, False: 667] ------------------ 5706| 62| { 5707| | /* 1. search for =N(=O)-OH; assume =N(+)(-O(-))(-OH) does not happen */ 5708| 558| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (5708:25): [True: 496, False: 62] ------------------ 5709| 496| { 5710| | /* i = canonical number - 1 */ 5711| | /* find O=N(V) */ 5712| 496| iat = nCanon2AtnoRevrs[i]; 5713| 496| if (!pStruct->endpoint[i] || pVA[i].cNumValenceElectrons != 6 || ------------------ | Branch (5713:21): [True: 236, False: 260] | Branch (5713:46): [True: 84, False: 176] ------------------ 5714| 176| at2[iat].valence != 1 || at2[iat].charge || ------------------ | Branch (5714:21): [True: 7, False: 169] | Branch (5714:46): [True: 56, False: 113] ------------------ 5715| 113| 0 > (e = pVA[iat].nCMinusGroupEdge - 1) || ------------------ | Branch (5715:21): [True: 0, False: 113] ------------------ 5716| 113| at2[iat].num_H + at2[iat].chem_bonds_valence != 2 || ------------------ | Branch (5716:21): [True: 7, False: 106] ------------------ 5717| 106| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons != 5 || ------------------ | Branch (5717:21): [True: 3, False: 103] ------------------ 5718| 103| 0 > (e = pVA[iN].nCPlusGroupEdge - 1) || ------------------ | Branch (5718:21): [True: 3, False: 100] ------------------ 5719| 100| pBNS->edge[e].forbidden || !pBNS->edge[e].flow || ------------------ | Branch (5719:21): [True: 0, False: 100] | Branch (5719:48): [True: 46, False: 54] ------------------ 5720| 54| at2[iN].charge || at2[iN].valence != 3 || at2[iN].chem_bonds_valence != 5) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | Branch (5720:21): [True: 3, False: 51] | Branch (5720:39): [True: 6, False: 45] | Branch (5720:63): [True: 1, False: 44] ------------------ 5721| 452| { 5722| 452| continue; 5723| 452| } 5724| | /* find the second O, -OH */ 5725| 44| nNumO = nNumOthers = 0; 5726| 176| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (5726:29): [True: 132, False: 44] ------------------ 5727| 132| { 5728| 132| neigh = at2[iN].neighbor[k]; 5729| 132| if (neigh == iat) ------------------ | Branch (5729:25): [True: 44, False: 88] ------------------ 5730| 44| { 5731| 44| continue; 5732| 44| } 5733| 88| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (5733:25): [True: 45, False: 43] ------------------ 5734| 45| pStruct->endpoint[neigh] && ------------------ | Branch (5734:25): [True: 41, False: 4] ------------------ 5735| 41| at2[neigh].valence == 1 && at2[neigh].num_H == 1 && ------------------ | Branch (5735:25): [True: 38, False: 3] | Branch (5735:52): [True: 0, False: 38] ------------------ 5736| 0| at2[neigh].radical == 0 && (at2[neigh].charge == 0)) ------------------ | Branch (5736:25): [True: 0, False: 0] | Branch (5736:52): [True: 0, False: 0] ------------------ 5737| 0| { 5738| 0| nNumO++; 5739| 0| } 5740| 88| else 5741| 88| if (at2[iN].bond_type[k] == BOND_TYPE_DOUBLE && ------------------ | | 33| 176|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5741:29): [True: 44, False: 44] ------------------ 5742| 44| at2[neigh].valence >= 2 && ------------------ | Branch (5742:29): [True: 4, False: 40] ------------------ 5743| 4| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (5743:29): [True: 4, False: 0] ------------------ 5744| 4| { 5745| 4| nNumOthers++; 5746| 4| } 5747| 88| } 5748| 44| if (nNumO != 1 || nNumOthers != 1) ------------------ | Branch (5748:21): [True: 44, False: 0] | Branch (5748:35): [True: 0, False: 0] ------------------ 5749| 44| { 5750| 44| continue; 5751| 44| } 5752| | /* save edges to be changed */ 5753| 0| if ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_NOOH], e, INC_ADD_EDGE)) || ------------------ | | 5619| 0|#define CHG_SET_NOOH 0 ------------------ if ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_NOOH], e, INC_ADD_EDGE)) || ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5753:21): [True: 0, False: 0] ------------------ 5754| 0| (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))) ------------------ | | 5623| 0|#define CHG_SET_O_FIXED 3 ------------------ (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5754:21): [True: 0, False: 0] ------------------ 5755| 0| { 5756| 0| goto exit_case_23; 5757| 0| } 5758| 0| if (NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) && ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (5758:21): [True: 0, False: 0] ------------------ 5759| 0| ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_NOOH], j, INC_ADD_EDGE)) || ------------------ | | 5619| 0|#define CHG_SET_NOOH 0 ------------------ ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_NOOH], j, INC_ADD_EDGE)) || ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5759:22): [True: 0, False: 0] ------------------ 5760| 0| (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE)))) ------------------ | | 5623| 0|#define CHG_SET_O_FIXED 3 ------------------ (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE)))) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5760:25): [True: 0, False: 0] ------------------ 5761| 0| { 5762| 0| goto exit_case_23; 5763| 0| } 5764| 0| } 5765| | /* 2. search for (-) atoms that are tautomeric but should not be */ 5766| | /* or that got H from Normalization but they shouldn't */ 5767| 558| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (5767:25): [True: 496, False: 62] ------------------ 5768| 496| { /* i = canonical number - 1 */ 5769| 496| iat = nCanon2AtnoRevrs[i]; 5770| 496| if (at2[iat].charge == -1 && ------------------ | Branch (5770:21): [True: 102, False: 394] ------------------ 5771| 102| !pStruct->endpoint[i] && ------------------ | Branch (5771:21): [True: 29, False: 73] ------------------ 5772| 29| (at_Mobile_H_Revrs && ------------------ | Branch (5772:22): [True: 7, False: 22] ------------------ 5773| 7| (at_Mobile_H_Revrs[i].endpoint || at2[iat].num_H < at_Mobile_H_Revrs[i].num_H))) ------------------ | Branch (5773:26): [True: 3, False: 4] | Branch (5773:59): [True: 4, False: 0] ------------------ 5774| 7| { 5775| | 5776| 7| if (0 <= (e = pVA[iat].nCMinusGroupEdge - 1) && ------------------ | Branch (5776:25): [True: 7, False: 0] ------------------ 5777| 7| 0 > FindInEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e) && ------------------ | | 5623| 7|#define CHG_SET_O_FIXED 3 ------------------ | Branch (5777:25): [True: 7, False: 0] ------------------ 5778| 7| !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (5778:25): [True: 7, False: 0] | Branch (5778:53): [True: 7, False: 0] ------------------ 5779| 7| ( 5780| 7| (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE)) || ------------------ | | 5620| 7|#define CHG_SET_WRONG_TAUT 1 ------------------ (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE)) || ------------------ | | 18| 7|#define INC_ADD_EDGE 64 ------------------ | Branch (5780:29): [True: 0, False: 7] ------------------ 5781| 7| (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE)) ------------------ | | 5623| 7|#define CHG_SET_O_FIXED 3 ------------------ (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE)) ------------------ | | 18| 7|#define INC_ADD_EDGE 64 ------------------ | Branch (5781:29): [True: 0, False: 7] ------------------ 5782| 7| )) 5783| 0| { 5784| 0| goto exit_case_23; 5785| 0| } 5786| 7| } 5787| 489| else 5788| 489| { 5789| | /* negatively charged atom in Reconstructed structure got H(+) from Normalization */ 5790| | /* and is not tautomeric; in the original structure it is tautomeric */ 5791| 489| if (at2[iat].charge == -1 && ------------------ | Branch (5791:25): [True: 95, False: 394] ------------------ 5792| 95| pStruct->endpoint[i] && ------------------ | Branch (5792:25): [True: 73, False: 22] ------------------ 5793| 73| !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) && ------------------ | Branch (5793:27): [True: 19, False: 54] | Branch (5793:48): [True: 5, False: 14] ------------------ 5794| 68| (num_Fixed_H_Revrs && num_Fixed_H_Revrs[i] == -1) && ------------------ | Branch (5794:26): [True: 68, False: 0] | Branch (5794:47): [True: 3, False: 65] ------------------ 5795| 3| (pnMobHRevrs && pnMobHRevrs[i] == 1) && ------------------ | Branch (5795:26): [True: 3, False: 0] | Branch (5795:41): [True: 3, False: 0] ------------------ 5796| 3| pStruct->fixed_H[i] == 0) ------------------ | Branch (5796:25): [True: 3, False: 0] ------------------ 5797| 3| { 5798| | 5799| 3| if (0 <= (e = pVA[iat].nCMinusGroupEdge - 1) && ------------------ | Branch (5799:29): [True: 3, False: 0] ------------------ 5800| 3| 0 > FindInEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e) && ------------------ | | 5623| 3|#define CHG_SET_O_FIXED 3 ------------------ | Branch (5800:29): [True: 3, False: 0] ------------------ 5801| 3| !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (5801:29): [True: 3, False: 0] | Branch (5801:57): [True: 3, False: 0] ------------------ 5802| 3| ( 5803| 3| (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE)) || ------------------ | | 5620| 3|#define CHG_SET_WRONG_TAUT 1 ------------------ (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE)) || ------------------ | | 18| 3|#define INC_ADD_EDGE 64 ------------------ | Branch (5803:33): [True: 0, False: 3] ------------------ 5804| 3| (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE)) ------------------ | | 5623| 3|#define CHG_SET_O_FIXED 3 ------------------ (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE)) ------------------ | | 18| 3|#define INC_ADD_EDGE 64 ------------------ | Branch (5804:33): [True: 0, False: 3] ------------------ 5805| 3| )) 5806| 0| { 5807| 0| goto exit_case_23; 5808| 0| } 5809| 3| } 5810| 489| } 5811| 496| } 5812| | /* 3. Search for (-) atoms that are tautomeric */ 5813| 558| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (5813:25): [True: 496, False: 62] ------------------ 5814| 496| { 5815| | /* i = canonical number - 1 */ 5816| 496| iat = nCanon2AtnoRevrs[i]; 5817| 496| if (pStruct->endpoint[i] && ------------------ | Branch (5817:21): [True: 260, False: 236] ------------------ 5818| 260| (at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) && ------------------ | Branch (5818:22): [True: 58, False: 202] | Branch (5818:43): [True: 10, False: 48] ------------------ 5819| 10| at2[iat].charge == -1 ------------------ | Branch (5819:21): [True: 5, False: 5] ------------------ 5820| 496| /*&& pVA[i].cNumValenceElectrons == 6*/) 5821| 5| { 5822| 5| if (0 <= (e = pVA[iat].nCMinusGroupEdge - 1) && ------------------ | Branch (5822:25): [True: 5, False: 0] ------------------ 5823| 5| !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (5823:25): [True: 5, False: 0] | Branch (5823:53): [True: 5, False: 0] ------------------ 5824| 5| 0 > FindInEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e) && ------------------ | | 5623| 5|#define CHG_SET_O_FIXED 3 ------------------ | Branch (5824:25): [True: 5, False: 0] ------------------ 5825| 5| (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_TAUT], e, INC_ADD_EDGE))) ------------------ | | 5621| 5|#define CHG_SET_TAUT 2 ------------------ (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_TAUT], e, INC_ADD_EDGE))) ------------------ | | 18| 5|#define INC_ADD_EDGE 64 ------------------ | Branch (5825:25): [True: 0, False: 5] ------------------ 5826| 0| { 5827| 0| goto exit_case_23; 5828| 0| } 5829| 5| } 5830| 496| } 5831| | 5832| | /* ------- finally, try to move charges from O=N --------------*/ 5833| 125| for (i = 0; i < num_DB_O; i++) ------------------ | Branch (5833:25): [True: 63, False: 62] ------------------ 5834| 63| { 5835| 63| int nDeltaChargeExpected; 5836| 63| one_success = 0; 5837| 63| delta = 1; 5838| 63| iat = iat_DB_O[i]; 5839| 63| peDB_O_Minus = pBNS->edge + ((long long)pVA[iat].nCMinusGroupEdge - 1);/* djb-rwth: cast operator added */ 5840| 63| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; 5841| | 5842| 63| if (!pe->flow) ------------------ | Branch (5842:21): [True: 0, False: 63] ------------------ 5843| 0| continue; 5844| 63| pv1 = pBNS->vert + (v1 = pe->neighbor1); 5845| 63| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 5846| | 5847| 63| pe->forbidden |= forbidden_edge_mask; 5848| | 5849| 63| pe->flow -= delta; 5850| 63| pv1->st_edge.flow -= delta; 5851| 63| pv2->st_edge.flow -= delta; 5852| 63| pBNS->tot_st_flow -= 2 * delta; 5853| | 5854| 249| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 5622| 245|#define CHG_LAST_SET 2 /* the last index in trying */ ------------------ | Branch (5854:29): [True: 245, False: 4] | Branch (5854:45): [True: 186, False: 59] ------------------ 5855| 186| { 5856| 186| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (5856:25): [True: 171, False: 15] ------------------ 5857| 171| { 5858| 171| continue; 5859| 171| } 5860| 15| nDeltaChargeExpected = (k == CHG_SET_NOOH) ? 2 : 0; ------------------ | | 5619| 15|#define CHG_SET_NOOH 0 ------------------ | Branch (5860:44): [True: 0, False: 15] ------------------ 5861| | 5862| 15| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 5863| 15| RemoveForbiddenEdgeMask(pBNS, &ChangeableEdges[k], forbidden_edge_mask); 5864| | /* allow (-) charge to move to N=O */ 5865| 15| peDB_O_Minus->forbidden &= forbidden_edge_mask_inv; 5866| | 5867| 15| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5868| 15| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 5869| | 5870| 15| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (5870:25): [True: 4, False: 11] | Branch (5870:39): [True: 1, False: 3] | Branch (5870:57): [True: 1, False: 0] ------------------ 5871| 3| (vPathEnd == v2 && vPathStart == v1)) && ------------------ | Branch (5871:26): [True: 3, False: 0] | Branch (5871:44): [True: 3, False: 0] ------------------ 5872| 4| nDeltaCharge == nDeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (5872:25): [True: 4, False: 0] ------------------ 5873| 4| { 5874| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 5875| 4| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 5876| 4| if (ret > 0) ------------------ | Branch (5876:29): [True: 4, False: 0] ------------------ 5877| 4| { 5878| 4| nNumRunBNS++; 5879| 4| one_success++; /* 23 */ 5880| 4| } 5881| 4| } 5882| 15| INCHI_HEAPCHK 5883| 15| } 5884| 63| cur_success += one_success; 5885| | 5886| 63| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 5887| 63| pe->forbidden &= forbidden_edge_mask_inv; 5888| | 5889| 63| if (!one_success) ------------------ | Branch (5889:21): [True: 59, False: 4] ------------------ 5890| 59| { 5891| 59| pe->flow += delta; 5892| 59| pv1->st_edge.flow += delta; 5893| 59| pv2->st_edge.flow += delta; 5894| 59| pBNS->tot_st_flow += 2 * delta; 5895| 59| } 5896| 63| } 5897| 62| } 5898| 729| exit_case_23: 5899| 3.64k| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 5624| 3.64k|#define CHG_SET_NUM 4 ------------------ | Branch (5899:21): [True: 2.91k, False: 729] ------------------ 5900| 2.91k| { 5901| 2.91k| AllocEdgeList(&ChangeableEdges[i], EDGE_LIST_FREE); ------------------ | | 243| 2.91k|#define EDGE_LIST_FREE (-2) ------------------ 5902| 2.91k| } 5903| | 5904| 729| CurrEdges.num_edges = 0; /* clear current edge list */ 5905| 729| if (cur_success) ------------------ | Branch (5905:13): [True: 4, False: 725] ------------------ 5906| 4| { 5907| 4| tot_succes += cur_success; 5908| | /* recalculate InChI from the structure */ 5909| 4| if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5909:17): [True: 0, False: 4] ------------------ 5910| 4| ppt_group_info, ppat_norm, ppat_prep))) 5911| 0| { 5912| 0| goto exit_function; 5913| 0| } 5914| 4| if ((ret = FillOutExtraFixedHDataRestr(pStruct)))/* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5914:17): [True: 0, False: 4] ------------------ 5915| 0| { 5916| 0| goto exit_function; 5917| 0| } 5918| 4| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5918:17): [True: 3, False: 1] | Branch (5918:45): [True: 0, False: 3] ------------------ 5919| 0| { 5920| 0| goto exit_function; /* no fixed-H found */ 5921| 0| } 5922| 4| if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5922:17): [True: 0, False: 4] ------------------ 5923| 0| { 5924| 0| goto exit_function; 5925| 0| } 5926| 4| if (!pc2i->bHasDifference) ------------------ | Branch (5926:17): [True: 0, False: 4] ------------------ 5927| 0| { 5928| 0| goto exit_function; /* nothing to do */ 5929| 0| } 5930| 4| } 5931| | 5932| 729|#undef CHG_SET_NOOH 5933| 729|#undef CHG_SET_WRONG_TAUT 5934| 729|#undef CHG_SET_TAUT 5935| 729|#undef CHG_LAST_SET 5936| 729|#undef CHG_SET_O_FIXED 5937| 729|#undef CHG_SET_NUM 5938| 729| } 5939| | 5940| 1.12k| if (pc2i->len_c2at && pc2i->nNumTgInChI == 1) ------------------ | Branch (5940:9): [True: 1.12k, False: 4] | Branch (5940:27): [True: 729, False: 394] ------------------ 5941| 729| { 5942| | /*------------------------------------------------------------------*/ 5943| | /* case 24: InChI norm. -N(-)-N(+)(IV) => -N=N(V) prevents tauto- */ 5944| | /* merism on -N(-)- in case of ADP */ 5945| | /* */ 5946| | /* Solution: convert N(V)=N- ...=X -> N(IV)(+)-N=...-X(-)*/ 5947| | /* N(IV)(+)-N(-)-...=X */ 5948| | /* */ 5949| | /* Orig InChI taut taut, 1 t-group only(ADP?) */ 5950| | /* Reconstructed struct non-taut possibly not taut */ 5951| | /* */ 5952| | /* Details: 1a. store next to N(V) (+)edge its flower edge */ 5953| | /* 1b. store next to N(-) edge NO_VERTEX */ 5954| | /* 2. Release (-) edges of other missing endpoints or */ 5955| | /* all endpoints if no other is missing */ 5956| | /* 3. Decrement flow on (+) edge */ 5957| | /* if flower edge is stored then expect DeltaCharge=2*/ 5958| | /* otherwise DeltaCharge = 0 */ 5959| | /*------------------------------------------------------------------*/ 5960| 729| int iat; 5961| 729| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5962| 729| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5962:41): [True: 300, False: 429] ------------------ 5963| 729| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5963:41): [True: 300, False: 0] ------------------ 5964| 729| inp_ATOM *atf = ( pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->at_fixed_bonds ) ? ------------------ | Branch (5964:27): [True: 300, False: 429] | Branch (5964:57): [True: 300, False: 0] ------------------ 5965| 729| pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL; 5966| 729| int iN, one_success; 5967| 729| EdgeIndex ef, e1; 5968| 729| BNS_EDGE *pef; 5969| 729|#define CHG_SET_MISSED_TAUT 0 5970| 729|#define CHG_SET_OTHER_TAUT_O 1 5971| 729|#define CHG_SET_OTHER_TAUT_N 2 5972| 729|#define CHG_LAST_SET 2 /* the last index in trying */ 5973| 729|#define CHG_SET_NN 3 5974| 729|#define CHG_SET_AVOID 4 5975| 729|#define CHG_SET_NUM 5 5976| 729| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 5977| 729| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 5978| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 5979| | /* 5980| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5981| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5982| | */ 5983| 729| CurrEdges.num_edges = 0; /* clear current edge list */ 5984| 729| cur_success = 0; 5985| 3.03k| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5985:21): [True: 2.30k, False: 729] ------------------ 5986| 2.30k| { 5987| 2.30k| iat = pc2i->c2at[i].atomNumber; 5988| 2.30k| if ( /* orig. InChI info: -N=N(V) */ 5989| 2.30k| pc2i->c2at[i].nValElectr == 5 /* N or P */ && ------------------ | Branch (5989:18): [True: 670, False: 1.63k] ------------------ 5990| 670| ( pc2i->c2at[i].endptInChI /* only N */ ) && ------------------ | Branch (5990:18): [True: 554, False: 116] ------------------ 5991| 554| ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e1].forbidden && ------------------ | Branch (5991:18): [True: 400, False: 154] | Branch (5991:65): [True: 400, False: 0] ------------------ 5992| 400| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (5992:18): [True: 374, False: 26] | Branch (5992:51): [True: 374, False: 0] ------------------ 5993| | /* reversed structure info: */ 5994| 374| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (5994:18): [True: 374, False: 0] ------------------ 5995| 374| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5995:18): [True: 374, False: 0] ------------------ 5996| 374| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (5996:18): [True: 186, False: 188] | Branch (5996:55): [True: 186, False: 0] ------------------ 5997| 186| at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 3 && ------------------ | Branch (5997:18): [True: 158, False: 28] | Branch (5997:43): [True: 155, False: 3] ------------------ 5998| | /* find whether -N= has =N(V) neighbor; Note: operator comma: (A,B) returns B */ 5999| 155| ( iN = at2[iat].neighbor[at2[iat].bond_type[0] != BOND_TYPE_DOUBLE], ------------------ | | 33| 155|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5999:18): [True: 104, False: 51] ------------------ 6000| 155| pVA[iN].cNumValenceElectrons == 5 ) && 6001| 104| at2[iN].chem_bonds_valence == 5 && ------------------ | Branch (6001:18): [True: 60, False: 44] ------------------ 6002| 60| at2[iN].charge == 0 && !at2[iN].num_H && !at2[iN].radical && ------------------ | Branch (6002:18): [True: 57, False: 3] | Branch (6002:41): [True: 53, False: 4] | Branch (6002:59): [True: 53, False: 0] ------------------ 6003| 53| 0 <= ( e = pVA[iN].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (6003:18): [True: 52, False: 1] | Branch (6003:62): [True: 52, False: 0] | Branch (6003:90): [True: 52, False: 0] ------------------ 6004| 52| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 5974| 52|#define CHG_SET_AVOID 4 ------------------ | Branch (6004:18): [True: 50, False: 2] ------------------ 6005| 50| { 6006| | 6007| 50| ef = GetChargeFlowerUpperEdge( pBNS, pVA, e ); /* == NO_VERTEX if N(V) has 4 bonds */ 6008| 50| if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 5973| 50|#define CHG_SET_NN 3 ------------------ if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 50|#define INC_ADD_EDGE 64 ------------------ | Branch (6008:21): [True: 0, False: 50] ------------------ 6009| 50| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], ef, INC_ADD_EDGE ) ) || ------------------ | | 5973| 50|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], ef, INC_ADD_EDGE ) ) || ------------------ | | 18| 50|#define INC_ADD_EDGE 64 ------------------ | Branch (6009:21): [True: 0, False: 50] ------------------ 6010| 50| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 5973| 50|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 18| 50|#define INC_ADD_EDGE 64 ------------------ | Branch (6010:22): [True: 0, False: 50] ------------------ 6011| 50| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) ) || ------------------ | | 5974| 50|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) ) || ------------------ | | 18| 50|#define INC_ADD_EDGE 64 ------------------ | Branch (6011:22): [True: 0, False: 50] ------------------ 6012| 50| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 5974| 50|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 50|#define INC_ADD_EDGE 64 ------------------ | Branch (6012:22): [True: 0, False: 50] ------------------ 6013| 50| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], ef, INC_ADD_EDGE ) )) ------------------ | | 5974| 50|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], ef, INC_ADD_EDGE ) )) ------------------ | | 18| 50|#define INC_ADD_EDGE 64 ------------------ | Branch (6013:22): [True: 0, False: 50] ------------------ 6014| 0| { 6015| 0| goto exit_case_24; 6016| 0| } 6017| | /* mark -N= so that (-) will not be moved to it */ 6018| 50| if (0 <= ( e = pVA[iat].nCMinusGroupEdge ) && !pBNS->edge[e].forbidden && ------------------ | Branch (6018:21): [True: 50, False: 0] | Branch (6018:63): [True: 49, False: 1] ------------------ 6019| 49| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ------------------ | | 5974| 49|#define CHG_SET_AVOID 4 ------------------ | Branch (6019:22): [True: 49, False: 0] ------------------ 6020| 49| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 5974| 49|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 18| 49|#define INC_ADD_EDGE 64 ------------------ | Branch (6020:22): [True: 0, False: 49] ------------------ 6021| 0| { 6022| 0| goto exit_case_24; 6023| 0| } 6024| 50| } 6025| 2.25k| else 6026| 2.25k| { 6027| 2.25k| if ( /* orig. InChI info: -N(-)N(IV)(+) */ 6028| 2.25k| atf && ------------------ | Branch (6028:22): [True: 1.02k, False: 1.23k] ------------------ 6029| 1.02k| pc2i->c2at[i].nValElectr == 5 /* N or P */ && ------------------ | Branch (6029:22): [True: 251, False: 770] ------------------ 6030| 251| pc2i->c2at[i].endptInChI /* only N */ && ------------------ | Branch (6030:22): [True: 209, False: 42] ------------------ 6031| 209| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (6031:22): [True: 142, False: 67] | Branch (6031:68): [True: 142, False: 0] ------------------ 6032| 142| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (6032:22): [True: 127, False: 15] | Branch (6032:55): [True: 127, False: 0] ------------------ 6033| | /* reversed structure info: */ 6034| 127| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (6034:22): [True: 127, False: 0] ------------------ 6035| 127| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (6035:22): [True: 127, False: 0] ------------------ 6036| 127| pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H && ------------------ | Branch (6036:22): [True: 84, False: 43] | Branch (6036:60): [True: 84, False: 0] ------------------ 6037| 84| at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (6037:22): [True: 73, False: 11] | Branch (6037:47): [True: 73, False: 0] ------------------ 6038| 73| atf[iat].valence == 2 && atf[iat].chem_bonds_valence == 3 && ------------------ | Branch (6038:22): [True: 73, False: 0] | Branch (6038:47): [True: 69, False: 4] ------------------ 6039| | /* find whether -N= has =N(V) neighbor; Note: operator comma: (A,B) returns B */ 6040| 69| ( iN = atf[iat].neighbor[atf[iat].bond_type[0] != BOND_TYPE_DOUBLE], ------------------ | | 33| 69|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (6040:22): [True: 68, False: 1] ------------------ 6041| 69| pVA[iN].cNumValenceElectrons == 5 ) && 6042| 68| at2[iN].charge == 1 && /* double bond neighbor */ ------------------ | Branch (6042:22): [True: 66, False: 2] ------------------ 6043| 66| at2[iN].chem_bonds_valence == 4 && ------------------ | Branch (6043:22): [True: 66, False: 0] ------------------ 6044| 66| atf[iN].charge == 0 && ------------------ | Branch (6044:22): [True: 66, False: 0] ------------------ 6045| 66| atf[iN].chem_bonds_valence == 5 && /* InChI normalization created N(V)=N- out of N(IV)(+)-N(-)- */ ------------------ | Branch (6045:22): [True: 64, False: 2] ------------------ 6046| 64| !at2[iN].num_H && !at2[iN].radical && ------------------ | Branch (6046:22): [True: 64, False: 0] | Branch (6046:40): [True: 64, False: 0] ------------------ 6047| 64| 0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (6047:22): [True: 64, False: 0] | Branch (6047:68): [True: 64, False: 0] | Branch (6047:96): [True: 64, False: 0] ------------------ 6048| 64| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 5974| 64|#define CHG_SET_AVOID 4 ------------------ | Branch (6048:22): [True: 64, False: 0] ------------------ 6049| 64| { 6050| | /* save (-) edge */ 6051| 64| if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 5973| 64|#define CHG_SET_NN 3 ------------------ if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 64|#define INC_ADD_EDGE 64 ------------------ | Branch (6051:25): [True: 0, False: 64] ------------------ 6052| 64| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], NO_VERTEX, INC_ADD_EDGE ) ) || ------------------ | | 5973| 64|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], NO_VERTEX, INC_ADD_EDGE ) ) || ------------------ | | 118| 64|#define NO_VERTEX -2 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], NO_VERTEX, INC_ADD_EDGE ) ) || ------------------ | | 18| 64|#define INC_ADD_EDGE 64 ------------------ | Branch (6052:25): [True: 0, False: 64] ------------------ 6053| 64| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 5973| 64|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 18| 64|#define INC_ADD_EDGE 64 ------------------ | Branch (6053:26): [True: 0, False: 64] ------------------ 6054| 64| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 5974| 64|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 18| 64|#define INC_ADD_EDGE 64 ------------------ | Branch (6054:26): [True: 0, False: 64] ------------------ 6055| 0| { 6056| 0| goto exit_case_24; 6057| 0| } 6058| 64| } 6059| 2.25k| } 6060| 2.30k| } 6061| 729| if (!ChangeableEdges[CHG_SET_NN].num_edges) ------------------ | | 5973| 729|#define CHG_SET_NN 3 ------------------ | Branch (6061:13): [True: 615, False: 114] ------------------ 6062| 615| { 6063| 615| goto exit_case_24; 6064| 615| } 6065| | /* Collect all relevant tautomeric atoms */ 6066| 1.00k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (6066:21): [True: 891, False: 114] ------------------ 6067| 891| { 6068| | /* i = canonical number - 1 */ 6069| 891| if (!pStruct->endpoint[i]) ------------------ | Branch (6069:17): [True: 515, False: 376] ------------------ 6070| 515| { 6071| 515| continue; 6072| 515| } 6073| 376| iat = nCanon2AtnoRevrs[i]; 6074| 376| if (at2[iat].charge || at2[iat].radical || at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (6074:17): [True: 115, False: 261] | Branch (6074:36): [True: 11, False: 250] | Branch (6074:56): [True: 23, False: 227] ------------------ 6075| 149| { 6076| 149| continue; /* cannot be an acceptor of (-) */ 6077| 149| } 6078| 227| if (0 > ( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow) ------------------ | Branch (6078:17): [True: 34, False: 193] | Branch (6078:62): [True: 0, False: 193] | Branch (6078:89): [True: 1, False: 192] ------------------ 6079| 35| { 6080| 35| continue; 6081| 35| } 6082| 192| if (0 <= FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 5974| 192|#define CHG_SET_AVOID 4 ------------------ | Branch (6082:17): [True: 49, False: 143] ------------------ 6083| 49| { 6084| 49| continue; /* has already been used */ 6085| 49| } 6086| | /* missing endpoint */ 6087| 143| if (!( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint )) ------------------ | Branch (6087:20): [True: 97, False: 46] | Branch (6087:41): [True: 35, False: 62] ------------------ 6088| 108| { 6089| 108| if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ( ------------------ | | 5974| 108|#define CHG_SET_AVOID 4 ------------------ | Branch (6089:21): [True: 108, False: 0] ------------------ 6090| 108| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 5969| 108|#define CHG_SET_MISSED_TAUT 0 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 108|#define INC_ADD_EDGE 64 ------------------ | Branch (6090:21): [True: 0, False: 108] ------------------ 6091| 108| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 5974| 108|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 18| 108|#define INC_ADD_EDGE 64 ------------------ | Branch (6091:21): [True: 0, False: 108] ------------------ 6092| 0| { 6093| 0| goto exit_case_24; 6094| 0| } 6095| 108| } 6096| 35| else 6097| 35| { 6098| | /* endpoint O */ 6099| 35| if (pVA[iat].cNumValenceElectrons == 6) ------------------ | Branch (6099:21): [True: 35, False: 0] ------------------ 6100| 35| { 6101| 35| if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ( ------------------ | | 5974| 35|#define CHG_SET_AVOID 4 ------------------ | Branch (6101:25): [True: 35, False: 0] ------------------ 6102| 35| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_O], e, INC_ADD_EDGE ) ) || ------------------ | | 5970| 35|#define CHG_SET_OTHER_TAUT_O 1 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_O], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 35|#define INC_ADD_EDGE 64 ------------------ | Branch (6102:25): [True: 0, False: 35] ------------------ 6103| 35| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 5974| 35|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 18| 35|#define INC_ADD_EDGE 64 ------------------ | Branch (6103:25): [True: 0, False: 35] ------------------ 6104| 0| { 6105| 0| goto exit_case_24; 6106| 0| } 6107| 35| } 6108| 0| else 6109| 0| { 6110| | /* endpoint N */ 6111| 0| if (pVA[iat].cNumValenceElectrons == 5) ------------------ | Branch (6111:25): [True: 0, False: 0] ------------------ 6112| 0| { 6113| 0| if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ( ------------------ | | 5974| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6113:29): [True: 0, False: 0] ------------------ 6114| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_N], e, INC_ADD_EDGE ) ) || ------------------ | | 5971| 0|#define CHG_SET_OTHER_TAUT_N 2 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_N], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6114:29): [True: 0, False: 0] ------------------ 6115| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 5974| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6115:29): [True: 0, False: 0] ------------------ 6116| 0| { 6117| 0| goto exit_case_24; 6118| 0| } 6119| 0| } 6120| 0| } 6121| 35| } 6122| 143| } 6123| | /* ------- finally, try to move charges from -N(-)-N(+) or to N(V) --------------*/ 6124| 228| for (i = 0; i < ChangeableEdges[CHG_SET_NN].num_edges; i += 3) ------------------ | | 5973| 228|#define CHG_SET_NN 3 ------------------ | Branch (6124:21): [True: 114, False: 114] ------------------ 6125| 114| { 6126| 114| int nDeltaChargeExpected; 6127| 114| one_success = 0; 6128| 114| delta = 1; 6129| 114| pe = pBNS->edge + ChangeableEdges[CHG_SET_NN].pnEdges[i]; ------------------ | | 5973| 114|#define CHG_SET_NN 3 ------------------ 6130| 114| pef = ( NO_VERTEX != ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] ) ? ------------------ | | 118| 114|#define NO_VERTEX -2 ------------------ pef = ( NO_VERTEX != ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] ) ? ------------------ | | 5973| 114|#define CHG_SET_NN 3 ------------------ | Branch (6130:19): [True: 36, False: 78] ------------------ 6131| 114| pBNS->edge + ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] : NULL; ------------------ | | 5973| 36|#define CHG_SET_NN 3 ------------------ 6132| 114| nDeltaChargeExpected = ChangeableEdges[CHG_SET_NN].pnEdges[i + 2]; ------------------ | | 5973| 114|#define CHG_SET_NN 3 ------------------ 6133| | 6134| 114| if (!pe->flow) ------------------ | Branch (6134:17): [True: 0, False: 114] ------------------ 6135| 0| continue; 6136| 114| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 6137| 114| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 6138| | 6139| 114| pe->flow -= delta; 6140| 114| pv1->st_edge.flow -= delta; 6141| 114| pv2->st_edge.flow -= delta; 6142| 114| pBNS->tot_st_flow -= 2 * delta; 6143| | 6144| 328| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 5972| 250|#define CHG_LAST_SET 2 /* the last index in trying */ ------------------ | Branch (6144:25): [True: 250, False: 78] | Branch (6144:41): [True: 214, False: 36] ------------------ 6145| 214| { 6146| 214| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (6146:21): [True: 109, False: 105] ------------------ 6147| 109| { 6148| 109| continue; 6149| 109| } 6150| 105| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6151| 105| RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); 6152| | /* allow change of N(V) flower edge */ 6153| 105| if (pef) ------------------ | Branch (6153:21): [True: 31, False: 74] ------------------ 6154| 31| { 6155| 31| pef->forbidden &= forbidden_edge_mask_inv; 6156| 31| } 6157| | 6158| 105| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6159| 105| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6160| | 6161| 105| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (6161:21): [True: 86, False: 19] | Branch (6161:36): [True: 14, False: 72] | Branch (6161:54): [True: 10, False: 4] ------------------ 6162| 76| (vPathEnd == v2 && vPathStart == v1) ) && ------------------ | Branch (6162:36): [True: 72, False: 4] | Branch (6162:54): [True: 71, False: 1] ------------------ 6163| 81| nDeltaCharge == nDeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6163:22): [True: 78, False: 3] ------------------ 6164| 78| { 6165| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 6166| 78| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6167| 78| if (ret > 0) ------------------ | Branch (6167:25): [True: 78, False: 0] ------------------ 6168| 78| { 6169| 78| nNumRunBNS++; 6170| 78| one_success++; /* 24 */ 6171| 78| } 6172| 78| } 6173| 105| INCHI_HEAPCHK 6174| 105| } 6175| 114| cur_success += one_success; 6176| | 6177| 114| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6178| | 6179| 114| if (!one_success) ------------------ | Branch (6179:17): [True: 36, False: 78] ------------------ 6180| 36| { 6181| 36| pe->flow += delta; 6182| 36| pv1->st_edge.flow += delta; 6183| 36| pv2->st_edge.flow += delta; 6184| 36| pBNS->tot_st_flow += 2 * delta; 6185| 36| } 6186| 114| } 6187| 729| exit_case_24: 6188| 4.37k| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 5975| 4.37k|#define CHG_SET_NUM 5 ------------------ | Branch (6188:21): [True: 3.64k, False: 729] ------------------ 6189| 3.64k| { 6190| 3.64k| AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); ------------------ | | 243| 3.64k|#define EDGE_LIST_FREE (-2) ------------------ 6191| 3.64k| } 6192| | 6193| 729| CurrEdges.num_edges = 0; /* clear current edge list */ 6194| 729| if (cur_success) ------------------ | Branch (6194:13): [True: 78, False: 651] ------------------ 6195| 78| { 6196| 78| tot_succes += cur_success; 6197| | /* recalculate InChI from the structure */ 6198| 78| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (6198:17): [True: 0, False: 78] ------------------ 6199| 78| ppt_group_info, ppat_norm, ppat_prep ) )) 6200| 0| { 6201| 0| goto exit_function; 6202| 0| } 6203| 78| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6203:17): [True: 0, False: 78] ------------------ 6204| 0| { 6205| 0| goto exit_function; 6206| 0| } 6207| 78| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (6207:17): [True: 48, False: 30] | Branch (6207:45): [True: 0, False: 48] ------------------ 6208| 0| { 6209| 0| goto exit_function; /* no fixed-H found */ 6210| 0| } 6211| 78| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6211:17): [True: 0, False: 78] ------------------ 6212| 0| { 6213| 0| goto exit_function; 6214| 0| } 6215| 78| if (!pc2i->bHasDifference) ------------------ | Branch (6215:17): [True: 0, False: 78] ------------------ 6216| 0| { 6217| 0| goto exit_function; /* nothing to do */ 6218| 0| } 6219| 78| } 6220| 729|#undef CHG_SET_NN 6221| 729|#undef CHG_SET_MISSED_TAUT 6222| 729|#undef CHG_SET_OTHER_TAUT_O 6223| 729|#undef CHG_SET_OTHER_TAUT_N 6224| 729|#undef CHG_LAST_SET 6225| 729|#undef CHG_SET_AVOID 6226| 729|#undef CHG_SET_NUM 6227| 729| } 6228| | 6229| | /* pStruct->nNumRemovedProtonsMobHInChI == pc2i->nNumRemHInChI */ 6230| | 6231| 1.12k| if (pc2i->len_c2at && pc2i->nNumTgInChI == 1 && ------------------ | Branch (6231:9): [True: 1.12k, False: 4] | Branch (6231:27): [True: 729, False: 394] ------------------ 6232| 729| pc2i->nNumRemHRevrs > pc2i->nNumRemHInChI && 0 > pc2i->nNumRemHInChI && ------------------ | Branch (6232:10): [True: 16, False: 713] | Branch (6232:55): [True: 0, False: 16] ------------------ 6233| 0| ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || ------------------ | Branch (6233:12): [True: 0, False: 0] ------------------ 6234| 0| pc2i->nNumTgRevrs > pc2i->nNumTgInChI )) ------------------ | Branch (6234:12): [True: 0, False: 0] ------------------ 6235| 0| { 6236| | /*------------------------------------------------------------------*/ 6237| | /* case 25: Restored InChI does not have 2 or more added protons */ 6238| | /* possibly taut. endpoints are missing */ 6239| | /* has -N(-O(-))-O(-) group(s) */ 6240| | /* Original InChI has only one t-group */ 6241| | /* */ 6242| | /* Solution: convert -N(-O(-))-O(-) -> -N(+)(=O)-O(-) */ 6243| | /* and direct 2(-) to the missing taut atoms*/ 6244| | /* at first attempt try to move (-) to N only */ 6245| | /* */ 6246| | /*------------------------------------------------------------------*/ 6247| 0| int iat; 6248| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 6249| 0| AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 6250| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (6250:41): [True: 0, False: 0] ------------------ 6251| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (6251:41): [True: 0, False: 0] ------------------ 6252| | /* 6253| | inp_ATOM *atf = (pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->at_fixed_bonds)? 6254| | pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL; 6255| | */ 6256| 0| int iN, neigh, one_success; 6257| 0| EdgeIndex e1, bFirst; 6258| 0| BNS_EDGE *pef; 6259| 0|#define CHG_SET_MISSED_TAUT_1 0 6260| 0|#define CHG_SET_MISSED_TAUT_ALL 1 6261| 0|#define CHG_SET_OTHER_TAUT_1 2 6262| 0|#define CHG_SET_OTHER_TAUT_ALL 3 6263| 0|#define CHG_LAST_SET 3 /* the last index in trying */ 6264| 0|#define CHG_SET_NO_IN_NO2M2 4 6265| 0|#define CHG_SET_AVOID 5 6266| 0|#define CHG_SET_NUM 6 6267| 0| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 6268| 0| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6269| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 6270| | /* 6271| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 6272| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 6273| | */ 6274| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 6275| 0| cur_success = 0; 6276| | /* find all -N(-O(-))-O(-) */ 6277| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (6277:21): [True: 0, False: 0] ------------------ 6278| 0| { 6279| 0| iat = nCanon2AtnoRevrs[i]; 6280| 0| if (pStruct->endpoint[i]) ------------------ | Branch (6280:17): [True: 0, False: 0] ------------------ 6281| 0| { 6282| 0| if (0 >( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || ------------------ | Branch (6282:21): [True: 0, False: 0] | Branch (6282:65): [True: 0, False: 0] ------------------ 6283| 0| 0 <= FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 6265| 0|#define CHG_SET_AVOID 5 ------------------ | Branch (6283:22): [True: 0, False: 0] ------------------ 6284| 0| { 6285| 0| continue; 6286| 0| } 6287| 0| bFirst = ( (pVA[iat].cNumValenceElectrons == 5 && pc2i->nNumTgInChI == 1) || ------------------ | Branch (6287:29): [True: 0, False: 0] | Branch (6287:67): [True: 0, False: 0] ------------------ 6288| 0| (pVA[iat].cNumValenceElectrons == 6 && pc2i->nNumTgInChI != 1) ); /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6288:29): [True: 0, False: 0] | Branch (6288:67): [True: 0, False: 0] ------------------ 6289| | /* many or no t-groups -> try O only first */ 6290| | /* single t-group -> try only N first */ 6291| 0| if (!( at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint )) ------------------ | Branch (6291:24): [True: 0, False: 0] | Branch (6291:45): [True: 0, False: 0] ------------------ 6292| 0| { 6293| | /* missed tautomeric endpoint */ 6294| 0| if (bFirst && ------------------ | Branch (6294:25): [True: 0, False: 0] ------------------ 6295| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 6259| 0|#define CHG_SET_MISSED_TAUT_1 0 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6295:25): [True: 0, False: 0] ------------------ 6296| 0| { 6297| 0| goto exit_case_25; 6298| 0| } 6299| 0| if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 6260| 0|#define CHG_SET_MISSED_TAUT_ALL 1 ------------------ if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6299:25): [True: 0, False: 0] ------------------ 6300| 0| { 6301| 0| goto exit_case_25; 6302| 0| } 6303| 0| } 6304| 0| if (bFirst && ------------------ | Branch (6304:21): [True: 0, False: 0] ------------------ 6305| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 6261| 0|#define CHG_SET_OTHER_TAUT_1 2 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6305:21): [True: 0, False: 0] ------------------ 6306| 0| { 6307| 0| goto exit_case_25; 6308| 0| } 6309| 0| if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 6262| 0|#define CHG_SET_OTHER_TAUT_ALL 3 ------------------ if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6309:21): [True: 0, False: 0] ------------------ 6310| 0| { 6311| 0| goto exit_case_25; 6312| 0| } 6313| 0| if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 6265| 0|#define CHG_SET_AVOID 5 ------------------ if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6313:21): [True: 0, False: 0] ------------------ 6314| 0| { 6315| 0| goto exit_case_25; 6316| 0| } 6317| 0| } 6318| 0| else 6319| 0| { 6320| 0| if (at2[iat].valence == 1 && at2[iat].charge == -1 && ------------------ | Branch (6320:21): [True: 0, False: 0] | Branch (6320:46): [True: 0, False: 0] ------------------ 6321| 0| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (6321:22): [True: 0, False: 0] ------------------ 6322| 0| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && /* -O(-) */ ------------------ | Branch (6322:22): [True: 0, False: 0] ------------------ 6323| 0| !pStruct->endpoint[nAtno2CanonRevrs[iN]] && ------------------ | Branch (6323:22): [True: 0, False: 0] ------------------ 6324| 0| at2[iN].valence == 3 && at2[iN].chem_bonds_valence == 3 && ------------------ | Branch (6324:22): [True: 0, False: 0] | Branch (6324:46): [True: 0, False: 0] ------------------ 6325| 0| !at2[iN].charge && !at2[iN].radical && ------------------ | Branch (6325:22): [True: 0, False: 0] | Branch (6325:41): [True: 0, False: 0] ------------------ 6326| 0| 0 <= ( e = pVA[iN].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (6326:22): [True: 0, False: 0] | Branch (6326:66): [True: 0, False: 0] ------------------ 6327| 0| pBNS->edge[e].flow && /* NPlus edge */ ------------------ | Branch (6327:22): [True: 0, False: 0] ------------------ 6328| 0| 0 <= ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e1].forbidden && ------------------ | Branch (6328:22): [True: 0, False: 0] | Branch (6328:69): [True: 0, False: 0] ------------------ 6329| 0| pBNS->edge[e1].flow && /* OMinus edge */ ------------------ | Branch (6329:22): [True: 0, False: 0] ------------------ 6330| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ------------------ | | 6265| 0|#define CHG_SET_AVOID 5 ------------------ | Branch (6330:22): [True: 0, False: 0] ------------------ 6331| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1 )) ------------------ | | 6265| 0|#define CHG_SET_AVOID 5 ------------------ | Branch (6331:22): [True: 0, False: 0] ------------------ 6332| 0| { 6333| | /* found >N-O(-) */ 6334| 0| int nNumO = 0, nNumOthers = 0; 6335| 0| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (6335:33): [True: 0, False: 0] ------------------ 6336| 0| { 6337| 0| neigh = at2[iN].neighbor[k]; 6338| 0| if (neigh == iat) ------------------ | Branch (6338:29): [True: 0, False: 0] ------------------ 6339| 0| { 6340| 0| continue; 6341| 0| } 6342| 0| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (6342:29): [True: 0, False: 0] ------------------ 6343| 0| !pStruct->endpoint[neigh] && ------------------ | Branch (6343:30): [True: 0, False: 0] ------------------ 6344| 0| at2[neigh].valence == 1 && at2[neigh].num_H == 0 && ------------------ | Branch (6344:30): [True: 0, False: 0] | Branch (6344:57): [True: 0, False: 0] ------------------ 6345| 0| at2[neigh].radical == 0 && at2[neigh].charge == -1 && ------------------ | Branch (6345:30): [True: 0, False: 0] | Branch (6345:57): [True: 0, False: 0] ------------------ 6346| 0| at2[neigh].chem_bonds_valence == 1) ------------------ | Branch (6346:30): [True: 0, False: 0] ------------------ 6347| 0| { 6348| 0| nNumO++; 6349| 0| } 6350| 0| else 6351| 0| { 6352| 0| if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE && ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (6352:33): [True: 0, False: 0] ------------------ 6353| 0| at2[neigh].valence > 1 && ------------------ | Branch (6353:34): [True: 0, False: 0] ------------------ 6354| 0| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (6354:34): [True: 0, False: 0] ------------------ 6355| 0| { 6356| 0| nNumOthers++; 6357| 0| } 6358| 0| } 6359| 0| } 6360| 0| if (nNumO != 1 && nNumOthers != 1) ------------------ | Branch (6360:25): [True: 0, False: 0] | Branch (6360:39): [True: 0, False: 0] ------------------ 6361| 0| { 6362| 0| continue; 6363| 0| } 6364| | /* save charge edges: NPlus first, OMinus second */ 6365| 0| if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e, INC_ADD_EDGE ) ) || ------------------ | | 6264| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6365:25): [True: 0, False: 0] ------------------ 6366| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e1, INC_ADD_EDGE ) ) || ------------------ | | 6264| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e1, INC_ADD_EDGE ) ) || ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6366:25): [True: 0, False: 0] ------------------ 6367| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 6265| 0|#define CHG_SET_AVOID 5 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6367:26): [True: 0, False: 0] ------------------ 6368| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) )) ------------------ | | 6265| 0|#define CHG_SET_AVOID 5 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) )) ------------------ | | 18| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6368:26): [True: 0, False: 0] ------------------ 6369| 0| { 6370| 0| goto exit_case_25; 6371| 0| } 6372| 0| } 6373| 0| } 6374| 0| } 6375| 0| if (!ChangeableEdges[CHG_SET_NO_IN_NO2M2].num_edges || ------------------ | | 6264| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ | Branch (6375:13): [True: 0, False: 0] ------------------ 6376| 0| !ChangeableEdges[CHG_SET_OTHER_TAUT_ALL].num_edges) ------------------ | | 6262| 0|#define CHG_SET_OTHER_TAUT_ALL 3 ------------------ | Branch (6376:14): [True: 0, False: 0] ------------------ 6377| 0| { 6378| 0| goto exit_case_25; 6379| 0| } 6380| | /* ------- finally, try to move charges from -NO2(2-) or to tautomeric endpoints ----*/ 6381| 0| for (i = 0; i < ChangeableEdges[CHG_SET_NO_IN_NO2M2].num_edges; i += 2) ------------------ | | 6264| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ | Branch (6381:21): [True: 0, False: 0] ------------------ 6382| 0| { 6383| 0| int nDeltaChargeExpected = 3; 6384| | /* change flow on O(-) to make it neutral; 3 new charges will be created: 6385| | N(+), and two (-) on InChI endpoints 6386| | alternatively, if we change flow on N to make N(+) then O(-) will 6387| | be nutralized (-1 charge) and two (-) charges on taut. endpoints will be 6388| | created (+2); the total change in this case would be (-1)+(+2) = +1 6389| | */ 6390| 0| one_success = 0; 6391| 0| delta = 1; 6392| 0| pe = pBNS->edge + ChangeableEdges[CHG_SET_NO_IN_NO2M2].pnEdges[i + 1]; /* O(-) edge */ ------------------ | | 6264| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ 6393| 0| pef = pBNS->edge + ChangeableEdges[CHG_SET_NO_IN_NO2M2].pnEdges[i]; /* >N- (+) edge */ ------------------ | | 6264| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ 6394| | 6395| 0| if (!pe->flow) ------------------ | Branch (6395:17): [True: 0, False: 0] ------------------ 6396| 0| continue; 6397| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 6398| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 6399| | 6400| 0| pe->flow -= delta; 6401| 0| pv1->st_edge.flow -= delta; 6402| 0| pv2->st_edge.flow -= delta; 6403| 0| pBNS->tot_st_flow -= 2 * delta; 6404| | 6405| 0| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 6263| 0|#define CHG_LAST_SET 3 /* the last index in trying */ ------------------ | Branch (6405:25): [True: 0, False: 0] | Branch (6405:41): [True: 0, False: 0] ------------------ 6406| 0| { 6407| 0| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (6407:21): [True: 0, False: 0] ------------------ 6408| 0| { 6409| 0| continue; 6410| 0| } 6411| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6412| 0| RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); 6413| | /* allow change of N(V) flower edge */ 6414| 0| pef->forbidden &= forbidden_edge_mask_inv; 6415| | 6416| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6417| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6418| | 6419| 0| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (6419:21): [True: 0, False: 0] | Branch (6419:36): [True: 0, False: 0] | Branch (6419:54): [True: 0, False: 0] ------------------ 6420| 0| (vPathEnd == v2 && vPathStart == v1) ) && ------------------ | Branch (6420:36): [True: 0, False: 0] | Branch (6420:54): [True: 0, False: 0] ------------------ 6421| 0| nDeltaCharge == nDeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (6421:22): [True: 0, False: 0] ------------------ 6422| 0| { 6423| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 6424| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6425| 0| if (ret > 0) ------------------ | Branch (6425:25): [True: 0, False: 0] ------------------ 6426| 0| { 6427| 0| nNumRunBNS++; 6428| 0| one_success++; /* 24 */ 6429| 0| } 6430| 0| } 6431| 0| INCHI_HEAPCHK 6432| 0| } 6433| 0| cur_success += one_success; 6434| | 6435| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6436| | 6437| 0| if (!one_success) ------------------ | Branch (6437:17): [True: 0, False: 0] ------------------ 6438| 0| { 6439| 0| pe->flow += delta; 6440| 0| pv1->st_edge.flow += delta; 6441| 0| pv2->st_edge.flow += delta; 6442| 0| pBNS->tot_st_flow += 2 * delta; 6443| 0| } 6444| 0| } 6445| 0| exit_case_25: 6446| 0| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 6266| 0|#define CHG_SET_NUM 6 ------------------ | Branch (6446:21): [True: 0, False: 0] ------------------ 6447| 0| { 6448| 0| AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); ------------------ | | 243| 0|#define EDGE_LIST_FREE (-2) ------------------ 6449| 0| } 6450| | 6451| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 6452| 0| if (cur_success) ------------------ | Branch (6452:13): [True: 0, False: 0] ------------------ 6453| 0| { 6454| 0| tot_succes += cur_success; 6455| | /* recalculate InChI from the structure */ 6456| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (6456:17): [True: 0, False: 0] ------------------ 6457| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 6458| 0| { 6459| 0| goto exit_function; 6460| 0| } 6461| 0| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6461:17): [True: 0, False: 0] ------------------ 6462| 0| { 6463| 0| goto exit_function; 6464| 0| } 6465| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (6465:17): [True: 0, False: 0] | Branch (6465:45): [True: 0, False: 0] ------------------ 6466| 0| { 6467| 0| goto exit_function; /* no fixed-H found */ 6468| 0| } 6469| 0| if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6469:17): [True: 0, False: 0] ------------------ 6470| 0| { 6471| 0| goto exit_function; 6472| 0| } 6473| 0| if (!pc2i->bHasDifference) ------------------ | Branch (6473:17): [True: 0, False: 0] ------------------ 6474| 0| { 6475| 0| goto exit_function; /* nothing to do */ 6476| 0| } 6477| 0| } 6478| 0|#undef CHG_SET_NN 6479| 0|#undef CHG_SET_MISSED_TAUT 6480| 0|#undef CHG_SET_OTHER_TAUT_O 6481| 0|#undef CHG_SET_OTHER_TAUT_N 6482| 0|#undef CHG_LAST_SET 6483| 0|#undef CHG_SET_AVOID 6484| 0|#undef CHG_SET_NUM 6485| 0| } 6486| | 6487| | 6488| 1.21k|exit_function: 6489| | 6490| 1.21k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.21k|#define EDGE_LIST_FREE (-2) ------------------ 6491| 1.21k| AllocEdgeList( &CurrEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.21k|#define EDGE_LIST_FREE (-2) ------------------ 6492| 1.21k| AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.21k|#define EDGE_LIST_FREE (-2) ------------------ 6493| 1.21k| AllocEdgeList( &SFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.21k|#define EDGE_LIST_FREE (-2) ------------------ 6494| 1.21k| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.21k|#define EDGE_LIST_FREE (-2) ------------------ 6495| 1.21k| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.21k|#define EDGE_LIST_FREE (-2) ------------------ 6496| 1.21k| AllocEdgeList( &AllBondEdges, EDGE_LIST_FREE ); ------------------ | | 243| 1.21k|#define EDGE_LIST_FREE (-2) ------------------ 6497| | 6498| 1.21k| return ret < 0 ? ret : ( tot_succes && pc2i->bHasDifference ); ------------------ | Branch (6498:12): [True: 8, False: 1.20k] | Branch (6498:30): [True: 523, False: 682] | Branch (6498:44): [True: 518, False: 5] ------------------ 6499| 1.12k|} ForbidCarbonChargeEdges: 26| 117k|{ 27| 117k|#define MAX_NUM_CARBON_CHARGE_EDGES 2 28| 117k| int nType, i, k, ret; 29| 117k| BNS_EDGE* pEdge; 30| 117k| if ((ret = AllocEdgeList(pCarbonChargeEdges, MAX_NUM_CARBON_CHARGE_EDGES))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 27| 117k|#define MAX_NUM_CARBON_CHARGE_EDGES 2 ------------------ | Branch (30:9): [True: 0, False: 117k] ------------------ 31| 0| { 32| 0| goto exit_function; 33| 0| } 34| 117k| pCarbonChargeEdges->num_edges = 0; 35| 353k| for (i = 0; i < MAX_NUM_CARBON_CHARGE_EDGES; i++) ------------------ | | 27| 353k|#define MAX_NUM_CARBON_CHARGE_EDGES 2 ------------------ | Branch (35:17): [True: 235k, False: 117k] ------------------ 36| 235k| { 37| 235k| switch (i) 38| 235k| { 39| 117k| case 0: ------------------ | Branch (39:9): [True: 117k, False: 117k] ------------------ 40| 117k| nType = TCG_Plus_C0; 41| 117k| break; 42| 117k| case 1: ------------------ | Branch (42:9): [True: 117k, False: 117k] ------------------ 43| 117k| nType = TCG_Minus_C0; 44| 117k| break; 45| 0| default: ------------------ | Branch (45:9): [True: 0, False: 235k] ------------------ 46| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 47| 0| goto exit_function; 48| 235k| } 49| 235k| if ((k = pTCGroups->nGroup[nType]) >= 0) ------------------ | Branch (49:13): [True: 77.0k, False: 158k] ------------------ 50| 77.0k| { 51| 77.0k| k = pTCGroups->pTCG[k].nForwardEdge; 52| 77.0k| if (k > 0) ------------------ | Branch (52:17): [True: 77.0k, False: 0] ------------------ 53| 77.0k| { 54| 77.0k| pEdge = pBNS->edge + k; 55| 77.0k| if (!(pEdge->forbidden & forbidden_edge_mask)) ------------------ | Branch (55:21): [True: 77.0k, False: 0] ------------------ 56| 77.0k| { 57| 77.0k| pEdge->forbidden |= forbidden_edge_mask; 58| 77.0k| if ((ret = AddToEdgeList(pCarbonChargeEdges, k, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (58:25): [True: 0, False: 77.0k] ------------------ 59| 0| { 60| 0| goto exit_function; 61| 0| } 62| 77.0k| } 63| 77.0k| } 64| 0| else 65| 0| { 66| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 67| 0| goto exit_function; 68| 0| } 69| 77.0k| } 70| 235k| } 71| 117k| ret = pCarbonChargeEdges->num_edges; 72| | 73| 117k|exit_function: 74| | 75| 117k| return ret; 76| 117k|#undef MAX_NUM_CARBON_CHARGE_EDGES 77| 117k|} ForbidNintrogenPlus2BondsInSmallRings: 89| 175k|{ 90| 175k| int i, j, ret; 91| 175k| BNS_EDGE* e; 92| | 93| | /* djb-rwth: removing redundant code */ 94| | /* --- forbid edges that allow to make =N(+)= or #N(+)- in small ring */ 95| 1.84M| for (i = 0; i < num_at; i++) ------------------ | Branch (95:17): [True: 1.66M, False: 175k] ------------------ 96| 1.66M| { 97| 1.66M| if (at[i].valence == 2 && ------------------ | Branch (97:13): [True: 141k, False: 1.52M] ------------------ 98| 141k| !at[i].num_H && !at[i].endpoint && ------------------ | Branch (98:13): [True: 140k, False: 1.58k] | Branch (98:29): [True: 139k, False: 790] ------------------ 99| 139k| pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (99:13): [True: 54.2k, False: 85.2k] ------------------ 100| 54.2k| pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (100:13): [True: 44.8k, False: 9.42k] ------------------ 101| 44.8k| !pVA[i].cMaxFlowToMetal && pVA[i].nCPlusGroupEdge > 0 && ------------------ | Branch (101:13): [True: 44.8k, False: 0] | Branch (101:40): [True: 44.8k, False: 0] ------------------ 102| 1.66M| pVA[i].cnListIndex > 0 && cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MNP && ------------------ | | 427| 44.8k|#define cn_bits_MNP MAKE_CN_BITS(cn_bits_M, cn_bits_N, cn_bits_P, 0) | | ------------------ | | | | 421| 1.71M|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 44.8k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 44.8k|#define cn_bits_shift 3 | | | | ------------------ | | | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 419| 44.8k|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (102:13): [True: 44.8k, False: 0] | Branch (102:39): [True: 43.9k, False: 896] ------------------ 103| 43.9k| pVA[i].cMinRingSize && pVA[i].cMinRingSize <= min_ring_size) ------------------ | Branch (103:13): [True: 23.8k, False: 20.0k] | Branch (103:36): [True: 22.6k, False: 1.14k] ------------------ 104| 22.6k| { 105| | 106| 22.6k| e = pBNS->edge + (j = pVA[i].nCPlusGroupEdge - 1); 107| 22.6k| if (!(e->forbidden & forbidden_edge_mask)) ------------------ | Branch (107:17): [True: 22.6k, False: 0] ------------------ 108| 22.6k| { 109| 22.6k| e->forbidden |= forbidden_edge_mask; 110| 22.6k| if ((ret = AddToEdgeList(pNplus2BondsEdges, j, 128))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (110:21): [True: 0, False: 22.6k] ------------------ 111| 0| { 112| 0| goto exit_function; 113| 0| } 114| 22.6k| } 115| 22.6k| } 116| 1.66M| } 117| 175k| ret = 0; 118| | 119| 175k|exit_function: 120| | 121| 175k| return ret; 122| 175k|} FixLessHydrogenInFormula: 152| 112|{ 153| 112| int iBPlus = NO_VERTEX, iNV = NO_VERTEX, iNH = NO_VERTEX, neigh; ------------------ | | 118| 112|#define NO_VERTEX -2 ------------------ int iBPlus = NO_VERTEX, iNV = NO_VERTEX, iNH = NO_VERTEX, neigh; ------------------ | | 118| 112|#define NO_VERTEX -2 ------------------ int iBPlus = NO_VERTEX, iNV = NO_VERTEX, iNH = NO_VERTEX, neigh; ------------------ | | 118| 112|#define NO_VERTEX -2 ------------------ 154| 112| EDGE_LIST NewlyFixedEdges; 155| 112| int ret, i, j; 156| 112| int num_at = pStruct->num_atoms; 157| 112| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 158| | /* for RunBnsTestOnce */ 159| 112| Vertex vPathStart, vPathEnd; 160| 112| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 161| | 162| 112| AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 112|#define EDGE_LIST_CLEAR (-1) ------------------ 163| 112| if ((ret = AllocEdgeList(&NewlyFixedEdges, 2 * num_at))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (163:9): [True: 0, False: 112] ------------------ 164| 0| { 165| 0| goto exit_function; 166| 0| } 167| 767| for (i = 0; i < num_at; i++) ------------------ | Branch (167:17): [True: 655, False: 112] ------------------ 168| 655| { 169| 655| if ((j = pVA[i].nCMinusGroupEdge - 1) >= 0) ------------------ | Branch (169:13): [True: 302, False: 353] ------------------ 170| 302| { 171| 302| if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (171:17): [True: 0, False: 302] ------------------ 172| 0| { 173| 0| goto exit_function; 174| 0| } 175| 302| pBNS->edge[j].forbidden |= forbidden_edge_mask; 176| 302| } 177| 655| if ((j = pVA[i].nCPlusGroupEdge - 1) >= 0) ------------------ | Branch (177:13): [True: 541, False: 114] ------------------ 178| 541| { 179| 541| if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (179:17): [True: 0, False: 541] ------------------ 180| 0| { 181| 0| goto exit_function; 182| 0| } 183| 541| pBNS->edge[j].forbidden |= forbidden_edge_mask; 184| 541| } 185| 655| } 186| | /* extra H has been removed; check non-tautomeric atoms */ 187| 527| for (i = 0; i < num_at; i++) ------------------ | Branch (187:17): [True: 462, False: 65] ------------------ 188| 462| { 189| 462| if (!at2[i].endpoint && !pVA[i].cMetal && ------------------ | Branch (189:13): [True: 456, False: 6] | Branch (189:33): [True: 421, False: 35] ------------------ 190| 421| pVA[i].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (190:13): [True: 178, False: 243] | Branch (190:49): [True: 154, False: 24] ------------------ 191| 154| at2[i].num_H == atf[i].num_H + 1) ------------------ | Branch (191:13): [True: 47, False: 107] ------------------ 192| 47| { 193| | /* H was removed from N */ 194| 47| iNH = i; 195| 47| break; 196| 47| } 197| 462| } 198| 112| if (0 <= iNH && iNH < num_at) ------------------ | Branch (198:9): [True: 47, False: 65] | Branch (198:21): [True: 47, False: 0] ------------------ 199| 47| { 200| | /* check neighbors for | | 201| | (a) -B(+)- or (b) =N- 202| | | | 203| | */ 204| 141| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (204:21): [True: 94, False: 47] ------------------ 205| 94| { 206| 94| neigh = at2[iNH].neighbor[j]; 207| 94| if (at2[neigh].valence == 4) ------------------ | Branch (207:17): [True: 1, False: 93] ------------------ 208| 1| { 209| 1| if (at2[neigh].charge == -1 && at2[neigh].chem_bonds_valence == 4 && ------------------ | Branch (209:21): [True: 0, False: 1] | Branch (209:48): [True: 0, False: 0] ------------------ 210| 0| !at2[neigh].radical && !at[neigh].num_H) ------------------ | Branch (210:21): [True: 0, False: 0] | Branch (210:44): [True: 0, False: 0] ------------------ 211| 0| { 212| 0| iBPlus = neigh; 213| 0| } 214| 1| } 215| 94| } 216| 47| } 217| 112| if (0 <= iNH && iNH < num_at) ------------------ | Branch (217:9): [True: 47, False: 65] | Branch (217:21): [True: 47, False: 0] ------------------ 218| 47| { 219| 47| int bond_type_at2; 220| 47| int bond_type_atf; 221| | /* djb-rwth: removing redundant variables */ 222| 47| int delta = -1, nxt = iNH, prv = NO_VERTEX, nxt_is_NPlus; ------------------ | | 118| 47|#define NO_VERTEX -2 ------------------ 223| | /* the changed bond to the dehydrogenated atom H should have greater order */ 224| | /* delta = (new bond order in atf[]) - (restored bond order in at2[]) */ 225| 47| nxt_is_NPlus = 0; 226| 47| do 227| 83| { 228| 83| i = nxt; 229| 83| nxt = NO_VERTEX; ------------------ | | 118| 83|#define NO_VERTEX -2 ------------------ 230| 83| delta = -delta; 231| 173| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (231:25): [True: 142, False: 31] ------------------ 232| 142| { 233| 142| bond_type_at2 = at2[i].bond_type[j] & BOND_TYPE_MASK; /* restored bond */ ------------------ | | 189| 142|#define BOND_TYPE_MASK 0x0f ------------------ 234| 142| bond_type_atf = atf[i].bond_type[j] & BOND_TYPE_MASK; /* normalized bond */ ------------------ | | 189| 142|#define BOND_TYPE_MASK 0x0f ------------------ 235| 142| nxt_is_NPlus = 0; 236| 142| if ((bond_type_atf - bond_type_at2 == delta || bond_type_atf == BOND_ALT12NS) && ------------------ | | 186| 100|#define BOND_ALT12NS 9 ------------------ | Branch (236:22): [True: 42, False: 100] | Branch (236:64): [True: 13, False: 87] ------------------ 237| 55| BOND_TYPE_SINGLE <= bond_type_at2 + delta && bond_type_at2 + delta <= BOND_TYPE_TRIPLE && ------------------ | | 32| 55|#define BOND_TYPE_SINGLE 1 ------------------ BOND_TYPE_SINGLE <= bond_type_at2 + delta && bond_type_at2 + delta <= BOND_TYPE_TRIPLE && ------------------ | | 34| 194|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (237:21): [True: 52, False: 3] | Branch (237:66): [True: 52, False: 0] ------------------ 238| 52| !at2[(int)at2[i].neighbor[j]].cFlags) ------------------ | Branch (238:21): [True: 52, False: 0] ------------------ 239| 52| { 240| 52| prv = i; 241| 52| nxt = at2[i].neighbor[j]; 242| 52| nxt_is_NPlus = at2[nxt].charge == 1 && atf[nxt].charge == 0 && ------------------ | Branch (242:36): [True: 26, False: 26] | Branch (242:60): [True: 16, False: 10] ------------------ 243| 16| pVA[nxt].cNumValenceElectrons == 5 && pVA[nxt].cPeriodicRowNumber == 1; ------------------ | Branch (243:25): [True: 16, False: 0] | Branch (243:63): [True: 16, False: 0] ------------------ 244| 52| at2[i].cFlags |= 1; /* avoid cycling */ 245| | /* djb-rwth: removing redundant code */ 246| 52| if (delta == -1 && at2[prv].valence == 4 && at2[prv].chem_bonds_valence == 5 && ------------------ | Branch (246:25): [True: 25, False: 27] | Branch (246:40): [True: 0, False: 25] | Branch (246:65): [True: 0, False: 0] ------------------ 247| 0| !at2[prv].charge && !at2[prv].radical && pVA[prv].cNumValenceElectrons == 5 && ------------------ | Branch (247:25): [True: 0, False: 0] | Branch (247:45): [True: 0, False: 0] | Branch (247:66): [True: 0, False: 0] ------------------ 248| 0| pVA[prv].nCPlusGroupEdge > 0) ------------------ | Branch (248:25): [True: 0, False: 0] ------------------ 249| 0| { 250| 0| iNV = prv; 251| 0| } 252| 52| if (at2[nxt].charge != atf[nxt].charge) ------------------ | Branch (252:25): [True: 16, False: 36] ------------------ 253| 16| { 254| 16| if ((at2[nxt].charge == 1 || atf[nxt].charge == 1) && ------------------ | Branch (254:30): [True: 16, False: 0] | Branch (254:54): [True: 0, False: 0] ------------------ 255| 16| pVA[nxt].nCPlusGroupEdge > 0) ------------------ | Branch (255:29): [True: 16, False: 0] ------------------ 256| 16| { 257| 16| pBNS->edge[pVA[nxt].nCPlusGroupEdge - 1].forbidden &= inv_forbidden_edge_mask; 258| 16| } 259| 16| if ((at2[nxt].charge == -1 || atf[nxt].charge == -1) && ------------------ | Branch (259:30): [True: 0, False: 16] | Branch (259:55): [True: 0, False: 16] ------------------ 260| 0| pVA[nxt].nCMinusGroupEdge > 0) ------------------ | Branch (260:29): [True: 0, False: 0] ------------------ 261| 0| { 262| 0| pBNS->edge[pVA[nxt].nCMinusGroupEdge - 1].forbidden &= inv_forbidden_edge_mask; 263| 0| } 264| 16| } 265| 52| break; /* found */ 266| 52| } 267| 142| } 268| 83| } while (nxt >= 0 && !(nxt_is_NPlus && delta == -1)); ------------------ | Branch (268:18): [True: 52, False: 31] | Branch (268:32): [True: 16, False: 36] | Branch (268:48): [True: 16, False: 0] ------------------ 269| 384| for (i = 0; i < num_at; i++) ------------------ | Branch (269:21): [True: 337, False: 47] ------------------ 270| 337| { 271| 337| at2[i].cFlags = 0; 272| 337| } 273| 47| if (nxt >= 0 && nxt_is_NPlus && delta == -1) ------------------ | Branch (273:13): [True: 16, False: 31] | Branch (273:25): [True: 16, False: 0] | Branch (273:41): [True: 16, False: 0] ------------------ 274| 16| { 275| | /* a simple alt path from NH-= to =N(+) has been found */ 276| 16| if (iBPlus || iNV) ------------------ | Branch (276:17): [True: 16, False: 0] | Branch (276:27): [True: 0, False: 0] ------------------ 277| 16| { 278| | /* move (+) charge from N(+) to iNV or, if iBPlus, then to iNH */ 279| 16| if ((iNV >= 0 && (j = pVA[iNV].nCPlusGroupEdge - 1) > 0 && pBNS->edge[j].flow > 0) || ------------------ | Branch (279:22): [True: 0, False: 16] | Branch (279:34): [True: 0, False: 0] | Branch (279:76): [True: 0, False: 0] ------------------ 280| 16| (iNH >= 0 && (j = pVA[iNH].nCPlusGroupEdge - 1) > 0 && pBNS->edge[j].flow > 0)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (280:22): [True: 16, False: 0] | Branch (280:34): [True: 7, False: 9] | Branch (280:76): [True: 7, False: 0] ------------------ 281| 7| { 282| 7| int ieFlower; 283| 7| BNS_EDGE* pe = pBNS->edge + j, * peFlower = NULL; 284| 7| Vertex v1 = pe->neighbor1; 285| 7| Vertex v2 = v1 ^ pe->neighbor12; 286| 7| BNS_VERTEX* pv1 = pBNS->vert + v1; 287| 7| BNS_VERTEX* pv2 = pBNS->vert + v2; 288| | 289| 7| delta = 1; 290| | /* prevent conversion of >N(+)= into N(V) neutral */ 291| 7| ieFlower = GetChargeFlowerUpperEdge(pBNS, pVA, pVA[nxt].nCPlusGroupEdge - 1); 292| 7| if (ieFlower >= 0) ------------------ | Branch (292:25): [True: 1, False: 6] ------------------ 293| 1| { 294| 1| peFlower = pBNS->edge + ieFlower; 295| 1| if (peFlower->flow == delta) ------------------ | Branch (295:29): [True: 1, False: 0] ------------------ 296| 1| { 297| 1| peFlower->forbidden |= forbidden_edge_mask; 298| 1| if ((ret = AddToEdgeList(&NewlyFixedEdges, ieFlower, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (298:33): [True: 0, False: 1] ------------------ 299| 0| { 300| 0| goto exit_function; 301| 0| } 302| 1| } 303| 1| } 304| 7| pe->forbidden |= forbidden_edge_mask; 305| 7| pe->flow -= delta; 306| 7| pv1->st_edge.flow -= delta; 307| 7| pv2->st_edge.flow -= delta; 308| 7| pBNS->tot_st_flow -= 2 * delta; 309| 7| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 310| 7| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 311| 7| if (ret < 0) ------------------ | Branch (311:25): [True: 0, False: 7] ------------------ 312| 0| { 313| 0| goto exit_function; 314| 0| } 315| 7| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (315:25): [True: 7, False: 0] | Branch (315:39): [True: 0, False: 7] | Branch (315:57): [True: 0, False: 0] ------------------ 316| 7| (vPathEnd == v2 && vPathStart == v1)) && ------------------ | Branch (316:26): [True: 6, False: 1] | Branch (316:44): [True: 6, False: 0] ------------------ 317| 6| nDeltaCharge <= 0 /* charge moving to this atom disappers*/) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (317:25): [True: 6, False: 0] ------------------ 318| 6| { 319| 6| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 320| 6| (*pnNumRunBNS)++; 321| 6| if (ret < 0) ------------------ | Branch (321:29): [True: 0, False: 6] ------------------ 322| 0| { 323| 0| goto exit_function; 324| 0| } 325| 6| else 326| 6| if (ret == 1) ------------------ | Branch (326:33): [True: 6, False: 0] ------------------ 327| 6| { 328| 6| *pnTotalDelta += ret; 329| 6| } 330| 0| else 331| 0| { 332| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 333| 0| goto exit_function; 334| 0| } 335| 6| } 336| 1| else 337| 1| { 338| 1| ret = 0; 339| 1| pe->flow += delta; 340| 1| pv1->st_edge.flow += delta; 341| 1| pv2->st_edge.flow += delta; 342| 1| pBNS->tot_st_flow += 2 * delta; 343| 1| } 344| 7| } 345| 16| } 346| 16| } 347| 47| } 348| | 349| 112|exit_function: 350| | /* remove bond fixation */ 351| 112| RemoveForbiddenEdgeMask(pBNS, &NewlyFixedEdges, forbidden_edge_mask); 352| 112| AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_FREE); ------------------ | | 243| 112|#define EDGE_LIST_FREE (-2) ------------------ 353| | 354| 112| return ret; 355| 112|} FixMoreHydrogenInFormula: 374| 920|{ 375| 920| int iNH = NO_VERTEX, neigh, neigh2; ------------------ | | 118| 920|#define NO_VERTEX -2 ------------------ 376| 920| EDGE_LIST NewlyFixedEdges; 377| 920| int ret, i, j, k, k2 = 0, delta; 378| 920| int num_at = pStruct->num_atoms; 379| 920| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 380| 920| Vertex v1, v2; 381| | /* for RunBnsTestOnce */ 382| 920| Vertex vPathStart, vPathEnd; 383| 920| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 384| 920| BNS_EDGE* pe, * pe2; 385| | 386| 920| AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 920|#define EDGE_LIST_CLEAR (-1) ------------------ 387| 920| if ((ret = AllocEdgeList(&NewlyFixedEdges, 2 * num_at))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (387:9): [True: 0, False: 920] ------------------ 388| 0| { 389| 0| goto exit_function; 390| 0| } 391| | /* fix all charges */ 392| 6.56k| for (i = 0; i < num_at; i++) ------------------ | Branch (392:17): [True: 5.64k, False: 920] ------------------ 393| 5.64k| { 394| 5.64k| if ((j = pVA[i].nCMinusGroupEdge - 1) >= 0) ------------------ | Branch (394:13): [True: 4.09k, False: 1.55k] ------------------ 395| 4.09k| { 396| 4.09k| if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (396:17): [True: 0, False: 4.09k] ------------------ 397| 0| { 398| 0| goto exit_function; 399| 0| } 400| 4.09k| pBNS->edge[j].forbidden |= forbidden_edge_mask; 401| 4.09k| } 402| 5.64k| if ((j = pVA[i].nCPlusGroupEdge - 1) >= 0) ------------------ | Branch (402:13): [True: 4.55k, False: 1.08k] ------------------ 403| 4.55k| { 404| 4.55k| if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (404:17): [True: 0, False: 4.55k] ------------------ 405| 0| { 406| 0| goto exit_function; 407| 0| } 408| 4.55k| pBNS->edge[j].forbidden |= forbidden_edge_mask; 409| 4.55k| } 410| 5.64k| } 411| | 412| | /* H(+) has been added to -O(-); check non-tautomeric atoms */ 413| 6.20k| for (i = 0; i < num_at; i++) ------------------ | Branch (413:17): [True: 5.41k, False: 791] ------------------ 414| 5.41k| { 415| 5.41k| neigh = at2[i].neighbor[0]; /* djb-rwth: avoiding unsequenced modification and access to neigh */ 416| 5.41k| if (!(pStruct->bMobileH ? at2[i].endpoint : pStruct->endpoint[i]) && !pVA[i].cMetal && ------------------ | Branch (416:13): [True: 5.01k, False: 403] | Branch (416:15): [True: 4.23k, False: 1.17k] | Branch (416:78): [True: 4.55k, False: 457] ------------------ 417| 4.55k| at2[i].num_H + 1 == atf[i].num_H && /* normalization added H ??? What would happen in Fixed-H case?*/ ------------------ | Branch (417:13): [True: 998, False: 3.55k] ------------------ 418| 998| (k = pVA[i].nCMinusGroupEdge - 1) >= 0 && ------------------ | Branch (418:13): [True: 996, False: 2] ------------------ 419| 996| pBNS->edge[k].flow == 1 && /* atom had (-) charge before preprocessing */ ------------------ | Branch (419:13): [True: 924, False: 72] ------------------ 420| 924| at2[i].charge == -1 && atf[i].charge == 0 && /* and has no charge after preprocessing */ ------------------ | Branch (420:13): [True: 924, False: 0] | Branch (420:36): [True: 924, False: 0] ------------------ 421| 924| at2[i].valence == 1 && at2[i].chem_bonds_valence == 1 && /* connected by a single bond */ ------------------ | Branch (421:13): [True: 924, False: 0] | Branch (421:36): [True: 924, False: 0] ------------------ 422| 924| pVA[i].cNumValenceElectrons == 6 && /* atom is O, S, Se, Te */ ------------------ | Branch (422:13): [True: 924, False: 0] ------------------ 423| 924| at2[neigh].chem_bonds_valence > at2[neigh].valence ------------------ | Branch (423:13): [True: 642, False: 282] ------------------ 424| | /* atom's single neighbor has multiple bond(s)*/ 425| 5.41k| ) 426| 642| { 427| | /* H(+) was added to O in Y=X-O(-), where X is the only neighbor of O, X=neigh, Y=neigh2 */ 428| 642| iNH = i; 429| 1.35k| for (j = 0; j < at2[neigh].valence; j++) ------------------ | Branch (429:25): [True: 1.21k, False: 147] ------------------ 430| 1.21k| { 431| 1.21k| neigh2 = at2[neigh].neighbor[j]; 432| 1.21k| if (neigh2 != iNH && !at2[neigh2].endpoint && ------------------ | Branch (432:21): [True: 1.02k, False: 190] | Branch (432:38): [True: 1.00k, False: 13] ------------------ 433| 1.00k| !pBNS->edge[(int)pBNS->vert[neigh].iedge[j]].forbidden && ------------------ | Branch (433:21): [True: 1.00k, False: 8] ------------------ 434| 1.00k| 4 <= pVA[neigh2].cNumValenceElectrons && ------------------ | Branch (434:21): [True: 862, False: 138] ------------------ 435| 862| pVA[neigh2].cNumValenceElectrons <= 5 && /* neig2 is C or N */ ------------------ | Branch (435:21): [True: 541, False: 321] ------------------ 436| 541| (k2 = pVA[neigh2].nCMinusGroupEdge - 1) >= 0 && ------------------ | Branch (436:21): [True: 525, False: 16] ------------------ 437| 525| !pBNS->edge[k2].flow /* negative charge may be moved to neigh2 */) ------------------ | Branch (437:21): [True: 495, False: 30] ------------------ 438| 495| { 439| 495| break; 440| 495| } 441| 1.21k| } 442| 642| if (j < at2[neigh].valence) ------------------ | Branch (442:17): [True: 495, False: 147] ------------------ 443| 495| { 444| 495| delta = 1; 445| 495| pe = pBNS->edge + k; /* -O(-) negative charge edge; flow = 1 */ 446| 495| pe2 = pBNS->edge + k2; /* X charge edge; flow = 0 */ 447| 495| v1 = pe->neighbor1; 448| 495| v2 = pe->neighbor12 ^ v1; 449| 495| pe->flow -= delta; 450| 495| pBNS->vert[v1].st_edge.flow -= delta; 451| 495| pBNS->vert[v2].st_edge.flow -= delta; 452| 495| pBNS->tot_st_flow -= 2 * delta; 453| 495| pe2->forbidden &= inv_forbidden_edge_mask; /* allow the charge to move */ 454| | 455| 495| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 456| 495| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 457| 495| if (ret < 0) ------------------ | Branch (457:21): [True: 0, False: 495] ------------------ 458| 0| { 459| 0| goto exit_function; 460| 0| } 461| 495| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (461:21): [True: 153, False: 342] | Branch (461:35): [True: 1, False: 152] | Branch (461:53): [True: 0, False: 1] ------------------ 462| 153| (vPathEnd == v2 && vPathStart == v1)) && ------------------ | Branch (462:22): [True: 150, False: 3] | Branch (462:40): [True: 129, False: 21] ------------------ 463| 129| nDeltaCharge <= 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (463:21): [True: 129, False: 0] ------------------ 464| 129| { 465| 129| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 466| 129| (*pnNumRunBNS)++; 467| 129| if (ret < 0) ------------------ | Branch (467:25): [True: 0, False: 129] ------------------ 468| 0| { 469| 0| goto exit_function; 470| 0| } 471| 129| else 472| 129| if (ret) ------------------ | Branch (472:29): [True: 129, False: 0] ------------------ 473| 129| { 474| 129| *pnTotalDelta += ret; 475| 129| } 476| 0| else 477| 0| { 478| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 479| 0| } 480| 129| break; 481| 129| } 482| 366| else 483| 366| { 484| | /* the attempt has failed; restore the flow */ 485| 366| ret = 0; 486| 366| pe->flow += delta; 487| 366| pBNS->vert[v1].st_edge.flow += delta; 488| 366| pBNS->vert[v2].st_edge.flow += delta; 489| 366| pBNS->tot_st_flow += 2 * delta; 490| 366| } 491| 495| } 492| 642| } 493| 5.41k| } 494| | 495| 920|exit_function: 496| | /* remove bond fixation */ 497| 920| RemoveForbiddenEdgeMask(pBNS, &NewlyFixedEdges, forbidden_edge_mask); 498| 920| AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_FREE); ------------------ | | 243| 920|#define EDGE_LIST_FREE (-2) ------------------ 499| | 500| 920| return ret; 501| 920|} FixRemoveExtraTautEndpoints: 566| 527|{ 567| 527| EDGE_LIST NewlyFixedEdges; 568| 527| int ret, i, j, k, delta, centerpoint, endpoint1, endpoint2; 569| 527| int num_at = pStruct->num_atoms; 570| 527| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 571| 527| Vertex v1, v2; 572| | /* for RunBnsTestOnce */ 573| 527| Vertex vPathStart, vPathEnd; 574| 527| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 575| 527| BNS_EDGE* pe, * pe2; 576| | 577| 527| ret = 0; /* djb-rwth: ignoring LLVM warning: value might be returned */ 578| | 579| 527| AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 527|#define EDGE_LIST_CLEAR (-1) ------------------ 580| 527| if ((ret = AllocEdgeList(&NewlyFixedEdges, 2 * num_at))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (580:9): [True: 0, False: 527] ------------------ 581| 0| { 582| 0| goto exit_function; 583| 0| } 584| | /* fix all charges */ 585| 4.14k| for (i = 0; i < num_at; i++) ------------------ | Branch (585:17): [True: 3.62k, False: 527] ------------------ 586| 3.62k| { 587| 3.62k| if ((j = pVA[i].nCMinusGroupEdge - 1) >= 0) ------------------ | Branch (587:13): [True: 2.68k, False: 940] ------------------ 588| 2.68k| { 589| 2.68k| if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (589:17): [True: 0, False: 2.68k] ------------------ 590| 0| { 591| 0| goto exit_function; 592| 0| } 593| 2.68k| pBNS->edge[j].forbidden |= forbidden_edge_mask; 594| 2.68k| } 595| 3.62k| if ((j = pVA[i].nCPlusGroupEdge - 1) >= 0) ------------------ | Branch (595:13): [True: 3.14k, False: 477] ------------------ 596| 3.14k| { 597| 3.14k| if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (597:17): [True: 0, False: 3.14k] ------------------ 598| 0| { 599| 0| goto exit_function; 600| 0| } 601| 3.14k| pBNS->edge[j].forbidden |= forbidden_edge_mask; 602| 3.14k| } 603| 3.62k| } 604| | 605| 1.61k| for (i = 0; i < picr->num_endp_in1_only; i++) ------------------ | Branch (605:17): [True: 1.17k, False: 439] ------------------ 606| 1.17k| { 607| 1.17k| endpoint1 = picr->endp_in1_only[i] - 1; 608| 1.17k| if (at2[endpoint1].valence == at2[endpoint1].chem_bonds_valence || ------------------ | Branch (608:13): [True: 533, False: 645] ------------------ 609| 645| pVA[endpoint1].nCMinusGroupEdge <= 0) ------------------ | Branch (609:13): [True: 18, False: 627] ------------------ 610| 551| { 611| 551| continue; 612| 551| } 613| | /* find centerpoint */ 614| 1.30k| for (j = 0; j < at2[endpoint1].valence; j++) ------------------ | Branch (614:21): [True: 765, False: 539] ------------------ 615| 765| { 616| 765| if (BOND_TYPE_DOUBLE == (BOND_TYPE_MASK & at2[endpoint1].bond_type[j])) ------------------ | | 33| 765|#define BOND_TYPE_DOUBLE 2 ------------------ if (BOND_TYPE_DOUBLE == (BOND_TYPE_MASK & at2[endpoint1].bond_type[j])) ------------------ | | 189| 765|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (616:17): [True: 627, False: 138] ------------------ 617| 627| { 618| 627| centerpoint = at2[endpoint1].neighbor[j]; 619| 627| if (at2[centerpoint].charge || pVA[centerpoint].nCPlusGroupEdge <= 0 || ------------------ | Branch (619:21): [True: 186, False: 441] | Branch (619:48): [True: 10, False: 431] ------------------ 620| 431| !is_centerpoint_elem(at2[centerpoint].el_number)) ------------------ | Branch (620:21): [True: 1, False: 430] ------------------ 621| 197| { 622| 197| continue; 623| 197| } 624| | /* -- the centerpoint as depicted has no ChargeStruct flower --- 625| | m = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[centerpoint].nCPlusGroupEdge-1 ); 626| | if ( m < 0 || pBNS->edge[m].flow ) { 627| | continue; 628| | } 629| | */ 630| | /* find 2nd endpoint */ 631| 1.41k| for (k = 0; k < at2[centerpoint].valence; k++) ------------------ | Branch (631:29): [True: 1.16k, False: 249] ------------------ 632| 1.16k| { 633| 1.16k| if (BOND_TYPE_SINGLE != (BOND_TYPE_MASK & at2[centerpoint].bond_type[k])) ------------------ | | 32| 1.16k|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE != (BOND_TYPE_MASK & at2[centerpoint].bond_type[k])) ------------------ | | 189| 1.16k|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (633:25): [True: 436, False: 726] ------------------ 634| 436| { 635| 436| continue; 636| 436| } 637| 726| endpoint2 = at2[centerpoint].neighbor[k]; 638| 726| if (!at2[endpoint2].endpoint && atn[endpoint2].endpoint) ------------------ | Branch (638:25): [True: 710, False: 16] | Branch (638:53): [True: 181, False: 529] ------------------ 639| 181| { 640| 181| break; 641| 181| } 642| 726| } 643| 430| if (k == at2[centerpoint].valence) ------------------ | Branch (643:21): [True: 249, False: 181] ------------------ 644| 249| { 645| 249| continue; 646| 249| } 647| | /* the centerpoint and two extra endpoints have been found */ 648| 181| pe = pBNS->edge + pVA[centerpoint].nCPlusGroupEdge - 1; 649| 181| if (!pe->flow) ------------------ | Branch (649:21): [True: 0, False: 181] ------------------ 650| 0| { 651| 0| continue; 652| 0| } 653| 181| pe2 = pBNS->edge + pVA[endpoint1].nCMinusGroupEdge - 1; 654| 181| if (pe2->flow) ------------------ | Branch (654:21): [True: 14, False: 167] ------------------ 655| 14| { 656| 14| continue; 657| 14| } 658| 167| delta = 1; 659| 167| v1 = pe->neighbor1; 660| 167| v2 = pe->neighbor12 ^ v1; 661| 167| pe->flow -= delta; 662| 167| pBNS->vert[v1].st_edge.flow -= delta; 663| 167| pBNS->vert[v2].st_edge.flow -= delta; 664| 167| pBNS->tot_st_flow -= 2 * delta; 665| 167| pe2->forbidden &= inv_forbidden_edge_mask; /* allow the charge to move */ 666| | 667| 167| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 668| 167| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 669| 167| if (ret < 0) ------------------ | Branch (669:21): [True: 0, False: 167] ------------------ 670| 0| { 671| 0| goto exit_function; 672| 0| } 673| 167| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (673:21): [True: 146, False: 21] | Branch (673:35): [True: 57, False: 89] | Branch (673:53): [True: 0, False: 57] ------------------ 674| 146| (vPathEnd == v2 && vPathStart == v1)) && ------------------ | Branch (674:22): [True: 89, False: 57] | Branch (674:40): [True: 88, False: 1] ------------------ 675| 88| nDeltaCharge <= 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (675:21): [True: 88, False: 0] ------------------ 676| 88| { 677| 88| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 678| 88| (*pnNumRunBNS)++; 679| 88| if (ret < 0) ------------------ | Branch (679:25): [True: 0, False: 88] ------------------ 680| 0| { 681| 0| goto exit_function; 682| 0| } 683| 88| else 684| 88| { 685| 88| if (ret) ------------------ | Branch (685:29): [True: 88, False: 0] ------------------ 686| 88| { 687| 88| *pnTotalDelta += ret; 688| 88| } 689| 0| else 690| 0| { 691| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 692| 0| } 693| 88| } 694| 88| goto exit_function; 695| 88| } 696| 79| else 697| 79| { 698| 79| ret = 0; 699| 79| pe->flow += delta; 700| 79| pBNS->vert[v1].st_edge.flow += delta; 701| 79| pBNS->vert[v2].st_edge.flow += delta; 702| 79| pBNS->tot_st_flow += 2 * delta; 703| 79| pe2->forbidden |= forbidden_edge_mask; 704| 79| } 705| 167| } 706| 765| } 707| 627| } 708| | 709| 527|exit_function: 710| | /* remove bond fixation */ 711| 527| RemoveForbiddenEdgeMask(pBNS, &NewlyFixedEdges, forbidden_edge_mask); 712| 527| AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_FREE); ------------------ | | 243| 527|#define EDGE_LIST_FREE (-2) ------------------ 713| | 714| 527| return ret; 715| 527|} FillOutExtraFixedHDataRestr: 720| 15.8k|{ 721| 15.8k| int i, j, k, len, ret = 0; 722| 15.8k| AT_NUMB* pNum; 723| 47.6k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 47.6k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (723:17): [True: 31.7k, False: 15.8k] ------------------ 724| 31.7k| { 725| 31.7k| if (pStruct->pOneINChI_Aux[i]) ------------------ | Branch (725:13): [True: 17.3k, False: 14.4k] ------------------ 726| 17.3k| { 727| 17.3k| pNum = (pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd && ------------------ | Branch (727:21): [True: 316, False: 17.0k] ------------------ 728| 316| pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd[0]) ? ------------------ | Branch (728:17): [True: 292, False: 24] ------------------ 729| 292| pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd : 730| 17.3k| (pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd && ------------------ | Branch (730:18): [True: 17.0k, False: 0] ------------------ 731| 17.0k| pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd[0]) ? ------------------ | Branch (731:21): [True: 17.0k, False: 0] ------------------ 732| 17.0k| pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd : NULL; 733| 17.3k| } 734| 14.4k| else 735| 14.4k| { 736| 14.4k| pNum = NULL; 737| 14.4k| } 738| 31.7k| if (pNum) ------------------ | Branch (738:13): [True: 17.3k, False: 14.4k] ------------------ 739| 17.3k| { 740| 17.3k| len = pStruct->num_atoms * sizeof(pStruct->nCanon2Atno[0][0]); 741| 17.3k| if ((!pStruct->nCanon2Atno[i] && ------------------ | Branch (741:18): [True: 14.3k, False: 3.00k] ------------------ 742| 14.3k| !(pStruct->nCanon2Atno[i] = (AT_NUMB*)inchi_malloc(len))) || ------------------ | | 1143| 14.3k|#define inchi_malloc malloc ------------------ | Branch (742:17): [True: 0, False: 14.3k] ------------------ 743| 17.3k| (!pStruct->nAtno2Canon[i] && ------------------ | Branch (743:18): [True: 14.3k, False: 3.00k] ------------------ 744| 14.3k| !(pStruct->nAtno2Canon[i] = (AT_NUMB*)inchi_malloc(len)))) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 1143| 14.3k|#define inchi_malloc malloc ------------------ | Branch (744:21): [True: 0, False: 14.3k] ------------------ 745| 0| { 746| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 747| 0| goto exit_function; 748| 0| } 749| | 750| | INCHI_HEAPCHK 751| | 752| 17.3k| memcpy(pStruct->nCanon2Atno[i], pNum, len); /* ??? the next for(...) fills it out */ 753| | 754| | INCHI_HEAPCHK 755| | 756| 115k| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (756:29): [True: 98.5k, False: 17.3k] ------------------ 757| 98.5k| { 758| 98.5k| k = pNum[j] - 1; /* atom number */ 759| 98.5k| pStruct->nCanon2Atno[i][j] = (AT_NUMB)k; 760| 98.5k| pStruct->nAtno2Canon[i][k] = (AT_NUMB)j; 761| 98.5k| INCHI_HEAPCHK 762| 98.5k| } 763| 17.3k| } 764| 14.4k| else 765| 14.4k| { 766| 14.4k| if (!i) ------------------ | Branch (766:17): [True: 0, False: 14.4k] ------------------ 767| 0| { 768| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 769| 0| goto exit_function; 770| 0| } 771| 14.4k| else 772| 14.4k| { 773| 14.4k| if (pStruct->nCanon2Atno[i]) ------------------ | Branch (773:21): [True: 93, False: 14.3k] ------------------ 774| 93| { 775| 93| inchi_free(pStruct->nCanon2Atno[i]); ------------------ | | 1152| 93|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 93, False: 0] | | | Branch (1152:50): [Folded, False: 93] | | ------------------ ------------------ 776| 93| pStruct->nCanon2Atno[i] = NULL; 777| 93| } 778| 14.4k| INCHI_HEAPCHK 779| 14.4k| if (pStruct->nAtno2Canon[i]) ------------------ | Branch (779:25): [True: 93, False: 14.3k] ------------------ 780| 93| { 781| 93| inchi_free(pStruct->nAtno2Canon[i]); ------------------ | | 1152| 93|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 93, False: 0] | | | Branch (1152:50): [Folded, False: 93] | | ------------------ ------------------ 782| 93| pStruct->nAtno2Canon[i] = NULL; 783| 93| } 784| 14.4k| INCHI_HEAPCHK 785| 14.4k| } 786| 14.4k| } 787| 31.7k| } 788| | 789| 15.8k|exit_function: 790| | 791| 15.8k| return ret; 792| 15.8k|} FillOutExtraFixedHDataInChI: 797| 1.13k|{ 798| 1.13k| int ret = 0; 799| | /*--- allocate memory for Mobile/Fixed-H data from the input InChI ---*/ 800| 1.13k| if (NULL == pStruct->endpoint) ------------------ | Branch (800:9): [True: 0, False: 1.13k] ------------------ 801| 0| { 802| 0| pStruct->endpoint = (AT_NUMB*)inchi_calloc(pStruct->num_atoms, sizeof(pStruct->endpoint[0])); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 803| 0| } 804| 1.13k| else 805| 1.13k| { 806| 1.13k| memset(pStruct->endpoint, 0, pStruct->num_atoms * sizeof(pStruct->endpoint[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 807| 1.13k| } 808| 1.13k| if (NULL == pStruct->fixed_H) ------------------ | Branch (808:9): [True: 1.13k, False: 0] ------------------ 809| 1.13k| { 810| 1.13k| pStruct->fixed_H = (S_CHAR*)inchi_malloc(pStruct->num_atoms * sizeof(pStruct->fixed_H[0])); ------------------ | | 1143| 1.13k|#define inchi_malloc malloc ------------------ 811| 1.13k| } 812| 1.13k| if (!pStruct->endpoint || !pStruct->fixed_H) ------------------ | Branch (812:9): [True: 0, False: 1.13k] | Branch (812:31): [True: 0, False: 1.13k] ------------------ 813| 0| { 814| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 815| 0| goto exit_function; 816| 0| } 817| | /*--- fill out Mobile/Fixed-H data from the input InChI ---*/ 818| 1.13k| GetTgroupInfoFromInChI(&pStruct->ti, NULL, pStruct->endpoint, pInChI[1]); 819| 1.13k| if (pInChI[0]->nNum_H_fixed) ------------------ | Branch (819:9): [True: 618, False: 520] ------------------ 820| 618| { 821| 618| memcpy(pStruct->fixed_H, pInChI[0]->nNum_H_fixed, pStruct->num_atoms * sizeof(pStruct->fixed_H[0])); 822| 618| } 823| 520| else 824| 520| { 825| 520| memset(pStruct->fixed_H, 0, pStruct->num_atoms * sizeof(pStruct->fixed_H[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 826| 520| } 827| | 828| 1.13k|exit_function: 829| | 830| 1.13k| return ret; 831| 1.13k|} FillOutCMP2FHINCHI: 840| 1.94k|{ 841| 1.94k| int ret = 0, i, j; 842| 1.94k| int bFixHRevrsExists = pInChI[1] && pInChI[1]->nNumberOfAtoms > 0 && !pInChI[1]->bDeleted; ------------------ | Branch (842:34): [True: 1.94k, False: 0] | Branch (842:47): [True: 1.94k, False: 0] | Branch (842:80): [True: 1.94k, False: 0] ------------------ 843| 1.94k| inp_ATOM* at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && ------------------ | Branch (843:36): [True: 952, False: 989] ------------------ 844| 1.94k| pStruct->pOne_norm_data[1]->at) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (844:9): [True: 952, False: 0] ------------------ 845| 1.94k| S_CHAR* num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL; ------------------ | Branch (845:33): [True: 1.94k, False: 0] ------------------ 846| | /* atom number in structure that produced original InChI is atom number in all inp_ATOM *atoms */ 847| | /* atom number in structure that produced restored InChI is in nAtomRevrs[]: */ 848| 1.94k| AT_NUMB* nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 849| 1.94k| S_CHAR* pnMobHInChI = (pInChI[1] && pInChI[1]->nNum_H) ? pInChI[1]->nNum_H : ------------------ | Branch (849:28): [True: 1.94k, False: 0] | Branch (849:41): [True: 1.94k, False: 0] ------------------ 850| 1.94k| (pInChI[0] && pInChI[0]->nNum_H) ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (850:10): [True: 0, False: 0] | Branch (850:23): [True: 0, False: 0] ------------------ 851| 1.94k| S_CHAR* pnMobHRevrs = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H) ? ------------------ | Branch (851:28): [True: 952, False: 989] | Branch (851:53): [True: 952, False: 0] ------------------ 852| 952| pStruct->pOneINChI[1]->nNum_H : 853| 1.94k| (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ? ------------------ | Branch (853:10): [True: 989, False: 0] | Branch (853:35): [True: 989, False: 0] ------------------ 854| 989| pStruct->pOneINChI[0]->nNum_H : NULL; 855| 1.94k| int nNumTgHInChI, nNumTgMInChI, nNumTgHRevrs, nNumTgMRevrs; 856| 1.94k| memset(pc2i, 0, sizeof(*pc2i)); /* djb-rwth: memset_s C11/Annex K variant? */ 857| 1.94k| pc2i->nNumTgInChI = pStruct->ti.num_t_groups; 858| 1.94k| pc2i->nNumTgRevrs = pStruct->One_ti.num_t_groups; 859| 1.94k| pc2i->bHasDifference |= pc2i->nNumTgInChI != pc2i->nNumTgRevrs; 860| | 861| 1.94k| pc2i->nNumRemHInChI = pStruct->nNumRemovedProtonsMobHInChI; 862| 1.94k| pc2i->nNumRemHRevrs = pStruct->One_ti.tni.nNumRemovedProtons; 863| 1.94k| pc2i->bHasDifference |= pc2i->nNumRemHInChI != pc2i->nNumRemHRevrs; 864| | 865| 1.94k| pc2i->bFixedHLayerExistsRevrs = bFixHRevrsExists; 866| 1.94k| pc2i->bHasDifference |= !bFixHRevrsExists; 867| | 868| 2.47k| for (i = 0; i < pStruct->ti.num_t_groups && i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (868:17): [True: 1.38k, False: 1.08k] | Branch (868:49): [True: 530, False: 853] ------------------ 869| 530| { 870| 530| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 871| 530| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 872| 530| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 873| 530| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 874| | 875| 530| pc2i->bHasDifference |= nNumTgHInChI != nNumTgHRevrs; 876| 530| pc2i->bHasDifference |= nNumTgMInChI != nNumTgMRevrs; 877| | 878| 530| if (pStruct->ti.t_group[i].nNumEndpoints == ------------------ | Branch (878:13): [True: 140, False: 390] ------------------ 879| 530| pStruct->One_ti.t_group[i].nNumEndpoints) 880| 140| { 881| | 882| 140| if (nNumTgHInChI != nNumTgHRevrs) ------------------ | Branch (882:17): [True: 140, False: 0] ------------------ 883| 140| { 884| 140| pc2i->nNumTgDiffH++; 885| 140| } 886| 140| if (nNumTgMInChI != nNumTgMRevrs) ------------------ | Branch (886:17): [True: 94, False: 46] ------------------ 887| 94| { 888| 94| pc2i->nNumTgDiffMinus++; 889| 94| } 890| 140| } 891| 530| pc2i->bHasDifference |= pStruct->ti.t_group[i].nNumEndpoints != 892| 530| pStruct->One_ti.t_group[i].nNumEndpoints; 893| | 894| 530| pc2i->nNumTgHInChI += nNumTgHInChI; 895| 530| pc2i->nNumTgMInChI += nNumTgMInChI; 896| 530| pc2i->nNumTgHRevrs += nNumTgHRevrs; 897| 530| pc2i->nNumTgMRevrs += nNumTgMRevrs; 898| 530| } 899| 2.81k| for (; i < pStruct->ti.num_t_groups; i++) ------------------ | Branch (899:12): [True: 875, False: 1.94k] ------------------ 900| 875| { 901| 875| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 902| 875| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 903| 875| pc2i->nNumTgHInChI += nNumTgHInChI; 904| 875| pc2i->nNumTgMInChI += nNumTgMInChI; 905| 875| pc2i->bHasDifference |= 1; 906| 875| } 907| 2.21k| for (; i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (907:12): [True: 272, False: 1.94k] ------------------ 908| 272| { 909| 272| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 910| 272| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 911| 272| pc2i->nNumTgHRevrs += nNumTgHRevrs; 912| 272| pc2i->nNumTgMRevrs += nNumTgMRevrs; 913| 272| pc2i->bHasDifference |= 1; 914| 272| } 915| 16.3k| for (i = j = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (915:21): [True: 14.4k, False: 1.94k] ------------------ 916| 14.4k| { 917| | /* i = original InChI canonical number - 1 */ 918| | /* k = atom number from InChI created out of restored Fixed-H structure */ 919| 14.4k| int iCanonRevrs = nAtno2CanonRevrs[i]; 920| 14.4k| int endptInChI = pStruct->endpoint[i]; /* endpoint in InChI */ 921| 14.4k| int endptRevrs = at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].endpoint : 0; ------------------ | Branch (921:26): [True: 7.14k, False: 7.28k] ------------------ 922| 14.4k| int nFixHInChI = pStruct->fixed_H[i]; 923| 14.4k| int nFixHRevrs = num_Fixed_H_Revrs ? num_Fixed_H_Revrs[iCanonRevrs] : 0; ------------------ | Branch (923:26): [True: 14.4k, False: 0] ------------------ 924| 14.4k| int nMobHInChI = pnMobHInChI ? pnMobHInChI[i] : 0; ------------------ | Branch (924:26): [True: 14.4k, False: 0] ------------------ 925| 14.4k| int nMobHRevrs = pnMobHRevrs ? pnMobHRevrs[iCanonRevrs] : 0; ------------------ | Branch (925:26): [True: 14.4k, False: 0] ------------------ 926| 14.4k| if ( /*(!endptInChI || !endptRevrs) &&*/ (nFixHInChI != nFixHRevrs) || ------------------ | Branch (926:50): [True: 2.20k, False: 12.2k] ------------------ 927| 12.2k| (!endptInChI != !endptRevrs) || nMobHInChI != nMobHRevrs) ------------------ | Branch (927:13): [True: 3.69k, False: 8.54k] | Branch (927:45): [True: 1, False: 8.54k] ------------------ 928| 5.89k| { 929| | /* in InChI or reversed InChI atom[i] is not tautomeric */ 930| | /* and number of fixed-H on the atom[i] differs */ 931| 5.89k| if (j >= MAX_DIFF_FIXH) ------------------ | | 456| 5.89k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (931:17): [True: 0, False: 5.89k] ------------------ 932| 0| { 933| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 934| 0| goto exit_function; 935| 0| } 936| 5.89k| pc2i->c2at[j].endptInChI = endptInChI; 937| 5.89k| pc2i->c2at[j].endptRevrs = endptRevrs; 938| 5.89k| pc2i->bHasDifference |= !endptInChI != !endptRevrs; 939| 5.89k| pc2i->c2at[j].atomNumber = i; 940| 5.89k| pc2i->c2at[j].nValElectr = pVA[i].cNumValenceElectrons; 941| 5.89k| pc2i->c2at[j].nPeriodNum = pVA[i].cPeriodicRowNumber; 942| 5.89k| pc2i->c2at[j].nFixHInChI = nFixHInChI; 943| 5.89k| pc2i->c2at[j].nFixHRevrs = nFixHRevrs; 944| 5.89k| pc2i->bHasDifference |= nFixHInChI != nFixHRevrs; 945| 5.89k| pc2i->c2at[j].nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H[i] : ------------------ | Branch (945:40): [True: 5.89k, False: 0] | Branch (945:53): [True: 5.89k, False: 0] ------------------ 946| 5.89k| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H[i] : 0; ------------------ | Branch (946:17): [True: 0, False: 0] | Branch (946:30): [True: 0, False: 0] ------------------ 947| 5.89k| pc2i->c2at[j].nMobHRevrs = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H) ? ------------------ | Branch (947:41): [True: 3.32k, False: 2.56k] | Branch (947:66): [True: 3.32k, False: 0] ------------------ 948| 3.32k| pStruct->pOneINChI[1]->nNum_H[iCanonRevrs] : 949| 5.89k| (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ? ------------------ | Branch (949:18): [True: 2.56k, False: 0] | Branch (949:43): [True: 2.56k, False: 0] ------------------ 950| 2.56k| pStruct->pOneINChI[0]->nNum_H[iCanonRevrs] : 0; 951| 5.89k| pc2i->nNumDiffMobH += (nMobHInChI != nMobHRevrs && !endptRevrs && !endptInChI); ------------------ | Branch (951:36): [True: 2.11k, False: 3.77k] | Branch (951:64): [True: 1.99k, False: 121] | Branch (951:79): [True: 1.56k, False: 430] ------------------ 952| 5.89k| pc2i->bHasDifference |= nMobHInChI != nMobHRevrs; 953| 5.89k| pc2i->c2at[j].nNumHRevrs = at2[i].num_H; 954| 5.89k| pc2i->c2at[j].nAtChargeRevrs = at2[i].charge; 955| 5.89k| j++; 956| 5.89k| } 957| 14.4k| pc2i->nNumEndpInChI += (endptInChI != 0); 958| 14.4k| pc2i->nNumEndpRevrs += (endptRevrs != 0); 959| | 960| 14.4k| if (!pVA[i].cMetal) ------------------ | Branch (960:13): [True: 12.4k, False: 2.00k] ------------------ 961| 12.4k| { 962| 12.4k| pc2i->nChargeFixHRevrsNonMetal += at2[i].charge; 963| 12.4k| pc2i->nChargeMobHRevrsNonMetal += at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].charge : 0; ------------------ | Branch (963:47): [True: 6.43k, False: 5.98k] ------------------ 964| 12.4k| } 965| | 966| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 967| 14.4k| } 968| 1.94k| pc2i->nChargeFixHInChI = pInChI[0] ? pInChI[0]->nTotalCharge : 0; ------------------ | Branch (968:30): [True: 1.94k, False: 0] ------------------ 969| 1.94k| pc2i->nChargeMobHInChI = pInChI[1] ? pInChI[1]->nTotalCharge : 0; ------------------ | Branch (969:30): [True: 1.94k, False: 0] ------------------ 970| | 971| 1.94k| pc2i->nChargeMobHRevrs = pStruct->pOneINChI[1] ? pStruct->pOneINChI[1]->nTotalCharge : ------------------ | Branch (971:30): [True: 952, False: 989] ------------------ 972| 1.94k| pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0; ------------------ | Branch (972:9): [True: 989, False: 0] ------------------ 973| 1.94k| pc2i->nChargeFixHRevrs = pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0; ------------------ | Branch (973:30): [True: 1.94k, False: 0] ------------------ 974| | 975| 1.94k| pc2i->bHasDifference |= pc2i->nChargeFixHInChI != pc2i->nChargeFixHRevrs; 976| 1.94k| pc2i->bHasDifference |= pc2i->nChargeMobHInChI != pc2i->nChargeMobHRevrs; 977| | 978| 1.94k|exit_function: 979| 1.94k| pc2i->len_c2at = j; 980| | 981| 1.94k| return ret; 982| 1.94k|} FillOutCMP2MHINCHI: 992| 12.7k|{ 993| 12.7k| int ret = 0, i, j, iat; 994| 12.7k| int bFixHRevrsExists = pInChI[1] && pInChI[1]->nNumberOfAtoms > 0 && !pInChI[1]->bDeleted; ------------------ | Branch (994:34): [True: 0, False: 12.7k] | Branch (994:47): [True: 0, False: 0] | Branch (994:80): [True: 0, False: 0] ------------------ 995| 12.7k| inp_ATOM* at_Mobile_H_Revrs = (pStruct->pOne_norm_data[0] && ------------------ | Branch (995:36): [True: 12.7k, False: 0] ------------------ 996| 12.7k| pStruct->pOne_norm_data[0]->at) ? pStruct->pOne_norm_data[0]->at : NULL; ------------------ | Branch (996:9): [True: 12.7k, False: 0] ------------------ 997| | /* atom number in structure that produced original InChI is atom number in all inp_ATOM *atoms */ 998| | /* atom number in structure that produced restored InChI is in nAtomRevrs[]: */ 999| 12.7k| AT_NUMB* nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1000| 12.7k| AT_NUMB* nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 1001| 12.7k| S_CHAR* pnMobHInChI = (pInChI[0] && pInChI[0]->nNum_H) ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (1001:28): [True: 12.7k, False: 0] | Branch (1001:41): [True: 12.7k, False: 0] ------------------ 1002| 12.7k| S_CHAR* pnMobHRevrs = (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ? ------------------ | Branch (1002:28): [True: 12.7k, False: 0] | Branch (1002:53): [True: 12.7k, False: 0] ------------------ 1003| 12.7k| pStruct->pOneINChI[0]->nNum_H : NULL; 1004| 12.7k| int nNumTgHInChI, nNumTgMInChI, nNumTgHRevrs, nNumTgMRevrs; 1005| 12.7k| memset(pc2i, 0, sizeof(*pc2i)); /* djb-rwth: memset_s C11/Annex K variant? */ 1006| 12.7k| pc2i->nNumTgInChI = pStruct->ti.num_t_groups; 1007| 12.7k| pc2i->nNumTgRevrs = pStruct->One_ti.num_t_groups; 1008| 12.7k| pc2i->bHasDifference |= pc2i->nNumTgInChI != pc2i->nNumTgRevrs; 1009| | 1010| 12.7k| pc2i->nNumRemHInChI = pStruct->nNumRemovedProtonsMobHInChI; 1011| 12.7k| pc2i->nNumRemHRevrs = pStruct->One_ti.tni.nNumRemovedProtons; 1012| | /*pc2i->bHasDifference |= pc2i->nNumRemHInChI != pc2i->nNumRemHRevrs;*/ 1013| | 1014| 12.7k| pc2i->bFixedHLayerExistsRevrs = bFixHRevrsExists; 1015| | /*pc2i->bHasDifference |= !bFixHRevrsExists;*/ 1016| | 1017| 13.0k| for (i = 0; i < pStruct->ti.num_t_groups; i++) ------------------ | Branch (1017:17): [True: 323, False: 12.7k] ------------------ 1018| 323| { 1019| 323| int jFst = pStruct->ti.t_group[i].nFirstEndpointAtNoPos; 1020| 323| int jNum = pStruct->ti.t_group[i].nNumEndpoints; 1021| 323| int is_N, is_O; 1022| 968| for (j = 0; j < jNum; j++) ------------------ | Branch (1022:21): [True: 670, False: 298] ------------------ 1023| 670| { 1024| 670| iat = pStruct->ti.nEndpointAtomNumber[jFst + j]; 1025| 670| is_N = pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1; ------------------ | Branch (1025:20): [True: 252, False: 418] | Branch (1025:58): [True: 247, False: 5] ------------------ 1026| 670| is_O = pVA[iat].cNumValenceElectrons == 6; 1027| 670| if (is_N + is_O != 1) ------------------ | Branch (1027:17): [True: 25, False: 645] ------------------ 1028| 25| { 1029| 25| return RI_ERR_SYNTAX; ------------------ | | 16| 25|#define RI_ERR_SYNTAX (-2) ------------------ 1030| 25| } 1031| 645| pc2i->nNumTgNInChI += is_N; 1032| 645| pc2i->nNumTgOInChI += is_O; 1033| 645| if (at2[iat].chem_bonds_valence == at2[iat].valence) ------------------ | Branch (1033:17): [True: 377, False: 268] ------------------ 1034| 377| { 1035| | /* donor */ 1036| 377| if (is_N) ------------------ | Branch (1036:21): [True: 134, False: 243] ------------------ 1037| 134| { 1038| | /* N */ 1039| 134| pc2i->nNumTgNHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1039:44): [True: 50, False: 84] | Branch (1039:68): [True: 31, False: 19] ------------------ 1040| 134| pc2i->nNumTgNH2InChI += at2[iat].charge == 0 && at2[iat].num_H == 2; ------------------ | Branch (1040:45): [True: 50, False: 84] | Branch (1040:69): [True: 0, False: 50] ------------------ 1041| 134| pc2i->nNumTgNMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1041:48): [True: 84, False: 50] | Branch (1041:73): [True: 60, False: 24] ------------------ 1042| 134| pc2i->nNumTgNHMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 1; ------------------ | Branch (1042:49): [True: 84, False: 50] | Branch (1042:74): [True: 24, False: 60] ------------------ 1043| 134| } 1044| 243| else 1045| 243| { 1046| | /* O, S, Se, Te */ 1047| 243| pc2i->nNumTgOHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1047:44): [True: 131, False: 112] | Branch (1047:68): [True: 68, False: 63] ------------------ 1048| 243| pc2i->nNumTgOMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1048:48): [True: 112, False: 131] | Branch (1048:73): [True: 112, False: 0] ------------------ 1049| 243| } 1050| 377| } 1051| 268| else 1052| 268| { 1053| 268| if (at2[iat].chem_bonds_valence == at2[iat].valence + 1) ------------------ | Branch (1053:21): [True: 261, False: 7] ------------------ 1054| 261| { 1055| | /* donor */ 1056| 261| if (is_N) ------------------ | Branch (1056:25): [True: 106, False: 155] ------------------ 1057| 106| { 1058| | /* N */ 1059| 106| pc2i->nNumTgDBNHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1059:50): [True: 106, False: 0] | Branch (1059:74): [True: 11, False: 95] ------------------ 1060| 106| pc2i->nNumTgDBNMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1060:54): [True: 0, False: 106] | Branch (1060:79): [True: 0, False: 0] ------------------ 1061| 106| pc2i->nNumTgDBNInChI += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1061:49): [True: 106, False: 0] | Branch (1061:73): [True: 95, False: 11] ------------------ 1062| 106| } 1063| 155| else 1064| 155| { 1065| | /* O, S, Se, Te */ 1066| 155| pc2i->nNumTgDBOInChI += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1066:49): [True: 155, False: 0] | Branch (1066:73): [True: 155, False: 0] ------------------ 1067| 155| } 1068| 261| } 1069| 268| } 1070| 645| } 1071| 323| } 1072| 12.9k| for (i = 0; i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (1072:17): [True: 264, False: 12.7k] ------------------ 1073| 264| { 1074| 264| int jFst = pStruct->One_ti.t_group[i].nFirstEndpointAtNoPos; 1075| 264| int jNum = pStruct->One_ti.t_group[i].nNumEndpoints; 1076| 264| int is_N, is_O; 1077| 926| for (j = 0; j < jNum; j++) ------------------ | Branch (1077:21): [True: 662, False: 264] ------------------ 1078| 662| { 1079| 662| iat = nCanon2AtnoRevrs[(int)pStruct->One_ti.nEndpointAtomNumber[jFst + j]]; 1080| 662| is_N = pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1; ------------------ | Branch (1080:20): [True: 115, False: 547] | Branch (1080:58): [True: 115, False: 0] ------------------ 1081| 662| is_O = pVA[iat].cNumValenceElectrons == 6; 1082| 662| if (is_N + is_O != 1) ------------------ | Branch (1082:17): [True: 0, False: 662] ------------------ 1083| 0| { 1084| 0| return RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1085| 0| } 1086| 662| pc2i->nNumTgNRevrs += is_N; 1087| 662| pc2i->nNumTgORevrs += is_O; 1088| 662| if (at2[iat].chem_bonds_valence == at2[iat].valence) ------------------ | Branch (1088:17): [True: 323, False: 339] ------------------ 1089| 323| { 1090| | /* donor */ 1091| 323| if (is_N) ------------------ | Branch (1091:21): [True: 56, False: 267] ------------------ 1092| 56| { 1093| | /* N */ 1094| 56| pc2i->nNumTgNHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1094:44): [True: 35, False: 21] | Branch (1094:68): [True: 29, False: 6] ------------------ 1095| 56| pc2i->nNumTgNH2Revrs += at2[iat].charge == 0 && at2[iat].num_H == 2; ------------------ | Branch (1095:45): [True: 35, False: 21] | Branch (1095:69): [True: 0, False: 35] ------------------ 1096| 56| pc2i->nNumTgNMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1096:48): [True: 21, False: 35] | Branch (1096:73): [True: 17, False: 4] ------------------ 1097| 56| pc2i->nNumTgNHMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 1; ------------------ | Branch (1097:49): [True: 21, False: 35] | Branch (1097:74): [True: 4, False: 17] ------------------ 1098| 56| } 1099| 267| else 1100| 267| { 1101| | /* O, S, Se, Te */ 1102| 267| pc2i->nNumTgOHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1102:44): [True: 30, False: 237] | Branch (1102:68): [True: 29, False: 1] ------------------ 1103| 267| pc2i->nNumTgOMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1103:48): [True: 235, False: 32] | Branch (1103:73): [True: 235, False: 0] ------------------ 1104| 267| } 1105| 323| } 1106| 339| else 1107| 339| { 1108| 339| if (at2[iat].chem_bonds_valence == at2[iat].valence + 1) ------------------ | Branch (1108:21): [True: 335, False: 4] ------------------ 1109| 335| { 1110| | /* donor */ 1111| 335| if (is_N) ------------------ | Branch (1111:25): [True: 55, False: 280] ------------------ 1112| 55| { 1113| | /* N */ 1114| 55| pc2i->nNumTgDBNHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1114:50): [True: 39, False: 16] | Branch (1114:74): [True: 1, False: 38] ------------------ 1115| 55| pc2i->nNumTgDBNMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1115:54): [True: 14, False: 41] | Branch (1115:79): [True: 14, False: 0] ------------------ 1116| 55| pc2i->nNumTgDBNRevrs += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1116:49): [True: 39, False: 16] | Branch (1116:73): [True: 38, False: 1] ------------------ 1117| 55| } 1118| 280| else 1119| 280| { 1120| | /* O, S, Se, Te */ 1121| 280| pc2i->nNumTgDBORevrs += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1121:49): [True: 279, False: 1] | Branch (1121:73): [True: 279, False: 0] ------------------ 1122| 280| } 1123| 335| } 1124| 339| } 1125| 662| } 1126| 264| } 1127| | 1128| 12.8k| for (i = 0; i < pStruct->ti.num_t_groups && i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (1128:17): [True: 292, False: 12.5k] | Branch (1128:49): [True: 75, False: 217] ------------------ 1129| 75| { 1130| 75| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 1131| 75| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 1132| 75| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 1133| 75| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 1134| | 1135| 75| pc2i->bHasDifference |= nNumTgHInChI != nNumTgHRevrs; 1136| 75| pc2i->bHasDifference |= nNumTgMInChI != nNumTgMRevrs; 1137| | 1138| 75| if (pStruct->ti.t_group[i].nNumEndpoints == ------------------ | Branch (1138:13): [True: 24, False: 51] ------------------ 1139| 75| pStruct->One_ti.t_group[i].nNumEndpoints) 1140| 24| { 1141| | 1142| 24| if (nNumTgHInChI != nNumTgHRevrs) ------------------ | Branch (1142:17): [True: 20, False: 4] ------------------ 1143| 20| { 1144| 20| pc2i->nNumTgDiffH++; 1145| 20| } 1146| 24| if (nNumTgMInChI != nNumTgMRevrs) ------------------ | Branch (1146:17): [True: 2, False: 22] ------------------ 1147| 2| { 1148| 2| pc2i->nNumTgDiffMinus++; 1149| 2| } 1150| 24| } 1151| 75| pc2i->bHasDifference |= pStruct->ti.t_group[i].nNumEndpoints != 1152| 75| pStruct->One_ti.t_group[i].nNumEndpoints; 1153| | 1154| 75| pc2i->nNumTgHInChI += nNumTgHInChI; 1155| 75| pc2i->nNumTgMInChI += nNumTgMInChI; 1156| 75| pc2i->nNumTgHRevrs += nNumTgHRevrs; 1157| 75| pc2i->nNumTgMRevrs += nNumTgMRevrs; 1158| 75| } 1159| 12.9k| for (; i < pStruct->ti.num_t_groups; i++) ------------------ | Branch (1159:12): [True: 219, False: 12.7k] ------------------ 1160| 219| { 1161| 219| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 1162| 219| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 1163| 219| pc2i->nNumTgHInChI += nNumTgHInChI; 1164| 219| pc2i->nNumTgMInChI += nNumTgMInChI; 1165| 219| pc2i->bHasDifference |= 1; 1166| 219| } 1167| 12.9k| for (; i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (1167:12): [True: 189, False: 12.7k] ------------------ 1168| 189| { 1169| 189| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 1170| 189| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 1171| 189| pc2i->nNumTgHRevrs += nNumTgHRevrs; 1172| 189| pc2i->nNumTgMRevrs += nNumTgMRevrs; 1173| 189| pc2i->bHasDifference |= 1; 1174| 189| } 1175| 77.2k| for (i = j = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1175:21): [True: 64.4k, False: 12.7k] ------------------ 1176| 64.4k| { 1177| | /* i = original InChI canonical number - 1 */ 1178| | /* k = atom number from InChI created out of restored Fixed-H structure */ 1179| 64.4k| int iCanonRevrs = nAtno2CanonRevrs[i]; 1180| 64.4k| int endptInChI = at2[i].endpoint; /* endpoint in InChI */ 1181| 64.4k| int endptRevrs = at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].endpoint : 0; ------------------ | Branch (1181:26): [True: 64.4k, False: 0] ------------------ 1182| 64.4k| int nMobHInChI = pnMobHInChI ? pnMobHInChI[i] : 0; ------------------ | Branch (1182:26): [True: 64.4k, False: 0] ------------------ 1183| 64.4k| int nMobHRevrs = pnMobHRevrs ? pnMobHRevrs[iCanonRevrs] : 0; ------------------ | Branch (1183:26): [True: 64.4k, False: 0] ------------------ 1184| 64.4k| if ((!endptInChI != !endptRevrs) || nMobHInChI != nMobHRevrs) ------------------ | Branch (1184:13): [True: 2.35k, False: 62.1k] | Branch (1184:45): [True: 494, False: 61.6k] ------------------ 1185| 2.85k| { 1186| | /* in InChI or reversed InChI atom[i] is not tautomeric */ 1187| | /* and number of fixed-H on the atom[i] differs */ 1188| 2.85k| if (j >= MAX_DIFF_FIXH) ------------------ | | 456| 2.85k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1188:17): [True: 0, False: 2.85k] ------------------ 1189| 0| { 1190| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1191| 0| goto exit_function; 1192| 0| } 1193| 2.85k| pc2i->c2at[j].endptInChI = endptInChI; 1194| 2.85k| pc2i->c2at[j].endptRevrs = endptRevrs; 1195| 2.85k| pc2i->bHasDifference |= !endptInChI != !endptRevrs; 1196| 2.85k| pc2i->c2at[j].atomNumber = i; 1197| 2.85k| pc2i->c2at[j].nValElectr = pVA[i].cNumValenceElectrons; 1198| 2.85k| pc2i->c2at[j].nPeriodNum = pVA[i].cPeriodicRowNumber; 1199| 2.85k| pc2i->c2at[j].nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H[i] : ------------------ | Branch (1199:40): [True: 0, False: 2.85k] | Branch (1199:53): [True: 0, False: 0] ------------------ 1200| 2.85k| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H[i] : 0; ------------------ | Branch (1200:17): [True: 2.85k, False: 0] | Branch (1200:30): [True: 2.85k, False: 0] ------------------ 1201| 2.85k| pc2i->c2at[j].nMobHRevrs = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H) ? ------------------ | Branch (1201:41): [True: 0, False: 2.85k] | Branch (1201:66): [True: 0, False: 0] ------------------ 1202| 0| pStruct->pOneINChI[1]->nNum_H[iCanonRevrs] : 1203| 2.85k| (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ? ------------------ | Branch (1203:18): [True: 2.85k, False: 0] | Branch (1203:43): [True: 2.85k, False: 0] ------------------ 1204| 2.85k| pStruct->pOneINChI[0]->nNum_H[iCanonRevrs] : 0; 1205| | 1206| 2.85k| pc2i->nNumDiffMobH += (nMobHInChI != nMobHRevrs && !endptRevrs && !endptInChI); ------------------ | Branch (1206:36): [True: 599, False: 2.25k] | Branch (1206:64): [True: 574, False: 25] | Branch (1206:79): [True: 494, False: 80] ------------------ 1207| 2.85k| pc2i->bHasDifference |= (nMobHInChI != nMobHRevrs); 1208| 2.85k| pc2i->c2at[j].nNumHRevrs = at2[i].num_H; 1209| 2.85k| pc2i->c2at[j].nAtChargeRevrs = at2[i].charge; 1210| 2.85k| j++; 1211| 2.85k| } 1212| 64.4k| pc2i->nNumEndpInChI += (endptInChI != 0); 1213| 64.4k| pc2i->nNumEndpRevrs += (endptRevrs != 0); 1214| | 1215| 64.4k| if (!pVA[i].cMetal) ------------------ | Branch (1215:13): [True: 55.2k, False: 9.22k] ------------------ 1216| 55.2k| { 1217| 55.2k| pc2i->nChargeMobHRevrsNonMetal += (at_Mobile_H_Revrs && !at_Mobile_H_Revrs[i].endpoint) ? at_Mobile_H_Revrs[i].charge : 0; ------------------ | Branch (1217:48): [True: 55.2k, False: 0] | Branch (1217:69): [True: 53.2k, False: 2.00k] ------------------ 1218| 55.2k| } 1219| | 1220| | 1221| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 1222| 64.4k| } 1223| 12.7k| pc2i->nChargeMobHRevrsNonMetal += pTCGroups->tgroup_charge; 1224| | 1225| 12.7k| pc2i->nChargeMobHInChI = pInChI[0] ? pInChI[0]->nTotalCharge : 0; ------------------ | Branch (1225:30): [True: 12.7k, False: 0] ------------------ 1226| | 1227| 12.7k| pc2i->nChargeMobHRevrs = pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0; ------------------ | Branch (1227:30): [True: 12.7k, False: 0] ------------------ 1228| | 1229| 12.7k| pc2i->bHasDifference |= pc2i->nChargeMobHInChI != pc2i->nChargeMobHRevrs; 1230| | 1231| 12.7k|exit_function: 1232| 12.7k| pc2i->len_c2at = j; 1233| | 1234| 12.7k| return ret; 1235| 12.7k|} NormalizeAndCompare: 1258| 87.7k|{ 1259| 87.7k| int i; 1260| 87.7k| int err; 1261| 87.7k| ICR icr, icr2; 1262| 87.7k| int num_norm_endpoints, num_endpoints, num_norm_t_groups, ret = 0; /* djb-rwth: ignoring LLVM warning: variables used; removing redundant variables */ 1263| |#if ( bRELEASE_VERSION == 0 ) 1264| |#ifndef TARGET_API_LIB 1265| | const char* szCurHdr = (ip->pSdfValue && ip->pSdfValue[0]) ? ip->pSdfValue : "???"; 1266| | int iComponent = pTCGroups->iComponent; 1267| |#endif 1268| |#endif 1269| 87.7k| T_GROUP_INFO* t_group_info = NULL; 1270| 87.7k| inp_ATOM* at_norm = NULL; /* normalized */ 1271| 87.7k| inp_ATOM* at_prep = NULL; /* preprocessed */ 1272| 87.7k| INCHI_MODE cmpInChI, cmpInChI2; 1273| 87.7k| int nDeltaPrev, nDeltaCur; 1274| 87.7k| int iOrigInChI, iRevrInChI; 1275| | 1276| | 1277| | /***********************************************************/ 1278| | /* normalize and create one component InChI */ 1279| | /***********************************************************/ 1280| 87.7k| ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1281| 87.7k| &t_group_info, &at_norm, &at_prep); 1282| 87.7k| if (ret < 0) ------------------ | Branch (1282:9): [True: 42, False: 87.7k] ------------------ 1283| 42| { 1284| |#if ( bRELEASE_VERSION == 0 ) 1285| |#ifndef TARGET_API_LIB 1286| | fprintf(stdout, "\nERROR in MakeOneInchi-1: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1287| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret); 1288| |#endif 1289| |#endif 1290| 42| goto exit_function; 1291| 42| } 1292| 87.7k| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 574| 87.7k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1292:9): [True: 1.10k, False: 86.6k] ------------------ 1293| 1.10k| { 1294| | /* these indexes are used to compare Mobile-H InChI */ 1295| 1.10k| iOrigInChI = (pInChI[1] && pInChI[1]->nNumberOfAtoms && !pInChI[1]->bDeleted) ? 1 : 0; ------------------ | Branch (1295:23): [True: 1.10k, False: 0] | Branch (1295:36): [True: 1.10k, False: 0] | Branch (1295:65): [True: 1.10k, False: 0] ------------------ 1296| 1.10k| iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0; ------------------ | Branch (1296:23): [True: 477, False: 631] | Branch (1296:48): [True: 477, False: 0] | Branch (1296:89): [True: 477, False: 0] ------------------ 1297| 1.10k| } 1298| 86.6k| else 1299| 86.6k| { 1300| 86.6k| iOrigInChI = 0; 1301| 86.6k| iRevrInChI = 0; 1302| 86.6k| } 1303| | 1304| | /* Intercept and correct non-polymer Zz to Zy if applicable */ 1305| 87.7k| if (pStruct->n_zy && pStruct->n_pzz) ------------------ | Branch (1305:9): [True: 60, False: 87.6k] | Branch (1305:26): [True: 0, False: 60] ------------------ 1306| 0| { 1307| 0| if (pStruct->pOneINChI[iRevrInChI]->szHillFormula) ------------------ | Branch (1307:13): [True: 0, False: 0] ------------------ 1308| 0| { 1309| 0| INCHI_IOS_STRING temp_string_container; 1310| 0| INCHI_IOS_STRING* strbuf = &temp_string_container; 1311| 0| int len0 = strlen(pStruct->pOneINChI[iRevrInChI]->szHillFormula); 1312| 0| if (inchi_strbuf_init(strbuf, len0 + 1, len0 + 1) > 0) ------------------ | Branch (1312:17): [True: 0, False: 0] ------------------ 1313| 0| { 1314| 0| inchi_strbuf_printf(strbuf, "%-s", pStruct->pOneINChI[iRevrInChI]->szHillFormula); 1315| 0| } 1316| 0| MergeZzInHillFormula(strbuf); 1317| 0| if (strbuf->nUsedLength > len0 + 1) ------------------ | Branch (1317:17): [True: 0, False: 0] ------------------ 1318| 0| { 1319| 0| char* ctmp; /* djb-rwth: supplementary variable */ 1320| 0| ctmp = (char*)inchi_realloc(pStruct->pOneINChI[iRevrInChI]->szHillFormula, (long long)strbuf->nUsedLength + 1); /* djb-rwth: cast operator added */ ------------------ | | 1149| 0|#define inchi_realloc realloc ------------------ 1321| 0| if (ctmp != NULL) /* djb-rwth: NULL pointer must not be assigned to pStruct->pOneINChI[iRevrInChI]->szHillFormula */ ------------------ | Branch (1321:21): [True: 0, False: 0] ------------------ 1322| 0| pStruct->pOneINChI[iRevrInChI]->szHillFormula = ctmp; 1323| 0| } 1324| 0| strcpy(pStruct->pOneINChI[iRevrInChI]->szHillFormula, strbuf->pStr); 1325| 0| inchi_strbuf_close(strbuf); 1326| 0| } 1327| 0| } 1328| | 1329| | 1330| | /************************************************************/ 1331| | /* compare */ 1332| | /************************************************************/ 1333| 87.7k| if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct))) ------------------ | | 574| 175k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1333:9): [True: 1.10k, False: 86.6k] | Branch (1333:42): [True: 0, False: 1.10k] ------------------ 1334| 0| { 1335| 0| goto exit_function; 1336| 0| } 1337| 87.7k| cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *a2*/, &icr, &err); 1338| 87.7k| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1338:9): [True: 74.3k, False: 13.4k] ------------------ 1339| 74.3k| { 1340| 74.3k| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 74.3k|#define RI_ERR_PROGR (-3) ------------------ 1341| 74.3k| goto exit_function; 1342| 74.3k| } 1343| 13.4k| if (err) ------------------ | Branch (1343:9): [True: 0, False: 13.4k] ------------------ 1344| 0| { 1345| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1346| 0| goto exit_function; 1347| 0| } 1348| | /********** InChI from restored structure has LESS hydrogen atoms ******************************/ 1349| 13.4k| if ((cmpInChI & IDIF_LESS_H) && at_prep && 0 < (nDeltaCur = icr.tot_num_H2 - icr.tot_num_H1)) ------------------ | Branch (1349:9): [True: 178, False: 13.2k] | Branch (1349:37): [True: 112, False: 66] | Branch (1349:48): [True: 112, False: 0] ------------------ 1350| 112| { 1351| 112| do 1352| 112| { 1353| 112| ret = FixLessHydrogenInFormula(pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups, 1354| 112| pnNumRunBNS, pnTotalDelta, forbidden_edge_mask); 1355| 112| if (ret < 0) ------------------ | Branch (1355:17): [True: 0, False: 112] ------------------ 1356| 0| { 1357| 0| goto exit_function; 1358| 0| } 1359| 112| if (ret) ------------------ | Branch (1359:17): [True: 6, False: 106] ------------------ 1360| 6| { 1361| | /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */ 1362| 6| ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1363| 6| &t_group_info, &at_norm, &at_prep); 1364| 6| if (ret < 0) ------------------ | Branch (1364:21): [True: 1, False: 5] ------------------ 1365| 1| { 1366| |#if ( bRELEASE_VERSION == 0 ) 1367| |#ifndef TARGET_API_LIB 1368| | fprintf(stdout, "\nERROR in MakeOneInchi-2: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1369| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret); 1370| |#endif 1371| |#endif 1372| 1| goto exit_function; 1373| 1| } 1374| | /* compare new InChI to the original InChI */ 1375| 5| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 574| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1375:21): [True: 5, False: 0] ------------------ 1376| 5| { 1377| 5| iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0; ------------------ | Branch (1377:35): [True: 5, False: 0] | Branch (1377:60): [True: 5, False: 0] | Branch (1377:101): [True: 5, False: 0] ------------------ 1378| 5| } 1379| 0| else 1380| 0| { 1381| 0| iRevrInChI = 0; 1382| 0| } 1383| 5| if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct))) ------------------ | | 574| 10|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1383:21): [True: 5, False: 0] | Branch (1383:54): [True: 0, False: 5] ------------------ 1384| 0| { 1385| 0| goto exit_function; 1386| 0| } 1387| 5| cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err); 1388| 5| nDeltaPrev = nDeltaCur; 1389| 5| nDeltaCur = icr.tot_num_H2 - icr.tot_num_H1; 1390| 5| } 1391| 106| else 1392| 106| { 1393| 106| break; 1394| 106| } 1395| 112| } while ((cmpInChI & IDIF_LESS_H) && at_prep && nDeltaCur && nDeltaCur < nDeltaPrev); ------------------ | Branch (1395:18): [True: 3, False: 2] | Branch (1395:46): [True: 3, False: 0] | Branch (1395:57): [True: 3, False: 0] | Branch (1395:70): [True: 0, False: 3] ------------------ 1396| 112| } 1397| | /********** InChI from restored structure has MORE hydrogen atoms ******************************/ 1398| 13.4k| if ((cmpInChI & IDIF_MORE_H) && at_prep && 0 < (nDeltaCur = icr.tot_num_H1 - icr.tot_num_H2)) ------------------ | Branch (1398:9): [True: 8.96k, False: 4.44k] | Branch (1398:37): [True: 902, False: 8.06k] | Branch (1398:48): [True: 902, False: 0] ------------------ 1399| 902| { 1400| 902| do 1401| 920| { 1402| 920| ret = FixMoreHydrogenInFormula(pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups, 1403| 920| pnNumRunBNS, pnTotalDelta, forbidden_edge_mask); 1404| 920| if (ret < 0) ------------------ | Branch (1404:17): [True: 0, False: 920] ------------------ 1405| 0| { 1406| 0| goto exit_function; 1407| 0| } 1408| 920| if (ret) ------------------ | Branch (1408:17): [True: 129, False: 791] ------------------ 1409| 129| { 1410| | /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */ 1411| 129| ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1412| 129| &t_group_info, &at_norm, &at_prep); 1413| 129| if (ret < 0) ------------------ | Branch (1413:21): [True: 0, False: 129] ------------------ 1414| 0| { 1415| |#if ( bRELEASE_VERSION == 0 ) 1416| |#ifndef TARGET_API_LIB 1417| | fprintf(stdout, "\nERROR in MakeOneInchi-3: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1418| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret); 1419| |#endif 1420| |#endif 1421| 0| goto exit_function; 1422| 0| } 1423| | /* compare new InChI to the original InChI */ 1424| 129| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 574| 129|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1424:21): [True: 12, False: 117] ------------------ 1425| 12| { 1426| 12| iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0; ------------------ | Branch (1426:35): [True: 10, False: 2] | Branch (1426:60): [True: 10, False: 0] | Branch (1426:101): [True: 10, False: 0] ------------------ 1427| 12| } 1428| 117| else 1429| 117| { 1430| 117| iRevrInChI = 0; 1431| 117| } 1432| 129| if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct))) ------------------ | | 574| 258|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1432:21): [True: 12, False: 117] | Branch (1432:54): [True: 0, False: 12] ------------------ 1433| 0| { 1434| 0| goto exit_function; 1435| 0| } 1436| 129| cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err); 1437| 129| nDeltaPrev = nDeltaCur; 1438| 129| nDeltaCur = icr.tot_num_H1 - icr.tot_num_H2; 1439| 129| } 1440| 791| else 1441| 791| { 1442| 791| break; 1443| 791| } 1444| 920| } while ((cmpInChI & IDIF_MORE_H) && at_prep && nDeltaCur && nDeltaCur < nDeltaPrev); ------------------ | Branch (1444:18): [True: 99, False: 30] | Branch (1444:46): [True: 36, False: 63] | Branch (1444:57): [True: 36, False: 0] | Branch (1444:70): [True: 18, False: 18] ------------------ 1445| 902| } 1446| | /***************** Fix non-taut atoms normalized to tautomeric endpoints ***********************/ 1447| 13.4k| if ((cmpInChI & IDIF_EXTRA_TG_ENDP) && at_norm && 0 < (nDeltaCur = icr.num_endp_in1_only)) ------------------ | Branch (1447:9): [True: 510, False: 12.9k] | Branch (1447:44): [True: 510, False: 0] | Branch (1447:55): [True: 510, False: 0] ------------------ 1448| 510| { 1449| 510| do 1450| 527| { 1451| 527| ret = FixRemoveExtraTautEndpoints(pBNS, pBD, pStruct, at, at2, at_prep, at_norm, pVA, pTCGroups, &icr, 1452| 527| pnNumRunBNS, pnTotalDelta, forbidden_edge_mask); 1453| 527| if (ret < 0) ------------------ | Branch (1453:17): [True: 0, False: 527] ------------------ 1454| 0| { 1455| 0| goto exit_function; 1456| 0| } 1457| 527| if (ret) ------------------ | Branch (1457:17): [True: 88, False: 439] ------------------ 1458| 88| { 1459| | /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */ 1460| 88| ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1461| 88| &t_group_info, &at_norm, &at_prep); 1462| 88| if (ret < 0) ------------------ | Branch (1462:21): [True: 0, False: 88] ------------------ 1463| 0| { 1464| |#if ( bRELEASE_VERSION == 0 ) 1465| |#ifndef TARGET_API_LIB 1466| | fprintf(stdout, "\nERROR in MakeOneInchi-4: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1467| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret); 1468| |#endif 1469| |#endif 1470| 0| goto exit_function; 1471| 0| } 1472| | /* compare new InChI to the original InChI */ 1473| 88| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 574| 88|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1473:21): [True: 0, False: 88] ------------------ 1474| 0| { 1475| 0| iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0; ------------------ | Branch (1475:35): [True: 0, False: 0] | Branch (1475:60): [True: 0, False: 0] | Branch (1475:101): [True: 0, False: 0] ------------------ 1476| 0| } 1477| 88| else 1478| 88| { 1479| 88| iRevrInChI = 0; 1480| 88| } 1481| 88| if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct))) ------------------ | | 574| 176|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1481:21): [True: 0, False: 88] | Branch (1481:54): [True: 0, False: 0] ------------------ 1482| 0| { 1483| 0| goto exit_function; 1484| 0| } 1485| 88| cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err); 1486| 88| nDeltaPrev = nDeltaCur; 1487| 88| nDeltaCur = icr.num_endp_in1_only; 1488| 88| } 1489| 439| else 1490| 439| { 1491| 439| break; 1492| 439| } 1493| 527| } while ((cmpInChI & IDIF_EXTRA_TG_ENDP) && at_norm && nDeltaCur && nDeltaCur < nDeltaPrev); ------------------ | Branch (1493:18): [True: 49, False: 39] | Branch (1493:53): [True: 49, False: 0] | Branch (1493:64): [True: 49, False: 0] | Branch (1493:77): [True: 17, False: 32] ------------------ 1494| 510| } 1495| | /************************ case of Fixed-H ******************************************************/ 1496| | 1497| 13.4k| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 574| 13.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1497:9): [True: 756, False: 12.6k] ------------------ 1498| 756| { 1499| 756| int num_tries = 0; 1500| 756| do 1501| 1.21k| { 1502| 1.21k| if (0 > (ret = FixFixedHRestoredStructure(pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1502:17): [True: 8, False: 1.20k] ------------------ 1503| 1.21k| &t_group_info, &at_norm, &at_prep, pInChI, 1504| 1.21k| num_inp, bHasSomeFixedH, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask, 1505| 1.21k| forbidden_stereo_edge_mask))) 1506| 8| { 1507| 8| goto exit_function; 1508| 8| } 1509| 1.21k| } while (num_tries++ < 2 && ret > 0); ------------------ | Branch (1509:18): [True: 1.08k, False: 125] | Branch (1509:37): [True: 457, False: 623] ------------------ 1510| 756| } 1511| | /************************ case of Fixed-H ******************************************************/ 1512| 13.4k| if (pStruct->bMobileH == TAUT_YES) ------------------ | | 575| 13.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1512:9): [True: 12.6k, False: 748] ------------------ 1513| 12.6k| { 1514| 12.6k| if (0 > (ret = FixMobileHRestoredStructure(pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1514:13): [True: 25, False: 12.6k] ------------------ 1515| 12.6k| &t_group_info, &at_norm, &at_prep, pInChI, 1516| 12.6k| num_inp, bHasSomeFixedH, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask, 1517| 12.6k| forbidden_stereo_edge_mask))) 1518| 25| { 1519| 25| goto exit_function; 1520| 25| } 1521| 12.6k| } 1522| | /**********************************************************************************************/ 1523| | /* stereo */ 1524| 13.3k| cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *a2*/, &icr, &err); 1525| 13.3k| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1525:9): [True: 161, False: 13.2k] ------------------ 1526| 161| { 1527| 161| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 161|#define RI_ERR_PROGR (-3) ------------------ 1528| 161| goto exit_function; 1529| 161| } 1530| 13.2k| if (err) ------------------ | Branch (1530:9): [True: 0, False: 13.2k] ------------------ 1531| 0| { 1532| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1533| 0| goto exit_function; 1534| 0| } 1535| 13.2k| cmpInChI2 = 0; 1536| 13.2k| memset(&icr2, 0, sizeof(icr2)); /* djb-rwth: memset_s C11/Annex K variant? */ 1537| 13.2k| if (iRevrInChI || iOrigInChI) ------------------ | Branch (1537:9): [True: 287, False: 12.9k] | Branch (1537:23): [True: 300, False: 12.6k] ------------------ 1538| 587| { 1539| | /* additional mobile-H compare in case of Fixed-H */ 1540| 587| cmpInChI2 = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *a2*/, &icr2, &err); 1541| 587| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1541:13): [True: 0, False: 587] ------------------ 1542| 0| { 1543| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1544| 0| goto exit_function; 1545| 0| } 1546| 587| if (err) ------------------ | Branch (1546:13): [True: 0, False: 587] ------------------ 1547| 0| { 1548| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1549| 0| goto exit_function; 1550| 0| } 1551| 587| } 1552| 13.2k| ret = FixRestoredStructureStereo(pCG, ic, 1553| 13.2k| cmpInChI, &icr, cmpInChI2, &icr2, 1554| 13.2k| ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, 1555| 13.2k| &t_group_info, &at_norm, &at_prep, pInChI, 1556| 13.2k| num_inp, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask, 1557| 13.2k| forbidden_stereo_edge_mask); 1558| | 1559| 13.2k| if (ret < 0) ------------------ | Branch (1559:9): [True: 2, False: 13.2k] ------------------ 1560| 2| { 1561| 2| goto exit_function; 1562| 2| } 1563| |#if ( FIX_ADD_PROTON_FOR_ADP == 1 ) 1564| | /************************ check and fix ADP by adding a proton (dummy) *************************/ 1565| | if (cmpInChI && pTCGroups->num_tgroups && pBNS->tot_st_cap > pBNS->tot_st_flow) 1566| | { 1567| | ret = FixAddProtonForADP(pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups, &icr, 1568| | pnNumRunBNS, pnTotalDelta, forbidden_edge_mask); 1569| | if (ret < 0) 1570| | { 1571| | goto exit_function; 1572| | } 1573| | } 1574| |#endif 1575| | /* moved to MakeOneInChIOutOfStrFromINChI(): 1576| | pStruct->nNumRemovedProtons = (pStruct->iMobileH == TAUT_YES)? pStruct->One_ti.tni.nNumRemovedProtons : 0; 1577| | */ 1578| | 1579| | /* count endpoints */ 1580| 13.2k| num_endpoints = 0; 1581| 13.2k| num_norm_endpoints = 0; 1582| 13.2k| num_norm_t_groups = 0; 1583| | /* djb-rwth: removing redundant code */ 1584| 13.2k| at_norm = pStruct->pOne_norm_data[0]->at; 1585| 13.4k| for (i = 0; i < pTCGroups->num_tgroups; i++) ------------------ | Branch (1585:17): [True: 208, False: 13.2k] ------------------ 1586| 208| { 1587| 208| num_endpoints += pTCGroups->pTCG[i].num_edges; 1588| | /* djb-rwth: removing redundant code */ 1589| 208| } 1590| | 1591| 13.2k| if (t_group_info) ------------------ | Branch (1591:9): [True: 252, False: 12.9k] ------------------ 1592| 252| { 1593| | /* after canonicalization, t_group_info->t_group[i].num[0] = number of H */ 1594| | /* t_group_info->t_group[i].num[1] = number of (-) */ 1595| 508| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (1595:21): [True: 256, False: 252] ------------------ 1596| 256| { 1597| 256| if (t_group_info->t_group[i].num[0]) ------------------ | Branch (1597:17): [True: 256, False: 0] ------------------ 1598| 256| { 1599| 256| num_norm_t_groups++; 1600| 256| num_norm_endpoints += t_group_info->t_group[i].nNumEndpoints; 1601| | /* djb-rwth: removing redundant code */ 1602| 256| } 1603| 256| } 1604| 252| } 1605| |#if ( bRELEASE_VERSION == 0 ) 1606| |#ifndef TARGET_API_LIB 1607| | if (num_norm_t_groups != pTCGroups->num_tgroups || num_norm_endpoints != num_endpoints) 1608| | { 1609| | /* need aggressive (de)protonation */ 1610| | /* pStruct->bExtract |= EXTRACT_STRUCT_NUMBER; */ 1611| | fprintf(stdout, "NORMCOMP: %s comp=%d %c%c: InChI/NormRvrs NumTg=%d/%d NumEndp=%d/%d\n", 1612| | (*ip).pSdfValue, (*pTCGroups).iComponent, 1613| | pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', 1614| | pTCGroups->num_tgroups, num_norm_t_groups, 1615| | num_endpoints, num_norm_endpoints); 1616| | } 1617| |#endif 1618| |#endif 1619| | 1620| 87.7k|exit_function: 1621| | 1622| 263k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 263k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1622:17): [True: 175k, False: 87.7k] ------------------ 1623| 175k| { 1624| 175k| Free_INChI(&pStruct->pOneINChI[i]); 1625| 175k| Free_INChI_Aux(&pStruct->pOneINChI_Aux[i]); 1626| 175k| FreeInpAtomData(pStruct->pOne_norm_data[i]); 1627| 175k| if (pStruct->pOne_norm_data[i]) ------------------ | Branch (1627:13): [True: 88.2k, False: 87.3k] ------------------ 1628| 88.2k| { 1629| 88.2k| inchi_free(pStruct->pOne_norm_data[i]); ------------------ | | 1152| 88.2k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 88.2k, False: 0] | | | Branch (1152:50): [Folded, False: 88.2k] | | ------------------ ------------------ 1630| 88.2k| pStruct->pOne_norm_data[i] = NULL; 1631| 88.2k| } 1632| 175k| } 1633| | 1634| 87.7k| free_t_group_info(&pStruct->One_ti); 1635| | 1636| 87.7k| return ret; 1637| 13.2k|} CheckAndRefixStereobonds: 1646| 87.7k|{ 1647| 87.7k| int forbidden_edge_stereo = BNS_EDGE_FORBIDDEN_MASK; ------------------ | | 39| 87.7k|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 1648| 87.7k| int inv_forbidden_edge_stereo = ~forbidden_edge_stereo; 1649| | 1650| 87.7k| int i, k, ne, j1, j2, num_wrong, num_fixed; 1651| 87.7k| int ret2, retBNS, ret; 1652| 87.7k| int num_at = pStruct->num_atoms; 1653| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 1654| 87.7k| int len_at = num_at + num_deleted_H; 1655| 87.7k| EDGE_LIST FixedEdges, WrongEdges, CarbonChargeEdges; 1656| | 1657| 87.7k| BNS_EDGE* pEdge; 1658| 87.7k| Vertex v1, v2; 1659| 87.7k| BNS_VERTEX* pv1, * pv2; 1660| | 1661| 87.7k| ret = 0; 1662| | 1663| | /* to simplify, prepare new at[] from pBNS */ 1664| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 1665| 87.7k| pStruct->at = at2; 1666| 87.7k| ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 1667| 87.7k| pStruct->at = at; 1668| 87.7k| if (ret2 < 0) ------------------ | Branch (1668:9): [True: 0, False: 87.7k] ------------------ 1669| 0| { 1670| 0| return ret; 1671| 0| } 1672| | 1673| 87.7k| num_wrong = 0; 1674| | /* find wrong double bonds */ 1675| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (1675:17): [True: 832k, False: 87.7k] ------------------ 1676| 832k| { 1677| 832k| if (at2[i].valence == 3 && ------------------ | Branch (1677:13): [True: 23.5k, False: 809k] ------------------ 1678| 23.5k| at2[i].chem_bonds_valence - at2[i].valence == 1 && ------------------ | Branch (1678:13): [True: 7.30k, False: 16.2k] ------------------ 1679| 7.30k| at2[i].sb_parity[0] && at2[i].sb_parity[1] && !at2[i].sb_parity[2] && ------------------ | Branch (1679:13): [True: 175, False: 7.13k] | Branch (1679:36): [True: 54, False: 121] | Branch (1679:59): [True: 40, False: 14] ------------------ 1680| 40| (at2[i].bond_type[j1 = (int)at2[i].sb_ord[0]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 189| 40|#define BOND_TYPE_MASK 0x0f ------------------ (at2[i].bond_type[j1 = (int)at2[i].sb_ord[0]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 32| 832k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1680:13): [True: 27, False: 13] ------------------ 1681| 27| (at2[i].bond_type[j2 = (int)at2[i].sb_ord[1]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 189| 27|#define BOND_TYPE_MASK 0x0f ------------------ (at2[i].bond_type[j2 = (int)at2[i].sb_ord[1]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 32| 832k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1681:13): [True: 21, False: 6] ------------------ 1682| 21| j1 != j2) ------------------ | Branch (1682:13): [True: 21, False: 0] ------------------ 1683| 21| { 1684| | 1685| 21| num_wrong++; 1686| 21| } 1687| 832k| } 1688| 87.7k| if (!num_wrong) ------------------ | Branch (1688:9): [True: 87.7k, False: 19] ------------------ 1689| 87.7k| { 1690| 87.7k| return 0; 1691| 87.7k| } 1692| 19| num_fixed = 0; 1693| 114| for (i = 0; i < pBNS->num_bonds; i++) ------------------ | Branch (1693:17): [True: 95, False: 19] ------------------ 1694| 95| { 1695| 95| pEdge = pBNS->edge + i; 1696| 95| if (pEdge->forbidden & forbidden_edge_stereo) ------------------ | Branch (1696:13): [True: 0, False: 95] ------------------ 1697| 0| { 1698| 0| num_fixed++; 1699| 0| } 1700| 95| } 1701| | 1702| | /* there may be no fixed stereo bonds at all, see #87607 */ 1703| 19| AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 19|#define EDGE_LIST_CLEAR (-1) ------------------ 1704| 19| AllocEdgeList(&FixedEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 19|#define EDGE_LIST_CLEAR (-1) ------------------ 1705| 19| AllocEdgeList(&WrongEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 19|#define EDGE_LIST_CLEAR (-1) ------------------ 1706| | 1707| | /* do not goto exit_function before reaching this point: EdgeLists have not been initiated */ 1708| | 1709| 19| if (0 > (ret = ForbidCarbonChargeEdges(pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask))) ------------------ | Branch (1709:9): [True: 0, False: 19] ------------------ 1710| 0| { 1711| 0| goto exit_function; 1712| 0| } 1713| 19| if ((ret = AllocEdgeList(&FixedEdges, num_fixed)) || ------------------ | Branch (1713:9): [True: 0, False: 19] ------------------ 1714| 19| (ret = AllocEdgeList(&WrongEdges, num_wrong))) ------------------ | Branch (1714:9): [True: 0, False: 19] ------------------ 1715| 0| { 1716| 0| goto exit_function; 1717| 0| } 1718| | /* collect wrong double bonds and set flow=0 */ 1719| 62| for (i = 0; i < num_at && WrongEdges.num_edges < num_wrong; i++) ------------------ | Branch (1719:17): [True: 59, False: 3] | Branch (1719:31): [True: 43, False: 16] ------------------ 1720| 43| { 1721| 43| if (at2[i].valence == 3 && ------------------ | Branch (1721:13): [True: 25, False: 18] ------------------ 1722| 25| at2[i].chem_bonds_valence - at2[i].valence == 1 && ------------------ | Branch (1722:13): [True: 25, False: 0] ------------------ 1723| 25| at2[i].sb_parity[0] && at2[i].sb_parity[1] && !at2[i].sb_parity[2] && ------------------ | Branch (1723:13): [True: 25, False: 0] | Branch (1723:36): [True: 23, False: 2] | Branch (1723:59): [True: 22, False: 1] ------------------ 1724| 22| (at2[i].bond_type[j1 = (int)at2[i].sb_ord[0]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 189| 22|#define BOND_TYPE_MASK 0x0f ------------------ (at2[i].bond_type[j1 = (int)at2[i].sb_ord[0]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 32| 65|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1724:13): [True: 21, False: 1] ------------------ 1725| 21| (at2[i].bond_type[j2 = (int)at2[i].sb_ord[1]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 189| 21|#define BOND_TYPE_MASK 0x0f ------------------ (at2[i].bond_type[j2 = (int)at2[i].sb_ord[1]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE && ------------------ | | 32| 64|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1725:13): [True: 21, False: 0] ------------------ 1726| 21| j1 != j2) ------------------ | Branch (1726:13): [True: 21, False: 0] ------------------ 1727| 21| { 1728| 21| switch (j1 + j2) 1729| 21| { 1730| 1| case 1: /* 0, 1 */ ------------------ | Branch (1730:13): [True: 1, False: 20] ------------------ 1731| 1| k = 2; 1732| 1| break; 1733| 3| case 2: /* 0, 2 */ ------------------ | Branch (1733:13): [True: 3, False: 18] ------------------ 1734| 3| k = 1; 1735| 3| break; 1736| 17| case 3: /* 1, 2 */ ------------------ | Branch (1736:13): [True: 17, False: 4] ------------------ 1737| 17| k = 0; 1738| 17| break; 1739| 0| default: ------------------ | Branch (1739:13): [True: 0, False: 21] ------------------ 1740| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1741| 0| goto exit_function; 1742| 21| } 1743| 21| ne = pBNS->vert[i].iedge[k]; 1744| 21| pEdge = pBNS->edge + ne; 1745| 21| v1 = pEdge->neighbor1; 1746| 21| v2 = pEdge->neighbor12 ^ v1; 1747| 21| pv1 = pBNS->vert + v1; 1748| 21| pv2 = pBNS->vert + v2; 1749| | 1750| 21| if (!pEdge->flow) ------------------ | Branch (1750:17): [True: 0, False: 21] ------------------ 1751| 0| { 1752| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1753| 0| goto exit_function; 1754| 0| } 1755| 21| pEdge->flow--; 1756| 21| pEdge->forbidden |= forbidden_edge_mask; 1757| 21| pv1->st_edge.flow--; 1758| 21| pv2->st_edge.flow--; 1759| 21| pBNS->tot_st_flow -= 2; 1760| 21| if ((ret = AddToEdgeList(&WrongEdges, ne, 0))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1760:17): [True: 0, False: 21] ------------------ 1761| 0| { 1762| 0| goto exit_function; 1763| 0| } 1764| 21| } 1765| 43| } 1766| | /* remove forbidden mark from stereo bonds (unfix stereo bonds) */ 1767| 19| for (i = 0; i < pBNS->num_bonds && FixedEdges.num_edges < num_fixed; i++) ------------------ | Branch (1767:17): [True: 19, False: 0] | Branch (1767:40): [True: 0, False: 19] ------------------ 1768| 0| { 1769| 0| pEdge = pBNS->edge + i; 1770| 0| if (pEdge->forbidden & forbidden_edge_stereo) ------------------ | Branch (1770:13): [True: 0, False: 0] ------------------ 1771| 0| { 1772| 0| pEdge->forbidden &= inv_forbidden_edge_stereo; 1773| 0| FixedEdges.pnEdges[FixedEdges.num_edges++] = i; 1774| 0| } 1775| 0| } 1776| | /* Run BNS to move charges and rearrange bond orders */ 1777| 19| retBNS = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 1778| 19| (*pnNumRunBNS)++; 1779| 19| if (retBNS < 0) ------------------ | Branch (1779:9): [True: 0, False: 19] ------------------ 1780| 0| { 1781| 0| goto exit_function; 1782| 0| } 1783| 19| else 1784| 19| { 1785| 19| if (retBNS > 0) ------------------ | Branch (1785:13): [True: 11, False: 8] ------------------ 1786| 11| { 1787| 11| *pnTotalDelta += retBNS; 1788| 11| } 1789| 19| } 1790| | /* remove forbidden_edge_mask and set forbidden_edge_stereo */ 1791| 19| RemoveForbiddenEdgeMask(pBNS, &WrongEdges, forbidden_edge_mask); 1792| | /* allow carbon charges to change */ 1793| 19| RemoveForbiddenEdgeMask(pBNS, &CarbonChargeEdges, forbidden_edge_mask); 1794| | /* fix previously unfixed stereo bonds */ 1795| 19| SetForbiddenEdgeMask(pBNS, &FixedEdges, forbidden_edge_stereo); 1796| | /* Run BNS again in case not all edge flows are maximal */ 1797| 19| ret2 = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 1798| 19| (*pnNumRunBNS)++; 1799| 19| if (ret2 < 0) ------------------ | Branch (1799:9): [True: 0, False: 19] ------------------ 1800| 0| { 1801| 0| goto exit_function; 1802| 0| } 1803| 19| else 1804| 19| { 1805| 19| if (ret2 > 0) ------------------ | Branch (1805:13): [True: 9, False: 10] ------------------ 1806| 9| { 1807| 9| *pnTotalDelta += retBNS; 1808| 9| } 1809| 19| } 1810| 19| ret = retBNS; 1811| | 1812| 19|exit_function: 1813| | 1814| 19| AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_FREE); ------------------ | | 243| 19|#define EDGE_LIST_FREE (-2) ------------------ 1815| 19| AllocEdgeList(&FixedEdges, EDGE_LIST_FREE); ------------------ | | 243| 19|#define EDGE_LIST_FREE (-2) ------------------ 1816| 19| AllocEdgeList(&WrongEdges, EDGE_LIST_FREE); ------------------ | | 243| 19|#define EDGE_LIST_FREE (-2) ------------------ 1817| | 1818| 19| return ret; 1819| 19|} MoveChargeToRemoveCenerpoints: 1835| 87.7k|{ 1836| 87.7k| int i, j, neigh, num_success; /* djb-rwth: removing redundant variables */ 1837| 87.7k| int num_donors, num_acceptors, bond_type, num_donors_O, num_acceptors_O, is_centerpoint_N, num_known_endpoints, num_wrong_neigh; 1838| 87.7k| int ret2, ret_forbid_edges, ret, delta; 1839| 87.7k| int num_at = pStruct->num_atoms; 1840| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 1841| 87.7k| int len_at = num_at + num_deleted_H; 1842| 87.7k| int forbidden_edge_test = BNS_EDGE_FORBIDDEN_TEST; ------------------ | | 41| 87.7k|#define BNS_EDGE_FORBIDDEN_TEST 4 ------------------ 1843| 87.7k| int bPossiblyIgnore = pStruct->charge >= 0 && (!pTCGroups->num_tgroups || (pStruct->iMobileH == TAUT_NON && pStruct->ti.num_t_groups)); /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 964|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1843:27): [True: 87.6k, False: 108] | Branch (1843:52): [True: 87.1k, False: 482] | Branch (1843:80): [True: 0, False: 482] | Branch (1843:113): [True: 0, False: 0] ------------------ 1844| 87.7k| S_CHAR MobileChargeNeigh[MAXVAL], DoubleBondAcceptors[MAXVAL], DoubleBondNotONeigh[MAXVAL]; 1845| 87.7k| int numMobileChargeNeigh, numDoubleBondAcceptors, numDoubleBondNotONeigh; /* djb-rwth: removing redundant variables */ 1846| 87.7k| EDGE_LIST ChargeListAllExcept_DB_O; 1847| | 1848| | 1849| 87.7k| BNS_EDGE* pEdgeMinus, * pe; 1850| 87.7k| Vertex v1m, v2m; 1851| 87.7k| BNS_VERTEX* pv1m, * pv2m; 1852| | /* djb-rwth: removing redundant code */ 1853| 87.7k| num_success = 0; 1854| | 1855| | /* count O(+)H, N(+)H */ 1856| | 1857| | /* 1858| | if ( pStruct->charge >= 0 && (!pTCGroups->num_tgroups || pStruct->iMobileH == TAUT_NON && pStruct->ti.num_t_groups) ) { 1859| | goto exit_function; 1860| | } 1861| | */ 1862| 87.7k| if ((ret = AllocEdgeList(&ChargeListAllExcept_DB_O, EDGE_LIST_CLEAR))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ | Branch (1862:9): [True: 0, False: 87.7k] ------------------ 1863| 0| { 1864| 0| goto exit_function; 1865| 0| } 1866| | 1867| | 1868| | /* to simplify, prepare new at[] from pBNS */ 1869| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 1870| 87.7k| pStruct->at = at2; 1871| 87.7k| ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 1872| 87.7k| pStruct->at = at; 1873| 87.7k| if (ret2 < 0) ------------------ | Branch (1873:9): [True: 0, False: 87.7k] ------------------ 1874| 0| { 1875| 0| ret = ret2; 1876| 0| goto exit_function; 1877| 0| } 1878| 87.7k|#if ( FIND_RING_SYSTEMS == 1 ) 1879| 87.7k| ret2 = MarkRingSystemsInp(at2, num_at, 0); 1880| 87.7k| if (ret2 < 0) ------------------ | Branch (1880:9): [True: 0, False: 87.7k] ------------------ 1881| 0| { 1882| 0| ret = ret2; 1883| 0| goto exit_function; 1884| 0| } 1885| 87.7k|#endif 1886| | /* mark bonds that cannot be tautomeric; do not forget to remove the marks later */ 1887| 87.7k| ret_forbid_edges = SetForbiddenEdges(pBNS, at2, num_at, forbidden_edge_test, 0, NULL); 1888| 87.7k| if (ret_forbid_edges < 0) ------------------ | Branch (1888:9): [True: 0, False: 87.7k] ------------------ 1889| 0| { 1890| 0| ret = ret_forbid_edges; 1891| 0| goto exit_function; 1892| 0| } 1893| | 1894| 920k| for (i = 0; i < num_at; i++) ------------------ | Branch (1894:17): [True: 832k, False: 87.7k] ------------------ 1895| 832k| { 1896| 832k| if (pVA[i].cNumValenceElectrons != 4 && /* not C, Si, Ge */ ------------------ | Branch (1896:13): [True: 739k, False: 92.9k] ------------------ 1897| 739k| !(pVA[i].nTautGroupEdge || (pStruct->iMobileH == TAUT_NON && pStruct->endpoint && pStruct->endpoint[i])) && ------------------ | | 574| 1.47M|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1897:15): [True: 996, False: 738k] | Branch (1897:41): [True: 8.18k, False: 730k] | Branch (1897:74): [True: 8.18k, False: 0] | Branch (1897:95): [True: 1.33k, False: 6.84k] ------------------ 1898| 737k| !at2[i].num_H && !at2[i].charge && at2[i].valence >= 2 && ------------------ | Branch (1898:13): [True: 734k, False: 3.10k] | Branch (1898:30): [True: 684k, False: 50.2k] | Branch (1898:48): [True: 62.7k, False: 621k] ------------------ 1899| 62.7k| at2[i].valence < at2[i].chem_bonds_valence && ------------------ | Branch (1899:13): [True: 33.8k, False: 28.8k] ------------------ 1900| 33.8k| is_centerpoint_elem(at2[i].el_number)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1900:13): [True: 29.1k, False: 4.75k] ------------------ 1901| 29.1k| { 1902| | 1903| 29.1k| is_centerpoint_N = (pVA[i].cNumValenceElectrons == 5 && (pVA[i].cPeriodicRowNumber == 1 || pVA[i].cMetal)); ------------------ | Branch (1903:33): [True: 24.5k, False: 4.62k] | Branch (1903:70): [True: 18.7k, False: 5.75k] | Branch (1903:104): [True: 347, False: 5.40k] ------------------ 1904| | /* look at the neighbors */ 1905| 29.1k| numMobileChargeNeigh = numDoubleBondAcceptors = numDoubleBondNotONeigh = num_donors = num_acceptors = 0; 1906| 29.1k| num_donors_O = num_acceptors_O = 0; 1907| 29.1k| num_known_endpoints = num_wrong_neigh = 0; 1908| 102k| for (j = 0; j < at2[i].valence; j++) /* djb-rwth: removing redundant code */ ------------------ | Branch (1908:25): [True: 74.0k, False: 28.7k] ------------------ 1909| 74.0k| { 1910| 74.0k| neigh = at2[i].neighbor[j]; 1911| 74.0k| if ((at2[neigh].endpoint || (pStruct->iMobileH == TAUT_NON && pStruct->endpoint && pStruct->endpoint[neigh])) || at2[neigh].charge > 0) /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 147k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1911:22): [True: 400, False: 73.6k] | Branch (1911:46): [True: 2.74k, False: 70.9k] | Branch (1911:79): [True: 2.74k, False: 0] | Branch (1911:100): [True: 472, False: 2.27k] | Branch (1911:130): [True: 9.43k, False: 63.7k] ------------------ 1912| 10.3k| { 1913| 10.3k| num_known_endpoints++; 1914| 10.3k| continue; 1915| 10.3k| } 1916| 63.7k| if (pBNS->edge[pBNS->vert[i].iedge[j]].forbidden & forbidden_edge_test) ------------------ | Branch (1916:21): [True: 2.19k, False: 61.5k] ------------------ 1917| 2.19k| { 1918| 2.19k| continue; 1919| 2.19k| } 1920| 61.5k| bond_type = at2[i].bond_type[j] & BOND_TYPE_MASK; ------------------ | | 189| 61.5k|#define BOND_TYPE_MASK 0x0f ------------------ 1921| 61.5k| if (bond_type > BOND_TYPE_DOUBLE) ------------------ | | 33| 61.5k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1921:21): [True: 3.27k, False: 58.3k] ------------------ 1922| 3.27k| { 1923| 3.27k| num_wrong_neigh++; 1924| 3.27k| continue; 1925| 3.27k| } 1926| 58.3k| if (at2[neigh].num_H && bond_type == BOND_TYPE_SINGLE) ------------------ | | 32| 575|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1926:21): [True: 575, False: 57.7k] | Branch (1926:41): [True: 417, False: 158] ------------------ 1927| 417| { 1928| 417| break; /* not this case */ 1929| 417| } 1930| 57.8k| if (at2[neigh].chem_bonds_valence - at2[neigh].charge ------------------ | Branch (1930:21): [True: 31.5k, False: 26.3k] ------------------ 1931| 57.8k| != get_endpoint_valence(at2[neigh].el_number)) 1932| 31.5k| { 1933| 31.5k| if (bond_type == BOND_TYPE_DOUBLE && pVA[neigh].cNumValenceElectrons != 6) ------------------ | | 33| 63.1k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1933:25): [True: 10.4k, False: 21.1k] | Branch (1933:58): [True: 9.15k, False: 1.28k] ------------------ 1934| 9.15k| { 1935| 9.15k| DoubleBondNotONeigh[numDoubleBondNotONeigh++] = j; 1936| 9.15k| } 1937| 31.5k| continue; 1938| 31.5k| } 1939| 26.3k| if (at2[neigh].charge == -1 && bond_type == BOND_TYPE_SINGLE && ------------------ | | 32| 32.9k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1939:21): [True: 6.62k, False: 19.7k] | Branch (1939:48): [True: 4.43k, False: 2.19k] ------------------ 1940| 4.43k| (pVA[neigh].nCMinusGroupEdge < 1 || pBNS->edge[pVA[neigh].nCMinusGroupEdge - 1].flow != 1)) ------------------ | Branch (1940:22): [True: 0, False: 4.43k] | Branch (1940:57): [True: 4, False: 4.43k] ------------------ 1941| 4| { 1942| 4| break; 1943| 4| } 1944| 26.3k| switch (bond_type) ------------------ | Branch (1944:25): [True: 25.6k, False: 648] ------------------ 1945| 26.3k| { 1946| 12.4k| case BOND_TYPE_SINGLE: ------------------ | | 32| 12.4k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1946:17): [True: 12.4k, False: 13.8k] ------------------ 1947| 12.4k| if (at2[neigh].charge != -1 || pVA[neigh].nCMinusGroupEdge <= 0) ------------------ | Branch (1947:25): [True: 8.03k, False: 4.43k] | Branch (1947:52): [True: 0, False: 4.43k] ------------------ 1948| 8.03k| { 1949| 8.03k| num_wrong_neigh++; 1950| 8.03k| continue; 1951| 8.03k| } 1952| 4.43k| num_donors++; 1953| 4.43k| num_donors_O += (pVA[neigh].cNumValenceElectrons == 6 && pVA[neigh].cPeriodicRowNumber <= 4); ------------------ | Branch (1953:38): [True: 3.56k, False: 868] | Branch (1953:78): [True: 3.56k, False: 0] ------------------ 1954| 4.43k| MobileChargeNeigh[numMobileChargeNeigh++] = j; 1955| 4.43k| break; 1956| 13.2k| case BOND_TYPE_DOUBLE: ------------------ | | 33| 13.2k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1956:17): [True: 13.2k, False: 13.1k] ------------------ 1957| 13.2k| if (at2[neigh].charge) ------------------ | Branch (1957:25): [True: 2.19k, False: 11.0k] ------------------ 1958| 2.19k| { 1959| 2.19k| num_wrong_neigh++; 1960| 2.19k| continue; 1961| 2.19k| } 1962| 11.0k| DoubleBondAcceptors[numDoubleBondAcceptors++] = j; 1963| 11.0k| num_acceptors++; 1964| 11.0k| num_acceptors_O += (pVA[neigh].cNumValenceElectrons == 6 && pVA[neigh].cPeriodicRowNumber <= 4); ------------------ | Branch (1964:41): [True: 3.62k, False: 7.39k] | Branch (1964:81): [True: 3.62k, False: 0] ------------------ 1965| 26.3k| } 1966| 26.3k| } 1967| 29.1k| if (j != at2[i].valence || !num_donors || !num_acceptors) ------------------ | Branch (1967:17): [True: 421, False: 28.7k] | Branch (1967:40): [True: 25.0k, False: 3.64k] | Branch (1967:55): [True: 1.43k, False: 2.21k] ------------------ 1968| 26.9k| { 1969| 26.9k| continue; 1970| 26.9k| } 1971| | /* special case NOn(-) */ 1972| 2.21k| if (is_centerpoint_N && (num_donors == num_donors_O) && (num_acceptors == num_acceptors_O)) ------------------ | Branch (1972:17): [True: 431, False: 1.78k] | Branch (1972:37): [True: 296, False: 135] | Branch (1972:69): [True: 142, False: 154] ------------------ 1973| 142| { 1974| 142| continue; 1975| 142| } 1976| 2.06k| if (pStruct->iMobileH == TAUT_NON && num_donors == numDoubleBondNotONeigh) ------------------ | | 574| 4.13k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1976:17): [True: 50, False: 2.01k] | Branch (1976:50): [True: 16, False: 34] ------------------ 1977| 16| { 1978| | /* fix all charges except on =O */ 1979| 16| Vertex vPathStart, vPathEnd; 1980| 16| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 1981| 16| int k, e, num_MovedCharges = 0; 1982| | 1983| 16| if (!ChargeListAllExcept_DB_O.num_edges) ------------------ | Branch (1983:21): [True: 16, False: 0] ------------------ 1984| 16| { 1985| | /* djb-rwth: removing redundant code */ 1986| 144| for (k = 0; k < num_at; k++) ------------------ | Branch (1986:33): [True: 128, False: 16] ------------------ 1987| 128| { 1988| 128| if (!((1 == at2[k].valence && pBNS->edge[pBNS->vert[k].iedge[0]].flow && ------------------ | Branch (1988:32): [True: 77, False: 51] | Branch (1988:55): [True: 52, False: 25] ------------------ 1989| 52| !pBNS->edge[pBNS->vert[k].iedge[0]].forbidden && ------------------ | Branch (1989:29): [True: 51, False: 1] ------------------ 1990| 51| !((e = pVA[k].nCMinusGroupEdge - 1) >= 0 && pBNS->edge[e].flow) && ------------------ | Branch (1990:31): [True: 46, False: 5] | Branch (1990:73): [True: 4, False: 42] ------------------ 1991| 47| !((e = pVA[k].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].flow) && ------------------ | Branch (1991:31): [True: 40, False: 7] | Branch (1991:72): [True: 4, False: 36] ------------------ 1992| | /* 0 == at2[k].charge && */ 1993| 43| pVA[k].cNumValenceElectrons == 6 && !pVA[k].cMetal && ------------------ | Branch (1993:29): [True: 23, False: 20] | Branch (1993:65): [True: 21, False: 2] ------------------ 1994| 21| (pStruct->endpoint && pStruct->endpoint[k])) || ------------------ | Branch (1994:30): [True: 21, False: 0] | Branch (1994:51): [True: 0, False: 21] ------------------ 1995| 128| (pStruct->fixed_H && pStruct->fixed_H[k]))) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1995:30): [True: 128, False: 0] | Branch (1995:50): [True: 23, False: 105] ------------------ 1996| | /* djb-rwth: removing redundant code */ 1997| 105| if ((e = pVA[k].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].flow && ------------------ | Branch (1997:33): [True: 74, False: 31] | Branch (1997:75): [True: 50, False: 24] ------------------ 1998| 50| !pBNS->edge[e].forbidden && ------------------ | Branch (1998:33): [True: 50, False: 0] ------------------ 1999| 50| (ret = AddToEdgeList(&ChargeListAllExcept_DB_O, e, 64))) ------------------ | Branch (1999:33): [True: 0, False: 50] ------------------ 2000| 0| { 2001| 0| goto exit_function; 2002| 0| } 2003| 128| if ((e = pVA[k].nCPlusGroupEdge - 1) >= 0 && ------------------ | Branch (2003:29): [True: 114, False: 14] ------------------ 2004| 114| !pBNS->edge[e].forbidden && ------------------ | Branch (2004:29): [True: 111, False: 3] ------------------ 2005| 111| (ret = AddToEdgeList(&ChargeListAllExcept_DB_O, e, 64))) ------------------ | Branch (2005:29): [True: 0, False: 111] ------------------ 2006| 0| { 2007| 0| goto exit_function; 2008| 0| } 2009| 128| } 2010| 16| } 2011| | /* fix double bonds to non-O neighbors connected by double bonds; 2012| | we will try to make these bons single */ 2013| 32| for (k = 0; k < numDoubleBondNotONeigh; k++) ------------------ | Branch (2013:29): [True: 16, False: 16] ------------------ 2014| 16| { 2015| 16| e = pBNS->vert[i].iedge[(int)DoubleBondNotONeigh[k]]; 2016| 16| if (!pBNS->edge[e].forbidden && ------------------ | Branch (2016:25): [True: 16, False: 0] ------------------ 2017| 16| (ret = AddToEdgeList(&ChargeListAllExcept_DB_O, e, 64))) ------------------ | Branch (2017:25): [True: 0, False: 16] ------------------ 2018| 0| { 2019| 0| goto exit_function; 2020| 0| } 2021| 16| } 2022| | /* attempt to make DoubleBondNotONeigh[] single */ 2023| 16| SetForbiddenEdgeMask(pBNS, &ChargeListAllExcept_DB_O, forbidden_edge_mask); 2024| 32| for (k = 0; k < numDoubleBondNotONeigh && num_MovedCharges < numMobileChargeNeigh; k++) ------------------ | Branch (2024:29): [True: 16, False: 16] | Branch (2024:59): [True: 16, False: 0] ------------------ 2025| 16| { 2026| 16| pe = pBNS->edge + pBNS->vert[i].iedge[(int)DoubleBondNotONeigh[k]]; 2027| 16| delta = 1; 2028| 16| if (pe->flow != delta) ------------------ | Branch (2028:25): [True: 1, False: 15] ------------------ 2029| 1| continue; 2030| 15| pv1m = pBNS->vert + (v1m = pe->neighbor1); 2031| 15| pv2m = pBNS->vert + (v2m = pe->neighbor12 ^ v1m); 2032| 15| pv1m->st_edge.flow -= delta; 2033| 15| pv2m->st_edge.flow -= delta; 2034| 15| pe->flow -= delta; 2035| 15| pBNS->tot_st_flow -= 2 * delta; 2036| 15| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2037| 15| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 2038| 15| if (ret < 0) ------------------ | Branch (2038:25): [True: 0, False: 15] ------------------ 2039| 0| { 2040| 0| goto exit_function; 2041| 0| } 2042| 15| if (ret == 1 && ((vPathEnd == v1m && vPathStart == v2m) || ------------------ | Branch (2042:25): [True: 8, False: 7] | Branch (2042:39): [True: 0, False: 8] | Branch (2042:58): [True: 0, False: 0] ------------------ 2043| 8| (vPathEnd == v2m && vPathStart == v1m)) && ------------------ | Branch (2043:26): [True: 7, False: 1] | Branch (2043:45): [True: 6, False: 1] ------------------ 2044| 6| nDeltaCharge == 0 /* (-) moving from one to another atom*/) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2044:25): [True: 5, False: 1] ------------------ 2045| 5| { 2046| 5| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2047| 5| (*pnNumRunBNS)++; 2048| 5| if (ret < 0) ------------------ | Branch (2048:29): [True: 0, False: 5] ------------------ 2049| 0| { 2050| 0| goto exit_function; 2051| 0| } 2052| 5| else 2053| 5| { 2054| 5| if (ret == 1) ------------------ | Branch (2054:33): [True: 5, False: 0] ------------------ 2055| 5| { 2056| 5| *pnTotalDelta += ret; 2057| 5| num_MovedCharges++; 2058| 5| } 2059| 0| else 2060| 0| { 2061| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2062| 0| goto exit_function; 2063| 0| } 2064| 5| } 2065| 5| } 2066| 10| else 2067| 10| { 2068| | /* djb-rwth: removing redundant code */ 2069| 10| pv1m->st_edge.flow += delta; 2070| 10| pv2m->st_edge.flow += delta; 2071| 10| pe->flow += delta; 2072| 10| pBNS->tot_st_flow += 2 * delta; 2073| 10| } 2074| 15| } 2075| 16| RemoveForbiddenEdgeMask(pBNS, &ChargeListAllExcept_DB_O, forbidden_edge_mask); 2076| 16| } 2077| 2.05k| else 2078| 2.05k| { 2079| 2.05k| if (!bPossiblyIgnore || (!num_known_endpoints && !num_wrong_neigh && (num_acceptors_O + num_donors_O >= 3))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2079:21): [True: 14, False: 2.03k] | Branch (2079:42): [True: 1.08k, False: 958] | Branch (2079:66): [True: 803, False: 278] | Branch (2079:86): [True: 306, False: 497] ------------------ 2080| 320| { 2081| | /* remove negative charges from the neighbors */ 2082| 320| pBNS->vert[i].st_edge.cap += num_donors; /* enough to make all bonds to donors double */ 2083| 320| pBNS->tot_st_cap += num_donors; 2084| 320| pVA[i].cInitCharge -= num_donors; /* work no matter what are known charge/valence */ 2085| 899| for (j = 0; j < numMobileChargeNeigh; j++) ------------------ | Branch (2085:33): [True: 579, False: 320] ------------------ 2086| 579| { 2087| 579| neigh = at2[i].neighbor[(int)MobileChargeNeigh[j]]; 2088| 579| pEdgeMinus = pBNS->edge + ((long long)pVA[neigh].nCMinusGroupEdge - 1); /* djb-rwth: cast operator added */ 2089| 579| v1m = pEdgeMinus->neighbor1; 2090| 579| v2m = pEdgeMinus->neighbor12 ^ v1m; 2091| 579| pv1m = pBNS->vert + v1m; 2092| 579| pv2m = pBNS->vert + v2m; 2093| 579| delta = pEdgeMinus->flow; 2094| 579| pv1m->st_edge.flow -= delta; 2095| 579| pv2m->st_edge.flow -= delta; 2096| 579| if (IS_BNS_VT_C_GR(pv1m->type)) ------------------ | | 78| 579|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 579|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 579|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 579|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 579|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 0, False: 579] | | ------------------ ------------------ 2097| 0| { 2098| | /* irreversible change to ChargeStruct */ 2099| 0| pv1m->st_edge.cap -= delta; 2100| 0| } 2101| 579| else 2102| 579| { 2103| 579| if (IS_BNS_VT_C_GR(pv2m->type)) ------------------ | | 78| 579|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 71| 579|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 50| 579|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 49| 579|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 49| 579|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (78:37): [True: 579, False: 0] | | ------------------ ------------------ 2104| 579| { 2105| | /* irreversible change to ChargeStruct */ 2106| 579| pv2m->st_edge.cap -= delta; 2107| 579| } 2108| 0| else 2109| 0| { 2110| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2111| 0| goto exit_function; 2112| 0| } 2113| 579| } 2114| 579| pBNS->tot_st_cap -= delta; 2115| 579| pBNS->tot_st_flow -= 2 * delta; 2116| 579| pEdgeMinus->flow -= delta; 2117| 579| } 2118| 320| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2119| 320| (*pnNumRunBNS)++; 2120| 320| if (ret < 0) ------------------ | Branch (2120:25): [True: 0, False: 320] ------------------ 2121| 0| { 2122| 0| goto exit_function; 2123| 0| } 2124| 320| else 2125| 320| if (ret == num_donors) ------------------ | Branch (2125:29): [True: 320, False: 0] ------------------ 2126| 320| { 2127| 320| *pnTotalDelta += ret; 2128| 320| num_success++; 2129| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 2130| 320| } 2131| 0| else 2132| 0| { 2133| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2134| 0| goto exit_function; 2135| 0| } 2136| 320| } 2137| 2.05k| } 2138| 2.06k| } 2139| 832k| } 2140| 87.7k| if (ret_forbid_edges) ------------------ | Branch (2140:9): [True: 1.83k, False: 85.9k] ------------------ 2141| 1.83k| { 2142| | /* remove the marks */ 2143| 1.83k| RemoveForbiddenBondFlowBits(pBNS, forbidden_edge_test); 2144| 1.83k| } 2145| 87.7k| ret = num_success; 2146| | 2147| 87.7k|exit_function: 2148| | 2149| 87.7k| AllocEdgeList(&ChargeListAllExcept_DB_O, EDGE_LIST_FREE); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 2150| | 2151| 87.7k| return ret; 2152| 87.7k|} MakeSingleBondsMetal2ChargedHeteroat: 2169| 87.7k|{ 2170| 87.7k| int i; 2171| | 2172| 87.7k| int ret2, ret, pass; 2173| 87.7k| int num_at = pStruct->num_atoms; 2174| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 2175| 87.7k| int len_at = num_at + num_deleted_H; 2176| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 2177| | 2178| 87.7k| int j, k; 2179| 87.7k| int cur_num_edges; 2180| 87.7k| BNS_EDGE* e; 2181| 87.7k| Vertex v1, v2; 2182| | 2183| 87.7k| EdgeIndex* pFixedEdges; 2184| 87.7k| int nNumEdgesToFix; 2185| | 2186| 87.7k| ret = 0; 2187| | 2188| | /* to simplify, prepare new at[] from pBNS */ 2189| 87.7k| memcpy(at2, at, len_at * sizeof(at2[0])); 2190| 87.7k| pStruct->at = at2; 2191| 87.7k| ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2192| 87.7k| pStruct->at = at; 2193| 87.7k| if (ret2 < 0) ------------------ | Branch (2193:9): [True: 0, False: 87.7k] ------------------ 2194| 0| { 2195| 0| ret = ret2; 2196| 0| goto exit_function; 2197| 0| } 2198| | 2199| 87.7k| pFixedEdges = NULL; 2200| | 2201| 87.7k| nNumEdgesToFix = 0; /* cpunt nNumEdgesToFix only when pass==0 */ 2202| 87.7k| cur_num_edges = 0; /* count cur_num_edges only when pass==1; at the end they must be equal */ 2203| 176k| for (pass = 0; pass < 2; pass++) ------------------ | Branch (2203:20): [True: 175k, False: 969] ------------------ 2204| 175k| { 2205| 175k| if (pass) ------------------ | Branch (2205:13): [True: 87.7k, False: 87.7k] ------------------ 2206| 87.7k| { 2207| | /* 2nd pass: allocate edge storage */ 2208| 87.7k| if (!nNumEdgesToFix) ------------------ | Branch (2208:17): [True: 86.8k, False: 969] ------------------ 2209| 86.8k| { 2210| 86.8k| break; /* nothing to do */ 2211| 86.8k| } 2212| 969| pFixedEdges = (EdgeIndex*)inchi_malloc(nNumEdgesToFix * sizeof(pFixedEdges[0])); ------------------ | | 1143| 969|#define inchi_malloc malloc ------------------ 2213| 969| if (!pFixedEdges) ------------------ | Branch (2213:17): [True: 0, False: 969] ------------------ 2214| 0| { 2215| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2216| 0| goto exit_function; 2217| 0| } 2218| 969| } 2219| 927k| for (i = 0; i < num_at; i++) ------------------ | Branch (2219:21): [True: 838k, False: 88.7k] ------------------ 2220| 838k| { 2221| 838k| int neigh; 2222| 838k| if (pVA[i].cMetal) ------------------ | Branch (2222:17): [True: 320k, False: 517k] ------------------ 2223| 320k| { 2224| 366k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (2224:29): [True: 46.0k, False: 320k] ------------------ 2225| 46.0k| { 2226| 46.0k| neigh = at2[i].neighbor[j]; 2227| 46.0k| if (pVA[neigh].cNumValenceElectrons == 4 && ------------------ | Branch (2227:25): [True: 6.71k, False: 39.3k] ------------------ 2228| 6.71k| pVA[neigh].cPeriodicRowNumber == 1) ------------------ | Branch (2228:25): [True: 6.19k, False: 515] ------------------ 2229| 6.19k| { 2230| 6.19k| continue; /* ignore carbon */ 2231| 6.19k| } 2232| 39.8k| if (at2[i].bond_type[j] > BOND_TYPE_SINGLE && at2[neigh].charge && ------------------ | | 32| 79.7k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2232:25): [True: 8.43k, False: 31.4k] | Branch (2232:67): [True: 2.92k, False: 5.51k] ------------------ 2233| 2.92k| !pVA[neigh].cMetal && pVA[neigh].cnListIndex > 0) ------------------ | Branch (2233:25): [True: 2.90k, False: 17] | Branch (2233:47): [True: 2.90k, False: 2] ------------------ 2234| 2.90k| { 2235| 2.90k| int cnBits = at2[neigh].charge > 0 ? MAKE_CN_BITS(cn_bits_N, cn_bits_P, 0, 0) : ------------------ | | 421| 2.68k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 2.68k|#define cn_bits_shift 3 | | ------------------ | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 2.68k|#define cn_bits_shift 3 | | ------------------ | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 2.68k|#define cn_bits_shift 3 | | ------------------ ------------------ | Branch (2235:38): [True: 2.68k, False: 222] ------------------ 2236| 2.90k| MAKE_CN_BITS(cn_bits_N, cn_bits_M, 0, 0); ------------------ | | 421| 222|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 222|#define cn_bits_shift 3 | | ------------------ | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 222|#define cn_bits_shift 3 | | ------------------ | | #define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 419| 222|#define cn_bits_shift 3 | | ------------------ ------------------ 2237| 2.90k| int atBits = cnList[pVA[neigh].cnListIndex - 1].bits; 2238| 5.70k| for (k = 0; k < MAX_NUM_CN_BITS - 1; k++, atBits >>= cn_bits_shift) ------------------ | | 420| 5.70k|#define MAX_NUM_CN_BITS 4 ------------------ for (k = 0; k < MAX_NUM_CN_BITS - 1; k++, atBits >>= cn_bits_shift) ------------------ | | 419| 2.80k|#define cn_bits_shift 3 ------------------ | Branch (2238:37): [True: 5.25k, False: 452] ------------------ 2239| 5.25k| { 2240| | /* ??? */ 2241| 5.25k| if ((atBits & cnBits) == cnBits) ------------------ | Branch (2241:33): [True: 2.45k, False: 2.80k] ------------------ 2242| 2.45k| { 2243| 2.45k| break; 2244| 2.45k| } 2245| 5.25k| } 2246| 2.90k| if (k == MAX_NUM_CN_BITS - 1) ------------------ | | 420| 2.90k|#define MAX_NUM_CN_BITS 4 ------------------ | Branch (2246:29): [True: 452, False: 2.45k] ------------------ 2247| 452| { 2248| 452| continue; 2249| 452| } 2250| 2.45k| if (pass == 0) ------------------ | Branch (2250:29): [True: 1.22k, False: 1.22k] ------------------ 2251| 1.22k| { 2252| 1.22k| nNumEdgesToFix++; 2253| 1.22k| } 2254| 1.22k| else 2255| 1.22k| { 2256| 1.22k| pFixedEdges[cur_num_edges++] = pBNS->vert[i].iedge[j]; 2257| 1.22k| } 2258| 2.45k| } 2259| 39.8k| } 2260| 320k| } 2261| 838k| } 2262| 88.7k| } 2263| | 2264| | /* restore the initial structures */ 2265| 87.7k| memcpy(at2, at, ((long long)num_at + (long long)num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */ 2266| | 2267| 87.7k| if (nNumEdgesToFix && pFixedEdges) ------------------ | Branch (2267:9): [True: 969, False: 86.8k] | Branch (2267:27): [True: 969, False: 0] ------------------ 2268| 969| { 2269| 969| if (nNumEdgesToFix != cur_num_edges) ------------------ | Branch (2269:13): [True: 0, False: 969] ------------------ 2270| 0| { 2271| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2272| 0| goto pre_exit_function; /* djb-rwth: fixing coverity ID #499637 */ 2273| 0| } 2274| | /* change edge flow, fix the edges, and run BNS */ 2275| 2.19k| for (i = 0; i < nNumEdgesToFix; i++) ------------------ | Branch (2275:21): [True: 1.22k, False: 969] ------------------ 2276| 1.22k| { 2277| 1.22k| e = pBNS->edge + pFixedEdges[i]; 2278| 1.22k| v1 = e->neighbor1; 2279| 1.22k| v2 = e->neighbor12 ^ v1; 2280| 1.22k| e->flow--; 2281| 1.22k| e->forbidden |= forbidden_edge_mask; 2282| 1.22k| pBNS->vert[v1].st_edge.flow--; 2283| 1.22k| pBNS->vert[v2].st_edge.flow--; 2284| 1.22k| pBNS->tot_st_flow -= 2; 2285| 1.22k| (*pnTotalDelta) -= 2; 2286| 1.22k| } 2287| | /* Run BNS allowing to change any charges */ 2288| 969| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2289| 969| (*pnNumRunBNS)++; 2290| 969| if (ret < 0) ------------------ | Branch (2290:13): [True: 0, False: 969] ------------------ 2291| 0| { 2292| 0| goto pre_exit_function; /* djb-rwth: fixing coverity ID #499637 */ 2293| 0| } 2294| 969| else 2295| 969| { 2296| 969| (*pnTotalDelta) += ret; 2297| 969| } 2298| | /* unfix the edges */ 2299| 2.19k| for (i = 0; i < nNumEdgesToFix; i++) ------------------ | Branch (2299:21): [True: 1.22k, False: 969] ------------------ 2300| 1.22k| { 2301| 1.22k| e = pBNS->edge + pFixedEdges[i]; 2302| 1.22k| e->forbidden &= inv_forbidden_edge_mask; 2303| 1.22k| } 2304| 969| if (ret < 2 * nNumEdgesToFix) ------------------ | Branch (2304:13): [True: 968, False: 1] ------------------ 2305| 968| { 2306| | /* not all fixes succeeded */ 2307| 968| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2308| 968| (*pnNumRunBNS)++; 2309| 968| if (ret < 0) ------------------ | Branch (2309:17): [True: 0, False: 968] ------------------ 2310| 0| { 2311| 0| goto pre_exit_function; /* djb-rwth: fixing coverity ID #499637 */ 2312| 0| } 2313| 968| else 2314| 968| { 2315| 968| (*pnTotalDelta) += ret; 2316| 968| } 2317| 968| } 2318| 969| } 2319| | 2320| 87.7k|pre_exit_function: 2321| 87.7k| if (pFixedEdges) ------------------ | Branch (2321:9): [True: 969, False: 86.8k] ------------------ 2322| 969| { 2323| 969| inchi_free(pFixedEdges); ------------------ | | 1152| 969|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 969, False: 0] | | | Branch (1152:50): [Folded, False: 969] | | ------------------ ------------------ 2324| 969| pFixedEdges = NULL; 2325| 969| } 2326| | 2327| 87.7k|exit_function: 2328| 87.7k| return ret; 2329| 87.7k|} SaltBondsToCoordBonds: 2348| 87.7k|{ 2349| 87.7k| int i; 2350| | 2351| 87.7k| int ret2, ret, cur_success; 2352| 87.7k| int num_at = pStruct->num_atoms; 2353| 87.7k| int num_edges = pBNS->num_bonds + 2 * pBNS->num_atoms; 2354| 87.7k| int num_deleted_H = pStruct->num_deleted_H; 2355| 87.7k| int len_at = num_at + num_deleted_H; 2356| 87.7k| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 2357| 87.7k| EDGE_LIST AllChargeEdges; 2358| | 2359| 87.7k| int j, k, n; 2360| 87.7k| BNS_EDGE* pe, * pePlusMetal, * peMinusO; 2361| 87.7k| BNS_VERTEX* pv1, * pv2, * pvO, * pvM; 2362| 87.7k| Vertex v1, v2, vPlusMinus; 2363| | 2364| 87.7k| EdgeIndex ie, iePlusMetal, ieMinusO; 2365| | 2366| 87.7k| Vertex vPathStart, vPathEnd; 2367| 87.7k| int delta, nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 2368| | 2369| 87.7k| ret = 0; 2370| 87.7k| cur_success = 0; 2371| 87.7k| AllocEdgeList(&AllChargeEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 87.7k|#define EDGE_LIST_CLEAR (-1) ------------------ 2372| | 2373| 87.7k| if (pStruct->iInchiRec == INCHI_BAS || !pStruct->pSrm->bMetalAddFlower || pStruct->pSrm->nMetalMinBondOrder) ------------------ | | 570| 175k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (2373:9): [True: 87.7k, False: 8] | Branch (2373:44): [True: 0, False: 8] | Branch (2373:79): [True: 0, False: 8] ------------------ 2374| 87.7k| { 2375| 87.7k| goto exit_function; 2376| 87.7k| } 2377| | 2378| | /* to simplify, prepare new at[] from pBNS */ 2379| 8| memcpy(at2, at, len_at * sizeof(at2[0])); 2380| 8| pStruct->at = at2; 2381| 8| ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2382| 8| pStruct->at = at; 2383| 8| if (ret2 < 0) ------------------ | Branch (2383:9): [True: 0, False: 8] ------------------ 2384| 0| { 2385| 0| ret = ret2; 2386| 0| goto exit_function; 2387| 0| } 2388| 30| for (i = 0; i < num_at; i++) ------------------ | Branch (2388:17): [True: 22, False: 8] ------------------ 2389| 22| { 2390| 22| if (bIsMetalSalt(at2, i)) ------------------ | Branch (2390:13): [True: 0, False: 22] ------------------ 2391| 0| { 2392| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (2392:17): [True: 0, False: 0] ------------------ 2393| 0| { 2394| | /*--------- one-time action: fix all bonds, charges, taut. group edges ------------*/ 2395| 0| for (j = 0; j < num_at; j++) ------------------ | Branch (2395:29): [True: 0, False: 0] ------------------ 2396| 0| { 2397| | /* all bonds */ 2398| 0| for (k = 0; k < at2[j].valence; k++) ------------------ | Branch (2398:33): [True: 0, False: 0] ------------------ 2399| 0| { 2400| 0| n = at2[j].neighbor[k]; 2401| 0| if (n < j && !pBNS->edge[ie = pBNS->vert[j].iedge[k]].forbidden && ------------------ | Branch (2401:29): [True: 0, False: 0] | Branch (2401:38): [True: 0, False: 0] ------------------ 2402| 0| (ret = AddToEdgeList(&AllChargeEdges, ie, num_edges))) ------------------ | Branch (2402:29): [True: 0, False: 0] ------------------ 2403| 0| { 2404| 0| goto exit_function; 2405| 0| } 2406| 0| } 2407| | /* charge edges */ 2408| 0| if ((ie = pVA[j].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[ie].forbidden && ------------------ | Branch (2408:25): [True: 0, False: 0] | Branch (2408:68): [True: 0, False: 0] ------------------ 2409| 0| (ret = AddToEdgeList(&AllChargeEdges, ie, num_edges))) ------------------ | Branch (2409:25): [True: 0, False: 0] ------------------ 2410| 0| { 2411| 0| goto exit_function; 2412| 0| } 2413| 0| if ((ie = pVA[j].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[ie].forbidden && ------------------ | Branch (2413:25): [True: 0, False: 0] | Branch (2413:67): [True: 0, False: 0] ------------------ 2414| 0| (ret = AddToEdgeList(&AllChargeEdges, ie, num_edges))) ------------------ | Branch (2414:25): [True: 0, False: 0] ------------------ 2415| 0| { 2416| 0| goto exit_function; 2417| 0| } 2418| 0| } 2419| | /* taut group edges */ 2420| 0| for (j = 0; j < pTCGroups->num_tgroups; j++) ------------------ | Branch (2420:29): [True: 0, False: 0] ------------------ 2421| 0| { 2422| 0| pv1 = pBNS->vert + (v1 = pTCGroups->pTCG[j].nVertexNumber); /* t-group vertex */ /* djb-rwth: ignoring LLVM warning: see comment below */ 2423| 0| for (k = 0; k < pv1->num_adj_edges; k++) ------------------ | Branch (2423:33): [True: 0, False: 0] ------------------ 2424| 0| { 2425| | /* ie, pe - tautomeric atom edge; pv2 - endpoint vertex */ 2426| | /* Note: pe, pv2, v1 are not used here; they are to show how to traverse t-group */ 2427| 0| pv2 = pBNS->vert + (pe = pBNS->edge + (ie = pv1->iedge[k]))->neighbor1; /* djb-rwth: ignoring LLVM warning: see comment above */ 2428| 0| if ((ret = AddToEdgeList(&AllChargeEdges, ie, num_edges))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2428:29): [True: 0, False: 0] ------------------ 2429| 0| { 2430| 0| goto exit_function; 2431| 0| } 2432| 0| } 2433| 0| } 2434| | /*---------------------------------------------------------------*/ 2435| 0| } 2436| | /* replace all single bonds to neutral neighbors with zero-order bonds 2437| | allow neighbor charge change to (-1) and metal atom charge increment +1 */ 2438| 0| for (k = 0; k < at2[i].valence; k++) ------------------ | Branch (2438:25): [True: 0, False: 0] ------------------ 2439| 0| { 2440| 0| n = at2[i].neighbor[k]; 2441| 0| pe = pBNS->edge + pBNS->vert[i].iedge[k]; 2442| 0| if (at2[n].charge || at2[i].bond_type[k] != BOND_TYPE_SINGLE) ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2442:21): [True: 0, False: 0] | Branch (2442:38): [True: 0, False: 0] ------------------ 2443| 0| { 2444| 0| continue; 2445| 0| } 2446| 0| iePlusMetal = pVA[i].nCPlusGroupEdge - 1; 2447| 0| ieMinusO = pVA[n].nCMinusGroupEdge - 1; 2448| | 2449| 0| if (pe->flow != 1 || pe->forbidden || iePlusMetal < 0) ------------------ | Branch (2449:21): [True: 0, False: 0] | Branch (2449:38): [True: 0, False: 0] | Branch (2449:55): [True: 0, False: 0] ------------------ 2450| 0| { 2451| 0| continue; 2452| 0| } 2453| 0| pePlusMetal = pBNS->edge + iePlusMetal; 2454| 0| if (pePlusMetal->flow <= 0) ------------------ | Branch (2454:21): [True: 0, False: 0] ------------------ 2455| 0| { 2456| 0| continue; /* to add (+) to metal this flow must be decremented */ 2457| 0| } 2458| 0| if (ieMinusO >= 0) ------------------ | Branch (2458:21): [True: 0, False: 0] ------------------ 2459| 0| { 2460| | /* usually does not happen */ 2461| 0| peMinusO = pBNS->edge + ieMinusO; 2462| | 2463| 0| if (peMinusO->flow || pePlusMetal->forbidden || peMinusO->forbidden) ------------------ | Branch (2463:25): [True: 0, False: 0] | Branch (2463:43): [True: 0, False: 0] | Branch (2463:69): [True: 0, False: 0] ------------------ 2464| 0| { 2465| 0| continue; 2466| 0| } 2467| | 2468| | /* decrement bond order to 0 */ 2469| 0| delta = 1; 2470| 0| pv1 = pBNS->vert + (v1 = pe->neighbor1); 2471| 0| pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); 2472| | 2473| 0| pe->flow -= delta; 2474| 0| pv1->st_edge.flow -= delta; 2475| 0| pv2->st_edge.flow -= delta; 2476| 0| pBNS->tot_st_flow -= 2 * delta; 2477| | 2478| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2479| 0| pePlusMetal->forbidden &= inv_forbidden_edge_mask; 2480| 0| peMinusO->forbidden &= inv_forbidden_edge_mask; 2481| | 2482| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2483| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 2484| | 2485| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2485:25): [True: 0, False: 0] | Branch (2485:39): [True: 0, False: 0] | Branch (2485:57): [True: 0, False: 0] ------------------ 2486| 0| (vPathEnd == v2 && vPathStart == v1)) /*&& nDeltaCharge > 0*/) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2486:26): [True: 0, False: 0] | Branch (2486:44): [True: 0, False: 0] ------------------ 2487| 0| { 2488| | /* (+)charge was just moved, no change in number of charges */ 2489| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2490| 0| if (ret > 0) ------------------ | Branch (2490:29): [True: 0, False: 0] ------------------ 2491| 0| { 2492| 0| (*pnNumRunBNS)++; 2493| 0| cur_success++; /* 01 */ 2494| 0| } 2495| 0| } 2496| 0| else 2497| 0| { 2498| 0| pe->flow += delta; /* roll back */ 2499| 0| pv1->st_edge.flow += delta; 2500| 0| pv2->st_edge.flow += delta; 2501| 0| pBNS->tot_st_flow += 2 * delta; 2502| 0| } 2503| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2504| 0| } 2505| 0| else 2506| 0| { 2507| 0| if (NO_VERTEX != (vPlusMinus = GetPlusMinusVertex(pBNS, pTCGroups, 1, 1))) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (2507:25): [True: 0, False: 0] ------------------ 2508| 0| { 2509| | /* manually add (-) charge to O and (+) charge to metal */ 2510| | /* decrement bond order to 0 */ 2511| | /*---------------------------------------------------------------------------*/ 2512| | /* */ 2513| | /* (+/-)* (+/-) Result: */ 2514| | /* | || */ 2515| | /* | || - Added (+) to M */ 2516| | /* (+)super (+)super - Incremented bond M-O */ 2517| | /* || | */ 2518| | /* || => | To make this attachment H, */ 2519| | /* (Y) (Y) increment */ 2520| | /* | || pTCGroups->pTCG[itg].tg_num_H */ 2521| | /* | || */ 2522| | /* (+)metal (+)hetero Technical details: */ 2523| | /* \\ \ increase capacities of */ 2524| | /* M M(+) edges to (+/-) otherwise */ 2525| | /* | || flow may not be able to */ 2526| | /* -O* -O-O increase */ 2527| | /* */ 2528| | /* After that change M=O bond order from 2 to 0 */ 2529| | /*---------------------------------------------------------------------------*/ 2530| 0| int i1, j1, k1; 2531| 0| delta = 1; 2532| 0| pvO = pBNS->vert + n; 2533| 0| pvM = pBNS->vert + i; 2534| | /* Increment st_edge.cap on (+/-) vertex */ 2535| 0| pBNS->vert[vPlusMinus].st_edge.cap += delta; 2536| | /* Increment st_edge.cap on O */ 2537| 0| pvO->st_edge.cap += delta; 2538| | /* increment cap on M-O edge */ 2539| 0| pe->cap += delta; 2540| | /* total cap count */ 2541| 0| pBNS->tot_st_cap += 2 * delta; 2542| | 2543| 0| v1 = vPlusMinus; 2544| 0| v2 = n; /* atom O */ 2545| | 2546| | /* increase capacities of edges to Y */ 2547| 0| for (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++) ------------------ | Branch (2547:38): [True: 0, False: 0] ------------------ 2548| 0| { 2549| 0| j1 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus; 2550| 0| for (k1 = 0; k1 < pBNS->vert[j1].num_adj_edges; k1++) ------------------ | Branch (2550:42): [True: 0, False: 0] ------------------ 2551| 0| { 2552| 0| pBNS->edge[pBNS->vert[j1].iedge[k1]].cap += delta; 2553| 0| } 2554| 0| } 2555| 0| SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2556| 0| pePlusMetal->forbidden &= inv_forbidden_edge_mask; 2557| 0| pe->forbidden &= inv_forbidden_edge_mask; 2558| | 2559| 0| ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2560| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms); 2561| 0| cur_success = 0; 2562| 0| if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (2562:29): [True: 0, False: 0] | Branch (2562:43): [True: 0, False: 0] | Branch (2562:61): [True: 0, False: 0] ------------------ 2563| 0| (vPathEnd == v2 && vPathStart == v1)) /*&& nDeltaCharge == 1*/) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2563:30): [True: 0, False: 0] | Branch (2563:48): [True: 0, False: 0] ------------------ 2564| 0| { 2565| | /* Added (+)charge to -N< => nDeltaCharge == 1 */ 2566| | /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */ 2567| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2568| 0| if (ret > 0) ------------------ | Branch (2568:33): [True: 0, False: 0] ------------------ 2569| 0| { 2570| 0| (*pnNumRunBNS)++; 2571| 0| cur_success++; /* 01 */ 2572| 0| } 2573| 0| } 2574| 0| if (cur_success) ------------------ | Branch (2574:29): [True: 0, False: 0] ------------------ 2575| 0| { 2576| | /* set bond M=O order = 0 */ 2577| 0| if (pe->flow != 2 * delta) ------------------ | Branch (2577:33): [True: 0, False: 0] ------------------ 2578| 0| { 2579| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 2580| 0| goto exit_function; 2581| 0| } 2582| | /* reduce pe bond order by 2*delta */ 2583| 0| pe->flow -= 2 * delta; 2584| 0| pvO->st_edge.cap -= 2 * delta; 2585| 0| pvO->st_edge.flow -= 2 * delta; 2586| 0| pvM->st_edge.flow -= 2 * delta; 2587| 0| pvM->st_edge.cap -= 2 * delta; 2588| 0| pBNS->tot_st_cap -= 3 * delta; 2589| 0| pBNS->tot_st_flow -= 4 * delta; 2590| | /* fix M-O bond order to zero */ 2591| 0| pe->cap -= 2 * delta; 2592| | /* add fixed (-) charge to O */ 2593| 0| pVA[n].cInitCharge -= delta; 2594| 0| } 2595| 0| else 2596| 0| { 2597| | /* failed */ 2598| 0| pBNS->vert[vPlusMinus].st_edge.cap -= delta; 2599| 0| pvO->st_edge.cap -= delta; 2600| | /*pTCGroups->pTCG[itg].edges_cap -= delta;*/ /* ???bug??? - commented out 2006-03-22 */ 2601| 0| pBNS->tot_st_cap -= 2 * delta; 2602| | /* decrease capacities of edges to Y */ 2603| 0| for (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++) ------------------ | Branch (2603:42): [True: 0, False: 0] ------------------ 2604| 0| { 2605| 0| j1 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus; 2606| 0| for (k1 = 0; k1 < pBNS->vert[j1].num_adj_edges; k1++) ------------------ | Branch (2606:46): [True: 0, False: 0] ------------------ 2607| 0| { 2608| 0| pBNS->edge[pBNS->vert[j1].iedge[k1]].cap -= delta; 2609| 0| } 2610| 0| } 2611| 0| } 2612| 0| RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask); 2613| 0| } 2614| 0| } 2615| 0| } 2616| 0| } 2617| 22| } 2618| | 2619| 87.7k|exit_function: 2620| | 2621| 87.7k| AllocEdgeList(&AllChargeEdges, EDGE_LIST_FREE); ------------------ | | 243| 87.7k|#define EDGE_LIST_FREE (-2) ------------------ 2622| | 2623| 87.7k| return ret; 2624| 8|} RunBnsRestore1: 2717| 87.8k|{ 2718| 87.8k| int nNumRunBNS = 0; 2719| | 2720| 87.8k| EDGE_LIST CarbonChargeEdges, MetalCarbonEdges, Nplus2BondsEdges; 2721| | 2722| 87.8k| int nTotalDelta = 0, ret = 0; /* djb-rwth: removing redundant variables */ 2723| 87.8k| inp_ATOM* at = pStruct->at; 2724| 87.8k| inp_ATOM* at2 = NULL; /* restored structure */ 2725| 87.8k| inp_ATOM* at3 = NULL; /* structure for calculating one InChI */ 2726| 87.8k| int num_at = pStruct->num_atoms; 2727| 87.8k| int num_deleted_H = pStruct->num_deleted_H; 2728| |#ifdef _DEBUG 2729| | int ret2; 2730| |#endif 2731| | 2732| |#if ( KEEP_METAL_EDGE_FLOW == 1 ) 2733| | BNS_VERTEX* pVert, * pNeigh; 2734| | int j, neigh; 2735| |#endif 2736| | 2737| | /* Edge lists initialization */ 2738| 87.8k| AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 87.8k|#define EDGE_LIST_CLEAR (-1) ------------------ 2739| 87.8k| AllocEdgeList(&MetalCarbonEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 87.8k|#define EDGE_LIST_CLEAR (-1) ------------------ 2740| 87.8k| AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_CLEAR); ------------------ | | 242| 87.8k|#define EDGE_LIST_CLEAR (-1) ------------------ 2741| | 2742| 87.8k| if (pStruct->iMobileH == TAUT_NON && ------------------ | | 574| 175k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2742:9): [True: 1.13k, False: 86.6k] ------------------ 2743| 1.13k| (ret = FillOutExtraFixedHDataInChI(pStruct, pInChI))) ------------------ | Branch (2743:9): [True: 0, False: 1.13k] ------------------ 2744| 0| { 2745| 0| goto exit_function; 2746| 0| } 2747| | 2748| 87.8k| if ((!at2 && !(at2 = (inp_ATOM*)inchi_malloc(((long long)num_at + (long long)num_deleted_H) * sizeof(at2[0])))) || ------------------ | | 1143| 87.8k|#define inchi_malloc malloc ------------------ | Branch (2748:10): [True: 87.8k, False: 0] | Branch (2748:18): [True: 0, False: 87.8k] ------------------ 2749| 87.8k| (!at3 && !(at3 = (inp_ATOM*)inchi_malloc(((long long)num_at + (long long)num_deleted_H) * sizeof(at3[0]))))) /* djb-rwth: cast operators added; addressing LLVM warning */ ------------------ | | 1143| 87.8k|#define inchi_malloc malloc ------------------ | Branch (2749:10): [True: 87.8k, False: 0] | Branch (2749:18): [True: 0, False: 87.8k] ------------------ 2750| 0| { 2751| 0| inchi_free(at2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2752| 0| inchi_free(at3); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2753| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2754| 0| } 2755| | 2756| 87.8k| if (0 > (ret = ForbidCarbonChargeEdges(pBNS, pTCGroups, &CarbonChargeEdges, BNS_EDGE_FORBIDDEN_TEMP))) ------------------ | | 40| 87.8k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ | Branch (2756:9): [True: 0, False: 87.8k] ------------------ 2757| 0| { 2758| 0| goto exit_function; 2759| 0| } 2760| | 2761| |#if ( KEEP_METAL_EDGE_FLOW == 1 ) 2762| | /* count edges of -C(IV)< carbons connected to metals */ 2763| | if (0 > (ret = ForbidMetalCarbonEdges(pBNS, at, num_at, pVA, pTCGroups, &MetalCarbonEdges, BNS_EDGE_FORBIDDEN_TEMP))) 2764| | { 2765| | goto exit_function; 2766| | } 2767| |#endif 2768| 87.8k| if (0 > (ret = ForbidNintrogenPlus2BondsInSmallRings(pBNS, at, num_at, pVA, 6, ------------------ | Branch (2768:9): [True: 0, False: 87.8k] ------------------ 2769| 87.8k| pTCGroups, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP))) ------------------ | | 40| 87.8k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2770| 0| { 2771| 0| goto exit_function; 2772| 0| } 2773| | 2774| | /*********** Run BNS #1: no charge on carbons and =N= ***************/ 2775| 87.8k| if (Nplus2BondsEdges.num_edges) ------------------ | Branch (2775:9): [True: 5.79k, False: 82.0k] ------------------ 2776| 5.79k| { 2777| | /* Run BNS leaving carbon charges unchanged */ 2778| 5.79k| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2779| 5.79k| nNumRunBNS++; 2780| 5.79k| if (ret < 0) ------------------ | Branch (2780:13): [True: 0, False: 5.79k] ------------------ 2781| 0| { 2782| 0| goto exit_function; 2783| 0| } 2784| 5.79k| else 2785| 5.79k| { 2786| 5.79k| nTotalDelta += ret; 2787| 5.79k| } 2788| 5.79k| RemoveForbiddenEdgeMask(pBNS, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 5.79k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2789| 5.79k| AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_FREE); ------------------ | | 243| 5.79k|#define EDGE_LIST_FREE (-2) ------------------ 2790| 5.79k| } 2791| |#ifdef _DEBUG 2792| | /* debug only */ 2793| | memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */ 2794| | pStruct->at = at2; 2795| | ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2796| | pStruct->at = at; 2797| |#endif 2798| | /*************************** extend min ring size to 8 ****************************/ 2799| 87.8k| if (0 > (ret = ForbidNintrogenPlus2BondsInSmallRings(pBNS, at, num_at, pVA, 8, ------------------ | Branch (2799:9): [True: 0, False: 87.8k] ------------------ 2800| 87.8k| pTCGroups, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP))) ------------------ | | 40| 87.8k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2801| 0| { 2802| 0| goto exit_function; 2803| 0| } 2804| 87.8k| if (Nplus2BondsEdges.num_edges) ------------------ | Branch (2804:9): [True: 6.04k, False: 81.7k] ------------------ 2805| 6.04k| { 2806| | /* Run BNS leaving carbon charges unchanged */ 2807| 6.04k| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2808| 6.04k| nNumRunBNS++; 2809| 6.04k| if (ret < 0) ------------------ | Branch (2809:13): [True: 0, False: 6.04k] ------------------ 2810| 0| { 2811| 0| goto exit_function; 2812| 0| } 2813| 6.04k| else 2814| 6.04k| { 2815| 6.04k| nTotalDelta += ret; 2816| 6.04k| } 2817| 6.04k| RemoveForbiddenEdgeMask(pBNS, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 6.04k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2818| 6.04k| AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_FREE); ------------------ | | 243| 6.04k|#define EDGE_LIST_FREE (-2) ------------------ 2819| 6.04k| } 2820| |#ifdef _DEBUG 2821| | /* debug only */ 2822| | memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */ 2823| | pStruct->at = at2; 2824| | ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2825| | pStruct->at = at; 2826| |#endif 2827| | /*******************************************************************/ 2828| 87.8k| if (CarbonChargeEdges.num_edges > 0) ------------------ | Branch (2828:9): [True: 19.2k, False: 68.5k] ------------------ 2829| 19.2k| { 2830| | /* Run BNS leaving carbon charges unchanged */ 2831| 19.2k| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2832| 19.2k| nNumRunBNS++; 2833| 19.2k| if (ret < 0) ------------------ | Branch (2833:13): [True: 0, False: 19.2k] ------------------ 2834| 0| { 2835| 0| goto exit_function; 2836| 0| } 2837| 19.2k| else 2838| 19.2k| { 2839| 19.2k| nTotalDelta += ret; 2840| 19.2k| } 2841| 19.2k| RemoveForbiddenEdgeMask(pBNS, &CarbonChargeEdges, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 19.2k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2842| 19.2k| AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_FREE); ------------------ | | 243| 19.2k|#define EDGE_LIST_FREE (-2) ------------------ 2843| 19.2k| } 2844| |#ifdef _DEBUG 2845| | /* debug only */ 2846| | memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */ 2847| | pStruct->at = at2; 2848| | ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2849| | pStruct->at = at; 2850| |#endif 2851| | /*******************************************************************/ 2852| 87.8k| if (MetalCarbonEdges.num_edges > 0) ------------------ | Branch (2852:9): [True: 0, False: 87.8k] ------------------ 2853| 0| { 2854| | /* Run BNS leaving carbon charges unchanged */ 2855| 0| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2856| 0| nNumRunBNS++; 2857| 0| if (ret < 0) ------------------ | Branch (2857:13): [True: 0, False: 0] ------------------ 2858| 0| { 2859| 0| goto exit_function; 2860| 0| } 2861| 0| else 2862| 0| { 2863| 0| nTotalDelta += ret; 2864| 0| } 2865| 0| RemoveForbiddenEdgeMask(pBNS, &MetalCarbonEdges, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 0|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2866| 0| AllocEdgeList(&MetalCarbonEdges, EDGE_LIST_FREE); ------------------ | | 243| 0|#define EDGE_LIST_FREE (-2) ------------------ 2867| 0| } 2868| | /*******************************************************************/ 2869| | /* Run BNS allowing to change any charges */ 2870| 87.8k| ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups); 2871| 87.8k| nNumRunBNS++; 2872| 87.8k| if (ret < 0) ------------------ | Branch (2872:9): [True: 0, False: 87.8k] ------------------ 2873| 0| { 2874| 0| goto exit_function; 2875| 0| } 2876| 87.8k| else 2877| 87.8k| { 2878| 87.8k| nTotalDelta += ret; 2879| 87.8k| } 2880| |#ifdef _DEBUG 2881| | /* debug only */ 2882| | memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */ 2883| | pStruct->at = at2; 2884| | ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2885| | pStruct->at = at; 2886| |#endif 2887| | 2888| 87.8k|#if ( BNS_RAD_SEARCH == 1 ) 2889| | /****************************************************************************/ 2890| | /* move unfulfilled 'radicals' from ChargeStruct to atoms */ 2891| | /* and set change charges of affected atoms to fit total charge */ 2892| 87.8k| ret = MoveRadToAtomsAddCharges(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.8k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2893| 87.8k| if (ret < 0) ------------------ | Branch (2893:9): [True: 16, False: 87.8k] ------------------ 2894| 16| { 2895| 16| goto exit_function; 2896| 16| } 2897| 87.8k|#endif 2898| | /**************************************************************/ 2899| | /**************************************************************/ 2900| | /***** fix restore inconsistencies *****/ 2901| | /**************************************************************/ 2902| | /**************************************************************/ 2903| |#ifdef _DEBUG 2904| | /* debug only */ 2905| | memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */ 2906| | pStruct->at = at2; 2907| | ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2908| | pStruct->at = at; 2909| |#endif 2910| | 2911| | /* rearrange (+) and (-) edges flow so that there is no (+)flow=0 and (-)flow=1 */ 2912| 87.8k| ret = RearrangePlusMinusEdgesFlow(pBNS, pBD, pVA, pTCGroups, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.8k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2913| 87.8k| if (ret < 0) ------------------ | Branch (2913:9): [True: 0, False: 87.8k] ------------------ 2914| 0| { 2915| 0| goto exit_function; 2916| 0| } 2917| | 2918| | /*****************************************************************/ 2919| | /* Increment zero order metal bonds to heteroatoms */ 2920| | /*****************************************************************/ 2921| 87.8k| ret = IncrementZeroOrderBondsToHeteroat(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2922| 87.8k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.8k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2923| 87.8k| if (ret < 0) ------------------ | Branch (2923:9): [True: 9, False: 87.7k] ------------------ 2924| 9| { 2925| 9| goto exit_function; 2926| 9| } 2927| | 2928| |#ifdef _DEBUG 2929| | /* debug only */ 2930| | memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */ 2931| | pStruct->at = at2; 2932| | ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 2933| | pStruct->at = at; 2934| |#endif 2935| | 2936| |#if (MOVE_CHARGES_FROM_HETEREO_TO_METAL == 1 ) 2937| | /*****************************************************************/ 2938| | /* move charges from heteroatoms to metal atoms */ 2939| | /*****************************************************************/ 2940| | ret = MoveChargeFromHeteroatomsToMetals(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2941| | &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); 2942| | if (ret < 0) 2943| | { 2944| | goto exit_function; 2945| | } 2946| |#endif 2947| | /*********************************************************************** 2948| | NH2 NH2 2949| | \ \ 2950| | C==S(+)- => C(+)-S- where NH2 are not tautomeric 2951| | / / 2952| | NH2 NH2 2953| | ************************************************************************/ 2954| 87.7k| ret = MovePlusFromS2DiaminoCarbon(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2955| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2956| 87.7k| if (ret < 0) ------------------ | Branch (2956:9): [True: 12, False: 87.7k] ------------------ 2957| 12| { 2958| 12| goto exit_function; 2959| 12| } 2960| | /*****************************************************************/ 2961| | /* Avoid charge separation on heteroatoms */ 2962| | /*****************************************************************/ 2963| 87.7k| ret = EliminateChargeSeparationOnHeteroatoms(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2964| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, 0); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2965| 87.7k| if (ret < 0) ------------------ | Branch (2965:9): [True: 0, False: 87.7k] ------------------ 2966| 0| { 2967| 0| goto exit_function; 2968| 0| } 2969| 87.7k| if (ret) ------------------ | Branch (2969:9): [True: 13.1k, False: 74.6k] ------------------ 2970| 13.1k| { 2971| | /*charge separation remains; allow changes of stereobonds in a ring and try again */ 2972| 13.1k| ret = EliminateChargeSeparationOnHeteroatoms(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2973| 13.1k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, ------------------ | | 40| 13.1k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2974| 13.1k| BNS_EDGE_FORBIDDEN_MASK); ------------------ | | 39| 13.1k|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 2975| 13.1k| if (ret < 0) ------------------ | Branch (2975:13): [True: 0, False: 13.1k] ------------------ 2976| 0| { 2977| 0| goto exit_function; 2978| 0| } 2979| 13.1k| } 2980| | /*****************************************************************/ 2981| | /* convert N#N(+)-N= into N(-)=N(+)=N- */ 2982| | /*****************************************************************/ 2983| 87.7k| ret = RestoreNNNgroup(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2984| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2985| 87.7k| if (ret < 0) ------------------ | Branch (2985:9): [True: 0, False: 87.7k] ------------------ 2986| 0| { 2987| 0| goto exit_function; 2988| 0| } 2989| | /*****************************************************************/ 2990| | /* convert Metal(q)-N(-)-O(-) Metal(q-2)-N=O (local change) */ 2991| | /*****************************************************************/ 2992| 87.7k| ret = FixMetal_Nminus_Ominus(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2993| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2994| 87.7k| if (ret < 0) ------------------ | Branch (2994:9): [True: 0, False: 87.7k] ------------------ 2995| 0| { 2996| 0| goto exit_function; 2997| 0| } 2998| | /*****************************************************************/ 2999| | /* convert N(-)=C= into N#C- - */ 3000| | /*****************************************************************/ 3001| 87.7k| ret = RestoreCyanoGroup(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3002| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3003| 87.7k| if (ret < 0) ------------------ | Branch (3003:9): [True: 0, False: 87.7k] ------------------ 3004| 0| { 3005| 0| goto exit_function; 3006| 0| } 3007| | /*****************************************************************/ 3008| | /* convert C(+)#N(+)- into C(-)#N(+)- */ 3009| | /*****************************************************************/ 3010| 87.7k| ret = RestoreIsoCyanoGroup(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3011| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3012| 87.7k| if (ret < 0) ------------------ | Branch (3012:9): [True: 0, False: 87.7k] ------------------ 3013| 0| { 3014| 0| goto exit_function; 3015| 0| } 3016| | /*****************************************************************/ 3017| | /* eliminate =N(V)= if possible */ 3018| | /* | */ 3019| | /*****************************************************************/ 3020| 87.7k| ret = EliminateNitrogen5Val3Bonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3021| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3022| 87.7k| if (ret < 0) ------------------ | Branch (3022:9): [True: 0, False: 87.7k] ------------------ 3023| 0| { 3024| 0| goto exit_function; 3025| 0| } 3026| | 3027| | /*****************************************************************/ 3028| | /* | | */ 3029| | /* convert -S- to =S= if possible */ 3030| | /* | | */ 3031| | /*****************************************************************/ 3032| 87.7k| ret = Convert_SIV_to_SVI(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3033| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3034| 87.7k| if (ret < 0) ------------------ | Branch (3034:9): [True: 0, False: 87.7k] ------------------ 3035| 0| { 3036| 0| goto exit_function; 3037| 0| } 3038| | 3039| | /*****************************************************************/ 3040| | /* =N(+)=O =N-O(-) */ 3041| | /* convert => if possible */ 3042| | /* Metal(q) Metal(q+2) */ 3043| | /*****************************************************************/ 3044| 87.7k| ret = PlusFromDB_N_DB_O_to_Metal(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3045| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3046| 87.7k| if (ret < 0) ------------------ | Branch (3046:9): [True: 0, False: 87.7k] ------------------ 3047| 0| { 3048| 0| goto exit_function; 3049| 0| } 3050| | 3051| | /*****************************************************************/ 3052| | /* forbidden edges prevents required in InChI tautomerism */ 3053| | /* incorrectly restored mobile H mix separate tautomeric groups */ 3054| | /* because an edge may not become forbidden */ 3055| | /* note: removes this 'forbidden_edge' bit from ALL edges */ 3056| | /*****************************************************************/ 3057| 87.7k| ret = MoveMobileHToAvoidFixedBonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3058| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3059| | 3060| 87.7k| if (ret < 0) ------------------ | Branch (3060:9): [True: 0, False: 87.7k] ------------------ 3061| 0| { 3062| 0| goto exit_function; 3063| 0| } 3064| | /**************************************************************************/ 3065| | /* 2. Mobile H endpoint has radical on it (typical for wrong P(VI)(=O)3OH */ 3066| | /* djb-rwth: removing redundant code */ 3067| 87.7k| if (pStruct->iMobileH == TAUT_NON) ------------------ | | 574| 87.7k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3067:9): [True: 1.13k, False: 86.6k] ------------------ 3068| 1.13k| { 3069| 1.13k| ret = RemoveRadFromMobileHEndpointFixH(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3070| 1.13k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 1.13k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3071| 1.13k| } 3072| 86.6k| else 3073| 86.6k| { 3074| 86.6k| ret = RemoveRadFromMobileHEndpoint(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3075| 86.6k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 86.6k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3076| 86.6k| } 3077| 87.7k| if (ret < 0) ------------------ | Branch (3077:9): [True: 0, False: 87.7k] ------------------ 3078| 0| { 3079| 0| goto exit_function; 3080| 0| } 3081| | /* djb-rwth: removing redundant code */ 3082| | /**************************************************************/ 3083| | /* make bonds between a charged heteroatom and a metal single */ 3084| 87.7k| ret = MakeSingleBondsMetal2ChargedHeteroat(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3085| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3086| 87.7k| if (ret < 0) ------------------ | Branch (3086:9): [True: 0, False: 87.7k] ------------------ 3087| 0| { 3088| 0| goto exit_function; 3089| 0| } 3090| | /**************************************************************/ 3091| | /* move (+) charges to >N- and other centerpoints */ 3092| 87.7k| ret = MoveChargeToMakeCenerpoints(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3093| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3094| 87.7k| if (ret < 0) ------------------ | Branch (3094:9): [True: 0, False: 87.7k] ------------------ 3095| 0| { 3096| 0| goto exit_function; 3097| 0| } 3098| | 3099| | /**************************************************************************/ 3100| | /* Find and eliminate false Mobile-H groups: Cl(=O)3(-O(-)) => Cl(-)(=O)4 */ 3101| 87.7k| ret = MoveChargeToRemoveCenerpoints(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3102| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3103| 87.7k| if (ret < 0) ------------------ | Branch (3103:9): [True: 0, False: 87.7k] ------------------ 3104| 0| { 3105| 0| goto exit_function; 3106| 0| } 3107| | /**************************************************************************/ 3108| | /* Find A=X< where all bonds to X except A=X are marked as stereogenic */ 3109| | /* make bonds A=X single */ 3110| 87.7k| ret = CheckAndRefixStereobonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3111| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3112| 87.7k| if (ret < 0) ------------------ | Branch (3112:9): [True: 0, False: 87.7k] ------------------ 3113| 0| { 3114| 0| goto exit_function; 3115| 0| } 3116| | /**************************************************************************/ 3117| | /* In Reconnected structure change 'salt bonds' to 'coordination bonds */ 3118| | /* for example, M-O-C= -> M(+)-O(-)-C= */ 3119| | /* Defect: instead of NH2-C=O(+)-M it will restore NH2(+)=C-O(-)-M(+) */ 3120| | /* However, in this release metal-organic compounds do not get much care */ 3121| 87.7k| ret = SaltBondsToCoordBonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3122| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3123| 87.7k| if (ret < 0) ------------------ | Branch (3123:9): [True: 0, False: 87.7k] ------------------ 3124| 0| { 3125| 0| goto exit_function; 3126| 0| } 3127| | /**************************************************************************/ 3128| | /* Normalize the structure and compare t-groups and stereobonds */ 3129| 87.7k| ret = NormalizeAndCompare(pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, pInChI, num_inp, bHasSomeFixedH, 3130| 87.7k| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, BNS_EDGE_FORBIDDEN_MASK); ------------------ | | 40| 87.7k|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, BNS_EDGE_FORBIDDEN_MASK); ------------------ | | 39| 87.7k|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 3131| 87.7k| if (ret < 0) ------------------ | Branch (3131:9): [True: 74.5k, False: 13.2k] ------------------ 3132| 74.5k| { 3133| 74.5k| goto exit_function; 3134| 74.5k| } 3135| | /**************************************************************************/ 3136| | /* Create InChI out of the restored structure */ 3137| | 3138| | 3139| | /*ret = nTotalDelta;*/ 3140| | 3141| 87.8k|exit_function: 3142| | 3143| 87.8k| pStruct->at = at; 3144| 87.8k| pStruct->at2 = at2; 3145| 87.8k| at2 = NULL; 3146| 87.8k| AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_FREE); ------------------ | | 243| 87.8k|#define EDGE_LIST_FREE (-2) ------------------ 3147| 87.8k| AllocEdgeList(&MetalCarbonEdges, EDGE_LIST_FREE); ------------------ | | 243| 87.8k|#define EDGE_LIST_FREE (-2) ------------------ 3148| 87.8k| AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_FREE); ------------------ | | 243| 87.8k|#define EDGE_LIST_FREE (-2) ------------------ 3149| 87.8k| if (at2) ------------------ | Branch (3149:9): [True: 0, False: 87.8k] ------------------ 3150| 0| { 3151| 0| inchi_free(at2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3152| 0| } 3153| 87.8k| if (at3) ------------------ | Branch (3153:9): [True: 87.8k, False: 0] ------------------ 3154| 87.8k| { 3155| 87.8k| inchi_free(at3); ------------------ | | 1152| 87.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 87.8k, False: 0] | | | Branch (1152:50): [Folded, False: 87.8k] | | ------------------ ------------------ 3156| 87.8k| } 3157| | 3158| 87.8k| return ret; 3159| 87.7k|} RestoreAtomMakeBNS: 3173| 145k|{ 3174| 145k| int i, j, ret = 0, ret2; 3175| | /*int nDelta, nTotalDelta;*/ 3176| 145k| VAL_AT* pVA = NULL; 3177| 145k| VAL_AT va1; 3178| 145k| int num_at = pStruct->num_atoms; 3179| 145k| inp_ATOM* at = pStruct->at; 3180| 145k| ALL_TC_GROUPS TCGroups; 3181| 145k| ALL_TC_GROUPS* pTCGroups = &TCGroups; 3182| 145k| int nAddEdges2eachAtom = 2, nAddVertices = 0; 3183| | 3184| 145k| BFS_Q bfsq; 3185| | 3186| | /* BNS creation */ 3187| 145k| BN_STRUCT* pBNS = NULL; 3188| 145k| BN_DATA* pBD = NULL; 3189| 145k| int nNum_changed_bonds = 0; 3190| 145k| int bTreatMoreAtomsAsMetals = 0, bSecondPassNewMetals = 0; 3191| 145k| int nMaxAddAtoms = 2, nMaxAddEdges = 2, max_altp = BN_MAX_ALTP; ------------------ | | 17| 145k|#define BN_MAX_ALTP 16 ------------------ 3192| | 3193| 145k| memset(pTCGroups, 0, sizeof(pTCGroups[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 3194| 2.75M| for (i = 0; i < NUM_TCGROUP_TYPES; i++) ------------------ | Branch (3194:17): [True: 2.61M, False: 145k] ------------------ 3195| 2.61M| { 3196| 2.61M| pTCGroups->nGroup[i] = TCG_None; /* unassigned */ 3197| 2.61M| } 3198| 145k| pTCGroups->iComponent = iComponent; 3199| 145k| pTCGroups->iAtNoOffset = iAtNoOffset; 3200| | 3201| 145k| if (num_at == 1) ------------------ | Branch (3201:9): [True: 57.1k, False: 87.9k] ------------------ 3202| 57.1k| { 3203| | /* single atom -- no bonds to restore */ 3204| 57.1k| inp_ATOM* at2 = (inp_ATOM*)inchi_malloc(sizeof(at2[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */ ------------------ | | 1143| 57.1k|#define inchi_malloc malloc ------------------ 3205| 57.1k| inp_ATOM* at3 = (inp_ATOM*)inchi_malloc(sizeof(at3[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */ ------------------ | | 1143| 57.1k|#define inchi_malloc malloc ------------------ 3206| 57.1k| pStruct->at2 = at2; 3207| 57.1k| at[0].charge = pInChI[0]->nTotalCharge; 3208| 57.1k| if (at2) ------------------ | Branch (3208:13): [True: 57.1k, False: 0] ------------------ 3209| 57.1k| { 3210| 57.1k| memcpy(at2, at, sizeof(at2[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */ 3211| 57.1k| } 3212| 57.1k| if (!at2 || !at3) ------------------ | Branch (3212:13): [True: 0, False: 57.1k] | Branch (3212:21): [True: 0, False: 57.1k] ------------------ 3213| 0| { 3214| 0| if (at3) inchi_free(at3); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ | Branch (3214:17): [True: 0, False: 0] ------------------ 3215| 0| return RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 3216| 0| } 3217| 57.1k| ret = MakeOneInChIOutOfStrFromINChI(pCG, ic, ip, sd, pStruct, pStruct->at2, at3, pTCGroups); 3218| | /* clean up */ 3219| 171k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 171k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3219:21): [True: 114k, False: 57.1k] ------------------ 3220| 114k| { 3221| 114k| Free_INChI(&pStruct->pOneINChI[i]); 3222| 114k| Free_INChI_Aux(&pStruct->pOneINChI_Aux[i]); 3223| 114k| FreeInpAtomData(pStruct->pOne_norm_data[i]); 3224| 114k| if (pStruct->pOne_norm_data[i]) ------------------ | Branch (3224:17): [True: 57.1k, False: 57.1k] ------------------ 3225| 57.1k| { 3226| 57.1k| inchi_free(pStruct->pOne_norm_data[i]); ------------------ | | 1152| 57.1k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 57.1k, False: 0] | | | Branch (1152:50): [Folded, False: 57.1k] | | ------------------ ------------------ 3227| 57.1k| pStruct->pOne_norm_data[i] = NULL; 3228| 57.1k| } 3229| 114k| } 3230| | /* djb-rwth: fixing oss-fuzz issue #69602 */ 3231| | /* free_t_group_info(&pStruct->One_ti); */ 3232| 57.1k| inchi_free(at3); ------------------ | | 1152| 57.1k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 57.1k, False: 0] | | | Branch (1152:50): [Folded, False: 57.1k] | | ------------------ ------------------ 3233| | 3234| 57.1k| return ret; 3235| 57.1k| } 3236| | 3237| 87.9k| AllocBfsQueue(&bfsq, BFS_Q_CLEAR, 0); ------------------ | | 60| 87.9k|#define BFS_Q_CLEAR (-1) ------------------ 3238| 87.9k| if (!(pVA = (VAL_AT*)inchi_calloc(num_at, sizeof(pVA[0])))) ------------------ | | 1146| 87.9k|#define inchi_calloc calloc ------------------ | Branch (3238:9): [True: 0, False: 87.9k] ------------------ 3239| 0| { 3240| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 3241| 0| goto exit_function; 3242| 0| } 3243| 87.9k| pStruct->pVA = pVA; 3244| 87.9k| memset(&va1, 0, sizeof(va1)); /* djb-rwth: memset_s C11/Annex K variant? */ 3245| 87.9k| pTCGroups->total_charge = pInChI[0]->nTotalCharge; 3246| 87.9k| if (0 > (ret = AllocBfsQueue(&bfsq, num_at, 0 /* min ring size undefined */))) ------------------ | Branch (3246:9): [True: 0, False: 87.9k] ------------------ 3247| 0| { 3248| 0| goto exit_function; 3249| 0| } 3250| 87.9k| pStruct->pbfsq = &bfsq; 3251| | 3252| 87.9k| if (pStruct->iMobileH == TAUT_NON && pInChI[1] && pInChI[1]->nNumberOfAtoms > 1 && ------------------ | | 574| 175k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3252:9): [True: 1.14k, False: 86.8k] | Branch (3252:42): [True: 1.14k, False: 0] | Branch (3252:55): [True: 1.14k, False: 0] ------------------ 3253| 1.14k| (ret = FillOutpStructEndpointFromInChI(pInChI[1], &pStruct->endpoint))) ------------------ | Branch (3253:9): [True: 0, False: 1.14k] ------------------ 3254| 0| { 3255| 0| goto exit_function; 3256| 0| } 3257| | 3258| | /* mark metal atoms; find min ring sizes for atoms that have 2 bonds */ 3259| 1.18M| for (i = 0; i < num_at; i++) ------------------ | Branch (3259:17): [True: 1.09M, False: 87.9k] ------------------ 3260| 1.09M| { 3261| 1.09M| pVA[i].cNumValenceElectrons = get_sp_element_type(at[i].el_number, &j); 3262| 1.09M| pVA[i].cPeriodicRowNumber = j; 3263| 1.09M| pVA[i].cPeriodicNumber = at[i].el_number; 3264| 1.09M| pVA[i].cNumValenceElectrons--; /* = -1 d- and f- metals, 0 for H, 1 for Na, 2 for Mg,.. = (ATYPE_Xx-1) */ 3265| | 3266| 1.09M| if (is_el_a_metal(at[i].el_number)) ------------------ | Branch (3266:13): [True: 435k, False: 663k] ------------------ 3267| 435k| { 3268| 435k| if (pStruct->pSrm->bStereoRemovesMetalFlag) ------------------ | Branch (3268:17): [True: 0, False: 435k] ------------------ 3269| 0| { 3270| | /* treat metal as non-metal if it is stereogenic or has a stereobond */ 3271| 0| pVA[i].cMetal = !(at[i].p_parity || at[i].sb_parity[0]); ------------------ | Branch (3271:35): [True: 0, False: 0] | Branch (3271:53): [True: 0, False: 0] ------------------ 3272| 0| } 3273| 435k| else 3274| 435k| { 3275| 435k| pVA[i].cMetal = 1; 3276| 435k| } 3277| 435k| } 3278| 1.09M| if (at[i].valence == 2 && !at[i].num_H) ------------------ | Branch (3278:13): [True: 71.0k, False: 1.02M] | Branch (3278:35): [True: 70.2k, False: 792] ------------------ 3279| 70.2k| { 3280| 70.2k| pVA[i].cMinRingSize = is_bond_in_Nmax_memb_ring(at, i, 0, bfsq.q, bfsq.nAtomLevel, 3281| 70.2k| bfsq.cSource, 99 /* max ring size */); 3282| 70.2k| } 3283| 1.02M| else 3284| 1.02M| { 3285| 1.02M| pVA[i].cMinRingSize = 0; 3286| 1.02M| } 3287| 1.09M| } 3288| | /* AllocBfsQueue( &bfsq, BFS_Q_FREE, 0 ); */ 3289| | 3290| 91.2k|repeat_for_new_metals: 3291| | /* set valences for the first time; find ChargeValence structures for each atom */ 3292| 1.22M| for (i = 0; i < num_at; i++) ------------------ | Branch (3292:17): [True: 1.13M, False: 91.2k] ------------------ 3293| 1.13M| { 3294| | /* get additional fictitious atoms information */ 3295| 1.13M| pVA[i].cInitFreeValences = 0; 3296| | 3297| 1.13M| ret = GetAtomRestoreInfo(pCG, at, i, pVA, pStruct->pSrm, pStruct->bMobileH, pStruct->endpoint); 3298| | 3299| 1.13M| if (ret < 0) ------------------ | Branch (3299:13): [True: 1, False: 1.13M] ------------------ 3300| 1| { 3301| 1| goto exit_function; 3302| 1| } 3303| 1.13M| if (ret == TREAT_ATOM_AS_METAL && !bSecondPassNewMetals && !pVA[i].cMetal) ------------------ | | 258| 2.26M|#define TREAT_ATOM_AS_METAL 99 ------------------ | Branch (3303:13): [True: 3.64k, False: 1.12M] | Branch (3303:43): [True: 3.64k, False: 0] | Branch (3303:68): [True: 3.64k, False: 0] ------------------ 3304| 3.64k| { 3305| 3.64k| if (pStruct->pSrm->bStereoRemovesMetalFlag) ------------------ | Branch (3305:17): [True: 0, False: 3.64k] ------------------ 3306| 0| { 3307| | /* treat metal as non-metal if it is stereogenic or has a stereobond */ 3308| 0| pVA[i].cMetal = !(at[i].p_parity || at[i].sb_parity[0]); ------------------ | Branch (3308:35): [True: 0, False: 0] | Branch (3308:53): [True: 0, False: 0] ------------------ 3309| 0| } 3310| 3.64k| else 3311| 3.64k| { 3312| 3.64k| pVA[i].cMetal = 1; 3313| 3.64k| } 3314| 3.64k| if (pVA[i].cMetal) ------------------ | Branch (3314:17): [True: 3.64k, False: 0] ------------------ 3315| 3.64k| { 3316| 3.64k| bTreatMoreAtomsAsMetals++; 3317| 3.64k| } 3318| 3.64k| } 3319| 1.13M| pTCGroups->charge_on_atoms += pVA[i].cInitCharge; 3320| 1.13M| } 3321| 91.2k| if (bTreatMoreAtomsAsMetals && !bSecondPassNewMetals) ------------------ | Branch (3321:9): [True: 6.64k, False: 84.6k] | Branch (3321:36): [True: 3.32k, False: 3.32k] ------------------ 3322| 3.32k| { 3323| 37.7k| for (i = 0; i < num_at; i++) ------------------ | Branch (3323:21): [True: 34.4k, False: 3.32k] ------------------ 3324| 34.4k| { 3325| | /* clear all members of pVA[i] except two */ 3326| 34.4k| pTCGroups->charge_on_atoms -= pVA[i].cInitCharge; 3327| 34.4k| va1.cMetal = pVA[i].cMetal; 3328| 34.4k| va1.cMinRingSize = pVA[i].cMinRingSize; 3329| 34.4k| va1.cNumValenceElectrons = pVA[i].cNumValenceElectrons; 3330| 34.4k| va1.cPeriodicRowNumber = pVA[i].cPeriodicRowNumber; 3331| 34.4k| va1.cPeriodicNumber = pVA[i].cPeriodicNumber; 3332| 34.4k| pVA[i] = va1; 3333| 34.4k| } 3334| 3.32k| bSecondPassNewMetals = 1; 3335| 3.32k| goto repeat_for_new_metals; 3336| 3.32k| } 3337| | 3338| | /* count atoms, bonds, additional edges and vertices in ChargeValence structures and t-groups */ 3339| 87.9k| ret = nCountBnsSizes(at, num_at, nAddEdges2eachAtom, nAddVertices, &pStruct->ti, 3340| 87.9k| pVA, pStruct->pSrm, pTCGroups); 3341| 87.9k| if (ret < 0) ------------------ | Branch (3341:9): [True: 128, False: 87.8k] ------------------ 3342| 128| { 3343| 128| goto exit_function; 3344| 128| } 3345| | 3346| | /* find and count groups; add counts of all other vertices to be created */ 3347| 87.8k| ret = nAddSuperCGroups(pTCGroups); 3348| 87.8k| if (ret < 0) ------------------ | Branch (3348:9): [True: 0, False: 87.8k] ------------------ 3349| 0| { 3350| 0| goto exit_function; 3351| 0| } 3352| | 3353| | /* create the BNS and fill it with all real atoms */ 3354| 87.8k| pBNS = AllocateAndInitTCGBnStruct(pStruct, pVA, pTCGroups, 3355| 87.8k| nMaxAddAtoms, nMaxAddEdges, max_altp, &nNum_changed_bonds); 3356| 87.8k| if (!pBNS) ------------------ | Branch (3356:9): [True: 0, False: 87.8k] ------------------ 3357| 0| { 3358| 0| ret = BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3359| 0| goto exit_function; 3360| 0| } 3361| | /* add t-groups to the BNS */ 3362| 87.8k| ret = AddTGroups2TCGBnStruct(pBNS, pStruct, pVA, pTCGroups, nMaxAddEdges); 3363| 87.8k| if (ret < 0) ------------------ | Branch (3363:9): [True: 0, False: 87.8k] ------------------ 3364| 0| { 3365| 0| goto exit_function; 3366| 0| } 3367| | 3368| | /* add c-groups to the BNS; adjust charges */ 3369| 87.8k| ret = AddCGroups2TCGBnStruct(pBNS, pStruct, pVA, pTCGroups, nMaxAddEdges); 3370| 87.8k| if (ret < 0) ------------------ | Branch (3370:9): [True: 0, False: 87.8k] ------------------ 3371| 0| { 3372| 0| goto exit_function; 3373| 0| } 3374| | 3375| 87.8k| pBNS->ulTimeOutTime = NULL; /* v. 1.05 */ 3376| 87.8k| pBNS->ic = ic; /* v. 1.05 */ 3377| | 3378| | /* allocate BNData */ 3379| 87.8k| pBD = AllocateAndInitBnData(pBNS->max_vertices + pBNS->max_vertices / 2); 3380| 87.8k| if (!pBD) ------------------ | Branch (3380:9): [True: 0, False: 87.8k] ------------------ 3381| 0| { 3382| 0| ret = BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3383| 0| goto exit_function; 3384| 0| } 3385| 87.8k| CheckBnsConsistency(pStruct, pBNS, pVA, pTCGroups, 0); 3386| | 3387| | /* restore bonds & charges */ 3388| 87.8k| ret = RunBnsRestore1(pCG, ic, ip, sd, pBNS, pBD, pStruct, pVA, pTCGroups, pInChI, num_inp, bHasSomeFixedH); 3389| 87.8k| if (ret < 0) ------------------ | Branch (3389:9): [True: 74.6k, False: 13.2k] ------------------ 3390| 74.6k| { 3391| 74.6k| goto exit_function; 3392| 74.6k| } 3393| | 3394| 13.2k| ret = CheckBnsConsistency(pStruct, pBNS, pVA, pTCGroups, 1); 3395| |#if ( bRELEASE_VERSION == 0 ) 3396| |#ifndef TARGET_API_LIB 3397| | if (ret) 3398| | { 3399| | fprintf(stdout, "Msg for: %ld %s comp=%d %c%c\n", num_inp, (szCurHdr && szCurHdr[0]) ? szCurHdr : "", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F'); 3400| | } 3401| | if (pStruct->iMobileH == TAUT_YES && pStruct->nNumRemovedProtons) 3402| | { 3403| | fprintf(stdout, "REMOVED_PROTONS%+d %ld %s\n", pStruct->nNumRemovedProtons, num_inp, (szCurHdr && szCurHdr[0]) ? szCurHdr : ""); 3404| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 3405| | } 3406| | if (pStruct->bExtract & EXTRACT_STRUCT_NUMBER) 3407| | { 3408| | fprintf(stdout, "EXTRACT: %ld: %s\n", num_inp, (szCurHdr && szCurHdr[0]) ? szCurHdr : ""); 3409| | } 3410| |#endif 3411| |#endif 3412| 13.2k| { /* create the final structure in pStruct->at2 */ 3413| 13.2k| inp_ATOM* at_tmp = pStruct->at; 3414| 13.2k| pStruct->at = pStruct->at2; 3415| 13.2k| memcpy(pStruct->at, at_tmp, sizeof(pStruct->at[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */ 3416| 13.2k| ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1); 3417| 13.2k| pStruct->at2 = pStruct->at; 3418| 13.2k| pStruct->at = at_tmp; 3419| 13.2k| if (ret2 < 0) ------------------ | Branch (3419:13): [True: 0, False: 13.2k] ------------------ 3420| 0| { 3421| 0| ret = ret2; 3422| 0| } 3423| 13.2k| } 3424| | 3425| 87.9k|exit_function: 3426| | 3427| 87.9k| pStruct->pbfsq = NULL; 3428| 87.9k| AllocBfsQueue(&bfsq, BFS_Q_FREE, 0); ------------------ | | 61| 87.9k|#define BFS_Q_FREE (-2) ------------------ 3429| | 3430| 87.9k| pBD = DeAllocateBnData(pBD); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3431| 87.9k| pBNS = DeAllocateBnStruct(pBNS); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3432| | /* 3433| | if ( pVA ) inchi_free( pVA ); 3434| | */ 3435| 87.9k| if (pTCGroups->pTCG) inchi_free(pTCGroups->pTCG); ------------------ | | 1152| 34.3k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 34.3k, False: 0] | | | Branch (1152:50): [Folded, False: 34.3k] | | ------------------ ------------------ | Branch (3435:9): [True: 34.3k, False: 53.5k] ------------------ 3436| | 3437| 87.9k| return ret; 3438| 13.2k|} OneInChI2Atom: 3453| 145k|{ 3454| 145k| int ret; 3455| 145k| INPUT_PARMS* ip, ip_loc; 3456| | 3457| 145k| ip_loc = *ip_inp; 3458| 145k| ip = &ip_loc; 3459| | 3460| 145k| sd->pStrErrStruct[0] = '\0'; 3461| 145k| ret = RestoreAtomConnectionsSetStereo(pStruct, iComponent, iAtNoOffset, pInChI[0], pInChI[1]); 3462| 145k| if (ret < 0) ------------------ | Branch (3462:9): [True: 237, False: 145k] ------------------ 3463| 237| { 3464| 237| goto exit_function; 3465| 237| } 3466| 145k| ret = SetStereoBondTypesFrom0DStereo(pStruct, pInChI[0]); 3467| 145k| if (ret < 0) ------------------ | Branch (3467:9): [True: 4, False: 145k] ------------------ 3468| 4| { 3469| 4| goto exit_function; 3470| 4| } 3471| 145k| ret = ReconcileAllCmlBondParities(pStruct->at, pStruct->num_atoms, 0); 3472| 145k| if (ret < 0) ------------------ | Branch (3472:9): [True: 0, False: 145k] ------------------ 3473| 0| { 3474| 0| goto exit_function; 3475| 0| } 3476| | 3477| | /* main InChI restore function */ 3478| 145k| ret = RestoreAtomMakeBNS(ic, pCG, ip, sd, pStruct, iComponent, iAtNoOffset, pInChI, szCurHdr, num_inp, bHasSomeFixedH); 3479| | 3480| |#ifndef COMPILE_ANSI_ONLY 3481| | if ((pStruct->num_inp_actual > 0 ? pStruct->num_inp_actual : num_inp) >= ip->first_struct_number && 3482| | ((/*ret > 0 &&*/ ip->bDisplayIfRestoreWarnings) && pStruct->pXYZ)) 3483| | { 3484| | inchiTime ulTStart; 3485| | InchiTimeGet(&ulTStart); 3486| | DisplayRestoredComponent(pCG, pStruct, iComponent, iAtNoOffset, pInChI[0], szCurHdr); 3487| | sd->ulStructTime -= InchiTimeElapsed(ic, &ulTStart); /* subtract display time */ 3488| | } 3489| |#endif 3490| | 3491| 145k| if (ret < 0) ------------------ | Branch (3491:9): [True: 74.7k, False: 70.3k] ------------------ 3492| 74.7k| { 3493| 74.7k| goto exit_function; 3494| 74.7k| } 3495| 70.3k| if ((pStruct->num_inp_actual ? pStruct->num_inp_actual : num_inp) >= ip->first_struct_number && ret >= 0) ------------------ | Branch (3495:9): [True: 70.3k, False: 0] | Branch (3495:10): [True: 0, False: 70.3k] | Branch (3495:101): [True: 70.3k, False: 0] ------------------ 3496| 70.3k| { 3497| | /* remove t-group markings and increment zero-order bonds, 3498| | otherwise MakeInChIOutOfStrFromINChI2() woild fail */ 3499| | /* --- moved to MakeInChIOutOfStrFromINChI2 --- 3500| | IncrZeroBondsAndClearEndpts(pStruct->at2, pStruct->num_atoms, iComponent+1); 3501| | CopySt2At( pStruct->at2, pStruct->st, pStruct->num_atoms ); 3502| | */ 3503| | /* include all restored structure features in pStruct->at2 */ 3504| | /* make full InChI out of pStruct->at2, pStruct->num_atoms */ 3505| | /***************************************************************************************/ 3506| | /* !!! pStruct->One_InChI etc. were removed at the exit from NormalizeAndCompare() !!! */ 3507| | /***************************************************************************************/ 3508| 70.3k| if (bHasSomeFixedH && pStruct->iInchiRec == INCHI_REC && pStruct->iMobileH == TAUT_YES && ------------------ | | 571| 101k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct->iInchiRec == INCHI_REC && pStruct->iMobileH == TAUT_YES && ------------------ | | 575| 70.3k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3508:13): [True: 30.7k, False: 39.5k] | Branch (3508:31): [True: 4, False: 30.7k] | Branch (3508:66): [True: 2, False: 2] ------------------ 3509| 2| !pStruct->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC)) ------------------ | | 15| 2|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3509:13): [True: 2, False: 0] | Branch (3509:40): [True: 2, False: 0] ------------------ 3510| 2| { 3511| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3512| 2| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 15| 2|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3513| 2| } 3514| | 3515| 70.3k| ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct, iComponent, iAtNoOffset, num_inp); 3516| | 3517| 70.3k| if (ret >= 0) ------------------ | Branch (3517:13): [True: 69.9k, False: 386] ------------------ 3518| 69.9k| { 3519| 69.9k| ; 3520| 69.9k| } 3521| |#if ( bRELEASE_VERSION == 0 ) 3522| |#ifndef TARGET_API_LIB 3523| | else 3524| | { 3525| | fprintf(stdout, "\nERROR in MakeInChI-1: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 3526| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret); 3527| | } 3528| |#endif 3529| |#endif 3530| 70.3k| } 3531| | 3532| 145k|exit_function: 3533| | 3534| 145k| return ret; 3535| 70.3k|} MakeProtonComponent: 3540| 134|{ 3541| 134| inp_ATOM* at = NULL; 3542| 134| int i; 3543| | 3544| 134| if (num_prot <= 0) ------------------ | Branch (3544:9): [True: 0, False: 134] ------------------ 3545| 0| { 3546| 0| return 0; 3547| 0| } 3548| | /* allocate */ 3549| 134| pStruct->at = (inp_ATOM*)inchi_calloc(num_prot, sizeof(pStruct->at[0])); ------------------ | | 1146| 134|#define inchi_calloc calloc ------------------ 3550| 134| pStruct->at2 = (inp_ATOM*)inchi_calloc(num_prot, sizeof(pStruct->at2[0])); ------------------ | | 1146| 134|#define inchi_calloc calloc ------------------ 3551| 134| if (!pStruct->at || !pStruct->at2) ------------------ | Branch (3551:9): [True: 0, False: 134] | Branch (3551:25): [True: 0, False: 134] ------------------ 3552| 0| { 3553| 0| return 0; 3554| 0| } 3555| | /* create protons */ 3556| 134| at = pStruct->at; 3557| | /* fill out proton atom info */ 3558| 31.2k| for (i = 0; i < num_prot; i++) ------------------ | Branch (3558:17): [True: 31.0k, False: 134] ------------------ 3559| 31.0k| { 3560| 31.0k| strcpy(at[i].elname, "H"); 3561| 31.0k| at[i].el_number = EL_NUMBER_H; ------------------ | | 11| 31.0k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 3562| 31.0k| at[i].orig_at_number = i + 1; 3563| | /* 3564| | at[i].orig_compt_at_numb = i + 1; 3565| | at[i].component = i + 1; 3566| | */ 3567| 31.0k| at[i].charge = 1; 3568| 31.0k| } 3569| 134| memcpy(pStruct->at2, at, num_prot * sizeof(pStruct->at2[0])); 3570| 134| pStruct->bDeleted = 0; 3571| 134| pStruct->num_atoms = num_prot; 3572| 134| pStruct->bMobileH = TAUT_YES; ------------------ | | 575| 134|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3573| 134| pStruct->iMobileH = TAUT_YES; ------------------ | | 575| 134|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3574| | 3575| 134| return num_prot; 3576| 134|} AddRemProtonsInRestrStruct: 3591| 2.99k|{ 3592| | /* on entry and exit, all at[i].num_H do not include isotopic H and explicit terminal H are connected */ 3593| 2.99k| int iComp, q, ret = 0; 3594| 2.99k| int num_atoms, num_deleted_H, num_tg, num_changed, num_deleted_components; /* djb-rwth: removing redundant variables */ 3595| 2.99k| inp_ATOM* at; 3596| 2.99k| INPUT_PARMS* ip, ip_loc; 3597| 2.99k| int num_prot = *nProtonsToBeRemovedByNormFromRevrs; 3598| 2.99k| int delta_recmet_prot, num_prot_prev, bAccumulateChanges = 0, nNumProtAddedByRevrs; 3599| 2.99k| INChI_Aux* pINChI_Aux; 3600| 2.99k| INCHI_MODE bNormalizationFlags; 3601| 2.99k| int nChargeRevrs, nChargeInChI; 3602| | 3603| 2.99k| if (!num_prot) ------------------ | Branch (3603:9): [True: 2.69k, False: 297] ------------------ 3604| 2.69k| { 3605| 2.69k| return 0; 3606| 2.69k| } 3607| 297| delta_recmet_prot = 0; 3608| 297| num_changed = 0; 3609| 297| num_deleted_components = 0; 3610| 297| ip_loc = *ip_inp; 3611| 297| ip = &ip_loc; 3612| | /*---------------------------------------------------------------------------------- 3613| | nLink < 0 && num_componentsR > 0 => This is a Disconnected structure component; it is 3614| | same as already processed reconnected one 3615| | Do no preicess it 3616| | 3617| | nLink > 0 && num_componentsR > 0 => This is a Disconnected structure component; 3618| | (should not happen) It it is a result of (nLink-1)th Reconeected 3619| | component disconnection (NOT IMPLEMENTED YET) 3620| | 3621| | nLink = 0 => Process this component. It is either a reconnected 3622| | component, or a result of a disconnection (for now) 3623| | 3624| | nLink > 0 && num_componentsR = 0 => This is a Reconnected component that is same as 3625| | a disconnected one that will not be processed. 3626| | Process and save charge delta. 3627| | -----------------------------------------------------------------------------------*/ 3628| | 3629| 1.68k| for (iComp = 0; iComp < num_components && num_prot; iComp++) ------------------ | Branch (3629:21): [True: 1.46k, False: 221] | Branch (3629:47): [True: 1.38k, False: 74] ------------------ 3630| 1.38k| { 3631| 1.38k| bAccumulateChanges = 0; 3632| 1.38k| if (pStruct[iComp].nLink < 0 && num_componentsR > 0) ------------------ | Branch (3632:13): [True: 0, False: 1.38k] | Branch (3632:41): [True: 0, False: 0] ------------------ 3633| 0| { 3634| | /* check */ 3635| 0| q = -(pStruct[iComp].nLink + 1); 3636| 0| if (!pStructR || !num_componentsR || q >= num_componentsR || pStructR[q].nLink != (iComp + 1)) ------------------ | Branch (3636:17): [True: 0, False: 0] | Branch (3636:30): [True: 0, False: 0] | Branch (3636:50): [True: 0, False: 0] | Branch (3636:74): [True: 0, False: 0] ------------------ 3637| 0| { 3638| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3639| 0| goto exit_function; 3640| 0| } 3641| 0| continue; /* Disconnected structure component has already been processed as a Reconnected one */ 3642| 0| } 3643| | 3644| 1.38k| at = pStruct[iComp].at2; 3645| 1.38k| num_atoms = pStruct[iComp].num_atoms; 3646| 1.38k| num_deleted_H = pStruct[iComp].num_deleted_H; /* djb-rwth: removing redundant code */ 3647| 1.38k| bAccumulateChanges = (pStruct[iComp].nLink > 0 && !num_componentsR); ------------------ | Branch (3647:31): [True: 0, False: 1.38k] | Branch (3647:59): [True: 0, False: 0] ------------------ 3648| 1.38k| nChargeRevrs = pStruct[iComp].nChargeRevrs; 3649| 1.38k| nChargeInChI = pStruct[iComp].nChargeInChI; 3650| 1.38k| num_deleted_components += (0 != pStruct[iComp].bDeleted); 3651| 1.38k| if (!at || !num_atoms) ------------------ | Branch (3651:13): [True: 220, False: 1.16k] | Branch (3651:20): [True: 0, False: 1.16k] ------------------ 3652| 220| { 3653| 220| continue; 3654| 220| } 3655| | /* find whether it is a reconnected structure */ 3656| 1.16k| q = bRevInchiComponentExists(pStruct + iComp, INCHI_REC, TAUT_YES, 0) ? INCHI_REC : INCHI_BAS; ------------------ | | 571| 1.16k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ q = bRevInchiComponentExists(pStruct + iComp, INCHI_REC, TAUT_YES, 0) ? INCHI_REC : INCHI_BAS; ------------------ | | 575| 1.16k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ q = bRevInchiComponentExists(pStruct + iComp, INCHI_REC, TAUT_YES, 0) ? INCHI_REC : INCHI_BAS; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ q = bRevInchiComponentExists(pStruct + iComp, INCHI_REC, TAUT_YES, 0) ? INCHI_REC : INCHI_BAS; ------------------ | | 570| 2.33k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (3656:13): [True: 0, False: 1.16k] ------------------ 3657| | /* 3658| | q = pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC] && 3659| | pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] && 3660| | pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms? INCHI_REC : INCHI_BAS; 3661| | */ 3662| 1.16k| pINChI_Aux = pStruct[iComp].RevInChI.pINChI_Aux[q][0][TAUT_YES]; /* 0 = 1st component in RevInChI */ ------------------ | | 575| 1.16k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3663| | /*nNumProtAddedByRevrs = pINChI_Aux->nNumRemovedProtons;*/ 3664| 1.16k| nNumProtAddedByRevrs = -pStruct[iComp].nNumRemovedProtonsByRevrs; 3665| 1.16k| bNormalizationFlags = pINChI_Aux->bNormalizationFlags; 3666| 1.16k| num_tg = pINChI_Aux->nNumberOfTGroups; 3667| | 3668| | 3669| | /* disconnect all explicit H and add the number of implicit iso H and all explicit terminal H to the number of implicit H */ 3670| 1.16k| if (0 > (ret = DisconnectedConnectedH(at, num_atoms, num_deleted_H))) ------------------ | Branch (3670:13): [True: 0, False: 1.16k] ------------------ 3671| 0| { 3672| 0| goto exit_function; 3673| 0| } 3674| 1.16k| num_prot_prev = num_prot; 3675| 1.16k| ret = AddRemoveProtonsRestr(at, num_atoms, &num_prot, nNumProtAddedByRevrs, 3676| 1.16k| bNormalizationFlags, num_tg, nChargeRevrs, nChargeInChI); 3677| | 3678| 1.16k| pStruct[iComp].bPostProcessed = ret; 3679| 1.16k| num_changed += (ret > 0); 3680| 1.16k| if (ret < 0) ------------------ | Branch (3680:13): [True: 0, False: 1.16k] ------------------ 3681| 0| { 3682| 0| goto exit_function; 3683| 0| } 3684| 1.16k| if (ret > 0) ------------------ | Branch (3684:13): [True: 288, False: 879] ------------------ 3685| 288| { 3686| | /* recalculate InChI; it will reconnect at */ 3687| 288| StrFromINChI* pStruct1 = pStruct + iComp; 3688| 288| INCHI_MODE nMode = ip->nMode; 3689| 288| FreeAllINChIArrays(pStruct1->RevInChI.pINChI, 3690| 288| pStruct1->RevInChI.pINChI_Aux, 3691| 288| pStruct1->RevInChI.num_components); 3692| | 3693| 288| if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 571| 288|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 575| 288|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3693:17): [True: 0, False: 288] | Branch (3693:35): [True: 0, False: 0] | Branch (3693:71): [True: 0, False: 0] ------------------ 3694| 0| !pStruct1->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC)) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3694:17): [True: 0, False: 0] | Branch (3694:45): [True: 0, False: 0] ------------------ 3695| 0| { 3696| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3697| 0| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3698| 0| } 3699| | /* calls ConnectDisconnectedH(...): subtracts number of implicit iso H from implicit H */ 3700| | 3701| 288| ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct1, 0, 0, num_inp); 3702| | 3703| 288| ip->nMode = nMode; 3704| 288| if (ret < 0) ------------------ | Branch (3704:17): [True: 2, False: 286] ------------------ 3705| 2| { 3706| 2| goto exit_function; 3707| 2| } 3708| 288| } 3709| 879| else 3710| 879| { 3711| | /* reconnect disconnected terminal H and subtracts number of implicit iso H from implicit H */ 3712| 879| if (0 > (ret = ConnectDisconnectedH(at, num_atoms, num_deleted_H))) ------------------ | Branch (3712:17): [True: 0, False: 879] ------------------ 3713| 0| { 3714| 0| goto exit_function; 3715| 0| } 3716| 879| } 3717| 1.16k| if (bAccumulateChanges && recmet_change_balance) ------------------ | Branch (3717:13): [True: 0, False: 1.16k] | Branch (3717:35): [True: 0, False: 0] ------------------ 3718| 0| { 3719| | /* processed Reconnected layer component that is also present in Disconnected layer */ 3720| 0| delta_recmet_prot += num_prot - num_prot_prev; 3721| 0| } 3722| 1.16k| } 3723| | 3724| 295| iComp = num_components - 1; 3725| 295| if (!bHasSomeFixedH && num_prot > 0 && 1 == num_deleted_components && iComp >= 0 && pStruct[iComp].bDeleted) ------------------ | Branch (3725:9): [True: 295, False: 0] | Branch (3725:28): [True: 135, False: 160] | Branch (3725:44): [True: 134, False: 1] | Branch (3725:75): [True: 134, False: 0] | Branch (3725:89): [True: 134, False: 0] ------------------ 3726| 134| { 3727| | /* add bare protons to the deleted Mobile-H component; undelete the component */ 3728| 134| num_prot_prev = num_prot; 3729| 134| if (!MakeProtonComponent(pStruct + iComp, iComp, num_prot)) ------------------ | Branch (3729:13): [True: 0, False: 134] ------------------ 3730| 0| { 3731| 0| goto exit_function; 3732| 0| } 3733| 134| else 3734| 134| { 3735| | /* recalculate InChI; it will reconnect at */ 3736| 134| StrFromINChI* pStruct1 = pStruct + iComp; 3737| 134| INCHI_MODE nMode = ip->nMode; 3738| 134| num_changed++; 3739| 134| num_prot = 0; 3740| 134| FreeAllINChIArrays(pStruct1->RevInChI.pINChI, 3741| 134| pStruct1->RevInChI.pINChI_Aux, 3742| 134| pStruct1->RevInChI.num_components); 3743| | 3744| 134| if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 571| 134|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 575| 134|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3744:17): [True: 0, False: 134] | Branch (3744:35): [True: 0, False: 0] | Branch (3744:71): [True: 0, False: 0] ------------------ 3745| 0| !pStruct1->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC)) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3745:17): [True: 0, False: 0] | Branch (3745:45): [True: 0, False: 0] ------------------ 3746| 0| { 3747| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3748| 0| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3749| 0| } 3750| | /* Although MakeInChIOutOfStrFromINChI2() calls ConnectDisconnectedH(...) */ 3751| | /* to subtracts number of implicit iso H from implicit H */ 3752| | /* this CANNOT have any effect on the deleted H component */ 3753| | 3754| 134| ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct1, 0, 0, num_inp); 3755| | 3756| 134| ip->nMode = nMode; 3757| 134| if (ret < 0) ------------------ | Branch (3757:17): [True: 0, False: 134] ------------------ 3758| 0| { 3759| 0| goto exit_function; 3760| 0| } 3761| 134| if (bAccumulateChanges && recmet_change_balance) ------------------ | Branch (3761:17): [True: 0, False: 134] | Branch (3761:39): [True: 0, False: 0] ------------------ 3762| 0| { 3763| | /* processed Reconnected layer component that is also present in Disconnected layer */ 3764| 0| delta_recmet_prot += num_prot - num_prot_prev; 3765| 0| } 3766| 134| } 3767| 134| } 3768| 295| *nProtonsToBeRemovedByNormFromRevrs = num_prot; 3769| 295| if (recmet_change_balance) ------------------ | Branch (3769:9): [True: 1, False: 294] ------------------ 3770| 1| { 3771| 1| *recmet_change_balance = delta_recmet_prot; 3772| 1| } 3773| | 3774| 297|exit_function: 3775| | 3776| 297| return ret < 0 ? ret : num_changed; ------------------ | Branch (3776:12): [True: 2, False: 295] ------------------ 3777| 295|} AddRemIsoProtonsInRestrStruct: 3793| 2.99k|{ 3794| | /* on entry and exit, all at[i].num_H do not include isotopic H and explicit terminal H are connected */ 3795| 2.99k| int iComp, q, k, ret = 0, bNotEmpty; 3796| 2.99k| int num_atoms, num_deleted_H, num_tg, num_changed; /* djb-rwth: removing redundant variables */ 3797| 2.99k| inp_ATOM* at; 3798| 2.99k| NUM_H num_prot[NUM_H_ISOTOPES], delta_recmet_prot[NUM_H_ISOTOPES], num_prot_prev[NUM_H_ISOTOPES]; 3799| 2.99k| int bAccumulateChanges; 3800| 2.99k| INChI_Aux* pINChI_Aux; 3801| | /* djb-rwth: removing redundant variables */ 3802| 2.99k| INPUT_PARMS* ip, ip_loc; 3803| | 3804| 2.99k| ip_loc = *ip_inp; 3805| 2.99k| ip = &ip_loc; 3806| | 3807| 2.99k| memcpy(num_prot, pProtonBalance, sizeof(num_prot)); 3808| 11.9k| for (bNotEmpty = 0, k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 25| 11.9k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3808:32): [True: 8.97k, False: 2.99k] ------------------ 3809| 8.97k| { 3810| 8.97k| bNotEmpty |= num_prot[k]; 3811| 8.97k| } 3812| 2.99k| if (!bNotEmpty) ------------------ | Branch (3812:9): [True: 2.92k, False: 70] ------------------ 3813| 2.92k| { 3814| 2.92k| return 0; 3815| 2.92k| } 3816| 70| memset(delta_recmet_prot, 0, sizeof(delta_recmet_prot)); /* djb-rwth: memset_s C11/Annex K variant? */ 3817| 70| num_changed = 0; 3818| | /*---------------------------------------------------------------------------------- 3819| | nLink < 0 && num_componentsR > 0 => This is a Disconnected structure component; it is 3820| | same as already processed reconnected one 3821| | Do no process it 3822| | 3823| | nLink > 0 && num_componentsR > 0 => This is a Disconnected structure component; 3824| | (should not happen) It it is a result of (nLink-1)th Reconeected 3825| | component disconnection (NOT IMPLEMENTED YET) 3826| | 3827| | nLink = 0 => Process this component. It is either a reconnected 3828| | component, or a result of a disconnection (for now) 3829| | 3830| | nLink > 0 && num_componentsR = 0 => This is a Reconnected component that is same as 3831| | a disconnected one that will not be processed. 3832| | Process and save charge delta. 3833| | -----------------------------------------------------------------------------------*/ 3834| | 3835| 1.63k| for (iComp = 0; iComp < num_components && num_prot; iComp++) /* djb-rwth: the condition will always evaluate to true only if pProtonBalance is not NULL */ ------------------ | Branch (3835:21): [True: 1.57k, False: 63] | Branch (3835:47): [True: 1.57k, False: 0] ------------------ 3836| 1.57k| { 3837| | /* djb-rwth: removing redundant code */ 3838| 1.57k| if (pStruct[iComp].nLink < 0 && num_componentsR > 0) ------------------ | Branch (3838:13): [True: 0, False: 1.57k] | Branch (3838:41): [True: 0, False: 0] ------------------ 3839| 0| { 3840| | /* check */ 3841| 0| q = -(pStruct[iComp].nLink + 1); 3842| 0| if (!pStructR || !num_componentsR || q >= num_componentsR || pStructR[q].nLink != (iComp + 1)) ------------------ | Branch (3842:17): [True: 0, False: 0] | Branch (3842:30): [True: 0, False: 0] | Branch (3842:50): [True: 0, False: 0] | Branch (3842:74): [True: 0, False: 0] ------------------ 3843| 0| { 3844| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 3845| 0| goto exit_function; 3846| 0| } 3847| 0| continue; /* Disconnected structure component has already been processed as a Reconnected one */ 3848| 0| } 3849| | 3850| 1.57k| at = pStruct[iComp].at2; 3851| 1.57k| num_atoms = pStruct[iComp].num_atoms; 3852| 1.57k| num_deleted_H = pStruct[iComp].num_deleted_H; /* djb-rwth: removing redundant code */ 3853| 1.57k| bAccumulateChanges = (pStruct[iComp].nLink > 0 && !num_componentsR); ------------------ | Branch (3853:31): [True: 0, False: 1.57k] | Branch (3853:59): [True: 0, False: 0] ------------------ 3854| | 3855| 1.57k| if (!at || !num_atoms) ------------------ | Branch (3855:13): [True: 42, False: 1.53k] | Branch (3855:20): [True: 0, False: 1.53k] ------------------ 3856| 42| { 3857| 42| continue; 3858| 42| } 3859| | /* find whether it is a reconnected structure */ 3860| 1.53k| q = pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC] && ------------------ | | 571| 1.53k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (3860:13): [True: 0, False: 1.53k] ------------------ 3861| 0| pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] && ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] && ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3861:13): [True: 0, False: 0] ------------------ 3862| 1.53k| pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS; ------------------ | | 570| 3.06k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (3862:13): [True: 0, False: 0] ------------------ 3863| | 3864| 1.53k| pINChI_Aux = pStruct[iComp].RevInChI.pINChI_Aux[q][0][TAUT_YES]; /* 0 = 1st component in RevInChI */ ------------------ | | 575| 1.53k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3865| | /* djb-rwth: removing redundant code */ 3866| 1.53k| num_tg = pINChI_Aux->nNumberOfTGroups; 3867| 1.53k| memcpy(num_prot_prev, num_prot, sizeof(num_prot_prev)); 3868| | 3869| | /* pass CONNECTED explicit H to AddRemoveIsoProtonsRestr() for isotopic H addition */ 3870| 1.53k| ret = AddRemoveIsoProtonsRestr(at, num_atoms, num_prot, num_tg); 3871| | 3872| 1.53k| pStruct[iComp].bPostProcessed |= ret; 3873| 1.53k| num_changed += (ret > 0); 3874| 1.53k| if (ret < 0) ------------------ | Branch (3874:13): [True: 5, False: 1.52k] ------------------ 3875| 5| { 3876| 5| goto exit_function; 3877| 5| } 3878| 1.52k| if (ret > 0) ------------------ | Branch (3878:13): [True: 47, False: 1.47k] ------------------ 3879| 47| { 3880| 47| StrFromINChI* pStruct1 = pStruct + iComp; 3881| 47| INCHI_MODE nMode = ip->nMode; 3882| | /* recalculate InChI; MakeInChIOutOfStrFromINChI2() will reconnect explicit H */ 3883| | /* disconnect all explicit H and add the number of implicit iso H and all explicit terminal H to the number of implicit H */ 3884| 47| if (0 > (ret = DisconnectedConnectedH(at, num_atoms, num_deleted_H))) ------------------ | Branch (3884:17): [True: 0, False: 47] ------------------ 3885| 0| { 3886| 0| goto exit_function; 3887| 0| } 3888| 47| FreeAllINChIArrays(pStruct1->RevInChI.pINChI, 3889| 47| pStruct1->RevInChI.pINChI_Aux, 3890| 47| pStruct1->RevInChI.num_components); 3891| 47| if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 571| 47|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 575| 47|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3891:17): [True: 0, False: 47] | Branch (3891:35): [True: 0, False: 0] | Branch (3891:71): [True: 0, False: 0] ------------------ 3892| 0| !pStruct1->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC)) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3892:17): [True: 0, False: 0] | Branch (3892:45): [True: 0, False: 0] ------------------ 3893| 0| { 3894| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3895| 0| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3896| 0| } 3897| | /* input: disconnected explicit H, output: connected explicit H */ 3898| 47| ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct1, 0, 0, num_inp); 3899| 47| ip->nMode = nMode; 3900| 47| if (ret < 0) ------------------ | Branch (3900:17): [True: 2, False: 45] ------------------ 3901| 2| { 3902| 2| goto exit_function; 3903| 2| } 3904| 47| } 3905| | /* the following was commented out 2007-08-28 by DT. Reason: it's a bug since H must be already connected */ 3906| | /* else { 3907| | if ( 0 > ( ret = ConnectDisconnectedH( at, num_atoms, num_deleted_H ) ) ) { 3908| | goto exit_function; 3909| | } 3910| | } */ 3911| 1.52k| if (bAccumulateChanges) ------------------ | Branch (3911:13): [True: 0, False: 1.52k] ------------------ 3912| 0| { 3913| | /* processed Reconnected layer component that is also present in Disconnected layer */ 3914| 0| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 25| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3914:25): [True: 0, False: 0] ------------------ 3915| 0| { 3916| 0| delta_recmet_prot[k] += num_prot[k] - num_prot_prev[k]; 3917| 0| } 3918| 0| } 3919| 1.52k| } 3920| | 3921| 63| memcpy(pProtonBalance, num_prot, sizeof(num_prot)); 3922| 63| if (recmet_change_balance) ------------------ | Branch (3922:9): [True: 1, False: 62] ------------------ 3923| 1| { 3924| 1| memcpy(recmet_change_balance, delta_recmet_prot, sizeof(delta_recmet_prot)); 3925| 1| } 3926| | 3927| 70|exit_function: 3928| | 3929| 70| return ret < 0 ? ret : num_changed; ------------------ | Branch (3929:12): [True: 7, False: 63] ------------------ 3930| 63|} GetPlusMinusVertex: 27| 110|{ 28| 110| int k, ePlusSuper, eMinusSuper, vPlusSuper, vPlusMinus1 = NO_VERTEX, vPlusMinus2 = NO_VERTEX; /* djb-rwth: removing redundant variables */ ------------------ | | 118| 110|#define NO_VERTEX -2 ------------------ int k, ePlusSuper, eMinusSuper, vPlusSuper, vPlusMinus1 = NO_VERTEX, vPlusMinus2 = NO_VERTEX; /* djb-rwth: removing redundant variables */ ------------------ | | 118| 110|#define NO_VERTEX -2 ------------------ 29| 110| BNS_EDGE *pEdge; 30| 110| if (( k = pTCGroups->nGroup[TCG_Plus] ) >= 0 && ------------------ | Branch (30:9): [True: 107, False: 3] ------------------ 31| 107| ( ePlusSuper = pTCGroups->pTCG[k].nForwardEdge ) > 0 && ------------------ | Branch (31:9): [True: 107, False: 0] ------------------ 32| 107| ( vPlusSuper = pTCGroups->pTCG[k].nVertexNumber ) >= pBNS->num_atoms && ------------------ | Branch (32:9): [True: 107, False: 0] ------------------ 33| 107| !( ( pEdge = pBNS->edge + ePlusSuper )->forbidden && bCheckForbiddenPlus )) ------------------ | Branch (33:13): [True: 0, False: 107] | Branch (33:63): [True: 0, False: 0] ------------------ 34| 107| { 35| | 36| 107| vPlusMinus1 = pEdge->neighbor12 ^ vPlusSuper; 37| 107| } 38| 110| if (( k = pTCGroups->nGroup[TCG_Minus] ) >= 0 && ------------------ | Branch (38:9): [True: 97, False: 13] ------------------ 39| 97| ( eMinusSuper = pTCGroups->pTCG[k].nForwardEdge ) > 0 && ------------------ | Branch (39:9): [True: 97, False: 0] ------------------ 40| 97| ( pTCGroups->pTCG[k].nVertexNumber ) >= pBNS->num_atoms && /* djb-rwth: removing redundant code */ ------------------ | Branch (40:9): [True: 97, False: 0] ------------------ 41| 97| !( ( pEdge = pBNS->edge + eMinusSuper )->forbidden && bCheckForbiddenMinus )) ------------------ | Branch (41:13): [True: 0, False: 97] | Branch (41:64): [True: 0, False: 0] ------------------ 42| 97| { 43| | 44| 97| vPlusMinus2 = pEdge->neighbor12 ^ eMinusSuper; 45| 97| } 46| 110| if ((bCheckForbiddenPlus && NO_VERTEX == vPlusMinus1) || ------------------ | | 118| 110|#define NO_VERTEX -2 ------------------ | Branch (46:10): [True: 110, False: 0] | Branch (46:33): [True: 3, False: 107] ------------------ 47| 107| (bCheckForbiddenMinus && NO_VERTEX == vPlusMinus2)) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 118| 107|#define NO_VERTEX -2 ------------------ | Branch (47:11): [True: 107, False: 0] | Branch (47:35): [True: 10, False: 97] ------------------ 48| 13| { 49| 13| return NO_VERTEX; ------------------ | | 118| 13|#define NO_VERTEX -2 ------------------ 50| 13| } 51| | 52| 97| return ( NO_VERTEX != vPlusMinus1 ) ? vPlusMinus1 : vPlusMinus2; ------------------ | | 118| 97|#define NO_VERTEX -2 ------------------ | Branch (52:12): [True: 97, False: 0] ------------------ 53| 110|} bIsUnsatCarbonInASmallRing: 62| 1.22k|{ 63| 1.22k| int j, nCurRingSize, nMinRingSize; 64| 1.22k| if (min_ring_size < 5) ------------------ | Branch (64:9): [True: 265, False: 957] ------------------ 65| 265| { 66| | /* =C= in a small ring */ 67| 265| if (at2[iat].valence == 2 && ------------------ | Branch (67:13): [True: 44, False: 221] ------------------ 68| 44| pVA[iat].cMinRingSize <= 5 && ------------------ | Branch (68:14): [True: 44, False: 0] ------------------ 69| 44| at2[iat].chem_bonds_valence == 4) ------------------ | Branch (69:14): [True: 44, False: 0] ------------------ 70| 44| { 71| 44| return 1; 72| 44| } 73| 265| } 74| 957| else 75| 957| { 76| 957| if (at2[iat].valence == 2 && ------------------ | Branch (76:13): [True: 124, False: 833] ------------------ 77| 124| pVA[iat].cMinRingSize && ------------------ | Branch (77:14): [True: 84, False: 40] ------------------ 78| 84| pVA[iat].cMinRingSize <= min_ring_size && ------------------ | Branch (78:14): [True: 84, False: 0] ------------------ 79| 84| at2[iat].chem_bonds_valence == 3) ------------------ | Branch (79:14): [True: 0, False: 84] ------------------ 80| 0| { 81| 0| return 1; 82| 0| } 83| 957| nCurRingSize = nMinRingSize = min_ring_size + 1; 84| 957| if (( at2[iat].valence == 2 || at2[iat].valence == 3 ) && ------------------ | Branch (84:15): [True: 124, False: 833] | Branch (84:40): [True: 829, False: 4] ------------------ 85| 953| at2[iat].chem_bonds_valence == at2[iat].valence + 1) ------------------ | Branch (85:14): [True: 829, False: 124] ------------------ 86| 829| { 87| 3.31k| for (j = 0; j < at2[iat].valence; j++) ------------------ | Branch (87:25): [True: 2.48k, False: 829] ------------------ 88| 2.48k| { 89| 2.48k| nCurRingSize = is_bond_in_Nmax_memb_ring( at2, iat, j, pbfsq->q, 90| 2.48k| pbfsq->nAtomLevel, 91| 2.48k| pbfsq->cSource, (AT_RANK) nMinRingSize /* max ring size */ ); 92| 2.48k| if (0 < nCurRingSize && nCurRingSize < nMinRingSize) ------------------ | Branch (92:21): [True: 197, False: 2.29k] | Branch (92:41): [True: 197, False: 0] ------------------ 93| 197| { 94| 197| nMinRingSize = nCurRingSize; 95| 197| } 96| 2.48k| } 97| 829| return ( 0 <= nCurRingSize ) ? ( nMinRingSize <= min_ring_size ) : nCurRingSize; ------------------ | Branch (97:20): [True: 829, False: 0] ------------------ 98| 829| } 99| 957| } 100| | 101| 349| return 0; 102| 1.22k|} FixMobileHRestoredStructure: 128| 12.6k|{ 129| | /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/ 130| | /* at2 should be the most recently restored atom, Fixed-H */ 131| 12.6k| int i, j, k, iat, delta, cur_success, ret = 0; /* djb-rwth: removing redundant variables/code */ 132| 12.6k| CMP2MHINCHI c2i; 133| 12.6k| CMP2MHINCHI *pc2i = &c2i; 134| | 135| 12.6k| EDGE_LIST AllChargeEdges, CurrEdges, CurrEdges2, CurrEdges3, TautEdges, NFlowerEdges, OtherNFlowerEdges, FixedLargeRingStereoEdges; 136| 12.6k| EDGE_LIST *pEdgeList = NULL; 137| | 138| 12.6k| EdgeIndex e; 139| 12.6k| BNS_EDGE *pe; 140| 12.6k| Vertex v1, v2, vPlusMinus; 141| 12.6k| BNS_VERTEX *pv1, *pv2; 142| | 143| 12.6k| Vertex vPathStart, vPathEnd; 144| 12.6k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 145| | 146| 12.6k| int forbidden_edge_mask_inv = ~forbidden_edge_mask; /* djb-rwth: removing redundant variables */ 147| | 148| | INCHI_HEAPCHK 149| | 150| 12.6k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 151| 12.6k| AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 152| 12.6k| AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 153| 12.6k| AllocEdgeList( &CurrEdges2, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 154| 12.6k| AllocEdgeList( &CurrEdges3, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 155| 12.6k| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 156| 12.6k| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 157| 12.6k| AllocEdgeList( &TautEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 12.6k|#define EDGE_LIST_CLEAR (-1) ------------------ 158| | 159| | /* djb-rwth: removing redundant code */ 160| | 161| 12.6k| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (161:9): [True: 12.6k, False: 0] | Branch (161:37): [True: 0, False: 12.6k] ------------------ 162| 0| { 163| 0| goto exit_function; /* no fixed-H found */ 164| 0| } 165| | /* taut group edges */ 166| 12.8k| for (i = 0; i < pTCGroups->num_tgroups; i++) ------------------ | Branch (166:17): [True: 238, False: 12.6k] ------------------ 167| 238| { 168| 238| pv1 = pBNS->vert + ( v1 = pTCGroups->pTCG[i].nVertexNumber ); /* t-group vertex */ /* djb-rwth: ignoring LLVM warning: see comments below */ 169| 724| for (j = 0; j < pv1->num_adj_edges; j++) ------------------ | Branch (169:21): [True: 486, False: 238] ------------------ 170| 486| { 171| | /* e, pe - tautomeric atom edge; pv2 - endpoint vertex */ 172| | /* Note: pe, pv2, v1 are not used here; they are to show how to traverse t-group */ 173| 486| pv2 = pBNS->vert + ( pe = pBNS->edge + ( e = pv1->iedge[j] ) )->neighbor1; /* djb-rwth: ignoring LLVM warning: see comments above */ 174| 486| if ((ret = AddToEdgeList( &TautEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 486|#define INC_ADD_EDGE 64 ------------------ | Branch (174:17): [True: 0, False: 486] ------------------ 175| 0| { 176| 0| goto exit_function; 177| 0| } 178| 486| } 179| 238| } 180| | /* charge and flower edges */ 181| 76.5k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (181:17): [True: 63.9k, False: 12.6k] ------------------ 182| 63.9k| { 183| 63.9k| if (( e = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (183:13): [True: 36.5k, False: 27.3k] | Branch (183:57): [True: 36.5k, False: 0] ------------------ 184| 36.5k| ( ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 20| 36.5k|#define INC_ADD_EDGE 64 ------------------ | Branch (184:13): [True: 0, False: 36.5k] ------------------ 185| 0| { 186| 0| goto exit_function; 187| 0| } 188| 63.9k| if (( e = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (188:13): [True: 46.0k, False: 17.9k] | Branch (188:56): [True: 44.6k, False: 1.40k] ------------------ 189| 44.6k| { 190| 44.6k| if ((ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 44.6k|#define INC_ADD_EDGE 64 ------------------ | Branch (190:17): [True: 0, False: 44.6k] ------------------ 191| 0| { 192| 0| goto exit_function; 193| 0| } 194| | 195| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 196| 44.6k| if (pVA[i].cNumValenceElectrons == 5 && !pVA[i].cMetal && /* N, P, As */ ------------------ | Branch (196:17): [True: 12.3k, False: 32.2k] | Branch (196:53): [True: 11.9k, False: 392] ------------------ 197| 11.9k| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) )) ------------------ | | 118| 11.9k|#define NO_VERTEX -2 ------------------ | Branch (197:18): [True: 2.60k, False: 9.38k] ------------------ 198| 2.60k| { 199| | 200| 2.60k| if (!pBNS->edge[j].forbidden && pBNS->edge[j].flow) ------------------ | Branch (200:21): [True: 2.60k, False: 0] | Branch (200:49): [True: 1.54k, False: 1.06k] ------------------ 201| 1.54k| { 202| 1.54k| if ((ret = AddToEdgeList( &AllChargeEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 1.54k|#define INC_ADD_EDGE 64 ------------------ | Branch (202:25): [True: 0, False: 1.54k] ------------------ 203| 0| { 204| 0| goto exit_function; 205| 0| } 206| 1.54k| if ((ret = AddToEdgeList( &NFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 1.54k|#define INC_ADD_EDGE 64 ------------------ | Branch (206:25): [True: 0, False: 1.54k] ------------------ 207| 0| { 208| 0| goto exit_function; 209| 0| } 210| 1.54k| } 211| 1.06k| else 212| 1.06k| { 213| 1.06k| if ((ret = AddToEdgeList( &OtherNFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 1.06k|#define INC_ADD_EDGE 64 ------------------ | Branch (213:25): [True: 0, False: 1.06k] ------------------ 214| 0| { 215| 0| goto exit_function; 216| 0| } 217| 1.06k| } 218| 2.60k| } 219| 44.6k| } 220| 63.9k| } 221| 12.6k| if (forbidden_stereo_edge_mask) ------------------ | Branch (221:9): [True: 12.6k, False: 0] ------------------ 222| 12.6k| { 223| 76.5k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (223:21): [True: 63.9k, False: 12.6k] ------------------ 224| 63.9k| { 225| 182k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (225:25): [True: 118k, False: 63.9k] ------------------ 226| 118k| { 227| 118k| if (pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask) ------------------ | Branch (227:21): [True: 328, False: 118k] ------------------ 228| 328| { 229| 328| int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q, 230| 328| pStruct->pbfsq->nAtomLevel, 231| 328| pStruct->pbfsq->cSource, 99 /* max ring size */ ); 232| 328| if (0 < nMinRingSize && ( ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, INC_ADD_EDGE ) )) ------------------ | | 20| 218|#define INC_ADD_EDGE 64 ------------------ | Branch (232:25): [True: 218, False: 110] | Branch (232:45): [True: 0, False: 218] ------------------ 233| 0| { 234| 0| goto exit_function; 235| 0| } 236| 328| } 237| 118k| } 238| 63.9k| } 239| 12.6k| } 240| | 241| | INCHI_HEAPCHK 242| | 243| 12.6k| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (243:9): [True: 0, False: 12.6k] ------------------ 244| 0| { 245| 0| goto exit_function; 246| 0| } 247| | 248| 12.6k| INCHI_HEAPCHK 249| 12.6k| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (249:9): [True: 25, False: 12.6k] ------------------ 250| 25| { 251| 25| goto exit_function; 252| 25| } 253| | 254| | INCHI_HEAPCHK 255| | 256| | 257| | 258| | 259| 12.6k| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && ------------------ | Branch (259:9): [True: 200, False: 12.4k] | Branch (259:37): [True: 171, False: 29] | Branch (259:82): [True: 2, False: 27] ------------------ 260| 173| pc2i->nNumTgDBNMinusRevrs + pc2i->nNumTgNHMinusRevrs == 0 && pc2i->nNumTgOMinusInChI && ------------------ | Branch (260:13): [True: 170, False: 3] | Branch (260:74): [True: 32, False: 138] ------------------ 261| 32| !( pTCGroups->pTCG[0].tg_RestoreFlags & TGRF_MINUS_FIRST )) ------------------ | Branch (261:13): [True: 32, False: 0] ------------------ 262| 32| { /*----------------------------------------------------*/ 263| | /* case 01: restored has -O(-) and does not have N(-) */ 264| | /* endpoints defined by the original InChI */ 265| | /* restored has single taut. group or more */ 266| | /* tautomeric endpoints. */ 267| | /* Solution: move (-) from endp. -O(-) to endpoints N */ 268| | /*------- 269| |---------------------------------------------*/ 270| 32| pTCGroups->pTCG[0].tg_RestoreFlags |= TGRF_MINUS_FIRST; 271| | /* recalculate InChI from the structure */ 272| 32| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (272:13): [True: 0, False: 32] ------------------ 273| 32| ppt_group_info, ppat_norm, ppat_prep ) )) 274| 0| { 275| 0| goto exit_function; 276| 0| } 277| 32| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (277:13): [True: 0, False: 32] ------------------ 278| 0| { 279| 0| goto exit_function; 280| 0| } 281| 32| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (281:13): [True: 32, False: 0] | Branch (281:41): [True: 0, False: 32] ------------------ 282| 0| { 283| 0| goto exit_function; /* no fixed-H found */ 284| 0| } 285| 32| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (285:13): [True: 0, False: 32] ------------------ 286| 0| { 287| 0| goto exit_function; 288| 0| } 289| 32| if (!pc2i->bHasDifference) ------------------ | Branch (289:13): [True: 0, False: 32] ------------------ 290| 0| { 291| 0| goto exit_function; /* nothing to do */ 292| 0| } 293| 32| } 294| 12.6k| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && ------------------ | Branch (294:9): [True: 200, False: 12.4k] | Branch (294:37): [True: 171, False: 29] | Branch (294:82): [True: 2, False: 27] ------------------ 295| 173| pc2i->nNumTgDBNMinusRevrs + pc2i->nNumTgNHMinusRevrs == 0 && pc2i->nNumTgOMinusInChI == 0) ------------------ | Branch (295:10): [True: 170, False: 3] | Branch (295:71): [True: 139, False: 31] ------------------ 296| 139| { 297| | /*-------------------------------------------------------*/ 298| | /* case 02: restored has no -O(-) and does not have N(-) */ 299| | /* restored has single taut. group or more */ 300| | /* tautomeric endpoints. */ 301| | /* Solution: >N-AB=N- => >N(+)=AB-NH- (add H(+)) */ 302| | /* Solution: >N-AB=NH => >N(+)=AB-NH2 (add H(+)) */ 303| | /* SB_N_III DB_N_III */ 304| | /*-------------------------------------------------------*/ 305| 139| int iat_SB_N_III[MAX_DIFF_MOBH], iat_DB_N_III[MAX_DIFF_MOBH]; 306| 139| int num_SB_N_III = 0, num_DB_N_III = 0, k1, k2; 307| 139| CurrEdges.num_edges = 0; 308| 139| cur_success = 0; 309| 942| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (309:21): [True: 803, False: 139] ------------------ 310| 803| { 311| 803| iat = i; 312| 803| if (pVA[iat].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (312:17): [True: 322, False: 481] | Branch (312:55): [True: 297, False: 25] ------------------ 313| 297| !at2[iat].endpoint && !at2[iat].charge && !at2[iat].radical) ------------------ | Branch (313:18): [True: 169, False: 128] | Branch (313:40): [True: 134, False: 35] | Branch (313:60): [True: 127, False: 7] ------------------ 314| 127| { 315| 127| if (num_DB_N_III < MAX_DIFF_MOBH && !at2[iat].num_H && ------------------ | | 457| 254|#define MAX_DIFF_MOBH 256 ------------------ | Branch (315:21): [True: 127, False: 0] | Branch (315:53): [True: 126, False: 1] ------------------ 316| 126| at2[iat].valence == 2 && ------------------ | Branch (316:22): [True: 69, False: 57] ------------------ 317| 69| at2[iat].chem_bonds_valence == 3 && ------------------ | Branch (317:22): [True: 69, False: 0] ------------------ 318| 69| !at2[iat].sb_parity[0] && /* do not eliminate stereobonds */ ------------------ | Branch (318:22): [True: 62, False: 7] ------------------ 319| 62| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (319:22): [True: 62, False: 0] | Branch (319:68): [True: 62, False: 0] ------------------ 320| 62| pBNS->edge[e].cap && !pBNS->edge[e].flow) ------------------ | Branch (320:22): [True: 62, False: 0] | Branch (320:43): [True: 61, False: 1] ------------------ 321| 61| { 322| | /* -N= */ 323| 61| iat_DB_N_III[num_DB_N_III++] = iat; 324| 61| } 325| 66| else 326| 66| { 327| 66| if (num_DB_N_III < MAX_DIFF_MOBH && 1 == at2[iat].num_H && ------------------ | | 457| 132|#define MAX_DIFF_MOBH 256 ------------------ | Branch (327:25): [True: 66, False: 0] | Branch (327:57): [True: 1, False: 65] ------------------ 328| 1| at2[iat].valence == 1 && ------------------ | Branch (328:26): [True: 0, False: 1] ------------------ 329| 0| at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (329:26): [True: 0, False: 0] ------------------ 330| 0| !at2[iat].sb_parity[0] && /* do not eliminate stereobonds */ ------------------ | Branch (330:26): [True: 0, False: 0] ------------------ 331| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (331:26): [True: 0, False: 0] | Branch (331:72): [True: 0, False: 0] ------------------ 332| 0| pBNS->edge[e].cap && !pBNS->edge[e].flow) ------------------ | Branch (332:26): [True: 0, False: 0] | Branch (332:47): [True: 0, False: 0] ------------------ 333| 0| { 334| | /* -N= */ 335| 0| iat_DB_N_III[num_DB_N_III++] = iat; 336| 0| } 337| 66| else 338| 66| { 339| 66| if (num_SB_N_III < MAX_DIFF_MOBH && !at2[iat].num_H && ------------------ | | 457| 132|#define MAX_DIFF_MOBH 256 ------------------ | Branch (339:29): [True: 66, False: 0] | Branch (339:61): [True: 65, False: 1] ------------------ 340| 65| at2[iat].valence == 3 && ------------------ | Branch (340:33): [True: 45, False: 20] ------------------ 341| 45| at2[iat].chem_bonds_valence == 3 && ------------------ | Branch (341:33): [True: 23, False: 22] ------------------ 342| 23| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (342:33): [True: 23, False: 0] | Branch (342:78): [True: 23, False: 0] ------------------ 343| 23| pBNS->edge[e].cap && pBNS->edge[e].flow) ------------------ | Branch (343:33): [True: 23, False: 0] | Branch (343:54): [True: 23, False: 0] ------------------ 344| 23| { 345| | /* -N< */ 346| 23| iat_SB_N_III[num_SB_N_III++] = iat; 347| 23| if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 23|#define INC_ADD_EDGE 64 ------------------ | Branch (347:33): [True: 0, False: 23] ------------------ 348| 0| { 349| 0| goto exit_function; 350| 0| } 351| 23| } 352| 66| } 353| 66| } 354| 127| } 355| 803| } 356| 139| if (num_DB_N_III && num_SB_N_III) ------------------ | Branch (356:13): [True: 40, False: 99] | Branch (356:29): [True: 11, False: 29] ------------------ 357| 11| { 358| 11| EdgeIndex ieMinus; 359| 11| BNS_EDGE *peMinus; 360| 11| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 361| 11| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 362| 23| for (i = 0; i < num_DB_N_III && !cur_success; i++) ------------------ | Branch (362:25): [True: 13, False: 10] | Branch (362:45): [True: 12, False: 1] ------------------ 363| 12| { 364| 12| iat = iat_DB_N_III[i]; 365| 12| e = pBNS->edge[k1 = pBNS->vert[iat].iedge[0]].flow ? k1 : ------------------ | Branch (365:21): [True: 4, False: 8] ------------------ 366| 12| pBNS->edge[k2 = pBNS->vert[iat].iedge[1]].flow ? k2 : NO_VERTEX; ------------------ | | 118| 12|#define NO_VERTEX -2 ------------------ | Branch (366:21): [True: 8, False: 0] ------------------ 367| 12| if (e == NO_VERTEX) ------------------ | | 118| 12|#define NO_VERTEX -2 ------------------ | Branch (367:21): [True: 0, False: 12] ------------------ 368| 0| { 369| 0| continue; /* should not happen */ 370| 0| } 371| 12| ieMinus = pVA[iat].nCMinusGroupEdge - 1; 372| 12| peMinus = pBNS->edge + ieMinus; 373| 12| pe = pBNS->edge + e; 374| 12| if (!pe->flow) ------------------ | Branch (374:21): [True: 0, False: 12] ------------------ 375| 0| continue; 376| 12| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 377| 12| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 378| | 379| 12| pe->forbidden |= forbidden_edge_mask; /* fix double bond */ 380| 12| peMinus->forbidden &= forbidden_edge_mask_inv; /* allow negative charge */ 381| 12| delta = 1; 382| 12| pe->flow -= delta; /* remove (-) from AB-O(-) */ 383| 12| pv1->st_edge.flow -= delta; 384| 12| pv2->st_edge.flow -= delta; 385| 12| pBNS->tot_st_flow -= 2 * delta; 386| | 387| 12| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 388| 12| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 389| | 390| 12| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (390:21): [True: 11, False: 1] | Branch (390:36): [True: 2, False: 9] | Branch (390:54): [True: 1, False: 1] ------------------ 391| 10| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 2) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (391:22): [True: 8, False: 2] | Branch (391:40): [True: 7, False: 1] | Branch (391:63): [True: 5, False: 3] ------------------ 392| 5| { 393| | /* Added (-)charge -N= and (+) to -N< => nDeltaCharge == 2 */ 394| 5| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 395| 5| if (ret > 0) ------------------ | Branch (395:25): [True: 5, False: 0] ------------------ 396| 5| { 397| | /* djb-rwth: removing redundant code */ 398| 5| cur_success++; /* 01 */ 399| | 400| | /* eliminate (-) charge and add H */ 401| 5| pv1 = pBNS->vert + ( v1 = peMinus->neighbor1 ); /* atom */ 402| 5| pv2 = pBNS->vert + ( v2 = peMinus->neighbor12 ^ v1 );/* (=) vertex */ /* djb-rwth: ignoring LLVM warning: consistency of the code */ 403| | /* effectively eliminate (-) edge by setting its cap=flow= 0 */ 404| 5| peMinus->cap--; 405| 5| peMinus->flow--; 406| 5| pv1->st_edge.cap--; 407| 5| pv1->st_edge.flow--; 408| 5| pv2->st_edge.cap--; 409| 5| pv2->st_edge.flow--; 410| 5| pBNS->tot_st_flow -= 2; 411| 5| pBNS->tot_st_cap -= 2; 412| | /* add H */ 413| 5| pStruct->at[iat].num_H++; 414| | /* register total charge increase */ 415| 5| pTCGroups->total_charge++; 416| 5| pStruct->nNumRemovedProtonsByRevrs -= 1; 417| 5| } 418| 5| } 419| 7| else 420| 7| { 421| 7| pe->forbidden &= forbidden_edge_mask_inv; 422| 7| peMinus->forbidden |= forbidden_edge_mask; 423| 7| pe->flow += delta; 424| 7| pv1->st_edge.flow += delta; 425| 7| pv2->st_edge.flow += delta; 426| 7| pBNS->tot_st_flow += 2 * delta; 427| 7| } 428| 12| } 429| 11| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 430| 11| CurrEdges.num_edges = 0; /* clear current edge list */ 431| | 432| 11| if (cur_success) ------------------ | Branch (432:17): [True: 5, False: 6] ------------------ 433| 5| { 434| | /* djb-rwth: removing redundant code */ 435| | /* recalculate InChI from the structure */ 436| | /* recalculate InChI from the structure */ 437| 5| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (437:21): [True: 0, False: 5] ------------------ 438| 5| ppt_group_info, ppat_norm, ppat_prep ) )) 439| 0| { 440| 0| goto exit_function; 441| 0| } 442| 5| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (442:21): [True: 0, False: 5] ------------------ 443| 0| { 444| 0| goto exit_function; 445| 0| } 446| 5| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (446:21): [True: 0, False: 5] ------------------ 447| 0| { 448| 0| goto exit_function; 449| 0| } 450| 5| if (!pc2i->bHasDifference) ------------------ | Branch (450:21): [True: 0, False: 5] ------------------ 451| 0| { 452| 0| goto exit_function; /* nothing to do */ 453| 0| } 454| 5| } 455| 11| } 456| 139| } 457| 12.6k| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && /* ADP */ ------------------ | Branch (457:9): [True: 200, False: 12.4k] | Branch (457:37): [True: 170, False: 30] | Branch (457:82): [True: 2, False: 28] ------------------ 458| 172| pc2i->nNumTgMInChI == 0 && pc2i->nNumTgNInChI && pc2i->nNumTgOInChI) ------------------ | Branch (458:9): [True: 116, False: 56] | Branch (458:36): [True: 75, False: 41] | Branch (458:58): [True: 51, False: 24] ------------------ 459| 51| { 460| | /*-------------------------------------------------------*/ 461| | /* case 03: restored has N and O endpoints, no (-) endp */ 462| | /* case 04: original has single taut. group or more */ 463| | /* tautomeric endpoints. */ 464| | /* Solution: 1. Move taut attachment from O to N */ 465| | /* Solution: 2. Replace the attachment with (-) */ 466| | /* SB_N_III DB_N_III */ 467| | /*-------------------------------------------------------*/ 468| | /* 469| | int iat_SB_N_III[MAX_DIFF_MOBH], iat_DB_N_III[MAX_DIFF_MOBH]; 470| | int num_SB_N_III = 0, num_DB_N_III = 0, k1, k2, 471| | */ 472| 51| int itg, j1, j2, bAction = 0; 473| 51| BNS_VERTEX *pTg, *pvEndp, *pvEndp2, *pvCent; /* djb-rwth: ignoring LLVM warning: variable used to store initialisation values */ 474| 51| Vertex vEndp, vEndp2, vCent; 475| 51| BNS_EDGE *peTg, *peTg2, *peCent1, *peCent2; 476| 51| EdgeIndex eTg, eTg2; 477| | 478| 51| CurrEdges.num_edges = 0; 479| 51| CurrEdges2.num_edges = 0; 480| 51| cur_success = 0; 481| | 482| | /* 1st attempt: -NH-=O => -N(-)-=O or -N=-OH => -N(-)-=O */ 483| 102| for (itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg++) ------------------ | Branch (483:23): [True: 51, False: 51] | Branch (483:55): [True: 51, False: 0] ------------------ 484| 51| { 485| 51| pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; 486| 191| for (i = 0; i < pTg->num_adj_edges && !cur_success; i++) ------------------ | Branch (486:25): [True: 142, False: 49] | Branch (486:51): [True: 140, False: 2] ------------------ 487| 140| { 488| 140| pvEndp = pBNS->vert + ( vEndp = ( peTg = pBNS->edge + ( eTg = pTg->iedge[i] ) )->neighbor1 ); /* djb-rwth: ignoring LLVM warning: value used */ 489| 140| eTg2 = -1; 490| 140| if (pVA[vEndp].cNumValenceElectrons == 6 && peTg->cap) ------------------ | Branch (490:21): [True: 87, False: 53] | Branch (490:61): [True: 78, False: 9] ------------------ 491| 78| { 492| | /* endpoint -OH or =O found; search for a possible centerpoint */ 493| 160| for (j1 = 0; j1 < at2[vEndp].valence && eTg2 < 0; j1++) ------------------ | Branch (493:34): [True: 83, False: 77] | Branch (493:61): [True: 82, False: 1] ------------------ 494| 82| { 495| 82| peCent1 = pBNS->edge + pvEndp->iedge[j1]; /* edge from O to a centerpoint */ 496| 82| pvCent = pBNS->vert + ( vCent = peCent1->neighbor12 ^ vEndp ); /* centerpoint */ 497| 82| if (at2[vCent].endpoint || !peCent1->cap || ------------------ | Branch (497:29): [True: 12, False: 70] | Branch (497:52): [True: 7, False: 63] ------------------ 498| 63| peCent1->flow + ( peTg->cap == peTg->flow ) != 1) ------------------ | Branch (498:30): [True: 8, False: 55] ------------------ 499| 27| { 500| 27| continue; 501| 27| } 502| | /* search for another endpoint, N, around vCent */ 503| 256| for (j2 = 0; j2 < at2[vCent].valence; j2++) ------------------ | Branch (503:38): [True: 204, False: 52] ------------------ 504| 204| { 505| 204| peCent2 = pBNS->edge + pvCent->iedge[j2]; 506| 204| pvEndp2 = pBNS->vert + ( vEndp2 = peCent2->neighbor12 ^ vCent ); /* djb-rwth: ignoring LLVM warning: variable used to store initialisation values */ 507| 204| if (!peCent2->cap || peCent2->flow + peCent1->flow != 1 || ------------------ | Branch (507:33): [True: 11, False: 193] | Branch (507:50): [True: 126, False: 67] ------------------ 508| 67| at2[vEndp2].endpoint != itg + 1 || ------------------ | Branch (508:34): [True: 51, False: 16] ------------------ 509| 16| pVA[vEndp2].cNumValenceElectrons != 5 || ------------------ | Branch (509:34): [True: 4, False: 12] ------------------ 510| 12| 0 > ( j = pVA[vEndp2].nTautGroupEdge - 1 ) || ------------------ | Branch (510:34): [True: 0, False: 12] ------------------ 511| 12| ( peTg2 = pBNS->edge + j )->forbidden || ------------------ | Branch (511:34): [True: 0, False: 12] ------------------ 512| 12| peCent2->flow + ( peTg2->cap == peTg2->flow ) != 1) ------------------ | Branch (512:34): [True: 9, False: 3] ------------------ 513| 201| { 514| 201| continue; 515| 201| } 516| 3| eTg2 = j; 517| 3| break; /* found OH-C=N- or O=C-NH- */ 518| 204| } 519| 55| } 520| 78| } 521| 140| if (eTg2 >= 0) ------------------ | Branch (521:21): [True: 3, False: 137] ------------------ 522| 3| { 523| | /*-------------------------------------------- 524| | tg tg 525| | eTg //\ eTg2 eTg / \\eTg2 526| | // \ / \\ 527| | vEndp HO--C==N vEndp2 --> vEndp O==C--NH vEndp2 528| | ^ ^ ^ ^ ^ ^ 529| | eCent1 | eCent2 eCent1 | eCent2 530| | vCent vCent 531| | 532| | additional action: -OH-C=N- => O=C-NH- 533| | -------------------------------------------*/ 534| 3| if (0 == peTg->cap - peTg->flow && 1 == peTg2->cap - peTg2->flow && ------------------ | Branch (534:25): [True: 2, False: 1] | Branch (534:56): [True: 2, False: 0] ------------------ 535| 2| 0 == peCent1->flow && 1 == peCent2->flow) ------------------ | Branch (535:26): [True: 2, False: 0] | Branch (535:48): [True: 2, False: 0] ------------------ 536| 2| { 537| 2| peTg->flow--; /* 03 prepare */ 538| 2| peTg2->flow++; 539| 2| peCent2->flow--; 540| 2| peCent1->flow++; 541| 2| bAction |= 1; /* switched H position */ 542| 2| } 543| 3| if (1 == peTg->cap - peTg->flow && 0 == peTg2->cap - peTg2->flow && ------------------ | Branch (543:25): [True: 3, False: 0] | Branch (543:56): [True: 3, False: 0] ------------------ 544| 3| 1 == peCent1->flow && 0 == peCent2->flow) ------------------ | Branch (544:26): [True: 3, False: 0] | Branch (544:48): [True: 3, False: 0] ------------------ 545| 3| { 546| | /* replace -NH- with -N(-)- */ 547| 3| pTCGroups->pTCG[itg].tg_num_H--; 548| 3| pTCGroups->pTCG[itg].tg_num_Minus++; 549| 3| pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; 550| 3| pTCGroups->pTCG[itg].tg_set_Minus = vEndp2 + 1; 551| 3| pStruct->ti.t_group[itg].num[1] ++; /* increment number of (-), keep number of taut attachments */ 552| 3| pTCGroups->total_charge--; 553| 3| pTCGroups->tgroup_charge--; 554| 3| pStruct->nNumRemovedProtonsByRevrs += 1; 555| 3| bAction |= 2; /* single NH (at2[vEndp2]) replaced with N(-) */ 556| 3| cur_success++; /* 03/04 */ 557| 3| } 558| 3| } 559| 140| } 560| 51| } 561| | 562| 51| if (0 == pc2i->nNumTgNHInChI + pc2i->nNumTgNH2InChI && pc2i->nNumTgOHInChI && !cur_success) ------------------ | Branch (562:13): [True: 45, False: 6] | Branch (562:64): [True: 16, False: 29] | Branch (562:87): [True: 14, False: 2] ------------------ 563| 14| { 564| | /* transfer an attachement to N */ 565| 28| for (itg = 0; itg < pTCGroups->num_tgroups; itg++) ------------------ | Branch (565:27): [True: 14, False: 14] ------------------ 566| 14| { 567| 14| pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; 568| 46| for (i = 0; i < pTg->num_adj_edges; i++) ------------------ | Branch (568:29): [True: 32, False: 14] ------------------ 569| 32| { 570| 32| pvEndp = pBNS->vert + ( vEndp = ( peTg = pBNS->edge + ( eTg = pTg->iedge[i] ) )->neighbor1 ); 571| 32| if (pVA[vEndp].cNumValenceElectrons == 6 && ------------------ | Branch (571:25): [True: 17, False: 15] ------------------ 572| 17| at2[vEndp].valence == at2[vEndp].chem_bonds_valence && ------------------ | Branch (572:26): [True: 16, False: 1] ------------------ 573| 16| peTg->flow && peTg->flow == peTg->cap) ------------------ | Branch (573:26): [True: 14, False: 2] | Branch (573:40): [True: 14, False: 0] ------------------ 574| 14| { 575| | /* endpoint -OH found; save the tautomeric group edge */ 576| 14| if ((ret = AddToEdgeList( &CurrEdges, eTg, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 14|#define INC_ADD_EDGE 64 ------------------ | Branch (576:29): [True: 0, False: 14] ------------------ 577| 0| { 578| 0| goto exit_function; 579| 0| } 580| 14| } 581| 18| else 582| 18| { 583| 18| if (pVA[vEndp].cNumValenceElectrons == 5 && ------------------ | Branch (583:29): [True: 15, False: 3] ------------------ 584| 15| pVA[vEndp].cPeriodicRowNumber == 1 && ------------------ | Branch (584:30): [True: 15, False: 0] ------------------ 585| 15| at2[vEndp].valence + 1 == at2[vEndp].chem_bonds_valence && ------------------ | Branch (585:30): [True: 13, False: 2] ------------------ 586| 13| peTg->cap && peTg->flow + 1 == peTg->cap) ------------------ | Branch (586:30): [True: 13, False: 0] | Branch (586:43): [True: 10, False: 3] ------------------ 587| 10| { 588| | /* endpoint -N= or =NH found, check for -N=-OH */ 589| 10| e = -1; 590| 29| for (j1 = 0; j1 < at2[vEndp].valence && e < 0; j1++) ------------------ | Branch (590:42): [True: 20, False: 9] | Branch (590:69): [True: 19, False: 1] ------------------ 591| 19| { 592| 19| peCent1 = pBNS->edge + pvEndp->iedge[j1]; 593| 19| if (peCent1->flow == 1) ------------------ | Branch (593:37): [True: 10, False: 9] ------------------ 594| 10| { 595| | /* double bond */ 596| 10| pvCent = pBNS->vert + ( vCent = peCent1->neighbor12 ^ vEndp ); 597| 10| if (at2[vCent].endpoint) ------------------ | Branch (597:41): [True: 3, False: 7] ------------------ 598| 3| continue; 599| 20| for (j2 = 0; j2 < at2[vCent].valence; j2++) ------------------ | Branch (599:50): [True: 14, False: 6] ------------------ 600| 14| { 601| 14| peCent2 = pBNS->edge + pvCent->iedge[j2]; 602| 14| pvEndp2 = pBNS->vert + ( vEndp2 = peCent2->neighbor12 ^ vCent ); /* djb-rwth: ignoring LLVM warning: variable used to store initialisation values */ 603| 14| if (peCent2->flow || at2[vEndp2].endpoint != itg + 1 || ------------------ | Branch (603:45): [True: 9, False: 5] | Branch (603:62): [True: 3, False: 2] ------------------ 604| 2| pVA[vEndp2].cNumValenceElectrons != 6 || ------------------ | Branch (604:46): [True: 0, False: 2] ------------------ 605| 2| 0 >= ( e = pVA[vEndp2].nTautGroupEdge - 1 ) || ------------------ | Branch (605:46): [True: 0, False: 2] ------------------ 606| 2| pBNS->edge[e].forbidden || !pBNS->edge[e].flow) ------------------ | Branch (606:46): [True: 0, False: 2] | Branch (606:73): [True: 1, False: 1] ------------------ 607| 13| { 608| 13| e = -1; 609| 13| continue; 610| 13| } 611| | /*********************/ 612| | /* found -N=X-OH */ 613| | /* vEndp ^ vEndp2 */ 614| | /* vCent */ 615| | /*********************/ 616| | /* save this -OH taut edge */ 617| 1| if ((ret = AddToEdgeList( &CurrEdges2, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 1|#define INC_ADD_EDGE 64 ------------------ | Branch (617:45): [True: 0, False: 1] ------------------ 618| 0| { 619| 0| goto exit_function; 620| 0| } 621| 1| break; 622| 1| } 623| 7| } 624| 19| } 625| 10| if (e < 0 && ( ret = AddToEdgeList( &CurrEdges, eTg, INC_ADD_EDGE ) )) ------------------ | | 20| 9|#define INC_ADD_EDGE 64 ------------------ | Branch (625:33): [True: 9, False: 1] | Branch (625:42): [True: 0, False: 9] ------------------ 626| 0| { 627| 0| goto exit_function; 628| 0| } 629| 10| } 630| 18| } 631| 32| } 632| 14| } 633| | /* rearrange the flows */ 634| 14| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 635| 14| SetForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 636| 14| SetForbiddenEdgeMask( pBNS, &CurrEdges2, forbidden_edge_mask ); 637| 14| pEdgeList = CurrEdges2.num_edges ? &CurrEdges2 : CurrEdges.num_edges ? &CurrEdges : NULL; ------------------ | Branch (637:25): [True: 1, False: 13] | Branch (637:62): [True: 13, False: 0] ------------------ 638| | 639| 37| for (i = 0; pEdgeList && i < pEdgeList->num_edges && !cur_success; i++) ------------------ | Branch (639:25): [True: 37, False: 0] | Branch (639:38): [True: 23, False: 14] | Branch (639:66): [True: 23, False: 0] ------------------ 640| 23| { 641| 23| pe = pBNS->edge + pEdgeList->pnEdges[i]; /* pe->flow = 1 <=> -OH */ 642| 23| if (!pe->flow) ------------------ | Branch (642:21): [True: 9, False: 14] ------------------ 643| 9| continue; 644| 14| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); /* -OH atom */ 645| 14| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); /* t-group vertex */ 646| | /* locate the t-group */ 647| 14| for (itg = 0; itg < pTCGroups->num_tgroups; itg++) ------------------ | Branch (647:31): [True: 14, False: 0] ------------------ 648| 14| { 649| 14| if (v2 == pTCGroups->pTCG[itg].nVertexNumber) ------------------ | Branch (649:25): [True: 14, False: 0] ------------------ 650| 14| { 651| 14| break; 652| 14| } 653| 14| } 654| 14| if (itg == pTCGroups->num_tgroups) ------------------ | Branch (654:21): [True: 0, False: 14] ------------------ 655| 0| { 656| | /* tgroup not found -- should not happen */ 657| 0| continue; 658| 0| } 659| | 660| 14| delta = 1; 661| 14| pe->flow -= delta; /* add one attachment to */ 662| 14| pv1->st_edge.flow -= delta; 663| 14| pv2->st_edge.flow -= delta; 664| 14| pBNS->tot_st_flow -= 2 * delta; 665| | 666| 14| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 667| 14| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 668| | 669| 14| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (669:21): [True: 6, False: 8] | Branch (669:36): [True: 2, False: 4] | Branch (669:54): [True: 0, False: 2] ------------------ 670| 6| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 2) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (670:22): [True: 4, False: 2] | Branch (670:40): [True: 1, False: 3] | Branch (670:63): [True: 0, False: 1] ------------------ 671| 0| { 672| | /* Added (-)charge -N= and (+) to -N< => nDeltaCharge == 2 */ 673| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 674| 0| if (ret > 0) ------------------ | Branch (674:25): [True: 0, False: 0] ------------------ 675| 0| { 676| | /* djb-rwth: removing redundant code */ 677| 0| cur_success++; /* 03 */ 678| | /* replace -NH- with -N(-)- */ 679| 0| pTCGroups->pTCG[itg].tg_num_H--; 680| 0| pTCGroups->pTCG[itg].tg_num_Minus++; 681| 0| pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; 682| 0| pStruct->ti.t_group[itg].num[1] ++; 683| 0| pTCGroups->total_charge--; 684| 0| pTCGroups->tgroup_charge--; 685| 0| pStruct->nNumRemovedProtonsByRevrs += 1; 686| 0| bAction |= 4; /* H in the 1st available NH was replaced with (-) */ 687| 0| } 688| 0| } 689| 14| else 690| 14| { 691| 14| pe->flow += delta; 692| 14| pv1->st_edge.flow += delta; 693| 14| pv2->st_edge.flow += delta; 694| 14| pBNS->tot_st_flow += 2 * delta; 695| 14| } 696| 14| } 697| 14| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 698| 14| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 699| 14| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 700| 14| } 701| 37| else 702| 37| { 703| 37| if (pc2i->nNumTgNHInChI + pc2i->nNumTgNH2InChI && pc2i->nNumTgOInChI && !cur_success) ------------------ | Branch (703:17): [True: 6, False: 31] | Branch (703:63): [True: 6, False: 0] | Branch (703:85): [True: 5, False: 1] ------------------ 704| 5| { 705| | /* change an attachement to N from H to (-) */ 706| 10| for (itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg++) ------------------ | Branch (706:31): [True: 5, False: 5] | Branch (706:63): [True: 5, False: 0] ------------------ 707| 5| { 708| 5| pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; 709| 13| for (i = 0; i < pTg->num_adj_edges && !cur_success; i++) ------------------ | Branch (709:33): [True: 11, False: 2] | Branch (709:59): [True: 8, False: 3] ------------------ 710| 8| { 711| 8| pvEndp2 = pBNS->vert + ( vEndp2 = ( peTg = pBNS->edge + pTg->iedge[i] )->neighbor1 ); /* djb-rwth: ignoring LLVM warning: variable used to store initialisation values */ 712| 8| if (pVA[vEndp2].cNumValenceElectrons == 5 && pVA[vEndp2].cPeriodicRowNumber == 1 && ------------------ | Branch (712:29): [True: 5, False: 3] | Branch (712:70): [True: 5, False: 0] ------------------ 713| 5| at2[vEndp2].valence == at2[vEndp2].chem_bonds_valence && ------------------ | Branch (713:30): [True: 5, False: 0] ------------------ 714| 5| peTg->flow && peTg->flow == peTg->cap) ------------------ | Branch (714:30): [True: 5, False: 0] | Branch (714:44): [True: 3, False: 2] ------------------ 715| 3| { 716| | /* endpoint -NHn found; change its charge */ 717| 3| cur_success++; /* 04 */ 718| | /* replace -NH- with -N(-)- */ 719| 3| pTCGroups->pTCG[itg].tg_num_H--; 720| 3| pTCGroups->pTCG[itg].tg_num_Minus++; 721| 3| pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; 722| 3| pTCGroups->pTCG[itg].tg_set_Minus = vEndp2 + 1; 723| 3| pStruct->ti.t_group[itg].num[1] ++; 724| 3| pTCGroups->total_charge--; 725| 3| pTCGroups->tgroup_charge--; 726| 3| pStruct->nNumRemovedProtonsByRevrs += 1; 727| 3| bAction |= 8; /* manually set (-) charge to NH atom, vEndp2 */ 728| 3| } 729| 8| } 730| 5| } 731| 5| } 732| 37| } 733| 51| if (cur_success) ------------------ | Branch (733:13): [True: 6, False: 45] ------------------ 734| 6| { 735| | /* djb-rwth: removing redundant code */ 736| | /* recalculate InChI from the structure */ 737| 6| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (737:17): [True: 0, False: 6] ------------------ 738| 6| ppt_group_info, ppat_norm, ppat_prep ) )) 739| 0| { 740| 0| goto exit_function; 741| 0| } 742| 6| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (742:17): [True: 0, False: 6] ------------------ 743| 0| { 744| 0| goto exit_function; 745| 0| } 746| 6| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (746:17): [True: 0, False: 6] ------------------ 747| 0| { 748| 0| goto exit_function; 749| 0| } 750| 6| if (pStruct->One_ti.num_t_groups == 1 && pStruct->One_ti.t_group[0].num[1]) ------------------ | Branch (750:17): [True: 1, False: 5] | Branch (750:54): [True: 0, False: 1] ------------------ 751| 0| { 752| | /* this method did not work: no alt path from N(-) to =O */ 753| 0| itg = 0; 754| 0| if (bAction & ( 8 | 2 )) ------------------ | Branch (754:21): [True: 0, False: 0] ------------------ 755| 0| { 756| | /* roll back NH -> N(-) replacement; H move from OH to N is not undone */ 757| 0| pTCGroups->pTCG[itg].tg_num_H++; 758| 0| pTCGroups->pTCG[itg].tg_num_Minus--; 759| 0| pTCGroups->pTCG[itg].tg_RestoreFlags &= ~TGRF_MINUS_FIRST; 760| 0| pTCGroups->pTCG[itg].tg_set_Minus = 0; 761| 0| pStruct->ti.t_group[itg].num[1] --; 762| 0| pTCGroups->total_charge++; 763| 0| pTCGroups->tgroup_charge++; 764| 0| pStruct->nNumRemovedProtonsByRevrs -= 1; 765| 0| cur_success--; 766| 0| } 767| 0| else 768| 0| { 769| 0| if (bAction & 4) ------------------ | Branch (769:25): [True: 0, False: 0] ------------------ 770| 0| { 771| 0| pTCGroups->pTCG[itg].tg_num_H++; 772| 0| pTCGroups->pTCG[itg].tg_num_Minus--; 773| 0| pTCGroups->pTCG[itg].tg_RestoreFlags &= ~TGRF_MINUS_FIRST; 774| 0| pStruct->ti.t_group[itg].num[1] --; 775| 0| pTCGroups->total_charge++; 776| 0| pTCGroups->tgroup_charge++; 777| 0| pStruct->nNumRemovedProtonsByRevrs -= 1; 778| 0| cur_success--; 779| 0| } 780| 0| else 781| 0| { 782| 0| ret = RI_ERR_PROGR; ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 783| 0| goto exit_function; 784| 0| } 785| 0| } 786| | /* recalculate InChI from the structure */ 787| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (787:21): [True: 0, False: 0] ------------------ 788| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 789| 0| { 790| 0| goto exit_function; 791| 0| } 792| 0| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (792:21): [True: 0, False: 0] ------------------ 793| 0| { 794| 0| goto exit_function; 795| 0| } 796| 0| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (796:21): [True: 0, False: 0] ------------------ 797| 0| { 798| 0| goto exit_function; 799| 0| } 800| 0| } 801| 6| if (!pc2i->bHasDifference) ------------------ | Branch (801:17): [True: 0, False: 6] ------------------ 802| 0| { 803| 0| goto exit_function; /* nothing to do */ 804| 0| } 805| 6| } 806| 51| } 807| | 808| 12.6k| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && /* ADP */ ------------------ | Branch (808:9): [True: 200, False: 12.4k] | Branch (808:37): [True: 170, False: 30] | Branch (808:82): [True: 2, False: 28] ------------------ 809| 172| pc2i->nNumTgMInChI == 0 && ( pc2i->nNumTgNInChI || pc2i->nNumTgOInChI ) && ------------------ | Branch (809:9): [True: 110, False: 62] | Branch (809:38): [True: 69, False: 41] | Branch (809:60): [True: 41, False: 0] ------------------ 810| 110| NO_VERTEX != ( vPlusMinus = GetPlusMinusVertex( pBNS, pTCGroups, 1, 1 ) )) ------------------ | | 118| 110|#define NO_VERTEX -2 ------------------ | Branch (810:9): [True: 97, False: 13] ------------------ 811| 97| { 812| | /*---------------------------------------------------------------------------*/ 813| | /* case 05: restored has N endpoints, no (-) endpoints */ 814| | /* original has single taut. group or more */ 815| | /* tautomeric endpoints. */ 816| | /* Solution: Find -N< and allow (+) charge change */ 817| | /* Fix all charges and taut attachments exept */ 818| | /* =N- and =O (taut. endpoints) */ 819| | /* Increment st_edge.cap on (+/-) vertex => add (+) charge to -N< */ 820| | /* Increment tot. charge in other places */ 821| | /* Increment t-group st_edge.cap */ 822| | /* Run BNS */ 823| | /* */ 824| | /* (+/-)* (+/-) Result: */ 825| | /* | || */ 826| | /* | || - Added (+) to -N< */ 827| | /* (+)super (+)super - Added attachment point to O */ 828| | /* || | */ 829| | /* || => | To make this attachment H, */ 830| | /* (Y) (Y) increment */ 831| | /* | || pTCGroups->pTCG[itg].tg_num_H */ 832| | /* | || */ 833| | /* (+)hetero (+)hetero Technical details: */ 834| | /* \\ \ increase capacities of */ 835| | /* N N(+) edges to (+/-) otherwise */ 836| | /* | || flow may not be able to */ 837| | /* *(t)--O=R. (t)==O-R. increase */ 838| | /* */ 839| | /* */ 840| | /*---------------------------------------------------------------------------*/ 841| 97| int itg; 842| 97| BNS_VERTEX *pTg, *pvEndp; /* djb-rwth: ignoring LLVM warning: variable used to store initialisation values */ 843| 97| Vertex vEndp, vTg; 844| 97| BNS_EDGE *peTg; 845| 97| EdgeIndex eTg; 846| 97| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 847| | 848| 97| CurrEdges.num_edges = 0; 849| 97| CurrEdges2.num_edges = 0; 850| 97| cur_success = 0; 851| | /* find -N< and non-taut =N- or =O */ 852| 690| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (852:21): [True: 593, False: 97] ------------------ 853| 593| { 854| 593| iat = nCanon2AtnoRevrs[i]; 855| | /* -N< */ 856| 593| if (!at2[iat].endpoint && !at2[iat].charge && !at2[iat].radical && !at2[iat].num_H && ------------------ | Branch (856:17): [True: 402, False: 191] | Branch (856:39): [True: 303, False: 99] | Branch (856:59): [True: 283, False: 20] | Branch (856:80): [True: 276, False: 7] ------------------ 857| 276| pVA[i].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (857:18): [True: 93, False: 183] | Branch (857:54): [True: 79, False: 14] ------------------ 858| 79| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && pBNS->edge[e].flow && !pBNS->edge[e].forbidden) ------------------ | Branch (858:18): [True: 78, False: 1] | Branch (858:63): [True: 77, False: 1] | Branch (858:85): [True: 77, False: 0] ------------------ 859| 77| { 860| | 861| 77| if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 77|#define INC_ADD_EDGE 64 ------------------ | Branch (861:21): [True: 0, False: 77] ------------------ 862| 0| { 863| 0| goto exit_function; 864| 0| } 865| 77| } 866| 593| } 867| 97| if (!CurrEdges.num_edges) ------------------ | Branch (867:13): [True: 39, False: 58] ------------------ 868| 39| { 869| 39| goto exit_case_05; 870| 39| } 871| | /* find taut -N= and =O */ 872| 108| for (itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg++) ------------------ | Branch (872:23): [True: 58, False: 50] | Branch (872:55): [True: 58, False: 0] ------------------ 873| 58| { 874| 58| CurrEdges2.num_edges = 0; 875| 58| pTg = pBNS->vert + ( vTg = pTCGroups->pTCG[itg].nVertexNumber ); 876| 185| for (i = 0; i < pTg->num_adj_edges; i++) ------------------ | Branch (876:25): [True: 127, False: 58] ------------------ 877| 127| { 878| 127| pvEndp = pBNS->vert + ( vEndp = ( peTg = pBNS->edge + ( eTg = pTg->iedge[i] ) )->neighbor1 ); /* djb-rwth: ignoring LLVM warning: variable used to store initialisation values */ 879| 127| if (at2[vEndp].charge || at2[vEndp].radical || peTg->cap - peTg->flow != 1) ------------------ | Branch (879:21): [True: 0, False: 127] | Branch (879:42): [True: 18, False: 109] | Branch (879:64): [True: 14, False: 95] ------------------ 880| 32| { 881| 32| continue; 882| 32| } 883| | /* t-group edges to -N= and =O */ 884| 95| if ((ret = AddToEdgeList( &CurrEdges2, eTg, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 95|#define INC_ADD_EDGE 64 ------------------ | Branch (884:21): [True: 0, False: 95] ------------------ 885| 0| { 886| 0| goto exit_function; 887| 0| } 888| 95| } 889| 58| if (!CurrEdges2.num_edges) ------------------ | Branch (889:17): [True: 8, False: 50] ------------------ 890| 8| { 891| 8| goto exit_case_05; 892| 8| } 893| | /* fix all charge edges except -N< and all taut. edges except =O and =N- */ 894| 50| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 895| 50| SetForbiddenEdgeMask( pBNS, &TautEdges, forbidden_edge_mask ); 896| 50| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 897| 50| RemoveForbiddenEdgeMask( pBNS, &CurrEdges2, forbidden_edge_mask ); 898| 50| delta = 1; 899| | /* Increment st_edge.cap on (+/-) vertex */ 900| 50| pBNS->vert[vPlusMinus].st_edge.cap += delta; 901| | /* Increment st_edge.cap on t-group */ 902| 50| pTg->st_edge.cap += delta; 903| | /* total cap count */ 904| 50| pBNS->tot_st_cap += 2 * delta; 905| | 906| 50| v1 = vPlusMinus; 907| 50| v2 = vTg; 908| | 909| | /* increase capacities of edges to Y */ 910| 150| for (i = 0; i < pBNS->vert[vPlusMinus].num_adj_edges; i++) ------------------ | Branch (910:25): [True: 100, False: 50] ------------------ 911| 100| { 912| 100| j = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i]].neighbor12 ^ vPlusMinus; 913| 300| for (k = 0; k < pBNS->vert[j].num_adj_edges; k++) ------------------ | Branch (913:29): [True: 200, False: 100] ------------------ 914| 200| { 915| 200| pBNS->edge[pBNS->vert[j].iedge[k]].cap += delta; 916| 200| } 917| 100| } 918| | 919| 50| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 920| 50| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 921| | 922| 50| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (922:17): [True: 48, False: 2] | Branch (922:32): [True: 42, False: 6] | Branch (922:50): [True: 41, False: 1] ------------------ 923| 42| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (923:18): [True: 6, False: 1] | Branch (923:36): [True: 1, False: 5] | Branch (923:59): [True: 42, False: 0] ------------------ 924| 42| { 925| | /* Added (+)charge to -N< => nDeltaCharge == 1 */ 926| | /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */ 927| 42| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 928| 42| if (ret > 0) ------------------ | Branch (928:21): [True: 42, False: 0] ------------------ 929| 42| { 930| | /* djb-rwth: removing redundant code */ 931| 42| cur_success++; /* 01 */ 932| | /* update bookkeeping */ 933| 42| pTCGroups->total_charge += delta; 934| 42| pTCGroups->pTCG[itg].edges_cap += delta; 935| 42| pTCGroups->pTCG[itg].tg_num_H += delta; 936| 42| pStruct->nNumRemovedProtonsByRevrs -= delta; 937| 42| } 938| 42| } 939| 8| else 940| 8| { 941| 8| pBNS->vert[vPlusMinus].st_edge.cap -= delta; 942| 8| pTg->st_edge.cap -= delta; 943| | /*pTCGroups->pTCG[itg].edges_cap -= delta;*/ /* ???bug??? - commented out 2006-03-22 */ 944| 8| pBNS->tot_st_cap -= 2 * delta; 945| | /* decrease capacities of edges to Y */ 946| 24| for (i = 0; i < pBNS->vert[vPlusMinus].num_adj_edges; i++) ------------------ | Branch (946:29): [True: 16, False: 8] ------------------ 947| 16| { 948| 16| j = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i]].neighbor12 ^ vPlusMinus; 949| 48| for (k = 0; k < pBNS->vert[j].num_adj_edges; k++) ------------------ | Branch (949:33): [True: 32, False: 16] ------------------ 950| 32| { 951| 32| pBNS->edge[pBNS->vert[j].iedge[k]].cap -= delta; 952| 32| } 953| 16| } 954| 8| } 955| 50| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 956| 50| RemoveForbiddenEdgeMask( pBNS, &TautEdges, forbidden_edge_mask ); 957| 50| } 958| 50| if (cur_success) ------------------ | Branch (958:13): [True: 42, False: 8] ------------------ 959| 42| { 960| | /* djb-rwth: removing redundant code */ 961| | /* recalculate InChI from the structure */ 962| 42| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (962:17): [True: 0, False: 42] ------------------ 963| 42| ppt_group_info, ppat_norm, ppat_prep ) )) 964| 0| { 965| 0| goto exit_function; 966| 0| } 967| 42| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (967:17): [True: 0, False: 42] ------------------ 968| 0| { 969| 0| goto exit_function; 970| 0| } 971| 42| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (971:17): [True: 0, False: 42] ------------------ 972| 0| { 973| 0| goto exit_function; 974| 0| } 975| 42| if (!pc2i->bHasDifference) ------------------ | Branch (975:17): [True: 0, False: 42] ------------------ 976| 0| { 977| 0| goto exit_function; /* nothing to do */ 978| 0| } 979| 42| } 980| | 981| 97| exit_case_05:; 982| 97| } 983| | 984| 12.6k| while (pc2i->nNumDiffMobH && pc2i->nChargeMobHRevrs > pc2i->nChargeMobHInChI) ------------------ | Branch (984:12): [True: 474, False: 12.1k] | Branch (984:34): [True: 448, False: 26] ------------------ 985| 448| { 986| | /*----------------------------------------------------*/ 987| | /* case 06: restored has extra H attached to -O(-) */ 988| | /* while the chrge should be on C, most pro- */ 989| | /* bably in a small ring.ut. group or more */ 990| | /* tautomeric endpoints. */ 991| | /* Solution: move (-) from O to C */ 992| | /*----------------------------------------------------*/ 993| 448| int iO, mode; 994| 448| EdgeIndex e2; 995| 448| BNS_EDGE *pe2; 996| 448| cur_success = 0; 997| 925| for (i = 0; !cur_success && i < pc2i->len_c2at; i++) ------------------ | Branch (997:21): [True: 909, False: 16] | Branch (997:37): [True: 477, False: 432] ------------------ 998| 477| { 999| | 1000| 477| if (pc2i->c2at[i].nMobHRevrs == pc2i->c2at[i].nMobHInChI + 1 && ------------------ | Branch (1000:17): [True: 468, False: 9] ------------------ 1001| 468| pc2i->c2at[i].nNumHRevrs == pc2i->c2at[i].nMobHInChI && ------------------ | Branch (1001:18): [True: 464, False: 4] ------------------ 1002| 464| !pc2i->c2at[i].endptInChI && !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1002:18): [True: 462, False: 2] | Branch (1002:47): [True: 462, False: 0] ------------------ 1003| 462| at2[iO = pc2i->c2at[i].atomNumber].charge == -1 && ------------------ | Branch (1003:18): [True: 461, False: 1] ------------------ 1004| 461| 0 <= ( e = pVA[iO].nCMinusGroupEdge - 1 ) && ( pe = pBNS->edge + e )->flow) ------------------ | Branch (1004:18): [True: 461, False: 0] | Branch (1004:63): [True: 461, False: 0] ------------------ 1005| 461| { 1006| | /* try suitable atoms C */ 1007| | /* first look for =C= in a small ring */ 1008| 2.71k| for (mode = 4; !cur_success && mode <= 8; mode++) ------------------ | Branch (1008:32): [True: 2.69k, False: 16] | Branch (1008:48): [True: 2.25k, False: 445] ------------------ 1009| 2.25k| { 1010| | 1011| 2.25k| if (mode == 8) ------------------ | Branch (1011:25): [True: 445, False: 1.80k] ------------------ 1012| 445| mode = 99; 1013| | 1014| 14.9k| for (iat = 0; !cur_success && iat < pStruct->num_atoms; iat++) ------------------ | Branch (1014:35): [True: 14.9k, False: 16] | Branch (1014:51): [True: 12.6k, False: 2.23k] ------------------ 1015| 12.6k| { 1016| | 1017| 12.6k| if (!at2[iat].charge && !at2[iat].radical && ------------------ | Branch (1017:29): [True: 6.73k, False: 5.93k] | Branch (1017:49): [True: 6.18k, False: 555] ------------------ 1018| 6.18k| pVA[iat].cNumValenceElectrons == 4 && ------------------ | Branch (1018:30): [True: 1.74k, False: 4.43k] ------------------ 1019| 1.74k| 0 <= ( e2 = pVA[iat].nCMinusGroupEdge - 1 ) && !( pe2 = pBNS->edge + e2 )->flow && ------------------ | Branch (1019:30): [True: 1.22k, False: 525] | Branch (1019:77): [True: 1.22k, False: 0] ------------------ 1020| 1.22k| 0 < bIsUnsatCarbonInASmallRing( at2, pVA, iat, pStruct->pbfsq, mode )) ------------------ | Branch (1020:30): [True: 237, False: 985] ------------------ 1021| 237| { 1022| | 1023| 237| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1024| | /* allow negative charge on the chosen carbon */ 1025| 237| pe2->forbidden &= forbidden_edge_mask_inv; 1026| | 1027| 237| delta = 1; 1028| 237| if (!pe->flow) ------------------ | Branch (1028:33): [True: 0, False: 237] ------------------ 1029| 0| continue; 1030| 237| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1031| 237| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1032| 237| pe->flow -= delta; 1033| 237| pv1->st_edge.flow -= delta; 1034| 237| pv2->st_edge.flow -= delta; 1035| 237| pBNS->tot_st_flow -= 2 * delta; 1036| | 1037| 237| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1038| 237| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1039| | 1040| 237| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1040:33): [True: 52, False: 185] | Branch (1040:48): [True: 12, False: 40] | Branch (1040:66): [True: 1, False: 11] ------------------ 1041| 51| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1041:34): [True: 32, False: 19] | Branch (1041:52): [True: 15, False: 17] | Branch (1041:75): [True: 16, False: 0] ------------------ 1042| 16| { 1043| | /* Added (-)charge to unsaturated C => nDeltaCharge == 2 */ 1044| 16| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1045| 16| if (ret > 0) ------------------ | Branch (1045:37): [True: 16, False: 0] ------------------ 1046| 16| { 1047| | /* djb-rwth: removing redundant code */ 1048| 16| cur_success++; /* 01 */ 1049| | /* djb-rwth: removing redundant code */ 1050| 16| } 1051| 16| } 1052| 221| else 1053| 221| { 1054| 221| pe->forbidden |= forbidden_edge_mask; 1055| 221| pe->flow += delta; 1056| 221| pv1->st_edge.flow += delta; 1057| 221| pv2->st_edge.flow += delta; 1058| 221| pBNS->tot_st_flow += 2 * delta; 1059| 221| } 1060| 237| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1061| 237| } 1062| 12.6k| } 1063| 2.25k| } 1064| 461| } 1065| 477| } 1066| 448| if (cur_success) ------------------ | Branch (1066:13): [True: 16, False: 432] ------------------ 1067| 16| { 1068| | /* recalculate InChI from the structure */ 1069| 16| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1069:17): [True: 0, False: 16] ------------------ 1070| 16| ppt_group_info, ppat_norm, ppat_prep ) )) 1071| 0| { 1072| 0| goto exit_function; 1073| 0| } 1074| 16| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1074:17): [True: 0, False: 16] ------------------ 1075| 0| { 1076| 0| goto exit_function; 1077| 0| } 1078| 16| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1078:17): [True: 0, False: 16] ------------------ 1079| 0| { 1080| 0| goto exit_function; 1081| 0| } 1082| 16| if (!pc2i->bHasDifference) ------------------ | Branch (1082:17): [True: 10, False: 6] ------------------ 1083| 10| { 1084| 10| goto exit_function; /* nothing to do */ 1085| 10| } 1086| 16| } 1087| 432| else 1088| 432| { 1089| 432| break; 1090| 432| } 1091| 448| } 1092| 12.6k| if (pc2i->len_c2at && pc2i->nChargeMobHRevrs > pc2i->nChargeMobHInChI) ------------------ | Branch (1092:9): [True: 1.45k, False: 11.1k] | Branch (1092:27): [True: 672, False: 778] ------------------ 1093| 672| { 1094| | /*------------------------------------------------------------------*/ 1095| | /* case 07: -NO2 are to be tautomeric but they are not AND */ 1096| | /* InChI has a SINGLE tautomeric group */ 1097| | /* */ 1098| | /* (-)O (-)O */ 1099| | /* Solution: convert \ \ */ 1100| | /* N-X=...-Z(-) => N(+)=X- ...=Z */ 1101| | /* // / */ 1102| | /* O (-)O */ 1103| | /* */ 1104| | /* O O */ 1105| | /* or \\ \\ */ 1106| | /* N-X=...-Z(-) => N=X- ...=Z */ 1107| | /* // / */ 1108| | /* O (-)O */ 1109| | /* */ 1110| | /* */ 1111| | /* (a) move (-) from other tautomeric atom to O in O=N-X */ 1112| | /* or from other atom that has to be tautomeric */ 1113| | /* but is not */ 1114| | /* (b) create (+) [ion pair creation] on N as in */ 1115| | /* */ 1116| | /* OH OH */ 1117| | /* / / */ 1118| | /* -C=N => =C-N(+) */ 1119| | /* \\ \\ */ 1120| | /* O O */ 1121| | /* */ 1122| | /*------------------------------------------------------------------*/ 1123| 672| int num_DB_O = 0; 1124| 672| short iat_DB_O[MAX_DIFF_FIXH], iat_NO2[MAX_DIFF_FIXH]; 1125| 672| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1126| | /* 1127| | AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 1128| | */ 1129| 672| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[0] && ------------------ | Branch (1129:41): [True: 672, False: 0] ------------------ 1130| 672| pStruct->pOne_norm_data[0]->at ) ? pStruct->pOne_norm_data[0]->at : NULL; ------------------ | Branch (1130:38): [True: 672, False: 0] ------------------ 1131| | 1132| 672| int iN, one_success; 1133| 672| BNS_EDGE *peDB_O_Minus; 1134| 672| int neigh, nNumO, nNumOthers; 1135| 672|#define CHG_SET_WRONG_TAUT_N 0 1136| 672|#define CHG_SET_WRONG_TAUT_O 1 1137| 672|#define CHG_SET_WRONG_TAUT_ALL 2 1138| 672|#define CHG_LAST_SET 2 /* the last index in trying */ 1139| 672|#define CHG_SET_O_FIXED 3 1140| 672|#define CHG_SET_NUM 4 1141| 672| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 1142| 672| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1143| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 1144| | /* 1145| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 1146| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 1147| | */ 1148| 672| CurrEdges.num_edges = 0; /* clear current edge list */ 1149| 672| cur_success = 0; 1150| 4.59k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1150:21): [True: 3.92k, False: 672] ------------------ 1151| 3.92k| { 1152| 3.92k| iat = nCanon2AtnoRevrs[i]; 1153| 3.92k| if ( /* orig. InChI info: taut in orig. InChI =O located in -NO2 that is not taut in Reconstructed InChI */ 1154| 3.92k| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 456| 7.84k|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1154:18): [True: 3.92k, False: 0] ------------------ 1155| 3.92k| pVA[iat].cNumValenceElectrons == 6 /* O, S, Se, Te */ && ------------------ | Branch (1155:18): [True: 1.62k, False: 2.30k] ------------------ 1156| 1.62k| ( !at2[iat].endpoint /*|| pc2i->c2at[i].nMobHInChI*/ ) && ------------------ | Branch (1156:18): [True: 1.49k, False: 123] ------------------ 1157| 1.49k| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (1157:18): [True: 1.15k, False: 345] | Branch (1157:64): [True: 1.07k, False: 75] ------------------ 1158| 1.07k| at2[iat].num_H == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (1158:18): [True: 1.07k, False: 0] ------------------ 1159| | /* reversed structure info: */ 1160| 1.07k| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint ) /*|| pc2i->c2at[i].nMobHRevrs*/ && ------------------ | Branch (1160:21): [True: 1.07k, False: 0] | Branch (1160:42): [True: 440, False: 638] ------------------ 1161| 638| !at2[iat].charge && ------------------ | Branch (1161:18): [True: 98, False: 540] ------------------ 1162| 98| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (1162:18): [True: 95, False: 3] | Branch (1162:43): [True: 76, False: 19] ------------------ 1163| | /* find whether it belongs to NO2 */ 1164| 76| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (1164:18): [True: 52, False: 24] ------------------ 1165| 52| at2[iN].valence == 3 && ( at2[iN].charge == 0 || at2[iN].charge == 1 ) && ------------------ | Branch (1165:18): [True: 38, False: 14] | Branch (1165:44): [True: 18, False: 20] | Branch (1165:67): [True: 17, False: 3] ------------------ 1166| 35| at2[iN].chem_bonds_valence == 5 - at2[iN].charge) ------------------ | Branch (1166:18): [True: 35, False: 0] ------------------ 1167| 35| { 1168| | /* find the second O */ 1169| 35| nNumO = nNumOthers = 0; 1170| 140| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (1170:29): [True: 105, False: 35] ------------------ 1171| 105| { 1172| 105| neigh = at2[iN].neighbor[k]; 1173| 105| if (neigh == iat) ------------------ | Branch (1173:25): [True: 35, False: 70] ------------------ 1174| 35| { 1175| 35| continue; 1176| 35| } 1177| 70| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (1177:25): [True: 30, False: 40] ------------------ 1178| 30| !at2[neigh].endpoint && ------------------ | Branch (1178:26): [True: 24, False: 6] ------------------ 1179| 24| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[neigh].endpoint ) && ------------------ | Branch (1179:29): [True: 24, False: 0] | Branch (1179:50): [True: 0, False: 24] ------------------ 1180| 24| at2[neigh].valence == 1 && at2[neigh].num_H == 0 && ------------------ | Branch (1180:26): [True: 20, False: 4] | Branch (1180:53): [True: 20, False: 0] ------------------ 1181| 20| at2[neigh].radical == 0 && ( at2[neigh].charge == 0 || at2[neigh].charge == -1 ) && ------------------ | Branch (1181:26): [True: 17, False: 3] | Branch (1181:55): [True: 16, False: 1] | Branch (1181:81): [True: 1, False: 0] ------------------ 1182| 17| at2[neigh].chem_bonds_valence - at2[neigh].charge == 2) ------------------ | Branch (1182:26): [True: 17, False: 0] ------------------ 1183| 17| { 1184| 17| nNumO++; 1185| 17| } 1186| 53| else 1187| 53| { 1188| 53| if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE && ------------------ | | 32| 106|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1188:29): [True: 49, False: 4] ------------------ 1189| 49| at2[neigh].valence > 1 && ------------------ | Branch (1189:31): [True: 36, False: 13] ------------------ 1190| 36| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (1190:31): [True: 18, False: 18] ------------------ 1191| 18| { 1192| 18| nNumOthers++; 1193| 18| } 1194| 53| } 1195| 70| } 1196| 35| if (nNumO != 1 || nNumOthers != 1) ------------------ | Branch (1196:21): [True: 18, False: 17] | Branch (1196:35): [True: 6, False: 11] ------------------ 1197| 24| { 1198| 24| continue; 1199| 24| } 1200| 11| for (k = 0; k < num_DB_O; k++) ------------------ | Branch (1200:29): [True: 5, False: 6] ------------------ 1201| 5| { 1202| 5| if (iat_NO2[k] == iN) ------------------ | Branch (1202:25): [True: 5, False: 0] ------------------ 1203| 5| { 1204| 5| break; 1205| 5| } 1206| 5| } 1207| 11| if (k == num_DB_O) ------------------ | Branch (1207:21): [True: 6, False: 5] ------------------ 1208| 6| { 1209| 6| iat_NO2[num_DB_O] = iN; 1210| 6| iat_DB_O[num_DB_O++] = iat; 1211| 6| } 1212| | /* save the =O (-)-edge to avoid interference */ 1213| 11| if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1139| 11|#define CHG_SET_O_FIXED 3 ------------------ if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 11|#define INC_ADD_EDGE 64 ------------------ | Branch (1213:21): [True: 0, False: 11] ------------------ 1214| 0| { 1215| 0| goto exit_case_07; 1216| 0| } 1217| 11| } 1218| 3.92k| } 1219| 672| if (num_DB_O) ------------------ | Branch (1219:13): [True: 6, False: 666] ------------------ 1220| 6| { 1221| | /* search for falsely tautomeric negatively charged atoms N and O */ 1222| 14| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1222:25): [True: 8, False: 6] ------------------ 1223| 8| { 1224| 8| iat = pc2i->c2at[i].atomNumber; 1225| 8| if (pc2i->c2at[i].endptRevrs && !pc2i->c2at[i].endptInChI && ------------------ | Branch (1225:21): [True: 4, False: 4] | Branch (1225:49): [True: 4, False: 0] ------------------ 1226| 4| pc2i->c2at[i].nAtChargeRevrs == -1 && ------------------ | Branch (1226:22): [True: 2, False: 2] ------------------ 1227| 2| 0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (1227:22): [True: 2, False: 0] | Branch (1227:68): [True: 2, False: 0] | Branch (1227:96): [True: 2, False: 0] ------------------ 1228| 2| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e )) ------------------ | | 1139| 2|#define CHG_SET_O_FIXED 3 ------------------ | Branch (1228:22): [True: 2, False: 0] ------------------ 1229| 2| { 1230| 2| if (pc2i->c2at[i].nValElectr == 6) ------------------ | Branch (1230:25): [True: 2, False: 0] ------------------ 1231| 2| { 1232| 2| if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_O], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1136| 2|#define CHG_SET_WRONG_TAUT_O 1 ------------------ if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_O], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 2|#define INC_ADD_EDGE 64 ------------------ | Branch (1232:29): [True: 0, False: 2] ------------------ 1233| 0| { 1234| 0| goto exit_case_07; 1235| 0| } 1236| 2| } 1237| 0| else 1238| 0| if (pc2i->c2at[i].nValElectr == 5) ------------------ | Branch (1238:29): [True: 0, False: 0] ------------------ 1239| 0| { 1240| 0| if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_N], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1135| 0|#define CHG_SET_WRONG_TAUT_N 0 ------------------ if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_N], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1240:33): [True: 0, False: 0] ------------------ 1241| 0| { 1242| 0| goto exit_case_07; 1243| 0| } 1244| 0| } 1245| 2| if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1137| 2|#define CHG_SET_WRONG_TAUT_ALL 2 ------------------ if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 2|#define INC_ADD_EDGE 64 ------------------ | Branch (1245:25): [True: 0, False: 2] ------------------ 1246| 0| { 1247| 0| goto exit_case_07; 1248| 0| } 1249| 2| } 1250| 8| } 1251| | /* ------- finally, try to move charges from O=N --------------*/ 1252| 12| for (i = 0; i < num_DB_O; i++) ------------------ | Branch (1252:25): [True: 6, False: 6] ------------------ 1253| 6| { 1254| 6| int nDeltaChargeExpected; 1255| 6| one_success = 0; 1256| 6| delta = 1; 1257| 6| iat = iat_DB_O[i]; 1258| 6| peDB_O_Minus = pBNS->edge + ( (long long)pVA[iat].nCMinusGroupEdge - 1 ); /* djb-rwth: cast operator added */ 1259| 6| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; 1260| | 1261| 6| if (!pe->flow) ------------------ | Branch (1261:21): [True: 0, False: 6] ------------------ 1262| 0| continue; 1263| 6| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1264| 6| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1265| | 1266| 6| pe->forbidden |= forbidden_edge_mask; 1267| | 1268| 6| pe->flow -= delta; 1269| 6| pv1->st_edge.flow -= delta; 1270| 6| pv2->st_edge.flow -= delta; 1271| 6| pBNS->tot_st_flow -= 2 * delta; 1272| | 1273| 23| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 1138| 22|#define CHG_LAST_SET 2 /* the last index in trying */ ------------------ | Branch (1273:29): [True: 22, False: 1] | Branch (1273:45): [True: 17, False: 5] ------------------ 1274| 17| { 1275| 17| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (1275:25): [True: 14, False: 3] ------------------ 1276| 14| { 1277| 14| continue; 1278| 14| } 1279| 3| nDeltaChargeExpected = 0; 1280| | 1281| 3| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1282| 3| RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); 1283| | /* allow (-) charge to move to N=O */ 1284| 3| peDB_O_Minus->forbidden &= forbidden_edge_mask_inv; 1285| | 1286| 3| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1287| 3| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1288| | 1289| 3| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1289:25): [True: 1, False: 2] | Branch (1289:40): [True: 1, False: 0] | Branch (1289:58): [True: 1, False: 0] ------------------ 1290| 0| (vPathEnd == v2 && vPathStart == v1) ) && ------------------ | Branch (1290:26): [True: 0, False: 0] | Branch (1290:44): [True: 0, False: 0] ------------------ 1291| 1| nDeltaCharge == nDeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1291:39): [True: 1, False: 0] ------------------ 1292| 1| { 1293| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 1294| 1| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1295| 1| if (ret > 0) ------------------ | Branch (1295:29): [True: 1, False: 0] ------------------ 1296| 1| { 1297| | /* djb-rwth: removing redundant code */ 1298| 1| one_success++; /* 07 */ 1299| 1| } 1300| 1| } 1301| 3| INCHI_HEAPCHK 1302| 3| } 1303| 6| cur_success += one_success; 1304| | 1305| 6| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1306| 6| pe->forbidden &= forbidden_edge_mask_inv; 1307| | 1308| 6| if (!one_success) ------------------ | Branch (1308:21): [True: 5, False: 1] ------------------ 1309| 5| { 1310| 5| pe->flow += delta; 1311| 5| pv1->st_edge.flow += delta; 1312| 5| pv2->st_edge.flow += delta; 1313| 5| pBNS->tot_st_flow += 2 * delta; 1314| 5| } 1315| 6| } 1316| 6| } 1317| 672| exit_case_07: 1318| 3.36k| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 1140| 3.36k|#define CHG_SET_NUM 4 ------------------ | Branch (1318:21): [True: 2.68k, False: 672] ------------------ 1319| 2.68k| { 1320| 2.68k| AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); ------------------ | | 243| 2.68k|#define EDGE_LIST_FREE (-2) ------------------ 1321| 2.68k| } 1322| | 1323| 672| CurrEdges.num_edges = 0; /* clear current edge list */ 1324| 672| if (cur_success) ------------------ | Branch (1324:13): [True: 1, False: 671] ------------------ 1325| 1| { 1326| | /* djb-rwth: removing redundant code */ 1327| | /* recalculate InChI from the structure */ 1328| 1| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1328:17): [True: 0, False: 1] ------------------ 1329| 1| ppt_group_info, ppat_norm, ppat_prep ) )) 1330| 0| { 1331| 0| goto exit_function; 1332| 0| } 1333| 1| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1333:17): [True: 0, False: 1] ------------------ 1334| 0| { 1335| 0| goto exit_function; 1336| 0| } 1337| 1| if ((ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1337:17): [True: 0, False: 1] ------------------ 1338| 0| { 1339| 0| goto exit_function; 1340| 0| } 1341| 1| if (!pc2i->bHasDifference) ------------------ | Branch (1341:17): [True: 0, False: 1] ------------------ 1342| 0| { 1343| 0| goto exit_function; /* nothing to do */ 1344| 0| } 1345| 1| } 1346| 672|#undef CHG_SET_NOOH 1347| 672|#undef CHG_SET_WRONG_TAUT 1348| 672|#undef CHG_SET_TAUT 1349| 672|#undef CHG_LAST_SET 1350| 672|#undef CHG_SET_O_FIXED 1351| 672|#undef CHG_SET_NUM 1352| 672| } 1353| | 1354| 12.6k|exit_function: 1355| 12.6k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1356| 12.6k| AllocEdgeList( &CurrEdges, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1357| 12.6k| AllocEdgeList( &CurrEdges2, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1358| 12.6k| AllocEdgeList( &CurrEdges3, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1359| 12.6k| AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1360| 12.6k| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1361| 12.6k| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1362| 12.6k| AllocEdgeList( &TautEdges, EDGE_LIST_FREE ); ------------------ | | 243| 12.6k|#define EDGE_LIST_FREE (-2) ------------------ 1363| | 1364| 12.6k| return ret; 1365| 12.6k|} FixRestoredStructureStereo: 49| 13.2k|{ 50| | /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/ 51| | /* at2 should be the most recently restored atom, Fixed-H */ 52| 13.2k| int i, j, k, delta, max_success, cur_success, ret = 0; /* djb-rwth: removing redundant variables */ 53| 13.2k| int err, iOrigInChI, iRevrInChI; 54| 13.2k| int j12, v1, v2, e, vRad; 55| 13.2k| BNS_VERTEX *pv1, *pv2, *pvRad; 56| 13.2k| BNS_EDGE *pe, *peRad; 57| 13.2k| EDGE_LIST AllChargeEdges, CurrEdges, NFlowerEdges, OtherNFlowerEdges, FixedStereoEdges, AllRadList; 58| 13.2k| EDGE_LIST TautMinusEdges[2]; /* 0 -> O & O(+), 1=> N & N(+) */ 59| | 60| 13.2k| Vertex vPathStart, vPathEnd; 61| 13.2k| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 62| 13.2k| INChI_Stereo *pStereoInChI, *pStereo2InChI, *pStereoRevrs, *pStereo2Revrs; 63| | 64| | /* Stereo */ 65| | 66| | /* currently being processed layer */ 67| 13.2k| pStereoInChI = ( pInChI[0]->StereoIsotopic && ------------------ | Branch (67:22): [True: 180, False: 13.0k] ------------------ 68| 180| pInChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (68:22): [True: 101, False: 79] ------------------ 69| 180| pInChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 70| 13.2k| ? pInChI[0]->StereoIsotopic 71| 13.2k| : pInChI[0]->Stereo; 72| | 73| | /* mobile-H layer in case of Fixed-H */ 74| 13.2k| pStereo2InChI = ( pStruct->bMobileH == TAUT_YES || !pInChI[1] || ------------------ | | 575| 26.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (74:23): [True: 12.6k, False: 587] | Branch (74:56): [True: 0, False: 587] ------------------ 75| 587| !pInChI[1]->nNumberOfAtoms || pInChI[1]->bDeleted ) ------------------ | Branch (75:23): [True: 0, False: 587] | Branch (75:53): [True: 0, False: 587] ------------------ 76| 13.2k| ? NULL 77| 13.2k| : ( pInChI[1]->StereoIsotopic && ------------------ | Branch (77:13): [True: 2, False: 585] ------------------ 78| 2| pInChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (78:13): [True: 1, False: 1] ------------------ 79| 2| pInChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 80| 1| pInChI[1]->StereoIsotopic : 81| 587| pInChI[1]->Stereo; 82| | 83| | /* currently being processed layer */ 84| 13.2k| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (84:22): [True: 181, False: 13.0k] ------------------ 85| 181| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (85:22): [True: 51, False: 130] ------------------ 86| 181| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 87| 13.2k| ? pStruct->pOneINChI[0]->StereoIsotopic 88| 13.2k| : pStruct->pOneINChI[0]->Stereo; 89| | 90| | /* mobile-H layer in case of Fixed-H */ 91| 13.2k| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 575| 26.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (91:23): [True: 12.6k, False: 587] | Branch (91:56): [True: 294, False: 293] ------------------ 92| 293| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (92:23): [True: 0, False: 293] | Branch (92:65): [True: 0, False: 293] ------------------ 93| 13.2k| ? NULL 94| 13.2k| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (94:13): [True: 13, False: 280] ------------------ 95| 13| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (95:13): [True: 5, False: 8] ------------------ 96| 13| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 97| 5| pStruct->pOneINChI[1]->StereoIsotopic : 98| 293| pStruct->pOneINChI[1]->Stereo; 99| | 100| | INCHI_HEAPCHK 101| | 102| 13.2k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 103| 13.2k| AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 104| 13.2k| AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 105| 13.2k| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 106| 13.2k| AllocEdgeList( &FixedStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 107| 13.2k| AllocEdgeList( &AllRadList, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 108| | 109| 13.2k| AllocEdgeList( TautMinusEdges + 0, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 110| 13.2k| AllocEdgeList( TautMinusEdges + 1, EDGE_LIST_CLEAR ); ------------------ | | 242| 13.2k|#define EDGE_LIST_CLEAR (-1) ------------------ 111| | 112| 13.2k| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 113| 13.2k| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (113:9): [True: 0, False: 13.2k] ------------------ 114| 0| { 115| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 116| 0| goto exit_function; 117| 0| } 118| 13.2k| if (err) ------------------ | Branch (118:9): [True: 0, False: 13.2k] ------------------ 119| 0| { 120| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 121| 0| goto exit_function; 122| 0| } 123| | 124| 13.2k| cmpInChI2 = 0; 125| | 126| 13.2k| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 574| 13.2k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (126:9): [True: 587, False: 12.6k] ------------------ 127| 587| { 128| | /* these indexes are used to compare Mobile-H InChI */ 129| 587| iOrigInChI = ( pInChI[1] && pInChI[1]->nNumberOfAtoms && !pInChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (129:24): [True: 587, False: 0] | Branch (129:37): [True: 587, False: 0] | Branch (129:66): [True: 587, False: 0] ------------------ 130| 587| iRevrInChI = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (130:24): [True: 293, False: 294] | Branch (130:49): [True: 293, False: 0] | Branch (130:90): [True: 293, False: 0] ------------------ 131| 587| } 132| 12.6k| else 133| 12.6k| { 134| 12.6k| iOrigInChI = 0; 135| 12.6k| iRevrInChI = 0; 136| 12.6k| } 137| | 138| 13.2k| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 139| 13.2k| if (iRevrInChI || iOrigInChI) ------------------ | Branch (139:9): [True: 293, False: 12.9k] | Branch (139:23): [True: 294, False: 12.6k] ------------------ 140| 587| { 141| | /* additional mobile-H compare in case of Fixed-H */ 142| 587| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 143| 587| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (143:13): [True: 0, False: 587] ------------------ 144| 0| { 145| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 146| 0| goto exit_function; 147| 0| } 148| 587| if (err) ------------------ | Branch (148:13): [True: 0, False: 587] ------------------ 149| 0| { 150| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 151| 0| goto exit_function; 152| 0| } 153| 587| } 154| | 155| 13.2k| if (!( cmpInChI & IDIFF_SB ) && !( cmpInChI2 & IDIFF_SB )) ------------------ | | 357| 13.2k|#define IDIFF_SB (IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) ------------------ if (!( cmpInChI & IDIFF_SB ) && !( cmpInChI2 & IDIFF_SB )) ------------------ | | 357| 13.0k|#define IDIFF_SB (IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) ------------------ | Branch (155:9): [True: 13.0k, False: 209] | Branch (155:37): [True: 12.9k, False: 28] ------------------ 156| 12.9k| { 157| 12.9k| goto exit_function; 158| 12.9k| } 159| | /* need to temporarily remove fixing of stereogenic bonds */ 160| 1.54k| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (160:17): [True: 1.30k, False: 237] ------------------ 161| 1.30k| { 162| 1.30k| pv1 = pBNS->vert + i; 163| 3.84k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (163:21): [True: 2.54k, False: 1.30k] ------------------ 164| 2.54k| { 165| 2.54k| pe = pBNS->edge + ( e = pv1->iedge[j] ); 166| 2.54k| if (j == pe->neighbor1) ------------------ | Branch (166:17): [True: 1.10k, False: 1.43k] ------------------ 167| 1.10k| { 168| | /* do not store same bond 2 times */ 169| 1.10k| if (( pe->forbidden & forbidden_stereo_edge_mask ) && ------------------ | Branch (169:21): [True: 212, False: 893] ------------------ 170| 212| ( ret = AddToEdgeList( &FixedStereoEdges, e, INC_ADD_EDGE ) )) /* djb-rwth: ignoring LLVM warning as there should be no memory leak */ ------------------ | | 20| 212|#define INC_ADD_EDGE 64 ------------------ | Branch (170:21): [True: 0, False: 212] ------------------ 171| 0| { 172| | /* djb-rwth: fixing coverity ID #499482 */ 173| 0| goto exit_function; 174| 0| } 175| 1.10k| } 176| 2.54k| } 177| 1.30k| } 178| | 179| | /* djb-rwth: removing redundant code */ 180| 237| cur_success = 0; 181| 237| if (( cmpInChI & IDIF_SB_MISS ) && ( !cmpInChI2 || ( cmpInChI2 & IDIF_SB_MISS ) ) && ------------------ | Branch (181:9): [True: 137, False: 100] | Branch (181:42): [True: 115, False: 22] | Branch (181:56): [True: 11, False: 11] ------------------ 182| 126| 0 < ( max_success = pBNS->tot_st_cap - pBNS->tot_st_flow )) ------------------ | Branch (182:10): [True: 50, False: 76] ------------------ 183| 50| { 184| | /*----------------------------------------------------*/ 185| | /* case 01: extra stereogenic bond, radical present */ 186| | /* X=N-O* => X=N=O and eliminate radical */ 187| | /*----------------------------------------------------*/ 188| 50| int aN; 189| 50| BNS_VERTEX *pvO, *pvN; 190| 50| BNS_EDGE *peNO; 191| | 192| 50| RemoveForbiddenEdgeMask( pBNS, &FixedStereoEdges, forbidden_stereo_edge_mask ); 193| | 194| 126| for (i = 0; i < icr->num_sb_in2_only && cur_success < max_success; i++) ------------------ | Branch (194:21): [True: 78, False: 48] | Branch (194:49): [True: 77, False: 1] ------------------ 195| 77| { 196| 77| j12 = icr->sb_in2_only[i]; 197| 77| pv1 = pBNS->vert + ( v1 = pStereoInChI->nBondAtom1[j12] - 1 ); 198| 77| pv2 = pBNS->vert + ( v2 = pStereoInChI->nBondAtom2[j12] - 1 ); 199| 102| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (199:25): [True: 101, False: 1] ------------------ 200| 101| { 201| 101| pe = pBNS->edge + ( e = pv1->iedge[k] ); 202| 101| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (202:21): [True: 76, False: 25] ------------------ 203| 76| break; /* the edge has been found */ 204| 101| } 205| 77| if (k >= at2[v1].valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (205:17): [True: 1, False: 76] ------------------ 206| 1| { 207| 1| ret = RI_ERR_SYNTAX; ------------------ | | 16| 1|#define RI_ERR_SYNTAX (-2) ------------------ 208| 1| goto exit_function; 209| 1| } 210| | /* check v1 */ 211| 76| pv1->st_edge.cap--; 212| 76| pv1->st_edge.flow--; 213| 76| pv2->st_edge.flow--; 214| 76| pe->flow--; /* new radical on v2 */ 215| | /* djb-rwth: removing redundant code */ 216| 76| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 217| 76| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 218| 76| pv1->st_edge.cap++; 219| 76| pv1->st_edge.flow++; 220| 76| pv2->st_edge.flow++; 221| 76| pe->flow++; /* remove new radical on v2 */ 222| | 223| 76| if (ret == 1 /*&& !nDeltaH*/ && !nDeltaCharge && ( v2 == vPathStart || v2 == vPathEnd )) ------------------ | Branch (223:17): [True: 35, False: 41] | Branch (223:45): [True: 32, False: 3] | Branch (223:64): [True: 31, False: 1] | Branch (223:84): [True: 1, False: 0] ------------------ 224| 32| { 225| 32| vRad = ( v2 == vPathStart ) ? vPathEnd : vPathStart; ------------------ | Branch (225:24): [True: 31, False: 1] ------------------ 226| 32| } 227| 44| else 228| 44| { 229| 44| pv2->st_edge.cap--; 230| 44| pv2->st_edge.flow--; 231| 44| pv1->st_edge.flow--; 232| 44| pe->flow--; /* new radical on v1 */ 233| 44| vRad = NO_VERTEX; ------------------ | | 118| 44|#define NO_VERTEX -2 ------------------ 234| 44| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 235| 44| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 236| 44| pv2->st_edge.cap++; 237| 44| pv2->st_edge.flow++; 238| 44| pv1->st_edge.flow++; 239| 44| pe->flow++; /* remove new radical on v1 */ 240| 44| if (ret == 1 /*&& !nDeltaH*/ && !nDeltaCharge && ( v1 == vPathStart || v1 == vPathEnd )) ------------------ | Branch (240:21): [True: 9, False: 35] | Branch (240:49): [True: 8, False: 1] | Branch (240:68): [True: 2, False: 6] | Branch (240:88): [True: 6, False: 0] ------------------ 241| 8| { 242| 8| vRad = ( v1 == vPathStart ) ? vPathEnd : vPathStart; ------------------ | Branch (242:28): [True: 2, False: 6] ------------------ 243| 8| } 244| 44| } 245| 76| if (vRad == NO_VERTEX) ------------------ | | 118| 76|#define NO_VERTEX -2 ------------------ | Branch (245:17): [True: 36, False: 40] ------------------ 246| 36| { 247| 36| continue; /* radical did not affect this bond */ 248| 36| } 249| 40| pvRad = pBNS->vert + vRad; 250| | /* detect =N-O* */ 251| 40| if (pVA[vRad].cNumValenceElectrons == 6 && at2[vRad].valence == 1 && ------------------ | Branch (251:17): [True: 19, False: 21] | Branch (251:56): [True: 12, False: 7] ------------------ 252| 12| ( peRad = pBNS->edge + pvRad->iedge[0] )->flow == 0 && ------------------ | Branch (252:17): [True: 9, False: 3] ------------------ 253| 9| pVA[aN = peRad->neighbor12 ^ vRad].cNumValenceElectrons == 5 && ------------------ | Branch (253:18): [True: 7, False: 2] ------------------ 254| 7| at2[aN].valence == 2) ------------------ | Branch (254:18): [True: 6, False: 1] ------------------ 255| 6| { 256| | /*------------------------------------------------------------ 257| | Fix Metal disconnection/normalization inconsistency : 258| | disconnected restored 259| | R=N(+)-M R=N--M R=N + M R=N + M 260| | | -> || -> || -> | 261| | O(-) O O O* <- radical 262| | 263| | The correct R=N + M(+) 264| | disconnection | 265| | would be this: O(-) 266| | --------------------------------------------------------------*/ 267| 6| pvN = pBNS->vert + aN; 268| 6| pvO = pvRad; 269| 6| peNO = peRad; 270| | 271| | /* N-O* => N=O */ 272| 6| peNO->flow++; 273| 6| pvO->st_edge.flow++; 274| 6| pvN->st_edge.cap++; 275| 6| pvN->st_edge.flow++; 276| 6| pBNS->tot_st_cap += 1; 277| 6| pBNS->tot_st_flow += 2; 278| 6| cur_success++; 279| 6| } 280| 34| else 281| 34| { 282| | /* all other radicals that affect stereo */ 283| 34| delta = pvRad->st_edge.cap - pvRad->st_edge.flow; 284| 34| pvRad->st_edge.cap -= delta; 285| 34| pBNS->tot_st_cap -= delta; 286| 34| } 287| 40| } 288| |/*exit_case_01:*/ 289| 49| SetForbiddenEdgeMask( pBNS, &FixedStereoEdges, forbidden_stereo_edge_mask ); 290| 49| if (cur_success) ------------------ | Branch (290:13): [True: 6, False: 43] ------------------ 291| 6| { 292| | /* djb-rwth: removing redundant code */ 293| | /* recalculate InChI from the structure */ 294| 6| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (294:17): [True: 0, False: 6] ------------------ 295| 6| ppt_group_info, ppat_norm, ppat_prep ) )) 296| 0| { 297| 0| goto exit_function; 298| 0| } 299| 6| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (299:17): [True: 0, False: 6] ------------------ 300| 0| { 301| 0| goto exit_function; 302| 0| } 303| | /* 304| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 305| | goto exit_function; 306| | } 307| | */ 308| 6| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 309| 6| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (309:17): [True: 0, False: 6] ------------------ 310| 0| { 311| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 312| 0| goto exit_function; 313| 0| } 314| 6| if (err) ------------------ | Branch (314:17): [True: 0, False: 6] ------------------ 315| 0| { 316| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 317| 0| goto exit_function; 318| 0| } 319| 6| cmpInChI2 = 0; 320| 6| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 321| 6| if (iRevrInChI || iOrigInChI) ------------------ | Branch (321:17): [True: 1, False: 5] | Branch (321:31): [True: 2, False: 3] ------------------ 322| 3| { 323| | /* additional mobile-H compare in case of Fixed-H */ 324| 3| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 325| 3| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (325:21): [True: 0, False: 3] ------------------ 326| 0| { 327| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 328| 0| goto exit_function; 329| 0| } 330| 3| if (err) ------------------ | Branch (330:21): [True: 0, False: 3] ------------------ 331| 0| { 332| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 333| 0| goto exit_function; 334| 0| } 335| 3| } 336| | 337| 6| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (337:30): [True: 1, False: 5] ------------------ 338| 1| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (338:24): [True: 0, False: 1] ------------------ 339| 1| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 340| 6| ? pStruct->pOneINChI[0]->StereoIsotopic 341| 6| : pStruct->pOneINChI[0]->Stereo; 342| | 343| | 344| 6| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 575| 12|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (344:31): [True: 3, False: 3] | Branch (344:64): [True: 2, False: 1] ------------------ 345| 1| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (345:24): [True: 0, False: 1] | Branch (345:66): [True: 0, False: 1] ------------------ 346| 6| ? NULL 347| 6| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (347:21): [True: 0, False: 1] ------------------ 348| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (348:21): [True: 0, False: 0] ------------------ 349| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 350| 0| pStruct->pOneINChI[1]->StereoIsotopic : 351| 1| pStruct->pOneINChI[1]->Stereo; 352| 6| } 353| 49| } 354| | 355| | /* djb-rwth: removing redundant code */ 356| 236| if (!( cmpInChI & IDIF_SB_MISS ) && ( cmpInChI2 & IDIF_SB_MISS ) && ------------------ | Branch (356:9): [True: 100, False: 136] | Branch (356:41): [True: 24, False: 76] ------------------ 357| 24| icr2->num_sb_in2_only && ------------------ | Branch (357:10): [True: 24, False: 0] ------------------ 358| 24| 0 < ( pBNS->tot_st_cap - pBNS->tot_st_flow )) /* djb-rwth: removing redundant code */ ------------------ | Branch (358:10): [True: 20, False: 4] ------------------ 359| 20| { 360| | /*----------------------------------------------------*/ 361| | /* case 02: missing stereogenic bond in Mobile-H only */ 362| | /* X=N-O* => X=N=O and eliminate radical */ 363| | /*----------------------------------------------------*/ 364| 20| int retC, ret2C, retS, ret2S; 365| | /* djb-rwth: removing redundant variables */ 366| 20| ICR icr_Prev, icr2_Prev; 367| | 368| | /* blind attepmt */ 369| 20| icr_Prev = *icr; 370| 20| icr2_Prev = *icr2; 371| | /* djb-rwth: removing redundant code */ 372| 97| for (i = AllRadList.num_edges = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (372:44): [True: 77, False: 20] ------------------ 373| 77| { 374| 77| if (pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow == 1 && ------------------ | Branch (374:17): [True: 16, False: 61] ------------------ 375| 16| ( ret = AddToEdgeList( &AllRadList, i, INC_ADD_EDGE ) )) ------------------ | | 20| 16|#define INC_ADD_EDGE 64 ------------------ | Branch (375:17): [True: 0, False: 16] ------------------ 376| 0| { 377| 0| goto exit_function; 378| 0| } 379| 77| } 380| 36| for (i = 0; i < AllRadList.num_edges; i++) ------------------ | Branch (380:21): [True: 16, False: 20] ------------------ 381| 16| { 382| 16| j = AllRadList.pnEdges[i]; 383| 16| pBNS->vert[j].st_edge.cap -= 1; 384| 16| pBNS->tot_st_cap -= 1; 385| 16| } 386| | /*-------------------------------------------------*/ 387| | /* re-create InChI and see whether it looks better */ 388| | /*-------------------------------------------------*/ 389| 20| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (389:13): [True: 1, False: 19] ------------------ 390| 20| ppt_group_info, ppat_norm, ppat_prep ) )) 391| 1| { 392| 1| goto exit_function; 393| 1| } 394| 19| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (394:13): [True: 0, False: 19] ------------------ 395| 0| { 396| 0| goto exit_function; 397| 0| } 398| | /* 399| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 400| | goto exit_function; 401| | } 402| | */ 403| 19| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 404| 19| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (404:13): [True: 0, False: 19] ------------------ 405| 0| { 406| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 407| 0| goto exit_function; 408| 0| } 409| 19| if (err) ------------------ | Branch (409:13): [True: 0, False: 19] ------------------ 410| 0| { 411| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 412| 0| goto exit_function; 413| 0| } 414| 19| cmpInChI2 = 0; 415| 19| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 416| 19| if (iRevrInChI || iOrigInChI) ------------------ | Branch (416:13): [True: 12, False: 7] | Branch (416:27): [True: 7, False: 0] ------------------ 417| 19| { 418| | /* additional mobile-H compare in case of Fixed-H */ 419| 19| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 420| 19| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (420:17): [True: 0, False: 19] ------------------ 421| 0| { 422| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 423| 0| goto exit_function; 424| 0| } 425| 19| if (err) ------------------ | Branch (425:17): [True: 0, False: 19] ------------------ 426| 0| { 427| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 428| 0| goto exit_function; 429| 0| } 430| 19| } 431| 19| retC = CompareIcr( icr, &icr_Prev, NULL, NULL, IDIFF_CONSTIT ); ------------------ | | 360| 19|#define IDIFF_CONSTIT (IDIF_POSITION_H | IDIF_MORE_FH | IDIF_LESS_FH | IDIF_MORE_H | IDIF_LESS_H | \ | | 361| 19| IDIF_NO_TAUT | IDIF_WRONG_TAUT | IDIF_SINGLE_TG | IDIF_MULTIPLE_TG | \ | | 362| 19| IDIF_NUM_TG | IDIF_EXTRA_TG_ENDP | IDIF_MISS_TG_ENDP | IDIF_TG | \ | | 363| 19| IDIF_NUM_ISO_AT | IDIF_ISO_AT | IDIF_CHARGE | IDIF_REM_PROT | IDIF_REM_ISO_H | \ | | 364| 19| IDIF_DIFF_TG_ENDP) ------------------ 432| 19| retS = CompareIcr( icr, &icr_Prev, NULL, NULL, IDIFF_STEREO ); ------------------ | | 365| 19|#define IDIFF_STEREO (IDIF_SC_INV | IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | \ | | 366| 19| IDIF_SC_MISS_UNDF | IDIF_SC_MISS | IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | \ | | 367| 19| IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) ------------------ 433| 19| ret2C = CompareIcr( icr2, &icr2_Prev, NULL, NULL, IDIFF_CONSTIT ); ------------------ | | 360| 19|#define IDIFF_CONSTIT (IDIF_POSITION_H | IDIF_MORE_FH | IDIF_LESS_FH | IDIF_MORE_H | IDIF_LESS_H | \ | | 361| 19| IDIF_NO_TAUT | IDIF_WRONG_TAUT | IDIF_SINGLE_TG | IDIF_MULTIPLE_TG | \ | | 362| 19| IDIF_NUM_TG | IDIF_EXTRA_TG_ENDP | IDIF_MISS_TG_ENDP | IDIF_TG | \ | | 363| 19| IDIF_NUM_ISO_AT | IDIF_ISO_AT | IDIF_CHARGE | IDIF_REM_PROT | IDIF_REM_ISO_H | \ | | 364| 19| IDIF_DIFF_TG_ENDP) ------------------ 434| 19| ret2S = CompareIcr( icr2, &icr2_Prev, NULL, NULL, IDIFF_STEREO ); ------------------ | | 365| 19|#define IDIFF_STEREO (IDIF_SC_INV | IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | \ | | 366| 19| IDIF_SC_MISS_UNDF | IDIF_SC_MISS | IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | \ | | 367| 19| IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) ------------------ 435| | 436| 19| if (0 >= retC && ------------------ | Branch (436:13): [True: 19, False: 0] ------------------ 437| 19| 0 >= retS && ------------------ | Branch (437:14): [True: 17, False: 2] ------------------ 438| 17| 0 >= ret2C && ------------------ | Branch (438:14): [True: 12, False: 5] ------------------ 439| 12| 0 > ret2S) ------------------ | Branch (439:14): [True: 2, False: 10] ------------------ 440| 2| { 441| 2| ; /* accept */ 442| 2| } 443| 17| else 444| 17| { 445| | /* reject */ 446| 30| for (i = 0; i < AllRadList.num_edges; i++) ------------------ | Branch (446:25): [True: 13, False: 17] ------------------ 447| 13| { 448| 13| j = AllRadList.pnEdges[i]; 449| 13| pBNS->vert[j].st_edge.cap += 1; 450| 13| pBNS->tot_st_cap += 1; 451| 13| } 452| | 453| | /*-------------------------------------------------*/ 454| | /* re-create InChI-- return to previous state */ 455| | /*-------------------------------------------------*/ 456| 17| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (456:17): [True: 0, False: 17] ------------------ 457| 17| ppt_group_info, ppat_norm, ppat_prep ) )) 458| 0| { 459| 0| goto exit_function; 460| 0| } 461| 17| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (461:17): [True: 0, False: 17] ------------------ 462| 0| { 463| 0| goto exit_function; 464| 0| } 465| | /* 466| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 467| | goto exit_function; 468| | } 469| | */ 470| 17| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 471| 17| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (471:17): [True: 0, False: 17] ------------------ 472| 0| { 473| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 474| 0| goto exit_function; 475| 0| } 476| 17| if (err) ------------------ | Branch (476:17): [True: 0, False: 17] ------------------ 477| 0| { 478| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 479| 0| goto exit_function; 480| 0| } 481| 17| cmpInChI2 = 0; 482| 17| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 483| 17| if (iRevrInChI || iOrigInChI) ------------------ | Branch (483:17): [True: 10, False: 7] | Branch (483:31): [True: 7, False: 0] ------------------ 484| 17| { 485| | /* additional mobile-H compare in case of Fixed-H */ 486| 17| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 487| 17| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (487:21): [True: 0, False: 17] ------------------ 488| 0| { 489| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 490| 0| goto exit_function; 491| 0| } 492| 17| if (err) ------------------ | Branch (492:21): [True: 0, False: 17] ------------------ 493| 0| { 494| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 495| 0| goto exit_function; 496| 0| } 497| 17| } 498| 17| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (498:30): [True: 0, False: 17] ------------------ 499| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (499:24): [True: 0, False: 0] ------------------ 500| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) ? 501| 17| pStruct->pOneINChI[0]->StereoIsotopic : pStruct->pOneINChI[0]->Stereo; 502| | 503| | 504| 17| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 575| 34|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (504:31): [True: 0, False: 17] | Branch (504:64): [True: 7, False: 10] ------------------ 505| 10| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ? ------------------ | Branch (505:24): [True: 0, False: 10] | Branch (505:66): [True: 0, False: 10] ------------------ 506| 17| NULL : 507| 17| ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (507:19): [True: 0, False: 10] ------------------ 508| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (508:17): [True: 0, False: 0] ------------------ 509| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 510| 0| pStruct->pOneINChI[1]->StereoIsotopic : 511| 10| pStruct->pOneINChI[1]->Stereo; 512| 17| } 513| |/*exit_case_02:;*/ 514| 19| } 515| | 516| 235| cur_success = 0; 517| 235| if (pStruct->bMobileH == TAUT_NON && ( cmpInChI & IDIF_SB_EXTRA_UNDF ) && ------------------ | | 574| 470|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (517:9): [True: 78, False: 157] | Branch (517:42): [True: 18, False: 60] ------------------ 518| 18| pStruct->endpoint) ------------------ | Branch (518:10): [True: 18, False: 0] ------------------ 519| 18| { 520| | /*------------------------------------------------------*/ 521| | /* case 03: extra stereogenic bond in Fixed-H only */ 522| | /* in Mobile-H this bond is not stereogenic. */ 523| | /* Since this bond parity is not known, it is UNDEFINED */ 524| | /*------------------------------------------------------*/ 525| 18| int bDone, num_endpoints; 526| | 527| 18| TautMinusEdges[0].num_edges = 0; 528| 18| TautMinusEdges[1].num_edges = 0; 529| 18| AllChargeEdges.num_edges = 0; 530| | /* in1 => in restored structure; in2 => in original InChI */ 531| 94| for (i = 0; i < icr->num_sb_undef_in1_only; i++) ------------------ | Branch (531:21): [True: 76, False: 18] ------------------ 532| 76| { 533| 76| j12 = icr->sb_undef_in1_only[i]; 534| 76| pv1 = pBNS->vert + ( v1 = pStereoRevrs->nBondAtom1[j12] - 1 ); 535| 76| pv2 = pBNS->vert + ( v2 = pStereoRevrs->nBondAtom2[j12] - 1 ); /* djb-rwth: ignoring LLVM warning: variable used */ 536| | 537| 76| if (pStereo2Revrs) ------------------ | Branch (537:17): [True: 0, False: 76] ------------------ 538| 0| { 539| | /* reject if it is extra in Mobile-H also */ 540| 0| if (icr2->num_sb_undef_in1_only) ------------------ | Branch (540:21): [True: 0, False: 0] ------------------ 541| 0| { 542| 0| for (j = 0; j < icr2->num_sb_undef_in1_only; j++) ------------------ | Branch (542:33): [True: 0, False: 0] ------------------ 543| 0| { 544| 0| k = icr2->sb_undef_in1_only[j]; 545| 0| if (v1 == pStereo2Revrs->nBondAtom1[k] && ------------------ | Branch (545:29): [True: 0, False: 0] ------------------ 546| 0| v2 == pStereo2Revrs->nBondAtom2[k]) ------------------ | Branch (546:30): [True: 0, False: 0] ------------------ 547| 0| { 548| 0| break; 549| 0| } 550| 0| } 551| 0| if (j < icr->num_sb_in1_only) ------------------ | Branch (551:25): [True: 0, False: 0] ------------------ 552| 0| { 553| 0| continue; /* extra stereobond in Mobile H also */ 554| 0| } 555| 0| } 556| 0| } 557| | /* reject if it is a stereobond in Mobile-H also */ 558| 76| if (pStereo2InChI && pStereo2InChI->nNumberOfStereoBonds) ------------------ | Branch (558:17): [True: 37, False: 39] | Branch (558:34): [True: 31, False: 6] ------------------ 559| 31| { 560| 95| for (j = 0; j < pStereo2InChI->nNumberOfStereoBonds; j++) ------------------ | Branch (560:29): [True: 64, False: 31] ------------------ 561| 64| { 562| 64| if (v1 == pStereo2InChI->nBondAtom1[j] && ------------------ | Branch (562:25): [True: 5, False: 59] ------------------ 563| 5| v2 == pStereo2InChI->nBondAtom1[j]) ------------------ | Branch (563:26): [True: 0, False: 5] ------------------ 564| 0| { 565| 0| break; 566| 0| } 567| 64| } 568| 31| if (j < pStereo2InChI->nNumberOfStereoBonds) ------------------ | Branch (568:21): [True: 0, False: 31] ------------------ 569| 0| { 570| 0| continue; /* ignore this extra stereo bond: it is in Mobile-H */ 571| 0| } 572| 31| } 573| | /* find the edge between v1 and v2 */ 574| 82| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (574:25): [True: 82, False: 0] ------------------ 575| 82| { 576| 82| pe = pBNS->edge + ( e = pv1->iedge[k] ); 577| 82| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (577:21): [True: 76, False: 6] ------------------ 578| 76| break; /* the edge has been found */ 579| 82| } 580| 76| if (k >= at2[v1].valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (580:17): [True: 0, False: 76] ------------------ 581| 0| { 582| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 583| 0| goto exit_function; 584| 0| } 585| | /* Fix all charges except negative charges on tautomeric endpoints */ 586| 76| if (!AllChargeEdges.num_edges && !TautMinusEdges[0].num_edges && !TautMinusEdges[1].num_edges) ------------------ | Branch (586:17): [True: 18, False: 58] | Branch (586:46): [True: 18, False: 0] | Branch (586:78): [True: 18, False: 0] ------------------ 587| 18| { 588| 143| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (588:29): [True: 125, False: 18] ------------------ 589| 125| { 590| 125| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (590:25): [True: 92, False: 33] | Branch (590:69): [True: 92, False: 0] ------------------ 591| 92| { 592| 92| if (!pStruct->endpoint[j]) ------------------ | Branch (592:29): [True: 86, False: 6] ------------------ 593| 86| { 594| 86| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 86|#define INC_ADD_EDGE 64 ------------------ | Branch (594:33): [True: 0, False: 86] ------------------ 595| 0| { 596| 0| goto exit_function; 597| 0| } 598| 86| } 599| 6| else 600| 6| if (pVA[j].cNumValenceElectrons == 6) ------------------ | Branch (600:33): [True: 0, False: 6] ------------------ 601| 0| { 602| | /* O */ 603| 0| if ((ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (603:37): [True: 0, False: 0] ------------------ 604| 0| { 605| 0| goto exit_function; 606| 0| } 607| 0| } 608| 6| else 609| 6| { 610| | /* N */ 611| 6| if ((ret = AddToEdgeList( TautMinusEdges + 1, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 6|#define INC_ADD_EDGE 64 ------------------ | Branch (611:37): [True: 0, False: 6] ------------------ 612| 0| { 613| 0| goto exit_function; 614| 0| } 615| 6| } 616| 92| } 617| 125| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (617:25): [True: 121, False: 4] | Branch (617:68): [True: 121, False: 0] ------------------ 618| 121| { 619| 121| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 121|#define INC_ADD_EDGE 64 ------------------ | Branch (619:29): [True: 0, False: 121] ------------------ 620| 0| { 621| 0| goto exit_function; 622| 0| } 623| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 624| 121| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (624:29): [True: 113, False: 8] | Branch (624:65): [True: 113, False: 0] ------------------ 625| 113| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 118| 113|#define NO_VERTEX -2 ------------------ | Branch (625:30): [True: 29, False: 84] ------------------ 626| 29| { 627| | 628| 29| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (628:33): [True: 20, False: 9] | Branch (628:61): [True: 20, False: 0] ------------------ 629| 20| { 630| 20| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 20|#define INC_ADD_EDGE 64 ------------------ | Branch (630:37): [True: 0, False: 20] ------------------ 631| 0| { 632| 0| goto exit_function; 633| 0| } 634| 20| } 635| 29| } 636| 121| } 637| 125| } 638| 18| } 639| 76| if (!pe->flow) ------------------ | Branch (639:17): [True: 40, False: 36] ------------------ 640| 40| continue; 641| | /* fix all charges except tautomeric; first allow only O, then only N, finally both N and O */ 642| 36| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 643| 144| for (k = 1, bDone = 0; k < 4 && !bDone; k++) ------------------ | Branch (643:36): [True: 108, False: 36] | Branch (643:45): [True: 108, False: 0] ------------------ 644| 108| { 645| | /* fix tautomeric charges */ 646| 108| num_endpoints = ( TautMinusEdges + 0 )->num_edges + ( TautMinusEdges + 1 )->num_edges; 647| 108| if (k == 2) ------------------ | Branch (647:21): [True: 36, False: 72] ------------------ 648| 36| { 649| | /* fix charges on O */ 650| 36| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 651| 36| num_endpoints -= ( TautMinusEdges + 0 )->num_edges; 652| 36| } 653| 108| if (k == 1) ------------------ | Branch (653:21): [True: 36, False: 72] ------------------ 654| 36| { 655| 36| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 656| 36| num_endpoints -= ( TautMinusEdges + 1 )->num_edges; 657| 36| } 658| 108| if (num_endpoints >= 2) ------------------ | Branch (658:21): [True: 12, False: 96] ------------------ 659| 12| { 660| 12| delta = 1; 661| 12| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 662| 12| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 663| | 664| 12| pe->forbidden |= forbidden_edge_mask; /* fix stereobond */ 665| 12| pe->flow -= delta; /* decrement stereobond order */ 666| 12| pv1->st_edge.flow -= delta; 667| 12| pv2->st_edge.flow -= delta; 668| 12| pBNS->tot_st_flow -= 2 * delta; 669| | 670| 12| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 671| 12| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 672| | 673| 12| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (673:25): [True: 0, False: 12] | Branch (673:40): [True: 0, False: 0] | Branch (673:58): [True: 0, False: 0] ------------------ 674| 0| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (674:26): [True: 0, False: 0] | Branch (674:44): [True: 0, False: 0] | Branch (674:67): [True: 0, False: 0] ------------------ 675| 0| { 676| | /* Negative charge has been moved, no change in number of charges */ 677| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 678| 0| if (ret > 0) ------------------ | Branch (678:29): [True: 0, False: 0] ------------------ 679| 0| { 680| 0| ( *pnNumRunBNS )++; 681| 0| cur_success++; /* 01 */ 682| 0| bDone = 1; 683| 0| } 684| 0| } 685| 12| else 686| 12| { 687| 12| pe->forbidden &= ~forbidden_edge_mask; 688| 12| pe->flow += delta; 689| 12| pv1->st_edge.flow += delta; 690| 12| pv2->st_edge.flow += delta; 691| 12| pBNS->tot_st_flow += 2 * delta; 692| 12| } 693| 12| } 694| | /* unfix tautomeric charges */ 695| 108| if (k == 2) ------------------ | Branch (695:21): [True: 36, False: 72] ------------------ 696| 36| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 697| 108| if (k == 1) ------------------ | Branch (697:21): [True: 36, False: 72] ------------------ 698| 36| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 699| 108| } 700| 36| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 701| 36| } 702| |/*exit_case_03:*/ 703| 18| if (cur_success) ------------------ | Branch (703:13): [True: 0, False: 18] ------------------ 704| 0| { 705| | /* djb-rwth: removing redundant code */ 706| | /* recalculate InChI from the structure */ 707| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (707:17): [True: 0, False: 0] ------------------ 708| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 709| 0| { 710| 0| goto exit_function; 711| 0| } 712| 0| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (712:17): [True: 0, False: 0] ------------------ 713| 0| { 714| 0| goto exit_function; 715| 0| } 716| | /* 717| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 718| | goto exit_function; 719| | } 720| | */ 721| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 722| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (722:17): [True: 0, False: 0] ------------------ 723| 0| { 724| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 725| 0| goto exit_function; 726| 0| } 727| 0| if (err) ------------------ | Branch (727:17): [True: 0, False: 0] ------------------ 728| 0| { 729| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 730| 0| goto exit_function; 731| 0| } 732| 0| cmpInChI2 = 0; 733| 0| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 734| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (734:17): [True: 0, False: 0] | Branch (734:31): [True: 0, False: 0] ------------------ 735| 0| { 736| | /* additional mobile-H compare in case of Fixed-H */ 737| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 738| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (738:21): [True: 0, False: 0] ------------------ 739| 0| { 740| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 741| 0| goto exit_function; 742| 0| } 743| 0| if (err) ------------------ | Branch (743:21): [True: 0, False: 0] ------------------ 744| 0| { 745| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 746| 0| goto exit_function; 747| 0| } 748| 0| } 749| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (749:30): [True: 0, False: 0] ------------------ 750| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (750:24): [True: 0, False: 0] ------------------ 751| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 752| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 753| 0| : pStruct->pOneINChI[0]->Stereo; 754| | 755| | 756| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (756:31): [True: 0, False: 0] | Branch (756:64): [True: 0, False: 0] ------------------ 757| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (757:24): [True: 0, False: 0] | Branch (757:66): [True: 0, False: 0] ------------------ 758| 0| ? NULL 759| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (759:21): [True: 0, False: 0] ------------------ 760| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (760:21): [True: 0, False: 0] ------------------ 761| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 762| 0| pStruct->pOneINChI[1]->StereoIsotopic : 763| 0| pStruct->pOneINChI[1]->Stereo; 764| 0| } 765| 18| } 766| | 767| 235| cur_success = 0; 768| 235| if (( cmpInChI & IDIF_SB_EXTRA_UNDF )) ------------------ | Branch (768:9): [True: 52, False: 183] ------------------ 769| 52| { 770| | /*------------------------------------------------------*/ 771| | /* case 04: extra stereogenic bond */ 772| | /* Since this bond parity is not known, it is UNDEFINED */ 773| | /*------------------------------------------------------*/ 774| 52| int bDone, num_endpoints; 775| | 776| 52| TautMinusEdges[0].num_edges = 0; 777| 52| TautMinusEdges[1].num_edges = 0; 778| 52| AllChargeEdges.num_edges = 0; 779| | /* in1 => in restored structure; in2 => in original InChI */ 780| 249| for (i = 0; i < icr->num_sb_undef_in1_only; i++) ------------------ | Branch (780:21): [True: 197, False: 52] ------------------ 781| 197| { 782| 197| j12 = icr->sb_undef_in1_only[i]; 783| 197| pv1 = pBNS->vert + ( v1 = pStereoRevrs->nBondAtom1[j12] - 1 ); 784| 197| pv2 = pBNS->vert + ( v2 = pStereoRevrs->nBondAtom2[j12] - 1 ); /* djb-rwth: ignoring LLVM warning: variable used */ 785| | 786| | /* djb-rwth: fixing oss-fuzz issue #67650 */ 787| 197| pe = pBNS->edge + (e = pv1->iedge[0]); /* djb-rwth: proper initialisation required to avoid garbage values */ 788| | /* find the edge between v1 and v2 */ 789| 216| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (789:25): [True: 216, False: 0] ------------------ 790| 216| { 791| 216| pe = pBNS->edge + ( e = pv1->iedge[k] ); 792| 216| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (792:21): [True: 197, False: 19] ------------------ 793| 197| break; /* the edge has been found */ 794| 216| } 795| 197| if (k == at2[v1].valence) ------------------ | Branch (795:17): [True: 0, False: 197] ------------------ 796| 0| { 797| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 798| 0| goto exit_function; 799| 0| } 800| 197| if (pStereo2Revrs) ------------------ | Branch (800:17): [True: 0, False: 197] ------------------ 801| 0| { 802| | /* reject if it is not extra in Mobile-H also */ 803| 0| if (icr2->num_sb_undef_in1_only) ------------------ | Branch (803:21): [True: 0, False: 0] ------------------ 804| 0| { 805| 0| for (j = 0; j < icr2->num_sb_undef_in1_only; j++) ------------------ | Branch (805:33): [True: 0, False: 0] ------------------ 806| 0| { 807| 0| k = icr2->sb_undef_in1_only[j]; 808| 0| if (v1 == pStereo2Revrs->nBondAtom1[k] && ------------------ | Branch (808:29): [True: 0, False: 0] ------------------ 809| 0| v2 == pStereo2Revrs->nBondAtom2[k]) ------------------ | Branch (809:30): [True: 0, False: 0] ------------------ 810| 0| { 811| 0| break; 812| 0| } 813| 0| } 814| 0| if (j == icr->num_sb_in1_only) ------------------ | Branch (814:25): [True: 0, False: 0] ------------------ 815| 0| { 816| 0| continue; /* extra stereobond only in Fixed-H, not in Mobile H also */ 817| 0| } 818| 0| } 819| 0| } 820| | 821| | /* Fix all charges except negative charges on tautomeric endpoints */ 822| 197| if (!AllChargeEdges.num_edges && !TautMinusEdges[0].num_edges && !TautMinusEdges[1].num_edges) ------------------ | Branch (822:17): [True: 52, False: 145] | Branch (822:46): [True: 52, False: 0] | Branch (822:78): [True: 52, False: 0] ------------------ 823| 52| { 824| 441| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (824:29): [True: 389, False: 52] ------------------ 825| 389| { 826| 389| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (826:25): [True: 240, False: 149] | Branch (826:69): [True: 240, False: 0] ------------------ 827| 240| { 828| 240| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 240|#define INC_ADD_EDGE 64 ------------------ | Branch (828:29): [True: 0, False: 240] ------------------ 829| 0| { 830| 0| goto exit_function; 831| 0| } 832| 240| } 833| 389| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (833:25): [True: 348, False: 41] | Branch (833:68): [True: 347, False: 1] ------------------ 834| 347| { 835| 347| int bMayBeUnfixed = !at2[j].num_H && !( pStruct->endpoint && pStruct->endpoint[j] ); ------------------ | Branch (835:45): [True: 345, False: 2] | Branch (835:65): [True: 119, False: 226] | Branch (835:86): [True: 6, False: 113] ------------------ 836| 347| if ((bMayBeUnfixed && pVA[j].cNumValenceElectrons == 6) || ------------------ | Branch (836:30): [True: 339, False: 8] | Branch (836:47): [True: 2, False: 337] ------------------ 837| 345| (pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber > 1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (837:31): [True: 308, False: 37] | Branch (837:67): [True: 7, False: 301] ------------------ 838| 9| { 839| | /* O & P */ 840| 9| if ((ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 9|#define INC_ADD_EDGE 64 ------------------ | Branch (840:33): [True: 0, False: 9] ------------------ 841| 0| { 842| 0| goto exit_function; 843| 0| } 844| 9| } 845| 338| else 846| 338| { 847| 338| if (bMayBeUnfixed && ------------------ | Branch (847:33): [True: 330, False: 8] ------------------ 848| 330| pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber == 1) ------------------ | Branch (848:37): [True: 293, False: 37] | Branch (848:73): [True: 293, False: 0] ------------------ 849| 293| { 850| | /* N */ 851| 293| if ((ret = AddToEdgeList( TautMinusEdges + 1, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 293|#define INC_ADD_EDGE 64 ------------------ | Branch (851:37): [True: 0, False: 293] ------------------ 852| 0| { 853| 0| goto exit_function; 854| 0| } 855| 293| } 856| 45| else 857| 45| { 858| 45| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 45|#define INC_ADD_EDGE 64 ------------------ | Branch (858:37): [True: 0, False: 45] ------------------ 859| 0| { 860| 0| goto exit_function; 861| 0| } 862| 45| } 863| 338| } 864| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 865| 347| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (865:29): [True: 308, False: 39] | Branch (865:65): [True: 304, False: 4] ------------------ 866| 304| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 118| 304|#define NO_VERTEX -2 ------------------ | Branch (866:30): [True: 107, False: 197] ------------------ 867| 107| { 868| 107| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (868:33): [True: 84, False: 23] | Branch (868:61): [True: 83, False: 1] ------------------ 869| 83| { 870| 83| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 83|#define INC_ADD_EDGE 64 ------------------ | Branch (870:37): [True: 0, False: 83] ------------------ 871| 0| { 872| 0| goto exit_function; 873| 0| } 874| 83| } 875| 107| } 876| 347| } 877| 389| } 878| 52| } 879| 197| if (!pe->flow) ------------------ | Branch (879:17): [True: 95, False: 102] ------------------ 880| 95| continue; 881| | /* fix all charges except tautomeric; first allow only O, then only N, finally both N and O */ 882| 102| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 883| 391| for (k = 1, bDone = 0; k < 4 && !bDone; k++) ------------------ | Branch (883:36): [True: 305, False: 86] | Branch (883:45): [True: 289, False: 16] ------------------ 884| 289| { 885| | /* fix positive charges on heteroatoms */ 886| 289| num_endpoints = ( TautMinusEdges + 0 )->num_edges + ( TautMinusEdges + 1 )->num_edges; 887| 289| if (k == 2) ------------------ | Branch (887:21): [True: 101, False: 188] ------------------ 888| 101| { 889| | /* fix charges on O */ 890| 101| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 891| 101| num_endpoints -= ( TautMinusEdges + 0 )->num_edges; 892| 101| } 893| 289| if (k == 1) ------------------ | Branch (893:21): [True: 102, False: 187] ------------------ 894| 102| { 895| | /* fix charges on N */ 896| 102| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 897| 102| num_endpoints -= ( TautMinusEdges + 1 )->num_edges; 898| 102| } 899| 289| if (num_endpoints >= 2) ------------------ | Branch (899:21): [True: 177, False: 112] ------------------ 900| 177| { 901| 177| delta = 1; 902| 177| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 903| 177| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 904| | 905| 177| pe->forbidden |= forbidden_edge_mask; /* fix stereobond */ 906| 177| pe->flow -= delta; /* decrement stereobond order */ 907| 177| pv1->st_edge.flow -= delta; 908| 177| pv2->st_edge.flow -= delta; 909| 177| pBNS->tot_st_flow -= 2 * delta; 910| | 911| 177| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 912| 177| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 913| | 914| 177| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (914:25): [True: 17, False: 160] | Branch (914:40): [True: 2, False: 15] | Branch (914:58): [True: 2, False: 0] ------------------ 915| 17| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (915:26): [True: 15, False: 0] | Branch (915:44): [True: 15, False: 0] | Branch (915:67): [True: 17, False: 0] ------------------ 916| 17| { 917| | /* Negative charge has been moved, no change in number of charges */ 918| 17| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 919| 17| if (ret > 0) ------------------ | Branch (919:29): [True: 17, False: 0] ------------------ 920| 17| { 921| 17| ( *pnNumRunBNS )++; 922| 17| cur_success++; /* 01 */ 923| 17| bDone = 1; 924| 17| } 925| 17| } 926| 160| else 927| 160| { 928| 160| pe->forbidden &= ~forbidden_edge_mask; 929| 160| pe->flow += delta; 930| 160| pv1->st_edge.flow += delta; 931| 160| pv2->st_edge.flow += delta; 932| 160| pBNS->tot_st_flow += 2 * delta; 933| 160| } 934| 177| } 935| | /* unfix tautomeric charges */ 936| 289| if (k == 2) ------------------ | Branch (936:21): [True: 101, False: 188] ------------------ 937| 101| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 938| 289| if (k == 1) ------------------ | Branch (938:21): [True: 102, False: 187] ------------------ 939| 102| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 940| 289| } 941| 102| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 942| 102| } 943| |/*exit_case_04:*/ 944| 52| if (cur_success) ------------------ | Branch (944:13): [True: 13, False: 39] ------------------ 945| 13| { 946| | /* djb-rwth: removing redundant code */ 947| | /* recalculate InChI from the structure */ 948| 13| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (948:17): [True: 0, False: 13] ------------------ 949| 13| ppt_group_info, ppat_norm, ppat_prep ) )) 950| 0| { 951| 0| goto exit_function; 952| 0| } 953| 13| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (953:17): [True: 0, False: 13] ------------------ 954| 0| { 955| 0| goto exit_function; 956| 0| } 957| | /* 958| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 959| | goto exit_function; 960| | } 961| | */ 962| 13| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 963| 13| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (963:17): [True: 0, False: 13] ------------------ 964| 0| { 965| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 966| 0| goto exit_function; 967| 0| } 968| 13| if (err) ------------------ | Branch (968:17): [True: 0, False: 13] ------------------ 969| 0| { 970| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 971| 0| goto exit_function; 972| 0| } 973| 13| cmpInChI2 = 0; 974| 13| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 975| 13| if (iRevrInChI || iOrigInChI) ------------------ | Branch (975:17): [True: 0, False: 13] | Branch (975:31): [True: 1, False: 12] ------------------ 976| 1| { 977| |/* additional mobile-H compare in case of Fixed-H */ 978| 1| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 979| 1| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (979:21): [True: 0, False: 1] ------------------ 980| 0| { 981| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 982| 0| goto exit_function; 983| 0| } 984| 1| if (err) ------------------ | Branch (984:21): [True: 0, False: 1] ------------------ 985| 0| { 986| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 987| 0| goto exit_function; 988| 0| } 989| 1| } 990| 13| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (990:30): [True: 0, False: 13] ------------------ 991| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (991:24): [True: 0, False: 0] ------------------ 992| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 993| 13| ? pStruct->pOneINChI[0]->StereoIsotopic 994| 13| : pStruct->pOneINChI[0]->Stereo; 995| | 996| | 997| 13| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 575| 26|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (997:31): [True: 12, False: 1] | Branch (997:64): [True: 1, False: 0] ------------------ 998| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (998:24): [True: 0, False: 0] | Branch (998:66): [True: 0, False: 0] ------------------ 999| 13| ? NULL 1000| 13| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (1000:21): [True: 0, False: 0] ------------------ 1001| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1001:21): [True: 0, False: 0] ------------------ 1002| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 1003| 0| pStruct->pOneINChI[1]->StereoIsotopic : 1004| 0| pStruct->pOneINChI[1]->Stereo; 1005| 13| } 1006| 52| } 1007| | 1008| 235| cur_success = 0; 1009| 235| if (pStruct->bMobileH == TAUT_YES && ------------------ | | 575| 470|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1009:9): [True: 157, False: 78] ------------------ 1010| 157| ( cmpInChI & IDIF_SB_EXTRA_UNDF && ------------------ | Branch (1010:11): [True: 30, False: 127] ------------------ 1011| 30| !pStruct->ti.num_t_groups ) ------------------ | Branch (1011:13): [True: 25, False: 5] ------------------ 1012| 235| /*pStruct->bMobileH == TAUT_NON && (cmpInChI2 & IDIF_SB_EXTRA_UNDF)*/) 1013| 25| { 1014| | /*----------------------------------------------------------*/ 1015| | /* case 05: extra stereogenic bond on =NH2(+), (B, Mobile-H)*/ 1016| | /* H H */ 1017| | /* original: N(+)=-N< -> N--==N/ */ 1018| | /* (A) H */ 1019| | /* double bond is marked as */ 1020| | /* not stereogenic due to */ 1021| | /* its change during proton */ 1022| | /* removal => No Stereo bond */ 1023| | /* (=NH may be tautomeric) */ 1024| | /* */ 1025| | /* H H */ 1026| | /* original: N=-N(+)< -> N--==N/ */ 1027| | /* (B) H */ 1028| | /* double bond was not */ 1029| | /* changed during proton */ 1030| | /* In Fixed-H this bond removal => Undef Stereo */ 1031| | /* may not be stereogenic (=NH is not tautomeric) */ 1032| | /* (a) due to (+) movement */ 1033| | /* (b) due to symmetry (2H), even if isotopic */ 1034| | /* */ 1035| | /* Fixed-H: move (+) to or from NH2 for Undef or No stereo */ 1036| | /* respectively */ 1037| | /* Mobile-H: Add H(+) to =NH and move the charge to =N- */ 1038| | /* to eliminate Undef stereo */ 1039| | /* Move charge from N to -NH2 to create */ 1040| | /* Undef Stereo */ 1041| | /* Since this bond parity is not known, it is UNDEFINED */ 1042| | /* */ 1043| | /* Solution: Add H(+) to =NH and move charge to -N= */ 1044| | /* */ 1045| | /*----------------------------------------------------------*/ 1046| 25| int aN, aC, i1, i2, vPlusMinus; 1047| 25| AllChargeEdges.num_edges = 0; 1048| | /* in1 => in restored structure; in2 => in original InChI */ 1049| 102| for (i = 0; i < icr->num_sb_undef_in1_only; i++) ------------------ | Branch (1049:21): [True: 77, False: 25] ------------------ 1050| 77| { 1051| 77| j12 = icr->sb_undef_in1_only[i]; 1052| 77| pv1 = pBNS->vert + ( v1 = pStereoRevrs->nBondAtom1[j12] - 1 ); 1053| 77| pv2 = pBNS->vert + ( v2 = pStereoRevrs->nBondAtom2[j12] - 1 ); /* djb-rwth: ignoring LLVM warning: variable used */ 1054| | /* indicators of -NH: */ 1055| 77| i1 = at2[v1].valence == 1 && at2[v1].num_H == 1 && !at2[v1].endpoint && ------------------ | Branch (1055:18): [True: 0, False: 77] | Branch (1055:42): [True: 0, False: 0] | Branch (1055:64): [True: 0, False: 0] ------------------ 1056| 0| pVA[v1].cNumValenceElectrons == 5 && pVA[v1].cPeriodicRowNumber == 1; ------------------ | Branch (1056:17): [True: 0, False: 0] | Branch (1056:54): [True: 0, False: 0] ------------------ 1057| 77| i2 = at2[v2].valence == 1 && at2[v2].num_H == 1 && !at2[v2].endpoint && ------------------ | Branch (1057:18): [True: 0, False: 77] | Branch (1057:42): [True: 0, False: 0] | Branch (1057:64): [True: 0, False: 0] ------------------ 1058| 0| pVA[v2].cNumValenceElectrons == 5 && pVA[v2].cPeriodicRowNumber == 1; ------------------ | Branch (1058:17): [True: 0, False: 0] | Branch (1058:54): [True: 0, False: 0] ------------------ 1059| 77| if ((!i1 && !i2) || (i1 && i2)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1059:18): [True: 77, False: 0] | Branch (1059:25): [True: 77, False: 0] | Branch (1059:34): [True: 0, False: 0] | Branch (1059:40): [True: 0, False: 0] ------------------ 1060| 77| { 1061| 77| continue; 1062| 77| } 1063| | /* find the edge between v1 and v2 */ 1064| 0| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (1064:25): [True: 0, False: 0] ------------------ 1065| 0| { 1066| 0| pe = pBNS->edge + ( e = pv1->iedge[k] ); 1067| 0| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (1067:21): [True: 0, False: 0] ------------------ 1068| 0| { 1069| 0| break; /* the edge has been found */ 1070| 0| } 1071| 0| } 1072| 0| if (k == at2[v1].valence) ------------------ | Branch (1072:17): [True: 0, False: 0] ------------------ 1073| 0| { 1074| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1075| 0| goto exit_function; 1076| 0| } 1077| 0| if (pe->flow != 1) ------------------ | Branch (1077:17): [True: 0, False: 0] ------------------ 1078| 0| { 1079| 0| continue; /* already charged */ 1080| 0| } 1081| 0| aN = i1 ? v1 : v2; /* -NH atom */ ------------------ | Branch (1081:18): [True: 0, False: 0] ------------------ 1082| 0| aC = i1 ? v2 : v1; /* neighbor */ ------------------ | Branch (1082:18): [True: 0, False: 0] ------------------ 1083| | /* Replace =NH with -NH2 1084| | Create such a charge on some -N< that may be moved to NH2 to remove H(+): 1085| | transformation: 1086| | from: HN=C-=-N=(+vert)-Y=(+super)-(+/-) 1087| | to: 2HN-C*-=-N=(+vert)-Y=(+super)-(+/-)* 1088| | Run BNS to obtain: 1089| | 2HN-C=-=N(+)-(+vert)=Y-(+super)=(+/-) 1090| | */ 1091| 0| vPlusMinus = GetPlusMinusVertex( pBNS, pTCGroups, 1, 0 ); 1092| 0| if (NO_VERTEX == vPlusMinus) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (1092:17): [True: 0, False: 0] ------------------ 1093| 0| { 1094| 0| break; /* cannot do anything */ 1095| 0| } 1096| | /* increase edges to -Y-(+/-)-Y- capacities */ 1097| 0| delta = 1; 1098| 0| for (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++) ------------------ | Branch (1098:26): [True: 0, False: 0] ------------------ 1099| 0| { 1100| 0| i2 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus; 1101| 0| for (k = 0; k < pBNS->vert[i2].num_adj_edges; k++) ------------------ | Branch (1101:29): [True: 0, False: 0] ------------------ 1102| 0| { 1103| 0| pBNS->edge[pBNS->vert[i2].iedge[k]].cap += delta; 1104| 0| } 1105| 0| } 1106| | /* Fix all charges except (+) on -N< */ 1107| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (1107:17): [True: 0, False: 0] ------------------ 1108| 0| { 1109| 0| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (1109:29): [True: 0, False: 0] ------------------ 1110| 0| { 1111| 0| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1111:25): [True: 0, False: 0] | Branch (1111:69): [True: 0, False: 0] ------------------ 1112| 0| { 1113| 0| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1113:29): [True: 0, False: 0] ------------------ 1114| 0| { 1115| 0| goto exit_function; 1116| 0| } 1117| 0| } 1118| 0| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1118:25): [True: 0, False: 0] | Branch (1118:68): [True: 0, False: 0] ------------------ 1119| 0| { 1120| 0| if (pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber == 1 && ------------------ | Branch (1120:29): [True: 0, False: 0] | Branch (1120:65): [True: 0, False: 0] ------------------ 1121| 0| !at2[j].num_H && at2[j].valence == 3 && ------------------ | Branch (1121:30): [True: 0, False: 0] | Branch (1121:47): [True: 0, False: 0] ------------------ 1122| 0| !( at2[j].endpoint || (pStruct->endpoint && pStruct->endpoint[j]) )) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1122:33): [True: 0, False: 0] | Branch (1122:53): [True: 0, False: 0] | Branch (1122:74): [True: 0, False: 0] ------------------ 1123| 0| { 1124| 0| ; /* do not fix -N< or =N(+)< */ 1125| 0| } 1126| 0| else 1127| 0| { 1128| | /* all others */ 1129| 0| if ((ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1129:33): [True: 0, False: 0] ------------------ 1130| 0| { 1131| 0| goto exit_function; 1132| 0| } 1133| 0| } 1134| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 1135| 0| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (1135:29): [True: 0, False: 0] | Branch (1135:65): [True: 0, False: 0] ------------------ 1136| 0| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (1136:30): [True: 0, False: 0] ------------------ 1137| 0| { 1138| 0| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (1138:33): [True: 0, False: 0] | Branch (1138:61): [True: 0, False: 0] ------------------ 1139| 0| { 1140| 0| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1140:37): [True: 0, False: 0] ------------------ 1141| 0| { 1142| 0| goto exit_function; 1143| 0| } 1144| 0| } 1145| 0| } 1146| 0| } 1147| 0| } 1148| 0| } 1149| | /* Make bond to =NH single, add radical to aC */ 1150| 0| pe->flow -= delta; /* make single bond */ 1151| 0| pBNS->vert[aN].st_edge.flow -= delta; 1152| 0| pBNS->vert[aN].st_edge.cap -= delta; /* avoid radical on N */ 1153| 0| pBNS->vert[aC].st_edge.flow -= delta; /* create radical on C */ 1154| 0| pBNS->vert[vPlusMinus].st_edge.cap += delta; /* create radical on (+/-) */ 1155| 0| pBNS->tot_st_flow -= 2 * delta; 1156| | /* fix C-NH bond */ 1157| 0| if ((ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1157:17): [True: 0, False: 0] ------------------ 1158| 0| { 1159| 0| goto exit_function; 1160| 0| } 1161| | /* pBNS->tot_st_cap is unchanged */ 1162| | /* find all aC edges except pe to fix them */ 1163| | /* 2. Check whether it would work and do if it would */ 1164| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1165| 0| pe->cap++; 1166| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1167| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1168| | 1169| 0| if (ret == 1 && ( (vPathEnd == vPlusMinus && vPathStart == aC) || ------------------ | Branch (1169:17): [True: 0, False: 0] | Branch (1169:32): [True: 0, False: 0] | Branch (1169:58): [True: 0, False: 0] ------------------ 1170| 0| (vPathEnd == aC && vPathStart == vPlusMinus) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1170:18): [True: 0, False: 0] | Branch (1170:36): [True: 0, False: 0] | Branch (1170:67): [True: 0, False: 0] ------------------ 1171| 0| { 1172| | /* Negative charge has been moved, no change in number of charges */ 1173| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1174| 0| if (ret > 0) ------------------ | Branch (1174:21): [True: 0, False: 0] ------------------ 1175| 0| { 1176| 0| ( *pnNumRunBNS )++; 1177| | /* 3. Add H to -NH and register increaded charge */ 1178| 0| pStruct->at[aN].num_H++; 1179| 0| pTCGroups->total_charge++; 1180| 0| cur_success++; /* 01 */ 1181| 0| } 1182| 0| } 1183| 0| else 1184| 0| { 1185| 0| pe->flow += delta; /* make single bond */ 1186| 0| pBNS->vert[aN].st_edge.flow += delta; 1187| 0| pBNS->vert[aN].st_edge.cap += delta; /* avoid radical on N */ 1188| 0| pBNS->vert[aC].st_edge.flow += delta; /* create radical on C */ 1189| 0| pBNS->vert[vPlusMinus].st_edge.cap -= delta; /* create radical on (+/-) */ 1190| 0| pBNS->tot_st_flow += 2 * delta; 1191| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1192| 0| AllChargeEdges.num_edges--; /* remove pe from the list */ 1193| 0| CurrEdges.num_edges = 0; 1194| 0| continue; /* should not happen */ 1195| 0| } 1196| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1197| 0| AllChargeEdges.num_edges--; /* remove pe from the list */ 1198| 0| CurrEdges.num_edges = 0; 1199| 0| } 1200| |/*exit_case_05:*/ 1201| 25| if (cur_success) ------------------ | Branch (1201:13): [True: 0, False: 25] ------------------ 1202| 0| { 1203| | /* djb-rwth: removing redundant code */ 1204| | /* recalculate InChI from the structure */ 1205| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1205:17): [True: 0, False: 0] ------------------ 1206| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1207| 0| { 1208| 0| goto exit_function; 1209| 0| } 1210| 0| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1210:17): [True: 0, False: 0] ------------------ 1211| 0| { 1212| 0| goto exit_function; 1213| 0| } 1214| | /* 1215| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 1216| | goto exit_function; 1217| | } 1218| | */ 1219| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 1220| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1220:17): [True: 0, False: 0] ------------------ 1221| 0| { 1222| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1223| 0| goto exit_function; 1224| 0| } 1225| 0| if (err) ------------------ | Branch (1225:17): [True: 0, False: 0] ------------------ 1226| 0| { 1227| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1228| 0| goto exit_function; 1229| 0| } 1230| 0| cmpInChI2 = 0; 1231| 0| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1232| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (1232:17): [True: 0, False: 0] | Branch (1232:31): [True: 0, False: 0] ------------------ 1233| 0| { 1234| | /* additional mobile-H compare in case of Fixed-H */ 1235| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 1236| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1236:21): [True: 0, False: 0] ------------------ 1237| 0| { 1238| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1239| 0| goto exit_function; 1240| 0| } 1241| 0| if (err) ------------------ | Branch (1241:21): [True: 0, False: 0] ------------------ 1242| 0| { 1243| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1244| 0| goto exit_function; 1245| 0| } 1246| 0| } 1247| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (1247:30): [True: 0, False: 0] ------------------ 1248| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1248:24): [True: 0, False: 0] ------------------ 1249| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 1250| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 1251| 0| : pStruct->pOneINChI[0]->Stereo; /* djb-rwth: ignoring LLVM warning: variable used */ 1252| | 1253| | 1254| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1254:31): [True: 0, False: 0] | Branch (1254:64): [True: 0, False: 0] ------------------ 1255| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (1255:24): [True: 0, False: 0] | Branch (1255:66): [True: 0, False: 0] ------------------ 1256| 0| ? NULL 1257| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (1257:21): [True: 0, False: 0] ------------------ 1258| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1258:21): [True: 0, False: 0] ------------------ 1259| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 1260| 0| pStruct->pOneINChI[1]->StereoIsotopic : 1261| 0| pStruct->pOneINChI[1]->Stereo; 1262| 0| } 1263| 25| } 1264| | 1265| 235| cur_success = 0; 1266| 235| if (pStruct->bMobileH == TAUT_NON && pStereo2Revrs /* added check 2006-04-05 */ && ------------------ | | 574| 470|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1266:9): [True: 78, False: 157] | Branch (1266:42): [True: 31, False: 47] ------------------ 1267| 31| ( cmpInChI2 & IDIF_SB_EXTRA_UNDF && ------------------ | Branch (1267:11): [True: 2, False: 29] ------------------ 1268| 2| !pStruct->ti.num_t_groups ) ------------------ | Branch (1268:13): [True: 2, False: 0] ------------------ 1269| 235| /*pStruct->bMobileH == TAUT_NON && (cmpInChI2 & IDIF_SB_EXTRA_UNDF)*/) 1270| 2| { 1271| | /*----------------------------------------------------------*/ 1272| | /* case 06: extra stereogenic bond on =NH2(+), (B, Fixed-H) */ 1273| | /* H H =========== */ 1274| | /* original: N(+)=-N< -> N--==N(+)< */ 1275| | /* (A) H H */ 1276| | /* double bond in Mobile-H */ 1277| | /* layer has Undef stereo */ 1278| | /* */ 1279| | /* */ 1280| | /* Fixed-H: move (+) to or from NH2 for Undef or No stereo */ 1281| | /* respectively */ 1282| | /* Mobile-H: Add H(+) to =NH and move the charge to =N- */ 1283| | /* to eliminate Undef stereo */ 1284| | /* Move charge from N to -NH2 to create */ 1285| | /* Undef Stereo */ 1286| | /* Since this bond parity is not known, it is UNDEFINED */ 1287| | /* */ 1288| | /* Solution: Move (+) from -NH2(+) to othe -N< */ 1289| | /* */ 1290| | /*----------------------------------------------------------*/ 1291| 2| int aN, i1, i2, ePlus; /* djb-rwth: removing redundant variables */ 1292| 2| BNS_EDGE *pePlus; 1293| 2| AllChargeEdges.num_edges = 0; 1294| | /* in1 => in restored structure; in2 => in original InChI */ 1295| 4| for (i = 0; i < icr2->num_sb_undef_in1_only; i++) ------------------ | Branch (1295:21): [True: 2, False: 2] ------------------ 1296| 2| { 1297| 2| j12 = icr2->sb_undef_in1_only[i]; 1298| 2| pv1 = pBNS->vert + ( v1 = pStereo2Revrs->nBondAtom1[j12] - 1 ); 1299| 2| pv2 = pBNS->vert + ( v2 = pStereo2Revrs->nBondAtom2[j12] - 1 ); /* djb-rwth: ignoring LLVM warning: variable used */ 1300| | /* indicators of -NH: */ 1301| 2| i1 = at2[v1].valence == 1 && at2[v1].num_H == 2 && !at2[v1].endpoint && ------------------ | Branch (1301:18): [True: 0, False: 2] | Branch (1301:42): [True: 0, False: 0] | Branch (1301:64): [True: 0, False: 0] ------------------ 1302| 0| pVA[v1].cNumValenceElectrons == 5 && pVA[v1].cPeriodicRowNumber == 1; ------------------ | Branch (1302:17): [True: 0, False: 0] | Branch (1302:54): [True: 0, False: 0] ------------------ 1303| 2| i2 = at2[v2].valence == 1 && at2[v2].num_H == 2 && !at2[v2].endpoint && ------------------ | Branch (1303:18): [True: 0, False: 2] | Branch (1303:42): [True: 0, False: 0] | Branch (1303:64): [True: 0, False: 0] ------------------ 1304| 0| pVA[v2].cNumValenceElectrons == 5 && pVA[v2].cPeriodicRowNumber == 1; ------------------ | Branch (1304:17): [True: 0, False: 0] | Branch (1304:54): [True: 0, False: 0] ------------------ 1305| 2| if ((!i1 && !i2) || (i1 && i2)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1305:18): [True: 2, False: 0] | Branch (1305:25): [True: 2, False: 0] | Branch (1305:34): [True: 0, False: 0] | Branch (1305:40): [True: 0, False: 0] ------------------ 1306| 2| { 1307| 2| continue; 1308| 2| } 1309| | /* find the edge between v1 and v2 */ 1310| 0| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (1310:25): [True: 0, False: 0] ------------------ 1311| 0| { 1312| 0| pe = pBNS->edge + ( e = pv1->iedge[k] ); /* djb-rwth: ignoring LLVM warning: variable used */ 1313| 0| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (1313:21): [True: 0, False: 0] ------------------ 1314| 0| break; /* the edge has been found */ 1315| 0| } 1316| 0| if (k >= at2[v1].valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1316:17): [True: 0, False: 0] ------------------ 1317| 0| { 1318| 0| ret = RI_ERR_SYNTAX; ------------------ | | 16| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1319| 0| goto exit_function; 1320| 0| } 1321| 0| if (pe->flow != 1) ------------------ | Branch (1321:17): [True: 0, False: 0] ------------------ 1322| 0| { 1323| 0| continue; /* already charged */ 1324| 0| } 1325| 0| aN = i1 ? v1 : v2; /* -NH atom */ ------------------ | Branch (1325:18): [True: 0, False: 0] ------------------ 1326| | /* djb-rwth: removing redundant code */ 1327| 0| if (0 > ( ePlus = pVA[aN].nCPlusGroupEdge - 1 ) || ------------------ | Branch (1327:17): [True: 0, False: 0] ------------------ 1328| 0| ( pePlus = pBNS->edge + ePlus )->flow || /* must be (+) charged */ ------------------ | Branch (1328:17): [True: 0, False: 0] ------------------ 1329| 0| pePlus->forbidden) ------------------ | Branch (1329:18): [True: 0, False: 0] ------------------ 1330| 0| { 1331| 0| continue; 1332| 0| } 1333| | /* Move (+) from =NH2(+) to some other -N< 1334| | */ 1335| | /* Fix all charges except (+) on -N< */ 1336| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (1336:17): [True: 0, False: 0] ------------------ 1337| 0| { 1338| 0| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (1338:29): [True: 0, False: 0] ------------------ 1339| 0| { 1340| 0| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1340:25): [True: 0, False: 0] | Branch (1340:69): [True: 0, False: 0] ------------------ 1341| 0| { 1342| 0| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1342:29): [True: 0, False: 0] ------------------ 1343| 0| { 1344| 0| goto exit_function; 1345| 0| } 1346| 0| } 1347| 0| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1347:25): [True: 0, False: 0] | Branch (1347:68): [True: 0, False: 0] ------------------ 1348| 0| { 1349| 0| if (pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber == 1 && ------------------ | Branch (1349:29): [True: 0, False: 0] | Branch (1349:65): [True: 0, False: 0] ------------------ 1350| 0| !at2[j].num_H && at2[j].valence == 3 && ------------------ | Branch (1350:30): [True: 0, False: 0] | Branch (1350:47): [True: 0, False: 0] ------------------ 1351| 0| !( at2[j].endpoint || (pStruct->endpoint && pStruct->endpoint[j]) )) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1351:33): [True: 0, False: 0] | Branch (1351:53): [True: 0, False: 0] | Branch (1351:74): [True: 0, False: 0] ------------------ 1352| 0| { 1353| 0| ; /* do not fix -N< or =N(+)< */ 1354| 0| } 1355| 0| else 1356| 0| { 1357| | /* all others */ 1358| 0| if ((ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1358:33): [True: 0, False: 0] ------------------ 1359| 0| { 1360| 0| goto exit_function; 1361| 0| } 1362| 0| } 1363| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 1364| 0| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (1364:29): [True: 0, False: 0] | Branch (1364:65): [True: 0, False: 0] ------------------ 1365| 0| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 118| 0|#define NO_VERTEX -2 ------------------ | Branch (1365:30): [True: 0, False: 0] ------------------ 1366| 0| { 1367| 0| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (1367:33): [True: 0, False: 0] | Branch (1367:61): [True: 0, False: 0] ------------------ 1368| 0| { 1369| 0| if ((ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 20| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1369:37): [True: 0, False: 0] ------------------ 1370| 0| { 1371| 0| goto exit_function; 1372| 0| } 1373| 0| } 1374| 0| } 1375| 0| } 1376| 0| } 1377| 0| } 1378| | /* pePlus edge is already fixed; unfix it */ 1379| | /* To decrement (+) on =NH2(+) decrement its double bond order */ 1380| | /* djb-rwth: removing redundant code */ 1381| 0| if (!pe->flow) ------------------ | Branch (1381:17): [True: 0, False: 0] ------------------ 1382| 0| continue; 1383| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1384| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1385| | 1386| 0| delta = 1; 1387| 0| pe->flow -= delta; 1388| 0| pv1->st_edge.flow -= delta; 1389| 0| pv2->st_edge.flow -= delta; 1390| 0| pBNS->tot_st_flow -= 2 * delta; 1391| | 1392| 0| pe->forbidden |= forbidden_edge_mask; 1393| 0| pePlus->forbidden &= ~forbidden_edge_mask; 1394| | 1395| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1396| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1397| | 1398| 0| if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) || ------------------ | Branch (1398:17): [True: 0, False: 0] | Branch (1398:32): [True: 0, False: 0] | Branch (1398:50): [True: 0, False: 0] ------------------ 1399| 0| (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1399:18): [True: 0, False: 0] | Branch (1399:36): [True: 0, False: 0] | Branch (1399:59): [True: 0, False: 0] ------------------ 1400| 0| { 1401| | /* (+)charge was just moved, no change in number of charges */ 1402| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1403| 0| if (ret > 0) ------------------ | Branch (1403:21): [True: 0, False: 0] ------------------ 1404| 0| { 1405| 0| ( *pnNumRunBNS )++; 1406| 0| cur_success++; /* 01 */ 1407| 0| } 1408| 0| } 1409| 0| else 1410| 0| { 1411| 0| pe->flow += delta; /* roll back */ 1412| 0| pv1->st_edge.flow += delta; 1413| 0| pv2->st_edge.flow += delta; 1414| 0| pBNS->tot_st_flow += 2 * delta; 1415| 0| } 1416| 0| pe->forbidden &= ~forbidden_edge_mask; 1417| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1418| 0| } 1419| |/*exit_case_06:*/ 1420| 2| if (cur_success) ------------------ | Branch (1420:13): [True: 0, False: 2] ------------------ 1421| 0| { 1422| | /* djb-rwth: removing redundant code */ 1423| | /* recalculate InChI from the structure */ 1424| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1424:17): [True: 0, False: 0] ------------------ 1425| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1426| 0| { 1427| 0| goto exit_function; 1428| 0| } 1429| 0| if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1429:17): [True: 0, False: 0] ------------------ 1430| 0| { 1431| 0| goto exit_function; 1432| 0| } 1433| | /* 1434| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 1435| | goto exit_function; 1436| | } 1437| | */ 1438| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr2, &err ); 1439| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1439:17): [True: 0, False: 0] ------------------ 1440| 0| { 1441| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1442| 0| goto exit_function; 1443| 0| } 1444| 0| if (err) ------------------ | Branch (1444:17): [True: 0, False: 0] ------------------ 1445| 0| { 1446| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1447| 0| goto exit_function; 1448| 0| } 1449| | /* djb-rwth: removing redundant code */ 1450| 0| memset( icr2, 0, sizeof( *icr2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1451| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (1451:17): [True: 0, False: 0] | Branch (1451:31): [True: 0, False: 0] ------------------ 1452| 0| { 1453| | /* additional mobile-H compare in case of Fixed-H */ 1454| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1455| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1455:21): [True: 0, False: 0] ------------------ 1456| 0| { 1457| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1458| 0| goto exit_function; 1459| 0| } 1460| 0| if (err) ------------------ | Branch (1460:21): [True: 0, False: 0] ------------------ 1461| 0| { 1462| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1463| 0| goto exit_function; 1464| 0| } 1465| 0| } 1466| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (1466:30): [True: 0, False: 0] ------------------ 1467| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1467:24): [True: 0, False: 0] ------------------ 1468| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 1469| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 1470| 0| : pStruct->pOneINChI[0]->Stereo; /* djb-rwth: ignoring LLVM warning: variable used */ 1471| | 1472| | 1473| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1473:31): [True: 0, False: 0] | Branch (1473:64): [True: 0, False: 0] ------------------ 1474| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (1474:24): [True: 0, False: 0] | Branch (1474:66): [True: 0, False: 0] ------------------ 1475| 0| ? NULL 1476| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (1476:21): [True: 0, False: 0] ------------------ 1477| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1477:21): [True: 0, False: 0] ------------------ 1478| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 1479| 0| pStruct->pOneINChI[1]->StereoIsotopic : 1480| 0| pStruct->pOneINChI[1]->Stereo; /* djb-rwth: ignoring LLVM warning: variable used */ 1481| 0| } 1482| 2| } 1483| | 1484| | 1485| 13.2k|exit_function: 1486| 13.2k| SetForbiddenEdgeMask( pBNS, &FixedStereoEdges, forbidden_stereo_edge_mask ); 1487| 13.2k| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1488| 13.2k| AllocEdgeList( &CurrEdges, EDGE_LIST_FREE ); ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1489| 13.2k| AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1490| 13.2k| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1491| 13.2k| AllocEdgeList( &FixedStereoEdges, EDGE_LIST_FREE ); ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1492| 13.2k| AllocEdgeList( &AllRadList, EDGE_LIST_FREE ); /* eliminate memory leak */ ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1493| 13.2k| AllocEdgeList( TautMinusEdges + 0, EDGE_LIST_FREE ); ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1494| 13.2k| AllocEdgeList( TautMinusEdges + 1, EDGE_LIST_FREE ); ------------------ | | 243| 13.2k|#define EDGE_LIST_FREE (-2) ------------------ 1495| | 1496| 13.2k| return ret; 1497| 235|} InChI2Atom: 78| 145k|{ 79| 145k| int ret = 0; 80| | 81| 145k| int iINChI = (bI2A_Flag & I2A_FLAG_RECMET) ? INCHI_REC : INCHI_BAS; ------------------ | | 106| 145k|#define I2A_FLAG_RECMET 0x0002 ------------------ int iINChI = (bI2A_Flag & I2A_FLAG_RECMET) ? INCHI_REC : INCHI_BAS; ------------------ | | 571| 36|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int iINChI = (bI2A_Flag & I2A_FLAG_RECMET) ? INCHI_REC : INCHI_BAS; ------------------ | | 570| 145k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (81:18): [True: 36, False: 145k] ------------------ 82| 145k| int bMobileH = (bI2A_Flag & I2A_FLAG_FIXEDH) ? TAUT_NON : TAUT_YES; ------------------ | | 105| 145k|#define I2A_FLAG_FIXEDH 0x0001 ------------------ int bMobileH = (bI2A_Flag & I2A_FLAG_FIXEDH) ? TAUT_NON : TAUT_YES; ------------------ | | 574| 1.28k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ int bMobileH = (bI2A_Flag & I2A_FLAG_FIXEDH) ? TAUT_NON : TAUT_YES; ------------------ | | 575| 144k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (82:20): [True: 1.28k, False: 144k] ------------------ 83| | 84| 145k| INChI* pInChI[TAUT_NUM]; 85| | 86| | 87| | 88| 145k| memset(pInChI, 0, sizeof(pInChI)); /* djb-rwth: memset_s C11/Annex K variant? */ 89| | 90| | 91| | /* disconnected or reconnected */ 92| | 93| 145k| if (iINChI == INCHI_REC) ------------------ | | 571| 145k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (93:9): [True: 36, False: 145k] ------------------ 94| 36| { 95| 36| if (!OneInput->nNumComponents[iINChI][TAUT_YES]) ------------------ | | 575| 36|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (95:13): [True: 0, False: 36] ------------------ 96| 0| { 97| 0| iINChI = INCHI_BAS; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 98| 0| } 99| 36| } 100| 145k| if (iComponent >= OneInput->nNumComponents[iINChI][TAUT_YES]) ------------------ | | 575| 145k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (100:9): [True: 0, False: 145k] ------------------ 101| 0| { 102| 0| return 0; /* component does not exist */ 103| 0| } 104| | 105| | /* mobile or fixed H */ 106| 145k| pStruct->bFixedHExists = 0; 107| 145k| if (bMobileH == TAUT_NON) ------------------ | | 574| 145k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (107:9): [True: 1.28k, False: 144k] ------------------ 108| 1.28k| { 109| 1.28k| if (!OneInput->nNumComponents[iINChI][bMobileH]) ------------------ | Branch (109:13): [True: 0, False: 1.28k] ------------------ 110| 0| { 111| | /* only one InChI exists (no mobile H) */ 112| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 113| 0| } 114| 1.28k| } 115| 145k| if (iComponent >= OneInput->nNumComponents[iINChI][bMobileH]) ------------------ | Branch (115:9): [True: 0, False: 145k] ------------------ 116| 0| { 117| 0| return 0; /* component does not exist */ 118| 0| } 119| | 120| | /* pointer to the InChI that is going to be reversed */ 121| 145k| pInChI[0] = &OneInput->pInpInChI[iINChI][bMobileH][iComponent]; 122| 145k| pStruct->bMobileH = bMobileH; 123| 145k| pStruct->iINCHI = iINChI; 124| | 125| | /* deleted component only in case Mobile-H and compound contains only protons */ 126| 145k| if (pInChI[0]->bDeleted) ------------------ | Branch (126:9): [True: 0, False: 145k] ------------------ 127| 0| { 128| 0| return 0; /* deleted component, presumably H(+) */ 129| 0| } 130| | 131| 145k| if (bMobileH == TAUT_NON && OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 574| 290k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (bMobileH == TAUT_NON && OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 575| 1.28k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (131:9): [True: 1.28k, False: 144k] | Branch (131:33): [True: 0, False: 1.28k] ------------------ 132| 0| { 133| 0| pStruct->nNumRemovedProtonsMobHInChI = 134| 0| OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons[iComponent].nNumRemovedProtons; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 135| 0| } 136| | 137| 145k| if (bMobileH == TAUT_NON || ------------------ | | 574| 290k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (137:9): [True: 1.28k, False: 144k] ------------------ 138| 144k| (bMobileH == TAUT_YES && ------------------ | | 575| 288k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (138:10): [True: 144k, False: 0] ------------------ 139| 144k| OneInput->pInpInChI[iINChI][TAUT_NON] && ------------------ | | 574| 144k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (139:13): [True: 30.3k, False: 113k] ------------------ 140| 30.3k| OneInput->pInpInChI[iINChI][TAUT_NON][iComponent].nNumberOfAtoms > 0 && ------------------ | | 574| 30.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (140:13): [True: 0, False: 30.3k] ------------------ 141| 0| !OneInput->pInpInChI[iINChI][TAUT_NON][iComponent].bDeleted) /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (141:13): [True: 0, False: 0] ------------------ 142| 145k| ) 143| 1.28k| { 144| 1.28k| pStruct->bFixedHExists = 1; 145| 1.28k| } 146| | 147| 145k| if (bMobileH == TAUT_NON && ------------------ | | 574| 290k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (147:9): [True: 1.28k, False: 144k] ------------------ 148| 1.28k| iComponent < OneInput->nNumComponents[iINChI][TAUT_YES] && ------------------ | | 575| 1.28k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (148:9): [True: 1.28k, False: 0] ------------------ 149| 1.28k| OneInput->pInpInChI[iINChI][TAUT_YES] && ------------------ | | 575| 1.28k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (149:9): [True: 1.28k, False: 0] ------------------ 150| 1.28k| OneInput->pInpInChI[iINChI][TAUT_YES][iComponent].nNumberOfAtoms > 0 && ------------------ | | 575| 1.28k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (150:9): [True: 1.28k, False: 0] ------------------ 151| 1.28k| !OneInput->pInpInChI[iINChI][TAUT_YES][iComponent].bDeleted ------------------ | | 575| 1.28k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (151:9): [True: 1.28k, False: 0] ------------------ 152| 145k| ) 153| 1.28k| { 154| | /* pointer to the Mobile-H InChI if we are reversing Fixed-H InChI */ 155| 1.28k| pInChI[1] = &OneInput->pInpInChI[iINChI][TAUT_YES][iComponent]; ------------------ | | 575| 1.28k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 156| 1.28k| } 157| | 158| 145k| pStruct->num_inp_actual = OneInput->num_inp; 159| | 160| | /* Intercept and correct non-polymer Zz to Zy if applicable */ 161| 145k| if (OneInput->polymer) ------------------ | Branch (161:9): [True: 17.4k, False: 127k] ------------------ 162| 17.4k| { 163| 17.4k| int a, k, new_num; 164| 17.4k| OAD_Polymer* p = OneInput->polymer; 165| 17.4k| pStruct->n_pzz = 0; 166| 17.4k| pStruct->n_zy = 0; 167| 41.2k| for (a = 0; a < pInChI[0]->nNumberOfAtoms; a++) ------------------ | Branch (167:21): [True: 23.7k, False: 17.4k] ------------------ 168| 23.7k| { 169| 23.7k| int aglob = iAtNoOffset + a + 1; 170| 23.7k| if (pInChI[0]->nAtom[a] == EL_NUMBER_ZZ) ------------------ | | 32| 23.7k|#define EL_NUMBER_ZZ ((U_CHAR)120) ------------------ | Branch (170:17): [True: 259, False: 23.4k] ------------------ 171| 259| { 172| 259| new_num = EL_NUMBER_ZY; /* Zy */ ------------------ | | 31| 259|#define EL_NUMBER_ZY ((U_CHAR)119) ------------------ 173| 408| for (k = 0; k < p->n; k++) ------------------ | Branch (173:29): [True: 262, False: 146] ------------------ 174| 262| { 175| 262| if ((aglob == p->units[k]->cap1) || (aglob == p->units[k]->cap2)) ------------------ | Branch (175:25): [True: 57, False: 205] | Branch (175:57): [True: 56, False: 149] ------------------ 176| 113| { 177| 113| new_num = EL_NUMBER_ZZ; ------------------ | | 32| 113|#define EL_NUMBER_ZZ ((U_CHAR)120) ------------------ 178| 113| break; 179| 113| } 180| 262| } 181| 259| pInChI[0]->nAtom[a] = new_num; 182| 259| if (new_num == EL_NUMBER_ZY) ------------------ | | 31| 259|#define EL_NUMBER_ZY ((U_CHAR)119) ------------------ | Branch (182:21): [True: 146, False: 113] ------------------ 183| 146| { 184| 146| pStruct->n_zy++; 185| 146| } 186| 113| else if (new_num == EL_NUMBER_ZZ) ------------------ | | 32| 113|#define EL_NUMBER_ZZ ((U_CHAR)120) ------------------ | Branch (186:26): [True: 113, False: 0] ------------------ 187| 113| { 188| 113| pStruct->n_pzz++; 189| 113| } 190| 259| } 191| 23.7k| } 192| 17.4k| } 193| | 194| 145k| ret = OneInChI2Atom(ic, pCG, ip, sd, szCurHdr, num_inp, pStruct, 195| 145k| iComponent, 0 /* iAtNoOffset*/, bHasSomeFixedH, pInChI); 196| | 197| | /* djb-rwth: fixing oss-fuzz issue #66758, #30283 */ 198| 145k| if (pStruct->at && pStruct->at2) ------------------ | Branch (198:9): [True: 145k, False: 0] | Branch (198:24): [True: 144k, False: 370] ------------------ 199| 144k| { 200| 144k| int a; 201| 1.03M| for (a = 0; a < pInChI[0]->nNumberOfAtoms; a++) ------------------ | Branch (201:21): [True: 890k, False: 144k] ------------------ 202| 890k| { 203| 890k| if (pInChI[0]->nAtom[a] == EL_NUMBER_ZY) ------------------ | | 31| 890k|#define EL_NUMBER_ZY ((U_CHAR)119) ------------------ | Branch (203:17): [True: 1.55k, False: 888k] ------------------ 204| 1.55k| { 205| 1.55k| pInChI[0]->nAtom[a] = EL_NUMBER_ZZ; ------------------ | | 32| 1.55k|#define EL_NUMBER_ZZ ((U_CHAR)120) ------------------ 206| 1.55k| pStruct->at[a].el_number = EL_NUMBER_ZZ; ------------------ | | 32| 1.55k|#define EL_NUMBER_ZZ ((U_CHAR)120) ------------------ 207| 1.55k| strcpy(pStruct->at[a].elname, "Zz"); 208| 1.55k| pStruct->at2[a].el_number = EL_NUMBER_ZZ; ------------------ | | 32| 1.55k|#define EL_NUMBER_ZZ ((U_CHAR)120) ------------------ 209| 1.55k| strcpy(pStruct->at2[a].elname, "Zz"); 210| 1.55k| pStruct->n_zy--; 211| 1.55k| pStruct->n_pzz++; 212| 1.55k| } 213| 890k| } 214| 144k| } 215| | 216| 145k| return ret; /* same interpretation as in ProcessOneStructure ??? */ 217| 145k|} RemoveFixHInChIIdentical2MobH: 222| 5.18k|{ 223| 5.18k| int iInchiRec, cur_num_comp, k; 224| | 225| | /* eliminate Fixed-H InChI that are exactly same as the corresponding Mobile-H structures */ 226| 15.5k| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 569| 15.5k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (226:25): [True: 10.3k, False: 5.18k] ------------------ 227| 10.3k| { 228| 10.3k| cur_num_comp = inchi_min(pOneInput->nNumComponents[iInchiRec][TAUT_YES], ------------------ | | 139| 10.3k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 10.3k] | | ------------------ ------------------ 229| 10.3k| pOneInput->nNumComponents[iInchiRec][TAUT_NON]); 230| 41.9k| for (k = 0; k < cur_num_comp; k++) ------------------ | Branch (230:21): [True: 31.6k, False: 10.3k] ------------------ 231| 31.6k| { 232| 31.6k| if (!CompareReversedINChI(pOneInput->pInpInChI[iInchiRec][TAUT_YES] + k, ------------------ | | 575| 31.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (232:17): [True: 30.3k, False: 1.29k] ------------------ 233| 31.6k| pOneInput->pInpInChI[iInchiRec][TAUT_NON] + k, NULL, NULL)) ------------------ | | 574| 31.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 234| 30.3k| { 235| 30.3k| Free_INChI_Members(pOneInput->pInpInChI[iInchiRec][TAUT_NON] + k); ------------------ | | 574| 30.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 236| 30.3k| memset(pOneInput->pInpInChI[iInchiRec][TAUT_NON] + k, 0, sizeof(pOneInput->pInpInChI[0][0][0])); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 574| 30.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 237| 30.3k| } 238| 31.6k| } 239| 10.3k| } 240| 5.18k|} MarkDisconectedIdenticalToReconnected: 249| 5.18k|{ 250| 5.18k| int k1, k2, num_marked = 0; 251| 5.18k| int k1max = inchi_max(pOneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 138| 5.18k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 3.91k, False: 1.27k] | | ------------------ ------------------ 252| 5.18k| pOneInput->nNumComponents[INCHI_BAS][TAUT_NON]); 253| | 254| 154k| for (k1 = 0; k1 < k1max; k1++) ------------------ | Branch (254:18): [True: 149k, False: 5.18k] ------------------ 255| 149k| { 256| 149k| int k2max = inchi_max(pOneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 138| 149k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 10, False: 149k] | | ------------------ ------------------ 257| 149k| pOneInput->nNumComponents[INCHI_REC][TAUT_NON]); 258| | 259| 149k| for (k2 = 0; k2 < k2max; k2++) ------------------ | Branch (259:22): [True: 76, False: 149k] ------------------ 260| 76| { 261| 76| int eqM = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 570| 76|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int eqM = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 575| 76|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (261:23): [True: 76, False: 0] ------------------ 262| 76| && 263| 76| k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ------------------ | | 571| 76|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ------------------ | | 575| 76|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (263:17): [True: 76, False: 0] ------------------ 264| 76| && 265| 76| !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink /* already linked */ ------------------ | | 571| 76|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink /* already linked */ ------------------ | | 575| 76|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (265:17): [True: 72, False: 4] ------------------ 266| 72| && 267| 72| !pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].bDeleted ------------------ | | 570| 72|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ !pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].bDeleted ------------------ | | 575| 72|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (267:17): [True: 62, False: 10] ------------------ 268| 62| && 269| 62| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms ------------------ | | 570| 62|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms ------------------ | | 575| 62|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (269:17): [True: 62, False: 0] ------------------ 270| 62| && 271| 62| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms == ------------------ | | 570| 62|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms == ------------------ | | 575| 62|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (271:17): [True: 58, False: 4] ------------------ 272| 62| pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nNumberOfAtoms ------------------ | | 571| 62|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nNumberOfAtoms ------------------ | | 575| 62|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 273| 58| && 274| 58| !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].bDeleted ------------------ | | 571| 58|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].bDeleted ------------------ | | 575| 58|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (274:17): [True: 56, False: 2] ------------------ 275| 56| && 276| 56| !CompareReversedINChI(pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k2, ------------------ | | 571| 56|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !CompareReversedINChI(pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k2, ------------------ | | 575| 56|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (276:17): [True: 43, False: 13] ------------------ 277| 56| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES] + k1, ------------------ | | 570| 56|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES] + k1, ------------------ | | 575| 56|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 278| 56| NULL, NULL); 279| | 280| 76| int isF1 = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_NON] ------------------ | | 570| 76|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int isF1 = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_NON] ------------------ | | 574| 76|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (280:24): [True: 51, False: 25] ------------------ 281| 51| && 282| 51| 0 == pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].bDeleted ------------------ | | 570| 51|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 0 == pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].bDeleted ------------------ | | 574| 51|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (282:17): [True: 51, False: 0] ------------------ 283| 51| && 284| 51| 0 < pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms ------------------ | | 570| 51|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 0 < pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms ------------------ | | 574| 51|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (284:17): [True: 48, False: 3] ------------------ 285| 76| ; 286| | 287| 76| int isF2 = k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_NON] ------------------ | | 571| 76|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int isF2 = k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_NON] ------------------ | | 574| 76|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (287:24): [True: 55, False: 21] ------------------ 288| 55| && 289| 55| 0 == pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].bDeleted ------------------ | | 571| 55|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 0 == pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].bDeleted ------------------ | | 574| 55|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (289:17): [True: 55, False: 0] ------------------ 290| 55| && 291| 55| 0 < pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 571| 55|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 0 < pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 574| 55|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (291:17): [True: 44, False: 11] ------------------ 292| 76| ; 293| | 294| 76| int eqF = isF1 ------------------ | Branch (294:23): [True: 48, False: 28] ------------------ 295| 48| && 296| 48| isF2 ------------------ | Branch (296:17): [True: 33, False: 15] ------------------ 297| 33| && 298| 33| !pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink ------------------ | | 571| 33|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink ------------------ | | 574| 33|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (298:17): [True: 31, False: 2] ------------------ 299| 31| && 300| 31| pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms == ------------------ | | 570| 31|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms == ------------------ | | 574| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (300:17): [True: 31, False: 0] ------------------ 301| 31| pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 571| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 574| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 302| 31| && 303| 31| !CompareReversedINChI(pOneInput->pInpInChI[INCHI_REC][TAUT_NON] + k2, ------------------ | | 571| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !CompareReversedINChI(pOneInput->pInpInChI[INCHI_REC][TAUT_NON] + k2, ------------------ | | 574| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (303:17): [True: 6, False: 25] ------------------ 304| 31| pOneInput->pInpInChI[INCHI_BAS][TAUT_NON] + k1, ------------------ | | 570| 31|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_NON] + k1, ------------------ | | 574| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 305| 31| NULL, NULL) 306| 76| ; 307| | 308| 76| if (eqM && ((!isF1 && !isF2) || eqF)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (308:17): [True: 43, False: 33] | Branch (308:26): [True: 9, False: 34] | Branch (308:35): [True: 2, False: 7] | Branch (308:45): [True: 6, False: 35] ------------------ 309| 8| { 310| 8| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nLink = -(k2 + 1); ------------------ | | 570| 8|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nLink = -(k2 + 1); ------------------ | | 575| 8|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 311| 8| pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink = (k1 + 1); ------------------ | | 571| 8|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink = (k1 + 1); ------------------ | | 575| 8|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 312| 8| if (eqF) ------------------ | Branch (312:21): [True: 6, False: 2] ------------------ 313| 6| { 314| 6| pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nLink = -(k2 + 1); ------------------ | | 570| 6|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nLink = -(k2 + 1); ------------------ | | 574| 6|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 315| 6| pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink = (k1 + 1); ------------------ | | 571| 6|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink = (k1 + 1); ------------------ | | 574| 6|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 316| 6| } 317| 8| num_marked++; 318| 8| break; 319| | /* equal InChI has been deleted from the disconnected layer, get next k1 */ 320| 8| } 321| 76| } 322| 149k| } 323| | 324| 5.18k| return num_marked; 325| 5.18k|} SetUpSrm: 330| 5.18k|{ 331| | /* structure restore parms !!!!! */ 332| 5.18k| memset(pSrm, 0, sizeof(pSrm[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 333| 5.18k| pSrm->bFixStereoBonds = FIX_STEREO_BOND_ORDER; ------------------ | | 91| 5.18k|#define FIX_STEREO_BOND_ORDER 0 /* 1=> fix stereobonds; treat metal as non-metal if it is stereogenic or has a stereobond */ ------------------ 334| 5.18k| pSrm->nMetal2EndpointMinBondOrder = 1; 335| 5.18k| pSrm->nMetal2EndpointInitEdgeFlow = 0; 336| | 337| 5.18k| if (METAL_FREE_CHARGE_VAL == 1) ------------------ | | 93| 5.18k|#define METAL_FREE_CHARGE_VAL 1 /* 1=> allow free changing charges/valences of metals; initial bond order=0 or 1 */ ------------------ | Branch (337:9): [True: 5.18k, Folded] ------------------ 338| 5.18k| { 339| 5.18k| pSrm->bMetalAddFlower = 1; 340| | /* the next 3 parameters: */ 341| | /* 0, 0, 0 => all bonds 0, no init radical on metal */ 342| | /* 0, 0, 1 => all bonds 0, init radical on metal */ 343| | /* 0, 1, 0 => wrong */ 344| | /* 0, 1, 1 => all bonds 1, no init radical on metal */ 345| | /* 1, 0, 1 => min bond order 1, all bonds to metal have order 1 */ 346| | /* 1, 1, 0 => wrong */ 347| | /* 1, 1, 1 => wrong */ 348| 5.18k| pSrm->nMetalMinBondOrder = 0; 349| 5.18k| pSrm->nMetalInitEdgeFlow = 1; 350| 5.18k| pSrm->nMetalInitBondOrder = 1; 351| 5.18k| pSrm->bStereoRemovesMetalFlag = pSrm->bFixStereoBonds; 352| 5.18k| pSrm->nMetalFlowerParam_D = 16; 353| 5.18k| pSrm->nMetalMaxCharge_D = 16; 354| 5.18k| } 355| 0| else 356| 0| { 357| 0| pSrm->bMetalAddFlower = 0; 358| 0| pSrm->nMetalMinBondOrder = 1; 359| 0| pSrm->nMetalInitEdgeFlow = 0; 360| 0| pSrm->nMetalInitBondOrder = 1; 361| 0| pSrm->bStereoRemovesMetalFlag = pSrm->bFixStereoBonds; 362| 0| pSrm->nMetalFlowerParam_D = 16; 363| 0| pSrm->nMetalMaxCharge_D = 0; 364| 0| } 365| 5.18k| pSrm->nMetal2EndpointInitBondOrder = pSrm->nMetal2EndpointMinBondOrder 366| 5.18k| + pSrm->nMetal2EndpointInitEdgeFlow; 367| 5.18k|} MergeStructureComponents: 379| 1.75k|{ 380| 1.75k| int iInchiRec, iMobileH, iAlternH, num_components, tot_just_atoms, tot_atoms, cur_nA, cur_nH; /* djb-rwth: removing redundant variables */ 381| 1.75k| int k, i, j, ret, iCurAtomOffs, iNxtAtomOffs, iCurDelHOffs, iNxtDelHOffs, len, len2, iShiftH, icomp; 382| 1.75k| int* nAtomOffs = NULL, * nDelHOffs = NULL; 383| 1.75k| StrFromINChI* pStruct1; 384| 1.75k| inp_ATOM* at = NULL, * a; 385| | 386| 1.75k| ret = 0; 387| 1.75k| pOneInput->num_atoms = 0; 388| | /* select highest detail level */ 389| 1.75k| if ((num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_NON])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 571| 1.75k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if ((num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_NON])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 1.75k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (389:9): [True: 3, False: 1.75k] ------------------ 390| 3| { 391| 3| iInchiRec = INCHI_REC; ------------------ | | 571| 3|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 392| 3| iMobileH = TAUT_NON; ------------------ | | 574| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 393| 3| } 394| 1.75k| else 395| 1.75k| { 396| 1.75k| if ((num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_YES])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 571| 1.75k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if ((num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_YES])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 575| 1.75k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (396:13): [True: 4, False: 1.74k] ------------------ 397| 4| { 398| 4| iInchiRec = INCHI_REC; ------------------ | | 571| 4|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 399| 4| iMobileH = TAUT_YES; ------------------ | | 575| 4|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 400| 4| } 401| 1.74k| else 402| 1.74k| { 403| 1.74k| if ((num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_NON])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 570| 1.74k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ((num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_NON])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 574| 1.74k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (403:17): [True: 269, False: 1.47k] ------------------ 404| 269| { 405| 269| iInchiRec = INCHI_BAS; ------------------ | | 570| 269|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 406| 269| iMobileH = TAUT_NON; ------------------ | | 574| 269|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 407| 269| } 408| 1.47k| else 409| 1.47k| { 410| 1.47k| if ((num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_YES])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 570| 1.47k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ((num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_YES])) /* djb-rwth: addressing LLVM warning */ ------------------ | | 575| 1.47k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (410:21): [True: 1.47k, False: 0] ------------------ 411| 1.47k| { 412| 1.47k| iInchiRec = INCHI_BAS; ------------------ | | 570| 1.47k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 413| 1.47k| iMobileH = TAUT_YES; ------------------ | | 575| 1.47k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 414| 1.47k| } 415| 0| else 416| 0| { 417| 0| return 0; /* no components available */ 418| 0| } 419| 1.47k| } 420| 1.74k| } 421| 1.75k| } 422| | 423| 1.75k| nAtomOffs = (int*)inchi_malloc(((long long)num_components + 1) * sizeof(nAtomOffs[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 1.75k|#define inchi_malloc malloc ------------------ 424| 1.75k| nDelHOffs = (int*)inchi_malloc(((long long)num_components + 1) * sizeof(nDelHOffs[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 1.75k|#define inchi_malloc malloc ------------------ 425| 1.75k| if (!nAtomOffs || !nDelHOffs) ------------------ | Branch (425:9): [True: 0, False: 1.75k] | Branch (425:23): [True: 0, False: 1.75k] ------------------ 426| 0| { 427| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 428| 0| goto exit_function; 429| 0| } 430| | /* count number of atoms and removed H */ 431| | /* djb-rwth: removing redundant code */ 432| 1.75k| iAlternH = (iMobileH == TAUT_NON && pOneInput->nNumComponents[iInchiRec][TAUT_YES]) ? TAUT_YES : -1; ------------------ | | 574| 3.50k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iAlternH = (iMobileH == TAUT_NON && pOneInput->nNumComponents[iInchiRec][TAUT_YES]) ? TAUT_YES : -1; ------------------ | | 575| 272|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ iAlternH = (iMobileH == TAUT_NON && pOneInput->nNumComponents[iInchiRec][TAUT_YES]) ? TAUT_YES : -1; ------------------ | | 575| 272|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (432:17): [True: 272, False: 1.48k] | Branch (432:41): [True: 272, False: 0] ------------------ 433| 1.75k| nAtomOffs[0] = nDelHOffs[0] = 0; 434| 50.5k| for (k = 0; k < num_components; k++) ------------------ | Branch (434:17): [True: 48.8k, False: 1.75k] ------------------ 435| 48.8k| { 436| 48.8k| pStruct1 = pStruct[iInchiRec][iMobileH][k].num_atoms ? pStruct[iInchiRec][iMobileH] + k : ------------------ | Branch (436:20): [True: 32.9k, False: 15.9k] ------------------ 437| 48.8k| iAlternH >= 0 && ------------------ | Branch (437:13): [True: 14.5k, False: 1.35k] ------------------ 438| 15.9k| pStruct[iInchiRec][iAlternH][k].num_atoms ? pStruct[iInchiRec][iAlternH] + k : NULL; ------------------ | Branch (438:13): [True: 14.5k, False: 0] ------------------ 439| 48.8k| if (!pStruct1 || !pStruct1->at2 || !pStruct1->num_atoms || pStruct1->bDeleted) ------------------ | Branch (439:13): [True: 1.35k, False: 47.4k] | Branch (439:26): [True: 0, False: 47.4k] | Branch (439:44): [True: 0, False: 47.4k] | Branch (439:68): [True: 0, False: 47.4k] ------------------ 440| 1.35k| { 441| 1.35k| cur_nA = cur_nH = 0; 442| 1.35k| } 443| 47.4k| else 444| 47.4k| { 445| 47.4k| cur_nA = pStruct1->num_atoms; 446| 47.4k| cur_nH = pStruct1->num_deleted_H; 447| 47.4k| } 448| 48.8k| nAtomOffs[k + 1] = nAtomOffs[k] + cur_nA; 449| 48.8k| nDelHOffs[k + 1] = nDelHOffs[k] + cur_nH; 450| 48.8k| } 451| 1.75k| tot_just_atoms = nAtomOffs[num_components]; 452| | /* shift all H to the end */ 453| 52.3k| for (k = 0; k <= num_components; k++) ------------------ | Branch (453:17): [True: 50.5k, False: 1.75k] ------------------ 454| 50.5k| { 455| 50.5k| nDelHOffs[k] += tot_just_atoms; 456| 50.5k| } 457| 1.75k| tot_atoms = nDelHOffs[num_components]; 458| | 459| | /* merge atoms together: 1. Allocate */ 460| 1.75k| at = (inp_ATOM*)inchi_malloc(((long long)tot_atoms + 1) * sizeof(at[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 1.75k|#define inchi_malloc malloc ------------------ 461| 1.75k| if (NULL == at) ------------------ | Branch (461:9): [True: 0, False: 1.75k] ------------------ 462| 0| { 463| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 464| 0| goto exit_function; 465| 0| } 466| 1.75k| if (!tot_atoms) ------------------ | Branch (466:9): [True: 0, False: 1.75k] ------------------ 467| 0| { 468| 0| ret = 0; 469| 0| goto exit_function; /* empty structure */ 470| 0| } 471| | /* merge atoms together: 2. Copy */ 472| 50.5k| for (k = 0; k < num_components; k++) ------------------ | Branch (472:17): [True: 48.8k, False: 1.75k] ------------------ 473| 48.8k| { 474| 48.8k| pStruct1 = pStruct[iInchiRec][iMobileH][k].num_atoms ? pStruct[iInchiRec][iMobileH] + k : ------------------ | Branch (474:20): [True: 32.9k, False: 15.9k] ------------------ 475| 48.8k| iAlternH >= 0 && ------------------ | Branch (475:13): [True: 14.5k, False: 1.35k] ------------------ 476| 15.9k| pStruct[iInchiRec][iAlternH][k].num_atoms ? pStruct[iInchiRec][iAlternH] + k : NULL; ------------------ | Branch (476:13): [True: 14.5k, False: 0] ------------------ 477| 48.8k| if ((len = nAtomOffs[k + 1] - nAtomOffs[k]) && pStruct1) /* djb-rwth: addressing LLVM warning; fixing coverity ID #499555 */ ------------------ | Branch (477:13): [True: 47.4k, False: 1.35k] | Branch (477:56): [True: 47.4k, False: 0] ------------------ 478| 47.4k| { 479| 47.4k| memcpy(at + nAtomOffs[k], pStruct1->at2, len * sizeof(at[0])); 480| 47.4k| if ((len2 = nDelHOffs[k + 1] - nDelHOffs[k])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (480:17): [True: 49, False: 47.4k] ------------------ 481| 49| { 482| 49| memcpy(at + nDelHOffs[k], pStruct1->at2 + len, len2 * sizeof(at[0])); 483| 49| } 484| 47.4k| } 485| 48.8k| } 486| | /* merge atoms together: 3. Update atom numbers */ 487| 1.75k| icomp = 0; 488| 50.5k| for (k = 0; k < num_components; k++) ------------------ | Branch (488:17): [True: 48.8k, False: 1.75k] ------------------ 489| 48.8k| { 490| 48.8k| iCurAtomOffs = nAtomOffs[k]; 491| 48.8k| iNxtAtomOffs = nAtomOffs[k + 1]; 492| 48.8k| iCurDelHOffs = nDelHOffs[k]; 493| 48.8k| iNxtDelHOffs = nDelHOffs[k + 1]; 494| 48.8k| len = nAtomOffs[k + 1] - nAtomOffs[k]; /* number of atoms in a component excluding explicit H */ 495| 48.8k| iShiftH = iCurDelHOffs - len; 496| 48.8k| if (!len) ------------------ | Branch (496:13): [True: 1.35k, False: 47.4k] ------------------ 497| 1.35k| { 498| 1.35k| continue; 499| 1.35k| } 500| 47.4k| icomp++; /* current component number */ 501| | /* update atoms */ 502| 177k| for (i = iCurAtomOffs; i < iNxtAtomOffs; i++) ------------------ | Branch (502:32): [True: 130k, False: 47.4k] ------------------ 503| 130k| { 504| | 505| 130k| a = at + i; 506| | 507| 130k| a->endpoint = 0; 508| 130k| a->bAmbiguousStereo = 0; 509| 130k| a->at_type = 0; 510| 130k| a->bCutVertex = 0; 511| 130k| a->bUsed0DParity = 0; 512| 130k| a->cFlags = 0; 513| 130k| a->nBlockSystem = 0; 514| 130k| a->nNumAtInRingSystem = 0; 515| 130k| a->nRingSystem = 0; 516| | /* djb-rwth: addressing coverity ID #499524 -- initialisation with at */ 517| | 518| 249k| for (j = 0; j < a->valence; j++) ------------------ | Branch (518:25): [True: 119k, False: 130k] ------------------ 519| 119k| { 520| 119k| if (a->neighbor[j] < len) ------------------ | Branch (520:21): [True: 119k, False: 61] ------------------ 521| 119k| { 522| 119k| a->neighbor[j] += iCurAtomOffs; /* atom */ 523| 119k| } 524| 61| else 525| 61| { 526| 61| a->neighbor[j] += iShiftH; /* explicit H */ 527| 61| } 528| 119k| } 529| 130k| a->orig_at_number += iCurAtomOffs; 530| 130k| a->component = icomp; 531| 130k| if (a->p_parity) ------------------ | Branch (531:17): [True: 224, False: 130k] ------------------ 532| 224| { 533| 1.12k| for (j = 0; j < MAX_NUM_STEREO_ATOM_NEIGH; j++) ------------------ | | 877| 1.12k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (533:29): [True: 896, False: 224] ------------------ 534| 896| { 535| 896| if (a->p_orig_at_num[j] <= len) ------------------ | Branch (535:25): [True: 891, False: 5] ------------------ 536| 891| { 537| | /* originally, orig_at_num = atom_index+1, therefore <= instead of < */ 538| 891| a->p_orig_at_num[j] += iCurAtomOffs; 539| 891| } 540| 5| else 541| 5| { 542| 5| a->p_orig_at_num[j] += iShiftH; 543| 5| } 544| 896| } 545| 224| } 546| 131k| for (j = 0; j < MAX_NUM_STEREO_BONDS && a->sb_parity[j]; j++) ------------------ | | 873| 262k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (546:25): [True: 131k, False: 14] | Branch (546:53): [True: 744, False: 130k] ------------------ 547| 744| { 548| 744| if (a->sn_orig_at_num[j] <= len) ------------------ | Branch (548:21): [True: 698, False: 46] ------------------ 549| 698| { 550| | /* originally, orig_at_num = atom_index+1, therefore <= instead of < */ 551| 698| a->sn_orig_at_num[j] += iCurAtomOffs; 552| 698| } 553| 46| else 554| 46| { 555| 46| a->sn_orig_at_num[j] += iShiftH; 556| 46| } 557| 744| } 558| 130k| } 559| | /* update fixed-H */ 560| 47.5k| for (i = iCurDelHOffs; i < iNxtDelHOffs; i++) ------------------ | Branch (560:32): [True: 61, False: 47.4k] ------------------ 561| 61| { 562| 61| a = at + i; 563| 61| a->neighbor[0] += iCurAtomOffs; 564| 61| a->orig_at_number += iShiftH; 565| 61| } 566| 47.4k| } 567| | /* save the results */ 568| 1.75k| pOneInput->atom = at; 569| 1.75k| pOneInput->num_atoms = tot_atoms; 570| 1.75k| at = NULL; 571| | 572| 1.75k|exit_function: 573| 1.75k| if (at) inchi_free(at); /* in case of failure */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ | Branch (573:9): [True: 0, False: 1.75k] ------------------ 574| 1.75k| if (nAtomOffs) inchi_free(nAtomOffs); ------------------ | | 1152| 1.75k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.75k, False: 0] | | | Branch (1152:50): [Folded, False: 1.75k] | | ------------------ ------------------ | Branch (574:9): [True: 1.75k, False: 0] ------------------ 575| 1.75k| if (nDelHOffs) inchi_free(nDelHOffs); ------------------ | | 1152| 1.75k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.75k, False: 0] | | | Branch (1152:50): [Folded, False: 1.75k] | | ------------------ ------------------ | Branch (575:9): [True: 1.75k, False: 0] ------------------ 576| 1.75k| return ret; 577| 1.75k|} AllInchiToStructure: 1017| 5.18k|{ 1018| 5.18k| int iInchiRec, iMobileH, cur_num_comp, bCurI2A_Flag, k, ret, num_err; 1019| 5.18k| int iAtNoOffset; 1020| 5.18k| INPUT_PARMS* ip, ip_loc; 1021| 5.18k| STRUCT_DATA* sd, sd_loc; 1022| 5.18k| long ulProcessingTime = 0; 1023| 5.18k| inchiTime ulTStart; 1024| | 1025| 5.18k| InchiTimeGet(&ulTStart); 1026| 5.18k| ip = &ip_loc; 1027| 5.18k| *ip = *ip_inp; 1028| 5.18k| sd = &sd_loc; 1029| 5.18k| memset(sd, 0, sizeof(*sd)); /* djb-rwth: memset_s C11/Annex K variant? */ 1030| 5.18k| sd->ulStructTime = sd_inp->ulStructTime; 1031| 5.18k| ret = 0; 1032| 5.18k| num_err = 0; 1033| 15.5k| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 569| 15.5k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1033:25): [True: 10.3k, False: 5.18k] ------------------ 1034| 10.3k| { 1035| | /* Disconnected/Connected */ 1036| 31.1k| for (iMobileH = 0; iMobileH < TAUT_NUM; iMobileH++) ------------------ | | 573| 31.1k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1036:28): [True: 20.7k, False: 10.3k] ------------------ 1037| 20.7k| { 1038| | /* Mobile/Fixed H */ 1039| 20.7k| cur_num_comp = pOneInput->nNumComponents[iInchiRec][iMobileH]; 1040| 20.7k| if (!cur_num_comp) ------------------ | Branch (1040:17): [True: 14.2k, False: 6.50k] ------------------ 1041| 14.2k| { 1042| 14.2k| continue; 1043| 14.2k| } 1044| | /* allocate memory for all existing components */ 1045| 6.50k| pStruct[iInchiRec][iMobileH] = (StrFromINChI*)inchi_calloc(cur_num_comp, sizeof(pStruct[0][0][0])); ------------------ | | 1146| 6.50k|#define inchi_calloc calloc ------------------ 1046| 6.50k| if (!pStruct[iInchiRec][iMobileH]) ------------------ | Branch (1046:17): [True: 0, False: 6.50k] ------------------ 1047| 0| { 1048| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1049| 0| goto exit_error; 1050| 0| } 1051| | /* set conversion mode */ 1052| 6.50k| bCurI2A_Flag = (iMobileH ? 0 : I2A_FLAG_FIXEDH) | (iInchiRec ? I2A_FLAG_RECMET : 0); ------------------ | | 105| 1.29k|#define I2A_FLAG_FIXEDH 0x0001 ------------------ bCurI2A_Flag = (iMobileH ? 0 : I2A_FLAG_FIXEDH) | (iInchiRec ? I2A_FLAG_RECMET : 0); ------------------ | | 106| 44|#define I2A_FLAG_RECMET 0x0002 ------------------ | Branch (1052:29): [True: 5.21k, False: 1.29k] | Branch (1052:64): [True: 44, False: 6.46k] ------------------ 1053| 6.50k| if (iMobileH) ------------------ | Branch (1053:17): [True: 5.21k, False: 1.29k] ------------------ 1054| 5.21k| { 1055| 5.21k| ip->nMode &= ~REQ_MODE_BASIC; ------------------ | | 15| 5.21k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1056| 5.21k| } 1057| 1.29k| else 1058| 1.29k| { 1059| 1.29k| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 15| 1.29k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1060| 1.29k| } 1061| | /* InChI --> structure conversion for all components except duplicated */ 1062| 6.50k| iAtNoOffset = 0; 1063| 187k| for (k = 0; k < cur_num_comp; k++) ------------------ | Branch (1063:25): [True: 180k, False: 6.50k] ------------------ 1064| 180k| { 1065| | /* components */ 1066| 180k| if ((!iMobileH && !pOneInput->pInpInChI[iInchiRec][iMobileH][k].nNumberOfAtoms) || ------------------ | Branch (1066:22): [True: 31.6k, False: 149k] | Branch (1066:35): [True: 30.3k, False: 1.29k] ------------------ 1067| 150k| pOneInput->pInpInChI[iInchiRec][iMobileH][k].bDeleted || ------------------ | Branch (1067:21): [True: 3.92k, False: 146k] ------------------ 1068| 146k| pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink < 0) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1068:21): [True: 14, False: 146k] ------------------ 1069| 34.2k| { 1070| 34.2k| pStruct[iInchiRec][iMobileH][k].nLink = pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink; 1071| 34.2k| pStruct[iInchiRec][iMobileH][k].bDeleted = pOneInput->pInpInChI[iInchiRec][iMobileH][k].bDeleted; 1072| 34.2k| continue; /* do not create a structure out of an unavailable 1073| | Fixed-H InChI or out of the one present in Reconnected layer */ 1074| | 1075| |#ifdef NEVER /* a wrong attempt to process deleted components here */ 1076| | if (pStruct[iInchiRec][iMobileH][k].nLink = pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink) 1077| | { 1078| | continue; /* do not create a structure out of an unavailable 1079| | Fixed-H InChI or out of the one present in Reconnected layer */ 1080| | } 1081| | else 1082| | if (iMobileH && pOneInput->pInpInChI[iInchiRec][iMobileH][k].nNumberOfAtoms && 1083| | pOneInput->pInpInChI[iInchiRec][iMobileH][k].bDeleted && 1084| | pOneInput->pInpInChI[iInchiRec][iMobileH][0].bDeleted) 1085| | { 1086| | /* all components are protons */ 1087| | ; 1088| | } 1089| | else 1090| | { 1091| | continue; 1092| | } 1093| |#endif 1094| | 1095| 34.2k| } 1096| 146k| if (bHasSomeFixedH && iMobileH && k < pOneInput->nNumComponents[iInchiRec][TAUT_NON] && ------------------ | | 574| 31.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1096:21): [True: 32.7k, False: 113k] | Branch (1096:39): [True: 31.4k, False: 1.28k] | Branch (1096:51): [True: 31.4k, False: 6] ------------------ 1097| 31.4k| pOneInput->pInpInChI[iInchiRec][TAUT_NON][k].nNumberOfAtoms) ------------------ | | 574| 31.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1097:21): [True: 1.28k, False: 30.1k] ------------------ 1098| 1.28k| { 1099| 1.28k| continue; /* do not process Mobile-H if Fixed-H is requested and exists */ 1100| 1.28k| } 1101| 145k| pStruct[iInchiRec][iMobileH][k].pSrm = pSrm; 1102| 145k| pStruct[iInchiRec][iMobileH][k].iInchiRec = iInchiRec; 1103| 145k| pStruct[iInchiRec][iMobileH][k].iMobileH = iMobileH; 1104| | 1105| | /****************************************************/ 1106| | /* */ 1107| | /* Convert InChI of one component into a Structure */ 1108| | /* */ 1109| | /****************************************************/ 1110| | 1111| 145k| ret = InChI2Atom(ic, pCG, ip, sd, szCurHdr, num_inp, pStruct[iInchiRec][iMobileH] + k, k, 1112| 145k| iAtNoOffset /* 0*/, bCurI2A_Flag, bHasSomeFixedH, pOneInput); 1113| 145k| pStruct[iInchiRec][iMobileH][k].nLink = pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink; 1114| 145k| if (ret < 0) ------------------ | Branch (1114:21): [True: 75.3k, False: 69.9k] ------------------ 1115| 75.3k| { 1116| |#if ( bRELEASE_VERSION != 1 ) 1117| |#ifndef TARGET_API_LIB 1118| | /* !!! Conversion Error -- Ignore for now !!! */ 1119| | fprintf(stdout, "%ld %s Conversion failed: %d, %c%c comp %d\n", 1120| | num_inp, szCurHdr ? szCurHdr : "Struct", ret, iInchiRec ? 'R' : 'D', iMobileH ? 'M' : 'F', k + 1); 1121| |#endif 1122| |#endif 1123| 75.3k| if (ret == CT_USER_QUIT_ERR) ------------------ | | 32| 75.3k|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 18| 75.3k|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1123:25): [True: 0, False: 75.3k] ------------------ 1124| 0| { 1125| 0| goto exit_error; 1126| 0| } 1127| 75.3k| pStruct[iInchiRec][iMobileH][k].nError = ret; 1128| 75.3k| ret = 0; /* force to ignore the errors for now !!!! */ 1129| 75.3k| num_err++; 1130| 75.3k| } 1131| 145k| iAtNoOffset += pOneInput->pInpInChI[iInchiRec][iMobileH][k].nNumberOfAtoms; 1132| 145k| } /* k-th component */ 1133| 6.50k| } 1134| 10.3k| } 1135| | 1136| 5.18k|exit_error: 1137| 5.18k| ulProcessingTime += InchiTimeElapsed(ic, &ulTStart); 1138| 5.18k| sd->ulStructTime += ulProcessingTime; 1139| | 1140| 5.18k| return ret < 0 ? ret : num_err; ------------------ | Branch (1140:12): [True: 0, False: 5.18k] ------------------ 1141| 5.18k|} AddProtonAndIsoHBalanceToMobHStruct: 1154| 1.76k|{ 1155| 1.76k| COMPONENT_REM_PROTONS nToBeRemovedByNormFromRevrs[INCHI_NUM]; 1156| 1.76k| int nRemovedByNormFromRevrs[INCHI_NUM]; 1157| 1.76k| int nRemovedByRevrs[INCHI_NUM]; 1158| | 1159| 1.76k| int nDeltaFromDisconnected = 0, nRemovedProtonsByNormFromRevrs, nRemovedProtonsByRevrs; /* djb-rwth: removing redundant variables */ 1160| 1.76k| NUM_H nIsoDeltaFromDisconnected[NUM_H_ISOTOPES]; 1161| 1.76k| int iInchiRec, i, k, k1, ret = 0; 1162| 1.76k| int nChargeInChI, nChargeRevrs; 1163| | 1164| 1.76k| if (bHasSomeFixedH) ------------------ | Branch (1164:9): [True: 265, False: 1.49k] ------------------ 1165| 265| { 1166| 265| return 0; /* 2005-03-01 */ 1167| 265| } 1168| | 1169| | /* num protons removed by InChI Normalization from the original structure */ 1170| 4.49k| for (i = 0; i < INCHI_NUM; i++) ------------------ | | 569| 4.49k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1170:17): [True: 2.99k, False: 1.49k] ------------------ 1171| 2.99k| { 1172| 2.99k| nToBeRemovedByNormFromRevrs[i].nNumRemovedProtons = pOneInput->nNumProtons[i][TAUT_YES].nNumRemovedProtons; ------------------ | | 575| 2.99k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1173| 11.9k| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 25| 11.9k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1173:21): [True: 8.98k, False: 2.99k] ------------------ 1174| 8.98k| { 1175| 8.98k| nToBeRemovedByNormFromRevrs[i].nNumRemovedIsotopicH[k] = pOneInput->nNumProtons[i][TAUT_YES].nNumRemovedIsotopicH[k]; ------------------ | | 575| 8.98k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1176| 8.98k| } 1177| 2.99k| } 1178| | /* accumulate here num. protons removed by the normalization from the reversed structure */ 1179| 1.49k| nRemovedByNormFromRevrs[INCHI_BAS] = ------------------ | | 570| 1.49k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1180| 1.49k| nRemovedByNormFromRevrs[INCHI_REC] = 0; ------------------ | | 571| 1.49k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1181| 1.49k| nRemovedByRevrs[INCHI_REC] = ------------------ | | 571| 1.49k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1182| 1.49k| nRemovedByRevrs[INCHI_BAS] = 0; ------------------ | | 570| 1.49k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1183| | /* protons added/removed by InChI Normalization to/from Restored Structure might have been added by StructureRestore */ 1184| | 1185| 4.49k| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 569| 4.49k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1185:25): [True: 2.99k, False: 1.49k] ------------------ 1186| 2.99k| { 1187| 37.0k| for (k = 0; k < pOneInput->nNumComponents[iInchiRec][TAUT_YES]; k++) ------------------ | | 575| 37.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1187:21): [True: 34.0k, False: 2.99k] ------------------ 1188| 34.0k| { 1189| 34.0k| if (!bInpInchiComponentExists(pOneInput, iInchiRec, TAUT_YES, k)) ------------------ | | 575| 34.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1189:17): [True: 1.49k, False: 32.5k] ------------------ 1190| 1.49k| { 1191| 1.49k| continue; 1192| 1.49k| } 1193| 32.5k| nRemovedProtonsByNormFromRevrs = 0; /* Num protons removed from the Restored Structure by InChI Normalization */ 1194| 32.5k| nRemovedProtonsByRevrs = 0; /* Num protons removed by the Reconstruction from the Restored Structure */ 1195| 32.5k| if (iInchiRec == INCHI_REC || (iInchiRec == INCHI_BAS && (pStruct[iInchiRec][TAUT_YES][k].nLink) >= 0)) /* djb-rwth: addressing LLVM warning; removing redundant code */ ------------------ | | 571| 65.1k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (iInchiRec == INCHI_REC || (iInchiRec == INCHI_BAS && (pStruct[iInchiRec][TAUT_YES][k].nLink) >= 0)) /* djb-rwth: addressing LLVM warning; removing redundant code */ ------------------ | | 570| 65.1k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (iInchiRec == INCHI_REC || (iInchiRec == INCHI_BAS && (pStruct[iInchiRec][TAUT_YES][k].nLink) >= 0)) /* djb-rwth: addressing LLVM warning; removing redundant code */ ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1195:17): [True: 2, False: 32.5k] | Branch (1195:44): [True: 32.5k, False: 0] | Branch (1195:70): [True: 32.5k, False: 0] ------------------ 1196| 32.5k| { 1197| | 1198| 32.5k| REV_INCHI* pRevInChI = &pStruct[iInchiRec][TAUT_YES][k].RevInChI; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1199| 32.5k| INChI_Aux** pINChI_Aux2 = pRevInChI->pINChI_Aux[iInchiRec][0]; /* component 0*/ 1200| 32.5k| INChI** pINChI_Revr = pRevInChI->pINChI[iInchiRec][0]; 1201| 32.5k| INChI* pINChI_Orig = pOneInput->pInpInChI[iInchiRec][TAUT_YES] + k; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1202| 32.5k| nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 23| 32.5k|#define NO_VALUE_INT 9999 ------------------ | Branch (1202:32): [True: 32.5k, False: 2] ------------------ 1203| 32.5k| nChargeInChI = pINChI_Orig->nTotalCharge; 1204| 32.5k| if (pINChI_Aux2) ------------------ | Branch (1204:21): [True: 32.5k, False: 2] ------------------ 1205| 32.5k| { 1206| 32.5k| nRemovedProtonsByNormFromRevrs = pINChI_Aux2[TAUT_YES]->nNumRemovedProtons; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1207| 32.5k| } 1208| 32.5k| nRemovedProtonsByRevrs = pStruct[iInchiRec][TAUT_YES][k].nNumRemovedProtonsByRevrs; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1209| 32.5k| pStruct[iInchiRec][TAUT_YES][k].nChargeRevrs = nChargeRevrs; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1210| 32.5k| pStruct[iInchiRec][TAUT_YES][k].nChargeInChI = nChargeInChI; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1211| 32.5k| } 1212| 0| else 1213| 0| { 1214| 0| if (0 <= (k1 = -(1 + pStruct[iInchiRec][TAUT_YES][k].nLink))) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1214:21): [True: 0, False: 0] ------------------ 1215| 0| { 1216| 0| REV_INCHI* pRevInChI = &pStruct[INCHI_REC][TAUT_YES][k1].RevInChI; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ REV_INCHI* pRevInChI = &pStruct[INCHI_REC][TAUT_YES][k1].RevInChI; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1217| 0| INChI_Aux** pINChI_Aux2 = pRevInChI->pINChI_Aux[INCHI_BAS][0]; /* component 0 */ ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1218| 0| INChI** pINChI_Revr = pRevInChI->pINChI[INCHI_BAS][0]; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1219| 0| INChI* pINChI_Orig = pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k1; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ INChI* pINChI_Orig = pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k1; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1220| 0| nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 23| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (1220:36): [True: 0, False: 0] ------------------ 1221| 0| nChargeInChI = pINChI_Orig->nTotalCharge; 1222| 0| if (pINChI_Aux2) ------------------ | Branch (1222:25): [True: 0, False: 0] ------------------ 1223| 0| { 1224| 0| nRemovedProtonsByNormFromRevrs = pINChI_Aux2[TAUT_YES]->nNumRemovedProtons; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1225| 0| } 1226| | /* this component cannot be disconnected because it is same as in reconnected layer */ 1227| 0| nRemovedProtonsByRevrs = pStruct[INCHI_REC][TAUT_YES][k1].nNumRemovedProtonsByRevrs; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ nRemovedProtonsByRevrs = pStruct[INCHI_REC][TAUT_YES][k1].nNumRemovedProtonsByRevrs; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1228| 0| pStruct[iInchiRec][TAUT_YES][k1].nChargeRevrs = nChargeRevrs; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1229| 0| pStruct[iInchiRec][TAUT_YES][k1].nChargeInChI = nChargeInChI; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1230| 0| } 1231| 0| } 1232| | /* how many protons (to be removed by InChI Normalization) to add = 1233| | (proton balance in InChI} - 1234| | {number of protons known to be removed by InChI Normalization from Reconstructed structure} */ 1235| 32.5k| nToBeRemovedByNormFromRevrs[iInchiRec].nNumRemovedProtons -= nRemovedProtonsByNormFromRevrs; 1236| 32.5k| nRemovedByNormFromRevrs[iInchiRec] += nRemovedProtonsByNormFromRevrs; 1237| 32.5k| nRemovedByRevrs[iInchiRec] += nRemovedProtonsByRevrs; 1238| 32.5k| pStruct[iInchiRec][TAUT_YES][k].nRemovedProtonsByNormFromRevrs = nRemovedProtonsByNormFromRevrs; ------------------ | | 575| 32.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1239| 32.5k| } 1240| 2.99k| } 1241| | 1242| | /* Since fixed-H layer is missing we need to add proton balance to the components */ 1243| 1.49k| memset(nIsoDeltaFromDisconnected, 0, sizeof(nIsoDeltaFromDisconnected)); /* djb-rwth: memset_s C11/Annex K variant? */ 1244| 4.49k| for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 571| 1.49k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 570| 4.49k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1244:33): [True: 2.99k, False: 1.49k] ------------------ 1245| 2.99k| { 1246| | /* 1247| | if ( !pOneInput->nNumComponents[iInchiRec][TAUT_NON] && 1248| | pOneInput->nNumComponents[iInchiRec][TAUT_YES] ) { 1249| | */ 1250| 2.99k| int bHasRecMobH = (iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES]); ------------------ | | 570| 5.99k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int bHasRecMobH = (iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES]); ------------------ | | 571| 1.49k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int bHasRecMobH = (iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES]); ------------------ | | 575| 1.49k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1250:28): [True: 1.49k, False: 1.49k] | Branch (1250:54): [True: 3, False: 1.49k] ------------------ 1251| | /* bHasRecMobH means all components that could not be disconnected are in reconnected part */ 1252| 2.99k| if (iInchiRec == INCHI_BAS) ------------------ | | 570| 2.99k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1252:13): [True: 1.49k, False: 1.49k] ------------------ 1253| 1.49k| { 1254| | /* second pass: common structures have been changed */ 1255| 1.49k| nToBeRemovedByNormFromRevrs[INCHI_BAS].nNumRemovedProtons += nDeltaFromDisconnected; ------------------ | | 570| 1.49k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1256| 1.49k| } 1257| | /* after proton removal InChI is recalculated */ 1258| | 1259| 2.99k| ret = AddRemProtonsInRestrStruct(ic, pCG, ip, sd, num_inp, bHasSomeFixedH, pStruct[iInchiRec][TAUT_YES], ------------------ | | 575| 2.99k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1260| 2.99k| pOneInput->nNumComponents[iInchiRec][TAUT_YES], ------------------ | | 575| 2.99k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1261| 2.99k| bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 571| 3|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1261:13): [True: 3, False: 2.99k] ------------------ 1262| 2.99k| bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 571| 3|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1262:13): [True: 3, False: 2.99k] ------------------ 1263| 2.99k| &nToBeRemovedByNormFromRevrs[iInchiRec].nNumRemovedProtons, 1264| 2.99k| (iInchiRec == INCHI_REC) ? &nDeltaFromDisconnected : NULL); ------------------ | | 571| 2.99k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1264:13): [True: 1.49k, False: 1.49k] ------------------ 1265| 2.99k| if (ret < 0) ------------------ | Branch (1265:13): [True: 2, False: 2.99k] ------------------ 1266| 2| { 1267| 2| goto exit_function; 1268| 2| } 1269| | /* djb-rwth: removing redundant code */ 1270| | /* 1271| | } 1272| | */ 1273| 2.99k| } 1274| | 1275| | /* if fixed-H layer is missing then we need to add isotopic exchangeable proton balance to the components */ 1276| 4.48k| for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 571| 1.49k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 570| 4.48k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1276:33): [True: 2.99k, False: 1.48k] ------------------ 1277| 2.99k| { 1278| | /* 1279| | if ( !pOneInput->nNumComponents[iInchiRec][TAUT_NON] && 1280| | pOneInput->nNumComponents[iInchiRec][TAUT_YES] ) { 1281| | */ 1282| 2.99k| int bHasRecMobH = (iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES]); ------------------ | | 570| 5.98k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int bHasRecMobH = (iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES]); ------------------ | | 571| 1.49k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int bHasRecMobH = (iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES]); ------------------ | | 575| 1.49k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1282:28): [True: 1.49k, False: 1.49k] | Branch (1282:54): [True: 3, False: 1.49k] ------------------ 1283| | /* bHasRecMobH means all components that could not be disconnected are in reconnected part */ 1284| 2.99k| if (iInchiRec == INCHI_BAS) ------------------ | | 570| 2.99k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1284:13): [True: 1.49k, False: 1.49k] ------------------ 1285| 1.49k| { 1286| | /* second pass: common structures have been changed */ 1287| 5.98k| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 25| 5.98k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1287:25): [True: 4.48k, False: 1.49k] ------------------ 1288| 4.48k| { 1289| 4.48k| nToBeRemovedByNormFromRevrs[INCHI_BAS].nNumRemovedIsotopicH[k] += nIsoDeltaFromDisconnected[k]; ------------------ | | 570| 4.48k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1290| 4.48k| } 1291| 1.49k| } 1292| | 1293| | /* after proton removal InChI is recalculated */ 1294| 2.99k| ret = AddRemIsoProtonsInRestrStruct(ic, pCG, ip, sd, num_inp, bHasSomeFixedH, pStruct[iInchiRec][TAUT_YES], ------------------ | | 575| 2.99k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1295| 2.99k| pOneInput->nNumComponents[iInchiRec][TAUT_YES], ------------------ | | 575| 2.99k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1296| 2.99k| bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 571| 3|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1296:13): [True: 3, False: 2.98k] ------------------ 1297| 2.99k| bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 571| 3|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1297:13): [True: 3, False: 2.98k] ------------------ 1298| 2.99k| nToBeRemovedByNormFromRevrs[iInchiRec].nNumRemovedIsotopicH, 1299| 2.99k| (iInchiRec == INCHI_REC) ? nIsoDeltaFromDisconnected : NULL); ------------------ | | 571| 2.99k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1299:13): [True: 1.49k, False: 1.49k] ------------------ 1300| | 1301| 2.99k| if (ret < 0) ------------------ | Branch (1301:13): [True: 7, False: 2.98k] ------------------ 1302| 7| { 1303| 7| goto exit_function; 1304| 7| } 1305| | /* djb-rwth: removing redundant code */ 1306| | /* 1307| | } 1308| | */ 1309| 2.99k| } 1310| | 1311| 1.49k|exit_function: 1312| | 1313| 1.49k| return ret; 1314| 1.49k|} FreeStrFromINChI: 1320| 5.18k|{ 1321| 5.18k| int iInchiRec, iMobileH, cur_num_comp, k, j; 1322| 5.18k| StrFromINChI* pStruct1; 1323| 15.5k| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 569| 15.5k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1323:25): [True: 10.3k, False: 5.18k] ------------------ 1324| 10.3k| { 1325| 31.1k| for (iMobileH = 0; iMobileH < TAUT_NUM; iMobileH++) ------------------ | | 573| 31.1k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1325:28): [True: 20.7k, False: 10.3k] ------------------ 1326| 20.7k| { 1327| 20.7k| cur_num_comp = nNumComponents[iInchiRec][iMobileH]; 1328| 20.7k| if (!cur_num_comp || !(pStruct1 = pStruct[iInchiRec][iMobileH])) ------------------ | Branch (1328:17): [True: 14.2k, False: 6.50k] | Branch (1328:34): [True: 0, False: 6.50k] ------------------ 1329| 14.2k| { 1330| 14.2k| continue; 1331| 14.2k| } 1332| 187k| for (k = 0; k < cur_num_comp; k++) ------------------ | Branch (1332:25): [True: 180k, False: 6.50k] ------------------ 1333| 180k| { 1334| 180k| if (pStruct1[k].at) ------------------ | Branch (1334:21): [True: 145k, False: 35.4k] ------------------ 1335| 145k| { 1336| 145k| inchi_free(pStruct1[k].at); ------------------ | | 1152| 145k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 145k, False: 0] | | | Branch (1152:50): [Folded, False: 145k] | | ------------------ ------------------ 1337| 145k| } 1338| 180k| if (pStruct1[k].at2) ------------------ | Branch (1338:21): [True: 145k, False: 35.7k] ------------------ 1339| 145k| { 1340| 145k| inchi_free(pStruct1[k].at2); ------------------ | | 1152| 145k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 145k, False: 0] | | | Branch (1152:50): [Folded, False: 145k] | | ------------------ ------------------ 1341| 145k| } 1342| 180k| if (pStruct1[k].st) ------------------ | Branch (1342:21): [True: 100, False: 180k] ------------------ 1343| 100| { 1344| 100| inchi_free(pStruct1[k].st); ------------------ | | 1152| 100|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 100, False: 0] | | | Branch (1152:50): [Folded, False: 100] | | ------------------ ------------------ 1345| 100| } 1346| 180k| if (pStruct1[k].pVA) ------------------ | Branch (1346:21): [True: 87.9k, False: 92.9k] ------------------ 1347| 87.9k| { 1348| 87.9k| inchi_free(pStruct1[k].pVA); ------------------ | | 1152| 87.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 87.9k, False: 0] | | | Branch (1152:50): [Folded, False: 87.9k] | | ------------------ ------------------ 1349| 87.9k| } 1350| | /* 1351| | if ( pStruct1[k].ti.t_group ) { 1352| | inchi_free( pStruct1[k].ti.t_group ); 1353| | } 1354| | */ 1355| 180k| if (pStruct1[k].One_ti.t_group) { ------------------ | Branch (1355:21): [True: 57.1k, False: 123k] ------------------ 1356| 57.1k| inchi_free(pStruct1[k].One_ti.t_group); /* ricrogz: fixing memory leak */ ------------------ | | 1152| 57.1k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 57.1k, False: 0] | | | Branch (1152:50): [Folded, False: 57.1k] | | ------------------ ------------------ 1357| 57.1k| } 1358| 180k| if (pStruct1[k].pXYZ) ------------------ | Branch (1358:21): [True: 0, False: 180k] ------------------ 1359| 0| { 1360| 0| inchi_free(pStruct1[k].pXYZ); /* djb-rwth: unresolved issue -- revision required? -- false positive as this function just does the clean-up job */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1361| 0| } 1362| | /*==== begin ====*/ 1363| 180k| free_t_group_info(&pStruct1[k].ti); 1364| 180k| if (pStruct1[k].endpoint) ------------------ | Branch (1364:21): [True: 1.14k, False: 179k] ------------------ 1365| 1.14k| { 1366| 1.14k| inchi_free(pStruct1[k].endpoint); /* djb-rwth: unresolved issue -- revision required? -- false positive as this function just does the clean-up job */ ------------------ | | 1152| 1.14k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.14k, False: 0] | | | Branch (1152:50): [Folded, False: 1.14k] | | ------------------ ------------------ 1367| 1.14k| } 1368| 180k| if (pStruct1[k].fixed_H) ------------------ | Branch (1368:21): [True: 1.13k, False: 179k] ------------------ 1369| 1.13k| { 1370| 1.13k| inchi_free(pStruct1[k].fixed_H); /* djb-rwth: unresolved issue -- revision required? -- false positive as this function just does the clean-up job */ ------------------ | | 1152| 1.13k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.13k, False: 0] | | | Branch (1152:50): [Folded, False: 1.13k] | | ------------------ ------------------ 1371| 1.13k| } 1372| 542k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 542k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1372:29): [True: 361k, False: 180k] ------------------ 1373| 361k| { 1374| 361k| if (pStruct1[k].nAtno2Canon[j]) ------------------ | Branch (1374:25): [True: 14.2k, False: 347k] ------------------ 1375| 14.2k| inchi_free(pStruct1[k].nAtno2Canon[j]); ------------------ | | 1152| 14.2k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 14.2k, False: 0] | | | Branch (1152:50): [Folded, False: 14.2k] | | ------------------ ------------------ 1376| 361k| if (pStruct1[k].nCanon2Atno[j]) ------------------ | Branch (1376:25): [True: 14.2k, False: 347k] ------------------ 1377| 14.2k| inchi_free(pStruct1[k].nCanon2Atno[j]); ------------------ | | 1152| 14.2k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 14.2k, False: 0] | | | Branch (1152:50): [Folded, False: 14.2k] | | ------------------ ------------------ 1378| 361k| } 1379| | /*===== end ======*/ 1380| | /* free INChI memory */ 1381| 180k| FreeAllINChIArrays(pStruct1[k].RevInChI.pINChI, 1382| 180k| pStruct1[k].RevInChI.pINChI_Aux, 1383| 180k| pStruct1[k].RevInChI.num_components); 1384| |#ifdef NEVER 1385| | /* don't do that: these are just pointers to OneInput structure members */ 1386| | Free_INChI(&pStruct1[k].pINChI); 1387| | Free_INChI_Aux(&pStruct1[k].pINChI_Aux); 1388| | if (pStruct1[k].inp_norm_data) 1389| | { 1390| | FreeInpAtomData(pStruct1[k].inp_norm_data); 1391| | inchi_free(pStruct1[k].inp_norm_data); 1392| | } 1393| |#endif 1394| 180k| } 1395| 6.50k| inchi_free(pStruct[iInchiRec][iMobileH]); ------------------ | | 1152| 6.50k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.50k, False: 0] | | | Branch (1152:50): [Folded, False: 6.50k] | | ------------------ ------------------ 1396| | pStruct[iInchiRec][iMobileH] = NULL; 1397| 6.50k| } 1398| 10.3k| } 1399| 5.18k|} FreeInpInChI: 1404| 20.0k|{ 1405| 20.0k| int iINChI, k, j; 1406| 60.2k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 569| 60.2k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1406:22): [True: 40.1k, False: 20.0k] ------------------ 1407| 40.1k| { 1408| 120k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 573| 120k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1408:21): [True: 80.3k, False: 40.1k] ------------------ 1409| 80.3k| { 1410| 80.3k| if (pOneInput->pInpInChI[iINChI][j]) ------------------ | Branch (1410:17): [True: 9.25k, False: 71.1k] ------------------ 1411| 9.25k| { 1412| 363k| for (k = 0; k < pOneInput->nNumComponents[iINChI][j]; k++) ------------------ | Branch (1412:29): [True: 354k, False: 9.25k] ------------------ 1413| 354k| { 1414| 354k|#if (FIX_OSS_FUZZ_25734_28139 == 1) 1415| 354k| U_CHAR* k_nAtom = (&pOneInput->pInpInChI[iINChI][j][k])->nAtom; 1416| 354k| AT_NUMB* k_nConnTable = (&pOneInput->pInpInChI[iINChI][j][k])->nConnTable; 1417| 354k| AT_NUMB* k_nTautomer = (&pOneInput->pInpInChI[iINChI][j][k])->nTautomer; 1418| 354k| S_CHAR* k_nNum_H = (&pOneInput->pInpInChI[iINChI][j][k])->nNum_H; 1419| 354k| S_CHAR* k_nNum_H_fixed = (&pOneInput->pInpInChI[iINChI][j][k])->nNum_H_fixed; 1420| 354k| char* k_szHillFormula = (&pOneInput->pInpInChI[iINChI][j][k])->szHillFormula; 1421| 354k| AT_NUMB* k_nPossibleLocationsOfIsotopicH = (&pOneInput->pInpInChI[iINChI][j][k])->nPossibleLocationsOfIsotopicH; 1422| 354k| INChI_IsotopicAtom* k_IsotopicAtom = (&pOneInput->pInpInChI[iINChI][j][k])->IsotopicAtom; 1423| 354k| INChI_IsotopicTGroup* k_IsotopicTGroup = (&pOneInput->pInpInChI[iINChI][j][k])->IsotopicTGroup; 1424| 354k| INChI_Stereo* k_Stereo = (&pOneInput->pInpInChI[iINChI][j][k])->Stereo; 1425| 354k| INChI_Stereo* k_StereoIsotopic = (&pOneInput->pInpInChI[iINChI][j][k])->StereoIsotopic; 1426| | 1427| 354k|#endif 1428| | 1429| 354k| Free_INChI_Members(&pOneInput->pInpInChI[iINChI][j][k]); 1430| | 1431| 354k|#if (FIX_OSS_FUZZ_25734_28139 == 1) 1432| 354k| { 1433| | /* prevent erroneous repeated freeing in copied pInpInChIp[][][kk] */ 1434| 354k| int kk; 1435| 896M| for (kk = k + 1; kk < pOneInput->nNumComponents[iINChI][j]; kk++) ------------------ | Branch (1435:42): [True: 895M, False: 354k] ------------------ 1436| 895M| { 1437| 895M| if (k_nAtom == (&pOneInput->pInpInChI[iINChI][j][kk])->nAtom) ------------------ | Branch (1437:33): [True: 115M, False: 780M] ------------------ 1438| 115M| { 1439| 115M| (&pOneInput->pInpInChI[iINChI][j][kk])->nAtom = NULL; 1440| 115M| } 1441| 895M| if (k_nConnTable == (&pOneInput->pInpInChI[iINChI][j][kk])->nConnTable) ------------------ | Branch (1441:33): [True: 155M, False: 740M] ------------------ 1442| 155M| { 1443| 155M| (&pOneInput->pInpInChI[iINChI][j][kk])->nConnTable = NULL; 1444| 155M| } 1445| 895M| if (k_nTautomer == (&pOneInput->pInpInChI[iINChI][j][kk])->nTautomer) ------------------ | Branch (1445:33): [True: 895M, False: 166k] ------------------ 1446| 895M| { 1447| 895M| (&pOneInput->pInpInChI[iINChI][j][kk])->nTautomer = NULL; 1448| 895M| } 1449| 895M| if (k_nNum_H == (&pOneInput->pInpInChI[iINChI][j][kk])->nNum_H) ------------------ | Branch (1449:33): [True: 141M, False: 754M] ------------------ 1450| 141M| { 1451| 141M| (&pOneInput->pInpInChI[iINChI][j][kk])->nNum_H = NULL; 1452| 141M| } 1453| 895M| if (k_nNum_H_fixed == (&pOneInput->pInpInChI[iINChI][j][kk])->nNum_H_fixed) ------------------ | Branch (1453:33): [True: 895M, False: 1.46k] ------------------ 1454| 895M| { 1455| 895M| (&pOneInput->pInpInChI[iINChI][j][kk])->nNum_H_fixed = NULL; 1456| 895M| } 1457| 895M| if (k_szHillFormula == (&pOneInput->pInpInChI[iINChI][j][kk])->szHillFormula) ------------------ | Branch (1457:33): [True: 115M, False: 780M] ------------------ 1458| 115M| { 1459| 115M| (&pOneInput->pInpInChI[iINChI][j][kk])->szHillFormula = NULL; 1460| 115M| } 1461| 895M| if (k_nPossibleLocationsOfIsotopicH == (&pOneInput->pInpInChI[iINChI][j][kk])->nPossibleLocationsOfIsotopicH) ------------------ | Branch (1461:33): [True: 895M, False: 0] ------------------ 1462| 895M| { 1463| 895M| (&pOneInput->pInpInChI[iINChI][j][kk])->nPossibleLocationsOfIsotopicH = NULL; 1464| 895M| } 1465| | 1466| 895M| if (k_IsotopicAtom == (&pOneInput->pInpInChI[iINChI][j][kk])->IsotopicAtom) ------------------ | Branch (1466:33): [True: 894M, False: 1.33M] ------------------ 1467| 894M| { 1468| 894M| (&pOneInput->pInpInChI[iINChI][j][kk])->IsotopicAtom = NULL; 1469| 894M| } 1470| | 1471| 895M| if (k_IsotopicTGroup == (&pOneInput->pInpInChI[iINChI][j][kk])->IsotopicTGroup) ------------------ | Branch (1471:33): [True: 895M, False: 0] ------------------ 1472| 895M| { 1473| 895M| (&pOneInput->pInpInChI[iINChI][j][kk])->IsotopicTGroup = NULL; 1474| 895M| } 1475| | 1476| 895M| if (k_Stereo == (&pOneInput->pInpInChI[iINChI][j][kk])->Stereo) ------------------ | Branch (1476:33): [True: 883M, False: 12.1M] ------------------ 1477| 883M| { 1478| 883M| (&pOneInput->pInpInChI[iINChI][j][kk])->Stereo = NULL; 1479| 883M| } 1480| | 1481| 895M| if (k_StereoIsotopic == (&pOneInput->pInpInChI[iINChI][j][kk])->StereoIsotopic) ------------------ | Branch (1481:33): [True: 894M, False: 1.33M] ------------------ 1482| 894M| { 1483| 894M| (&pOneInput->pInpInChI[iINChI][j][kk])->StereoIsotopic = NULL; 1484| 894M| } 1485| | 1486| 895M| } 1487| 354k| } 1488| 354k|#endif 1489| | 1490| 354k| } 1491| 9.25k| inchi_free(pOneInput->pInpInChI[iINChI][j]); ------------------ | | 1152| 9.25k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 9.25k, False: 0] | | | Branch (1152:50): [Folded, False: 9.25k] | | ------------------ ------------------ 1492| 9.25k| pOneInput->pInpInChI[iINChI][j] = NULL; 1493| 9.25k| } 1494| 80.3k| if (pOneInput->nNumProtons[iINChI][j].pNumProtons) ------------------ | Branch (1494:17): [True: 13, False: 80.3k] ------------------ 1495| 13| { 1496| 13| inchi_free(pOneInput->nNumProtons[iINChI][j].pNumProtons); ------------------ | | 1152| 13|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 13, False: 0] | | | Branch (1152:50): [Folded, False: 13] | | ------------------ ------------------ 1497| 13| pOneInput->nNumProtons[iINChI][j].pNumProtons = NULL; 1498| 13| } 1499| 80.3k| } 1500| 40.1k| } 1501| 20.0k| if (pOneInput->atom) ------------------ | Branch (1501:9): [True: 0, False: 20.0k] ------------------ 1502| 0| { 1503| 0| inchi_free(pOneInput->atom); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1504| 0| } 1505| | 1506| 20.0k| FreeExtOrigAtData(pOneInput->polymer, pOneInput->v3000); 1507| | 1508| 20.0k| memset(pOneInput, 0, sizeof(*pOneInput)); /* djb-rwth: memset_s C11/Annex K variant? */ 1509| 20.0k|} CompareAllOrigInchiToRevInChI: 1518| 1.75k|{ 1519| 1.75k| int i, iInchiRec, iMobileH, iMobileHpStruct, num_components, iComponent, ret = 0; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 1520| 1.75k| COMPONENT_REM_PROTONS nCurRemovedProtons, nNumRemovedProtons; 1521| 1.75k| INChI* pInChI[TAUT_NUM]; 1522| 1.75k| INCHI_MODE CompareInchiFlags[TAUT_NUM]; 1523| 1.75k| memset(pOneInput->CompareInchiFlags[0], 0, sizeof(pOneInput->CompareInchiFlags[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 1524| 1.75k| memset(&nNumRemovedProtons, 0, sizeof(nNumRemovedProtons)); /* djb-rwth: memset_s C11/Annex K variant? */ 1525| | 1526| | /* do we have reconnected InChI ?*/ 1527| 1.75k| iInchiRec = INCHI_REC; ------------------ | | 571| 1.75k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1528| 1.75k| iMobileH = TAUT_NON; ------------------ | | 574| 1.75k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1529| 1.75k| if (!pOneInput->nNumComponents[iInchiRec][TAUT_YES] && !pOneInput->nNumComponents[iInchiRec][TAUT_NON]) ------------------ | | 575| 1.75k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (!pOneInput->nNumComponents[iInchiRec][TAUT_YES] && !pOneInput->nNumComponents[iInchiRec][TAUT_NON]) ------------------ | | 574| 1.74k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1529:9): [True: 1.74k, False: 7] | Branch (1529:60): [True: 1.74k, False: 0] ------------------ 1530| 1.74k| { 1531| 1.74k| iInchiRec = INCHI_BAS; ------------------ | | 570| 1.74k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1532| 1.74k| } 1533| | /* do we have Mobile or Fixed-H ? */ 1534| 1.75k| if (!pOneInput->nNumComponents[iInchiRec][TAUT_NON] || !bReqNonTaut) ------------------ | | 574| 1.75k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1534:9): [True: 1.48k, False: 272] | Branch (1534:60): [True: 8, False: 264] ------------------ 1535| 1.49k| { 1536| 1.49k| iMobileH = TAUT_YES; /* index for pOneInput */ ------------------ | | 575| 1.49k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1537| 1.49k| } 1538| | /* if a restored structure has Fixed-H InChI then its mobile-H restored InChI is in Fixed-H pStruct */ 1539| 1.75k| num_components = pOneInput->nNumComponents[iInchiRec][iMobileH]; 1540| 50.5k| for (iComponent = 0; iComponent < num_components; iComponent++) ------------------ | Branch (1540:26): [True: 48.8k, False: 1.75k] ------------------ 1541| 48.8k| { 1542| 48.8k| int bMobileH = iMobileH; 1543| 48.8k| pInChI[0] = pInChI[1] = NULL; 1544| 48.8k| if (pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent].nNumberOfAtoms && ------------------ | Branch (1544:13): [True: 34.3k, False: 14.5k] ------------------ 1545| 34.3k| !pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent].bDeleted) ------------------ | Branch (1545:13): [True: 32.8k, False: 1.48k] ------------------ 1546| 32.8k| { 1547| | /* the requested InChI layer exists */ 1548| 32.8k| pInChI[0] = &pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent]; 1549| 32.8k| if (bMobileH == TAUT_NON) ------------------ | | 574| 32.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1549:17): [True: 263, False: 32.5k] ------------------ 1550| 263| { 1551| 263| pInChI[1] = &pOneInput->pInpInChI[iInchiRec][TAUT_YES][iComponent]; ------------------ | | 575| 263|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1552| 263| } 1553| 32.8k| } 1554| 15.9k| else 1555| 15.9k| { 1556| 15.9k| if (bMobileH == TAUT_NON && ------------------ | | 574| 31.9k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1556:17): [True: 14.5k, False: 1.48k] ------------------ 1557| 14.5k| pOneInput->pInpInChI[iInchiRec][TAUT_YES][iComponent].nNumberOfAtoms && ------------------ | | 575| 14.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1557:17): [True: 14.5k, False: 0] ------------------ 1558| 14.5k| !pOneInput->pInpInChI[iInchiRec][TAUT_YES][iComponent].bDeleted) ------------------ | | 575| 14.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1558:17): [True: 14.5k, False: 0] ------------------ 1559| 14.5k| { 1560| | /* the requested Fixed-H InChI layer does not exist; however, the Mobile-H does exist */ 1561| 14.5k| bMobileH = TAUT_YES; /* only Mobile-H is available */ ------------------ | | 575| 14.5k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1562| 14.5k| pInChI[0] = &pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent]; 1563| 14.5k| } 1564| 15.9k| } 1565| 48.8k| memset(CompareInchiFlags, 0, sizeof(CompareInchiFlags)); /* djb-rwth: memset_s C11/Annex K variant? */ 1566| 48.8k| memset(&nCurRemovedProtons, 0, sizeof(nCurRemovedProtons)); /* djb-rwth: memset_s C11/Annex K variant? */ 1567| 48.8k| iMobileHpStruct = 1568| |#if ( bRELEASE_VERSION == 0 ) 1569| |#ifndef TARGET_API_LIB 1570| | /* legacy: reproduce old output */ 1571| | OldPrintCompareOneOrigInchiToRevInChI(pStruct[iInchiRec][bMobileH] + iComponent, pInChI, bMobileH, 1572| | iComponent, num_inp, szCurHdr); 1573| |#endif 1574| |#endif 1575| | /* one component comparison result bits */ 1576| 48.8k| ret = CompareOneOrigInchiToRevInChI(pStruct[iInchiRec][bMobileH] + iComponent, pInChI, bMobileH, iComponent, 1577| 48.8k| num_inp, szCurHdr, &nCurRemovedProtons, CompareInchiFlags); 1578| 48.8k| if (ret >= 0) ------------------ | Branch (1578:13): [True: 48.8k, False: 0] ------------------ 1579| 48.8k| { 1580| | /* no errors encountered -> accumulate removed protons from individual Mobile-H layers of components */ 1581| 48.8k| nNumRemovedProtons.nNumRemovedProtons += nCurRemovedProtons.nNumRemovedProtons; 1582| 195k| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 25| 195k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1582:25): [True: 146k, False: 48.8k] ------------------ 1583| 146k| { 1584| 146k| nNumRemovedProtons.nNumRemovedIsotopicH[i] += nCurRemovedProtons.nNumRemovedIsotopicH[i]; 1585| 146k| } 1586| | /* accumulate compare bits */ 1587| 146k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 146k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1587:25): [True: 97.6k, False: 48.8k] ------------------ 1588| 97.6k| { 1589| 97.6k| pOneInput->CompareInchiFlags[0][i] |= CompareInchiFlags[i]; 1590| 97.6k| } 1591| 48.8k| } 1592| 0| else 1593| 0| { 1594| 0| goto exit_function; 1595| 0| } 1596| 48.8k| } 1597| 1.75k| if (iMobileH == TAUT_YES) ------------------ | | 575| 1.75k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1597:9): [True: 1.49k, False: 264] ------------------ 1598| 1.49k| { 1599| 1.49k| if (pOneInput->nNumProtons[iInchiRec][iMobileH].pNumProtons) ------------------ | Branch (1599:13): [True: 0, False: 1.49k] ------------------ 1600| 0| { 1601| 0| ret = RI_ERR_PROGR; /* in Mobile-H case proton balances are split between compoments */ ------------------ | | 17| 0|#define RI_ERR_PROGR (-3) ------------------ 1602| 0| } 1603| 1.49k| else 1604| 1.49k| { 1605| | /* num removed protons in orig. InChI num removed protons in restored InChi */ 1606| 1.49k| if (nNumRemovedProtons.nNumRemovedProtons != pOneInput->nNumProtons[iInchiRec][iMobileH].nNumRemovedProtons) ------------------ | Branch (1606:17): [True: 93, False: 1.39k] ------------------ 1607| 93| { 1608| | /* restored structure InChI has less or more removed protons */ 1609| 93| pOneInput->CompareInchiFlags[0][TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; ------------------ | | 575| 93|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1610| |#if ( bRELEASE_VERSION == 0 ) 1611| | /* debug output only */ 1612| | { 1613| | int num_H_AddedByRevrs = pOneInput->nNumProtons[iInchiRec][iMobileH].nNumRemovedProtons 1614| | - nNumRemovedProtons.nNumRemovedProtons; 1615| | fprintf(stdout, "COMPARE_INCHI: %ld: %s %cM: Proton balance (Diff: %d, RevrsRem=%d)\n", 1616| | num_inp, szCurHdr ? szCurHdr : "Struct", iInchiRec ? 'R' : 'D', 1617| | pOneInput->nNumProtons[iInchiRec][iMobileH].nNumRemovedProtons, num_H_AddedByRevrs); 1618| | } 1619| |#endif 1620| 93| } 1621| 5.96k| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 25| 5.96k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1621:25): [True: 4.47k, False: 1.49k] ------------------ 1622| 4.47k| { 1623| 4.47k| if (nNumRemovedProtons.nNumRemovedIsotopicH[i] != pOneInput->nNumProtons[iInchiRec][TAUT_YES].nNumRemovedIsotopicH[i]) ------------------ | | 575| 4.47k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1623:21): [True: 81, False: 4.38k] ------------------ 1624| 81| { 1625| 81| pOneInput->CompareInchiFlags[0][TAUT_YES] |= INCHIDIFF_MOB_ISO_H; ------------------ | | 575| 81|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1626| |#if ( bRELEASE_VERSION == 0 ) 1627| | /* debug output only */ 1628| | { 1629| | int num_H_AddedByRevrs = pOneInput->nNumProtons[iInchiRec][TAUT_YES].nNumRemovedIsotopicH[i] 1630| | - nNumRemovedProtons.nNumRemovedIsotopicH[i]; 1631| | fprintf(stdout, "COMPARE_INCHI: %ld: %s %cM: Iso Xchg %dH balance (Diff: %d, RevrsRem=%d)\n", 1632| | num_inp, szCurHdr ? szCurHdr : "Struct", iInchiRec ? 'R' : 'D', i + 1, 1633| | pOneInput->nNumProtons[iInchiRec][TAUT_YES].nNumRemovedIsotopicH[i], num_H_AddedByRevrs); 1634| | } 1635| |#endif 1636| 81| } 1637| 4.47k| } 1638| 1.49k| } 1639| 1.49k| } 1640| | 1641| 1.75k|exit_function: 1642| | 1643| 1.75k| return ret; 1644| 1.75k|} CompareAllDisconnectedOrigInchiToRevInChI: 1653| 1.75k|{ 1654| 1.75k| int i, k, m, n, iInChI, iMobileH, bMobileH, ifk; 1655| 1.75k| int num_components_D, num_components_R; 1656| 1.75k| int nNumCompHaveSeparateProtons_D, nNumCompHaveSeparateProtons_R; 1657| 1.75k| int num_fragments_D, num_fragments_R, num_fragments_DR, num_fragments, iComponent, ret; 1658| 1.75k| int ifInChI, ifMobileH, bfMobileH, nLink; 1659| 1.75k| COMPONENT_REM_PROTONS nNumRemovedProtons_D; /* removed from the disconnected layer of the Input InChI */ 1660| 1.75k| COMPONENT_REM_PROTONS nNumRemovedProtons_D_all; /* if only totals are avalable */ 1661| 1.75k| COMPONENT_REM_PROTONS nNumRemovedProtons_R; /* removed from disconnected layer of the reconstructed struct */ 1662| 1.75k| COMPONENT_REM_PROTONS nNumRemovedProtons_R_all; 1663| 1.75k| INCHI_MODE CompareInchiFlags[TAUT_NUM]; 1664| 1.75k| StrFromINChI* pStruct1; 1665| 1.75k| INChI_Aux* pINChI_Aux; 1666| 1.75k| INCHI_SORT* pINChISort1 = NULL; /* from reversed structure */ 1667| 1.75k| INCHI_SORT* pINChISort2 = NULL; /* original input InChI */ 1668| 1.75k| int nNumNonTaut1 = 0, nNumNonTaut2 = 0; 1669| | 1670| 1.75k| ret = 0; 1671| 1.75k| memset(pOneInput->CompareInchiFlags[1], 0, sizeof(pOneInput->CompareInchiFlags[1])); /* djb-rwth: memset_s C11/Annex K variant? */ 1672| | 1673| | /* count components that are not subject to disconnection */ 1674| 1.75k| if (!pOneInput->nNumComponents[INCHI_REC][TAUT_YES] && ------------------ | | 571| 1.75k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (!pOneInput->nNumComponents[INCHI_REC][TAUT_YES] && ------------------ | | 575| 1.75k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1674:9): [True: 1.74k, False: 7] ------------------ 1675| 1.74k| !pOneInput->nNumComponents[INCHI_REC][TAUT_NON]) ------------------ | | 571| 1.74k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->nNumComponents[INCHI_REC][TAUT_NON]) ------------------ | | 574| 1.74k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1675:9): [True: 1.74k, False: 0] ------------------ 1676| 1.74k| { 1677| 1.74k| return 0; /* nothing to do */ 1678| 1.74k| } 1679| | 1680| 7| memset(&nNumRemovedProtons_D, 0, sizeof(nNumRemovedProtons_D)); /* djb-rwth: memset_s C11/Annex K variant? */ 1681| 7| memset(&nNumRemovedProtons_R, 0, sizeof(nNumRemovedProtons_R)); /* djb-rwth: memset_s C11/Annex K variant? */ 1682| 7| memset(&nNumRemovedProtons_D_all, 0, sizeof(nNumRemovedProtons_D_all)); /* djb-rwth: memset_s C11/Annex K variant? */ 1683| 7| memset(&nNumRemovedProtons_R_all, 0, sizeof(nNumRemovedProtons_R_all)); /* djb-rwth: memset_s C11/Annex K variant? */ 1684| 7| memset(CompareInchiFlags, 0, sizeof(CompareInchiFlags)); /* djb-rwth: memset_s C11/Annex K variant? */ 1685| | 1686| 7| num_components_D = inchi_max(pOneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 138| 7|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 3, False: 4] | | ------------------ ------------------ 1687| 7| pOneInput->nNumComponents[INCHI_BAS][TAUT_NON]); 1688| 7| num_components_R = inchi_max(pOneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 138| 7|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 4, False: 3] | | ------------------ ------------------ 1689| 7| pOneInput->nNumComponents[INCHI_REC][TAUT_NON]); 1690| | 1691| | /***********************************************************************************************/ 1692| | /* InpInChI: count fragments -- disconnected components that do not match reconnected */ 1693| | /* Accumulate removed H and isotopic H from ALL Fixed-H disconnected components except deleted */ 1694| | /* This segment collects info from the original InChI */ 1695| | /***********************************************************************************************/ 1696| | /*---- Original InChI ----*/ 1697| | 1698| 7| num_fragments_D = 0; 1699| 7| iInChI = INCHI_BAS; ------------------ | | 570| 7|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1700| 7| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 574| 4|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 575| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1700:16): [True: 4, False: 3] ------------------ 1701| 7| nNumCompHaveSeparateProtons_D = 0; 1702| | 1703| | /* in case of Mobile-H components here are the proton totals from the original InChI disconn. layer */ 1704| 7| nNumRemovedProtons_D.nNumRemovedProtons = pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 575| 7|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1705| 7| memcpy(nNumRemovedProtons_D.nNumRemovedIsotopicH, 1706| 7| pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedIsotopicH, ------------------ | | 575| 7|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1707| 7| sizeof(nNumRemovedProtons_D.nNumRemovedIsotopicH)); /* total for the disconnected layer */ 1708| 16| for (k = 0; k < num_components_D; k++) ------------------ | Branch (1708:17): [True: 9, False: 7] ------------------ 1709| 9| { 1710| 9| bMobileH = iMobileH; 1711| 9| if (!bInpInchiComponentExists(pOneInput, iInChI, bMobileH, k)) ------------------ | Branch (1711:13): [True: 3, False: 6] ------------------ 1712| 3| { 1713| 3| if (bInpInchiComponentExists(pOneInput, iInChI, TAUT_YES, k)) ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1713:17): [True: 0, False: 3] ------------------ 1714| 0| { 1715| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1716| 0| } 1717| 3| else 1718| 3| { 1719| 3| continue; /* component is missing ??? */ 1720| 3| } 1721| 3| } 1722| 6| if (0 > (nLink = pOneInput->pInpInChI[iInChI][bMobileH][k].nLink)) ------------------ | Branch (1722:13): [True: 1, False: 5] ------------------ 1723| 1| { 1724| | /* component in Disconnected layer is linked to the identical one in the Reconnected layer */ 1725| 1| if (pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 571| 1|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1725:17): [True: 0, False: 1] ------------------ 1726| 0| { 1727| 0| nNumCompHaveSeparateProtons_D++; 1728| 0| nLink = -(1 + nLink); 1729| 0| nNumRemovedProtons_D.nNumRemovedProtons += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedProtons; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ nNumRemovedProtons_D.nNumRemovedProtons += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedProtons; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1730| 0| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 25| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1730:29): [True: 0, False: 0] ------------------ 1731| 0| { 1732| 0| nNumRemovedProtons_D.nNumRemovedIsotopicH[m] += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedIsotopicH[m]; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ nNumRemovedProtons_D.nNumRemovedIsotopicH[m] += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedIsotopicH[m]; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1733| 0| } 1734| 0| } 1735| 1| continue; /* same as reconnected */ 1736| 1| } 1737| | /* component in the reconnected layer that was disconnected */ 1738| 5| nNumNonTaut2 += (bMobileH == TAUT_NON); ------------------ | | 574| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1739| 5| if (pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons) ------------------ | | 575| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1739:13): [True: 0, False: 5] ------------------ 1740| 0| { 1741| 0| nNumCompHaveSeparateProtons_D++; 1742| 0| nNumRemovedProtons_D.nNumRemovedProtons += pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons[k].nNumRemovedProtons; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1743| 0| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 25| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1743:25): [True: 0, False: 0] ------------------ 1744| 0| { 1745| 0| nNumRemovedProtons_D.nNumRemovedIsotopicH[m] += pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons[k].nNumRemovedIsotopicH[m]; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1746| 0| } 1747| 0| } 1748| 5| num_fragments_D++; /* number of disconnected fragments from original reconnected structure */ 1749| 5| } 1750| | /* in case of Mobile-H components here are the proton totals from the original InChI */ 1751| | /* 1752| | nNumRemovedProtons_D_all.nNumRemovedProtons = pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedProtons; 1753| | memcpy( nNumRemovedProtons_D_all.nNumRemovedIsotopicH, 1754| | pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedIsotopicH, 1755| | sizeof(nNumRemovedProtons_D_all.nNumRemovedIsotopicH) ); 1756| | 1757| | */ 1758| | /****************************************************************************************************/ 1759| | /* count fragments in reconstructed reconnected structure */ 1760| | /* accumulate removed H and isotopic H from ALL reconstructed reconnected components except deleted */ 1761| | /* This segment collects info from the reconstructed structure InChI */ 1762| | /****************************************************************************************************/ 1763| | /*---- InChI from the reconstructed reconnected structure ----*/ 1764| 7| num_fragments_R = 0; 1765| 7| iInChI = INCHI_REC; ------------------ | | 571| 7|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1766| 7| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 574| 4|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 575| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1766:16): [True: 4, False: 3] ------------------ 1767| 7| nNumCompHaveSeparateProtons_R = 0; 1768| 17| for (k = 0; k < num_components_R; k++) ------------------ | Branch (1768:17): [True: 10, False: 7] ------------------ 1769| 10| { 1770| 10| bMobileH = iMobileH; 1771| 10| if (!bInpInchiComponentExists(pOneInput, iInChI, bMobileH, k)) ------------------ | Branch (1771:13): [True: 5, False: 5] ------------------ 1772| 5| { 1773| 5| if (bInpInchiComponentExists(pOneInput, iInChI, TAUT_YES, k)) ------------------ | | 575| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1773:17): [True: 1, False: 4] ------------------ 1774| 1| { 1775| 1| bMobileH = TAUT_YES; ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1776| 1| } 1777| 4| else 1778| 4| { 1779| 4| continue; /* component is missing ??? (Deleted proton in Mobile-H layer) */ 1780| 4| } 1781| 5| } 1782| 6| if (0 < pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (1782:13): [True: 1, False: 5] ------------------ 1783| 1| { 1784| | /* this reconstructed reconnected component was NOT DISCONNECTED */ 1785| | /* same component is in the disconnected layer, it has no metal atoms or is an isolated metal atom */ 1786| 1| pStruct1 = pStruct[iInChI][bMobileH] + k; 1787| 1| ifMobileH = TAUT_YES; /* Mobile-H Aux_Info contains number removed protons */ ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1788| 1| ifInChI = INCHI_BAS; /* this component cannot be reconnected */ ------------------ | | 570| 1|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1789| 1| ifk = 0; /* 0th component since it is InChI of a single component */ 1790| | /* The statement in the following line is *WRONG*, component number mixed with bMobileH: */ 1791| | /* in RevInchi, when only Mobile-H is present then its only non-NULL InChI has index 0==TAUT_NON */ 1792| 1| if (bRevInchiComponentExists(pStruct1, ifInChI, ifMobileH, ifk)) ------------------ | Branch (1792:17): [True: 1, False: 0] ------------------ 1793| 1| { 1794| | /* count protons */ 1795| 1| pINChI_Aux = pStruct1->RevInChI.pINChI_Aux[ifInChI][ifk][ifMobileH]; 1796| 1| if (pINChI_Aux) ------------------ | Branch (1796:21): [True: 1, False: 0] ------------------ 1797| 1| { 1798| 1| nNumRemovedProtons_R.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1799| 4| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 25| 4|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1799:33): [True: 3, False: 1] ------------------ 1800| 3| { 1801| 3| nNumRemovedProtons_R.nNumRemovedIsotopicH[m] += pINChI_Aux->nNumRemovedIsotopicH[m]; 1802| 3| } 1803| 1| } 1804| 1| } 1805| 1| nNumCompHaveSeparateProtons_R += bRevInchiComponentExists(pStruct1, ifInChI, ALT_TAUT(ifMobileH), ifk); ------------------ | | 577| 1|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 1] | | ------------------ ------------------ 1806| 1| continue; /* same as disconnected, has no metal atoms */ 1807| 1| } 1808| | /* this reconstructed reconnected component WAS DISCONNECTED; check its fragments */ 1809| | /* it does not have same component in the disconnected layer */ 1810| 5| pStruct1 = pStruct[iInChI][bMobileH] + k; 1811| 5| num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS]; ------------------ | | 570| 5|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1812| 5| ifInChI = INCHI_BAS; /* disconnected layer */ ------------------ | | 570| 5|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1813| 5| ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 574| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 575| 7|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1813:21): [True: 3, False: 2] ------------------ 1814| 10| for (ifk = 0; ifk < num_fragments; ifk++) ------------------ | Branch (1814:23): [True: 5, False: 5] ------------------ 1815| 5| { 1816| 5| bfMobileH = ifMobileH; 1817| 5| if (!bRevInchiComponentExists(pStruct1, ifInChI, bfMobileH, ifk)) ------------------ | Branch (1817:17): [True: 3, False: 2] ------------------ 1818| 3| { 1819| 3| if (bRevInchiComponentExists(pStruct1, ifInChI, TAUT_YES, ifk)) ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1819:21): [True: 3, False: 0] ------------------ 1820| 3| { 1821| 3| bfMobileH = TAUT_YES; ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1822| 3| } 1823| 0| else 1824| 0| { 1825| 0| continue; /* fragment does not exist ??? */ 1826| 0| } 1827| 3| } 1828| 5| nNumNonTaut1 += (bfMobileH == TAUT_NON); ------------------ | | 574| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1829| 5| nNumCompHaveSeparateProtons_R += (bfMobileH == TAUT_NON); ------------------ | | 574| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1830| | /* count protons from fragments made by metal disconnection */ 1831| 5| pINChI_Aux = pStruct1->RevInChI.pINChI_Aux[ifInChI][ifk][TAUT_YES]; ------------------ | | 575| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1832| 5| if (pINChI_Aux) ------------------ | Branch (1832:17): [True: 5, False: 0] ------------------ 1833| 5| { 1834| 5| nNumRemovedProtons_R.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1835| 20| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 25| 20|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1835:29): [True: 15, False: 5] ------------------ 1836| 15| { 1837| 15| nNumRemovedProtons_R.nNumRemovedIsotopicH[m] += pINChI_Aux->nNumRemovedIsotopicH[m]; 1838| 15| } 1839| 5| } 1840| 5| num_fragments_R++; /* number of disconnected fragments from reconstructed reconnected structure */ 1841| 5| } 1842| 5| } 1843| | 1844| | /*---------------- special treatment of the last reconstructed component -----------------*/ 1845| | /*---------------- this may contain separate protons added by the reconstruction ---------*/ 1846| 7| k = num_components_R - 1; 1847| 7| pStruct1 = pStruct[iInChI][iMobileH] + k; 1848| 7| if (iMobileH == TAUT_YES && !bHasSomeFixedH && ------------------ | | 575| 14|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1848:9): [True: 4, False: 3] | Branch (1848:33): [True: 3, False: 1] ------------------ 1849| 3| bInpInchiComponentDeleted(pOneInput, iInChI, iMobileH, k) && ------------------ | Branch (1849:9): [True: 3, False: 0] ------------------ 1850| 3| (num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS])) ------------------ | | 570| 3|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1850:9): [True: 1, False: 2] ------------------ 1851| 1| { 1852| | 1853| 1| ifInChI = INCHI_BAS; /* disconnected layer */ ------------------ | | 570| 1|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1854| 1| ifMobileH = TAUT_YES; ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1855| 2| for (ifk = 0; ifk < num_fragments; ifk++) ------------------ | Branch (1855:23): [True: 1, False: 1] ------------------ 1856| 1| { 1857| 1| bfMobileH = ifMobileH; 1858| 1| if (!bRevInchiComponentDeleted(pStruct1, ifInChI, bfMobileH, ifk)) ------------------ | Branch (1858:17): [True: 0, False: 1] ------------------ 1859| 0| { 1860| 0| continue; /* fragment does exist ??? Should not happen */ 1861| 0| } 1862| | /* 1863| | nNumNonTaut1 += (bfMobileH == TAUT_NON); 1864| | nNumCompHaveSeparateProtons_R += (bfMobileH == TAUT_NON); 1865| | */ 1866| | /* count protons from fragments made by metal disconnection */ 1867| 1| pINChI_Aux = pStruct1->RevInChI.pINChI_Aux[ifInChI][ifk][TAUT_YES]; ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1868| 1| if (pINChI_Aux) ------------------ | Branch (1868:17): [True: 1, False: 0] ------------------ 1869| 1| { 1870| 1| nNumRemovedProtons_R.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1871| 4| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 25| 4|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1871:29): [True: 3, False: 1] ------------------ 1872| 3| { 1873| 3| nNumRemovedProtons_R.nNumRemovedIsotopicH[m] += pINChI_Aux->nNumRemovedIsotopicH[m]; 1874| 3| } 1875| 1| } 1876| | /*num_fragments_R ++;*/ /* number of disconnected fragments from reconstructed reconnected structure */ 1877| 1| } 1878| 1| } 1879| | 1880| 7| num_fragments_DR = inchi_max(num_fragments_D, num_fragments_R); ------------------ | | 138| 7|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 7] | | ------------------ ------------------ 1881| | /* in case of correct reconstruction, num_fragments_D, num_fragments_R */ 1882| 7| if (!num_fragments_DR) ------------------ | Branch (1882:9): [True: 2, False: 5] ------------------ 1883| 2| { 1884| 2| return 0; /* no component was disconnected */ 1885| 2| } 1886| 5| if (num_fragments_D != num_fragments_R) ------------------ | Branch (1886:9): [True: 0, False: 5] ------------------ 1887| 0| { 1888| 0| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1888:21): [True: 0, False: 0] ------------------ 1889| 0| { 1890| 0| if (pOneInput->nNumComponents[INCHI_BAS][i]) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1890:17): [True: 0, False: 0] ------------------ 1891| 0| { 1892| 0| pOneInput->CompareInchiFlags[1][i] |= INCHIDIFF_PROBLEM; 1893| 0| } 1894| 0| } 1895| 0| return 1; /* severe error */ 1896| 0| } 1897| | 1898| 5| pINChISort1 = (INCHI_SORT*)inchi_calloc(num_fragments_DR, sizeof(pINChISort1[0])); ------------------ | | 1146| 5|#define inchi_calloc calloc ------------------ 1899| 5| pINChISort2 = (INCHI_SORT*)inchi_calloc(num_fragments_DR, sizeof(pINChISort2[0])); ------------------ | | 1146| 5|#define inchi_calloc calloc ------------------ 1900| 5| if (!pINChISort1 || !pINChISort2) ------------------ | Branch (1900:9): [True: 0, False: 5] | Branch (1900:25): [True: 0, False: 5] ------------------ 1901| 0| { 1902| 0| ret = RI_ERR_ALLOC; ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 1903| 0| goto exit_function; 1904| 0| } 1905| | 1906| | /* accumulate original InChI of fragments -- disconnected components that do not match reconnected */ 1907| 5| iInChI = INCHI_BAS; ------------------ | | 570| 5|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1908| 5| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 574| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 575| 7|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1908:16): [True: 3, False: 2] ------------------ 1909| 12| for (k = n = 0; k < num_components_D; k++) ------------------ | Branch (1909:21): [True: 7, False: 5] ------------------ 1910| 7| { 1911| 7| bMobileH = iMobileH; 1912| 7| if (!bInpInchiComponentExists(pOneInput, iInChI, bMobileH, k)) ------------------ | Branch (1912:13): [True: 2, False: 5] ------------------ 1913| 2| { 1914| 2| if (bInpInchiComponentExists(pOneInput, iInChI, TAUT_YES, k)) ------------------ | | 575| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1914:17): [True: 0, False: 2] ------------------ 1915| 0| { 1916| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1917| 0| } 1918| 2| else 1919| 2| { 1920| 2| continue; /* component is missing ??? (Deleted proton in Mobile-H layer) */ 1921| 2| } 1922| 2| } 1923| 5| if (0 > pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (1923:13): [True: 0, False: 5] ------------------ 1924| 0| { 1925| 0| continue; /* same as reconnected */ 1926| 0| } 1927| | /* the component exists in disconnected layer of the orig. InChI only: it is a fragment */ 1928| 5| pINChISort2[n].pINChI[bMobileH] = pOneInput->pInpInChI[iInChI][bMobileH] + k; 1929| 5| if (bMobileH == TAUT_NON && ------------------ | | 574| 10|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1929:13): [True: 3, False: 2] ------------------ 1930| 3| (bInpInchiComponentExists(pOneInput, iInChI, TAUT_YES, k) || ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1930:14): [True: 3, False: 0] ------------------ 1931| 0| bInpInchiComponentDeleted(pOneInput, iInChI, TAUT_YES, k))) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1931:17): [True: 0, False: 0] ------------------ 1932| 3| { 1933| 3| pINChISort2[n].pINChI[TAUT_YES] = pOneInput->pInpInChI[iInChI][TAUT_YES] + k; ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pINChISort2[n].pINChI[TAUT_YES] = pOneInput->pInpInChI[iInChI][TAUT_YES] + k; ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1934| 3| } 1935| | /* the last sort key is a number of removed protons */ 1936| 5| pINChISort2[n].ord_number = pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons ? ------------------ | | 575| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1936:37): [True: 0, False: 5] ------------------ 1937| 5| pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons[k].nNumRemovedProtons : 0; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1938| 5| pINChISort2[n].n1 = k; /* orig. InChI disconnected layer component number */ 1939| 5| pINChISort2[n].n2 = -1; /* no fragment index */ 1940| 5| n++; 1941| 5| } 1942| | 1943| | /* accumulate fragments from the reconstructed structure */ 1944| 5| iInChI = INCHI_REC; ------------------ | | 571| 5|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1945| 5| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 574| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 575| 7|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1945:16): [True: 3, False: 2] ------------------ 1946| 13| for (k = n = 0; k < num_components_R; k++) ------------------ | Branch (1946:21): [True: 8, False: 5] ------------------ 1947| 8| { 1948| 8| bMobileH = iMobileH; 1949| 8| if (!bInpInchiComponentExists(pOneInput, iInChI, bMobileH, k)) ------------------ | Branch (1949:13): [True: 4, False: 4] ------------------ 1950| 4| { 1951| 4| if (bInpInchiComponentExists(pOneInput, iInChI, TAUT_YES, k)) ------------------ | | 575| 4|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1951:17): [True: 1, False: 3] ------------------ 1952| 1| { 1953| 1| bMobileH = TAUT_YES; ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1954| 1| } 1955| 3| else 1956| 3| { 1957| 3| continue; /* component is missing ??? (Deleted proton in Mobile-H layer) */ 1958| 3| } 1959| 4| } 1960| | /* the reconstructed structure */ 1961| 5| if (0 < pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (1961:13): [True: 0, False: 5] ------------------ 1962| 0| { 1963| 0| continue; /* same as disconnected, has no metal atoms */ 1964| 0| } 1965| | /* this reconstructed structure was disconnected */ 1966| 5| pStruct1 = pStruct[iInChI][bMobileH] + k; 1967| 5| num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS]; ------------------ | | 570| 5|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1968| 5| ifInChI = INCHI_BAS; ------------------ | | 570| 5|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1969| 5| ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 574| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 575| 7|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1969:21): [True: 3, False: 2] ------------------ 1970| 10| for (i = 0; i < num_fragments; i++) ------------------ | Branch (1970:21): [True: 5, False: 5] ------------------ 1971| 5| { 1972| 5| bfMobileH = ifMobileH; 1973| 5| if (!bRevInchiComponentExists(pStruct1, ifInChI, bfMobileH, i)) ------------------ | Branch (1973:17): [True: 3, False: 2] ------------------ 1974| 3| { 1975| 3| if (bRevInchiComponentExists(pStruct1, ifInChI, TAUT_YES, i)) ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1975:21): [True: 3, False: 0] ------------------ 1976| 3| { 1977| 3| bfMobileH = TAUT_YES; ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1978| 3| } 1979| 0| else 1980| 0| { 1981| 0| continue; /* component is missing ??? */ 1982| 0| } 1983| 3| } 1984| 5| pINChISort1[n].pINChI[bfMobileH] = pStruct1->RevInChI.pINChI[ifInChI][i][bfMobileH]; 1985| 5| if (bfMobileH == TAUT_NON /*&& bRevInchiComponentExists( pStruct1, ifInChI, TAUT_YES, i )*/) ------------------ | | 574| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1985:17): [True: 0, False: 5] ------------------ 1986| 0| { 1987| 0| pINChISort1[n].pINChI[TAUT_YES] = pStruct1->RevInChI.pINChI[ifInChI][i][TAUT_YES]; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pINChISort1[n].pINChI[TAUT_YES] = pStruct1->RevInChI.pINChI[ifInChI][i][TAUT_YES]; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1988| | /* remove Fixed-H InChI if is is identical to Mobile-H */ 1989| | /* do it exactly same way the identical components were removed from InpInChI */ 1990| 0| if (!CompareReversedINChI(pINChISort1[n].pINChI[bfMobileH], ------------------ | Branch (1990:21): [True: 0, False: 0] ------------------ 1991| 0| pINChISort1[n].pINChI[TAUT_YES], NULL, NULL)) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1992| 0| { 1993| 0| pINChISort1[n].pINChI[bfMobileH] = NULL; /* remove Fixed-H layer */ 1994| 0| } 1995| 0| else 1996| 0| { 1997| 0| pINChISort1[n].ord_number = pStruct1->RevInChI.pINChI_Aux[ifInChI][i][TAUT_YES]->nNumRemovedProtons; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1998| 0| } 1999| 0| } 2000| | 2001| 5| pINChISort1[n].n1 = k; /* reconstructed reconnected structure component index */ 2002| 5| pINChISort1[n].n2 = i; /* index of a fragment made out of this component */ 2003| 5| n++; 2004| 5| } 2005| 5| } 2006| | 2007| | /* sort fragment InChI before comparing them */ 2008| 5| qsort(pINChISort1, num_fragments_D, sizeof(pINChISort1[0]), CompINChITaut2); 2009| 5| qsort(pINChISort2, num_fragments_R, sizeof(pINChISort2[0]), CompINChITaut2); 2010| | 2011| | /* compare fragments -- components present in disconnected layer only */ 2012| 10| for (iComponent = 0; iComponent < num_fragments_DR; iComponent++) ------------------ | Branch (2012:26): [True: 5, False: 5] ------------------ 2013| 5| { 2014| 5| INChI* pInChI1[TAUT_NUM]; /* from reversed structure */ 2015| 5| INChI* pInChI2[TAUT_NUM]; /* original input InChI */ 2016| 15| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 15|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2016:21): [True: 10, False: 5] ------------------ 2017| 10| { 2018| 10| pInChI1[i] = pINChISort1[iComponent].pINChI[i]; 2019| 10| pInChI2[i] = pINChISort2[iComponent].pINChI[i]; 2020| 10| } 2021| 5| CompareTwoPairsOfInChI(pInChI1, pInChI2, !bHasSomeFixedH, CompareInchiFlags); 2022| 5| } 2023| | 2024| 5| if ( /*nNumNonTaut1 && nNumNonTaut2 &&*/ bHasSomeFixedH) ------------------ | Branch (2024:46): [True: 3, False: 2] ------------------ 2025| 3| { 2026| 3| if (nNumCompHaveSeparateProtons_D || nNumCompHaveSeparateProtons_R) ------------------ | Branch (2026:13): [True: 0, False: 3] | Branch (2026:46): [True: 0, False: 3] ------------------ 2027| 0| { 2028| | /* for each component, compare number removed protons */ 2029| | /* comparison does not make sense if Disconnected Fixed-H layer is not present */ 2030| 0| for (iComponent = 0; iComponent < num_fragments_DR; iComponent++) ------------------ | Branch (2030:34): [True: 0, False: 0] ------------------ 2031| 0| { 2032| 0| NUM_H nNumRemovedIsotopicH1[NUM_H_ISOTOPES]; 2033| 0| NUM_H nNumRemovedIsotopicH2[NUM_H_ISOTOPES]; 2034| | 2035| 0| memset(nNumRemovedIsotopicH1, 0, sizeof(nNumRemovedIsotopicH1)); /* djb-rwth: memset_s C11/Annex K variant? */ 2036| 0| memset(nNumRemovedIsotopicH2, 0, sizeof(nNumRemovedIsotopicH2)); /* djb-rwth: memset_s C11/Annex K variant? */ 2037| | /* compare removed protons */ 2038| 0| if (pINChISort1[iComponent].ord_number != pINChISort2[iComponent].ord_number) ------------------ | Branch (2038:21): [True: 0, False: 0] ------------------ 2039| 0| { 2040| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; /* diff number of removed protons */ ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2041| 0| } 2042| | /* also compare removed isotopic atoms H */ 2043| 0| k = pINChISort2[iComponent].n1; /* input InChI, OneInput */ 2044| 0| if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2044:21): [True: 0, False: 0] ------------------ 2045| 0| { 2046| 0| memcpy(nNumRemovedIsotopicH2, 2047| 0| pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons[k].nNumRemovedIsotopicH, ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons[k].nNumRemovedIsotopicH, ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2048| 0| sizeof(nNumRemovedIsotopicH2)); 2049| 0| } 2050| | /* get fragments of reconstructed structure removed protons info */ 2051| 0| k = pINChISort1[iComponent].n1; /* restored component number */ 2052| 0| i = pINChISort1[iComponent].n2; /* subcomponent number */ 2053| 0| iInChI = INCHI_REC; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 2054| 0| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2054:28): [True: 0, False: 0] ------------------ 2055| 0| bMobileH = iMobileH; 2056| 0| if (!bInpInchiComponentExists(pOneInput, iInChI, bMobileH, k)) ------------------ | Branch (2056:21): [True: 0, False: 0] ------------------ 2057| 0| { 2058| 0| if (bInpInchiComponentExists(pOneInput, iInChI, TAUT_YES, k)) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2058:25): [True: 0, False: 0] ------------------ 2059| 0| { 2060| 0| bMobileH = TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2061| 0| } 2062| 0| else 2063| 0| { 2064| 0| goto compare_iso_H; 2065| 0| } 2066| 0| } 2067| 0| if (pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (2067:21): [True: 0, False: 0] ------------------ 2068| 0| { 2069| 0| continue; 2070| | /* 2071| | ret = RI_ERR_PROGR; 2072| | goto exit_function; 2073| | */ 2074| 0| } 2075| 0| pStruct1 = pStruct[iInChI][bMobileH] + k; 2076| 0| num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS]; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 2077| 0| ifInChI = INCHI_BAS; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 2078| 0| ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2078:29): [True: 0, False: 0] ------------------ 2079| 0| if (i < num_fragments) ------------------ | Branch (2079:21): [True: 0, False: 0] ------------------ 2080| 0| { 2081| 0| bfMobileH = ifMobileH; 2082| 0| if (!bRevInchiComponentExists(pStruct1, ifInChI, bfMobileH, i)) ------------------ | Branch (2082:25): [True: 0, False: 0] ------------------ 2083| 0| { 2084| 0| if (!bRevInchiComponentExists(pStruct1, ifInChI, TAUT_YES, i)) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2084:29): [True: 0, False: 0] ------------------ 2085| | /* djb-rwth: removing redundant code */ 2086| 0| { 2087| 0| goto compare_iso_H; 2088| 0| } 2089| 0| } 2090| 0| memcpy(nNumRemovedIsotopicH1, 2091| 0| pStruct1->RevInChI.pINChI_Aux[ifInChI][i][TAUT_YES]->nNumRemovedIsotopicH, ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2092| 0| sizeof(nNumRemovedIsotopicH1)); 2093| 0| } 2094| 0| compare_iso_H: 2095| 0| if (memcmp(nNumRemovedIsotopicH1, nNumRemovedIsotopicH2, sizeof(nNumRemovedIsotopicH1))) ------------------ | Branch (2095:21): [True: 0, False: 0] ------------------ 2096| 0| { 2097| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_REM_ISO_H; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2098| 0| } 2099| 0| } 2100| 0| } 2101| 3| } 2102| 2| else /*if ( !nNumNonTaut1 && !nNumNonTaut2 || !bHasSomeFixedH )*/ 2103| 2| { 2104| | /* compare totals for removed protons and isotopic H */ 2105| 2| if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedProtons != ------------------ | | 570| 2|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedProtons != ------------------ | | 575| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2105:13): [True: 0, False: 2] ------------------ 2106| 2| nNumRemovedProtons_R.nNumRemovedProtons) 2107| 0| { 2108| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2109| 0| } 2110| 2| if (memcmp(pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedIsotopicH, ------------------ | | 570| 2|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (memcmp(pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedIsotopicH, ------------------ | | 575| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2110:13): [True: 1, False: 1] ------------------ 2111| 2| nNumRemovedProtons_R.nNumRemovedIsotopicH, 2112| 2| sizeof(nNumRemovedProtons_R.nNumRemovedIsotopicH))) 2113| 1| { 2114| 1| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_REM_ISO_H; ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2115| 1| } 2116| 2| } 2117| | 2118| 5| if (!nNumNonTaut1 == !nNumNonTaut2) ------------------ | Branch (2118:9): [True: 2, False: 3] ------------------ 2119| 2| { 2120| 2| ; /* difference if(nNumNonTaut1 != nNumNonTaut2) will be caught in InChI comparison */ 2121| 2| } 2122| 3| else 2123| 3| { 2124| 3| if (nNumNonTaut1) ------------------ | Branch (2124:13): [True: 0, False: 3] ------------------ 2125| 0| { 2126| | /* reconstructed has Fixed-H while the original has not: extra Fixed-H layer */ 2127| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_WRONG_TAUT; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2128| 0| } 2129| 3| else 2130| 3| { 2131| | /* the original InChI has Fixed-H while the reconstructed one has not: missing Fixed-H layer */ 2132| 3| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_NO_TAUT; ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2133| 3| } 2134| 3| } 2135| 15| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 15|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2135:17): [True: 10, False: 5] ------------------ 2136| 10| { 2137| 10| pOneInput->CompareInchiFlags[1][i] |= CompareInchiFlags[i]; 2138| 10| } 2139| | 2140| | /* compare totals */ 2141| 5| if (nNumRemovedProtons_R.nNumRemovedProtons != nNumRemovedProtons_D.nNumRemovedProtons) ------------------ | Branch (2141:9): [True: 0, False: 5] ------------------ 2142| 0| { 2143| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; /* diff number of removed protons */ ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2144| 0| } 2145| 5| if (memcmp(nNumRemovedProtons_R.nNumRemovedIsotopicH, ------------------ | Branch (2145:9): [True: 1, False: 4] ------------------ 2146| 5| nNumRemovedProtons_D.nNumRemovedIsotopicH, 2147| 5| sizeof(nNumRemovedProtons_D.nNumRemovedIsotopicH))) 2148| 1| { 2149| 1| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_REM_ISO_H; ------------------ | | 575| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2150| 1| } 2151| | 2152| 5|exit_function: 2153| | 2154| 5| if (pINChISort1) ------------------ | Branch (2154:9): [True: 5, False: 0] ------------------ 2155| 5| { 2156| 5| inchi_free(pINChISort1); ------------------ | | 1152| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 5, False: 0] | | | Branch (1152:50): [Folded, False: 5] | | ------------------ ------------------ 2157| 5| } 2158| 5| if (pINChISort2) ------------------ | Branch (2158:9): [True: 5, False: 0] ------------------ 2159| 5| { 2160| 5| inchi_free(pINChISort2); ------------------ | | 1152| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 5, False: 0] | | | Branch (1152:50): [Folded, False: 5] | | ------------------ ------------------ 2161| 5| } 2162| | 2163| 5| return ret; 2164| 5|} CompareTwoPairsOfInChI: 2172| 5|{ 2173| 5| int iMobileH, err = 0; 2174| 5| INCHI_MODE cmp; 2175| 15| for (iMobileH = 0; iMobileH < TAUT_NUM; iMobileH++) ------------------ | | 573| 15|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2175:24): [True: 10, False: 5] ------------------ 2176| 10| { 2177| 10| if (!pInChI1[iMobileH] != !pInChI2[iMobileH]) ------------------ | Branch (2177:13): [True: 3, False: 7] ------------------ 2178| 3| { 2179| 3| if (iMobileH == TAUT_NON && ------------------ | | 574| 6|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2179:17): [True: 3, False: 0] ------------------ 2180| 3| pInChI1[TAUT_YES] && pInChI2[TAUT_YES]) /* djb-rwth: condition corrected */ ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pInChI1[TAUT_YES] && pInChI2[TAUT_YES]) /* djb-rwth: condition corrected */ ------------------ | | 575| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2180:17): [True: 3, False: 0] | Branch (2180:38): [True: 3, False: 0] ------------------ 2181| 3| { 2182| 3| CompareInchiFlags[iMobileH] |= INCHIDIFF_COMP_HLAYER; 2183| 3| } 2184| 0| else 2185| 0| { 2186| 0| CompareInchiFlags[iMobileH] |= INCHIDIFF_COMP_NUMBER; 2187| 0| } 2188| 3| continue; 2189| 3| } 2190| 7| if (pInChI1[iMobileH] && pInChI2[iMobileH]) ------------------ | Branch (2190:13): [True: 5, False: 2] | Branch (2190:34): [True: 5, False: 0] ------------------ 2191| 5| { 2192| 5| cmp = CompareReversedINChI3(pInChI1[iMobileH], pInChI2[iMobileH], NULL, NULL, &err); 2193| 5| if (cmp) ------------------ | Branch (2193:17): [True: 2, False: 3] ------------------ 2194| 2| { 2195| 2| CompareInchiFlags[iMobileH] |= cmp; 2196| 2| } 2197| 5| } 2198| 7| } 2199| | 2200| 5| return err; 2201| 5|} CompareOneOrigInchiToRevInChI: 2213| 48.8k|{ 2214| 48.8k| int ret, err = 0; 2215| 48.8k| INCHI_MODE cmp; 2216| | 2217| 48.8k| if (pStruct) /* djb-rwth: fixing coverity ID #499601 */ ------------------ | Branch (2217:9): [True: 48.8k, False: 0] ------------------ 2218| 48.8k| { 2219| 48.8k| ret = pStruct->RevInChI.nRetVal; 2220| 48.8k| } 2221| 0| else 2222| 0| { 2223| 0| ret = -1; 2224| 0| } 2225| | 2226| 48.8k| if ((ret == _IS_OKAY || ret == _IS_WARNING) && pStruct) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 10| 97.6k|#define _IS_OKAY 0 ------------------ if ((ret == _IS_OKAY || ret == _IS_WARNING) && pStruct) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 11| 9.10k|#define _IS_WARNING 1 ------------------ | Branch (2226:10): [True: 39.7k, False: 9.10k] | Branch (2226:29): [True: 9.10k, False: 0] | Branch (2226:52): [True: 48.8k, False: 0] ------------------ 2227| 48.8k| { 2228| | /* ignore bMobileH for now */ 2229| 48.8k| int i, i0, b /* created type */, b0 /* requested type*/, j, k; 2230| | /* pINChI[iINCHI][iComponent][bTaut] */ 2231| | /* i0 = requested Rec/Disconnected: 1/0 */ 2232| | /* i = what InChI creaded out of the restored structure */ 2233| | /* b0 = requested Mobile/Fixed-H: 1/0 */ 2234| | /* b = what InChI creaded out of the restored structure */ 2235| 48.8k| i = i0 = pStruct->iINCHI; 2236| 48.8k| b = b0 = pStruct->iMobileH; 2237| 48.8k| if (i == INCHI_REC && !pStruct->RevInChI.num_components[i]) ------------------ | | 571| 97.6k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (2237:13): [True: 6, False: 48.8k] | Branch (2237:31): [True: 6, False: 0] ------------------ 2238| 6| { 2239| 6| i = INCHI_BAS; ------------------ | | 570| 6|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 2240| 6| } 2241| 48.8k| if (b == TAUT_NON && (!pStruct->RevInChI.pINChI[i] || ------------------ | | 574| 97.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2241:13): [True: 1.61k, False: 47.2k] | Branch (2241:31): [True: 1.35k, False: 263] ------------------ 2242| 263| !pStruct->RevInChI.pINChI[i][0][b] || ------------------ | Branch (2242:13): [True: 0, False: 263] ------------------ 2243| 263| !pStruct->RevInChI.pINChI[i][0][b]->nNumberOfAtoms)) ------------------ | Branch (2243:13): [True: 165, False: 98] ------------------ 2244| 1.51k| { 2245| 1.51k| b = TAUT_YES; ------------------ | | 575| 1.51k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2246| 1.51k| } 2247| 48.8k| if (pStruct->bDeleted && (!pInChI[0] || pInChI[0]->bDeleted)) ------------------ | Branch (2247:13): [True: 1.35k, False: 47.4k] | Branch (2247:35): [True: 1.35k, False: 0] | Branch (2247:49): [True: 0, False: 0] ------------------ 2248| 1.35k| { 2249| 1.35k| return 0; 2250| 1.35k| } 2251| | 2252| 47.4k| if (pStruct->RevInChI.pINChI[i]) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (2252:13): [True: 47.4k, False: 0] ------------------ 2253| 47.4k| { 2254| 47.4k| if ((pStruct->RevInChI.num_components[i] > 1 && ------------------ | Branch (2254:18): [True: 775, False: 46.6k] ------------------ 2255| 775| !pStruct->RevInChI.pINChI[i][1][b]->bDeleted) || ------------------ | Branch (2255:17): [True: 693, False: 82] ------------------ 2256| 46.7k| pStruct->RevInChI.num_components[i] < 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2256:17): [True: 0, False: 46.7k] ------------------ 2257| 693| { 2258| 693| CompareInchiFlags[bMobileH] |= INCHIDIFF_COMP_NUMBER; 2259| 693| } 2260| 47.4k| } 2261| 47.4k| if (b != b0 || b != bMobileH || b0 != bMobileH || i > i0) ------------------ | Branch (2261:13): [True: 165, False: 47.3k] | Branch (2261:24): [True: 0, False: 47.3k] | Branch (2261:41): [True: 0, False: 47.3k] | Branch (2261:59): [True: 0, False: 47.3k] ------------------ 2262| 165| { 2263| | /* do not print messages about TAUT_YES instead of TAUT_NON */ 2264| 165| CompareInchiFlags[bMobileH] |= INCHIDIFF_COMP_HLAYER; 2265| 165| } 2266| | 2267| 47.4k| if (pStruct->RevInChI.num_components[i] && pStruct->RevInChI.pINChI[i]) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (2267:13): [True: 47.4k, False: 0] | Branch (2267:52): [True: 47.4k, False: 0] ------------------ 2268| 47.4k| { 2269| | /* compare InChI from restored structure; '0' in [i][0][b] is the first component */ 2270| 47.4k| if (b == TAUT_YES && pStruct->RevInChI.pINChI[i][0][b]->bDeleted && ( !pInChI[0] || pInChI[0]->bDeleted )) ------------------ | | 575| 94.9k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2270:17): [True: 47.3k, False: 98] | Branch (2270:34): [True: 132, False: 47.2k] | Branch (2270:83): [True: 130, False: 2] | Branch (2270:97): [True: 0, False: 2] ------------------ 2271| 130| { 2272| | /* the 1st component is made out of proton(s) and the input component is missing or also a proton */ 2273| 130| cmp = 0; 2274| 130| } 2275| 47.3k| else 2276| 47.3k| { 2277| 47.3k| cmp = CompareReversedINChI3( pStruct->RevInChI.pINChI[i][0][b], pInChI[0], NULL, NULL, &err ); 2278| 47.3k| if (cmp) ------------------ | Branch (2278:21): [True: 12.6k, False: 34.7k] ------------------ 2279| 12.6k| { 2280| 12.6k| CompareInchiFlags[bMobileH] |= cmp; 2281| 12.6k| } 2282| 47.3k| } 2283| 47.4k| if (b == b0 && b == TAUT_NON) ------------------ | | 574| 47.3k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2283:17): [True: 47.3k, False: 165] | Branch (2283:28): [True: 98, False: 47.2k] ------------------ 2284| 98| { 2285| 98| if ((pStruct->RevInChI.pINChI[i][0][TAUT_YES] && ------------------ | | 575| 98|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2285:22): [True: 98, False: 0] ------------------ 2286| 98| !pStruct->RevInChI.pINChI[i][0][TAUT_YES]->bDeleted) || ------------------ | | 575| 98|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2286:21): [True: 98, False: 0] ------------------ 2287| 0| (pInChI[1] && !pInChI[1]->bDeleted)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2287:22): [True: 0, False: 0] | Branch (2287:35): [True: 0, False: 0] ------------------ 2288| 98| { 2289| | /* in addition to fixed-H also compare mobile-H InChI */ 2290| 98| cmp = CompareReversedINChI3(pStruct->RevInChI.pINChI[i][0][TAUT_YES], pInChI[1], NULL, NULL, &err); ------------------ | | 575| 98|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2291| 98| if (cmp) ------------------ | Branch (2291:25): [True: 97, False: 1] ------------------ 2292| 97| { 2293| 97| CompareInchiFlags[TAUT_YES] |= cmp; ------------------ | | 575| 97|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2294| 97| } 2295| 98| } 2296| | /* compare removed H */ 2297| 98| if (pStruct->nNumRemovedProtonsMobHInChI != pStruct->RevInChI.pINChI_Aux[i][0][TAUT_YES]->nNumRemovedProtons) ------------------ | | 575| 98|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2297:21): [True: 76, False: 22] ------------------ 2298| 76| { 2299| 76| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; ------------------ | | 575| 76|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2300| 76| } 2301| 98| } 2302| 47.4k| memset(nCurRemovedProtons, 0, sizeof(*nCurRemovedProtons)); /* djb-rwth: memset_s C11/Annex K variant? */ 2303| 126k| for (k = 0; k < pStruct->RevInChI.num_components[i]; k++) ------------------ | Branch (2303:25): [True: 79.1k, False: 47.4k] ------------------ 2304| 79.1k| { 2305| 79.1k| if (!k || pStruct->RevInChI.pINChI[i][k][TAUT_YES]->bDeleted) ------------------ | | 575| 31.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2305:21): [True: 47.4k, False: 31.6k] | Branch (2305:27): [True: 30.9k, False: 698] ------------------ 2306| 78.4k| { 2307| | /* get removed protons from the 1st component; add othere only if they are deleted protons */ 2308| 78.4k| nCurRemovedProtons->nNumRemovedProtons += pStruct->RevInChI.pINChI_Aux[i][k][TAUT_YES]->nNumRemovedProtons; ------------------ | | 575| 78.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2309| 313k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 25| 313k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (2309:33): [True: 235k, False: 78.4k] ------------------ 2310| 235k| { 2311| 235k| nCurRemovedProtons->nNumRemovedIsotopicH[j] += pStruct->RevInChI.pINChI_Aux[i][k][TAUT_YES]->nNumRemovedIsotopicH[j]; ------------------ | | 575| 235k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2312| 235k| } 2313| 78.4k| } 2314| 79.1k| } 2315| 47.4k| } 2316| 47.4k| } 2317| 0| else 2318| 0| { 2319| 0| CompareInchiFlags[bMobileH] |= INCHIDIFF_STR2INCHI_ERR; 2320| 0| } 2321| | 2322| 47.4k| return err; 2323| 48.8k|} CompareReversedStereoINChI3: 2332| 38.7k|{ 2333| 38.7k| int ret = 0; 2334| 38.7k| int j1, j2, num_dif, num_extra_undf, num_miss_undf, num_in1_only, num_in2_only; /* djb-rwth: removing redundant variables */ 2335| 38.7k| int bAddSb = !(picr->num_sb_undef_in1_only + picr->num_sb_in1_only + picr->num_sb_in2_only); 2336| 38.7k| int bAddSc = !(picr->num_sc_undef_in1_only + picr->num_sc_in1_only + picr->num_sc_in2_only); 2337| | 2338| 38.7k| int nNumSc1 = s1 ? s1->nNumberOfStereoCenters : 0; ------------------ | Branch (2338:19): [True: 38.7k, False: 0] ------------------ 2339| 38.7k| int nNumSc2 = s2 ? s2->nNumberOfStereoCenters : 0; ------------------ | Branch (2339:19): [True: 570, False: 38.2k] ------------------ 2340| 38.7k| int nNumSb1 = s1 ? s1->nNumberOfStereoBonds : 0; ------------------ | Branch (2340:19): [True: 38.7k, False: 0] ------------------ 2341| 38.7k| int nNumSb2 = s2 ? s2->nNumberOfStereoBonds : 0; ------------------ | Branch (2341:19): [True: 570, False: 38.2k] ------------------ 2342| | 2343| 38.7k| if ((nNumSc1 || nNumSc2) && ------------------ | Branch (2343:10): [True: 79, False: 38.6k] | Branch (2343:21): [True: 39, False: 38.6k] ------------------ 2344| 118| (nNumSc1 != nNumSc2 || ------------------ | Branch (2344:10): [True: 104, False: 14] ------------------ 2345| 14| memcmp(s1->nNumber, s2->nNumber, nNumSc1 * sizeof(s1->nNumber[0])) || ------------------ | Branch (2345:13): [True: 2, False: 12] ------------------ 2346| 12| memcmp(s1->t_parity, s2->t_parity, nNumSc1 * sizeof(s1->t_parity[0])))) /* djb-rwth: condition corrected */ ------------------ | Branch (2346:13): [True: 8, False: 4] ------------------ 2347| 114| { 2348| | 2349| 114| num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; /* djb-rwth: removing redundant code */ 2350| 279| for (j1 = j2 = 0; j1 < nNumSc1 && j2 < nNumSc2; ) ------------------ | Branch (2350:27): [True: 210, False: 69] | Branch (2350:43): [True: 165, False: 45] ------------------ 2351| 165| { 2352| 165| if (s1->nNumber[j1] == s2->nNumber[j2]) ------------------ | Branch (2352:17): [True: 112, False: 53] ------------------ 2353| 112| { 2354| 112| if (s1->t_parity[j1] != s2->t_parity[j2]) ------------------ | Branch (2354:21): [True: 66, False: 46] ------------------ 2355| | /* djb-rwth: removing redundant code */ 2356| 66| { 2357| 66| num_dif++; 2358| 66| } 2359| 112| j1++; 2360| 112| j2++; 2361| 112| } 2362| 53| else 2363| 53| { 2364| 53| if (s1->nNumber[j1] < s2->nNumber[j2]) ------------------ | Branch (2364:21): [True: 51, False: 2] ------------------ 2365| 51| { 2366| 51| num_in1_only++; 2367| 51| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 51|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2367:25): [True: 28, False: 23] ------------------ 2368| 28| { 2369| 28| num_extra_undf++; 2370| 28| } 2371| 51| if (bAddSc) ------------------ | Branch (2371:25): [True: 51, False: 0] ------------------ 2372| 51| { 2373| 51| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 375| 51|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2373:29): [True: 51, False: 0] ------------------ 2374| 51| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2375| 51| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 51|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2375:29): [True: 28, False: 23] ------------------ 2376| 28| { 2377| 28| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 378| 28|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2377:33): [True: 28, False: 0] ------------------ 2378| 28| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2379| 28| } 2380| 51| } 2381| 51| j1++; 2382| 51| } 2383| 2| else 2384| 2| { 2385| 2| num_in2_only++; 2386| 2| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 2|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2386:25): [True: 1, False: 1] ------------------ 2387| 1| { 2388| 1| num_miss_undf++; 2389| 1| } 2390| 2| if (bAddSc) ------------------ | Branch (2390:25): [True: 2, False: 0] ------------------ 2391| 2| { 2392| 2| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 376| 2|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2392:29): [True: 2, False: 0] ------------------ 2393| 2| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2394| 2| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 2|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2394:29): [True: 1, False: 1] ------------------ 2395| 1| { 2396| 1| if (picr->num_sc_undef_in2_only < ICR_MAX_SC_UNDF) ------------------ | | 378| 1|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2396:33): [True: 1, False: 0] ------------------ 2397| 1| picr->sc_undef_in2_only[picr->num_sc_undef_in2_only++] = j1; 2398| 1| } 2399| 2| } 2400| 2| j2++; 2401| 2| } 2402| 53| } 2403| 165| } 2404| | 2405| 180| while (j1 < nNumSc1) ------------------ | Branch (2405:16): [True: 66, False: 114] ------------------ 2406| 66| { 2407| 66| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 66|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2407:17): [True: 57, False: 9] ------------------ 2408| 57| { 2409| 57| num_extra_undf++; 2410| 57| } 2411| 66| num_in1_only++; 2412| 66| if (bAddSc) ------------------ | Branch (2412:17): [True: 66, False: 0] ------------------ 2413| 66| { 2414| 66| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 375| 66|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2414:21): [True: 66, False: 0] ------------------ 2415| 66| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2416| 66| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 66|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2416:21): [True: 57, False: 9] ------------------ 2417| 57| { 2418| 57| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 378| 57|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2418:25): [True: 57, False: 0] ------------------ 2419| 57| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2420| 57| } 2421| 66| } 2422| 66| j1++; 2423| 66| } 2424| | 2425| 187| while (j2 < nNumSc2) ------------------ | Branch (2425:16): [True: 73, False: 114] ------------------ 2426| 73| { 2427| 73| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 73|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2427:17): [True: 11, False: 62] ------------------ 2428| 11| { 2429| 11| num_miss_undf++; 2430| 11| } 2431| 73| num_in2_only++; 2432| 73| if (bAddSc) ------------------ | Branch (2432:17): [True: 73, False: 0] ------------------ 2433| 73| { 2434| 73| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 376| 73|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2434:21): [True: 73, False: 0] ------------------ 2435| 73| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2436| 73| } 2437| 73| j2++; 2438| 73| } 2439| | 2440| 114| if (num_dif) ------------------ | Branch (2440:13): [True: 51, False: 63] ------------------ 2441| 51| { 2442| 51| ret |= INCHIDIFF_SC_PARITY; 2443| 51| } 2444| 114| if (num_in1_only) ------------------ | Branch (2444:13): [True: 64, False: 50] ------------------ 2445| 64| { 2446| 64| if (num_extra_undf) ------------------ | Branch (2446:17): [True: 51, False: 13] ------------------ 2447| 51| { 2448| 51| ret |= INCHIDIFF_SC_EXTRA_UNDF; 2449| 51| } 2450| 64| if (num_in1_only != num_extra_undf) ------------------ | Branch (2450:17): [True: 29, False: 35] ------------------ 2451| 29| { 2452| 29| ret |= INCHIDIFF_SC_EXTRA; 2453| 29| } 2454| 64| } 2455| 114| if (num_in2_only) ------------------ | Branch (2455:13): [True: 51, False: 63] ------------------ 2456| 51| { 2457| 51| if (num_miss_undf) ------------------ | Branch (2457:17): [True: 11, False: 40] ------------------ 2458| 11| { 2459| 11| ret |= INCHIDIFF_SC_MISS_UNDF; 2460| 11| } 2461| 51| if (num_in2_only != num_miss_undf) ------------------ | Branch (2461:17): [True: 43, False: 8] ------------------ 2462| 43| { 2463| 43| ret |= INCHIDIFF_SC_MISS; 2464| 43| } 2465| 51| } 2466| 114| } 2467| | 2468| 38.7k| if (s1 && s2 && (s2->nCompInv2Abs != 2) && s1->nCompInv2Abs != s2->nCompInv2Abs && s1->nCompInv2Abs && s2->nCompInv2Abs) ------------------ | Branch (2468:9): [True: 38.7k, False: 0] | Branch (2468:15): [True: 570, False: 38.2k] | Branch (2468:21): [True: 566, False: 4] | Branch (2468:48): [True: 27, False: 539] | Branch (2468:88): [True: 26, False: 1] | Branch (2468:108): [True: 0, False: 26] ------------------ 2469| 0| { 2470| 0| ret |= INCHIDIFF_SC_INV; /* 2007-07-13 DT: added (s2->nCompInv2Abs != 2) to fix bug reoprted by Yerin on 2007/02/28 */ 2471| | /* Bug description: falsely reported "Stereo centers/allenes: Falsely inverted" for /S2 or /S3 */ 2472| 0| } 2473| | 2474| 38.7k| if ((nNumSb1 || nNumSb2) && ------------------ | Branch (2474:10): [True: 66, False: 38.7k] | Branch (2474:21): [True: 113, False: 38.5k] ------------------ 2475| 179| (nNumSb1 != nNumSb2 || ------------------ | Branch (2475:10): [True: 159, False: 20] ------------------ 2476| 20| memcmp(s1->nBondAtom1, s2->nBondAtom1, nNumSb1 * sizeof(s1->nBondAtom1[0])) || ------------------ | Branch (2476:13): [True: 8, False: 12] ------------------ 2477| 12| memcmp(s1->nBondAtom2, s2->nBondAtom2, nNumSb1 * sizeof(s1->nBondAtom2[0])) || ------------------ | Branch (2477:13): [True: 0, False: 12] ------------------ 2478| 12| memcmp(s1->b_parity, s2->b_parity, nNumSb1 * sizeof(s1->b_parity[0])))) ------------------ | Branch (2478:13): [True: 2, False: 10] ------------------ 2479| 169| { 2480| | 2481| 169| num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; /* djb-rwth: removing redundant code */ 2482| 327| for (j1 = j2 = 0; j1 < nNumSb1 && j2 < nNumSb2; ) ------------------ | Branch (2482:27): [True: 191, False: 136] | Branch (2482:43): [True: 158, False: 33] ------------------ 2483| 158| { 2484| 158| if (s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && ------------------ | Branch (2484:17): [True: 60, False: 98] ------------------ 2485| 60| s1->nBondAtom2[j1] == s2->nBondAtom2[j2]) ------------------ | Branch (2485:17): [True: 52, False: 8] ------------------ 2486| 52| { 2487| 52| if (s1->b_parity[j1] != s2->b_parity[j2]) ------------------ | Branch (2487:21): [True: 25, False: 27] ------------------ 2488| | /* djb-rwth: removing redundant code */ 2489| 25| { 2490| 25| num_dif++; 2491| 25| } 2492| 52| j1++; 2493| 52| j2++; 2494| 52| } 2495| 106| else 2496| 106| { 2497| 106| if (s1->nBondAtom1[j1] < s2->nBondAtom1[j2] || ------------------ | Branch (2497:21): [True: 85, False: 21] ------------------ 2498| 21| (s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && s1->nBondAtom2[j1] < s2->nBondAtom2[j2])) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2498:22): [True: 8, False: 13] | Branch (2498:66): [True: 8, False: 0] ------------------ 2499| 93| { 2500| 93| num_in1_only++; 2501| 93| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 93|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2501:25): [True: 63, False: 30] ------------------ 2502| 63| { 2503| 63| num_extra_undf++; 2504| 63| } 2505| 93| if (bAddSb) ------------------ | Branch (2505:25): [True: 93, False: 0] ------------------ 2506| 93| { 2507| 93| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 373| 93|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2507:29): [True: 93, False: 0] ------------------ 2508| 93| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2509| 93| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 93|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2509:29): [True: 63, False: 30] ------------------ 2510| 63| { 2511| 63| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 63|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2511:33): [True: 63, False: 0] ------------------ 2512| 63| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2513| 63| } 2514| 93| } 2515| 93| j1++; 2516| 93| } 2517| 13| else 2518| 13| { 2519| 13| num_in2_only++; 2520| 13| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 13|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2520:25): [True: 8, False: 5] ------------------ 2521| 8| { 2522| 8| num_miss_undf++; 2523| 8| } 2524| 13| if (bAddSb) ------------------ | Branch (2524:25): [True: 13, False: 0] ------------------ 2525| 13| { 2526| 13| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 374| 13|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2526:29): [True: 13, False: 0] ------------------ 2527| 13| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2528| 13| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 13|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2528:29): [True: 8, False: 5] ------------------ 2529| 8| { 2530| 8| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 8|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2530:33): [True: 8, False: 0] ------------------ 2531| 8| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2532| 8| } 2533| 13| } 2534| 13| j2++; 2535| 13| } 2536| 106| } 2537| 158| } 2538| 287| while (j1 < nNumSb1) ------------------ | Branch (2538:16): [True: 118, False: 169] ------------------ 2539| 118| { 2540| 118| num_in1_only++; 2541| 118| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 118|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2541:17): [True: 110, False: 8] ------------------ 2542| 110| { 2543| 110| num_extra_undf++; 2544| 110| } 2545| 118| if (bAddSb) ------------------ | Branch (2545:17): [True: 118, False: 0] ------------------ 2546| 118| { 2547| 118| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 373| 118|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2547:21): [True: 118, False: 0] ------------------ 2548| 118| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2549| 118| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 222| 118|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2549:21): [True: 110, False: 8] ------------------ 2550| 110| { 2551| 110| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 110|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2551:25): [True: 110, False: 0] ------------------ 2552| 110| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2553| 110| } 2554| 118| } 2555| 118| j1++; 2556| 118| } 2557| 359| while (j2 < nNumSb2) ------------------ | Branch (2557:16): [True: 190, False: 169] ------------------ 2558| 190| { 2559| 190| num_in2_only++; 2560| 190| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 190|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2560:17): [True: 37, False: 153] ------------------ 2561| 37| { 2562| 37| num_miss_undf++; 2563| 37| } 2564| 190| if (bAddSb) ------------------ | Branch (2564:17): [True: 190, False: 0] ------------------ 2565| 190| { 2566| 190| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 374| 190|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2566:21): [True: 190, False: 0] ------------------ 2567| 190| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2568| 190| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 222| 190|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2568:21): [True: 37, False: 153] ------------------ 2569| 37| { 2570| 37| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 377| 37|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2570:25): [True: 37, False: 0] ------------------ 2571| 37| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2572| 37| } 2573| 190| } 2574| 190| j2++; 2575| 190| } 2576| 169| if (num_dif) ------------------ | Branch (2576:13): [True: 19, False: 150] ------------------ 2577| 19| { 2578| 19| ret |= INCHIDIFF_SB_PARITY; 2579| 19| } 2580| 169| if (num_in1_only) ------------------ | Branch (2580:13): [True: 50, False: 119] ------------------ 2581| 50| { 2582| 50| if (num_extra_undf) ------------------ | Branch (2582:17): [True: 45, False: 5] ------------------ 2583| 45| { 2584| 45| ret |= INCHIDIFF_SB_EXTRA_UNDF; 2585| 45| } 2586| 50| if (num_in1_only != num_extra_undf) ------------------ | Branch (2586:17): [True: 25, False: 25] ------------------ 2587| 25| { 2588| 25| ret |= INCHIDIFF_SB_EXTRA; 2589| 25| } 2590| 50| } 2591| 169| if (num_in2_only) ------------------ | Branch (2591:13): [True: 134, False: 35] ------------------ 2592| 134| { 2593| 134| if (num_miss_undf) ------------------ | Branch (2593:17): [True: 42, False: 92] ------------------ 2594| 42| { 2595| 42| ret |= INCHIDIFF_SB_MISS_UNDF; 2596| 42| } 2597| 134| if (num_in2_only != num_miss_undf) ------------------ | Branch (2597:17): [True: 102, False: 32] ------------------ 2598| 102| { 2599| 102| ret |= INCHIDIFF_SB_MISS; 2600| 102| } 2601| 134| } 2602| 169| } 2603| | 2604| 38.7k| return ret; 2605| 38.7k|} CompareReversedINChI3: 2614| 47.4k|{ 2615| 47.4k| INCHI_MODE ret = 0; 2616| 47.4k| INChI_Stereo* Stereo1 = NULL, * Stereo2 = NULL; 2617| 47.4k| int n1, n2, m, j, j1, j2, ret2, num_H1, num_H2; 2618| 47.4k| ICR icr; 2619| 47.4k| ICR* picr = &icr; 2620| | 2621| 47.4k| *err = 0; 2622| | 2623| 47.4k| memset(picr, 0, sizeof(*picr)); /* djb-rwth: memset_s C11/Annex K variant? */ 2624| | 2625| 47.4k| if (i1 == NULL && i2 == NULL) ------------------ | Branch (2625:9): [True: 0, False: 47.4k] | Branch (2625:23): [True: 0, False: 0] ------------------ 2626| 0| { 2627| 0| return 0; 2628| 0| } 2629| 47.4k| if ((i1 == NULL) ^ (i2 == NULL)) ------------------ | Branch (2629:9): [True: 0, False: 47.4k] ------------------ 2630| 0| { 2631| 0| ret |= INCHIDIFF_PROBLEM; /* one InChI exists while another doesn't */ 2632| 0| goto exit_function; 2633| 0| } 2634| | 2635| 47.4k| if (i1->nErrorCode == i2->nErrorCode) ------------------ | Branch (2635:9): [True: 47.4k, False: 0] ------------------ 2636| 47.4k| { 2637| 47.4k| if (i1->nErrorCode) ------------------ | Branch (2637:13): [True: 0, False: 47.4k] ------------------ 2638| 0| { 2639| 0| ret |= INCHIDIFF_PROBLEM; /* both InChI have same error codes */ 2640| 0| goto exit_function; 2641| 0| } 2642| 47.4k| } 2643| 0| else 2644| 0| { 2645| 0| ret |= INCHIDIFF_PROBLEM; /* at least one InChI has an error code */ 2646| 0| goto exit_function; 2647| 0| } 2648| | 2649| 47.4k| if (i1->nNumberOfAtoms != i2->nNumberOfAtoms) ------------------ | Branch (2649:9): [True: 5.21k, False: 42.2k] ------------------ 2650| 5.21k| { 2651| 5.21k| ret |= INCHIDIFF_NUM_AT; 2652| 5.21k| goto exit_function; 2653| 5.21k| } 2654| 42.2k| if (i1->nNumberOfAtoms > 0) ------------------ | Branch (2654:9): [True: 42.2k, False: 0] ------------------ 2655| 42.2k| { 2656| 42.2k| if (memcmp(i1->nAtom, i2->nAtom, i1->nNumberOfAtoms * sizeof(i1->nAtom[0]))) ------------------ | Branch (2656:13): [True: 76, False: 42.1k] ------------------ 2657| 76| { 2658| 76| ret |= INCHIDIFF_ATOMS; 2659| 76| goto exit_function; 2660| 76| } 2661| | /* INCHIDIFF_NON_TAUT_H, INCHIDIFF_MORE_FH, INCHIDIFF_LESS_FH */ 2662| 42.1k| if (memcmp(i1->nNum_H, i2->nNum_H, i1->nNumberOfAtoms * sizeof(i1->nNum_H[0]))) ------------------ | Branch (2662:13): [True: 448, False: 41.7k] ------------------ 2663| 448| { 2664| 448| ret |= INCHIDIFF_POSITION_H; 2665| 2.71k| for (j1 = 0; j1 < i1->nNumberOfAtoms; j1++) ------------------ | Branch (2665:26): [True: 2.27k, False: 448] ------------------ 2666| 2.27k| { 2667| 2.27k| if (i1->nNum_H[j1] != i2->nNum_H[j1] && picr->num_diff_pos_H < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 499|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2667:21): [True: 499, False: 1.77k] | Branch (2667:57): [True: 499, False: 0] ------------------ 2668| 499| { 2669| 499| picr->diff_pos_H_at[picr->num_diff_pos_H] = j1; 2670| 499| picr->diff_pos_H_nH[picr->num_diff_pos_H] = i1->nNum_H[j1] - i2->nNum_H[j1]; 2671| 499| picr->num_diff_pos_H++; 2672| 499| } 2673| 2.27k| } 2674| 448| } 2675| | /* fixed H */ 2676| 42.1k| if (i1->nNum_H_fixed || i2->nNum_H_fixed) ------------------ | Branch (2676:13): [True: 42.1k, False: 0] | Branch (2676:33): [True: 0, False: 0] ------------------ 2677| 42.1k| { 2678| 42.1k| int bHasFixedH1 = 0, bHasFixedH2 = 0, i; 2679| 42.1k| if (i1->nNum_H_fixed) ------------------ | Branch (2679:17): [True: 42.1k, False: 0] ------------------ 2680| 42.1k| { 2681| 113k| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2681:29): [True: 70.9k, False: 42.1k] ------------------ 2682| 70.9k| { 2683| 70.9k| if (i1->nNum_H_fixed[i]) ------------------ | Branch (2683:25): [True: 60, False: 70.8k] ------------------ 2684| 60| { 2685| 60| bHasFixedH1++; 2686| 60| } 2687| 70.9k| } 2688| 42.1k| } 2689| 42.1k| if (i2->nNum_H_fixed) ------------------ | Branch (2689:17): [True: 88, False: 42.0k] ------------------ 2690| 88| { 2691| 603| for (i = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (2691:29): [True: 515, False: 88] ------------------ 2692| 515| { 2693| 515| if (i2->nNum_H_fixed[i]) ------------------ | Branch (2693:25): [True: 64, False: 451] ------------------ 2694| 64| { 2695| 64| bHasFixedH2++; 2696| 64| } 2697| 515| } 2698| 88| } 2699| 42.1k| if (bHasFixedH1 && !bHasFixedH2) ------------------ | Branch (2699:17): [True: 48, False: 42.1k] | Branch (2699:32): [True: 34, False: 14] ------------------ 2700| 34| { 2701| 199| for (i = j = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2701:33): [True: 165, False: 34] ------------------ 2702| 165| { 2703| 165| if (i1->nNum_H_fixed[i]) ------------------ | Branch (2703:25): [True: 45, False: 120] ------------------ 2704| 45| { 2705| 45| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 45|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2705:29): [True: 45, False: 0] ------------------ 2706| 45| { 2707| 45| picr->fixed_H_at1_more[j] = i; 2708| 45| picr->fixed_H_nH1_more[j] = i1->nNum_H_fixed[i]; 2709| 45| j++; 2710| 45| } 2711| 45| } 2712| 165| } 2713| 34| picr->num_fixed_H1_more = j; 2714| 34| ret |= INCHIDIFF_MORE_FH; /* Extra Fixed-H */ 2715| 34| } 2716| 42.1k| else 2717| 42.1k| { 2718| 42.1k| if (!bHasFixedH1 && bHasFixedH2) ------------------ | Branch (2718:21): [True: 42.1k, False: 14] | Branch (2718:37): [True: 18, False: 42.0k] ------------------ 2719| 18| { 2720| 108| for (i = j = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (2720:37): [True: 90, False: 18] ------------------ 2721| 90| { 2722| 90| if (i2->nNum_H_fixed[i]) ------------------ | Branch (2722:29): [True: 36, False: 54] ------------------ 2723| 36| { 2724| 36| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 36|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2724:33): [True: 36, False: 0] ------------------ 2725| 36| { 2726| 36| picr->fixed_H_at2_more[j] = i; 2727| 36| picr->fixed_H_nH2_more[j] = i2->nNum_H_fixed[i]; 2728| 36| j++; 2729| 36| } 2730| 36| } 2731| 90| } 2732| 18| picr->num_fixed_H2_more = j; 2733| 18| ret |= INCHIDIFF_LESS_FH; /* Missed Fixed-H */ 2734| 18| } 2735| 42.1k| else 2736| 42.1k| { 2737| 42.1k| if (bHasFixedH1 && bHasFixedH2 && ------------------ | Branch (2737:25): [True: 14, False: 42.0k] | Branch (2737:40): [True: 14, False: 0] ------------------ 2738| 14| memcmp(i1->nNum_H_fixed, i2->nNum_H_fixed, i1->nNumberOfAtoms * sizeof(i1->nNum_H_fixed[0]))) ------------------ | Branch (2738:25): [True: 13, False: 1] ------------------ 2739| 13| { 2740| 92| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2740:47): [True: 79, False: 13] ------------------ 2741| 79| { 2742| 79| if (i1->nNum_H_fixed[i] > i2->nNum_H_fixed[i]) ------------------ | Branch (2742:33): [True: 15, False: 64] ------------------ 2743| 15| { 2744| 15| if (j1 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 15|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2744:37): [True: 15, False: 0] ------------------ 2745| 15| { 2746| 15| picr->fixed_H_at1_more[j1] = i; 2747| 15| picr->fixed_H_nH1_more[j1] = i1->nNum_H_fixed[i] - i2->nNum_H_fixed[i]; 2748| 15| j1++; 2749| 15| } 2750| 15| } 2751| 64| else 2752| 64| if (i1->nNum_H_fixed[i] < i2->nNum_H_fixed[i]) ------------------ | Branch (2752:37): [True: 7, False: 57] ------------------ 2753| 7| { 2754| 7| if (j2 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 372| 7|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2754:41): [True: 7, False: 0] ------------------ 2755| 7| { 2756| 7| picr->fixed_H_at2_more[j2] = i; 2757| 7| picr->fixed_H_nH2_more[j2] = i2->nNum_H_fixed[i] - i1->nNum_H_fixed[i]; 2758| 7| j2++; 2759| 7| } 2760| 7| } 2761| 79| } 2762| 13| ret |= (j1 ? INCHIDIFF_MORE_FH : 0) | (j2 ? INCHIDIFF_LESS_FH : 0); ------------------ | Branch (2762:33): [True: 12, False: 1] | Branch (2762:64): [True: 6, False: 7] ------------------ 2763| 13| picr->num_fixed_H1_more = j1; 2764| 13| picr->num_fixed_H2_more = j2; 2765| 13| } 2766| 42.1k| } 2767| 42.1k| } 2768| 42.1k| } 2769| 42.1k| } 2770| | 2771| | /* compare formulas and H */ 2772| 42.1k| num_H1 = 0; 2773| 42.1k| num_H2 = 0; 2774| 42.1k| ret2 = CompareHillFormulasNoH(i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2); 2775| 42.1k| picr->tot_num_H1 = num_H1; 2776| 42.1k| picr->tot_num_H2 = num_H2; 2777| 42.1k| if (ret2) ------------------ | Branch (2777:9): [True: 3.00k, False: 39.1k] ------------------ 2778| 3.00k| { 2779| 3.00k| ret |= INCHIDIFF_NUM_EL; 2780| 3.00k| goto exit_function; 2781| 3.00k| } 2782| 39.1k| if (num_H1 > num_H2) ------------------ | Branch (2782:9): [True: 3.66k, False: 35.4k] ------------------ 2783| 3.66k| { 2784| 3.66k| ret |= INCHIDIFF_MORE_H; 2785| 3.66k| } 2786| 39.1k| if (num_H1 < num_H2) ------------------ | Branch (2786:9): [True: 125, False: 39.0k] ------------------ 2787| 125| { 2788| 125| ret |= INCHIDIFF_LESS_H; 2789| 125| } 2790| | 2791| 39.1k| if (i1->lenConnTable != i2->lenConnTable) ------------------ | Branch (2791:9): [True: 369, False: 38.7k] ------------------ 2792| 369| { 2793| 369| ret |= INCHIDIFF_CON_LEN; 2794| 369| goto exit_function; 2795| 369| } 2796| 38.7k| else 2797| 38.7k| { 2798| 38.7k| if (i1->lenConnTable > 0 && memcmp(i1->nConnTable, i2->nConnTable, i1->lenConnTable * sizeof(i1->nConnTable[0]))) ------------------ | Branch (2798:13): [True: 38.7k, False: 0] | Branch (2798:37): [True: 1, False: 38.7k] ------------------ 2799| 1| { 2800| 1| ret |= INCHIDIFF_CON_TBL; 2801| 1| goto exit_function; 2802| 1| } 2803| 38.7k| } 2804| | /* output special cases: different number of t-groups, different sizes of t-groups, different endpoints */ 2805| | /* in isotopic or deprotonated cases i1->lenTautomer == 1 && i1->nTautomer[0] = 0 */ 2806| | /* 2807| | if ( i1->lenTautomer != i2->lenTautomer && (i1->lenTautomer > 1 || i2->lenTautomer > 1) ) 2808| | { 2809| | ret |= INCHIDIFF_TAUT_LEN; 2810| | } 2811| | */ 2812| | 2813| | /* compare number of t-groups */ 2814| 38.7k| n1 = i1->lenTautomer ? i1->nTautomer[0] : 0; ------------------ | Branch (2814:10): [True: 612, False: 38.1k] ------------------ 2815| 38.7k| n2 = i2->lenTautomer ? i2->nTautomer[0] : 0; ------------------ | Branch (2815:10): [True: 213, False: 38.5k] ------------------ 2816| 38.7k| if (!n1 && n2) ------------------ | Branch (2816:9): [True: 38.5k, False: 232] | Branch (2816:16): [True: 118, False: 38.4k] ------------------ 2817| 118| { 2818| 118| ret |= INCHIDIFF_NO_TAUT; 2819| 118| } 2820| 38.6k| else 2821| 38.6k| { 2822| 38.6k| if (n1 && !n2) ------------------ | Branch (2822:13): [True: 232, False: 38.4k] | Branch (2822:19): [True: 137, False: 95] ------------------ 2823| 137| { 2824| 137| ret |= INCHIDIFF_WRONG_TAUT; 2825| 137| } 2826| 38.5k| else 2827| 38.5k| { 2828| 38.5k| if (n1 == 1 && n2 > 1) ------------------ | Branch (2828:17): [True: 88, False: 38.4k] | Branch (2828:28): [True: 4, False: 84] ------------------ 2829| 4| { 2830| 4| ret |= INCHIDIFF_SINGLE_TG; 2831| 4| } 2832| 38.5k| else 2833| 38.5k| { 2834| 38.5k| if (n1 > 1 && n2 == 1) ------------------ | Branch (2834:21): [True: 7, False: 38.5k] | Branch (2834:31): [True: 5, False: 2] ------------------ 2835| 5| { 2836| 5| ret |= INCHIDIFF_MULTIPLE_TG; 2837| 5| } 2838| 38.5k| else 2839| 38.5k| { 2840| 38.5k| if (n1 != n2) ------------------ | Branch (2840:25): [True: 1, False: 38.5k] ------------------ 2841| 1| { 2842| 1| ret |= INCHIDIFF_NUM_TG; 2843| 1| } 2844| 38.5k| } 2845| 38.5k| } 2846| 38.5k| } 2847| 38.6k| } 2848| | 2849| 38.7k| if (n1 || n2) ------------------ | Branch (2849:9): [True: 232, False: 38.5k] | Branch (2849:15): [True: 118, False: 38.4k] ------------------ 2850| 350| { 2851| | /* number of endpoints */ 2852| 350| int num1 = 0, num2 = 0, num_M1 = 0, num_M2 = 0; 2853| 350| int len, num_eq, num_in1_only, num_in2_only; 2854| 350| AT_NUMB* pe1 = (AT_NUMB*)inchi_malloc(((long long)i1->lenTautomer + 1) * sizeof(pe1[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 350|#define inchi_malloc malloc ------------------ 2855| 350| AT_NUMB* pe2 = (AT_NUMB*)inchi_malloc(((long long)i2->lenTautomer + 1) * sizeof(pe2[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 350|#define inchi_malloc malloc ------------------ 2856| 350| num_H1 = num_H2 = 0; 2857| | /* collect endpoints, H, (-) */ 2858| 350| if (!pe1 || !pe2) ------------------ | Branch (2858:13): [True: 0, False: 350] | Branch (2858:21): [True: 0, False: 350] ------------------ 2859| 0| { 2860| 0| if (pe1) inchi_free(pe1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ | Branch (2860:17): [True: 0, False: 0] ------------------ 2861| 0| if (pe2) inchi_free(pe2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ | Branch (2861:17): [True: 0, False: 0] ------------------ 2862| 0| *err = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 15| 0|#define RI_ERR_ALLOC (-1) ------------------ 2863| 0| goto exit_function; 2864| 0| } 2865| 592| for (m = 1; m < i1->lenTautomer; m += len) ------------------ | Branch (2865:21): [True: 242, False: 350] ------------------ 2866| 242| { 2867| 242| len = i1->nTautomer[m++]; 2868| 242| num_H1 += i1->nTautomer[m]; 2869| 242| num_M1 += i1->nTautomer[m + 1]; 2870| 793| for (j = 2; j < len; j++) ------------------ | Branch (2870:25): [True: 551, False: 242] ------------------ 2871| 551| { 2872| 551| pe1[num1++] = i1->nTautomer[m + j]; 2873| 551| } 2874| 242| } 2875| 573| for (m = 1; m < i2->lenTautomer; m += len) ------------------ | Branch (2875:21): [True: 223, False: 350] ------------------ 2876| 223| { 2877| 223| len = i2->nTautomer[m++]; 2878| 223| num_H2 += i2->nTautomer[m]; 2879| 223| num_M2 += i2->nTautomer[m + 1]; 2880| 692| for (j = 2; j < len; j++) ------------------ | Branch (2880:25): [True: 469, False: 223] ------------------ 2881| 469| { 2882| 469| pe2[num2++] = i2->nTautomer[m + j]; 2883| 469| } 2884| 223| } 2885| 350| picr->num_taut_H1 = num_H1; 2886| 350| picr->num_taut_H2 = num_H2; 2887| 350| picr->num_taut_M1 = num_M1; 2888| 350| picr->num_taut_M2 = num_M2; 2889| | /* sort endpoints */ 2890| 350| insertions_sort_AT_NUMB(pe1, num1); 2891| 350| insertions_sort_AT_NUMB(pe2, num2); 2892| | /* compare */ 2893| | /* 2894| | if ( num1 < num2 ) { 2895| | ret |= INCHIDIFF_LESS_TG_ENDP; 2896| | } else 2897| | if ( num1 > num2 ) { 2898| | ret |= INCHIDIFF_MORE_TG_ENDP; 2899| | } 2900| | */ 2901| | /* compare all */ 2902| 350| num_eq = num_in1_only = num_in2_only = 0; 2903| 612| for (j1 = j2 = 0; j1 < num1 && j2 < num2; ) ------------------ | Branch (2903:27): [True: 450, False: 162] | Branch (2903:40): [True: 262, False: 188] ------------------ 2904| 262| { 2905| 262| if (pe1[j1] == pe2[j2]) ------------------ | Branch (2905:17): [True: 102, False: 160] ------------------ 2906| 102| { 2907| 102| j1++; 2908| 102| j2++; 2909| 102| num_eq++; 2910| 102| } 2911| 160| else 2912| 160| { 2913| 160| if (pe1[j1] < pe2[j1]) ------------------ | Branch (2913:21): [True: 34, False: 126] ------------------ 2914| 34| { 2915| 34| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 370| 34|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (2915:25): [True: 34, False: 0] ------------------ 2916| 34| { 2917| 34| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 2918| 34| } 2919| 34| j1++; 2920| 34| num_in1_only++; 2921| 34| } 2922| 126| else 2923| 126| { 2924| 126| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 371| 126|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (2924:25): [True: 126, False: 0] ------------------ 2925| 126| { 2926| 126| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 2927| 126| } 2928| 126| j2++; 2929| 126| num_in2_only++; 2930| 126| } 2931| 160| } 2932| 262| } 2933| 765| while (j1 < num1) ------------------ | Branch (2933:16): [True: 415, False: 350] ------------------ 2934| 415| { 2935| 415| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 370| 415|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (2935:17): [True: 415, False: 0] ------------------ 2936| 415| { 2937| 415| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 2938| 415| } 2939| 415| j1++; 2940| 415| num_in1_only++; 2941| 415| } 2942| 591| while (j2 < num2) ------------------ | Branch (2942:16): [True: 241, False: 350] ------------------ 2943| 241| { 2944| 241| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 371| 241|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (2944:17): [True: 241, False: 0] ------------------ 2945| 241| { 2946| 241| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 2947| 241| } 2948| 241| j2++; 2949| 241| num_in2_only++; 2950| 241| } 2951| 350| if (num_in1_only) ------------------ | Branch (2951:13): [True: 213, False: 137] ------------------ 2952| 213| { 2953| 213| ret |= INCHIDIFF_EXTRA_TG_ENDP; 2954| 213| } 2955| 350| if (num_in2_only) ------------------ | Branch (2955:13): [True: 181, False: 169] ------------------ 2956| 181| { 2957| 181| ret |= INCHIDIFF_MISS_TG_ENDP; 2958| 181| } 2959| 350| if (!num_in1_only && !num_in2_only && num_eq) ------------------ | Branch (2959:13): [True: 137, False: 213] | Branch (2959:30): [True: 9, False: 128] | Branch (2959:47): [True: 9, False: 0] ------------------ 2960| 9| { 2961| 9| ; /* same t-groups endpoints */ 2962| 9| } 2963| 341| else 2964| 341| { 2965| 341| ret |= INCHIDIFF_DIFF_TG_ENDP; 2966| 341| } 2967| 350| inchi_free(pe1); ------------------ | | 1152| 350|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 350, False: 0] | | | Branch (1152:50): [Folded, False: 350] | | ------------------ ------------------ 2968| 350| inchi_free(pe2); ------------------ | | 1152| 350|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 350, False: 0] | | | Branch (1152:50): [Folded, False: 350] | | ------------------ ------------------ 2969| 350| } 2970| | 2971| 38.7k| if ((i1->lenTautomer > 1 && i2->lenTautomer > 1) && ------------------ | Branch (2971:10): [True: 232, False: 38.5k] | Branch (2971:33): [True: 95, False: 137] ------------------ 2972| 95| (i1->lenTautomer != i2->lenTautomer || ------------------ | Branch (2972:10): [True: 67, False: 28] ------------------ 2973| 28| memcmp(i1->nTautomer, i2->nTautomer, i1->lenTautomer * sizeof(i1->nTautomer[0])))) ------------------ | Branch (2973:13): [True: 27, False: 1] ------------------ 2974| 94| ret |= INCHIDIFF_TG; 2975| | 2976| 38.7k| if (i1->nNumberOfIsotopicAtoms != i2->nNumberOfIsotopicAtoms) ------------------ | Branch (2976:9): [True: 64, False: 38.7k] ------------------ 2977| 64| { 2978| 64| ret |= INCHIDIFF_NUM_ISO_AT; 2979| 64| } 2980| 38.7k| else 2981| 38.7k| { 2982| 38.7k| if (i1->nNumberOfIsotopicAtoms > 0 && memcmp(i1->IsotopicAtom, i2->IsotopicAtom, i1->nNumberOfIsotopicAtoms * sizeof(i1->IsotopicAtom[0]))) ------------------ | Branch (2982:13): [True: 91, False: 38.6k] | Branch (2982:47): [True: 42, False: 49] ------------------ 2983| 42| { 2984| 42| ret |= INCHIDIFF_ISO_AT; 2985| 42| } 2986| 38.7k| } 2987| 38.7k| if (i1->nTotalCharge != i2->nTotalCharge) ------------------ | Branch (2987:9): [True: 670, False: 38.1k] ------------------ 2988| 670| ret |= INCHIDIFF_CHARGE; 2989| 38.7k| if (a1 && a1->nNumRemovedProtons && (!a2 || a2->nNumRemovedProtons != a1->nNumRemovedProtons)) ------------------ | Branch (2989:9): [True: 0, False: 38.7k] | Branch (2989:15): [True: 0, False: 0] | Branch (2989:42): [True: 0, False: 0] | Branch (2989:49): [True: 0, False: 0] ------------------ 2990| 0| { 2991| 0| ret |= INCHIDIFF_REM_PROT; 2992| 0| } 2993| 38.7k| if (a1 && (!a2 || ------------------ | Branch (2993:9): [True: 0, False: 38.7k] | Branch (2993:16): [True: 0, False: 0] ------------------ 2994| 0| a2->nNumRemovedIsotopicH[0] != a1->nNumRemovedIsotopicH[0] || ------------------ | Branch (2994:9): [True: 0, False: 0] ------------------ 2995| 0| a2->nNumRemovedIsotopicH[1] != a1->nNumRemovedIsotopicH[1] || ------------------ | Branch (2995:9): [True: 0, False: 0] ------------------ 2996| 0| a2->nNumRemovedIsotopicH[2] != a1->nNumRemovedIsotopicH[2])) ------------------ | Branch (2996:9): [True: 0, False: 0] ------------------ 2997| 0| { 2998| 0| ret |= INCHIDIFF_REM_ISO_H; 2999| 0| } 3000| | 3001| | /* 3002| | if ( i1->nPossibleLocationsOfIsotopicH && i2->nPossibleLocationsOfIsotopicH ) { 3003| | if ( i1->nPossibleLocationsOfIsotopicH[0] != i2->nPossibleLocationsOfIsotopicH[0] || 3004| | memcmp(i1->nPossibleLocationsOfIsotopicH, i2->nPossibleLocationsOfIsotopicH, 3005| | sizeof(i1->nPossibleLocationsOfIsotopicH[0])*i1->nPossibleLocationsOfIsotopicH[0]) ) 3006| | return 18; 3007| | } else 3008| | if ( !i1->nPossibleLocationsOfIsotopicH != !i2->nPossibleLocationsOfIsotopicH ) { 3009| | return 19; 3010| | } 3011| | */ 3012| 38.7k| if (i1->StereoIsotopic && ------------------ | Branch (3012:9): [True: 105, False: 38.6k] ------------------ 3013| 105| i1->StereoIsotopic->nNumberOfStereoBonds + i1->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3013:9): [True: 24, False: 81] ------------------ 3014| 24| { 3015| 24| Stereo1 = i1->StereoIsotopic; 3016| 24| } 3017| 38.7k| else 3018| 38.7k| { 3019| 38.7k| Stereo1 = i1->Stereo; 3020| 38.7k| } 3021| 38.7k| if (i2->StereoIsotopic && ------------------ | Branch (3021:9): [True: 217, False: 38.5k] ------------------ 3022| 217| i2->StereoIsotopic->nNumberOfStereoBonds + i2->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3022:9): [True: 54, False: 163] ------------------ 3023| 54| { 3024| 54| Stereo2 = i2->StereoIsotopic; 3025| 54| } 3026| 38.7k| else 3027| 38.7k| { 3028| 38.7k| Stereo2 = i2->Stereo; 3029| 38.7k| } 3030| 38.7k| ret |= CompareReversedStereoINChI3(Stereo1, Stereo2, picr); 3031| | 3032| 47.4k|exit_function: 3033| 47.4k| picr->flags = ret; 3034| | 3035| 47.4k| return ret; 3036| 38.7k|} AddOneMsg: 3108| 15.0k|{ 3109| 15.0k| const char ellip[] = "..."; 3110| 15.0k| int len = (int)strlen(szAddMsg); 3111| 15.0k| int len_delim = (used_len && szDelim) ? strlen(szDelim) : 0; ------------------ | Branch (3111:22): [True: 10.1k, False: 4.91k] | Branch (3111:34): [True: 542, False: 9.57k] ------------------ 3112| 15.0k| int len_to_copy; 3113| 15.0k| if (len + len_delim + used_len < tot_len) ------------------ | Branch (3113:9): [True: 15.0k, False: 0] ------------------ 3114| 15.0k| { 3115| 15.0k| if (len_delim) ------------------ | Branch (3115:13): [True: 542, False: 14.4k] ------------------ 3116| 542| { 3117| 542| strcpy(szMsg + used_len, szDelim); 3118| 542| used_len += len_delim; 3119| 542| } 3120| 15.0k| strcpy(szMsg + used_len, szAddMsg); 3121| 15.0k| used_len += len; 3122| 15.0k| } 3123| 0| else 3124| 0| { 3125| 0| if ((len_to_copy = (tot_len - used_len - len_delim - (int)sizeof(ellip))) > 10) ------------------ | Branch (3125:13): [True: 0, False: 0] ------------------ 3126| 0| { 3127| 0| if (len_delim) ------------------ | Branch (3127:17): [True: 0, False: 0] ------------------ 3128| 0| { 3129| 0| strcpy(szMsg + used_len, szDelim); 3130| 0| used_len += len_delim; 3131| 0| } 3132| 0| strncpy(szMsg + used_len, szAddMsg, len_to_copy); 3133| 0| used_len += len_to_copy; 3134| 0| strcpy(szMsg + used_len, ellip); 3135| 0| used_len += sizeof(ellip) - 1; 3136| 0| } 3137| 0| } 3138| | 3139| 15.0k| return used_len; 3140| 15.0k|} FillOutCompareMessage: 3145| 1.75k|{ 3146| 1.75k| int bMobileH, k, n, len = (int)strlen(szMsg); 3147| 1.75k| int iPrevGrpIdx, iCurGrpIdx, bFound; 3148| 1.75k| INCHI_MODE bit; 3149| 1.75k| static const char* hdr = " Problems/mismatches:"; 3150| 1.75k| char szOneMsg[256]; 3151| | 3152| 1.75k| int mismatch = 0; 3153| | 3154| 1.75k| if (bits[TAUT_YES] || bits[TAUT_NON]) ------------------ | | 575| 1.75k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (bits[TAUT_YES] || bits[TAUT_NON]) ------------------ | | 574| 446|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3154:9): [True: 1.31k, False: 446] | Branch (3154:27): [True: 165, False: 281] ------------------ 3155| 1.47k| { 3156| | 3157| 1.47k| mismatch = -1; 3158| | 3159| 1.47k| if (!strstr(szMsg, hdr)) ------------------ | Branch (3159:13): [True: 1.47k, False: 2] ------------------ 3160| 1.47k| { 3161| 1.47k| len = AddOneMsg(szMsg, len, nLenMsg, hdr, NULL); 3162| 1.47k| } 3163| | 3164| 4.43k| for (bMobileH = TAUT_YES; 0 <= bMobileH; bMobileH--) ------------------ | | 575| 1.47k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3164:35): [True: 2.95k, False: 1.47k] ------------------ 3165| 2.95k| { 3166| | /* bMobileH = TAUT_YES, TAUT_NON */ 3167| | 3168| 2.95k| if (bits[bMobileH]) ------------------ | Branch (3168:17): [True: 1.54k, False: 1.41k] ------------------ 3169| 1.54k| { 3170| 1.54k| strcpy(szOneMsg, bMobileH == TAUT_YES ? " Mobile-H(" : " Fixed-H("); ------------------ | | 575| 1.54k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3170:34): [True: 1.31k, False: 231] ------------------ 3171| 1.54k| len = AddOneMsg(szMsg, len, nLenMsg, szOneMsg, NULL); 3172| 1.54k| } 3173| | 3174| 2.95k| bit = 1; 3175| 2.95k| iPrevGrpIdx = -1; 3176| | 3177| 2.95k| do 3178| 189k| { 3179| 189k| if (bit & bits[bMobileH]) ------------------ | Branch (3179:21): [True: 3.20k, False: 185k] ------------------ 3180| 3.20k| { 3181| | /* search for the message */ 3182| 3.20k| bFound = 0; 3183| 45.3k| for (k = 0; CompareInchiMsgs[k].nBit != INCHIDIFF_ZERO && !bFound; k++) ------------------ | Branch (3183:33): [True: 45.3k, False: 0] | Branch (3183:79): [True: 42.1k, False: 3.20k] ------------------ 3184| 42.1k| { 3185| 42.1k| if (bit & (INCHI_MODE)CompareInchiMsgs[k].nBit) ------------------ | Branch (3185:29): [True: 3.20k, False: 38.9k] ------------------ 3186| 3.20k| { 3187| | /* message found */ 3188| 13.2k| for (n = 0; CompareInchiMsgsGroup[n].nGroupID != IDGRP_ZERO; n++) ------------------ | Branch (3188:41): [True: 13.2k, False: 0] ------------------ 3189| 13.2k| { 3190| 13.2k| if (CompareInchiMsgsGroup[n].nGroupID == CompareInchiMsgs[k].nGroupID) ------------------ | Branch (3190:37): [True: 3.20k, False: 10.0k] ------------------ 3191| 3.20k| { 3192| 3.20k| iCurGrpIdx = n; 3193| 3.20k| if (iCurGrpIdx != iPrevGrpIdx) ------------------ | Branch (3193:41): [True: 2.67k, False: 531] ------------------ 3194| 2.67k| { 3195| 2.67k| if (iPrevGrpIdx >= 0) ------------------ | Branch (3195:45): [True: 1.13k, False: 1.54k] ------------------ 3196| 1.13k| { 3197| 1.13k| len = AddOneMsg(szMsg, len, nLenMsg, ";", NULL); 3198| 1.13k| } 3199| 2.67k| len = AddOneMsg(szMsg, len, nLenMsg, CompareInchiMsgsGroup[iCurGrpIdx].szGroupName, NULL); 3200| 2.67k| } 3201| 3.20k| len = AddOneMsg(szMsg, len, nLenMsg, CompareInchiMsgs[k].szMsg, iCurGrpIdx == iPrevGrpIdx ? "," : NULL); ------------------ | Branch (3201:101): [True: 531, False: 2.67k] ------------------ 3202| 3.20k| iPrevGrpIdx = iCurGrpIdx; 3203| 3.20k| bFound = 1; 3204| 3.20k| break; 3205| 3.20k| } 3206| 13.2k| } 3207| 3.20k| } 3208| 42.1k| } 3209| 3.20k| } 3210| 189k| bit <<= 1; 3211| 189k| } while (bit); ------------------ | Branch (3211:22): [True: 186k, False: 2.95k] ------------------ 3212| | 3213| 2.95k| if (bits[bMobileH]) ------------------ | Branch (3213:17): [True: 1.54k, False: 1.41k] ------------------ 3214| 1.54k| { 3215| 1.54k| len = AddOneMsg(szMsg, len, nLenMsg, ")", NULL); 3216| 1.54k| } 3217| | 3218| 2.95k| } 3219| 1.47k| } 3220| | 3221| 1.75k| return mismatch; /*len; */ 3222| 1.75k|} inchi_qsort: 36| 1.21M|{ 37| 1.21M| char *lo, *hi; /* ends of sub-array currently sorting */ 38| 1.21M| char *mid; /* points to middle of subarray */ 39| 1.21M| char *loguy, *higuy; /* traveling pointers for partition step */ 40| 1.21M| size_t size; /* size of the sub-array */ 41| 1.21M| char *lostk[STKSIZ], *histk[STKSIZ]; 42| 1.21M| int stkptr; /* stack for saving sub-array to be processed */ 43| | 44| 1.21M| if (num < 2) ------------------ | Branch (44:9): [True: 779k, False: 432k] ------------------ 45| 779k| return; /* nothing to do */ 46| | 47| 432k| stkptr = 0; /* initialize stack */ 48| | 49| 432k| lo = (char *) base; 50| 432k| hi = (char *) base + width * ( num - 1 ); /* initialize limits */ 51| | 52| | /* This entry point is for pseudo-recursion calling: setting 53| | lo and hi and jumping to here is like recursion, but stkptr is 54| | preserved, locals aren't, so we preserve stuff on the stack */ 55| 2.09M|recurse: 56| | 57| 2.09M| size = ( hi - lo ) / width + 1; /* number of el's to sort */ 58| | 59| | /* First we pick a partitioning element. The efficiency of the 60| | algorithm demands that we find one that is approximately the median 61| | of the values, but also that we select one fast. We choose the 62| | median of the first, middle, and last elements, to avoid bad 63| | performance in the face of already sorted data, or data that is made 64| | up of multiple sorted runs appended together. Testing shows that a 65| | median-of-three algorithm provides better performance than simply 66| | picking the middle element for the latter case. */ 67| | 68| 2.09M| mid = lo + ( size / 2 ) * width; /* find middle element */ 69| | 70| | /* Sort the first, middle, last elements into order */ 71| 2.09M| if (comp( lo, mid, pParam ) > 0) ------------------ | Branch (71:9): [True: 156k, False: 1.94M] ------------------ 72| 156k| { 73| 156k| inchi_swap( lo, mid, width ); 74| 156k| } 75| 2.09M| if (comp( lo, hi, pParam ) > 0) ------------------ | Branch (75:9): [True: 98.3k, False: 1.99M] ------------------ 76| 98.3k| { 77| 98.3k| inchi_swap( lo, hi, width ); 78| 98.3k| } 79| 2.09M| if (comp( mid, hi, pParam ) > 0) ------------------ | Branch (79:9): [True: 224k, False: 1.87M] ------------------ 80| 224k| { 81| 224k| inchi_swap( mid, hi, width ); 82| 224k| } 83| | 84| | /* We now wish to partition the array into three pieces, one consisting 85| | of elements <= partition element, one of elements equal to the 86| | partition element, and one of elements > than it. This is done 87| | below; comments indicate conditions established at every step. */ 88| | 89| 2.09M| loguy = lo; 90| 2.09M| higuy = hi; 91| | 92| | /* Note that higuy decreases and loguy increases on every iteration, 93| | so loop must terminate. */ 94| 2.09M| for (;;) 95| 2.40M| { 96| | /* lo <= loguy < hi, lo < higuy <= hi, 97| | A[i] <= A[mid] for lo <= i <= loguy, 98| | A[i] > A[mid] for higuy <= i < hi, 99| | A[hi] >= A[mid] */ 100| | 101| | /* The doubled loop is to avoid calling comp(mid,mid), since some 102| | existing comparison funcs don't work when passed the same 103| | value for both pointers. */ 104| | 105| 2.40M| if (mid > loguy) ------------------ | Branch (105:13): [True: 2.22M, False: 170k] ------------------ 106| 2.22M| { 107| 2.22M| do 108| 4.40M| { 109| 4.40M| loguy += width; 110| 4.40M| } 111| 4.40M| while (loguy < mid && comp( loguy, mid, pParam ) <= 0); ------------------ | Branch (111:20): [True: 2.43M, False: 1.97M] | Branch (111:35): [True: 2.17M, False: 257k] ------------------ 112| 2.22M| } 113| 2.40M| if (mid <= loguy) ------------------ | Branch (113:13): [True: 2.14M, False: 257k] ------------------ 114| 2.14M| { 115| 2.14M| do 116| 2.25M| { 117| 2.25M| loguy += width; 118| 2.25M| } 119| 2.25M| while (loguy <= hi && comp( loguy, mid, pParam ) <= 0); ------------------ | Branch (119:20): [True: 1.49M, False: 760k] | Branch (119:35): [True: 110k, False: 1.38M] ------------------ 120| 2.14M| } 121| | 122| | /* lo < loguy <= hi+1, A[i] <= A[mid] for lo <= i < loguy, 123| | either loguy > hi or A[loguy] > A[mid] */ 124| | 125| 2.40M| do 126| 4.34M| { 127| 4.34M| higuy -= width; 128| 4.34M| } 129| 4.34M| while (higuy > mid && comp( higuy, mid, pParam ) > 0); ------------------ | Branch (129:16): [True: 2.21M, False: 2.13M] | Branch (129:31): [True: 1.94M, False: 265k] ------------------ 130| | 131| | /* lo <= higuy < hi, A[i] > A[mid] for higuy < i < hi, 132| | either higuy == lo or A[higuy] <= A[mid] */ 133| | 134| 2.40M| if (higuy < loguy) ------------------ | Branch (134:13): [True: 2.09M, False: 302k] ------------------ 135| 2.09M| { 136| 2.09M| break; 137| 2.09M| } 138| | 139| | /* if loguy > hi or higuy == lo, then we would have exited, so 140| | A[loguy] > A[mid], A[higuy] <= A[mid], 141| | loguy <= hi, higuy > lo */ 142| | 143| 302k| inchi_swap( loguy, higuy, width ); 144| | 145| | /* If the partition element was moved, follow it. Only need 146| | to check for mid == higuy, since before the swap, 147| | A[loguy] > A[mid] implies loguy != mid. */ 148| | 149| 302k| if (mid == higuy) ------------------ | Branch (149:13): [True: 125k, False: 176k] ------------------ 150| 125k| { 151| 125k| mid = loguy; 152| 125k| } 153| | 154| | /* A[loguy] <= A[mid], A[higuy] > A[mid]; so condition at top 155| | of loop is re-established */ 156| 302k| } 157| | 158| | /* A[i] <= A[mid] for lo <= i < loguy, 159| | A[i] > A[mid] for higuy < i < hi, 160| | A[hi] >= A[mid] 161| | higuy < loguy 162| | implying: 163| | higuy == loguy-1 164| | or higuy == hi - 1, loguy == hi + 1, A[hi] == A[mid] */ 165| | 166| | /* Find adjacent elements equal to the partition element. The 167| | doubled loop is to avoid calling comp(mid,mid), since some 168| | existing comparison funcs don't work when passed the same value 169| | for both pointers. */ 170| | 171| 2.09M| higuy += width; 172| 2.09M| if (mid < higuy) ------------------ | Branch (172:9): [True: 1.33M, False: 760k] ------------------ 173| 1.33M| { 174| 1.33M| do 175| 1.33M| { 176| 1.33M| higuy -= width; 177| 1.33M| } 178| 1.33M| while (higuy > mid && comp( higuy, mid, pParam ) == 0); ------------------ | Branch (178:16): [True: 89.2k, False: 1.24M] | Branch (178:31): [True: 0, False: 89.2k] ------------------ 179| 1.33M| } 180| 2.09M| if (mid >= higuy) ------------------ | Branch (180:9): [True: 2.00M, False: 89.2k] ------------------ 181| 2.00M| { 182| 2.00M| do 183| 2.00M| { 184| 2.00M| higuy -= width; 185| 2.00M| } 186| 2.00M| while (higuy > lo && comp( higuy, mid, pParam ) == 0); ------------------ | Branch (186:16): [True: 789k, False: 1.21M] | Branch (186:30): [True: 0, False: 789k] ------------------ 187| 2.00M| } 188| | 189| | /* OK, now we have the following: 190| | higuy < loguy 191| | lo <= higuy <= hi 192| | A[i] <= A[mid] for lo <= i <= higuy 193| | A[i] == A[mid] for higuy < i < loguy 194| | A[i] > A[mid] for loguy <= i < hi 195| | A[hi] >= A[mid] */ 196| | 197| | /* We've finished the partition, now we want to sort the subarrays 198| | [lo, higuy] and [loguy, hi]. 199| | We do the smaller one first to minimize stack usage. 200| | We only sort arrays of length 2 or more.*/ 201| | 202| 2.09M| if (higuy - lo >= hi - loguy) ------------------ | Branch (202:9): [True: 1.97M, False: 123k] ------------------ 203| 1.97M| { 204| 1.97M| if (lo < higuy) ------------------ | Branch (204:13): [True: 789k, False: 1.18M] ------------------ 205| 789k| { 206| 789k| lostk[stkptr] = lo; 207| 789k| histk[stkptr] = higuy; 208| 789k| ++stkptr; 209| 789k| } /* save big recursion for later */ 210| | 211| 1.97M| if (loguy < hi) ------------------ | Branch (211:13): [True: 662k, False: 1.31M] ------------------ 212| 662k| { 213| 662k| lo = loguy; 214| 662k| goto recurse; /* do small recursion */ 215| 662k| } 216| 1.97M| } 217| 123k| else 218| 123k| { 219| 123k| if (loguy < hi) ------------------ | Branch (219:13): [True: 123k, False: 0] ------------------ 220| 123k| { 221| 123k| lostk[stkptr] = loguy; 222| 123k| histk[stkptr] = hi; 223| 123k| ++stkptr; /* save big recursion for later */ 224| 123k| } 225| | 226| 123k| if (lo < higuy) ------------------ | Branch (226:13): [True: 89.3k, False: 34.3k] ------------------ 227| 89.3k| { 228| 89.3k| hi = higuy; 229| 89.3k| goto recurse; /* do small recursion */ 230| 89.3k| } 231| 123k| } 232| | 233| | /* We have sorted the array, except for any pending sorts on the stack. 234| | Check if there are any, and do them. */ 235| | 236| 1.34M| --stkptr; 237| 1.34M| if (stkptr >= 0) ------------------ | Branch (237:9): [True: 913k, False: 432k] ------------------ 238| 913k| { 239| 913k| lo = lostk[stkptr]; 240| 913k| hi = histk[stkptr]; 241| 913k| goto recurse; /* pop subarray from stack */ 242| 913k| } 243| 432k| else 244| 432k| { 245| 432k| return; /* all subarrays done */ 246| 432k| } 247| 1.34M|} inchi_swap: 252| 2.47M|{ 253| 2.47M| char tmp; 254| 2.47M| if (a != b) ------------------ | Branch (254:9): [True: 2.47M, False: 0] ------------------ 255| 2.47M| { 256| 15.9M| while (width--) ------------------ | Branch (256:16): [True: 13.4M, False: 2.47M] ------------------ 257| 13.4M| { 258| 13.4M| tmp = *a; 259| 13.4M| *a++ = *b; 260| 13.4M| *b++ = tmp; 261| 13.4M| } 262| 2.47M| } 263| 2.47M|} insertions_sort: 273| 1.90M|{ 274| 1.90M| char *i, *j, *pk = (char*) base; 275| 1.90M| int num_trans = 0; 276| 1.90M| size_t k; 277| 4.50M| for (k = 1; k < num; k++, pk += width) ------------------ | Branch (277:17): [True: 2.59M, False: 1.90M] ------------------ 278| 2.59M| { 279| | /*for( i = pk, j = pk + width; j > (char*)base && (*compare)(i,j) > 0; j=i, i -= width )*/ 280| 2.59M| for (i = j = pk + width; 281| 3.40M| j > ( char* )base && ( i -= width, ( *compare )( i, j, pCG ) ) > 0; ------------------ | Branch (281:14): [True: 3.24M, False: 152k] | Branch (281:35): [True: 802k, False: 2.44M] ------------------ 282| 2.59M| j = i) /* changed to keep BoundsChecker happy 2007-09-24 DT */ 283| 802k| { 284| 802k| inchi_swap( i, j, width ); 285| 802k| num_trans++; 286| 802k| } 287| 2.59M| } 288| | 289| 1.90M| return num_trans; 290| 1.90M|} insertions_sort_AT_NUMBERS: 300| 13.3M|{ 301| 13.3M| AT_NUMB *i, *j, *pk, tmp; 302| 13.3M| int k, num_trans = 0; 303| 316M| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (303:28): [True: 303M, False: 13.3M] ------------------ 304| 303M| { 305| 303M| for (j = ( i = pk ) + 1, tmp = *j; j > base && ( *compare )( i, &tmp, pCG ) > 0; j = i, i--) ------------------ | Branch (305:44): [True: 303M, False: 6.68k] | Branch (305:56): [True: 11.4k, False: 303M] ------------------ 306| 11.4k| { 307| 11.4k| *j = *i; 308| 11.4k| num_trans++; 309| 11.4k| } 310| 303M| *j = tmp; 311| 303M| } 312| | 313| 13.3M| return num_trans; 314| 13.3M|} insertions_sort_NeighList_AT_NUMBERS: 321| 730k|{ 322| 730k| AT_NUMB *i, *j, *pk, tmp; 323| 730k| AT_RANK rj; /* optimization */ 324| 730k| int k, num = (int) *base++; 325| 2.42M| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (325:28): [True: 1.69M, False: 730k] ------------------ 326| 1.69M| { 327| 1.98M| for (j = ( i = pk ) + 1, rj = nRank[(int) *j]; j > base && nRank[(int) *i] > rj; j = i, i--) ------------------ | Branch (327:56): [True: 1.88M, False: 101k] | Branch (327:68): [True: 291k, False: 1.59M] ------------------ 328| 291k| { 329| 291k| tmp = *i; 330| 291k| *i = *j; 331| 291k| *j = tmp; 332| 291k| } 333| 1.69M| } 334| 730k|} insertions_sort_AT_RANK: 341| 5.50k|{ 342| 5.50k| AT_RANK *i, *j, *pk, tmp; 343| 5.50k| int k, num_trans = 0; 344| 10.4k| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (344:28): [True: 4.98k, False: 5.50k] ------------------ 345| 4.98k| { 346| 7.59k| for (j = ( i = pk ) + 1, tmp = *j; j > base && *i > tmp; j = i, i--) ------------------ | Branch (346:44): [True: 6.55k, False: 1.03k] | Branch (346:56): [True: 2.60k, False: 3.95k] ------------------ 347| 2.60k| { 348| 2.60k| *j = *i; 349| 2.60k| num_trans++; 350| 2.60k| } 351| 4.98k| *j = tmp; 352| 4.98k| } 353| | 354| 5.50k| return num_trans; 355| 5.50k|} insertions_sort_NeighList_AT_NUMBERS3: 362| 77.8k|{ 363| 77.8k| AT_NUMB *i, *j, *pk, tmp; 364| 77.8k| AT_RANK rj; 365| 77.8k| int k, n, num = (int) *base++; 366| 170k| for (k = 1, pk = base, n = 0; k < num; k++, pk++) ------------------ | Branch (366:35): [True: 92.9k, False: 77.8k] ------------------ 367| 92.9k| { 368| 92.9k| for (j = ( i = pk ) + 1, rj = nRank[(int) ( tmp = *j )]; 369| 98.0k| j > base && nRank[(int) *i] > rj; ------------------ | Branch (369:14): [True: 94.0k, False: 3.95k] | Branch (369:26): [True: 5.03k, False: 89.0k] ------------------ 370| 92.9k| j = i, i--) 371| 5.03k| { 372| 5.03k| *j = *i; 373| 5.03k| n++; 374| 5.03k| } 375| 92.9k| *j = tmp; 376| 92.9k| } 377| | 378| 77.8k| return n; 379| 77.8k|} insertions_sort_NeighListBySymmAndCanonRank: 389| 134k|{ 390| 134k| AT_NUMB *i, *j, *pk, tmp; 391| 134k| int diff; 392| 134k| int k, num = (int) *base++; 393| 472k| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (393:28): [True: 338k, False: 134k] ------------------ 394| 338k| { 395| 338k| for (j = ( i = pk ) + 1; 396| 561k| j > base && /* always j > i */ ------------------ | Branch (396:14): [True: 459k, False: 102k] ------------------ 397| 459k| ( 0 > ( diff = (int) nSymmRank[(int) *i] - (int) nSymmRank[(int) *j] ) || ------------------ | Branch (397:16): [True: 188k, False: 270k] ------------------ 398| 270k| (!diff && nCanonRank[(int) *i] < nCanonRank[(int) *j]) ); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (398:15): [True: 85.9k, False: 184k] | Branch (398:24): [True: 35.4k, False: 50.5k] ------------------ 399| 338k| j = i, i--) 400| 223k| { 401| 223k| tmp = *i; 402| 223k| *i = *j; 403| 223k| *j = tmp; 404| 223k| } 405| 338k| } 406| | 407| 134k|} CompNeighborsAT_NUMBER: 419| 271k|{ 420| 271k| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 421| 271k|#ifdef CT_NEIGH_INCREASE 422| 271k| return (int) pCG->m_pn_RankForSort[pCG->m_pNeighborsForSort[( int )*(const AT_NUMB*) a1]] - 423| 271k| (int) pCG->m_pn_RankForSort[pCG->m_pNeighborsForSort[( int )*(const AT_NUMB*) a2]]; 424| |#else 425| | return (int) ( (CANON_GLOBALS *) pCG )->m_pn_RankForSort[pNeighborsForSort[( int )*(const AT_NUMB*) a2]] - 426| | (int) ( (CANON_GLOBALS *) pCG )->m_pn_RankForSort[pNeighborsForSort[( int )*(const AT_NUMB*) a1]]; 427| |#endif 428| 271k|} comp_AT_RANK: 433| 83.1k|{ 434| 83.1k| return ( int )*(const AT_RANK*) a1 - ( int )*(const AT_RANK*) a2; 435| 83.1k|} CompRank: 441| 386k|{ 442| 386k| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 443| 386k| int ret = (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a1] - 444| 386k| (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a2]; 445| | 446| 386k| return ret; 447| 386k|} CompRanksOrd: 452| 9.41M|{ 453| 9.41M| int ret; 454| 9.41M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 455| 9.41M| ret = (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a1] - 456| 9.41M| (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a2]; 457| 9.41M| if (!ret) ------------------ | Branch (457:9): [True: 3.89M, False: 5.51M] ------------------ 458| 3.89M| { 459| 3.89M| ret = ( int )*(const AT_RANK*) a1 - ( int )*(const AT_RANK*) a2; 460| 3.89M| } 461| | 462| 9.41M| return ret; 463| 9.41M|} CompAtomInvariants2Only: 468| 4.85M|{ 469| 4.85M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 470| 4.85M| const ATOM_INVARIANT2 *pAI1 = pCG->m_pAtomInvariant2ForSort + ( int )*(const AT_RANK*) a1; 471| 4.85M| const ATOM_INVARIANT2 *pAI2 = pCG->m_pAtomInvariant2ForSort + ( int )*(const AT_RANK*) a2; 472| 4.85M| int i; 473| 18.0M| for (i = 0; i < AT_INV_BREAK1; i++) ------------------ | Branch (473:17): [True: 16.1M, False: 1.86M] ------------------ 474| 16.1M| { 475| 16.1M| if (pAI1->val[i] == pAI2->val[i]) ------------------ | Branch (475:13): [True: 13.1M, False: 2.99M] ------------------ 476| 13.1M| continue; 477| 2.99M| return (int) pAI1->val[i] - (int) pAI2->val[i]; 478| 16.1M| } 479| 1.86M| if (pAI1->iso_sort_key != pAI2->iso_sort_key) ------------------ | Branch (479:9): [True: 3.46k, False: 1.85M] ------------------ 480| 3.46k| { 481| 3.46k| return ( pAI1->iso_sort_key > pAI2->iso_sort_key ) ? 1 : -1; ------------------ | Branch (481:16): [True: 1.32k, False: 2.14k] ------------------ 482| 3.46k| } 483| 1.85M| for (; i < AT_INV_LENGTH; i++) ------------------ | Branch (483:12): [True: 1.85M, False: 0] ------------------ 484| 1.85M| { 485| 1.85M| if (pAI1->val[i] != pAI2->val[i]) ------------------ | Branch (485:13): [True: 6, False: 1.85M] ------------------ 486| 6| { 487| 6| continue; 488| 6| } 489| 1.85M| return (int) pAI1->val[i] - (int) pAI2->val[i]; 490| 1.85M| } 491| 0| if (pAI1->iso_aux_key != pAI2->iso_aux_key) ------------------ | Branch (491:9): [True: 0, False: 0] ------------------ 492| 0| { 493| 0| return ( pAI1->iso_aux_key > pAI2->iso_aux_key ) ? 1 : -1; ------------------ | Branch (493:16): [True: 0, False: 0] ------------------ 494| 0| } 495| | 496| 0| return 0; 497| 0|} CompAtomInvariants2: 502| 3.95M|{ 503| | /* Warning: the following line may be compiler implementation dependent */ 504| 3.95M| int ret = CompAtomInvariants2Only( a1, a2, p ); 505| 3.95M| if (!ret) ------------------ | Branch (505:9): [True: 1.43M, False: 2.52M] ------------------ 506| 1.43M| { 507| 1.43M| ret = ( int )*(const AT_RANK*) a1 - ( int )*(const AT_RANK*) a2; 508| 1.43M| } 509| | 510| 3.95M| return ret; 511| 3.95M|} CompChemElemLex: 517| 464k|{ 518| 464k| return memcmp( a1, a2, 2 ); 519| 464k|} CompareNeighListLex: 526| 488M|{ 527| 488M| int len1 = (int) *pp1++; 528| 488M| int len2 = (int) *pp2++; 529| 488M| int len = inchi_min( len1, len2 ); ------------------ | | 139| 488M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 488M] | | ------------------ ------------------ 530| 488M| int diff = 0; 531| 488M| int ret; 532| | /* djb-rwth: fixing oss-fuzz issue #25642 */ 533| 489M| while ((len > 0) && !diff) ------------------ | Branch (533:12): [True: 1.42M, False: 488M] | Branch (533:25): [True: 1.37M, False: 53.8k] ------------------ 534| 1.37M| { 535| 1.37M| len--; 536| 1.37M| diff = (int)nRank[*pp1++] - (int)nRank[*pp2++]; 537| 1.37M| }; 538| | 539| 488M| ret = diff ? diff : (len1 - len2); ------------------ | Branch (539:11): [True: 89.0k, False: 488M] ------------------ 540| 488M| return ret; 541| 488M|} CompareNeighListLexUpToMaxRank: 548| 119M|{ 549| 119M| int len1 = (int) *pp1++; 550| 119M| int len2 = (int) *pp2++; 551| 119M| int diff = 0; 552| 119M| int len; 553| 120M| while (0 < len1 && nRank[pp1[len1 - 1]] > nMaxAtNeighRank) ------------------ | Branch (553:12): [True: 503k, False: 119M] | Branch (553:24): [True: 459k, False: 44.4k] ------------------ 554| 459k| { 555| 459k| len1--; 556| 459k| } 557| 119M| while (0 < len2 && nRank[pp2[len2 - 1]] > nMaxAtNeighRank) ------------------ | Branch (557:12): [True: 272k, False: 119M] | Branch (557:24): [True: 227k, False: 44.4k] ------------------ 558| 227k| { 559| 227k| len2--; 560| 227k| } 561| 119M| len = inchi_min( len1, len2 ); ------------------ | | 139| 119M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 119M] | | ------------------ ------------------ 562| 119M| while (len-- > 0 && !( diff = (int) nRank[*pp1++] - (int) nRank[*pp2++] )) ------------------ | Branch (562:12): [True: 62.4k, False: 119M] | Branch (562:25): [True: 53.0k, False: 9.40k] ------------------ 563| 53.0k| { 564| 53.0k| ; 565| 53.0k| } 566| | 567| 119M| return diff ? diff : ( len1 - len2 ); ------------------ | Branch (567:12): [True: 9.40k, False: 119M] ------------------ 568| 119M|} compare_NeighLists: 573| 244M|{ 574| 244M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 575| 244M| return CompareNeighListLex( *op1, *op2, pCG->m_pn_RankForSort ); 576| 244M|} CompNeighListRanks: 581| 2.67M|{ 582| 2.67M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 583| 2.67M| int ret; 584| 2.67M| ret = (int) pCG->m_pn_RankForSort[*( (const AT_RANK*) a1 )] - 585| 2.67M| (int) pCG->m_pn_RankForSort[*( (const AT_RANK*) a2 )]; 586| 2.67M| if (!ret) ------------------ | Branch (586:9): [True: 1.12M, False: 1.55M] ------------------ 587| 1.12M| { 588| 1.12M| ret = compare_NeighLists( pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a1 ), 589| 1.12M| pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a2 ), p ); 590| 1.12M| } 591| | 592| 2.67M| return ret; 593| 2.67M|} CompNeighLists: 598| 243M|{ 599| 243M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 600| 243M| int ret; 601| 243M| ret = compare_NeighLists( pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a1 ), 602| 243M| pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a2 ), p ); 603| | 604| 243M| return ret; 605| 243M|} CompNeighListsUpToMaxRank: 610| 59.7M|{ 611| 59.7M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 612| 59.7M| int ret; 613| 59.7M| ret = CompareNeighListLexUpToMaxRank( pCG->m_pNeighList_RankForSort[*( (const AT_RANK*) a1 )], 614| 59.7M| pCG->m_pNeighList_RankForSort[*( (const AT_RANK*) a2 )], 615| 59.7M| pCG->m_pn_RankForSort, pCG->m_nMaxAtNeighRankForSort ); 616| | 617| 59.7M| return ret; 618| 59.7M|} CompNeighListRanksOrd: 623| 1.02M|{ 624| 1.02M| int ret = CompNeighListRanks( a1, a2, p ); 625| 1.02M| if (!ret) ------------------ | Branch (625:9): [True: 408k, False: 617k] ------------------ 626| 408k| { 627| 408k| ret = ( int )*( (const AT_RANK*) a1 ) - ( int )*( (const AT_RANK*) a2 ); /* keep original order if identical */ 628| 408k| } 629| | 630| 1.02M| return ret; 631| 1.02M|} CompRanksInvOrd: 636| 4.37k|{ 637| 4.37k| return ( int )*(const AT_RANK*) a2 - ( int )*(const AT_RANK*) a1; 638| 4.37k|} CompNeighborsRanksCountEql: 643| 63.3k|{ 644| 63.3k| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 645| 63.3k|#ifdef CT_NEIGH_INCREASE 646| 63.3k| int ret = (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a1] - 647| 63.3k| (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a2]; 648| |#else 649| | int ret = (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a2] - 650| | (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a1]; 651| |#endif 652| 63.3k| pCG->m_nNumCompNeighborsRanksCountEql += !ret; 653| | 654| 63.3k| return ret; 655| 63.3k|} CreateNeighListFromLinearCT: 667| 4.30k|{ 668| | /* Atom numbers in LinearCT are canonical numbers 669| | * order: parent[i] > neigh[i][0] < neigh[i][1]... neigh[i+1][0] < ... 670| | * parent[i] < parent[i+1] 671| | */ 672| 4.30k| int i, j; 673| 4.30k| S_CHAR *valence = NULL; 674| 4.30k| NEIGH_LIST *pp = NULL; 675| 4.30k| AT_NUMB *pAtList = NULL; 676| 4.30k| AT_RANK n_vertex, n_neigh; 677| 4.30k| int err = 1, num_bonds; 678| 4.30k| int length, start; 679| | 680| 4.30k| if ((int) LinearCT[0] > num_atoms) ------------------ | Branch (680:9): [True: 0, False: 4.30k] ------------------ 681| 0| { 682| 0| goto exit_function; 683| 0| } 684| 4.30k| valence = (S_CHAR*)inchi_calloc((long long)num_atoms + 1, sizeof(valence[0])); ------------------ | | 1146| 4.30k|#define inchi_calloc calloc ------------------ 685| 4.30k| if (!valence) /* djb-rwth: cast operator added */ ------------------ | Branch (685:9): [True: 0, False: 4.30k] ------------------ 686| 0| { 687| 0| goto exit_function; 688| 0| } 689| | 690| 53.0k| for (i = 1, num_bonds = 0, n_vertex = LinearCT[0]; i < nLenCT; i++) ------------------ | Branch (690:56): [True: 48.7k, False: 4.30k] ------------------ 691| 48.7k| { 692| 48.7k| if (( n_neigh = LinearCT[i] ) < n_vertex) ------------------ | Branch (692:13): [True: 26.2k, False: 22.4k] ------------------ 693| 26.2k| { 694| 26.2k| valence[n_neigh] ++; 695| 26.2k| valence[n_vertex] ++; 696| 26.2k| num_bonds += 2; 697| 26.2k| } 698| 22.4k| else 699| 22.4k| { 700| 22.4k| if ((int) ( n_vertex = n_neigh ) > num_atoms) ------------------ | Branch (700:17): [True: 0, False: 22.4k] ------------------ 701| 0| { 702| 0| goto exit_function; 703| 0| } 704| 22.4k| } 705| 48.7k| } 706| 4.30k| if ((int) n_vertex != num_atoms) ------------------ | Branch (706:9): [True: 0, False: 4.30k] ------------------ 707| 0| { 708| 0| goto exit_function; 709| 0| } 710| 4.30k| length = num_bonds + num_atoms + 1; 711| 4.30k| pp = (NEIGH_LIST*)inchi_calloc(((long long)num_atoms + 1), sizeof(NEIGH_LIST)); ------------------ | | 1146| 4.30k|#define inchi_calloc calloc ------------------ 712| 4.30k| pAtList = (AT_NUMB*)inchi_malloc(length * sizeof(AT_NUMB)); ------------------ | | 1143| 4.30k|#define inchi_malloc malloc ------------------ 713| 4.30k| if (pp && pAtList) /* djb-rwth: cast operator added; addressing LLVM warning */ ------------------ | Branch (713:9): [True: 4.30k, False: 0] | Branch (713:15): [True: 4.30k, False: 0] ------------------ 714| 4.30k| { 715| | /* Create empty connection table */ 716| 31.0k| for (i = 1, length = 0; i <= num_atoms; i++) ------------------ | Branch (716:33): [True: 26.7k, False: 4.30k] ------------------ 717| 26.7k| { 718| 26.7k| start = length; 719| 26.7k| length += ( valence[i] + 1 ); 720| 26.7k| pp[i - 1] = pAtList + start; 721| 26.7k| pp[i - 1][0] = 0; 722| 26.7k| } 723| | /* Fill out the CT */ 724| 53.0k| for (i = 1, n_vertex = LinearCT[0] - 1; i < nLenCT; i++) ------------------ | Branch (724:49): [True: 48.7k, False: 4.30k] ------------------ 725| 48.7k| { 726| 48.7k| if (( n_neigh = LinearCT[i] - 1 ) < n_vertex) ------------------ | Branch (726:17): [True: 26.2k, False: 22.4k] ------------------ 727| 26.2k| { 728| | /* Vertex - neighbor connection */ 729| 26.2k| j = (int) ( ++pp[(int) n_vertex][0] ); 730| 26.2k| pp[(int) n_vertex][j] = n_neigh; 731| | /* neighbor - vertex connection */ 732| 26.2k| j = (int) ( ++pp[(int) n_neigh][0] ); 733| 26.2k| pp[(int) n_neigh][j] = n_vertex; 734| 26.2k| } 735| 22.4k| else 736| 22.4k| { 737| 22.4k| if ((int) ( n_vertex = n_neigh ) >= num_atoms) ------------------ | Branch (737:21): [True: 0, False: 22.4k] ------------------ 738| 0| { 739| 0| goto exit_function; 740| 0| } 741| 22.4k| } 742| 48.7k| } 743| 4.30k| err = 0; 744| 4.30k| } 745| | 746| 4.30k|exit_function: 747| 4.30k| if (valence) ------------------ | Branch (747:9): [True: 4.30k, False: 0] ------------------ 748| 4.30k| { 749| 4.30k| inchi_free( valence ); ------------------ | | 1152| 4.30k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 4.30k, False: 0] | | | Branch (1152:50): [Folded, False: 4.30k] | | ------------------ ------------------ 750| 4.30k| } 751| 4.30k| if (err) /* djb-rwth: ignoring LLVM warning */ ------------------ | Branch (751:9): [True: 0, False: 4.30k] ------------------ 752| 0| { 753| 0| if (pAtList) ------------------ | Branch (753:13): [True: 0, False: 0] ------------------ 754| 0| { 755| 0| inchi_free( pAtList ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 756| 0| } 757| 0| if (pp) ------------------ | Branch (757:13): [True: 0, False: 0] ------------------ 758| 0| { 759| 0| inchi_free( pp ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 760| 0| pp = NULL; 761| 0| } 762| 0| } 763| | 764| 4.30k| return pp; /* djb-rwth: ignoring LLVM warning: since a pointer is returned, memory should be freed in a function which calls *CreateNeighListFromLinearCT */ 765| 4.30k|} CreateNeighList: 780| 298k|{ 781| | /* +1 to add NULL termination */ 782| 298k| NEIGH_LIST *pp = (NEIGH_LIST *) inchi_calloc( ( (long long)num_at_tg + 1 ), sizeof( NEIGH_LIST ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 298k|#define inchi_calloc calloc ------------------ 783| 298k| T_GROUP *t_group = NULL; 784| 298k| AT_NUMB *nEndpointAtomNumber = NULL; 785| 298k| int num_t_groups = 0; 786| 298k| int nFirstEndpointAtNoPos; 787| | 788| 298k| AT_NUMB *pAtList = NULL; 789| 298k| int length, start, val, i, j; 790| 298k| if (pp) ------------------ | Branch (790:9): [True: 298k, False: 0] ------------------ 791| 298k| { 792| 298k| if (num_at_tg > num_atoms) ------------------ | Branch (792:13): [True: 3.46k, False: 295k] ------------------ 793| 3.46k| { 794| 3.46k| t_group = t_group_info->t_group; 795| 3.46k| num_t_groups = t_group_info->num_t_groups; 796| 3.46k| nEndpointAtomNumber = t_group_info->nEndpointAtomNumber; 797| 3.46k| } 798| | 799| 298k| if (!bDoubleBondSquare) ------------------ | Branch (799:13): [True: 298k, False: 0] ------------------ 800| 298k| { 801| 1.45M| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (801:37): [True: 1.15M, False: 298k] ------------------ 802| 1.15M| { 803| 1.15M| length += (int) at[i].valence + ( num_t_groups && at[i].endpoint ); ------------------ | Branch (803:51): [True: 22.5k, False: 1.13M] | Branch (803:67): [True: 8.58k, False: 13.9k] ------------------ 804| 1.15M| } 805| 298k| length += num_atoms; 806| 302k| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (806:25): [True: 3.56k, False: 298k] ------------------ 807| 3.56k| { 808| 3.56k| length += (int) t_group[i].nNumEndpoints; 809| 3.56k| } 810| 298k| length += num_t_groups; 811| 298k| } 812| 0| else 813| 0| { 814| 0| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (814:37): [True: 0, False: 0] ------------------ 815| 0| { 816| 0| val = (int) at[i].valence; 817| 0| for (j = 0; j < val; j++) ------------------ | Branch (817:29): [True: 0, False: 0] ------------------ 818| 0| { 819| 0| length += 1 + ( bDoubleBondSquare && BOND_DOUBLE == at[i].bond_type[j] ); ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (819:37): [True: 0, False: 0] | Branch (819:58): [True: 0, False: 0] ------------------ 820| 0| } 821| 0| length += ( num_t_groups && at[i].endpoint ); ------------------ | Branch (821:29): [True: 0, False: 0] | Branch (821:45): [True: 0, False: 0] ------------------ 822| 0| } 823| 0| length += num_atoms; 824| 0| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (824:25): [True: 0, False: 0] ------------------ 825| 0| { 826| 0| length += (int) t_group[i].nNumEndpoints; 827| 0| } 828| 0| length += num_t_groups; 829| 0| } 830| 298k| length++; /* +1 to save number of neighbors */ 831| 298k| pAtList = (AT_NUMB*)inchi_malloc(length * sizeof(AT_NUMB)); ------------------ | | 1143| 298k|#define inchi_malloc malloc ------------------ 832| 298k| if (pAtList) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (832:13): [True: 298k, False: 0] ------------------ 833| 298k| { 834| 298k| if (!bDoubleBondSquare) ------------------ | Branch (834:17): [True: 298k, False: 0] ------------------ 835| 298k| { 836| 1.45M| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (836:41): [True: 1.15M, False: 298k] ------------------ 837| 1.15M| { 838| 1.15M| val = at[i].valence; 839| 1.15M| start = length++; 840| 1.77M| for (j = 0; j < val; j++) ------------------ | Branch (840:33): [True: 619k, False: 1.15M] ------------------ 841| 619k| { 842| 619k| pAtList[length++] = at[i].neighbor[j]; 843| 619k| } 844| | /* add endpoint */ 845| 1.15M| if (num_t_groups && at[i].endpoint) ------------------ | Branch (845:25): [True: 22.5k, False: 1.13M] | Branch (845:41): [True: 8.58k, False: 13.9k] ------------------ 846| 8.58k| { 847| 8.58k| pAtList[length++] = num_atoms + (int) at[i].endpoint - 1; 848| 8.58k| } 849| 1.15M| pAtList[start] = length - start - 1; /* number of neighbors before the list of neighbors */ 850| 1.15M| pp[i] = pAtList + start; /* pointer to the */ 851| 1.15M| } 852| 298k| } 853| 0| else 854| 0| { 855| 0| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (855:41): [True: 0, False: 0] ------------------ 856| 0| { 857| 0| val = at[i].valence; 858| 0| start = length++; 859| 0| for (j = 0; j < val; j++) ------------------ | Branch (859:33): [True: 0, False: 0] ------------------ 860| 0| { 861| 0| pAtList[length++] = at[i].neighbor[j]; /* djb-rwth: buffer overrun avoided implicitly */ 862| 0| if (bDoubleBondSquare && BOND_DOUBLE == at[i].bond_type[j]) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (862:29): [True: 0, False: 0] | Branch (862:50): [True: 0, False: 0] ------------------ 863| 0| { 864| 0| pAtList[length++] = at[i].neighbor[j]; /* a list of neighbor orig. numbers */ 865| 0| } 866| 0| } 867| | /* Add endpoint */ 868| 0| if (num_t_groups && at[i].endpoint) ------------------ | Branch (868:25): [True: 0, False: 0] | Branch (868:41): [True: 0, False: 0] ------------------ 869| 0| { 870| 0| pAtList[length++] = num_atoms + (int) at[i].endpoint - 1; 871| 0| } 872| 0| pAtList[start] = length - start - 1; /* number of neighbors before the list of neighbors */ 873| 0| pp[i] = pAtList + start; /* pointer to the */ 874| 0| } 875| 0| } 876| | 877| | /* Add t-groups */ 878| 302k| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (878:25): [True: 3.56k, False: 298k] ------------------ 879| 3.56k| { 880| 3.56k| val = (int) t_group[i].nNumEndpoints; 881| 3.56k| start = length++; 882| 3.56k| nFirstEndpointAtNoPos = (int) t_group[i].nFirstEndpointAtNoPos; 883| 12.1k| for (j = 0; j < val; j++) ------------------ | Branch (883:29): [True: 8.58k, False: 3.56k] ------------------ 884| 8.58k| { 885| 8.58k| pAtList[length++] = nEndpointAtomNumber[nFirstEndpointAtNoPos + j]; 886| 8.58k| } 887| 3.56k| pAtList[start] = length - start - 1; /* number of neighbors before the list of neighbors */ 888| 3.56k| pp[num_atoms + i] = pAtList + start; /* pointer to the */ 889| 3.56k| } 890| 298k| } 891| 0| else 892| 0| { 893| 0| inchi_free(pAtList); /* djb-rwth: fixing coverity ID #499598 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 894| 0| inchi_free( pp ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 895| 0| return NULL; 896| 0| } 897| 298k| } /* djb-rwth: ignoring LLVM warning */ 898| | 899| | /* djb-rwth: fixing coverity ID #499598 -- pp uses pAtList values */ 900| | 901| 298k| return pp; /* djb-rwth: ignoring LLVM warning: since a pointer is returned, memory should be freed in a function which calls *CreateNeighList */ 902| 298k|} FreeNeighList: 907| 1.59M|{ 908| 1.59M| if (pp) ------------------ | Branch (908:9): [True: 303k, False: 1.29M] ------------------ 909| 303k| { 910| 303k| if (pp[0]) ------------------ | Branch (910:13): [True: 303k, False: 0] ------------------ 911| 303k| { 912| 303k| inchi_free( pp[0] ); ------------------ | | 1152| 303k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 303k, False: 0] | | | Branch (1152:50): [Folded, False: 303k] | | ------------------ ------------------ 913| 303k| } 914| 303k| inchi_free( pp ); ------------------ | | 1152| 303k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 303k, False: 0] | | | Branch (1152:50): [Folded, False: 303k] | | ------------------ ------------------ 915| 303k| } 916| | 917| 1.59M|} BreakAllTies: 928| 4.02k|{ 929| 4.02k| int i, nRet = -1, nNumRanks = 1 /* value does not matter*/; 930| | 931| 4.02k| AT_RANK *nPrevRank = *pRankStack++; 932| 4.02k| AT_RANK *nPrevAtomNumber = *pRankStack++; 933| | 934| 4.02k| AT_RANK *nNewRank = NULL; 935| 4.02k| AT_RANK *nNewAtomNumber = NULL; 936| | 937| 4.02k| if (!pRankStack[0]) ------------------ | Branch (937:9): [True: 1.22k, False: 2.80k] ------------------ 938| 1.22k| { 939| 1.22k| pRankStack[0] = (AT_RANK *) inchi_malloc( num_max * sizeof( *nNewRank ) ); ------------------ | | 1143| 1.22k|#define inchi_malloc malloc ------------------ 940| 1.22k| } 941| 4.02k| if (!pRankStack[1]) ------------------ | Branch (941:9): [True: 1.28k, False: 2.74k] ------------------ 942| 1.28k| { 943| 1.28k| pRankStack[1] = (AT_RANK *) inchi_malloc( num_max * sizeof( *nNewAtomNumber ) ); ------------------ | | 1143| 1.28k|#define inchi_malloc malloc ------------------ 944| 1.28k| } 945| 4.02k| if (!pRankStack[0] || !pRankStack[1]) ------------------ | Branch (945:9): [True: 0, False: 4.02k] | Branch (945:27): [True: 0, False: 4.02k] ------------------ 946| 0| { 947| 0| return CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 948| 0| } 949| 4.02k| nNewRank = pRankStack[0]; 950| 4.02k| nNewAtomNumber = pRankStack[1]; 951| | 952| 4.02k| if (nNewRank && nNewAtomNumber) ------------------ | Branch (952:9): [True: 4.02k, False: 0] | Branch (952:21): [True: 4.02k, False: 0] ------------------ 953| 4.02k| { 954| 4.02k| memcpy(nNewAtomNumber, nPrevAtomNumber, num_atoms * sizeof(nNewAtomNumber[0])); 955| 4.02k| memcpy(nNewRank, nPrevRank, num_atoms * sizeof(nNewRank[0])); 956| 23.9k| for (i = 1, nRet = 0; i < num_atoms; i++) ------------------ | Branch (956:31): [True: 19.9k, False: 4.02k] ------------------ 957| 19.9k| { 958| | /* 12-12-2001: replaced Prev... with New... */ 959| 19.9k| if (nNewRank[(int) nNewAtomNumber[i - 1]] == nNewRank[(int) nNewAtomNumber[i]]) ------------------ | Branch (959:17): [True: 1.24k, False: 18.6k] ------------------ 960| 1.24k| { 961| 1.24k| nNewRank[nNewAtomNumber[i - 1]] = (AT_RANK) i; 962| 1.24k| nNumRanks = DifferentiateRanks2( pCG, num_atoms, NeighList, 963| 1.24k| nNumRanks, nNewRank, nTempRank, 964| 1.24k| nNewAtomNumber, 965| 1.24k| &pCS->lNumNeighListIter, 1 ); 966| 1.24k| pCS->lNumBreakTies++; 967| 1.24k| nRet++; 968| 1.24k| } 969| 19.9k| } 970| 4.02k| } 971| | 972| 4.02k| return nRet; 973| 4.02k|} comp_AT_NUMB: 106| 3.49k|{ 107| 3.49k| return (int)(*(const AT_NUMB*)a1) - (int)(*(const AT_NUMB*)a2); 108| 3.49k|} dot_prod3: 269| 10|{ 270| 10| return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; 271| 10|} cross_prod3: 296| 10|{ 297| 10| double tmp[3]; 298| | 299| 10| tmp[0] = ( a[1] * b[2] - a[2] * b[1] ); 300| 10| tmp[1] = -( a[0] * b[2] - a[2] * b[0] ); 301| 10| tmp[2] = ( a[0] * b[1] - a[1] * b[0] ); 302| | 303| 10| result[0] = tmp[0]; 304| 10| result[1] = tmp[1]; 305| 10| result[2] = tmp[2]; 306| | 307| 10| return result; 308| 10|} bCanInpAtomBeAStereoCenter: 1401| 2.18M|{ 1402| |/************************************************************************************* 1403| | * current version 1404| | ************************************************************************************* 1405| | * Use #define to split the stereocenter description table into parts 1406| | * to make it easier to read 1407| | * 1408| | * --------- 4 single bonds stereocenters ------- 1409| | * 0 1 2 3 4 5 1410| | * 1411| | * | | | | | | 1412| | * -C- -Si- -Ge- -Sn- >As[+] >B[-] 1413| | * | | | | | | 1414| | */ 1415| 2.18M|#define SZELEM1 "C\000","Si", "Ge", "Sn", "As", "B\000", 1416| 2.18M|#define CCHARGE1 0, 0, 0, 0, 1, -1, 1417| 2.18M|#define CNUMBONDSANDH1 4, 4, 4, 4, 4, 4, 1418| 2.18M|#define CCHEMVALENCEH1 4, 4, 4, 4, 4, 4, 1419| 2.18M|#define CHAS3MEMBRING1 0, 0, 0, 0, 0, 0, 1420| 2.18M|#define CREQUIRDNEIGH1 0, 0, 0, 0, 3, 0, 1421| |/* 1422| | * --------------- S, Se stereocenters ---------- 1423| | * 6 7 8 9 10 11 12 13 1424| | * 1425| | * | | || | | || 1426| | * -S= =S= -S[+] >S[+] -Se= =Se= -Se[+] >Se[+] 1427| | * | | | | | | | | 1428| | */ 1429| 2.18M|#define SZELEM2 "S\000","S\000","S\000","S\000","Se", "Se", "Se", "Se", 1430| 2.18M|#define CCHARGE2 0, 0, 1, 1, 0, 0, 1, 1, 1431| 2.18M|#define CNUMBONDSANDH2 3, 4, 3, 4, 3, 4, 3, 4, 1432| 2.18M|#define CCHEMVALENCEH2 4, 6, 3, 5, 4, 6, 3, 5, 1433| 2.18M|#define CHAS3MEMBRING2 0, 0, 0, 0, 0, 0, 0, 0, 1434| 2.18M|#define CREQUIRDNEIGH2 3, 3, 3, 3, 3, 3, 3, 3, 1435| |/* 1436| | * ------------------ N, P stereocenters ----------------- 1437| | * 14 15 16 17 18 19 20 1438| | * 1439| | * Phosphine Arsine 1440| | * X---Y 1441| | * | | \ / | | \ / \ / 1442| | * =N- >N[+] N >P[+] =P- P As 1443| | * | | | | | | | 1444| | */ 1445| 2.18M|#define SZELEM3 "N\000","N\000","N\000","P\000","P\000","P\000", "As", 1446| 2.18M|#define CCHARGE3 0, 1, 0, 1, 0, 0, 0, 1447| 2.18M|#define CNUMBONDSANDH3 4, 4, 3, 4, 4, 3, 3, 1448| 2.18M|#define CCHEMVALENCEH3 5, 4, 3, 4, 5, 3, 3, 1449| 2.18M|#define CHAS3MEMBRING3 0, 0, 1, 0, 0, 0, 0, 1450| 2.18M|#define CREQUIRDNEIGH3 3, 3, 1, 3, 3, 2, 2, 1451| | 1452| 2.18M|#define PHOSPHINE_STEREO 19 /* the number must match Phosphine number in the comments, see above */ 1453| 2.18M|#define ARSINE_STEREO 20 /* the number must match Arsine number in the comments, see above */ 1454| | 1455| 2.18M| static const char szElem[][3] = { SZELEM1 SZELEM2 SZELEM3 }; ------------------ | | 1415| 2.18M|#define SZELEM1 "C\000","Si", "Ge", "Sn", "As", "B\000", ------------------ static const char szElem[][3] = { SZELEM1 SZELEM2 SZELEM3 }; ------------------ | | 1429| 2.18M|#define SZELEM2 "S\000","S\000","S\000","S\000","Se", "Se", "Se", "Se", ------------------ static const char szElem[][3] = { SZELEM1 SZELEM2 SZELEM3 }; ------------------ | | 1445| 2.18M|#define SZELEM3 "N\000","N\000","N\000","P\000","P\000","P\000", "As", ------------------ 1456| 2.18M| static const S_CHAR cCharge[] = { CCHARGE1 CCHARGE2 CCHARGE3 }; ------------------ | | 1416| 2.18M|#define CCHARGE1 0, 0, 0, 0, 1, -1, ------------------ static const S_CHAR cCharge[] = { CCHARGE1 CCHARGE2 CCHARGE3 }; ------------------ | | 1430| 2.18M|#define CCHARGE2 0, 0, 1, 1, 0, 0, 1, 1, ------------------ static const S_CHAR cCharge[] = { CCHARGE1 CCHARGE2 CCHARGE3 }; ------------------ | | 1446| 2.18M|#define CCHARGE3 0, 1, 0, 1, 0, 0, 0, ------------------ 1457| 2.18M| static const S_CHAR cNumBondsAndH[] = { CNUMBONDSANDH1 CNUMBONDSANDH2 CNUMBONDSANDH3 }; ------------------ | | 1417| 2.18M|#define CNUMBONDSANDH1 4, 4, 4, 4, 4, 4, ------------------ static const S_CHAR cNumBondsAndH[] = { CNUMBONDSANDH1 CNUMBONDSANDH2 CNUMBONDSANDH3 }; ------------------ | | 1431| 2.18M|#define CNUMBONDSANDH2 3, 4, 3, 4, 3, 4, 3, 4, ------------------ static const S_CHAR cNumBondsAndH[] = { CNUMBONDSANDH1 CNUMBONDSANDH2 CNUMBONDSANDH3 }; ------------------ | | 1447| 2.18M|#define CNUMBONDSANDH3 4, 4, 3, 4, 4, 3, 3, ------------------ 1458| 2.18M| static const S_CHAR cChemValenceH[] = { CCHEMVALENCEH1 CCHEMVALENCEH2 CCHEMVALENCEH3 }; ------------------ | | 1418| 2.18M|#define CCHEMVALENCEH1 4, 4, 4, 4, 4, 4, ------------------ static const S_CHAR cChemValenceH[] = { CCHEMVALENCEH1 CCHEMVALENCEH2 CCHEMVALENCEH3 }; ------------------ | | 1432| 2.18M|#define CCHEMVALENCEH2 4, 6, 3, 5, 4, 6, 3, 5, ------------------ static const S_CHAR cChemValenceH[] = { CCHEMVALENCEH1 CCHEMVALENCEH2 CCHEMVALENCEH3 }; ------------------ | | 1448| 2.18M|#define CCHEMVALENCEH3 5, 4, 3, 4, 5, 3, 3, ------------------ 1459| 2.18M| static const S_CHAR cHas3MembRing[] = { CHAS3MEMBRING1 CHAS3MEMBRING2 CHAS3MEMBRING3 }; ------------------ | | 1419| 2.18M|#define CHAS3MEMBRING1 0, 0, 0, 0, 0, 0, ------------------ static const S_CHAR cHas3MembRing[] = { CHAS3MEMBRING1 CHAS3MEMBRING2 CHAS3MEMBRING3 }; ------------------ | | 1433| 2.18M|#define CHAS3MEMBRING2 0, 0, 0, 0, 0, 0, 0, 0, ------------------ static const S_CHAR cHas3MembRing[] = { CHAS3MEMBRING1 CHAS3MEMBRING2 CHAS3MEMBRING3 }; ------------------ | | 1449| 2.18M|#define CHAS3MEMBRING3 0, 0, 1, 0, 0, 0, 0, ------------------ 1460| 2.18M| static const S_CHAR cRequirdNeigh[] = { CREQUIRDNEIGH1 CREQUIRDNEIGH2 CREQUIRDNEIGH3 }; ------------------ | | 1420| 2.18M|#define CREQUIRDNEIGH1 0, 0, 0, 0, 3, 0, ------------------ static const S_CHAR cRequirdNeigh[] = { CREQUIRDNEIGH1 CREQUIRDNEIGH2 CREQUIRDNEIGH3 }; ------------------ | | 1434| 2.18M|#define CREQUIRDNEIGH2 3, 3, 3, 3, 3, 3, 3, 3, ------------------ static const S_CHAR cRequirdNeigh[] = { CREQUIRDNEIGH1 CREQUIRDNEIGH2 CREQUIRDNEIGH3 }; ------------------ | | 1450| 2.18M|#define CREQUIRDNEIGH3 3, 3, 1, 3, 3, 2, 2, ------------------ 1461| | 1462| 2.18M| static const int n = sizeof( szElem ) / sizeof( szElem[0] ); 1463| | /* reqired neighbor types (bitmap): 1464| | 0 => check bonds only 1465| | 1 => no terminal hydrogen atom neighbors 1466| | 2 => no terminal -X and -XH together (don't care the bond type, charge, radical) 1467| | (X = tautomeric endpoint atom) 1468| | Note: whenever cChemValenceH[] > cNumBondsAndH[] 1469| | the tautomeric and/or alternating bonds 1470| | are permitted 1471| | 1472| | */ 1473| 2.18M| int i, ret = 0; 1474| 47.9M| for (i = 0; i < n; i++) ------------------ | Branch (1474:17): [True: 45.8M, False: 2.16M] ------------------ 1475| 45.8M| { 1476| 45.8M| if (!strcmp( at[cur_at].elname, szElem[i] ) && ------------------ | Branch (1476:13): [True: 1.46M, False: 44.3M] ------------------ 1477| 1.46M| ( at[cur_at].charge == cCharge[i] ------------------ | Branch (1477:13): [True: 809k, False: 659k] ------------------ 1478| |#ifdef ALLOW_NO_CHARGE_ON_STEREO_CENTERS 1479| | || at[cur_at].charge == 0 1480| |#endif 1481| 1.46M| ) && 1482| 809k| ( !at[cur_at].radical || at[cur_at].radical == 1 ) && ------------------ | Branch (1482:17): [True: 772k, False: 36.2k] | Branch (1482:40): [True: 0, False: 36.2k] ------------------ 1483| 772k| at[cur_at].valence + at[cur_at].num_H == cNumBondsAndH[i] && ------------------ | Branch (1483:14): [True: 43.4k, False: 729k] ------------------ 1484| 43.4k| at[cur_at].chem_bonds_valence + at[cur_at].num_H == cChemValenceH[i] && ------------------ | Branch (1484:14): [True: 26.7k, False: 16.7k] ------------------ 1485| 26.7k| ( cHas3MembRing[i] ? is_atom_in_3memb_ring( at, cur_at ) : 1 ) && ------------------ | Branch (1485:14): [True: 22.6k, False: 4.04k] | Branch (1485:16): [True: 7.90k, False: 18.8k] ------------------ 1486| 22.6k| bInpAtomHasRequirdNeigh( at, cur_at, cRequirdNeigh[i], cChemValenceH[i] - cNumBondsAndH[i], bStereoAtZz )) ------------------ | Branch (1486:14): [True: 18.4k, False: 4.21k] ------------------ 1487| | /* 1488| | if (!strcmp( at[cur_at].elname, szElem[i] ) && 1489| | at[cur_at].charge == cCharge[i] && 1490| | ( !at[cur_at].radical || at[cur_at].radical == 1 ) && 1491| | at[cur_at].valence + at[cur_at].num_H == cNumBondsAndH[i] && 1492| | at[cur_at].chem_bonds_valence + at[cur_at].num_H == cChemValenceH[i] && 1493| | ( cHas3MembRing[i] ? is_atom_in_3memb_ring( at, cur_at ) : 1 ) && 1494| | bInpAtomHasRequirdNeigh( at, cur_at, cRequirdNeigh[i], cChemValenceH[i] - cNumBondsAndH[i], bStereoAtZz ))*/ 1495| 18.4k| { 1496| 18.4k| ret = cNumBondsAndH[i]; 1497| 18.4k| break; 1498| 18.4k| } 1499| 45.8M| } 1500| | 1501| 2.18M| if (i == PHOSPHINE_STEREO && !( bPointedEdgeStereo & PES_BIT_PHOSPHINE_STEREO )) ------------------ | | 1452| 4.37M|#define PHOSPHINE_STEREO 19 /* the number must match Phosphine number in the comments, see above */ ------------------ if (i == PHOSPHINE_STEREO && !( bPointedEdgeStereo & PES_BIT_PHOSPHINE_STEREO )) ------------------ | | 45| 1.26k|#define PES_BIT_PHOSPHINE_STEREO 2 ------------------ | Branch (1501:9): [True: 1.26k, False: 2.18M] | Branch (1501:34): [True: 892, False: 377] ------------------ 1502| 892| { 1503| 892| ret = 0; 1504| 892| } 1505| 2.18M| if (i == ARSINE_STEREO && !( bPointedEdgeStereo & PES_BIT_ARSINE_STEREO )) ------------------ | | 1453| 4.37M|#define ARSINE_STEREO 20 /* the number must match Arsine number in the comments, see above */ ------------------ if (i == ARSINE_STEREO && !( bPointedEdgeStereo & PES_BIT_ARSINE_STEREO )) ------------------ | | 46| 440|#define PES_BIT_ARSINE_STEREO 4 ------------------ | Branch (1505:9): [True: 440, False: 2.18M] | Branch (1505:31): [True: 434, False: 6] ------------------ 1506| 434| { 1507| 434| ret = 0; 1508| 434| } 1509| | 1510| 2.18M| return ret; 1511| 2.18M|} bAtomHasValence3: 1540| 4.16k|{ 1541| 4.16k| static const char szElem[][3] = { "N\000" }; 1542| 4.16k| static const S_CHAR cCharge[] = { 0, }; 1543| 4.16k| int i, ret = 0; 1544| 4.66k| for (i = 0; i < (int) ( sizeof( szElem ) / sizeof( szElem[0] ) ); i++) ------------------ | Branch (1544:17): [True: 4.16k, False: 504] ------------------ 1545| 4.16k| { 1546| 4.16k| if (!strcmp( elname, szElem[i] ) && ( charge == cCharge[i] )) ------------------ | Branch (1546:13): [True: 3.92k, False: 241] | Branch (1546:45): [True: 3.66k, False: 263] ------------------ 1547| 3.66k| { 1548| 3.66k| ret = ( !radical || radical == RADICAL_SINGLET ); ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (1548:21): [True: 3.66k, False: 0] | Branch (1548:33): [True: 0, False: 0] ------------------ 1549| 3.66k| break; 1550| 3.66k| } 1551| 4.16k| } 1552| 4.16k| return ret; 1553| 4.16k|} bCanAtomHaveAStereoBond: 1560| 330k|{ 1561| 330k| static const char szElem[][3] = { "C\000", "Si", "Ge", "N\000", "N\000" }; 1562| 330k| static const S_CHAR cCharge[] = { 0, 0, 0, 0, 1, }; 1563| 330k| static const int n = sizeof( szElem ) / sizeof( szElem[0] ); 1564| 330k| int i, ret = 0; 1565| 1.57M| for (i = 0; i < n; i++) ------------------ | Branch (1565:17): [True: 1.38M, False: 181k] ------------------ 1566| 1.38M| { 1567| 1.38M| if (!strcmp( elname, szElem[i] ) && ( charge == cCharge[i] )) ------------------ | Branch (1567:13): [True: 188k, False: 1.20M] | Branch (1567:45): [True: 148k, False: 39.3k] ------------------ 1568| 148k| { 1569| 148k| ret = ( !radical || radical == RADICAL_SINGLET ); ------------------ | | 75| 7.27k|#define RADICAL_SINGLET 1 ------------------ | Branch (1569:21): [True: 141k, False: 7.27k] | Branch (1569:33): [True: 0, False: 7.27k] ------------------ 1570| 148k| break; 1571| 148k| } 1572| 1.38M| } 1573| 330k| return ret; 1574| 330k|} bCanAtomBeMiddleAllene: 1581| 1.62k|{ 1582| 1.62k| static const char szElem[][3] = { "C\000", "Si", "Ge", }; 1583| 1.62k| static const S_CHAR cCharge[] = { 0, 0, 0, }; 1584| 1.62k| static const int n = sizeof( szElem ) / sizeof( szElem[0] ); 1585| 1.62k| int i, ret = 0; 1586| 2.71k| for (i = 0; i < n; i++) ------------------ | Branch (1586:17): [True: 2.45k, False: 252] ------------------ 1587| 2.45k| { 1588| 2.45k| if (!strcmp( elname, szElem[i] ) && ( charge == cCharge[i] )) ------------------ | Branch (1588:13): [True: 1.37k, False: 1.08k] | Branch (1588:45): [True: 1.37k, False: 0] ------------------ 1589| 1.37k| { 1590| 1.37k| ret = ( !radical || radical == RADICAL_SINGLET ); ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (1590:21): [True: 1.37k, False: 0] | Branch (1590:33): [True: 0, False: 0] ------------------ 1591| 1.37k| break; 1592| 1.37k| } 1593| 2.45k| } 1594| 1.62k| return ret; 1595| 1.62k|} bCanAtomBeTerminalAllene: 1671| 24.0k|{ 1672| 24.0k| static const char szElem[][3] = { "C\000", "Si", "Ge", }; 1673| 24.0k| static const S_CHAR cCharge[] = { 0, 0, 0, }; 1674| 24.0k| static const int n = sizeof( szElem ) / sizeof( szElem[0] ); 1675| 24.0k| int i, ret = 0; 1676| 82.1k| for (i = 0; i < n; i++) ------------------ | Branch (1676:17): [True: 62.8k, False: 19.2k] ------------------ 1677| 62.8k| { 1678| 62.8k| if (!strcmp( elname, szElem[i] ) && ( charge == cCharge[i] )) ------------------ | Branch (1678:13): [True: 4.86k, False: 58.0k] | Branch (1678:45): [True: 4.80k, False: 65] ------------------ 1679| 4.80k| { 1680| 4.80k| ret = ( !radical || radical == RADICAL_SINGLET ); ------------------ | | 75| 24|#define RADICAL_SINGLET 1 ------------------ | Branch (1680:21): [True: 4.77k, False: 24] | Branch (1680:33): [True: 0, False: 24] ------------------ 1681| 4.80k| break; 1682| 4.80k| } 1683| 62.8k| } 1684| | 1685| 24.0k| return ret; 1686| 24.0k|} GetHalfStereobond0DParity: 1696| 1.02k|{ 1697| 1.02k| int m, last_parity, cur_parity; 1698| 1.02k| int i, icur2nxt, icur2neigh, cur_order_parity, nxt_at; 1699| 1.02k| AT_NUMB nNextSbAtOrigNumb; 1700| | /* find atom parities for all valid streobonds incident to at[cur_at] */ 1701| 2.13k| for (m = 0, last_parity = 0; m < MAX_NUM_STEREO_BONDS && at[cur_at].sb_parity[m]; m++) ------------------ | | 873| 4.27k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1701:34): [True: 2.13k, False: 8] | Branch (1701:62): [True: 1.11k, False: 1.01k] ------------------ 1702| 1.11k| { 1703| 1.11k| icur2nxt = icur2neigh = -1; /* ordering number of neighbors in nSbNeighOrigAtNumb[] */ 1704| 1.11k| cur_parity = 0; /* parity for mth stereobond incident to the cur_at */ 1705| 1.11k| nxt_at = at[cur_at].neighbor[(int)at[cur_at].sb_ord[m]]; /* djb-rwth: fixing coverity ID #499549 */ 1706| 1.11k| if (0 <= at[cur_at].sb_ord[m] && at[cur_at].sb_ord[m] < at[cur_at].valence && ------------------ | Branch (1706:13): [True: 1.11k, False: 0] | Branch (1706:42): [True: 1.11k, False: 0] ------------------ 1707| 1.11k| at[nxt_at].valence <= MAX_NUM_STEREO_BONDS && /* make sure it is a valid stereobond */ ------------------ | | 873| 2.23k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1707:14): [True: 1.11k, False: 0] ------------------ 1708| 1.11k| ( nNextSbAtOrigNumb = at[nxt_at].orig_at_number )) ------------------ | Branch (1708:14): [True: 1.11k, False: 0] ------------------ 1709| 1.11k| { 1710| | /* since at[cur_at].sn_ord[m] = -1 for explicit H use at[cur_at].sn_orig_at_num[m] */ 1711| 3.51k| for (i = 0; i < nNumExplictAttachments; i++) ------------------ | Branch (1711:25): [True: 2.39k, False: 1.11k] ------------------ 1712| 2.39k| { 1713| 2.39k| if (at[cur_at].sn_orig_at_num[m] == nSbNeighOrigAtNumb[i]) ------------------ | Branch (1713:21): [True: 1.11k, False: 1.27k] ------------------ 1714| 1.11k| { 1715| 1.11k| icur2neigh = i; /* neighbor */ 1716| 1.11k| } 1717| 1.27k| else 1718| 1.27k| { 1719| 1.27k| if (nNextSbAtOrigNumb == nSbNeighOrigAtNumb[i]) ------------------ | Branch (1719:25): [True: 1.11k, False: 157] ------------------ 1720| 1.11k| { 1721| 1.11k| icur2nxt = i; /* atom connected by a stereobond */ 1722| 1.11k| } 1723| 1.27k| } 1724| 2.39k| } 1725| 1.11k| if (icur2neigh >= 0 && icur2nxt >= 0) ------------------ | Branch (1725:17): [True: 1.11k, False: 0] | Branch (1725:36): [True: 1.11k, False: 0] ------------------ 1726| 1.11k| { 1727| 1.11k| if (ATOM_PARITY_WELL_DEF( at[cur_at].sb_parity[m] )) ------------------ | | 259| 1.11k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.11k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.11k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 1.11k, False: 0] | | | Branch (259:75): [True: 889, False: 229] | | ------------------ ------------------ 1728| 889| { 1729| | /* parity of at[cur_atom] neighbor permutation to reach this order: { next_atom, neigh_atom, ...} */ 1730| 889| cur_order_parity = ( icur2nxt + icur2neigh + ( icur2nxt > icur2neigh ) - 1 ) % 2; 1731| 889| cur_parity = 2 - ( cur_order_parity + at[cur_at].sb_parity[m] ) % 2; 1732| 889| } 1733| 229| else 1734| 229| { 1735| | /* unknowm/undef parities do not depend on the neighbor order */ 1736| 229| cur_parity = at[cur_at].sb_parity[m]; 1737| 229| } 1738| 1.11k| } 1739| 1.11k| } 1740| 0| else 1741| 0| { 1742| 0| continue; 1743| 0| } 1744| | /* use a well-known parity if available; if not then use preferably the unknown */ 1745| 1.11k| if (!last_parity) ------------------ | Branch (1745:13): [True: 1.02k, False: 91] ------------------ 1746| 1.02k| { 1747| 1.02k| last_parity = cur_parity; 1748| 1.02k| } 1749| 91| else 1750| 91| { 1751| 91| if (last_parity != cur_parity && cur_parity) ------------------ | Branch (1751:17): [True: 31, False: 60] | Branch (1751:46): [True: 31, False: 0] ------------------ 1752| 31| { 1753| 31| if (ATOM_PARITY_WELL_DEF( last_parity )) ------------------ | | 259| 31|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 31|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 31|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 31, False: 0] | | | Branch (259:75): [True: 15, False: 16] | | ------------------ ------------------ 1754| 15| { 1755| 15| if (ATOM_PARITY_WELL_DEF( cur_parity )) ------------------ | | 259| 15|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 15|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 15|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 15, False: 0] | | | Branch (259:75): [True: 6, False: 9] | | ------------------ ------------------ 1756| 6| { 1757| 6| last_parity = 0; /* error: all well-defined parities should be same */ 1758| 6| break; 1759| 6| } 1760| 15| } 1761| 16| else 1762| 16| { 1763| 16| if (ATOM_PARITY_WELL_DEF( cur_parity )) ------------------ | | 259| 16|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 16|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 16|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 16, False: 0] | | | Branch (259:75): [True: 15, False: 1] | | ------------------ ------------------ 1764| 15| { 1765| | /* replace unknown/undefined parity with well-known */ 1766| 15| last_parity = cur_parity; 1767| 15| } 1768| 1| else 1769| 1| { 1770| | /* select min unknown/undefined parity (out of AB_PARITY_UNKN and AB_PARITY_UNDF) */ 1771| 1| last_parity = inchi_min( cur_parity, last_parity ); ------------------ | | 139| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 1] | | ------------------ ------------------ 1772| 1| } 1773| 16| } 1774| 31| } 1775| 91| } 1776| 1.11k| } 1777| | 1778| 1.02k| if (last_parity) ------------------ | Branch (1778:9): [True: 1.02k, False: 6] ------------------ 1779| 1.02k| { 1780| 1.02k| bond_parity = last_parity; 1781| 1.02k| at[cur_at].bUsed0DParity |= nFlag; /* set flag: used stereobond 0D parity */ 1782| 1.02k| } 1783| | 1784| 1.02k| return bond_parity; 1785| 1.02k|} FixSb0DParities: 1801| 682|{ 1802| 682| int k, parity1, parity2, abs_parity1, abs_parity2; 1803| 682| int j1, j2, parity_sign; 1804| | /* 1805| | AT_NUMB nSbNeighOrigAtNumb1[MAX_NUM_STEREO_BOND_NEIGH], nSbNeighOrigAtNumb2[MAX_NUM_STEREO_BOND_NEIGH]; 1806| | int nNumExplictAttachments1, nNumExplictAttachments2; 1807| | */ 1808| 682| parity1 = parity2 = AB_PARITY_NONE; ------------------ | | 218| 682|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 1809| 682| j1 = j2 = -1; 1810| 682| parity_sign = ( *pparity1 < 0 || *pparity2 < 0 ) ? -1 : 1; ------------------ | Branch (1810:21): [True: 8, False: 674] | Branch (1810:38): [True: 0, False: 674] ------------------ 1811| | 1812| 682| abs_parity1 = abs( *pparity1 ); 1813| 682| abs_parity2 = abs( *pparity2 ); 1814| | 1815| 1.17k| for (k = 0; k < MAX_NUM_STEREO_BONDS && at[at_1].sb_parity[k]; k++) ------------------ | | 873| 2.35k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1815:17): [True: 1.17k, False: 0] | Branch (1815:45): [True: 494, False: 682] ------------------ 1816| 494| { 1817| 494| if (at[at_1].sb_ord[k] == i_next_at_1) ------------------ | Branch (1817:13): [True: 349, False: 145] ------------------ 1818| 349| { 1819| 349| parity1 = at[at_1].sb_parity[k]; 1820| 349| j1 = k; 1821| 349| } 1822| 494| } 1823| 1.31k| for (k = 0; k < MAX_NUM_STEREO_BONDS && at[at_2].sb_parity[k]; k++) ------------------ | | 873| 2.63k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1823:17): [True: 1.31k, False: 8] | Branch (1823:45): [True: 637, False: 674] ------------------ 1824| 637| { 1825| 637| if (at[at_2].sb_ord[k] == i_next_at_2) ------------------ | Branch (1825:13): [True: 349, False: 288] ------------------ 1826| 349| { 1827| 349| parity2 = at[at_2].sb_parity[k]; 1828| 349| j2 = k; 1829| 349| } 1830| 637| } 1831| 682| switch (( j1 >= 0 ) + 2 * ( j2 >= 0 )) ------------------ | Branch (1831:13): [True: 682, False: 0] ------------------ 1832| 682| { 1833| 333| case 0: ------------------ | Branch (1833:9): [True: 333, False: 349] ------------------ 1834| | /* the bond has no 0D parity */ 1835| 333| *pparity1 = *pparity2 = parity_sign * AB_PARITY_UNDF; ------------------ | | 222| 333|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 1836| 333| return 0; 1837| 0| case 1: ------------------ | Branch (1837:9): [True: 0, False: 682] ------------------ 1838| 0| case 2: ------------------ | Branch (1838:9): [True: 0, False: 682] ------------------ 1839| | /* 0D parity data error */ 1840| 0| *pparity1 = *pparity2 = AB_PARITY_NONE; ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 1841| 0| return -1; 1842| 349| case 3: ------------------ | Branch (1842:9): [True: 349, False: 333] ------------------ 1843| | /* the bond has 0D parity */ 1844| 349| switch (!( ATOM_PARITY_WELL_DEF( abs_parity1 ) && ATOM_PARITY_WELL_DEF( parity1 ) ) + ------------------ | | 259| 698|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 349|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 349|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 349, False: 0] | | | Branch (259:75): [True: 270, False: 79] | | ------------------ ------------------ switch (!( ATOM_PARITY_WELL_DEF( abs_parity1 ) && ATOM_PARITY_WELL_DEF( parity1 ) ) + ------------------ | | 259| 270|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 270|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 270|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 270, False: 0] | | | Branch (259:75): [True: 264, False: 6] | | ------------------ ------------------ | Branch (1844:21): [True: 349, False: 0] ------------------ 1845| 349| 2 * !( ATOM_PARITY_WELL_DEF( abs_parity2 ) && ATOM_PARITY_WELL_DEF( parity2 ) )) ------------------ | | 259| 698|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 349|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 349|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 349, False: 0] | | | Branch (259:75): [True: 267, False: 82] | | ------------------ ------------------ 2 * !( ATOM_PARITY_WELL_DEF( abs_parity2 ) && ATOM_PARITY_WELL_DEF( parity2 ) )) ------------------ | | 259| 267|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 267|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 267|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 267, False: 0] | | | Branch (259:75): [True: 263, False: 4] | | ------------------ ------------------ 1846| 349| { 1847| 257| case 0: ------------------ | Branch (1847:17): [True: 257, False: 92] ------------------ 1848| | /* both parities are well-defined; continue */ 1849| 257| break; 1850| 6| case 1: ------------------ | Branch (1850:17): [True: 6, False: 343] ------------------ 1851| | /* 0D parity not well-defined for at_1 */ 1852| 6| *pparity1 = parity_sign * ( ATOM_PARITY_WELL_DEF( parity1 ) ? abs_parity1 : ------------------ | | 259| 6|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 6|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 6|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 6, False: 0] | | | Branch (259:75): [True: 6, False: 0] | | ------------------ ------------------ 1853| 6| ATOM_PARITY_WELL_DEF( abs_parity1 ) ? parity1 : ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 1854| 0| inchi_min( abs_parity1, parity1 ) ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 1855| 6| *pparity2 = parity_sign * abs_parity2; 1856| 6| return -1; 1857| 7| case 2: ------------------ | Branch (1857:17): [True: 7, False: 342] ------------------ 1858| | /* 0D parity not well-defined for at_2 */ 1859| 7| *pparity1 = parity_sign * abs_parity1; 1860| 7| *pparity2 = parity_sign * ( ATOM_PARITY_WELL_DEF( parity2 ) ? abs_parity2 : ------------------ | | 259| 7|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 7|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 7|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 7, False: 0] | | | Branch (259:75): [True: 7, False: 0] | | ------------------ ------------------ 1861| 7| ATOM_PARITY_WELL_DEF( abs_parity2 ) ? parity2 : ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 1862| 0| inchi_min( abs_parity2, parity2 ) ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 1863| 7| return -1; 1864| 79| case 3: ------------------ | Branch (1864:17): [True: 79, False: 270] ------------------ 1865| 79| abs_parity1 = ( ATOM_PARITY_WELL_DEF( parity1 ) ? abs_parity1 : ------------------ | | 259| 79|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 79|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 79|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 79, False: 0] | | | Branch (259:75): [True: 0, False: 79] | | ------------------ ------------------ 1866| 79| ATOM_PARITY_WELL_DEF( abs_parity1 ) ? parity1 : ------------------ | | 259| 79|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 79|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 79|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 79, False: 0] | | | Branch (259:75): [True: 6, False: 73] | | ------------------ ------------------ 1867| 79| inchi_min( abs_parity1, parity1 ) ); ------------------ | | 139| 73|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 73] | | ------------------ ------------------ 1868| 79| abs_parity2 = ( ATOM_PARITY_WELL_DEF( parity2 ) ? abs_parity2 : ------------------ | | 259| 79|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 79|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 79|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 79, False: 0] | | | Branch (259:75): [True: 0, False: 79] | | ------------------ ------------------ 1869| 79| ATOM_PARITY_WELL_DEF( abs_parity2 ) ? parity2 : ------------------ | | 259| 79|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 79|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 79|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 79, False: 0] | | | Branch (259:75): [True: 4, False: 75] | | ------------------ ------------------ 1870| 79| inchi_min( abs_parity2, parity2 ) ); ------------------ | | 139| 75|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 75] | | ------------------ ------------------ 1871| 79| *pparity1 = *pparity2 = parity_sign * inchi_min( abs_parity1, abs_parity2 ); ------------------ | | 139| 79|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 79] | | ------------------ ------------------ 1872| | /*return (parity1 == parity2)? 0 : -1;*/ 1873| 79| return -1; 1874| 349| } 1875| 257| break; 1876| 682| } 1877| | /* we are here if both end-atoms of the bond have well-defined 0D parities */ 1878| | /* 1879| | nNumExplictAttachments1 = GetSbNeighOrigAtNumb( at, at_1, at_removed_H, num_removed_H, nSbNeighOrigAtNumb1 ); 1880| | nNumExplictAttachments2 = GetSbNeighOrigAtNumb( at, at_2, at_removed_H, num_removed_H, nSbNeighOrigAtNumb2 ); 1881| | parity1 = GetHalfStereobond0DParity( at, at_1, nSbNeighOrigAtNumb1, nNumExplictAttachments1, *pparity1, 0 ); 1882| | parity2 = GetHalfStereobond0DParity( at, at_2, nSbNeighOrigAtNumb2, nNumExplictAttachments2, *pparity2, 0 ); 1883| | */ 1884| 257| *pparity1 = parity_sign * abs_parity1; 1885| 257| *pparity2 = parity_sign * abs_parity2; 1886| | 1887| 257| if (chain_length % 2) ------------------ | Branch (1887:9): [True: 10, False: 247] ------------------ 1888| 10| { 1889| | /* allene; chain_length = (number of double bonds) - 1 */ 1890| | /* 1891| | int zer1 = ( !z_dir1[0] && !z_dir1[1] && !z_dir1[2] ); 1892| | int zer2 = ( !z_dir2[0] && !z_dir2[1] && !z_dir2[2] ); 1893| | */ 1894| 10| int bWrong_z_dir1 = ( 0 != ( at[at_1].bUsed0DParity & FlagSB_0D ) ); ------------------ | | 60| 10|#define FlagSB_0D 2 /**< bUsed0DParity */ ------------------ 1895| 10| int bWrong_z_dir2 = ( 0 != ( at[at_2].bUsed0DParity & FlagSB_0D ) ); ------------------ | | 60| 10|#define FlagSB_0D 2 /**< bUsed0DParity */ ------------------ 1896| | 1897| 10| if (bWrong_z_dir1 && bWrong_z_dir2) ------------------ | Branch (1897:13): [True: 10, False: 0] | Branch (1897:30): [True: 10, False: 0] ------------------ 1898| 10| { 1899| 10| goto set_default; 1900| 10| } 1901| 0| else 1902| 0| { 1903| 0| if (bWrong_z_dir1 || bWrong_z_dir2) ------------------ | Branch (1903:17): [True: 0, False: 0] | Branch (1903:34): [True: 0, False: 0] ------------------ 1904| 0| { 1905| 0| double r12[3], zi1[3], zi2[3], abs_r12, abs_zi2; 1906| 0| int at_i1, at_i2, j; /* djb-rwth: ignoring LLVM warning: variables used */ 1907| 0| S_CHAR z_dir[3]; 1908| 0| r12[0] = at[at_2].x - at[at_1].x; 1909| 0| r12[1] = at[at_2].y - at[at_1].y; 1910| 0| r12[2] = at[at_2].z - at[at_1].z; 1911| 0| abs_r12 = len3( r12 ); 1912| 0| if (abs_r12 < MIN_BOND_LEN) ------------------ | | 39| 0|#define MIN_BOND_LEN 0.000001 ------------------ | Branch (1912:21): [True: 0, False: 0] ------------------ 1913| 0| { 1914| 0| goto set_default; 1915| 0| } 1916| | /* make r12[] point to the atom with 'good' z_dir[] */ 1917| 0| if (bWrong_z_dir1) ------------------ | Branch (1917:21): [True: 0, False: 0] ------------------ 1918| 0| { 1919| 0| at_i1 = at_2; /* has good z_dir2[] */ /* djb-rwth: ignoring LLVM warning: variable used */ 1920| 0| at_i2 = at_1; /* has bad z_dir1[] */ /* djb-rwth: ignoring LLVM warning: variable used */ 1921| 0| zi1[0] = z_dir2[0]; 1922| 0| zi1[1] = z_dir2[1]; 1923| 0| zi1[2] = z_dir2[2]; 1924| 0| mult3( r12, 1.0 / abs_r12, r12 ); /* make length = 1 */ 1925| 0| } 1926| 0| else 1927| 0| { 1928| 0| at_i1 = at_1; /* has good z_dir1[] */ /* djb-rwth: ignoring LLVM warning: variable used */ 1929| 0| at_i2 = at_2; /* has bad z_dir2[] */ /* djb-rwth: ignoring LLVM warning: variable used */ 1930| 0| zi1[0] = z_dir1[0]; 1931| 0| zi1[1] = z_dir1[1]; 1932| 0| zi1[2] = z_dir1[2]; 1933| 0| mult3( r12, -1.0 / abs_r12, r12 ); /* make length = 1 */ 1934| 0| } 1935| 0| cross_prod3( r12, zi1, zi2 ); 1936| 0| abs_zi2 = len3( zi2 ); 1937| 0| mult3( zi2, 100.0 / abs_zi2, zi2 ); /* make length = 100 */ 1938| 0| for (j = 0; j < 3; j++) ------------------ | Branch (1938:29): [True: 0, False: 0] ------------------ 1939| 0| { 1940| 0| z_dir[j] = (S_CHAR) ( zi2[j] >= 0.0 ? floor( 0.5 + zi2[j] ) : ------------------ | Branch (1940:43): [True: 0, False: 0] ------------------ 1941| 0| -floor( 0.5 - zi2[j] ) ); /* abs(z_dir) = 100 */ 1942| 0| } 1943| 0| if (bWrong_z_dir1) ------------------ | Branch (1943:21): [True: 0, False: 0] ------------------ 1944| 0| { 1945| 0| memcpy(z_dir1, z_dir, sizeof(z_dir)); 1946| 0| } 1947| 0| else 1948| 0| { 1949| 0| memcpy(z_dir2, z_dir, sizeof(z_dir)); 1950| 0| } 1951| 0| } 1952| 0| } 1953| 0| return 0; 1954| | 1955| 10| set_default: 1956| | /* z_dir1[] = x-direction; z_dir2[] = z-direction; r12[] = y-direction */ 1957| 10| z_dir1[0] = 100; 1958| 10| z_dir1[1] = z_dir1[2] = 0; 1959| 10| z_dir2[0] = z_dir2[1] = 0; 1960| 10| z_dir2[2] = 100; 1961| 10| } 1962| | 1963| 257| return 0; 1964| 257|} FixUnkn0DStereoBonds: 1972| 216k|{ 1973| 216k| int i, m, num = 0; 1974| | 1975| | /* Add usual Unknown stereobond descriptors to each Unknown bond */ 1976| 1.27M| for (i = 0; i < num_at; i++) ------------------ | Branch (1976:17): [True: 1.05M, False: 216k] ------------------ 1977| 1.05M| { 1978| 1.05M| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) ------------------ | | 873| 2.11M|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1978:21): [True: 1.05M, False: 38] | Branch (1978:49): [True: 2.27k, False: 1.05M] ------------------ 1979| 2.27k| { 1980| 2.27k| if (AB_PARITY_UNKN == at[i].sb_parity[m]) ------------------ | | 221| 2.27k|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (1980:17): [True: 264, False: 2.01k] ------------------ 1981| 264| { 1982| 264| at[i].bond_stereo[(int) at[i].sb_ord[m]] = STEREO_DBLE_EITHER; ------------------ | | 40| 264|#define STEREO_DBLE_EITHER 3 ------------------ 1983| 264| num++; 1984| 264| } 1985| 2.27k| } 1986| 1.05M| } 1987| |#ifdef NEVER 1988| | if (num) 1989| | { 1990| | int j; 1991| | /* how to remove Unknown stereo bond parities */ 1992| | for (i = 0; i < num_at; i++) 1993| | { 1994| | for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) 1995| | { 1996| | if (AB_PARITY_UNKN == at[i].sb_parity[m]) 1997| | { 1998| | for (j = m + 1; j < MAX_NUM_STEREO_BONDS; j++) 1999| | { 2000| | at[i].sb_parity[j - 1] = at[i].sb_parity[j]; 2001| | at[i].sb_ord[j - 1] = at[i].sb_ord[j]; 2002| | at[i].sn_ord[j - 1] = at[i].sn_ord[j]; 2003| | at[i].sn_orig_at_num[j - 1] = at[i].sn_orig_at_num[j]; 2004| | } 2005| | at[i].sb_parity[j - 1] = 0; 2006| | at[i].sb_ord[j - 1] = 0; 2007| | at[i].sn_ord[j - 1] = 0; 2008| | at[i].sn_orig_at_num[j - 1] = 0; 2009| | } 2010| | } 2011| | } 2012| | } 2013| |#endif 2014| | 2015| 216k| return num; 2016| 216k|} GetStereocenter0DParity: 3705| 8.38k|{ 3706| 8.38k| int parity = AB_PARITY_NONE; ------------------ | | 218| 8.38k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 3707| 8.38k| if (at[cur_at].p_parity && ( j1 == MAX_NUM_STEREO_ATOM_NEIGH - 1 || j1 == MAX_NUM_STEREO_ATOM_NEIGH )) ------------------ | | 877| 614|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ if (at[cur_at].p_parity && ( j1 == MAX_NUM_STEREO_ATOM_NEIGH - 1 || j1 == MAX_NUM_STEREO_ATOM_NEIGH )) ------------------ | | 877| 402|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3707:9): [True: 614, False: 7.77k] | Branch (3707:34): [True: 212, False: 402] | Branch (3707:73): [True: 402, False: 0] ------------------ 3708| 614| { 3709| 614| int i, num_trans_inp, num_trans_neigh; 3710| 614| AT_NUMB nInpNeighOrigAtNumb[MAX_NUM_STEREO_ATOM_NEIGH]; 3711| 3.07k| for (i = 0; i < MAX_NUM_STEREO_ATOM_NEIGH; i++) ------------------ | | 877| 3.07k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3711:21): [True: 2.45k, False: 614] ------------------ 3712| 2.45k| { 3713| 2.45k| nInpNeighOrigAtNumb[i] = at[cur_at].p_orig_at_num[i]; 3714| 2.45k| if (nInpNeighOrigAtNumb[i] == at[cur_at].orig_at_number) ------------------ | Branch (3714:17): [True: 211, False: 2.24k] ------------------ 3715| 211| { 3716| 211| nInpNeighOrigAtNumb[i] = 0; /* lone pair or explicit H */ 3717| 211| } 3718| 2.45k| } 3719| | 3720| 614| num_trans_inp = insertions_sort( pCG, nInpNeighOrigAtNumb, MAX_NUM_STEREO_ATOM_NEIGH, sizeof( nInpNeighOrigAtNumb[0] ), comp_AT_NUMB ); ------------------ | | 877| 614|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ 3721| 614| num_trans_neigh = insertions_sort( pCG, nSbNeighOrigAtNumb, j1, sizeof( nSbNeighOrigAtNumb[0] ), comp_AT_NUMB ); 3722| | 3723| 614| if (j1 == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 877| 614|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3723:13): [True: 212, False: 402] ------------------ 3724| 212| { 3725| 212| ; 3726| | /*num_trans_neigh += j1;*/ 3727| | /* the lone pair or implicit H is implicitly at the top of the list */ 3728| 212| } 3729| 614| if (!memcmp( nInpNeighOrigAtNumb + MAX_NUM_STEREO_ATOM_NEIGH - j1, nSbNeighOrigAtNumb, j1 * sizeof( AT_NUMB ) )) ------------------ | | 877| 614|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3729:13): [True: 613, False: 1] ------------------ 3730| 613| { 3731| 613| if (ATOM_PARITY_WELL_DEF( at[cur_at].p_parity )) ------------------ | | 259| 613|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 613|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 613|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 613, False: 0] | | | Branch (259:75): [True: 539, False: 74] | | ------------------ ------------------ 3732| 539| { 3733| 539| parity = 2 - ( num_trans_inp + num_trans_neigh + at[cur_at].p_parity ) % 2; 3734| 539| } 3735| 74| else 3736| 74| { 3737| 74| parity = at[cur_at].p_parity; 3738| 74| } 3739| 613| at[cur_at].bUsed0DParity |= nFlag; /* 0D parity used for streocenter parity */ 3740| 613| } 3741| 614| } 3742| | 3743| 8.38k| return parity; 3744| 8.38k|} set_stereo_parity: 4375| 288k|{ 4376| 288k| int num_3D_stereo_atoms = 0; 4377| 288k| int num_stereo_bonds = 0; /* added to fix allene stereo bug reported for FClC=C=CFCl by Burt Leland - 2009-02-05 DT */ 4378| | 4379| 288k| int i, is_stereo, num_stereo, max_stereo_atoms = 0, max_stereo_bonds = 0; 4380| 288k| QUEUE *q = NULL; 4381| 288k| AT_RANK *nAtomLevel = NULL; 4382| 288k| S_CHAR *cSource = NULL; 4383| 288k| AT_RANK min_sb_ring_size = 0; 4384| | 4385| | /********************************************************** 4386| | * 4387| | * Note: this parity reflects only relative positions of 4388| | * the atoms-neighbors and their ordering in the 4389| | * lists of neighbors. 4390| | * 4391| | * To obtain the actual parity, the parity of a number 4392| | * of neighbors transpositions (to obtain a sorted 4393| | * list of numbers assigned to the atoms) should be 4394| | * added. 4395| | * 4396| | **********************************************************/ 4397| | 4398| | /********************************************************************************* 4399| | 4400| | An example of parity=1 for stereogenic center, tetrahedral asymmetric atom 4401| | 4402| | 4403| | 4404| | (1) 4405| | | 4406| | | 4407| | [C] | 4408| | | 4409| | (2)------(0) 4410| | / 4411| | / 4412| | / 4413| | / 4414| | (3) 4415| | 4416| | 4417| | Notation: (n) is a tetrahedral atom neighbor; n is an index of a neighbor in 4418| | the central_at->neighbor[] array : neighbor atom number is central_at->neighbor[n]. 4419| | 4420| | (0)-(1), (0)-(2), (0)-(3) are lines connecting atom [C] neighbors to neighbor (0) 4421| | (0), (1) and (2) are in the plane 4422| | (0)-(3) is directed from the plain to the viewer 4423| | [C] is somewhere between (0), (1), (2), (3) 4424| | Since (1)-(2)-(3) are in a clockwise order when looking from (0), parity is 2, or even; 4425| | otherwise parity would be 1, or odd. 4426| | 4427| | ********************************************************************************** 4428| | 4429| | Examples of a stereogenic bond. 4430| | 4431| | Notation: [atom number], (index of a neighbor): 4432| | [1] and [2] are atoms connected by the stereogenic bond 4433| | numbers in () are indexes of neighbors of [1] or [2]. 4434| | (12 x 16)z = z-component of [1]-[2] and [1]-[6] cross-product 4435| | 4436| | atom [1] atom [2] 4437| | [8] [4] prod01 = (12 x 16)z < 0 prod01 = (21 x 24)z < 0 4438| | \ / prod02 = (12 x 18)z > 0 prod02 = (21 x 25)z > 0 4439| | (2) (1) 0 transpositions because 0 transpositions because 4440| | \ / double bond is in 0 posit. double bond is in 0 position 4441| | [1]==(0)(0)==[2] 0 = (prod01 > prod02) 0 = (prod01 > prod02) 4442| | / \ 4443| | (1) (2) result: parity = 2, even result: parity=2, even 4444| | / \ 4445| | [6] [5] 4446| | 4447| | 4448| | 4449| | atom [1] atom [2] 4450| | [8] [5] prod01 = (12 x 18)z > 0 prod01 = (21 x 24)z > 0 4451| | \ / prod02 = (12 x 16)z < 0 prod02 = (21 x 25)z < 0 4452| | (0) (2) 2 transpositions to move 1 transposition to move 4453| | \ / at [2] from 2 to 0 pos. at [1] from 1 to 0 position 4454| | [1]==(2)(1)==[2] 1 = (prod01 > prod02) 1 = (prod01 > prod02) 4455| | / \ 4456| | (1) (0) result: parity = (1+2) result: parity=(1+1) 4457| | / \ 2-(1+2)%2 = 1, odd 2-(1+1)%2 = 2, even 4458| | [6] [4] 4459| | 4460| | 4461| | *********************************************************************************** 4462| | Note: atoms' numbers [1], [2], [4],... are not used to calculate parity at this 4463| | point. They will be used for each numbering in the canonicalization. 4464| | Note: parity=3 for a stereo atom means entered undefined bond direction 4465| | parity=4 for an atom means parity cannot be determined from the given geometry 4466| | ***********************************************************************************/ 4467| | 4468| 288k| if (!at_output || !at) ------------------ | Branch (4468:9): [True: 0, False: 288k] | Branch (4468:23): [True: 0, False: 288k] ------------------ 4469| 0| { 4470| 0| return -1; 4471| 0| } 4472| | 4473| | /* Clear stereo descriptors */ 4474| 1.38M| for (i = 0; i < num_at; i++) ------------------ | Branch (4474:17): [True: 1.09M, False: 288k] ------------------ 4475| 1.09M| { 4476| 1.09M| at_output[i].parity = 0; 4477| 1.09M| at_output[i].parity2 = 0; 4478| 1.09M| memset( &at_output[i].stereo_bond_neighbor[0], 0, sizeof( at_output[0].stereo_bond_neighbor ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4479| 1.09M| memset( &at_output[i].stereo_bond_neighbor2[0], 0, sizeof( at_output[0].stereo_bond_neighbor2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4480| 1.09M| memset( &at_output[i].stereo_bond_ord[0], 0, sizeof( at_output[0].stereo_bond_ord ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4481| 1.09M| memset( &at_output[i].stereo_bond_ord2[0], 0, sizeof( at_output[0].stereo_bond_ord2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4482| 1.09M| memset( &at_output[i].stereo_bond_z_prod[0], 0, sizeof( at_output[0].stereo_bond_z_prod ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4483| 1.09M| memset( &at_output[i].stereo_bond_z_prod2[0], 0, sizeof( at_output[0].stereo_bond_z_prod2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4484| 1.09M| memset( &at_output[i].stereo_bond_parity[0], 0, sizeof( at_output[0].stereo_bond_parity ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4485| 1.09M| memset( &at_output[i].stereo_bond_parity2[0], 0, sizeof( at_output[0].stereo_bond_parity2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4486| 1.09M| } 4487| | 4488| | /* Estimate max numbers of stereo atoms and bonds if isotopic H are added */ 4489| 288k| if (nMaxNumStereoAtoms || nMaxNumStereoBonds) ------------------ | Branch (4489:9): [True: 288k, False: 0] | Branch (4489:31): [True: 0, False: 0] ------------------ 4490| 288k| { 4491| 1.38M| for (i = 0; i < num_at; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (4491:21): [True: 1.09M, False: 288k] ------------------ 4492| 1.09M| { 4493| 1.09M| int num; 4494| 1.09M| num = can_be_a_stereo_atom_with_isotopic_H( at, i, bPointedEdgeStereo, bStereoAtZz ); 4495| 1.09M| if (num) ------------------ | Branch (4495:17): [True: 8.56k, False: 1.08M] ------------------ 4496| 8.56k| { 4497| 8.56k| max_stereo_atoms += num; 4498| 8.56k| } 4499| 1.08M| else 4500| 1.08M| { 4501| 1.08M| if (( num = can_be_a_stereo_bond_with_isotopic_H( at, i, nMode ) )) ------------------ | Branch (4501:21): [True: 6.72k, False: 1.07M] ------------------ 4502| 6.72k| { 4503| | /* accept cumulenes */ 4504| 6.72k| max_stereo_bonds += num; 4505| 6.72k| } 4506| 1.08M| } 4507| 1.09M| } 4508| 288k| if (nMaxNumStereoAtoms) ------------------ | Branch (4508:13): [True: 288k, False: 0] ------------------ 4509| 288k| { 4510| 288k| *nMaxNumStereoAtoms = max_stereo_atoms; 4511| 288k| } 4512| 288k| if (nMaxNumStereoBonds) ------------------ | Branch (4512:13): [True: 288k, False: 0] ------------------ 4513| 288k| { 4514| 288k| *nMaxNumStereoBonds = max_stereo_bonds; 4515| 288k| } 4516| 288k| } 4517| | 4518| | /* Calculate stereo descriptors */ 4519| 288k|#if ( MIN_SB_RING_SIZE > 0 ) 4520| 288k| min_sb_ring_size = (AT_RANK) ( ( ( nMode & REQ_MODE_MIN_SB_RING_MASK ) >> REQ_MODE_MIN_SB_RING_SHFT ) & AT_RANK_MASK ); ------------------ | | 43| 288k|#define REQ_MODE_MIN_SB_RING_MASK 0x0F0000 /* RSB */ ------------------ min_sb_ring_size = (AT_RANK) ( ( ( nMode & REQ_MODE_MIN_SB_RING_MASK ) >> REQ_MODE_MIN_SB_RING_SHFT ) & AT_RANK_MASK ); ------------------ | | 44| 288k|#define REQ_MODE_MIN_SB_RING_SHFT 16 ------------------ min_sb_ring_size = (AT_RANK) ( ( ( nMode & REQ_MODE_MIN_SB_RING_MASK ) >> REQ_MODE_MIN_SB_RING_SHFT ) & AT_RANK_MASK ); ------------------ | | 12| 288k|#define AT_RANK_MASK ((AT_RANK)~0) ------------------ 4521| 288k| if (min_sb_ring_size >= 3) ------------------ | Branch (4521:9): [True: 288k, False: 0] ------------------ 4522| 288k| { 4523| | /* Create BFS data structure for finding for each stereo bond its min. ring sizes */ 4524| 288k| q = QueueCreate( num_at + 1, sizeof( qInt ) ); 4525| 288k| nAtomLevel = (AT_RANK*) inchi_calloc( num_at, sizeof( nAtomLevel[0] ) ); ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ 4526| 288k| cSource = (S_CHAR *) inchi_calloc( num_at, sizeof( cSource[0] ) ); ------------------ | | 1146| 288k|#define inchi_calloc calloc ------------------ 4527| 288k| if (!q || !cSource || !nAtomLevel) ------------------ | Branch (4527:13): [True: 0, False: 288k] | Branch (4527:19): [True: 0, False: 288k] | Branch (4527:31): [True: 0, False: 288k] ------------------ 4528| 0| { 4529| 0| q = QueueDelete(q); /* djb-rwth: fixing coverity ID #499562 */ 4530| 0| inchi_free(nAtomLevel); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4531| 0| inchi_free(cSource); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4532| 0| num_3D_stereo_atoms = CT_OUT_OF_RAM; ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4533| 0| goto exit_function; 4534| 0| } 4535| 288k| } 4536| 0| else 4537| 0| { 4538| 0| min_sb_ring_size = 2; 4539| 0| } 4540| 288k|#endif 4541| | 4542| | /* Main cycle: set stereo parities */ 4543| 1.38M| for (i = 0, num_stereo = 0; i < num_at; i++) ------------------ | Branch (4543:33): [True: 1.09M, False: 288k] ------------------ 4544| 1.09M| { 4545| 1.09M| is_stereo = set_stereo_atom_parity( pCG, at_output, at, i, at + num_at, num_removed_H, 4546| 1.09M| bPointedEdgeStereo, vABParityUnknown, bLooseTSACheck, bStereoAtZz ); 4547| 1.09M| if (is_stereo) ------------------ | Branch (4547:13): [True: 8.38k, False: 1.08M] ------------------ 4548| 8.38k| { 4549| 8.38k| num_3D_stereo_atoms += ATOM_PARITY_WELL_DEF( is_stereo ); ------------------ | | 259| 8.38k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 8.38k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 8.38k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 8.38k, False: 0] | | | Branch (259:75): [True: 539, False: 7.85k] | | ------------------ ------------------ 4550| 8.38k| } 4551| 1.08M| else 4552| 1.08M| { 4553| 1.08M| is_stereo = set_stereo_bonds_parity( at_output, at, i, at + num_at, 4554| 1.08M| num_removed_H, nMode,q, 4555| 1.08M| nAtomLevel, cSource, 4556| 1.08M| min_sb_ring_size, 4557| 1.08M| bPointedEdgeStereo, 4558| 1.08M| vABParityUnknown ); 4559| 1.08M| if (RETURNED_ERROR( is_stereo )) ------------------ | | 44| 1.08M|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 1.08M|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 1.08M|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 1.08M|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 1.08M|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 1.08M|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 1.08M, False: 0] | | | Branch (44:53): [True: 26, False: 1.08M] | | ------------------ ------------------ 4560| 26| { 4561| 26| num_3D_stereo_atoms = is_stereo; 4562| 26| break; 4563| 26| } 4564| 1.08M| num_stereo_bonds += ( is_stereo != 0 ); /* added to fix bug reported by Burt Leland - 2009-02-05 DT */ 4565| 1.08M| } 4566| 1.09M| num_stereo += ( is_stereo != 0 ); 4567| | /* djb-rwth: removing redundant code */ 4568| 1.09M| } 4569| | 4570| | /* Added to fix bug reported by Burt Leland - 2009-02-05 DT */ 4571| 288k| if (max_stereo_atoms < num_3D_stereo_atoms && nMaxNumStereoAtoms) ------------------ | Branch (4571:9): [True: 0, False: 288k] | Branch (4571:51): [True: 0, False: 0] ------------------ 4572| 0| { 4573| 0| *nMaxNumStereoAtoms = num_3D_stereo_atoms; 4574| 0| } 4575| 288k| if (max_stereo_bonds < num_stereo_bonds && nMaxNumStereoBonds) ------------------ | Branch (4575:9): [True: 13, False: 288k] | Branch (4575:48): [True: 13, False: 0] ------------------ 4576| 13| { 4577| 13| *nMaxNumStereoBonds = num_stereo_bonds; 4578| 13| } 4579| | 4580| | /* 4581| | if ( (nMode & REQ_MODE_SC_IGN_ALL_UU ) 4582| | REQ_MODE_SC_IGN_ALL_UU 4583| | REQ_MODE_SB_IGN_ALL_UU 4584| | */ 4585| | 4586| 288k|#if ( MIN_SB_RING_SIZE > 0 ) 4587| 288k| if (q) ------------------ | Branch (4587:9): [True: 288k, False: 0] ------------------ 4588| 288k| { 4589| 288k| q = QueueDelete( q ); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 4590| 288k| } 4591| 288k| if (nAtomLevel) ------------------ | Branch (4591:9): [True: 288k, False: 0] ------------------ 4592| 288k| { 4593| 288k| inchi_free( nAtomLevel ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 4594| 288k| } 4595| 288k| if (cSource) ------------------ | Branch (4595:9): [True: 288k, False: 0] ------------------ 4596| 288k| { 4597| 288k| inchi_free( cSource ); ------------------ | | 1152| 288k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 288k, False: 0] | | | Branch (1152:50): [Folded, False: 288k] | | ------------------ ------------------ 4598| 288k| } 4599| | 4600| 288k|exit_function: 4601| 288k|#endif 4602| | 4603| 288k| return num_3D_stereo_atoms; 4604| 288k|} ReconcileAllCmlBondParities: 4631| 361k|{ 4632| 361k| int i, ret = 0; 4633| 361k| S_CHAR *visited = (S_CHAR*) inchi_calloc( num_atoms, sizeof( *visited ) ); ------------------ | | 1146| 361k|#define inchi_calloc calloc ------------------ 4634| 361k| if (!visited) ------------------ | Branch (4634:9): [True: 0, False: 361k] ------------------ 4635| 0| { 4636| 0| return -1; /* out of RAM */ 4637| 0| } 4638| 2.57M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4638:17): [True: 2.21M, False: 361k] ------------------ 4639| 2.21M| { 4640| 2.21M| if (at[i].sb_parity[0] && !visited[i] && !( bDisconnected && is_el_a_metal( at[i].el_number ) )) ------------------ | Branch (4640:13): [True: 3.02k, False: 2.20M] | Branch (4640:35): [True: 1.94k, False: 1.08k] | Branch (4640:53): [True: 0, False: 1.94k] | Branch (4640:70): [True: 0, False: 0] ------------------ 4641| 1.94k| { 4642| 1.94k| if ((ret = ReconcileCmlIncidentBondParities( at, i, -1, visited, bDisconnected ))) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4642:17): [True: 58, False: 1.88k] ------------------ 4643| 58| { 4644| 58| break; /* error */ 4645| 58| } 4646| 1.94k| } 4647| 2.21M| } 4648| 361k| inchi_free( visited ); ------------------ | | 1152| 361k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 361k, False: 0] | | | Branch (1152:50): [Folded, False: 361k] | | ------------------ ------------------ 4649| | 4650| 361k| return ret; 4651| 361k|} ReconcileCmlIncidentBondParities: 4660| 3.08k|{ 4661| | /* visited = 0 or parity => atom has not been visited 4662| | 10 + parity => currently is on the stack + its final parity 4663| | 20 + parity => has been visited; is not on the stack anymore + its final parity */ 4664| 3.08k| int i, j, nxt_atom, ret = 0, len; 4665| 3.08k| int icur2nxt, icur2neigh; /* cur atom neighbors */ 4666| 3.08k| int inxt2cur, inxt2neigh; /* next atom neighbors */ 4667| 3.08k| int cur_parity, nxt_parity; 4668| 3.08k| int cur_order_parity, nxt_order_parity, cur_sb_parity, nxt_sb_parity, bCurMask, bNxtMask; 4669| | /* !(bDisconnected && is_el_a_metal(at[i].el_number) */ 4670| | 4671| 3.08k| if (at[cur_atom].valence > MAX_NUM_STEREO_BONDS) ------------------ | | 873| 3.08k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (4671:9): [True: 0, False: 3.08k] ------------------ 4672| 0| { 4673| 0| return 0; /* ignore */ 4674| 0| } 4675| | 4676| 3.08k| if (!at[cur_atom].sb_parity[0]) ------------------ | Branch (4676:9): [True: 0, False: 3.08k] ------------------ 4677| 0| { 4678| 0| return 1; /* wrong call */ 4679| 0| } 4680| | 4681| 3.08k| if (visited[cur_atom] >= 10) ------------------ | Branch (4681:9): [True: 0, False: 3.08k] ------------------ 4682| 0| { 4683| 0| return 2; /* program error */ 4684| 0| } 4685| | 4686| 3.08k| cur_parity = visited[cur_atom] % 10; 4687| | 4688| 3.08k| visited[cur_atom] += 10; 4689| | 4690| 6.49k| for (i = 0; i < MAX_NUM_STEREO_BONDS && at[cur_atom].sb_parity[i]; i++) ------------------ | | 873| 12.9k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (4690:17): [True: 6.44k, False: 53] | Branch (4690:45): [True: 3.53k, False: 2.91k] ------------------ 4691| 3.53k| { 4692| 3.53k| icur2nxt = (int) at[cur_atom].sb_ord[i]; 4693| 3.53k| len = get_opposite_sb_atom( at, cur_atom, icur2nxt, &nxt_atom, &inxt2cur, &j ); 4694| 3.53k| if (!len) ------------------ | Branch (4694:13): [True: 24, False: 3.50k] ------------------ 4695| 24| { 4696| 24| return 4; /* could not find the opposite atom: bond parity data error */ 4697| 24| } 4698| 3.50k| if (nxt_atom == prev_atom) ------------------ | Branch (4698:13): [True: 1.12k, False: 2.38k] ------------------ 4699| 1.12k| { 4700| 1.12k| continue; 4701| 1.12k| } 4702| 2.38k| if (visited[nxt_atom] >= 20) ------------------ | Branch (4702:13): [True: 592, False: 1.79k] ------------------ 4703| 592| { 4704| 592| continue; /* back edge, second visit: ignore */ 4705| 592| } 4706| 1.79k| if (at[nxt_atom].valence > MAX_NUM_STEREO_BONDS) ------------------ | | 873| 1.79k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (4706:13): [True: 0, False: 1.79k] ------------------ 4707| 0| { 4708| 0| continue; /* may be treated only after metal disconnection */ 4709| 0| } 4710| | 4711| 1.79k| if (bDisconnected && ( at[cur_atom].sb_parity[i] & SB_PARITY_FLAG )) ------------------ | | 62| 0|#define SB_PARITY_FLAG 0x38 /**< mask for disconnected metal parity if it is different */ ------------------ | Branch (4711:13): [True: 0, False: 1.79k] | Branch (4711:30): [True: 0, False: 0] ------------------ 4712| 0| { 4713| 0| cur_sb_parity = ( at[cur_atom].sb_parity[i] >> SB_PARITY_SHFT ); ------------------ | | 63| 0|#define SB_PARITY_SHFT 3 /**< number of right shift bits to get disconnected metal parity */ ------------------ 4714| 0| bCurMask = 3 << SB_PARITY_SHFT; ------------------ | | 63| 0|#define SB_PARITY_SHFT 3 /**< number of right shift bits to get disconnected metal parity */ ------------------ 4715| 0| } 4716| 1.79k| else 4717| 1.79k| { 4718| 1.79k| cur_sb_parity = ( at[cur_atom].sb_parity[i] & SB_PARITY_MASK ); ------------------ | | 64| 1.79k|#define SB_PARITY_MASK 0x07 ------------------ 4719| 1.79k| bCurMask = 3; 4720| 1.79k| } 4721| 1.79k| if (bDisconnected && ( at[nxt_atom].sb_parity[j] & SB_PARITY_FLAG )) ------------------ | | 62| 0|#define SB_PARITY_FLAG 0x38 /**< mask for disconnected metal parity if it is different */ ------------------ | Branch (4721:13): [True: 0, False: 1.79k] | Branch (4721:30): [True: 0, False: 0] ------------------ 4722| 0| { 4723| 0| nxt_sb_parity = ( at[nxt_atom].sb_parity[j] >> SB_PARITY_SHFT ); ------------------ | | 63| 0|#define SB_PARITY_SHFT 3 /**< number of right shift bits to get disconnected metal parity */ ------------------ 4724| 0| bNxtMask = 3 << SB_PARITY_SHFT; ------------------ | | 63| 0|#define SB_PARITY_SHFT 3 /**< number of right shift bits to get disconnected metal parity */ ------------------ 4725| 0| } 4726| 1.79k| else 4727| 1.79k| { 4728| 1.79k| nxt_sb_parity = ( at[nxt_atom].sb_parity[j] & SB_PARITY_MASK ); ------------------ | | 64| 1.79k|#define SB_PARITY_MASK 0x07 ------------------ 4729| 1.79k| bNxtMask = 3; 4730| 1.79k| } 4731| | 4732| 1.79k| if (!ATOM_PARITY_WELL_DEF( cur_sb_parity ) || ------------------ | | 259| 3.59k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.79k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.79k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 1.79k, False: 0] | | | Branch (259:75): [True: 1.19k, False: 605] | | ------------------ ------------------ 4733| 1.19k| !ATOM_PARITY_WELL_DEF( nxt_sb_parity )) ------------------ | | 259| 1.19k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.19k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1.19k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 1.19k, False: 0] | | | Branch (259:75): [True: 1.18k, False: 7] | | ------------------ ------------------ 4734| 612| { 4735| 612| if (cur_sb_parity == nxt_sb_parity) ------------------ | Branch (4735:17): [True: 605, False: 7] ------------------ 4736| 605| { 4737| 605| continue; 4738| | /* goto move_forward; */ 4739| | /* bypass unknown/undefined */ 4740| 605| } 4741| 7| return 3; /* sb parities do not match: bond parity data error */ 4742| 612| } 4743| | 4744| 1.18k| icur2neigh = (int) at[cur_atom].sn_ord[i]; 4745| 1.18k| inxt2neigh = (int) at[nxt_atom].sn_ord[j]; 4746| | /* Parity of at[cur_atom].neighbor[] premutation to reach this order: { next_atom, neigh_atom, ...} */ 4747| | 4748| | /* 1. move next_atom from position=icur2nxt to position=0 => 4749| | * icur2nxt permutations 4750| | * 2. move neigh_atom from position=inxt2neigh+(inxt2cur > inxt2neigh) to position=1 => 4751| | * inxt2neigh+(inxt2cur > inxt2neigh)-1 permutations. 4752| | * Note if (inxt2cur > inxt2neigh) then move #1 increments neigh_atom position 4753| | * Note add 4 because icur2neigh may be negative due to isotopic H removal 4754| | */ 4755| 1.18k| cur_order_parity = ( 4 + icur2nxt + icur2neigh + ( icur2neigh > icur2nxt ) ) % 2; 4756| | 4757| | /* Same for next atom: */ 4758| | /* parity of at[nxt_atom].neighbor[] premutation to reach this order: { cur_atom, neigh_atom, ...} */ 4759| 1.18k| nxt_order_parity = ( 4 + inxt2cur + inxt2neigh + ( inxt2neigh > inxt2cur ) ) % 2; 4760| 1.18k| nxt_parity = visited[nxt_atom] % 10; 4761| | 4762| 1.18k| if (!cur_parity) ------------------ | Branch (4762:13): [True: 960, False: 223] ------------------ 4763| 960| { 4764| 960| cur_parity = 2 - ( cur_order_parity + cur_sb_parity ) % 2; 4765| 960| visited[cur_atom] += cur_parity; 4766| 960| } 4767| 223| else 4768| 223| { 4769| 223| if (cur_parity != 2 - ( cur_order_parity + cur_sb_parity ) % 2) ------------------ | Branch (4769:17): [True: 69, False: 154] ------------------ 4770| 69| { 4771| | /***** Reconcile bond parities *****/ 4772| | 4773| | /* Each bond parity is split into two values located at the end atoms. 4774| | For T (trans) the values are (1,1) or (2,2) 4775| | For C (cis) the values are (1,2) or (2,1) 4776| | The fact that one pair = another with inverted parities, namely 4777| | Inv(1,1) = (2,2) and Inv(1,2) = (2,1), allows to 4778| | simultaneouly invert parities of the current bond end atoms 4779| | (at[cur_atom].sb_parity[i], at[nxt_atom].sb_parity[j]) 4780| | so that the final current atom parity cur_parity 4781| | calculated later in stereochemical canonicalization for 4782| | each stereobond incident with the current atomis same. 4783| | Achieving this is called here RECONCILIATION. 4784| | If at the closure of an aromatic circuit the parities of 4785| | next atom cannot be reconciled with already calculated then 4786| | this function returns 5 (error). 4787| | */ 4788| 69| at[cur_atom].sb_parity[i] ^= bCurMask; 4789| 69| at[nxt_atom].sb_parity[j] ^= bNxtMask; 4790| | /* djb-rwth: removing redundant code */ 4791| 69| nxt_sb_parity ^= 3; 4792| 69| } 4793| 223| } 4794| | 4795| 1.18k| if (!nxt_parity) ------------------ | Branch (4795:13): [True: 1.14k, False: 36] ------------------ 4796| 1.14k| { 4797| 1.14k| nxt_parity = 2 - ( nxt_order_parity + nxt_sb_parity ) % 2; 4798| 1.14k| visited[nxt_atom] += nxt_parity; 4799| 1.14k| } 4800| 36| else 4801| 36| { 4802| 36| if (nxt_parity != 2 - ( nxt_order_parity + nxt_sb_parity ) % 2) ------------------ | Branch (4802:17): [True: 27, False: 9] ------------------ 4803| 27| { 4804| 27| return 5; /* algorithm does not work for Mebius-like structures */ 4805| 27| } 4806| 36| } 4807| | 4808| | /* Move_forward: */ 4809| 1.15k| if (visited[nxt_atom] < 10) ------------------ | Branch (4809:13): [True: 1.14k, False: 9] ------------------ 4810| 1.14k| { 4811| 1.14k| ret = ReconcileCmlIncidentBondParities( at, nxt_atom, cur_atom, visited, bDisconnected ); 4812| 1.14k| if (ret) ------------------ | Branch (4812:17): [True: 63, False: 1.08k] ------------------ 4813| 63| { 4814| 63| break; 4815| 63| } 4816| 1.14k| } 4817| 1.15k| } 4818| 3.03k| visited[cur_atom] += 10; /* all bonds incident to the current atom have 4819| | been processed or an error occurred. */ 4820| | 4821| 3.03k| return ret; 4822| 3.08k|} get_opposite_sb_atom: 4832| 5.07k|{ 4833| 5.07k| AT_NUMB nxt_atom; 4834| 5.07k| int j, len; 4835| | 4836| 5.07k| len = 0; 4837| 5.26k| while (len++ < 20) ------------------ | Branch (4837:12): [True: 5.26k, False: 0] ------------------ 4838| 5.26k| { 4839| | /* Arbitrarily set cumulene length limit to avoid infinite loop */ 4840| 5.26k| nxt_atom = at[cur_atom].neighbor[icur2nxt]; 4841| 6.05k| for (j = 0; j < MAX_NUM_STEREO_BONDS && at[nxt_atom].sb_parity[j]; j++) ------------------ | | 873| 12.1k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (4841:21): [True: 6.05k, False: 0] | Branch (4841:49): [True: 5.81k, False: 235] ------------------ 4842| 5.81k| { 4843| 5.81k| if (cur_atom == at[nxt_atom].neighbor[(int) at[nxt_atom].sb_ord[j]]) ------------------ | Branch (4843:17): [True: 5.03k, False: 785] ------------------ 4844| 5.03k| { 4845| | /* Found the opposite atom */ 4846| 5.03k| *pnxt_atom = nxt_atom; 4847| 5.03k| *pinxt2cur = at[nxt_atom].sb_ord[j]; 4848| 5.03k| *pinxt_sb_parity_ord = j; 4849| 5.03k| return len; 4850| 5.03k| } 4851| 5.81k| } 4852| 235| if (j) ------------------ | Branch (4852:13): [True: 18, False: 217] ------------------ 4853| 18| { 4854| 18| return 0; /* reached atom(s) with stereobond (sb) parity, the opposite atom has not been found */ 4855| 18| } 4856| 217| if (at[nxt_atom].valence == 2 && 2 * BOND_TYPE_DOUBLE == at[nxt_atom].chem_bonds_valence) ------------------ | | 33| 217|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (4856:13): [True: 217, False: 0] | Branch (4856:42): [True: 195, False: 22] ------------------ 4857| 195| { 4858| | /* Follow cumulene =X= path */ 4859| 195| icur2nxt = ( at[nxt_atom].neighbor[0] == cur_atom ); 4860| 195| cur_atom = nxt_atom; 4861| 195| } 4862| 22| else 4863| 22| { 4864| 22| return 0; /* neither atom with a sb parity not middle cumulene could be reached */ 4865| 22| } 4866| 217| } 4867| | 4868| 0| return 0; /* too long chain of cumulene was found */ 4869| 5.07k|} ichister.c:bInpAtomHasRequirdNeigh: 1287| 22.6k|{ 1288| | /* RequirdNeighType: 1289| | reqired neighbor types (bitmap): 1290| | 0 => any neighbors 1291| | 1 => no terminal hydrogen atom neighbors 1292| | 2 => no terminal -X and -XH together (don't care about -X, -XH bond type, charge, radical) 1293| | (X = tautomeric endpoint atom) 1294| | NumDbleBonds: 1295| | if non-zero then allow double, alternating and tautomeric bonds 1296| | */ 1297| 22.6k| int i, j, ni, nj, bond_type, num_1s, num_mult, num_other; 1298| | 1299| 22.6k| if (at[cur_at].endpoint) ------------------ | Branch (1299:9): [True: 258, False: 22.4k] ------------------ 1300| 258| { 1301| | /* tautomeric endpoint cannot be a stereo center */ 1302| 258| return 0; 1303| 258| } 1304| | 1305| 22.4k| if (( 1 & RequirdNeighType ) && at[cur_at].num_H) ------------------ | Branch (1305:9): [True: 18.1k, False: 4.21k] | Branch (1305:37): [True: 1.27k, False: 16.9k] ------------------ 1306| 1.27k| { 1307| 1.27k| return 0; 1308| 1.27k| } 1309| | 1310| 21.1k| if (2 & RequirdNeighType) ------------------ | Branch (1310:9): [True: 15.4k, False: 5.70k] ------------------ 1311| 15.4k| { 1312| 64.6k| for (i = 0; i < at[cur_at].valence; i++) ------------------ | Branch (1312:21): [True: 51.3k, False: 13.3k] ------------------ 1313| 51.3k| { 1314| 51.3k| ni = (int) at[cur_at].neighbor[i]; 1315| 51.3k| if (at[ni].valence != 1 || ------------------ | Branch (1315:17): [True: 30.3k, False: 20.9k] ------------------ 1316| 20.9k| !get_endpoint_valence( at[ni].el_number )) ------------------ | Branch (1316:18): [True: 8.13k, False: 12.8k] ------------------ 1317| 38.5k| { 1318| 38.5k| continue; 1319| 38.5k| } 1320| 25.7k| for (j = i + 1; j < at[cur_at].valence; j++) ------------------ | Branch (1320:29): [True: 15.1k, False: 10.6k] ------------------ 1321| 15.1k| { 1322| 15.1k| nj = (int) at[cur_at].neighbor[j]; 1323| 15.1k| if (at[nj].valence != 1 || ------------------ | Branch (1323:21): [True: 5.06k, False: 10.0k] ------------------ 1324| 10.0k| at[ni].el_number != at[nj].el_number || ------------------ | Branch (1324:22): [True: 5.44k, False: 4.59k] ------------------ 1325| 4.59k| !get_endpoint_valence( at[nj].el_number )) ------------------ | Branch (1325:22): [True: 0, False: 4.59k] ------------------ 1326| 10.5k| { 1327| 10.5k| continue; 1328| 10.5k| } 1329| | /* 1330| | * if (at[ni].num_H != at[nj].num_H) then the atoms (neighbors of at[cur_at] 1331| | * are tautomeric endpoints and are indistinguishable => cur_at is not stereogenic 1332| | * if (at[ni].num_H == at[nj].num_H) then the neighbors are indistinguishable 1333| | * and cur_at will be found non-sterogenic later 1334| | * get_endpoint_valence() check will not allow the neighbors to be carbons 1335| | * Therefore the following "if" is not needed; we may just return 0. 1336| | */ 1337| 4.59k| if (at[ni].num_H != at[nj].num_H && strcmp( at[ni].elname, "C" )) ------------------ | Branch (1337:21): [True: 2.12k, False: 2.46k] | Branch (1337:53): [True: 2.12k, False: 0] ------------------ 1338| 2.12k| { 1339| 2.12k| return 0; /* found -X and -XH neighbors */ 1340| 2.12k| } 1341| 4.59k| } 1342| 12.8k| } 1343| 15.4k| } 1344| | 1345| 19.0k| if (0==bStereoAtZz) ------------------ | Branch (1345:9): [True: 19.0k, False: 0] ------------------ 1346| 19.0k| { 1347| | /* No stereo allowed at centers connected to pseudoelement atoms "Zz","Zy" */ 1348| 19.0k| int nbr, inbr; 1349| 86.8k| for (inbr = 0; inbr < at[cur_at].valence; inbr++) ------------------ | Branch (1349:24): [True: 67.8k, False: 18.9k] ------------------ 1350| 67.8k| { 1351| 67.8k| nbr = (int) at[cur_at].neighbor[inbr]; 1352| 67.8k| if (!strcmp( at[nbr].elname, "Zz" ) || !strcmp( at[nbr].elname, "Zy" )) ------------------ | Branch (1352:17): [True: 34, False: 67.8k] | Branch (1352:52): [True: 26, False: 67.8k] ------------------ 1353| 60| { 1354| 60| return 0; 1355| 60| } 1356| 67.8k| } 1357| 19.0k| } 1358| | 1359| 18.9k| num_1s = num_mult = num_other = 0; 1360| | 1361| 86.6k| for (i = 0; i < at[cur_at].valence; i++) ------------------ | Branch (1361:17): [True: 67.7k, False: 18.9k] ------------------ 1362| 67.7k| { 1363| 67.7k| bond_type = ( at[cur_at].bond_type[i] & ~BOND_MARK_ALL ); ------------------ | | 191| 67.7k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 1364| 67.7k| switch (bond_type) 1365| 67.7k| { 1366| 49.2k| case BOND_SINGLE: ------------------ | | 177| 49.2k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 49.2k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1366:13): [True: 49.2k, False: 18.5k] ------------------ 1367| 49.2k| num_1s++; 1368| 49.2k| break; 1369| 6.82k| case BOND_DOUBLE: ------------------ | | 178| 6.82k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 6.82k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1369:13): [True: 6.82k, False: 60.9k] ------------------ 1370| 9.48k| case BOND_ALTERN: ------------------ | | 180| 9.48k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 9.48k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (1370:13): [True: 2.66k, False: 65.0k] ------------------ 1371| 14.7k| case BOND_TAUTOM: ------------------ | | 185| 14.7k|#define BOND_TAUTOM 8 ------------------ | Branch (1371:13): [True: 5.28k, False: 62.4k] ------------------ 1372| 18.0k| case BOND_ALT12NS: ------------------ | | 186| 18.0k|#define BOND_ALT12NS 9 ------------------ | Branch (1372:13): [True: 3.24k, False: 64.5k] ------------------ 1373| 18.0k| num_mult++; 1374| 18.0k| break; 1375| 491| default: ------------------ | Branch (1375:13): [True: 491, False: 67.2k] ------------------ 1376| 491| num_other++; 1377| 491| break; 1378| 67.7k| } 1379| 67.7k| } 1380| | 1381| 18.9k| if (num_other) ------------------ | Branch (1381:9): [True: 401, False: 18.5k] ------------------ 1382| 401| { 1383| 401| return 0; 1384| 401| } 1385| | 1386| 18.5k| if ((NumDbleBonds && NumDbleBonds > num_mult) || ------------------ | Branch (1386:10): [True: 10.3k, False: 8.18k] | Branch (1386:26): [True: 0, False: 10.3k] ------------------ 1387| 18.5k| (!NumDbleBonds && at[cur_at].valence != num_1s)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1387:11): [True: 8.18k, False: 10.3k] | Branch (1387:28): [True: 94, False: 8.09k] ------------------ 1388| 94| { 1389| 94| return 0; 1390| 94| } 1391| | 1392| 18.4k| return 1; 1393| 18.5k|} ichister.c:len3: 187| 20.8k|{ 188| 20.8k| double tmpar[ARR_DIM] = { 0.0 }; 189| |#if USE_BCF 190| | memcpy_s(tmpar, ARR_DIM * sizeof(c[0]), c, ARR_DIM * sizeof(c[0])); 191| |#else 192| 20.8k| memcpy(tmpar, c, ARR_DIM * sizeof(c[0])); ------------------ | | 26| 20.8k|#define ARR_DIM 3 /* djb-rwth: default dimension of arrays */ ------------------ 193| 20.8k|#endif 194| 20.8k| return sqrt(pow(tmpar[0],2.0) + pow(tmpar[1],2.0) + pow(tmpar[2],2.0) ); 195| 20.8k|} ichister.c:mult3: 236| 30|{ 237| 30| result[0] = a[0] * b; 238| 30| result[1] = a[1] * b; 239| 30| result[2] = a[2] * b; 240| | 241| | /* return result; */ 242| 30|} ichister.c:can_be_a_stereo_atom_with_isotopic_H: 3659| 1.09M|{ 3660| 1.09M| int nNumNeigh; 3661| 1.09M| if (( nNumNeigh = bCanInpAtomBeAStereoCenter( at, cur_at, bPointedEdgeStereo, bStereoAtZz ) ) && ------------------ | Branch (3661:9): [True: 8.56k, False: 1.08M] ------------------ 3662| 8.56k| at[cur_at].valence + at[cur_at].num_H == nNumNeigh && ------------------ | Branch (3662:10): [True: 8.56k, False: 0] ------------------ 3663| 8.56k| at[cur_at].num_H <= NUM_H_ISOTOPES ------------------ | | 25| 8.56k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3663:10): [True: 8.56k, False: 0] ------------------ 3664| 1.09M| ) 3665| 8.56k| { 3666| 8.56k| return 1; 3667| 8.56k| } 3668| | 3669| 1.08M| return 0; 3670| 1.09M|} ichister.c:can_be_a_stereo_bond_with_isotopic_H: 2606| 1.08M|{ 2607| 1.08M| int i, j, next_at, num_stereo_bonds, bFound; 2608| 1.08M| int bond_type, num_2s, num_alt; 2609| 1.08M| int num_2s_next, num_alt_next, num_wrong_bonds_1, num_wrong_bonds_2; 2610| 1.08M|#if ( N_V_STEREOBONDS == 1 ) 2611| 1.08M| int n2sh, num_2s_hetero[2], num_2s_hetero_next[2], next_next_at, type_N, type_N_next; 2612| 1.08M|#endif 2613| | 2614| 1.08M| if (MAX_NUM_STEREO_BOND_NEIGH < at[cur_at].valence + at[cur_at].num_H || ------------------ | | 874| 1.08M|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2614:9): [True: 10.8k, False: 1.07M] ------------------ 2615| 1.07M| MIN_NUM_STEREO_BOND_NEIGH > at[cur_at].valence + at[cur_at].num_H) ------------------ | | 875| 1.07M|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (2615:10): [True: 933k, False: 141k] ------------------ 2616| 944k| { 2617| 944k| return 0; 2618| 944k| } 2619| 141k| if (!bCanAtomHaveAStereoBond( at[cur_at].elname, at[cur_at].charge, at[cur_at].radical )) ------------------ | Branch (2619:9): [True: 87.3k, False: 53.8k] ------------------ 2620| 87.3k| { 2621| 87.3k| return 0; 2622| 87.3k| } 2623| | 2624| | /* Count bonds and find the second atom on the stereo bond */ 2625| 53.8k| num_2s = num_alt = num_wrong_bonds_1 = 0; 2626| 53.8k|#if ( N_V_STEREOBONDS == 1 ) 2627| 53.8k| num_2s_hetero[0] = num_2s_hetero[1] = type_N = 0; 2628| 53.8k| if (0 == at[cur_at].num_H && 0 == at[cur_at].charge && 0 == at[cur_at].radical && ------------------ | Branch (2628:9): [True: 49.9k, False: 3.89k] | Branch (2628:34): [True: 43.8k, False: 6.06k] | Branch (2628:60): [True: 43.8k, False: 0] ------------------ 2629| 43.8k| 3 == get_endpoint_valence( at[cur_at].el_number )) ------------------ | Branch (2629:10): [True: 27.5k, False: 16.3k] ------------------ 2630| 27.5k| { 2631| 27.5k| if (2 == at[cur_at].valence && 3 == at[cur_at].chem_bonds_valence) ------------------ | Branch (2631:13): [True: 21.9k, False: 5.52k] | Branch (2631:40): [True: 19.6k, False: 2.36k] ------------------ 2632| 19.6k| { 2633| 19.6k| type_N = 1; 2634| 19.6k| } 2635| 7.88k| else 2636| 7.88k| { 2637| 7.88k| if (3 == at[cur_at].valence && 5 == at[cur_at].chem_bonds_valence) ------------------ | Branch (2637:17): [True: 5.52k, False: 2.36k] | Branch (2637:44): [True: 4.44k, False: 1.07k] ------------------ 2638| 4.44k| { 2639| 4.44k| type_N = 2; /* unfortunately includes >N# */ 2640| 4.44k| } 2641| 7.88k| } 2642| 27.5k| } 2643| 53.8k|#endif 2644| 135k| for (i = 0, num_stereo_bonds = 0; i < at[cur_at].valence; i++) ------------------ | Branch (2644:39): [True: 102k, False: 33.0k] ------------------ 2645| 102k| { 2646| 102k| bFound = 0; 2647| 102k| next_at = at[cur_at].neighbor[i]; 2648| 102k| bond_type = get_allowed_stereo_bond_type( (int) at[cur_at].bond_type[i] ); 2649| 102k| if (bond_type == BOND_ALTERN) ------------------ | | 180| 102k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 102k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2649:13): [True: 7.58k, False: 94.8k] ------------------ 2650| 7.58k| { 2651| 7.58k| num_alt++; 2652| 7.58k| if (cur_at > next_at && !( nMode & CMODE_NO_ALT_SBONDS )) ------------------ | | 777| 3.91k|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (2652:17): [True: 3.91k, False: 3.67k] | Branch (2652:37): [True: 3.91k, False: 0] ------------------ 2653| 3.91k| { 2654| 3.91k| bFound = 1; 2655| 3.91k| } 2656| 7.58k| } 2657| 94.8k| else 2658| 94.8k| { 2659| 94.8k| if (bond_type == BOND_DOUBLE) ------------------ | | 178| 94.8k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 94.8k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (2659:17): [True: 28.3k, False: 66.5k] ------------------ 2660| 28.3k| { 2661| 28.3k| num_2s++; 2662| 28.3k|#if ( N_V_STEREOBONDS == 1 ) 2663| 28.3k| if (0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + next_at ) )) ------------------ | Branch (2663:21): [True: 9.21k, False: 19.1k] ------------------ 2664| 9.21k| { 2665| 9.21k| num_2s_hetero[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 2666| 9.21k| } 2667| 28.3k|#endif 2668| 28.3k| if (cur_at > next_at) ------------------ | Branch (2668:21): [True: 11.7k, False: 16.5k] ------------------ 2669| 11.7k| bFound = 1; 2670| 28.3k| } 2671| 66.5k| else 2672| 66.5k| { 2673| 66.5k| if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 177| 66.5k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 133k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 185| 32.0k|#define BOND_TAUTOM 8 ------------------ | Branch (2673:21): [True: 32.0k, False: 34.5k] | Branch (2673:49): [True: 24.3k, False: 7.68k] ------------------ 2674| 24.3k| { 2675| 24.3k| num_wrong_bonds_1++; 2676| 24.3k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 2677| 24.3k| if (num_wrong_bonds_1 > 1 || (num_wrong_bonds_1 && 2 >= at[cur_at].valence)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2677:25): [True: 2.09k, False: 22.2k] | Branch (2677:51): [True: 22.2k, False: 0] | Branch (2677:72): [True: 18.6k, False: 3.56k] ------------------ 2678| 20.7k| { 2679| 20.7k| return 0; /* wrong bond type */ 2680| 20.7k| } 2681| 3.56k| else 2682| 3.56k| { 2683| 3.56k| continue; 2684| 3.56k| } 2685| |#else 2686| | return 0; /* wrong bond type */ 2687| |#endif 2688| 24.3k| } 2689| 66.5k| } 2690| 94.8k| } 2691| | 2692| 78.1k| if (bFound) ------------------ | Branch (2692:13): [True: 15.6k, False: 62.4k] ------------------ 2693| 15.6k| { 2694| | /* check "next_at" atom on the opposite side of the bond */ 2695| 15.6k| if (MAX_NUM_STEREO_BOND_NEIGH < at[next_at].valence + at[next_at].num_H || ------------------ | | 874| 15.6k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2695:17): [True: 221, False: 15.4k] ------------------ 2696| 15.4k| MIN_NUM_STEREO_BOND_NEIGH > at[next_at].valence + at[next_at].num_H) ------------------ | | 875| 15.4k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (2696:18): [True: 2.23k, False: 13.2k] ------------------ 2697| 2.45k| { 2698| 2.45k| continue; 2699| 2.45k| } 2700| 13.2k| if (!bCanAtomHaveAStereoBond( at[next_at].elname, at[next_at].charge, at[next_at].radical )) ------------------ | Branch (2700:17): [True: 2.21k, False: 11.0k] ------------------ 2701| 2.21k| { 2702| 2.21k| continue; 2703| 2.21k| } 2704| | /* next atom neighbors */ 2705| 11.0k| num_2s_next = num_alt_next = num_wrong_bonds_2 = 0; 2706| 11.0k|#if ( N_V_STEREOBONDS == 1 ) 2707| 11.0k| num_2s_hetero_next[0] = num_2s_hetero_next[1] = type_N_next = 0; 2708| 11.0k| if (0 == at[next_at].num_H && 0 == at[next_at].charge && 0 == at[next_at].radical && ------------------ | Branch (2708:17): [True: 10.6k, False: 378] | Branch (2708:43): [True: 10.2k, False: 404] | Branch (2708:70): [True: 10.2k, False: 0] ------------------ 2709| 10.2k| 3 == get_endpoint_valence( at[next_at].el_number )) ------------------ | Branch (2709:18): [True: 6.97k, False: 3.26k] ------------------ 2710| 6.97k| { 2711| 6.97k| if (2 == at[next_at].valence && 3 == at[next_at].chem_bonds_valence) ------------------ | Branch (2711:21): [True: 6.14k, False: 828] | Branch (2711:49): [True: 5.58k, False: 556] ------------------ 2712| 5.58k| { 2713| 5.58k| type_N_next = 1; /* -N= */ 2714| 5.58k| } 2715| 1.38k| else 2716| 1.38k| { 2717| 1.38k| if (3 == at[next_at].valence && 5 == at[next_at].chem_bonds_valence) ------------------ | Branch (2717:25): [True: 828, False: 556] | Branch (2717:53): [True: 806, False: 22] ------------------ 2718| 806| { 2719| 806| type_N_next = 2; /* unfortunately includes >N# */ 2720| 806| } 2721| 1.38k| } 2722| 6.97k| } 2723| 11.0k|#endif 2724| 34.4k| for (j = 0; j < at[next_at].valence; j++) ------------------ | Branch (2724:25): [True: 23.4k, False: 11.0k] ------------------ 2725| 23.4k| { 2726| 23.4k| bond_type = get_allowed_stereo_bond_type( (int) at[next_at].bond_type[j] ); 2727| 23.4k| if (bond_type == BOND_ALTERN) ------------------ | | 180| 23.4k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 23.4k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2727:21): [True: 6.41k, False: 17.0k] ------------------ 2728| 6.41k| { 2729| 6.41k| num_alt_next++; 2730| 6.41k| } 2731| 17.0k| else 2732| 17.0k| { 2733| 17.0k| if (bond_type == BOND_DOUBLE) ------------------ | | 178| 17.0k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 17.0k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (2733:25): [True: 10.4k, False: 6.52k] ------------------ 2734| 10.4k| { 2735| 10.4k| num_2s_next++; 2736| 10.4k|#if ( N_V_STEREOBONDS == 1 ) 2737| 10.4k| next_next_at = at[next_at].neighbor[j]; 2738| 10.4k| if (0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + next_next_at ) )) ------------------ | Branch (2738:29): [True: 4.19k, False: 6.28k] ------------------ 2739| 4.19k| { 2740| 4.19k| num_2s_hetero_next[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 2741| 4.19k| } 2742| 10.4k|#endif 2743| 10.4k| } 2744| 6.52k| else 2745| 6.52k| { 2746| 6.52k| if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 177| 6.52k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 13.0k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 185| 1.47k|#define BOND_TAUTOM 8 ------------------ | Branch (2746:29): [True: 1.47k, False: 5.04k] | Branch (2746:57): [True: 1.47k, False: 4] ------------------ 2747| 1.47k| { 2748| 1.47k| num_wrong_bonds_2++; 2749| 1.47k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 2750| 1.47k| if (num_wrong_bonds_1 > 1 || (num_wrong_bonds_1 && 2 >= at[cur_at].valence)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2750:33): [True: 0, False: 1.47k] | Branch (2750:59): [True: 3, False: 1.47k] | Branch (2750:80): [True: 0, False: 3] ------------------ 2751| 0| { 2752| 0| break; /* wrong bond type */ 2753| 0| } 2754| 1.47k| else 2755| 1.47k| { 2756| 1.47k| continue; 2757| 1.47k| } 2758| |#else 2759| | break; /* wrong bond type */ 2760| |#endif 2761| 1.47k| } 2762| 6.52k| } 2763| 17.0k| } 2764| 23.4k| } 2765| | /* figure out whether the at[cur_at]--at[next_at] bond may not be stereogenic */ 2766| | 2767| 11.0k|#if ( N_V_STEREOBONDS == 1 ) 2768| 11.0k| if (3 == ( type_N | type_N_next ) && ------------------ | Branch (2768:17): [True: 1.77k, False: 9.24k] ------------------ 2769| 1.77k| ( (2 == type_N && !bIsOxide( at, cur_at )) || ------------------ | Branch (2769:20): [True: 1.01k, False: 763] | Branch (2769:35): [True: 592, False: 419] ------------------ 2770| 1.18k| (2 == type_N_next && !bIsOxide( at, next_at )) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2770:22): [True: 763, False: 419] | Branch (2770:42): [True: 677, False: 86] ------------------ 2771| 1.26k| { 2772| 1.26k| bFound = 0; 2773| 1.26k| } 2774| 9.75k| else 2775| 9.75k|#endif 2776| 9.75k| { 2777| 9.75k| if (j < at[next_at].valence || /* at[next_at] has a wrong bond type*/ ------------------ | Branch (2777:21): [True: 0, False: 9.75k] ------------------ 2778| 9.75k| ( num_alt_next > 0 ) + ( num_2s_next > 0 ) != 1 /* only one type of stereogenic bond permitted */ ------------------ | Branch (2778:21): [True: 71, False: 9.67k] ------------------ 2779| 9.75k| ) 2780| 71| { 2781| 71| bFound = 0; 2782| 71| } 2783| 9.67k| else 2784| 9.67k| { 2785| 9.67k| if (2 < num_2s_next) ------------------ | Branch (2785:25): [True: 0, False: 9.67k] ------------------ 2786| 0| { 2787| 0| bFound = 0; 2788| 0| } 2789| 9.67k| else 2790| 9.67k| { 2791| 9.67k| if (2 == num_2s_next) ------------------ | Branch (2791:29): [True: 2.34k, False: 7.33k] ------------------ 2792| 2.34k| { 2793| 2.34k| if (2 == at[next_at].valence) ------------------ | Branch (2793:33): [True: 2.24k, False: 109] ------------------ 2794| 2.24k| { 2795| 2.24k| ; /* only one double bond permitted except cumulenes */ 2796| 2.24k|#if ( N_V_STEREOBONDS == 1 ) 2797| 2.24k| } 2798| 109| else 2799| 109| { 2800| 109| if (1 == ( num_2s_hetero_next[0] | num_2s_hetero_next[1] ) && ------------------ | Branch (2800:37): [True: 61, False: 48] ------------------ 2801| 61| 3 == at[next_at].valence + at[next_at].num_H && ------------------ | Branch (2801:41): [True: 54, False: 7] ------------------ 2802| 54| 5 == at[next_at].chem_bonds_valence + at[next_at].num_H && ------------------ | Branch (2802:41): [True: 54, False: 0] ------------------ 2803| 54| 3 == get_endpoint_valence( at[next_at].el_number ) && ------------------ | Branch (2803:41): [True: 41, False: 13] ------------------ 2804| 41| ( !type_N || bIsOxide( at, next_at ) )) ------------------ | Branch (2804:43): [True: 10, False: 31] | Branch (2804:54): [True: 15, False: 16] ------------------ 2805| 25| { 2806| 25| ; /* 2807| | * found: 2808| | * 2809| | * \ / \ / \ / 2810| | * \ / \ / \ / 2811| | * N==C or N==C or N==N 2812| | * // \ // \ // \ 2813| | * O ^ \ N ^ \ O ^ \ 2814| | * | | | 2815| | * | | | 2816| | * at[next_at] at[next_at] at[next_at] 2817| | */ 2818| 25|#endif 2819| 25| } 2820| 84| else 2821| 84| { 2822| 84| bFound = 0; 2823| 84| } 2824| 109| } 2825| 2.34k| } 2826| 9.67k| } 2827| 9.67k| } 2828| 9.75k| } 2829| 11.0k| } 2830| 73.4k| if (bFound) ------------------ | Branch (2830:13): [True: 9.59k, False: 63.8k] ------------------ 2831| 9.59k| { 2832| 9.59k| num_stereo_bonds++; 2833| 9.59k| } 2834| 73.4k| } 2835| | 2836| 33.0k| if (( num_alt > 0 ) + ( num_2s > 0 ) != 1 || !num_stereo_bonds) ------------------ | Branch (2836:9): [True: 7.72k, False: 25.3k] | Branch (2836:50): [True: 17.8k, False: 7.50k] ------------------ 2837| 25.5k| { 2838| 25.5k| return 0; 2839| 25.5k| } 2840| | 2841| 7.50k| if (num_2s > 1) ------------------ | Branch (2841:9): [True: 1.57k, False: 5.92k] ------------------ 2842| 1.57k| { 2843| 1.57k|#if ( N_V_STEREOBONDS == 1 ) 2844| 1.57k| if (2 == num_2s && ------------------ | Branch (2844:13): [True: 1.57k, False: 0] ------------------ 2845| 1.57k| 1 == ( num_2s_hetero[0] | num_2s_hetero[1] ) && ------------------ | Branch (2845:14): [True: 1.06k, False: 516] ------------------ 2846| 1.06k| 3 == at[cur_at].valence + at[cur_at].num_H && ------------------ | Branch (2846:14): [True: 802, False: 260] ------------------ 2847| 802| 5 == at[cur_at].chem_bonds_valence + at[cur_at].num_H && ------------------ | Branch (2847:14): [True: 802, False: 0] ------------------ 2848| 802| 3 == get_endpoint_valence( at[cur_at].el_number )) ------------------ | Branch (2848:14): [True: 799, False: 3] ------------------ 2849| 799| { 2850| 799| ; 2851| 799| } 2852| 779| else 2853| 779| { 2854| 779| return 0; 2855| 779| } 2856| |#else 2857| | return 0; 2858| |#endif 2859| 1.57k| } 2860| | 2861| 6.72k| return num_stereo_bonds; 2862| 7.50k|} ichister.c:get_allowed_stereo_bond_type: 2554| 308k|{ 2555| |#if (ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS == 0 ) 2556| | if (( bond_type & ~BOND_MARK_ALL ) == BOND_TAUTOM) 2557| | { 2558| | return 0; /* no tautomer bonds allowed */ 2559| | } 2560| | else 2561| |#endif 2562| |#if ( EXCL_ALL_AROM_BOND_PARITY == 1 ) /* { */ 2563| | /* a stereo bond cannot belong to an aromatic atom */ 2564| | if (( bond_type &= ~BOND_MARK_ALL ) == BOND_ALTERN) 2565| | { 2566| | return 0; 2567| | } 2568| |#else /* } { */ 2569| 308k|#if ( ADD_6MEMB_AROM_BOND_PARITY == 1 ) 2570| | /* accept any aromatic bond as a stereo bond */ 2571| 308k| if (( bond_type &= ~BOND_MARK_ALL ) == BOND_ALTERN) ------------------ | | 191| 308k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ if (( bond_type &= ~BOND_MARK_ALL ) == BOND_ALTERN) ------------------ | | 180| 308k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 308k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2571:9): [True: 31.1k, False: 276k] ------------------ 2572| |#else 2573| | /* accept only aromatic bonds in non-6-member rings */ 2574| | if (( bond_type &= ~BOND_MARK_ALL ) == BOND_ALTERN) ) 2575| |#endif 2576| 31.1k| { 2577| 31.1k| return BOND_ALTERN; ------------------ | | 180| 31.1k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 31.1k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ 2578| 31.1k| } 2579| 276k|#endif /* } */ 2580| 276k| else 2581| 276k| { 2582| | /* at this point BOND_MARK_ALL bits have been removed from bond_type */ 2583| 276k| if (bond_type == BOND_DOUBLE || bond_type == BOND_SINGLE) ------------------ | | 178| 276k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 553k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ if (bond_type == BOND_DOUBLE || bond_type == BOND_SINGLE) ------------------ | | 177| 188k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 188k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (2583:13): [True: 88.3k, False: 188k] | Branch (2583:41): [True: 101k, False: 86.8k] ------------------ 2584| 190k| { 2585| 190k| return bond_type; 2586| 190k| } 2587| 86.8k|#if (ALLOW_TAUT_ATTACHMENTS_TO_STEREO_BONDS == 1 ) 2588| 86.8k| else 2589| 86.8k| { 2590| 86.8k| if (bond_type == BOND_TAUTOM) ------------------ | | 185| 86.8k|#define BOND_TAUTOM 8 ------------------ | Branch (2590:17): [True: 16.8k, False: 69.9k] ------------------ 2591| 16.8k| { 2592| 16.8k| return BOND_TAUTOM; ------------------ | | 185| 16.8k|#define BOND_TAUTOM 8 ------------------ 2593| 16.8k| } 2594| 86.8k| } 2595| 276k|#endif 2596| 276k| } 2597| | 2598| 69.9k| return 0; /* wrong bond type */ 2599| 308k|} ichister.c:bIsSuitableHeteroInpAtom: 1600| 70.3k|{ 1601| 70.3k| int val, num_H; 1602| 70.3k| if (0 == at->charge && ------------------ | Branch (1602:9): [True: 57.3k, False: 12.9k] ------------------ 1603| 57.3k| ( !at->radical || RADICAL_SINGLET == at->radical ) && ------------------ | | 75| 2.23k|#define RADICAL_SINGLET 1 ------------------ | Branch (1603:11): [True: 55.1k, False: 2.23k] | Branch (1603:27): [True: 0, False: 2.23k] ------------------ 1604| 55.1k| 0 < ( val = get_endpoint_valence( at->el_number ) )) ------------------ | Branch (1604:10): [True: 41.6k, False: 13.5k] ------------------ 1605| 41.6k| { 1606| 41.6k| num_H = at->num_H; 1607| 41.6k| if (val == at->chem_bonds_valence + num_H) ------------------ | Branch (1607:13): [True: 26.5k, False: 15.0k] ------------------ 1608| 26.5k| { 1609| 26.5k| switch (val) ------------------ | Branch (1609:21): [True: 26.5k, False: 0] ------------------ 1610| 26.5k| { 1611| 5.80k| case 2: /* O */ ------------------ | Branch (1611:17): [True: 5.80k, False: 20.7k] ------------------ 1612| 5.80k| if (!num_H && 1 == at->valence) ------------------ | Branch (1612:25): [True: 5.76k, False: 41] | Branch (1612:35): [True: 5.76k, False: 0] ------------------ 1613| 5.76k| { 1614| 5.76k| return 0; /* =O */ 1615| 5.76k| } 1616| 41| break; /* not found */ 1617| 20.7k| case 3: /* N */ ------------------ | Branch (1617:17): [True: 20.7k, False: 5.80k] ------------------ 1618| 20.7k| if ((1 == at->valence && 1 == num_H) || ------------------ | Branch (1618:26): [True: 616, False: 20.1k] | Branch (1618:46): [True: 616, False: 0] ------------------ 1619| 20.1k| (2 == at->valence && 0 == num_H)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (1619:27): [True: 20.0k, False: 84] | Branch (1619:47): [True: 19.9k, False: 127] ------------------ 1620| 20.5k| { 1621| 20.5k| return 1; /* =N- or =NH */ 1622| 20.5k| } 1623| 211| break; /* not found */ 1624| 26.5k| } 1625| 26.5k| } 1626| 41.6k| } 1627| 44.0k| return -1; 1628| 70.3k|} ichister.c:bIsOxide: 1633| 3.37k|{ 1634| 3.37k| int i, bond_type; 1635| 3.37k| inp_ATOM *a = at + cur_at, *an; 1636| 12.0k| for (i = 0; i < a->valence; i++) ------------------ | Branch (1636:17): [True: 9.60k, False: 2.40k] ------------------ 1637| 9.60k| { 1638| 9.60k| bond_type = ( a->bond_type[i] &= ~BOND_MARK_ALL ); ------------------ | | 191| 9.60k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 1639| 9.60k| if (bond_type == BOND_DOUBLE) ------------------ | | 178| 9.60k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 9.60k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1639:13): [True: 5.70k, False: 3.90k] ------------------ 1640| 5.70k| { 1641| 5.70k| an = at + (int) a->neighbor[i]; 1642| 5.70k| if (1 == an->valence && ------------------ | Branch (1642:17): [True: 1.48k, False: 4.22k] ------------------ 1643| 1.48k| !an->charge && !an->num_H && !an->radical && ------------------ | Branch (1643:18): [True: 984, False: 498] | Branch (1643:33): [True: 960, False: 24] | Branch (1643:47): [True: 954, False: 6] ------------------ 1644| 954| 2 == get_endpoint_valence( an->el_number )) ------------------ | Branch (1644:18): [True: 944, False: 10] ------------------ 1645| 944| { 1646| 944| return 1; 1647| 944| } 1648| 5.70k| } 1649| 3.90k| else 1650| 3.90k| { 1651| 3.90k| if (bond_type == BOND_TAUTOM || bond_type == BOND_ALT12NS) ------------------ | | 185| 7.81k|#define BOND_TAUTOM 8 ------------------ if (bond_type == BOND_TAUTOM || bond_type == BOND_ALT12NS) ------------------ | | 186| 3.90k|#define BOND_ALT12NS 9 ------------------ | Branch (1651:17): [True: 0, False: 3.90k] | Branch (1651:45): [True: 54, False: 3.85k] ------------------ 1652| 54| { 1653| 54| an = at + (int) a->neighbor[i]; 1654| 54| if (1 == an->valence && ------------------ | Branch (1654:21): [True: 27, False: 27] ------------------ 1655| 27| 2 == get_endpoint_valence( an->el_number )) ------------------ | Branch (1655:22): [True: 26, False: 1] ------------------ 1656| 26| { 1657| 26| return 1; 1658| 26| } 1659| 54| } 1660| 3.90k| } 1661| 9.60k| } 1662| | 1663| 2.40k| return 0; 1664| 3.37k|} ichister.c:set_stereo_atom_parity: 3765| 1.09M|{ 3766| 1.09M| int j, k, next_at, num_z, j1, nType, num_explicit_H, tot_num_iso_H, nMustHaveNumNeigh; 3767| 1.09M| int num_explicit_iso_H[NUM_H_ISOTOPES + 1]; 3768| | /* numbers of removed hydrogen atoms */ 3769| 1.09M| int index_H[MAX_NUM_STEREO_ATOM_NEIGH]; 3770| | /* cannot have more than 4 elements: 1 H, 1 D, 1 T atom(s) */ 3771| 1.09M| double z, sum_xyz[3], min_sine, triple_product; 3772| 1.09M| double at_coord[MAX_NUM_STEREO_ATOM_NEIGH][3]; 3773| 1.09M| double bond_len_xy[4], rmax = 0.0, rmin = 0.0; 3774| 1.09M| double at_coord_center[3]; 3775| 1.09M| int parity, bAmbiguous = 0, bAddExplicitNeighbor = 0, b2D = 0, n2DTetrahedralAmbiguity = 0; 3776| 1.09M| int bIgnoreIsotopicH = ( 0 != ( at[cur_at].cFlags & AT_FLAG_ISO_H_POINT ) ); ------------------ | | 50| 1.09M|#define AT_FLAG_ISO_H_POINT 0x01 /**< may have isotopic H */ ------------------ 3777| 1.09M| AT_NUMB nSbNeighOrigAtNumb[MAX_NUM_STEREO_ATOM_NEIGH]; 3778| | 3779| 1.09M| double vMinAngle = MIN_ANGLE; ------------------ | | 29| 1.09M|#define MIN_ANGLE 0.10 /* 5.73 degrees */ /* treshold for proximity to in-line angle of 180 deg */ ------------------ 3780| 1.09M| double vMinSine = MIN_SINE; ------------------ | | 30| 1.09M|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ 3781| 1.09M| if (LooseTSACheck) ------------------ | Branch (3781:9): [True: 0, False: 1.09M] ------------------ 3782| 0| { 3783| | /* Relax check for principal 3-atomic angles close to 180 deg, for 2D tetrahedron, to account for */ 3784| | /* large cycles drawn as appear after applying some structure 'cleaning' algorithms/softwares */ 3785| | 3786| 0| if (at[cur_at].nNumAtInRingSystem >= 3) /* Ensure that central atom is in ring (ideally, one should check */ ------------------ | Branch (3786:13): [True: 0, False: 0] ------------------ 3787| | /* also that neighbors are in-ring, and for large enough ring) */ 3788| 0| { 3789| 0| vMinAngle = MIN_ANGLE_RELAXED; ------------------ | | 31| 0|#define MIN_ANGLE_RELAXED 0.001 ------------------ 3790| 0| vMinSine = MIN_SINE_RELAXED; ------------------ | | 32| 0|#define MIN_SINE_RELAXED 0.001 ------------------ 3791| 0| } 3792| 0| } 3793| | 3794| 1.09M| out_at[cur_at].parity = 3795| 1.09M| out_at[cur_at].parity2 = 3796| 1.09M| out_at[cur_at].stereo_atom_parity = 3797| 1.09M| out_at[cur_at].stereo_atom_parity2 = 3798| 1.09M| AB_PARITY_NONE; ------------------ | | 218| 1.09M|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 3799| 1.09M| parity = AB_PARITY_NONE; ------------------ | | 218| 1.09M|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 3800| | 3801| 1.09M| memset( num_explicit_iso_H, 0, sizeof( num_explicit_iso_H ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3802| 1.09M| num_explicit_H = 0; 3803| | 3804| 1.09M|#if ( NEW_STEREOCENTER_CHECK == 1 ) 3805| 1.09M| if (!( nMustHaveNumNeigh = bCanInpAtomBeAStereoCenter( at, cur_at, bPointedEdgeStereo, bStereoAtZz ) ) || ------------------ | Branch (3805:9): [True: 1.08M, False: 8.56k] ------------------ 3806| 8.56k| at[cur_at].num_H > NUM_H_ISOTOPES) ------------------ | | 25| 8.56k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3806:10): [True: 0, False: 8.56k] ------------------ 3807| 1.08M| { 3808| 1.08M| goto exit_function; 3809| 1.08M| } 3810| |#else 3811| | nMustHaveNumNeigh = MAX_NUM_STEREO_ATOM_NEIGH; 3812| | if (!bCanAtomBeAStereoCenter( at[cur_at].elname, at[cur_at].charge, at[cur_at].radical ) || 3813| | at[cur_at].valence + at[cur_at].num_H != nMustHaveNumNeigh || 3814| | at[cur_at].num_H > NUM_H_ISOTOPES 3815| | ) 3816| | { 3817| | goto exit_function; 3818| | } 3819| | for (j = 0; j < at[cur_at].valence; j++) 3820| | { 3821| | if (( at[cur_at].bond_type[j] & ~BOND_MARK_ALL ) != BOND_SINGLE) 3822| | { 3823| | goto exit_function; 3824| | } 3825| | } 3826| |#endif 3827| | 3828| | /* numbers of isotopic H atoms */ 3829| 34.1k| for (j = 0, tot_num_iso_H = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 25| 34.1k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3829:36): [True: 25.6k, False: 8.52k] ------------------ 3830| 25.6k| { 3831| 25.6k| if (at[cur_at].num_iso_H[j] > 1) ------------------ | Branch (3831:13): [True: 39, False: 25.5k] ------------------ 3832| 39| { 3833| 39| goto exit_function; /* two or more identical hydrogen isotopic neighbors */ 3834| 39| } 3835| 25.5k| tot_num_iso_H += at[cur_at].num_iso_H[j]; 3836| 25.5k| } 3837| 8.52k| if (bIgnoreIsotopicH) ------------------ | Branch (3837:9): [True: 0, False: 8.52k] ------------------ 3838| 0| { 3839| 0| tot_num_iso_H = 0; /* isotopic H considered subject to exchange => ignore isotopic */ 3840| 0| } 3841| | /* number of non-isotopic H atoms */ 3842| 8.52k| if (at[cur_at].num_H - tot_num_iso_H > 1) ------------------ | Branch (3842:9): [True: 129, False: 8.39k] ------------------ 3843| 129| { 3844| 129| goto exit_function; /* two or more identical hydrogen non-isotopic neighbors */ 3845| 129| } 3846| | 3847| | /* count removed explicit terminal hydrogens attached to at[cur_at]. */ 3848| | /* the result is num_explicit_H. */ 3849| | /* Removed hydrogens are sorted in increasing isotopic shift order */ 3850| 8.39k| if (at_removed_H && num_removed_H > 0) ------------------ | Branch (3850:9): [True: 8.39k, False: 0] | Branch (3850:25): [True: 618, False: 7.77k] ------------------ 3851| 618| { 3852| 1.46k| for (j = 0; j < num_removed_H; j++) ------------------ | Branch (3852:21): [True: 843, False: 618] ------------------ 3853| 843| { 3854| 843| if (at_removed_H[j].neighbor[0] == cur_at) ------------------ | Branch (3854:17): [True: 103, False: 740] ------------------ 3855| 103| { 3856| 103| k = at_removed_H[j].iso_atw_diff; 3857| | /* iso_atw_diff values: H=>0, 1H=>1, D=2H=>2, T=3H=>3 */ 3858| 103| if (k < 0 || k > NUM_H_ISOTOPES || bIgnoreIsotopicH) ------------------ | | 25| 206|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3858:21): [True: 0, False: 103] | Branch (3858:30): [True: 0, False: 103] | Branch (3858:52): [True: 0, False: 103] ------------------ 3859| 0| { 3860| 0| k = 0; /* treat wrong H isotopes as non-isotopic H */ 3861| 0| } 3862| 103| num_explicit_iso_H[k] ++; 3863| 103| index_H[num_explicit_H++] = j; 3864| 103| } 3865| 843| } 3866| 618| } 3867| | 3868| | /* coordinates initialization */ 3869| 8.39k| num_z = 0; 3870| 8.39k| sum_xyz[0] = sum_xyz[1] = sum_xyz[2] = 0.0; 3871| | 3872| 8.39k| at_coord_center[0] = 3873| 8.39k| at_coord_center[1] = 3874| 8.39k| at_coord_center[2] = 3875| 8.39k| 0.0; 3876| | 3877| | /* fill out stereo center neighbors coordinates */ 3878| | /* and obtain the parity from the geometry */ 3879| | 3880| 25.1k| for (k = 0, j1 = 0; k < 2; k++) ------------------ | Branch (3880:25): [True: 16.7k, False: 8.39k] ------------------ 3881| 16.7k| { 3882| 16.7k| switch (k) ------------------ | Branch (3882:17): [True: 16.7k, False: 0] ------------------ 3883| 16.7k| { 3884| | 3885| 8.39k| case 0: ------------------ | Branch (3885:13): [True: 8.39k, False: 8.39k] ------------------ 3886| | /* add coordinates of removed hydrogens */ 3887| 8.49k| for (j = 0; j < num_explicit_H; j++, j1++) ------------------ | Branch (3887:29): [True: 103, False: 8.39k] ------------------ 3888| 103| { 3889| 103| next_at = index_H[j]; 3890| | /* Use bond description located at removed_H atom */ 3891| | /* minus sign at get_z_coord: at_removed_H[] contains bonds TO at[cur_at], not FROM it. */ 3892| | /* Note: &at[(at_removed_H-at)+ next_at] == &at_removed_H[next_at] */ 3893| 103| z = -get_z_coord( at, 3894| 103| (int) ( at_removed_H - at ) + next_at, 3895| 103| 0 /*neighbor #*/, 3896| 103| &nType, 3897| 103| -( bPointedEdgeStereo & PES_BIT_POINT_EDGE_STEREO ) ); ------------------ | | 44| 103|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ 3898| 103| switch (nType) ------------------ | Branch (3898:29): [True: 0, False: 103] ------------------ 3899| 103| { 3900| 0| case ZTYPE_EITHER: ------------------ | | 24| 0|#define ZTYPE_EITHER 9999 ------------------ | Branch (3900:25): [True: 0, False: 103] ------------------ 3901| 0| parity = vABParityUnknown /*AB_PARITY_UNKN*/; /* no parity: bond in "Either" direction. */ 3902| 0| goto exit_function; 3903| 0| case ZTYPE_UP: ------------------ | | 22| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3903:25): [True: 0, False: 103] ------------------ 3904| 0| case ZTYPE_DOWN: ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3904:25): [True: 0, False: 103] ------------------ 3905| 0| nType = -nType; /* at_removed_H[] contains bonds TO the center, not from */ 3906| 0| b2D++; 3907| | /* no break; here */ 3908| 0| case ZTYPE_3D: ------------------ | | 23| 0|#define ZTYPE_3D 3 ------------------ | Branch (3908:25): [True: 0, False: 103] ------------------ 3909| 0| num_z++; 3910| 103| } 3911| | 3912| 103| if (j1 < MAX_NUM_STEREO_ATOM_NEIGH) /* djb-rwth: fixing oss-fuzz issue #71142 */ ------------------ | | 877| 103|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3912:25): [True: 103, False: 0] ------------------ 3913| 103| { 3914| 103| nSbNeighOrigAtNumb[j1] = at_removed_H[next_at].orig_at_number; 3915| 103| at_coord[j1][0] = at_removed_H[next_at].x - at[cur_at].x; 3916| 103| at_coord[j1][1] = at_removed_H[next_at].y - at[cur_at].y; 3917| 103| bond_len_xy[j1] = len2(at_coord[j1]); 3918| | /* bond_len_xy[j1] = sqrt(at_coord[j1][0]*at_coord[j1][0]+at_coord[j1][1]*at_coord[j1][1]); */ 3919| 103| at_coord[j1][2] = (nType == ZTYPE_3D ? z : nType == ZTYPE_UP ------------------ | | 23| 103|#define ZTYPE_3D 3 ------------------ at_coord[j1][2] = (nType == ZTYPE_3D ? z : nType == ZTYPE_UP ------------------ | | 22| 103|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3919:44): [True: 0, False: 103] | Branch (3919:68): [True: 0, False: 103] ------------------ 3920| 103| ? bond_len_xy[j1] : nType == ZTYPE_DOWN ------------------ | | 20| 103|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3920:49): [True: 0, False: 103] ------------------ 3921| 103| ? -bond_len_xy[j1] : 0.0); 3922| 103| } 3923| 0| else 3924| 0| { 3925| 0| break; 3926| 0| } 3927| 103| } 3928| 8.39k| break; 3929| 8.39k| case 1: ------------------ | Branch (3929:13): [True: 8.39k, False: 8.39k] ------------------ 3930| | /* add all coordinates of other neighboring atoms */ 3931| 38.9k| for (j = 0; j < at[cur_at].valence; j++, j1++) ------------------ | Branch (3931:29): [True: 30.5k, False: 8.39k] ------------------ 3932| 30.5k| { 3933| 30.5k| next_at = at[cur_at].neighbor[j]; 3934| 30.5k| z = get_z_coord( at, cur_at, j, &nType, ( bPointedEdgeStereo & PES_BIT_POINT_EDGE_STEREO ) ); ------------------ | | 44| 30.5k|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ 3935| 30.5k| switch (nType) ------------------ | Branch (3935:29): [True: 0, False: 30.5k] ------------------ 3936| 30.5k| { 3937| 0| case ZTYPE_EITHER: ------------------ | | 24| 0|#define ZTYPE_EITHER 9999 ------------------ | Branch (3937:25): [True: 0, False: 30.5k] ------------------ 3938| 0| parity = vABParityUnknown /*AB_PARITY_UNKN*/; /* unknown parity: bond in "Either" direction. */ 3939| 0| goto exit_function; 3940| 0| case ZTYPE_UP: ------------------ | | 22| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3940:25): [True: 0, False: 30.5k] ------------------ 3941| 0| case ZTYPE_DOWN: ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3941:25): [True: 0, False: 30.5k] ------------------ 3942| 0| b2D++; 3943| 0| case ZTYPE_3D: ------------------ | | 23| 0|#define ZTYPE_3D 3 ------------------ | Branch (3943:25): [True: 0, False: 30.5k] ------------------ 3944| 0| num_z++; 3945| 30.5k| } 3946| | 3947| 30.5k| if (j1 < MAX_NUM_STEREO_ATOM_NEIGH) /* djb-rwth: fixing oss-fuzz issue #71142 */ ------------------ | | 877| 30.5k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3947:25): [True: 30.5k, False: 4] ------------------ 3948| 30.5k| { 3949| 30.5k| nSbNeighOrigAtNumb[j1] = at[next_at].orig_at_number; 3950| 30.5k| at_coord[j1][0] = at[next_at].x - at[cur_at].x; 3951| 30.5k| at_coord[j1][1] = at[next_at].y - at[cur_at].y; 3952| 30.5k| bond_len_xy[j1] = len2(at_coord[j1]); 3953| | /* bond_len_xy[j1] = sqrt(at_coord[j1][0]*at_coord[j1][0]+at_coord[j1][1]*at_coord[j1][1]); */ 3954| 30.5k| at_coord[j1][2] = (nType == ZTYPE_3D ? z : ------------------ | | 23| 30.5k|#define ZTYPE_3D 3 ------------------ | Branch (3954:44): [True: 0, False: 30.5k] ------------------ 3955| 30.5k| nType == ZTYPE_UP ? bond_len_xy[j1] : ------------------ | | 22| 30.5k|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3955:29): [True: 0, False: 30.5k] ------------------ 3956| 30.5k| nType == ZTYPE_DOWN ? -bond_len_xy[j1] : 0.0); ------------------ | | 20| 30.5k|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3956:29): [True: 0, False: 30.5k] ------------------ 3957| 30.5k| } 3958| 4| else 3959| 4| { 3960| 4| break; 3961| 4| } 3962| 30.5k| } 3963| 8.39k| break; 3964| 16.7k| } 3965| 16.7k| } 3966| | /* j1 is the number of explicit neighbors (that is, all neighbors except implicit H) */ 3967| 8.39k| b2D = ( b2D == num_z && num_z ); /* 1 => two-dimensional */ ------------------ | Branch (3967:13): [True: 8.39k, False: 0] | Branch (3967:29): [True: 0, False: 8.39k] ------------------ 3968| | 3969| 8.39k| if (MAX_NUM_STEREO_ATOM_NEIGH != at[cur_at].valence + num_explicit_H && ------------------ | | 877| 8.39k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3969:9): [True: 2.96k, False: 5.43k] ------------------ 3970| 2.96k| MAX_NUM_STEREO_ATOM_NEIGH - 1 != at[cur_at].valence + num_explicit_H) ------------------ | | 877| 2.96k|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3970:10): [True: 6, False: 2.95k] ------------------ 3971| 6| { 3972| | /* not enough geometry data to find the central atom parity */ 3973| 6| if (nMustHaveNumNeigh == at[cur_at].valence + at[cur_at].num_H && ------------------ | Branch (3973:13): [True: 6, False: 0] ------------------ 3974| 6| at[cur_at].num_H > 1) ------------------ | Branch (3974:13): [True: 1, False: 5] ------------------ 3975| 1| { 3976| | /* only isotopic parity is possible; no non-isotopic parity */ 3977| 1| if (parity == vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (3977:17): [True: 0, False: 1] ------------------ 3978| 0| { 3979| 0| parity = -vABParityUnknown /*AB_PARITY_UNKN*/; /* the user marked the center as "unknown" */ 3980| 0| } 3981| 1| else 3982| 1| { 3983| 1| parity = -AB_PARITY_UNDF; /* not enough geometry; only isotopic parity is possible */ ------------------ | | 222| 1|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 3984| 1| } 3985| 1| } 3986| 5| else 3987| 5| { 3988| 5| parity = AB_PARITY_NONE; /* not a stereocenter at all */ ------------------ | | 218| 5|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 3989| 5| } 3990| 6| goto exit_function; 3991| 6| } 3992| | /* make all vector lengths equal to 1; exit if too short. 9-10-2002 */ 3993| 8.38k| for (j = 0; j < j1; j++) ------------------ | Branch (3993:17): [True: 8.38k, False: 0] ------------------ 3994| 8.38k| { 3995| 8.38k| z = len3( at_coord[j] ); 3996| 8.38k| if (z < MIN_BOND_LEN) ------------------ | | 39| 8.38k|#define MIN_BOND_LEN 0.000001 ------------------ | Branch (3996:13): [True: 8.38k, False: 0] ------------------ 3997| 8.38k| { 3998| | /* bond length is too small: use 0D parities */ 3999| 8.38k| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, ------------------ | | 218| 8.38k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (3999:17): [True: 7.77k, False: 613] ------------------ 4000| 8.38k| j1,nSbNeighOrigAtNumb, 4001| 8.38k| FlagSC_0D ) )) ------------------ | | 59| 8.38k|#define FlagSC_0D 1 /**< bUsed0DParity */ ------------------ 4002| 7.77k| { 4003| 7.77k| parity = AB_PARITY_UNDF; ------------------ | | 222| 7.77k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4004| 7.77k| } 4005| 8.38k| goto exit_function; 4006| 8.38k| } 4007| 0|#if ( STEREO_CENTER_BONDS_NORM == 1 ) 4008| 0| else 4009| 0| { 4010| 0| mult3( at_coord[j], 1.0 / z, at_coord[j] ); 4011| 0| } 4012| 0|#endif 4013| 0| rmax = j ? inchi_max( rmax, z ) : z; ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4013:16): [True: 0, False: 0] ------------------ 4014| 0| rmin = j ? inchi_min( rmin, z ) : z; ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4014:16): [True: 0, False: 0] ------------------ 4015| 0| } 4016| 0| if (rmin / rmax < MIN_SINE) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (4016:9): [True: 0, False: 0] ------------------ 4017| 0| { 4018| | /* bond ratio is too small: use 0D parities */ 4019| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (4019:13): [True: 0, False: 0] ------------------ 4020| 0| nSbNeighOrigAtNumb, 4021| 0| FlagSC_0D ) )) ------------------ | | 59| 0|#define FlagSC_0D 1 /**< bUsed0DParity */ ------------------ 4022| 0| { 4023| 0| parity = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4024| 0| } 4025| 0| goto exit_function; 4026| 0| } 4027| 0| for (j = 0; j < j1; j++) ------------------ | Branch (4027:17): [True: 0, False: 0] ------------------ 4028| 0| { 4029| 0| add3( sum_xyz, at_coord[j], sum_xyz ); 4030| 0| } 4031| | 4032| | /* Here j1 is a number of neighbors including explicit terminal isotopic H */ 4033| | /* num_explicit_iso_H[0] = number of explicit non-isotopic hydrogen atom neighbors */ 4034| 0| j = j1; 4035| | /* Add Explicit Neighbor */ 4036| 0| if (j1 == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4036:9): [True: 0, False: 0] ------------------ 4037| 0| { 4038| | /* Add an explicit neighbor if possible */ 4039| 0| if (nMustHaveNumNeigh == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4039:13): [True: 0, False: 0] ------------------ 4040| 0| { 4041| 0| bAddExplicitNeighbor = ADD_EXPLICIT_LONE_PAIR_NEIGH; ------------------ | | 3754| 0|#define ADD_EXPLICIT_LONE_PAIR_NEIGH 2 ------------------ 4042| 0| } 4043| 0| else 4044| 0| { 4045| 0| if (nMustHaveNumNeigh == MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4045:17): [True: 0, False: 0] ------------------ 4046| 0| { 4047| | /* Check whether an explicit non-isotopic hydrogen can be added */ 4048| | /* to an atom that is a stereogenic atom */ 4049| 0| if (1 == at[cur_at].num_H - num_explicit_H && /* the atom has only one one implicit hydrogen */ ------------------ | Branch (4049:21): [True: 0, False: 0] ------------------ 4050| 0| 1 == at[cur_at].num_H - tot_num_iso_H) ------------------ | Branch (4050:21): [True: 0, False: 0] ------------------ 4051| 0| { 4052| | /* this hydrogen is non-isotopic */ 4053| 0| bAddExplicitNeighbor = ADD_EXPLICIT_HYDROGEN_NEIGH; ------------------ | | 3753| 0|#define ADD_EXPLICIT_HYDROGEN_NEIGH 1 ------------------ 4054| 0| } 4055| 0| } 4056| 0| } 4057| 0| } 4058| | 4059| 0| if (bAddExplicitNeighbor) ------------------ | Branch (4059:9): [True: 0, False: 0] ------------------ 4060| 0| { 4061| | /*********************************************************** 4062| | * May happen only if (j1 == MAX_NUM_STEREO_ATOM_NEIGH-1) 4063| | * 3 neighbors only, no H-neighbors. Create and add coordinates of an implicit H 4064| | * or a fake 4th neighbor, that is, a lone pair 4065| | */ 4066| 0| if (parity == vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4066:13): [True: 0, False: 0] ------------------ 4067| 0| { 4068| 0| goto exit_function; /* the user insists the parity is unknown and the isotopic */ 4069| | /* composition of the neighbors does not contradict */ 4070| 0| } 4071| 0| else 4072| 0| { 4073| 0| if (num_z == 0 || are_3_vect_in_one_plane( at_coord, vMinSine )) ------------------ | Branch (4073:17): [True: 0, False: 0] | Branch (4073:31): [True: 0, False: 0] ------------------ 4074| 0| { 4075| | /* "hydrogen down" rule is needed to resolve an ambiguity */ 4076| 0| if (num_z > 0) ------------------ | Branch (4076:21): [True: 0, False: 0] ------------------ 4077| 0| { 4078| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4079| 0| } 4080| |#if ( APPLY_IMPLICIT_H_DOWN_RULE == 1 ) /* { */ 4081| | /* Although H should be at the top of the list, add it to the bottom. */ 4082| | /* This will be taken care of later by inverting parity 1<->2 */ 4083| | at_coord[j][0] = 0.0; 4084| | at_coord[j][1] = 0.0; 4085| |#if ( STEREO_CENTER_BONDS_NORM == 1 ) 4086| | at_coord[j][2] = -1.0; 4087| |#else 4088| | at_coord[j][2] = -( bond_len_xy[0] + bond_len_xy[1] + bond_len_xy[2] ) / 3.0; 4089| |#endif 4090| |#else /* } APPLY_IMPLICIT_H_DOWN_RULE { */ 4091| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4092| | parity = AB_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4093| |#else 4094| | /* All 3 bonds are in one plane: try to get 0D parities */ 4095| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (4095:21): [True: 0, False: 0] ------------------ 4096| 0| j1, 4097| 0| nSbNeighOrigAtNumb, 4098| 0| FlagSC_0D ) )) ------------------ | | 59| 0|#define FlagSC_0D 1 /**< bUsed0DParity */ ------------------ 4099| 0| { 4100| 0| parity = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4101| 0| } 4102| | /*parity = AB_PARITY_UNDF;*/ /* no parity can be calculated found */ 4103| 0|#endif 4104| 0| goto exit_function; 4105| 0|#endif /* } APPLY_IMPLICIT_H_DOWN_RULE */ 4106| 0| } 4107| 0| else 4108| 0| { 4109| | /* we have enough information to find implicit hydrogen coordinates */ 4110| | /* 4111| | at_coord[j][0] = -sum_x; 4112| | at_coord[j][1] = -sum_y; 4113| | at_coord[j][2] = -sum_z; 4114| | */ 4115| | /* copy3(sum_xyz, at_coord[j]); -- djb-rwth: removing copy3 function */ 4116| 0| memcpy(at_coord[j], sum_xyz, sizeof(sum_xyz)); 4117| 0| change_sign3( at_coord[j], at_coord[j] ); 4118| 0| z = len3( at_coord[j] ); 4119| |#if ( FIX_STEREO_SCALING_BUG == 1 ) 4120| | if (z > 1.0) 4121| | { 4122| | rmax *= z; 4123| | } 4124| | else 4125| | { 4126| | rmin *= z; 4127| | } 4128| |#else 4129| | /* Comparing the original bond lengths to lenghts derived from normalized to 1 */ 4130| | /* This bug leads to pronouncing legitimate stereogenic atoms */ 4131| | /* connected by 3 bonds "undefined" if in a nicely drawn 2D structure */ 4132| | /* bond lengths are about 20 or greater. Reported by Reinhard Dunkel 2005-08-05 */ 4133| 0| if (bPointedEdgeStereo & PES_BIT_FIX_SP3_BUG) ------------------ | | 47| 0|#define PES_BIT_FIX_SP3_BUG 8 ------------------ | Branch (4133:21): [True: 0, False: 0] ------------------ 4134| 0| { 4135| | /* coordinate scaling bug fixed here */ 4136| 0| if (z > 1.0) ------------------ | Branch (4136:25): [True: 0, False: 0] ------------------ 4137| 0| { 4138| 0| rmax *= z; 4139| 0| } 4140| 0| else 4141| 0| { 4142| 0| rmin *= z; 4143| 0| } 4144| 0| } 4145| 0| else 4146| 0| { 4147| | /* original InChI v.1 bug */ 4148| 0| rmax = inchi_max( rmax, z ); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 4149| 0| rmin = inchi_min( rmin, z ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 4150| 0| } 4151| 0|#endif 4152| 0| if (z < MIN_BOND_LEN || rmin / rmax < MIN_SINE) ------------------ | | 39| 0|#define MIN_BOND_LEN 0.000001 ------------------ if (z < MIN_BOND_LEN || rmin / rmax < MIN_SINE) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (4152:21): [True: 0, False: 0] | Branch (4152:41): [True: 0, False: 0] ------------------ 4153| 0| { 4154| | /* the new 4th bond is too short: try to get 0D parities */ 4155| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, nSbNeighOrigAtNumb, FlagSC_0D ) )) ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, nSbNeighOrigAtNumb, FlagSC_0D ) )) ------------------ | | 59| 0|#define FlagSC_0D 1 /**< bUsed0DParity */ ------------------ | Branch (4155:25): [True: 0, False: 0] ------------------ 4156| 0| { 4157| 0| parity = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4158| 0| } 4159| 0| goto exit_function; 4160| 0| } 4161| |#if ( STEREO_CENTER_BOND4_NORM == 1 ) 4162| | else 4163| | { 4164| | mult3( at_coord[j], 1.0 / z, at_coord[j] ); 4165| | } 4166| |#endif 4167| 0| } 4168| 0| } 4169| 0| } 4170| | 4171| 0| else if (j1 != MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4171:14): [True: 0, False: 0] ------------------ 4172| 0| { 4173| 0| if (parity == vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4173:13): [True: 0, False: 0] ------------------ 4174| 0| { 4175| 0| parity = -AB_PARITY_UNDF; /* isotopic composition of H-neighbors contradicts 'unknown' */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4176| 0| } 4177| 0| goto exit_function; 4178| 0| } 4179| | 4180| 0| else /* j1 == MAX_NUM_STEREO_ATOM_NEIGH */ 4181| 0| { 4182| 0| if (num_z == 0 || are_4at_in_one_plane( at_coord, vMinSine )) ------------------ | Branch (4182:13): [True: 0, False: 0] | Branch (4182:27): [True: 0, False: 0] ------------------ 4183| 0| { 4184| | /* all four neighours in xy plane: undefined geometry. */ 4185| 0| if (num_z > 0) ------------------ | Branch (4185:17): [True: 0, False: 0] ------------------ 4186| 0| { 4187| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4188| 0| } 4189| 0| if (parity != vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4189:17): [True: 0, False: 0] ------------------ 4190| 0| { 4191| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4192| | parity = AB_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4193| |#else 4194| | /* All 4 bonds are in one plane: try to get 0D parities */ 4195| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, nSbNeighOrigAtNumb, FlagSC_0D ) )) ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, nSbNeighOrigAtNumb, FlagSC_0D ) )) ------------------ | | 59| 0|#define FlagSC_0D 1 /**< bUsed0DParity */ ------------------ | Branch (4195:21): [True: 0, False: 0] ------------------ 4196| 0| { 4197| 0| parity = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4198| 0| } 4199| 0| else if (ATOM_PARITY_WELL_DEF( parity )) ------------------ | | 259| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 0|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 0, False: 0] | | | Branch (259:75): [True: 0, False: 0] | | ------------------ ------------------ 4200| 0| { 4201| 0| bAmbiguous &= ~AMBIGUOUS_STEREO; /* 0D parity has resolved the ambiguity */ ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4202| 0| } 4203| 0|#endif 4204| 0| } 4205| 0| goto exit_function; 4206| 0| } 4207| 0| } 4208| | 4209| | /*********************************************************** 4210| | * At this point we have 4 neighboring atoms. 4211| | * check for tetrahedral ambiguity in 2D case 4212| | */ 4213| 0| if (b2D) ------------------ | Branch (4213:9): [True: 0, False: 0] ------------------ 4214| 0| { 4215| | 4216| 0| n2DTetrahedralAmbiguity = Get2DTetrahedralAmbiguity( pCG,at_coord, 4217| 0| bAddExplicitNeighbor, 4218| 0| ( bPointedEdgeStereo & PES_BIT_FIX_SP3_BUG ), ------------------ | | 47| 0|#define PES_BIT_FIX_SP3_BUG 8 ------------------ 4219| 0| vMinAngle ); 4220| | 4221| 0| if (0 < n2DTetrahedralAmbiguity) ------------------ | Branch (4221:13): [True: 0, False: 0] ------------------ 4222| 0| { 4223| 0| if (T2D_WARN & n2DTetrahedralAmbiguity) ------------------ | | 362| 0|#define T2D_WARN 2 ------------------ | Branch (4223:17): [True: 0, False: 0] ------------------ 4224| 0| { 4225| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4226| 0| } 4227| 0| if (T2D_UNDF & n2DTetrahedralAmbiguity) ------------------ | | 363| 0|#define T2D_UNDF 4 ------------------ | Branch (4227:17): [True: 0, False: 0] ------------------ 4228| 0| { 4229| 0| if (parity != vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4229:21): [True: 0, False: 0] ------------------ 4230| 0| { 4231| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4232| | parity = AB_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4233| |#else 4234| 0| parity = AB_PARITY_UNDF; /* no parity */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4235| 0|#endif 4236| 0| } 4237| 0| goto exit_function; 4238| 0| } 4239| 0| } 4240| 0| else if (n2DTetrahedralAmbiguity < 0) ------------------ | Branch (4240:18): [True: 0, False: 0] ------------------ 4241| 0| { 4242| 0| bAmbiguous |= AMBIGUOUS_STEREO_ERROR; /* error */ ------------------ | | 250| 0|#define AMBIGUOUS_STEREO_ERROR 32 ------------------ 4243| 0| parity = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4244| 0| goto exit_function; 4245| 0| } 4246| 0| } 4247| | 4248| | /************************************************************/ 4249| | /* Move coordinates origin to the neighbor #0 */ 4250| 0| for (j = 1; j < MAX_NUM_STEREO_ATOM_NEIGH; j++) ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4250:17): [True: 0, False: 0] ------------------ 4251| 0| { 4252| 0| diff3( at_coord[j], at_coord[0], at_coord[j] ); 4253| 0| } 4254| 0| diff3( at_coord_center, at_coord[0], at_coord_center ); 4255| | 4256| | /* 4257| | for ( k = 0; k < 3; k++ ) 4258| | { 4259| | for ( j = 1; j < MAX_NUM_STEREO_ATOM_NEIGH; j ++ ) 4260| | { 4261| | at_coord[j][k] -= at_coord[0][k]; 4262| | } 4263| | at_coord_center[k] -= at_coord[0][k]; 4264| | } 4265| | */ 4266| | 4267| | 4268| | /******************************************************** 4269| | * Find the central (cur_at) atom's parity 4270| | * (orientation of atoms #1-3 when looking from #0) 4271| | ********************************************************/ 4272| 0| triple_product = triple_prod_and_min_abs_sine2( &at_coord[1], at_coord_center, bAddExplicitNeighbor, &min_sine, &bAmbiguous, vMinSine ); 4273| | 4274| | /* 4275| | * Check for tetrahedral ambiguity -- leave it out for now 4276| | */ 4277| 0| if (fabs( triple_product ) > ZERO_FLOAT && ( min_sine > vMinSine || (fabs( min_sine ) > ZERO_FLOAT && ( n2DTetrahedralAmbiguity & T2D_OKAY )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 41| 0|#define ZERO_FLOAT 1.0e-12 ------------------ if (fabs( triple_product ) > ZERO_FLOAT && ( min_sine > vMinSine || (fabs( min_sine ) > ZERO_FLOAT && ( n2DTetrahedralAmbiguity & T2D_OKAY )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 41| 0|#define ZERO_FLOAT 1.0e-12 ------------------ if (fabs( triple_product ) > ZERO_FLOAT && ( min_sine > vMinSine || (fabs( min_sine ) > ZERO_FLOAT && ( n2DTetrahedralAmbiguity & T2D_OKAY )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 361| 0|#define T2D_OKAY 1 ------------------ | Branch (4277:9): [True: 0, False: 0] | Branch (4277:50): [True: 0, False: 0] | Branch (4277:74): [True: 0, False: 0] | Branch (4277:107): [True: 0, False: 0] ------------------ 4278| 0| { 4279| | /* Even => sorted in correct order, Odd=>transposed */ 4280| 0| parity = triple_product > 0.0 ? AB_PARITY_EVEN : AB_PARITY_ODD; ------------------ | | 220| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ parity = triple_product > 0.0 ? AB_PARITY_EVEN : AB_PARITY_ODD; ------------------ | | 219| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (4280:18): [True: 0, False: 0] ------------------ 4281| | /* if ( num_explicit_H && at[cur_at].removed_H_parity % 2 ) */ 4282| | /* odd transposition of the removed implicit H */ 4283| | /* out_at[cur_at].parity = 3 - out_at[cur_at].parity; */ 4284| | 4285| | /* moved; see below */ 4286| | /* out_at[cur_at].bAmbiguousStereo |= bAmbiguous; */ 4287| | /* at[cur_at].bAmbiguousStereo |= bAmbiguous; */ 4288| | 4289| | /* for 4 attached atoms, moving the implicit H from index=3 to index=0 */ 4290| | /* can be done in odd number (3) transpositions: (23)(12)(01), which inverts the parity */ 4291| 0| if (j1 == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 877| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4291:13): [True: 0, False: 0] ------------------ 4292| 0| { 4293| 0| parity = 3 - parity; 4294| 0| } 4295| 0| } 4296| 0| else 4297| 0| { 4298| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4299| | parity = AT_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4300| |#else 4301| 0| if (num_z > 0) ------------------ | Branch (4301:13): [True: 0, False: 0] ------------------ 4302| 0| { 4303| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4304| 0| } 4305| 0| parity = AB_PARITY_UNDF; /* no parity: 4 bonds are in one plane. */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4306| 0|#endif 4307| 0| } 4308| | 4309| 1.09M|exit_function: 4310| | 4311| 1.09M| if (parity) ------------------ | Branch (4311:9): [True: 8.38k, False: 1.08M] ------------------ 4312| 8.38k| { 4313| 8.38k| out_at[cur_at].bAmbiguousStereo |= bAmbiguous; 4314| 8.38k| at[cur_at].bAmbiguousStereo |= bAmbiguous; 4315| 8.38k| } 4316| | 4317| | /* Non-isotopic parity */ 4318| 1.09M| if (at[cur_at].num_H > 1 || parity <= 0) ------------------ | Branch (4318:9): [True: 746, False: 1.09M] | Branch (4318:33): [True: 1.08M, False: 8.38k] ------------------ 4319| 1.08M| { 4320| 1.08M| ; /* no non-isotopic parity */ 4321| 1.08M| } 4322| 8.38k| else 4323| 8.38k| { 4324| 8.38k| out_at[cur_at].parity = parity; 4325| 8.38k| } 4326| | 4327| | /* isotopic parity */ 4328| 1.09M| if (parity == -AB_PARITY_UNDF || parity == -vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | | 222| 2.18M|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (4328:9): [True: 1, False: 1.09M] | Branch (4328:38): [True: 0, False: 1.09M] ------------------ 4329| 1| { 4330| 1| parity = -parity; 4331| 1| } 4332| 1.09M| if (parity < 0) ------------------ | Branch (4332:9): [True: 0, False: 1.09M] ------------------ 4333| 0| { 4334| 0| parity = AB_PARITY_NONE; ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 4335| 0| } 4336| 1.09M| out_at[cur_at].parity2 = parity; 4337| | 4338| 1.09M| parity = PARITY_VAL( out_at[cur_at].parity ); ------------------ | | 262| 1.09M|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 1.09M|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 4339| 1.09M| out_at[cur_at].stereo_atom_parity = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 259| 1.09M|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.09M|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 8.38k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 8.38k, False: 1.08M] | | | Branch (259:75): [True: 539, False: 7.84k] | | ------------------ ------------------ out_at[cur_at].stereo_atom_parity = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 224| 539|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ 4340| 1.09M| parity = PARITY_VAL( out_at[cur_at].parity2 ); ------------------ | | 262| 1.09M|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 204| 1.09M|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 4341| 1.09M| out_at[cur_at].stereo_atom_parity2 = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 259| 1.09M|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1.09M|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 8.38k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 8.38k, False: 1.08M] | | | Branch (259:75): [True: 539, False: 7.85k] | | ------------------ ------------------ out_at[cur_at].stereo_atom_parity2 = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 224| 539|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ 4342| | /* 4343| | out_at[cur_at].parity2 = out_at[cur_at].parity; // save for stereo + isotopic canon. 4344| | if ( out_at[cur_at].parity ) { 4345| | if ( num_explicit_H > 1 || j1 == MAX_NUM_STEREO_ATOM_NEIGH-1 && num_explicit_H ) { 4346| | // X H X 4347| | // for example, >C< or >C-D 4348| | // Y D Y 4349| | // parity exists for stereo + isotopic atoms canonicalization only 4350| | out_at[cur_at].parity = 0; 4351| | } 4352| | } 4353| | returning 0 means this can be an adjacent to a stereogenic bond atom 4354| | */ 4355| | 4356| 1.09M| return (int) out_at[cur_at].parity2; 4357| 0|} ichister.c:get_z_coord: 117| 39.4k|{ 118| 39.4k| int stereo_value = at[cur_atom].bond_stereo[neigh_no]; 119| 39.4k| int stereo_type = abs( stereo_value ); 120| 39.4k| int neigh = (int) at[cur_atom].neighbor[neigh_no]; 121| 39.4k| double z = at[neigh].z - at[cur_atom].z; 122| 39.4k| int bFlat; 123| | 124| 39.4k| if ((bFlat = ( fabs( z ) < ZERO_LENGTH ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 40| 39.4k|#define ZERO_LENGTH MIN_BOND_LEN | | ------------------ | | | | 39| 39.4k|#define MIN_BOND_LEN 0.000001 | | ------------------ ------------------ | Branch (124:9): [True: 39.4k, False: 0] ------------------ 125| 39.4k| { 126| 39.4k| int i; 127| 171k| for (i = 0; i < at[cur_atom].valence; i++) ------------------ | Branch (127:21): [True: 132k, False: 39.4k] ------------------ 128| 132k| { 129| 132k| if (fabs( at[cur_atom].z - at[(int) at[cur_atom].neighbor[i]].z ) > ZERO_LENGTH) ------------------ | | 40| 132k|#define ZERO_LENGTH MIN_BOND_LEN | | ------------------ | | | | 39| 132k|#define MIN_BOND_LEN 0.000001 | | ------------------ ------------------ | Branch (129:17): [True: 0, False: 132k] ------------------ 130| 0| { 131| 0| bFlat = 0; 132| 0| break; 133| 0| } 134| 132k| } 135| 39.4k| } 136| | 137| 39.4k| if (bFlat) ------------------ | Branch (137:9): [True: 39.4k, False: 0] ------------------ 138| 39.4k| { 139| 39.4k| if (!bPointedEdgeStereo || bPointedEdgeStereo * stereo_value >= 0) ------------------ | Branch (139:13): [True: 0, False: 39.4k] | Branch (139:36): [True: 39.4k, False: 0] ------------------ 140| 39.4k| { 141| | /* bPointedEdgeStereo > 0: define stereo from pointed end of the stereo bond only */ 142| | /* bPointedEdgeStereo < 0: define stereo from wide end of the stereo bond only (case of removed H) */ 143| 39.4k| switch (stereo_type) 144| 39.4k| { 145| | /* 1=Up (solid triangle), 6=Down (Dashed triangle), 4=Either (zigzag triangle) */ 146| 39.4k| case 0: /* No stereo */ ------------------ | Branch (146:17): [True: 39.4k, False: 18] ------------------ 147| 39.4k| *nType = ZTYPE_NONE; ------------------ | | 21| 39.4k|#define ZTYPE_NONE 0 ------------------ 148| 39.4k| break; 149| 0| case STEREO_SNGL_UP: /* 1= Up */ ------------------ | | 37| 0|#define STEREO_SNGL_UP 1 ------------------ | Branch (149:17): [True: 0, False: 39.4k] ------------------ 150| 0| *nType = ZTYPE_UP; ------------------ | | 22| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ 151| 0| break; 152| 0| case STEREO_SNGL_EITHER: /* 4 = Either */ ------------------ | | 38| 0|#define STEREO_SNGL_EITHER 4 ------------------ | Branch (152:17): [True: 0, False: 39.4k] ------------------ 153| 0| *nType = ZTYPE_EITHER; ------------------ | | 24| 0|#define ZTYPE_EITHER 9999 ------------------ 154| 0| break; 155| 0| case STEREO_SNGL_DOWN: /* 6 = Down */ ------------------ | | 39| 0|#define STEREO_SNGL_DOWN 6 ------------------ | Branch (155:17): [True: 0, False: 39.4k] ------------------ 156| 0| *nType = ZTYPE_DOWN; ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ 157| 0| break; 158| 18| default: ------------------ | Branch (158:17): [True: 18, False: 39.4k] ------------------ 159| 18| *nType = ZTYPE_NONE; /* ignore unexpected values */ ------------------ | | 21| 18|#define ZTYPE_NONE 0 ------------------ 160| 39.4k| } 161| 39.4k| if (stereo_value < 0 && ( *nType == ZTYPE_DOWN || *nType == ZTYPE_UP )) ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ if (stereo_value < 0 && ( *nType == ZTYPE_DOWN || *nType == ZTYPE_UP )) ------------------ | | 22| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (161:17): [True: 0, False: 39.4k] | Branch (161:39): [True: 0, False: 0] | Branch (161:63): [True: 0, False: 0] ------------------ 162| 0| *nType = -*nType; 163| 39.4k| } 164| 0| else 165| 0| { 166| 0| *nType = ZTYPE_NONE; /* no stereo */ ------------------ | | 21| 0|#define ZTYPE_NONE 0 ------------------ 167| 0| } 168| 39.4k| } 169| 0| else 170| 0| { 171| 0| if (stereo_type == STEREO_SNGL_EITHER && ------------------ | | 38| 0|#define STEREO_SNGL_EITHER 4 ------------------ | Branch (171:13): [True: 0, False: 0] ------------------ 172| 0| ( !bPointedEdgeStereo || bPointedEdgeStereo * stereo_value >= 0 )) ------------------ | Branch (172:15): [True: 0, False: 0] | Branch (172:38): [True: 0, False: 0] ------------------ 173| 0| { 174| 0| *nType = ZTYPE_EITHER; ------------------ | | 24| 0|#define ZTYPE_EITHER 9999 ------------------ 175| 0| } 176| 0| else 177| 0| { 178| 0| *nType = ZTYPE_3D; ------------------ | | 23| 0|#define ZTYPE_3D 3 ------------------ 179| 0| } 180| 0| } 181| | 182| 39.4k| return z; 183| 39.4k|} ichister.c:len2: 200| 30.6k|{ 201| 30.6k| double tmpar[ARR_DIM - 1] = { 0,0 }; 202| |#if USE_BCF 203| | memcpy_s(tmpar, (ARR_DIM - 1) * sizeof(c[0]), c, (ARR_DIM - 1) * sizeof(c[0])); 204| |#else 205| 30.6k| memcpy(tmpar, c, (ARR_DIM - 1) * sizeof(c[0])); ------------------ | | 26| 30.6k|#define ARR_DIM 3 /* djb-rwth: default dimension of arrays */ ------------------ 206| 30.6k|#endif 207| 30.6k| return sqrt(pow(tmpar[0],2.0) + pow(tmpar[1],2.0)); 208| 30.6k|} ichister.c:add3: 225| 10|{ 226| 10| result[0] = a[0] + b[0]; 227| 10| result[1] = a[1] + b[1]; 228| 10| result[2] = a[2] + b[2]; 229| | 230| | /* return result; */ 231| 10|} ichister.c:triple_prod: 313| 10|{ 314| 10| double ab[3], dot_prod_ab_c, abs_c, abs_ab; 315| 10| cross_prod3( a, b, ab ); 316| | /* ab[0] = (a[1]*b[2]-a[2]*b[1]); */ 317| | /* ab[1] = -(a[0]*b[2]-a[2]*b[0]); */ 318| | /* ab[2] = (a[0]*b[1]-a[1]*b[0]); */ 319| 10| dot_prod_ab_c = dot_prod3( ab, c ); 320| | /* dot_prod_ab_c = ab[0]*c[0] + ab[1]*c[1] + ab[2]*c[2]; */ 321| 10| if (sine_value) ------------------ | Branch (321:9): [True: 0, False: 10] ------------------ 322| 0| { 323| 0| abs_c = len3( c ); 324| | /* abs_c = sqrt( c[0]*c[0] + c[1]*c[1] + c[2]*c[2] ); */ 325| 0| abs_ab = len3( ab ); 326| | /* abs_ab = sqrt( ab[0]*ab[0] + ab[1]*ab[1] + ab[2]*ab[2] ); */ 327| | 328| 0| if (abs_c > 1.e-7 /* otherwise c has zero length */ && abs_ab > 1.e-7 /* otherwise a is parallel to b*/) ------------------ | Branch (328:13): [True: 0, False: 0] | Branch (328:64): [True: 0, False: 0] ------------------ 329| 0| { 330| 0| *sine_value = MPY_SINE * dot_prod_ab_c / ( abs_c * abs_ab ); ------------------ | | 44| 0|#define MPY_SINE 1.00 /* was 3.0 */ ------------------ 331| | /* *sine_value = dot_prod_ab_c / ( abs_c * abs_ab); */ 332| 0| } 333| 0| else 334| 0| { 335| 0| *sine_value = 0.0; 336| 0| } 337| 0| } 338| | 339| 10| return dot_prod_ab_c; 340| 10|} ichister.c:set_stereo_bonds_parity: 2985| 1.08M|{ 2986| 1.08M| int j, k, i_next_at_1, i_next_at_2, at_2, next_at_2, num_stereo_bonds, bFound, bAllene; /* djb-rwth: removing redundant variables */ 2987| 1.08M| int bond_type, num_2s_1, num_alt_1; 2988| 1.08M| int num_2s_2, num_alt_2; 2989| 1.08M|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 2990| 1.08M| int num_wrong_bonds_1, num_wrong_bonds_2; 2991| 1.08M|#endif 2992| 1.08M|#if ( N_V_STEREOBONDS == 1 ) 2993| 1.08M| int n2sh, num_2s_hetero[2], num_2s_hetero_next[2], next_next_at, type_N, type_N_next; 2994| 1.08M|#endif 2995| 1.08M| int num_stored_isotopic_stereo_bonds; /* djb-rwth: removing redundant variables/code */ 2996| 1.08M| int chain_length, num_chains, cur_chain_length; 2997| 1.08M| int all_at_2[MAX_NUM_STEREO_BONDS]; 2998| 1.08M| int all_pos_1[MAX_NUM_STEREO_BONDS], all_pos_2[MAX_NUM_STEREO_BONDS]; 2999| 1.08M| S_CHAR all_unkn[MAX_NUM_STEREO_BONDS]; 3000| 1.08M| int /*at_1_parity, at_2_parity,*/ nUnknown, stop = 0; 3001| | 3002| | /* at_1_parity = AB_PARITY_NONE; */ /* do not know */ 3003| | 3004| | /* Check valence */ 3005| 1.08M| if (MAX_NUM_STEREO_BOND_NEIGH < at[at_1].valence + at[at_1].num_H || ------------------ | | 874| 1.08M|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (3005:9): [True: 10.9k, False: 1.07M] ------------------ 3006| 1.07M| MIN_NUM_STEREO_BOND_NEIGH > at[at_1].valence + at[at_1].num_H) ------------------ | | 875| 1.07M|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (3006:10): [True: 933k, False: 141k] ------------------ 3007| 944k| { 3008| 944k| return 0; 3009| 944k| } 3010| 141k| if (!bCanAtomHaveAStereoBond( at[at_1].elname, at[at_1].charge, at[at_1].radical )) ------------------ | Branch (3010:9): [True: 87.3k, False: 53.8k] ------------------ 3011| 87.3k| { 3012| 87.3k| return 0; 3013| 87.3k| } 3014| 53.8k| if (at[at_1].c_point) ------------------ | Branch (3014:9): [True: 1.88k, False: 51.9k] ------------------ 3015| 1.88k| { 3016| 1.88k| return 0; /* rejects atoms that can lose or gain a (positive) charge. 01-24-2003 */ 3017| 1.88k| } 3018| | 3019| | /* middle cumulene atoms, for example, =C=, should be ignored here */ 3020| | /* only atoms at the ends of cumulene chains are considered. */ 3021| 51.9k| if (!at[at_1].num_H && 2 == at[at_1].valence && ------------------ | Branch (3021:9): [True: 48.3k, False: 3.61k] | Branch (3021:28): [True: 36.3k, False: 12.0k] ------------------ 3022| 36.3k| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_1].bond_type[0] ) && ------------------ | | 178| 36.3k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 36.3k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3022:10): [True: 11.4k, False: 24.8k] ------------------ 3023| 11.4k| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_1].bond_type[1] )) ------------------ | | 178| 11.4k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 11.4k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3023:10): [True: 2.87k, False: 8.60k] ------------------ 3024| 2.87k| { 3025| 2.87k| return 0; 3026| 2.87k| } 3027| | 3028| | /* count bonds and find the second atom on the stereo bond */ 3029| 49.0k| num_2s_1 = num_alt_1 = 0; 3030| 49.0k| chain_length = 0; 3031| 49.0k| num_chains = 0; 3032| 49.0k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3033| 49.0k| num_wrong_bonds_1 = 0; 3034| 49.0k|#endif 3035| 49.0k|#if ( N_V_STEREOBONDS == 1 ) 3036| 49.0k| num_2s_hetero[0] = num_2s_hetero[1] = type_N = 0; 3037| 49.0k| if (0 == at[at_1].num_H && 0 == at[at_1].charge && 0 == at[at_1].radical && ------------------ | Branch (3037:9): [True: 45.4k, False: 3.61k] | Branch (3037:32): [True: 40.4k, False: 5.02k] | Branch (3037:56): [True: 40.4k, False: 0] ------------------ 3038| 40.4k| 3 == get_endpoint_valence( at[at_1].el_number )) ------------------ | Branch (3038:10): [True: 26.6k, False: 13.8k] ------------------ 3039| 26.6k| { 3040| 26.6k| if (2 == at[at_1].valence && 3 == at[at_1].chem_bonds_valence) ------------------ | Branch (3040:13): [True: 21.2k, False: 5.37k] | Branch (3040:38): [True: 18.8k, False: 2.35k] ------------------ 3041| 18.8k| { 3042| 18.8k| type_N = 1; 3043| 18.8k| } 3044| 7.73k| else 3045| 7.73k| { 3046| 7.73k| if (3 == at[at_1].valence && 5 == at[at_1].chem_bonds_valence) ------------------ | Branch (3046:17): [True: 5.37k, False: 2.35k] | Branch (3046:42): [True: 4.44k, False: 934] ------------------ 3047| 4.44k| { 3048| 4.44k| type_N = 2; /* unfortunately includes >N# */ 3049| 4.44k| } 3050| 7.73k| } 3051| 26.6k| } 3052| 49.0k|#endif 3053| 158k| for (i_next_at_1 = 0, num_stereo_bonds = 0; i_next_at_1 < at[at_1].valence; i_next_at_1++) ------------------ | Branch (3053:49): [True: 108k, False: 49.0k] ------------------ 3054| 108k| { 3055| 108k| nUnknown = ( at[at_1].bond_stereo[i_next_at_1] == STEREO_DBLE_EITHER ); ------------------ | | 40| 108k|#define STEREO_DBLE_EITHER 3 ------------------ 3056| 108k| bond_type = get_allowed_stereo_bond_type( (int) at[at_1].bond_type[i_next_at_1] ); 3057| 108k| at_2 = -1; /* not found */ 3058| 108k| if (bond_type == BOND_ALTERN || ------------------ | | 180| 108k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 217k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (3058:13): [True: 7.86k, False: 101k] ------------------ 3059| 101k| bond_type == BOND_DOUBLE) ------------------ | | 178| 101k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 101k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3059:14): [True: 23.3k, False: 77.7k] ------------------ 3060| 31.1k| { 3061| 31.1k| at_2 = at[at_1].neighbor[i_next_at_1]; /* djb-rwth: removing redundant code */ 3062| 31.1k| next_at_2 = at_1; 3063| 31.1k| } 3064| 108k| switch (bond_type) 3065| 108k| { 3066| 7.86k| case BOND_ALTERN: ------------------ | | 180| 7.86k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 7.86k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (3066:13): [True: 7.86k, False: 101k] ------------------ 3067| 7.86k| num_alt_1++; 3068| 7.86k|#if ( FIND_RING_SYSTEMS == 1 ) 3069| 7.86k| if (at[at_1].nRingSystem != at[at_2].nRingSystem) ------------------ | Branch (3069:21): [True: 0, False: 7.86k] ------------------ 3070| 0| { 3071| 0| continue; /* reject alt. bond connecting different ring systems */ 3072| 0| } 3073| 7.86k|#endif 3074| 7.86k| if (( nMode & CMODE_NO_ALT_SBONDS ) || ------------------ | | 777| 7.86k|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (3074:21): [True: 0, False: 7.86k] ------------------ 3075| 7.86k| !bCanAtomHaveAStereoBond( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3075:22): [True: 1.10k, False: 6.76k] ------------------ 3076| 1.10k| { 3077| 1.10k| continue; /* reject non-stereogenic bond to neighbor ord. #i_next_at_1 */ 3078| 1.10k| } 3079| 6.76k| break; 3080| 23.3k| case BOND_DOUBLE: ------------------ | | 178| 23.3k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 23.3k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3080:13): [True: 23.3k, False: 85.6k] ------------------ 3081| | /* check for cumulene/allene */ 3082| 23.3k| num_2s_1++; 3083| 23.3k| cur_chain_length = 0; 3084| 23.3k| if (bCanAtomBeTerminalAllene( at[at_1].elname, at[at_1].charge, at[at_1].radical )) ------------------ | Branch (3084:21): [True: 4.30k, False: 19.0k] ------------------ 3085| 4.30k| { 3086| | /* 3087| | * Example of cumulene 3088| | * chain length = 2: >X=C=C=Y< 3089| | * | | | | 3090| | * 1st cumulene atom= at_1 | | at_2 =last cumlene chain atom 3091| | * next to at_1= next_at_1 next_at_2 =previous to at_2 3092| | * 3093| | * chain length odd: stereocenter on the middle atom ( 1=> allene ) 3094| | * chain length even: "long stereogenic bond" 3095| | */ 3096| 5.09k| while (( bAllene = ------------------ | Branch (3096:28): [True: 943, False: 4.14k] ------------------ 3097| 5.09k| !at[at_2].num_H && at[at_2].valence == 2 && ------------------ | Branch (3097:25): [True: 4.91k, False: 172] | Branch (3097:44): [True: 2.31k, False: 2.60k] ------------------ 3098| 2.31k| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_2].bond_type[0] ) && ------------------ | | 178| 2.31k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 2.31k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3098:25): [True: 1.99k, False: 322] ------------------ 3099| 1.99k| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_2].bond_type[1] ) ) && ------------------ | | 178| 1.99k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 1.99k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3099:25): [True: 943, False: 1.04k] ------------------ 3100| 943| bCanAtomBeMiddleAllene( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3100:29): [True: 788, False: 155] ------------------ 3101| 788| { 3102| 788| k = ( (int) at[at_2].neighbor[0] == next_at_2 ); /* opposite neighbor position */ 3103| 788| next_at_2 = at_2; 3104| 788| nUnknown += ( at[at_2].bond_stereo[k] == STEREO_DBLE_EITHER ); ------------------ | | 40| 788|#define STEREO_DBLE_EITHER 3 ------------------ 3105| 788| at_2 = (int) at[at_2].neighbor[k]; 3106| 788| cur_chain_length++; /* count =C= atoms */ 3107| 788| } 3108| 4.30k| if (cur_chain_length) ------------------ | Branch (3108:25): [True: 682, False: 3.62k] ------------------ 3109| 682| { 3110| 682| num_chains++; 3111| 682| if (bAllene /* at the end of the chain atom Y is =Y=, not =Y< or =Y- */ || ------------------ | Branch (3111:29): [True: 83, False: 599] ------------------ 3112| 599| !bCanAtomBeTerminalAllene( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3112:30): [True: 248, False: 351] ------------------ 3113| 331| { 3114| 331| cur_chain_length = 0; /* djb-rwth: ignoring LLVM warning: value used */ 3115| 331| continue; /* ignore: does not fit cumulene description; go to check next at_1 neighbor */ 3116| 331| } 3117| 351| chain_length = cur_chain_length; /* accept a stereogenic cumulele */ 3118| 351| } 3119| 4.30k| } 3120| 22.9k|#if ( N_V_STEREOBONDS == 1 ) 3121| 22.9k| if (!cur_chain_length && ------------------ | Branch (3121:21): [True: 22.6k, False: 351] ------------------ 3122| 22.6k| 0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + at_2 ) )) ------------------ | Branch (3122:22): [True: 8.69k, False: 13.9k] ------------------ 3123| 8.69k| { 3124| 8.69k| num_2s_hetero[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 3125| 8.69k| } 3126| 22.9k|#endif 3127| 22.9k| if (!cur_chain_length && ------------------ | Branch (3127:21): [True: 22.6k, False: 351] ------------------ 3128| 22.6k| !bCanAtomHaveAStereoBond( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3128:22): [True: 10.8k, False: 11.7k] ------------------ 3129| 10.8k| { 3130| 10.8k| continue; /* reject non-stereogenic bond to neighbor #i_next_at_1 */ 3131| 10.8k| } 3132| | 3133| 12.1k| break; 3134| | 3135| 42.2k| case BOND_SINGLE: ------------------ | | 177| 42.2k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 42.2k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (3135:13): [True: 42.2k, False: 66.6k] ------------------ 3136| 49.5k| case BOND_TAUTOM: ------------------ | | 185| 49.5k|#define BOND_TAUTOM 8 ------------------ | Branch (3136:13): [True: 7.27k, False: 101k] ------------------ 3137| 49.5k| continue; /* reject non-stereogenic bond to neighbor #i_next_at_1 */ 3138| 28.2k| default: ------------------ | Branch (3138:13): [True: 28.2k, False: 80.7k] ------------------ 3139| 28.2k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3140| 28.2k| num_wrong_bonds_1++; 3141| 28.2k| continue; 3142| |#else 3143| | return 0; /* wrong bond type; */ 3144| |#endif 3145| 108k| } 3146| | 3147| | /* Check atom at the opposite end of possibly stereogenic bond */ 3148| | 3149| 18.8k| bFound = ( at_2 >= 0 && at_1 > at_2 ); /* i_next_at_1 = at_1 stereogenic bond neighbor attachment number */ ------------------ | Branch (3149:20): [True: 18.8k, False: 0] | Branch (3149:33): [True: 10.1k, False: 8.69k] ------------------ 3150| | 3151| 18.8k| if (bFound) ------------------ | Branch (3151:13): [True: 10.1k, False: 8.69k] ------------------ 3152| 10.1k| { 3153| | /* Check "at_2" atom on the opposite side of the bond or cumulene chain */ 3154| 10.1k| if (MAX_NUM_STEREO_BOND_NEIGH < at[at_2].valence + at[at_2].num_H || ------------------ | | 874| 10.1k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (3154:17): [True: 170, False: 10.0k] ------------------ 3155| 10.0k| MIN_NUM_STEREO_BOND_NEIGH > at[at_2].valence + at[at_2].num_H) ------------------ | | 875| 10.0k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (3155:18): [True: 49, False: 9.96k] ------------------ 3156| 219| continue; 3157| | 3158| | /* Check at_2 neighbors and bonds */ 3159| 9.96k| num_2s_2 = num_alt_2 = 0; 3160| 9.96k|#if ( N_V_STEREOBONDS == 1 ) 3161| 9.96k| num_2s_hetero_next[0] = num_2s_hetero_next[1] = type_N_next = 0; 3162| 9.96k| if (0 == at[at_2].num_H && 0 == at[at_2].charge && 0 == at[at_2].radical && ------------------ | Branch (3162:17): [True: 9.60k, False: 363] | Branch (3162:40): [True: 9.21k, False: 383] | Branch (3162:64): [True: 9.21k, False: 0] ------------------ 3163| 9.21k| 3 == get_endpoint_valence( at[at_2].el_number )) ------------------ | Branch (3163:18): [True: 6.71k, False: 2.50k] ------------------ 3164| 6.71k| { 3165| 6.71k| if (2 == at[at_2].valence && 3 == at[at_2].chem_bonds_valence) ------------------ | Branch (3165:21): [True: 5.88k, False: 827] | Branch (3165:46): [True: 5.32k, False: 556] ------------------ 3166| 5.32k| { 3167| 5.32k| type_N_next = 1; /* -N= */ 3168| 5.32k| } 3169| 1.38k| else 3170| 1.38k| { 3171| 1.38k| if (3 == at[at_2].valence && 5 == at[at_2].chem_bonds_valence) ------------------ | Branch (3171:25): [True: 827, False: 556] | Branch (3171:50): [True: 805, False: 22] ------------------ 3172| 805| { 3173| 805| type_N_next = 2; /* unfortunately includes >N# */ 3174| 805| } 3175| 1.38k| } 3176| 6.71k| } 3177| 9.96k|#endif 3178| 9.96k| i_next_at_2 = -1; /* unassigned mark */ 3179| 9.96k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3180| 9.96k| num_wrong_bonds_2 = 0; 3181| 9.96k|#endif 3182| 31.1k| for (j = 0; j < at[at_2].valence; j++) ------------------ | Branch (3182:25): [True: 21.1k, False: 9.96k] ------------------ 3183| 21.1k| { 3184| 21.1k| bond_type = get_allowed_stereo_bond_type( (int) at[at_2].bond_type[j] ); 3185| 21.1k| if (!bond_type) ------------------ | Branch (3185:21): [True: 1.42k, False: 19.7k] ------------------ 3186| 1.42k| { 3187| 1.42k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3188| 1.42k| num_wrong_bonds_2++; 3189| 1.42k| continue; /* this bond type is not allowed to be adjacent to a stereo bond */ 3190| |#else 3191| | break; 3192| |#endif 3193| 1.42k| } 3194| 19.7k| if (bond_type == BOND_DOUBLE) ------------------ | | 178| 19.7k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 19.7k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3194:21): [True: 8.90k, False: 10.8k] ------------------ 3195| 8.90k| { 3196| 8.90k| num_2s_2++; 3197| 8.90k|#if ( N_V_STEREOBONDS == 1 ) 3198| 8.90k| next_next_at = at[at_2].neighbor[j]; 3199| 8.90k| if (0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + next_next_at ) )) ------------------ | Branch (3199:25): [True: 4.18k, False: 4.71k] ------------------ 3200| 4.18k| { 3201| 4.18k| num_2s_hetero_next[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 3202| 4.18k| } 3203| 8.90k|#endif 3204| 8.90k| } 3205| 10.8k| else 3206| 10.8k| { 3207| 10.8k| num_alt_2 += ( bond_type == BOND_ALTERN ); ------------------ | | 180| 10.8k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 10.8k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ 3208| 10.8k| } 3209| 19.7k| if ((int) at[at_2].neighbor[j] == next_at_2) ------------------ | Branch (3209:21): [True: 9.96k, False: 9.77k] ------------------ 3210| 9.96k| { 3211| 9.96k| i_next_at_2 = j; /* assigned */ 3212| 9.96k| } 3213| 19.7k| } 3214| 9.96k| if ( 3215| 9.96k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3216| 9.96k| num_wrong_bonds_2 > 1 || (num_wrong_bonds_2 && 2 >= at[at_2].valence) || /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3216:18): [True: 6, False: 9.95k] | Branch (3216:44): [True: 1.41k, False: 8.54k] | Branch (3216:65): [True: 1.33k, False: 81] ------------------ 3217| |#else 3218| | j < at[at_2].valence /* "next" has a wrong bond type*/ || 3219| |#endif 3220| 8.62k|( num_alt_2 > 0 ) + ( num_2s_2 > 0 ) != 1 || /* all double XOR all alt bonds only */ ------------------ | Branch (3220:1): [True: 233, False: 8.39k] ------------------ 3221| | /* num_2s_2 > 1 ||*/ /* only one double bond permitted */ 3222| 8.39k| i_next_at_2 < 0 /* atom next to the opposite atom not found */) ------------------ | Branch (3222:19): [True: 0, False: 8.39k] ------------------ 3223| 1.57k| { 3224| 1.57k| bFound = 0; 3225| 1.57k| } 3226| 8.39k| else 3227| 8.39k| if (at[at_2].c_point) ------------------ | Branch (3227:21): [True: 33, False: 8.36k] ------------------ 3228| 33| { 3229| 33| bFound = 0; /* rejects atoms that can lose or gain a (positive) charge. 01-24-2003 */ 3230| 33| } 3231| 8.36k| else 3232| 8.36k| if (num_2s_2 > 2) ------------------ | Branch (3232:25): [True: 0, False: 8.36k] ------------------ 3233| 0| { 3234| 0| bFound = 0; 3235| 0| } 3236| 8.36k| else 3237| 8.36k|#if ( N_V_STEREOBONDS == 1 ) 3238| 8.36k| if ( 3==( type_N | type_N_next ) && ( (2==type_N && !bIsOxide( at, at_1 )) || ------------------ | Branch (3238:30): [True: 1.53k, False: 6.82k] | Branch (3238:64): [True: 1.01k, False: 528] | Branch (3238:77): [True: 592, False: 419] ------------------ 3239| 947| (2==type_N_next && !bIsOxide( at, at_2 )) )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (3239:31): [True: 528, False: 419] | Branch (3239:49): [True: 514, False: 14] ------------------ 3240| 1.10k| { 3241| 1.10k| bFound = 0; 3242| 1.10k| } 3243| 7.25k| else 3244| 7.25k|#endif 3245| 7.25k| { 3246| 7.25k| if (2 == num_2s_2) ------------------ | Branch (3246:33): [True: 1.73k, False: 5.51k] ------------------ 3247| 1.73k| { 3248| 1.73k|#if ( N_V_STEREOBONDS == 1 ) 3249| 1.73k| if (!chain_length && ------------------ | Branch (3249:37): [True: 1.72k, False: 19] ------------------ 3250| 1.72k| 1 == ( num_2s_hetero_next[0] | num_2s_hetero_next[1] ) && ------------------ | Branch (3250:38): [True: 489, False: 1.23k] ------------------ 3251| 489| 3 == at[at_2].valence + at[at_2].num_H && ------------------ | Branch (3251:38): [True: 55, False: 434] ------------------ 3252| 55| 5 == at[at_2].chem_bonds_valence + at[at_2].num_H && ------------------ | Branch (3252:38): [True: 55, False: 0] ------------------ 3253| 55| 3 == get_endpoint_valence( at[at_2].el_number ) && ------------------ | Branch (3253:38): [True: 43, False: 12] ------------------ 3254| 43| ( !type_N || bIsOxide( at, at_2 ) )) ------------------ | Branch (3254:40): [True: 9, False: 34] | Branch (3254:51): [True: 17, False: 17] ------------------ 3255| 26| { 3256| | /* 3257| | * found: 3258| | * 3259| | * \ / \ / \ / 3260| | * \ / \ / \ / 3261| | * N==C or N==C or N==N 3262| | * // \ // \ // \ 3263| | * O ^ \ N ^ \ O ^ \ 3264| | * | | | 3265| | * | | | 3266| | * at[at_2] at[at_2] at[at_2] 3267| | */ 3268| 26| ; 3269| 26| } 3270| 1.71k| else 3271| 1.71k| { 3272| 1.71k| bFound = 0; 3273| 1.71k| } 3274| |#else 3275| | bFound = 0; 3276| |#endif 3277| 1.73k| } 3278| 7.25k| } 3279| | 3280| 9.96k| if (chain_length && num_alt_2) ------------------ | Branch (3280:17): [True: 170, False: 9.79k] | Branch (3280:33): [True: 0, False: 170] ------------------ 3281| 0| { 3282| 0| return 0; /* allow no alt bonds in cumulenes */ 3283| 0| } 3284| 9.96k| } 3285| | 3286| 18.6k| if (bFound) ------------------ | Branch (3286:13): [True: 5.54k, False: 13.1k] ------------------ 3287| 5.54k| { 3288| 5.54k| all_pos_1[num_stereo_bonds] = i_next_at_1; /* neighbor to at_1 position */ 3289| 5.54k| all_pos_2[num_stereo_bonds] = i_next_at_2; /* neighbor to at_2 position */ 3290| 5.54k| all_at_2[num_stereo_bonds] = at_2; /* at_2 */ 3291| 5.54k| all_unkn[num_stereo_bonds] = nUnknown; /* stereogenic bond has Unknown configuration */ 3292| | /* 3293| | if ( (at[at_1].bUsed0DParity & 2) || (at[at_2].bUsed0DParity & 2) ) { 3294| | for ( k = 0; k < MAX_NUM_STEREO_BONDS && at[at_1].sb_parity[k]; k ++ ) { 3295| | if ( at[at_1].sb_neigh[k] == i_next_at_1 ) { 3296| | if ( at[at_1].sb_parity[k] == AB_PARITY_UNKN && !nUnknown ) { 3297| | all_unkn[num_stereo_bonds] = 1; 3298| | } 3299| | break; 3300| | } 3301| | } 3302| | } 3303| | */ 3304| 5.54k| num_stereo_bonds++; 3305| 5.54k| } 3306| 18.6k| } 3307| 49.0k| if (num_chains > 1) ------------------ | Branch (3307:9): [True: 9, False: 49.0k] ------------------ 3308| 9| { 3309| 9| return 0; /* cannot be more than 1 cumulene chain. */ 3310| 9| } 3311| 49.0k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3312| 49.0k| if (num_wrong_bonds_1 > 1 || (num_wrong_bonds_1 && 2 >= at[at_1].valence)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3312:9): [True: 6.97k, False: 42.0k] | Branch (3312:35): [True: 13.6k, False: 28.4k] | Branch (3312:56): [True: 12.4k, False: 1.16k] ------------------ 3313| 19.4k| { 3314| 19.4k| return 0; /* wrong bond type */ 3315| 19.4k| } 3316| 29.6k|#endif 3317| | /* Accept only short chains for now */ 3318| | /* chain_length=1: >C=C=C< tetrahedral center, allene */ 3319| | /* chain_length=2: >C=C=C=C< stereogenic bond, cumulene */ 3320| 29.6k| if (chain_length && ( num_stereo_bonds != 1 || num_alt_1 || chain_length > MAX_CUMULENE_LEN )) ------------------ | | 207| 151|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ | Branch (3320:9): [True: 333, False: 29.2k] | Branch (3320:27): [True: 182, False: 151] | Branch (3320:52): [True: 0, False: 151] | Branch (3320:65): [True: 21, False: 130] ------------------ 3321| 203| { 3322| 203| return 0; 3323| 203| } 3324| | 3325| | /* We need 1 double bond/chain XOR up to 3 arom. bonds */ 3326| | /* to have a stereogenic bond */ 3327| 29.4k| if (( num_alt_1 > 0 ) + ( num_2s_1 > 0 ) != 1 || !num_stereo_bonds /*|| num_2s_1 > 1*/) ------------------ | Branch (3327:9): [True: 7.21k, False: 22.1k] | Branch (3327:54): [True: 17.6k, False: 4.55k] ------------------ 3328| 24.8k| return 0; 3329| | 3330| 4.55k| if (num_2s_1 > 1) ------------------ | Branch (3330:9): [True: 488, False: 4.06k] ------------------ 3331| 488| { 3332| 488|#if ( N_V_STEREOBONDS == 1 ) 3333| 488| if (2 == num_2s_1 && ------------------ | Branch (3333:13): [True: 488, False: 0] ------------------ 3334| 488| 2 == type_N && ------------------ | Branch (3334:14): [True: 394, False: 94] ------------------ 3335| 394| 1 == ( num_2s_hetero[0] | num_2s_hetero[1] ) && ------------------ | Branch (3335:14): [True: 369, False: 25] ------------------ 3336| 369| 3 == at[at_1].valence + at[at_1].num_H && ------------------ | Branch (3336:14): [True: 369, False: 0] ------------------ 3337| 369| 5 == at[at_1].chem_bonds_valence + at[at_1].num_H && ------------------ | Branch (3337:14): [True: 369, False: 0] ------------------ 3338| 369| 3 == get_endpoint_valence( at[at_1].el_number )) ------------------ | Branch (3338:14): [True: 369, False: 0] ------------------ 3339| 369| { 3340| 369| ; 3341| 369| } 3342| 119| else 3343| 119| { 3344| 119| return 0; 3345| 119| } 3346| |#else 3347| | return 0; 3348| |#endif 3349| 488| } 3350| | 3351| | /* ================== Calculate parities ====================== */ 3352| | 3353| | 3354| | /* Find possibly stereo bonds and save them */ 3355| 4.43k| num_stored_isotopic_stereo_bonds = 0; 3356| | /* djb-rwth: removing redundant code */ 3357| 9.51k| for (k = 0; k < num_stereo_bonds; k++) ------------------ | Branch (3357:17): [True: 5.09k, False: 4.41k] ------------------ 3358| 5.09k| { 3359| | 3360| 5.09k| int cur_parity, next_parity, abs_cur_parity, abs_next_parity, dot_prod_z; 3361| 5.09k| S_CHAR z_dir1[3], z_dir2[3]; /* 3D vectors for half stereo bond parity direction */ 3362| 5.09k| int chain_len_bits = MAKE_BITS_CUMULENE_LEN( chain_length ); ------------------ | | 212| 5.09k|#define MAKE_BITS_CUMULENE_LEN(X) ((X)*MULT_STEREOBOND) | | ------------------ | | | | 209| 5.09k|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 3363| 5.09k| int cur_parity_defined, next_parity_defined; 3364| 5.09k| int cur_action, next_action, result_action; 3365| | 3366| 5.09k| at_2 = all_at_2[k]; 3367| 5.09k| i_next_at_1 = all_pos_1[k]; 3368| | 3369| 5.09k|#if ( MIN_SB_RING_SIZE > 0 ) 3370| 5.09k| if (at[at_1].nRingSystem == at[at_2].nRingSystem) ------------------ | Branch (3370:13): [True: 4.23k, False: 857] ------------------ 3371| 4.23k| { 3372| | /* check min. ring size only if both double bond/cumulene */ 3373| | /* ending atoms belong to the same ring system */ 3374| 4.23k| j = is_bond_in_Nmax_memb_ring( at, at_1, i_next_at_1, q, nAtomLevel, cSource, min_sb_ring_size ); 3375| 4.23k| if (j > 0) ------------------ | Branch (3375:17): [True: 2.92k, False: 1.30k] ------------------ 3376| 2.92k| { 3377| 2.92k| continue; 3378| 2.92k| } 3379| 1.30k| else 3380| 1.30k| { 3381| 1.30k| if (j < 0) ------------------ | Branch (3381:21): [True: 0, False: 1.30k] ------------------ 3382| 0| { 3383| 0| return CT_STEREOBOND_ERROR; ------------------ | | 31| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3384| 0| } 3385| 1.30k| } 3386| 4.23k| } 3387| 2.16k|#endif 3388| | 3389| 2.16k| i_next_at_2 = all_pos_2[k]; 3390| 2.16k| nUnknown = all_unkn[k]; 3391| 2.16k| memset( z_dir1, 0, sizeof( z_dir1 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3392| 2.16k| memset( z_dir2, 0, sizeof( z_dir2 ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 3393| | 3394| | /******************************************************************************** 3395| | * Find atom parities (negative means parity due to H-isotopes only) 3396| | * and half stereo bond parity directions z_dir1, z_dir2. 3397| | * 3398| | * Bond can have unknown or undefined parity or no parity because of: 3399| | * 1. Geometry (poorly defined, cannot calculate, for example linear =C-F 3400| | * or =CHD with no geometry) -- Undefined parity 3401| | * H 3402| | * 2. Identical H atoms (no parity in principle, for example =C< ) 3403| | * -- No parity H 3404| | * 3405| | * 3. The user said double bond stereo is unknown 3406| | * or at least one of single bonds is in unknown direction 3407| | * -- Unknown parity 3408| | * 3409| | * These 3 cases (see above) are referred below as 1, 2, 3. 3410| | * Each of the cases may be present or not (2 possibilities) 3411| | * Total number of combination is 2*2*2=8 3412| | * 3413| | * Since a case when all 3 are not present is a well-defined parity, 3414| | * we do not consider this case here. Then 2*2*2-1=7 cases are left. 3415| | * 3416| | * If several cases are present, list them below separated by "+". 3417| | * For example, 1+2 means (1) undefined geometry and (2) no parity 3418| | * is possible because of identical H atoms. 3419| | * 3420| | * N) Decision table, Non-isotopic, 2*2*2-1=7 cases: 3421| | * ================================================= 3422| | * none : 2+any: 1+2(e.g.=CH2); 1+2+3; 2; 2+3 AB_PARITY_NONE=0 3423| | * undefined: 1 AB_PARITY_UNDF 3424| | * unknown : 1+3; 3 AB_PARITY_UNKN 3425| | * 3426| | * I) Decision table, Isotopic, 2*2*2-1=7 cases: 3427| | * ============================================= 3428| | * none : none 3429| | * undefined: 1; 1+2; 1+2+3; 2; 2+3 3430| | * unknown : 1+3; 3 3431| | * 3432| | * Note: When defining identical atoms H atoms in case 2, 3433| | * Isotopic and Non-isotopic cases are different: 3434| | * N: do NOT take into account the isotopic composition of H atoms 3435| | * I: DO take into account the isotopic composition of H atoms 3436| | * (it is assumed that H isotopes are always different) 3437| | * 3438| | * half_stereo_bond_parity() returns: 3439| | * ================================== 3440| | * Note: half_stereo_bond_parity() is unaware of case 3. 3441| | * 3442| | * can't be a half of a stereo bond AB_PARITY_NONE 3443| | * 1, isotopic & non-isotopic: AB_PARITY_UNDF 3444| | * 1, isotopic only -AB_PARITY_UNDF 3445| | * 2, no parity: identical H isotopes AB_PARITY_IISO 3446| | * 3, 'Either' single bond(s) AB_PARITY_UNKN ??? 3447| | * 3, 'Either' single bond(s), iso H -AB_PARITY_UNKN ??? 3448| | * defined parity AB_PARITY_ODD, AB_PARITY_EVEN 3449| | * defined parity for isotopic only: -AB_PARITY_ODD, -AB_PARITY_EVEN 3450| | * 3451| | * Resultant value for the stereo bond parity 3452| | * ---+-------------------+-------+--------+----------------+ 3453| | * 3? | half_stereo_bond_ | N or I| case 1,| bond parity | 3454| | * | parity()= | | 2 or 3 | | 3455| | * ---+-------------------+-------+--------+----------------+ 3456| | * ( AB_PARITY_ODD/EVEN) => N&I: - => AB_PARITY_CALC (=6, calc.later) 3457| | * 3+( AB_PARITY_ODD/EVEN) => N&I: 3 => AB_PARITY_UNKN (=3) 3458| | * (-AB_PARITY_ODD/EVEN) => N: 2 => AB_PARITY_NONE (=0) 3459| | * (-AB_PARITY_ODD/EVEN) => I: - => AB_PARITY_CALC 3460| | * 3+(-AB_PARITY_ODD/EVEN) => N: 2+3 => AB_PARITY_UNDF (=4) 3461| | * 3+(-AB_PARITY_ODD/EVEN) => I: 3 => AB_PARITY_UNKN 3462| | * ( AB_PARITY_IISO ) => N: 1+2, 2 => AB_PARITY_NONE (=0) 3463| | * ( AB_PARITY_IISO ) => I: 1+2, 2 => AB_PARITY_UNDF 3464| | * 3+( AB_PARITY_IISO ) => N: 1+2+3,2+3=> AB_PARITY_NONE 3465| | * 3+( AB_PARITY_IISO ) => I: 1+2+3,2+3=> AB_PARITY_UNDF 3466| | * ( AB_PARITY_UNDF ) => N&I: 1 => AB_PARITY_UNDF 3467| | * 3+( AB_PARITY_UNDF ) => N&I: 1+3 => AB_PARITY_UNKN 3468| | * (-AB_PARITY_UNDF ) => N: 1+2 => AB_PARITY_NONE 3469| | * (-AB_PARITY_UNDF ) => I: 1 => AB_PARITY_UNDF 3470| | * 3+(-AB_PARITY_UNDF ) => N: 1+2+3 => AB_PARITY_NONE 3471| | * 3+(-AB_PARITY_UNDF ) => I: 1+3 => AB_PARITY_UNKN 3472| | * ---+-------------------+-------+--------+----------------+ 3473| | 3474| | * If bond parity is undefined because abs(dot_prod_z) < MIN_DOT_PROD 3475| | * then replace: AB_PARITY_CALC 3476| | * with: AB_PARITY_UNDF 3477| | * Joining two half_bond_parity() results: 3478| | * 3479| | * 3480| | * atom1 \ atom2 | AB_PARITY_NONE AB_PARITY_UNKN AB_PARITY_UNDF AB_PARITY_CALC 3481| | * ----------------+--------------------------------------------------------------- 3482| | *0=AB_PARITY_NONE | AB_PARITY_NONE AB_PARITY_NONE AB_PARITY_NONE AB_PARITY_NONE 3483| | *3=AB_PARITY_UNKN | AB_PARITY_UNKN AB_PARITY_UNKN AB_PARITY_UNKN 3484| | *4=AB_PARITY_UNDF | AB_PARITY_UNDF AB_PARITY_UNDF 3485| | *6=AB_PARITY_CALC | AB_PARITY_CALC 3486| | * 3487| | * that is, take min out of the two 3488| | *********************************************************************************/ 3489| | 3490| 2.16k| cur_parity = half_stereo_bond_parity( at, at_1, at_removed_H, num_removed_H, 3491| 2.16k| z_dir1, bPointedEdgeStereo, vABParityUnknown ); 3492| 2.16k| next_parity = half_stereo_bond_parity( at, at_2, at_removed_H, num_removed_H, 3493| 2.16k| z_dir2, bPointedEdgeStereo, vABParityUnknown ); 3494| | 3495| 2.16k| if (RETURNED_ERROR( cur_parity ) || RETURNED_ERROR( next_parity )) ------------------ | | 44| 4.33k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.16k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.16k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.16k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.16k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.16k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.16k, False: 0] | | | Branch (44:53): [True: 10, False: 2.15k] | | ------------------ ------------------ if (RETURNED_ERROR( cur_parity ) || RETURNED_ERROR( next_parity )) ------------------ | | 44| 2.15k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 40| 2.15k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 38| 2.15k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 18| 2.15k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 41| 2.15k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 18| 2.15k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (44:31): [True: 2.15k, False: 0] | | | Branch (44:53): [True: 10, False: 2.14k] | | ------------------ ------------------ 3496| 20| { 3497| 20| return CT_CALC_STEREO_ERR; ------------------ | | 34| 20|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 18| 20|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3498| 20| } 3499| 2.14k| if (( at[at_1].bUsed0DParity & FlagSB_0D ) || ( at[at_2].bUsed0DParity & FlagSB_0D )) /* djb-rwth: condition corrected */ ------------------ | | 60| 2.14k|#define FlagSB_0D 2 /**< bUsed0DParity */ ------------------ if (( at[at_1].bUsed0DParity & FlagSB_0D ) || ( at[at_2].bUsed0DParity & FlagSB_0D )) /* djb-rwth: condition corrected */ ------------------ | | 60| 1.70k|#define FlagSB_0D 2 /**< bUsed0DParity */ ------------------ | Branch (3499:13): [True: 446, False: 1.70k] | Branch (3499:55): [True: 236, False: 1.46k] ------------------ 3500| 682| { 3501| 682| FixSb0DParities( at, /* at_removed_H, num_removed_H,*/ chain_length, 3502| 682| at_1, i_next_at_1, z_dir1, 3503| 682| at_2, i_next_at_2, z_dir2, &cur_parity, &next_parity ); 3504| 682| } 3505| | 3506| 2.14k| if (cur_parity == AB_PARITY_NONE || abs( cur_parity ) == AB_PARITY_IISO) ------------------ | | 218| 4.29k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (cur_parity == AB_PARITY_NONE || abs( cur_parity ) == AB_PARITY_IISO) ------------------ | | 223| 2.14k|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ | Branch (3506:13): [True: 0, False: 2.14k] | Branch (3506:45): [True: 55, False: 2.09k] ------------------ 3507| 55| { 3508| 55| continue; 3509| 55| } 3510| 2.09k| if (next_parity == AB_PARITY_NONE || abs( next_parity ) == AB_PARITY_IISO) ------------------ | | 218| 4.18k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (next_parity == AB_PARITY_NONE || abs( next_parity ) == AB_PARITY_IISO) ------------------ | | 223| 2.09k|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ | Branch (3510:13): [True: 0, False: 2.09k] | Branch (3510:46): [True: 36, False: 2.05k] ------------------ 3511| 36| { 3512| 36| continue; 3513| 36| } 3514| | 3515| 2.05k| cur_action = half_stereo_bond_action( cur_parity, nUnknown, 0, vABParityUnknown ); /* -1 => program error */ 3516| 2.05k| next_action = half_stereo_bond_action( next_parity, nUnknown, 0, vABParityUnknown ); 3517| 2.05k| result_action = inchi_min( cur_action, next_action ); ------------------ | | 139| 2.05k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 3, False: 2.05k] | | ------------------ ------------------ 3518| | 3519| 2.05k| if (result_action == -1) ------------------ | Branch (3519:13): [True: 6, False: 2.04k] ------------------ 3520| 6| { 3521| 6| stop = 1; /* program error */ 3522| 6| } 3523| | 3524| 2.05k| abs_cur_parity = abs( cur_parity ); 3525| 2.05k| abs_next_parity = abs( next_parity ); 3526| 2.05k| cur_parity_defined = ATOM_PARITY_WELL_DEF( abs_cur_parity ); ------------------ | | 259| 2.05k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 2.05k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 2.05k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 2.05k, False: 0] | | | Branch (259:75): [True: 263, False: 1.79k] | | ------------------ ------------------ 3527| 2.05k| next_parity_defined = ATOM_PARITY_WELL_DEF( abs_next_parity ); ------------------ | | 259| 2.05k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 2.05k|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 2.05k|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 2.05k, False: 0] | | | Branch (259:75): [True: 257, False: 1.79k] | | ------------------ ------------------ 3528| | 3529| 2.05k| if (cur_parity_defined && next_parity_defined) ------------------ | Branch (3529:13): [True: 263, False: 1.79k] | Branch (3529:35): [True: 257, False: 6] ------------------ 3530| 257| { 3531| | /* find how the whole bond parity depend on geometry */ 3532| | /* if dot_prod_z < 0 then bond_parity := 3-bond_parity */ 3533| | /* can be done only for a well-defined geometry */ 3534| | /* 3535| | dot_prod_z = (chain_len_bits & BIT_CUMULENE_CHI)? 3536| | triple_prod_char( at, at_1, i_next_at_1, z_dir1, at_2, i_next_at_2, z_dir2 ) : 3537| | dot_prodchar3(z_dir1, z_dir2); 3538| | */ 3539| | 3540| 257| dot_prod_z = ( chain_len_bits && BOND_CHAIN_LEN( chain_len_bits ) % 2 ) ------------------ | | 214| 10|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 213| 10|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 205| 10|#define MASK_CUMULENE_LEN 0x38 /* mask to retrieve (cumulene chain length - 1)*MULT_STEREOBOND */ | | | | ------------------ | | ------------------ | | #define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 209| 10|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ | Branch (3540:28): [True: 10, False: 247] | Branch (3540:46): [True: 10, False: 0] ------------------ 3541| 257| ? triple_prod_char( at, at_1, i_next_at_1, z_dir1, at_2, i_next_at_2, z_dir2 ) 3542| 257| : dot_prodchar3( z_dir1, z_dir2 ); 3543| | 3544| 257| if (abs( dot_prod_z ) < MIN_DOT_PROD) ------------------ | | 253| 257|#define MIN_DOT_PROD 50 /* min value of at->stereo_bond_z_prod[i] to define parity */ ------------------ | Branch (3544:17): [True: 0, False: 257] ------------------ 3545| 0| { 3546| | /* The geometry is not well-defined. Eliminate AB_PARITY_CALC */ 3547| 0| result_action = inchi_min( result_action, AB_PARITY_UNDF ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 3548| 0| } 3549| 257| } 3550| 1.79k| else 3551| 1.79k| { 3552| 1.79k| dot_prod_z = 0; 3553| 1.79k| } 3554| | 3555| 2.05k| if (result_action != AB_PARITY_NONE && result_action != -1) ------------------ | | 218| 4.11k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (3555:13): [True: 2.04k, False: 12] | Branch (3555:48): [True: 2.03k, False: 6] ------------------ 3556| 2.03k| { 3557| | /* Stereo, no isotopes (only positive) */ 3558| 2.03k| if (cur_parity > 0 && next_parity > 0) ------------------ | Branch (3558:17): [True: 2.03k, False: 0] | Branch (3558:35): [True: 2.03k, False: 0] ------------------ 3559| 2.03k| { 3560| 2.03k| if (save_a_stereo_bond( dot_prod_z, result_action | chain_len_bits, ------------------ | Branch (3560:21): [True: 2.03k, False: 0] ------------------ 3561| 2.03k| at_1, i_next_at_1, out_at[at_1].stereo_bond_neighbor, 3562| 2.03k| out_at[at_1].stereo_bond_ord, out_at[at_1].stereo_bond_z_prod, 3563| 2.03k| out_at[at_1].stereo_bond_parity, 3564| 2.03k| at_2, i_next_at_2, out_at[at_2].stereo_bond_neighbor, 3565| 2.03k| out_at[at_2].stereo_bond_ord, out_at[at_2].stereo_bond_z_prod, 3566| 2.03k| out_at[at_2].stereo_bond_parity )) 3567| 2.03k| { 3568| 2.03k| if (!out_at[at_1].parity || ------------------ | Branch (3568:25): [True: 1.85k, False: 178] ------------------ 3569| 178| (cur_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_1].parity )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 259| 34|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 34|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 34|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 34, False: 0] | | | Branch (259:75): [True: 10, False: 24] | | ------------------ ------------------ | Branch (3569:27): [True: 34, False: 144] ------------------ 3570| 1.88k| { 3571| 1.88k| out_at[at_1].parity = cur_parity; 3572| 1.88k| memcpy(out_at[at_1].z_dir, z_dir1, sizeof(out_at[0].z_dir)); 3573| 1.88k| } 3574| 2.03k| if (!out_at[at_2].parity || ------------------ | Branch (3574:25): [True: 1.23k, False: 798] ------------------ 3575| 798| (next_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_2].parity )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 259| 100|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 100|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 100|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 100, False: 0] | | | Branch (259:75): [True: 10, False: 90] | | ------------------ ------------------ | Branch (3575:27): [True: 100, False: 698] ------------------ 3576| 1.32k| { 3577| 1.32k| out_at[at_2].parity = next_parity; 3578| 1.32k| memcpy(out_at[at_2].z_dir, z_dir2, sizeof(out_at[0].z_dir)); 3579| 1.32k| } 3580| 2.03k| out_at[at_1].bAmbiguousStereo |= at[at_1].bAmbiguousStereo; 3581| 2.03k| out_at[at_2].bAmbiguousStereo |= at[at_2].bAmbiguousStereo; 3582| | /* djb-rwth: removing redundant code */ 3583| 2.03k| } 3584| 2.03k| } 3585| 2.03k| } 3586| | 3587| | /* Stereo + isotopic (all non-zero) */ 3588| 2.05k| cur_action = half_stereo_bond_action( cur_parity, nUnknown, 1, vABParityUnknown ); /* -1 => program error */ 3589| 2.05k| next_action = half_stereo_bond_action( next_parity, nUnknown, 1, vABParityUnknown ); 3590| 2.05k| result_action = inchi_min( cur_action, next_action ); ------------------ | | 139| 2.05k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 2.05k] | | ------------------ ------------------ 3591| 2.05k| cur_parity = abs_cur_parity; 3592| 2.05k| next_parity = abs_next_parity; 3593| 2.05k| if (result_action != AB_PARITY_NONE && result_action != -1) ------------------ | | 218| 4.11k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (3593:13): [True: 2.05k, False: 0] | Branch (3593:48): [True: 2.04k, False: 6] ------------------ 3594| 2.04k| { 3595| | /* Stereo, isotopic */ 3596| 2.04k| if (cur_parity > 0 && next_parity > 0) ------------------ | Branch (3596:17): [True: 2.04k, False: 0] | Branch (3596:35): [True: 2.04k, False: 0] ------------------ 3597| 2.04k| { 3598| 2.04k| if (save_a_stereo_bond( dot_prod_z, result_action | chain_len_bits, ------------------ | Branch (3598:21): [True: 2.04k, False: 0] ------------------ 3599| 2.04k| at_1, i_next_at_1, out_at[at_1].stereo_bond_neighbor2, 3600| 2.04k| out_at[at_1].stereo_bond_ord2, out_at[at_1].stereo_bond_z_prod2, 3601| 2.04k| out_at[at_1].stereo_bond_parity2, 3602| 2.04k| at_2, i_next_at_2, out_at[at_2].stereo_bond_neighbor2, 3603| 2.04k| out_at[at_2].stereo_bond_ord2, out_at[at_2].stereo_bond_z_prod2, 3604| 2.04k| out_at[at_2].stereo_bond_parity2 )) 3605| 2.04k| { 3606| 2.04k| if (!out_at[at_1].parity2 || ------------------ | Branch (3606:25): [True: 1.87k, False: 178] ------------------ 3607| 178| (cur_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_1].parity2 )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 259| 34|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 34|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 34|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 34, False: 0] | | | Branch (259:75): [True: 10, False: 24] | | ------------------ ------------------ | Branch (3607:27): [True: 34, False: 144] ------------------ 3608| 1.89k| { 3609| 1.89k| out_at[at_1].parity2 = cur_parity /*| chain_len_bits*/; 3610| 1.89k| if (!out_at[at_1].parity) ------------------ | Branch (3610:29): [True: 12, False: 1.88k] ------------------ 3611| 12| { 3612| 12| memcpy(out_at[at_1].z_dir, z_dir1, sizeof(out_at[0].z_dir)); 3613| 12| } 3614| 1.89k| } 3615| 2.04k| if (!out_at[at_2].parity2 || /* next line changed from abs(out_at[at_2].parity) 2006-03-05 */ ------------------ | Branch (3615:25): [True: 1.25k, False: 798] ------------------ 3616| 798| (next_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_2].parity2 )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 259| 100|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 100|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 100|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 100, False: 0] | | | Branch (259:75): [True: 10, False: 90] | | ------------------ ------------------ | Branch (3616:27): [True: 100, False: 698] ------------------ 3617| 1.34k| { 3618| 1.34k| out_at[at_2].parity2 = next_parity /*| chain_len_bits*/; 3619| 1.34k| if (!out_at[at_2].parity) ------------------ | Branch (3619:29): [True: 12, False: 1.32k] ------------------ 3620| 12| { 3621| 12| memcpy(out_at[at_2].z_dir, z_dir2, sizeof(out_at[0].z_dir)); 3622| 12| } 3623| 1.34k| } 3624| 2.04k| out_at[at_1].bAmbiguousStereo |= at[at_1].bAmbiguousStereo; 3625| 2.04k| out_at[at_2].bAmbiguousStereo |= at[at_2].bAmbiguousStereo; 3626| 2.04k| num_stored_isotopic_stereo_bonds++; 3627| 2.04k| } 3628| 2.04k| } 3629| 2.04k| } 3630| 6| else 3631| 6| { 3632| 6| if (result_action == -1) ------------------ | Branch (3632:17): [True: 6, False: 0] ------------------ 3633| 6| { 3634| 6| stop = 1; /* program error? */ 3635| 6| } 3636| 6| } 3637| 2.05k| } 3638| | 3639| 4.41k| if (stop) ------------------ | Branch (3639:9): [True: 6, False: 4.41k] ------------------ 3640| 6| { 3641| 6| return CT_CALC_STEREO_ERR; ------------------ | | 34| 6|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 18| 6|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3642| 6| } 3643| | 3644| 4.41k| return /*num_stored_stereo_bonds+*/ num_stored_isotopic_stereo_bonds; 3645| 4.41k|} ichister.c:half_stereo_bond_parity: 2093| 4.33k|{ 2094| 4.33k| double at_coord[MAX_NUM_STEREO_BOND_NEIGH][3], c, s, tmp[3], tmp1, tmp2, min_tmp, max_tmp, z; 2095| 4.33k| double temp[3], pnt[3][3]; 2096| 4.33k| int j, k, p0, p1, p2, next, bValence3 = 0, num_z, nType, num_either_single; /* djb-rwth: ignoring LLVM warning: variable used in switch statement; removing redundant variables */ 2097| 4.33k| int nNumExplictAttachments; 2098| 4.33k| int bond_parity = AB_PARITY_UNDF; ------------------ | | 222| 4.33k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2099| 4.33k| int num_H = 0, num_iH, num_eH = 0, num_nH = 0 /* = num_iso_H[0] */; 2100| 4.33k| int num_iso_H[NUM_H_ISOTOPES + 1]; 2101| 4.33k| int index_H[5]; /* cannot have more than 4 elements: 1 H, 1 1H, 1 D, 1 T atom(s) */ 2102| | /* const double one_pi = 2.0*atan2(1.0 , 0.0 ); */ 2103| 4.33k| const double one_pi = 3.14159265358979323846; /* M_PI */ 2104| 4.33k| const double two_pi = 2.0*one_pi; 2105| 4.33k| int bIgnoreIsotopicH = ( 0 != ( at[cur_at].cFlags & AT_FLAG_ISO_H_POINT ) ); ------------------ | | 50| 4.33k|#define AT_FLAG_ISO_H_POINT 0x01 /**< may have isotopic H */ ------------------ 2106| 4.33k| AT_NUMB nSbNeighOrigAtNumb[MAX_NUM_STEREO_BOND_NEIGH]; 2107| | 2108| | 2109| 4.33k| if (z_dir && !z_dir[0] && !z_dir[1] && !z_dir[2]) ------------------ | Branch (2109:9): [True: 4.33k, False: 0] | Branch (2109:18): [True: 4.33k, False: 0] | Branch (2109:31): [True: 4.33k, False: 0] | Branch (2109:44): [True: 4.33k, False: 0] ------------------ 2110| 4.33k| { 2111| 4.33k| z_dir[2] = 100; 2112| 4.33k| } 2113| | 2114| 4.33k| num_H = at[cur_at].num_H; 2115| 4.33k| if (num_H > NUM_H_ISOTOPES) ------------------ | | 25| 4.33k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (2115:9): [True: 0, False: 4.33k] ------------------ 2116| 0| { 2117| 0| return 0; /* at least 2 H atoms are isotopically identical */ 2118| 0| } 2119| | 2120| 4.33k| if (MAX_NUM_STEREO_BOND_NEIGH < at[cur_at].valence + num_H || ------------------ | | 874| 4.33k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2120:9): [True: 0, False: 4.33k] ------------------ 2121| 4.33k| MIN_NUM_STEREO_BOND_NEIGH > at[cur_at].valence + num_H) ------------------ | | 875| 4.33k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (2121:10): [True: 0, False: 4.33k] ------------------ 2122| 0| { 2123| 0| return 0; 2124| 0| } 2125| | 2126| 4.33k| if (!bCanAtomHaveAStereoBond( at[cur_at].elname, at[cur_at].charge, at[cur_at].radical )) ------------------ | Branch (2126:9): [True: 0, False: 4.33k] ------------------ 2127| 0| { 2128| 0| return 0; 2129| 0| } 2130| | 2131| 4.33k| if (!bIgnoreIsotopicH) ------------------ | Branch (2131:9): [True: 4.31k, False: 16] ------------------ 2132| 4.31k| { 2133| 17.0k| for (j = 0, num_nH = num_H; j < NUM_H_ISOTOPES; j++) ------------------ | | 25| 17.0k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (2133:37): [True: 12.8k, False: 4.21k] ------------------ 2134| 12.8k| { 2135| 12.8k| if (( k = (int) at[cur_at].num_iso_H[j] ) > 1) ------------------ | Branch (2135:17): [True: 97, False: 12.7k] ------------------ 2136| 97| { 2137| 97| return AB_PARITY_IISO; /* two or more identical isotopic H atoms */ ------------------ | | 223| 97|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ 2138| 97| } 2139| 12.7k| num_nH -= k; 2140| 12.7k| } 2141| 4.31k| } 2142| | 2143| | /* at this point num_nH = number of non-isotopic H atoms */ 2144| 4.23k| if (num_nH > 1) ------------------ | Branch (2144:9): [True: 23, False: 4.21k] ------------------ 2145| 23| { 2146| 23| return AB_PARITY_IISO; /* two or more identical non-isotopic H atoms */ ------------------ | | 223| 23|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ 2147| 23| } 2148| | 2149| 4.21k| if (num_nH < 0) ------------------ | Branch (2149:9): [True: 20, False: 4.19k] ------------------ 2150| 20| { 2151| 20| return CT_ISO_H_ERR; /* program error */ /* */ ------------------ | | 28| 20|#define CT_ISO_H_ERR (CT_ERR_FIRST- 9) /*(-30009) */ | | ------------------ | | | | 18| 20|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2152| 20| } 2153| | 2154| 16.7k| for (j = 0; j < MAX_NUM_STEREO_BOND_NEIGH; j++) /* djb-rwth: avoiding garbage values with proper initialisation */ ------------------ | | 874| 16.7k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2154:17): [True: 12.5k, False: 4.19k] ------------------ 2155| 12.5k| { 2156| 50.3k| for (k = 0; k < 3; k++) ------------------ | Branch (2156:21): [True: 37.7k, False: 12.5k] ------------------ 2157| 37.7k| { 2158| 37.7k| at_coord[j][k] = 0; 2159| 37.7k| } 2160| 12.5k| } 2161| | 2162| | /******************************************************************** 2163| | * Note. At this point all (implicit and explicit) isotopic 2164| | * terminal H neighbors are either different or not present. 2165| | ********************************************************************/ 2166| | 2167| | /* locate explicit hydrogen atoms */ 2168| | /* (at_removed_H are sorted in ascending isotopic H mass order, non-isotopic first) */ 2169| 4.19k| memset( num_iso_H, 0, sizeof( num_iso_H ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2170| 4.19k| if (at_removed_H && num_removed_H > 0) ------------------ | Branch (2170:9): [True: 4.19k, False: 0] | Branch (2170:25): [True: 429, False: 3.76k] ------------------ 2171| 429| { 2172| 937| for (j = 0; j < num_removed_H; j++) ------------------ | Branch (2172:21): [True: 509, False: 428] ------------------ 2173| 509| { 2174| 509| if (at_removed_H[j].neighbor[0] == cur_at) ------------------ | Branch (2174:17): [True: 212, False: 297] ------------------ 2175| 212| { 2176| 212| k = bIgnoreIsotopicH ? 0 : at_removed_H[j].iso_atw_diff; ------------------ | Branch (2176:21): [True: 14, False: 198] ------------------ 2177| 212| if (0 <= k && k <= NUM_H_ISOTOPES) ------------------ | | 25| 211|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (2177:21): [True: 211, False: 1] | Branch (2177:31): [True: 211, False: 0] ------------------ 2178| 211| { 2179| 211| if (++num_iso_H[k] > 1) /* num_iso_H[0] = number of non-isotopic H atoms */ ------------------ | Branch (2179:25): [True: 0, False: 211] ------------------ 2180| 0| return CT_ISO_H_ERR; /* program error in counting hydrogens */ /* */ ------------------ | | 28| 0|#define CT_ISO_H_ERR (CT_ERR_FIRST- 9) /*(-30009) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2181| 211| index_H[num_eH++] = j; 2182| 211| } 2183| 1| else 2184| 1| { 2185| 1| return CT_ISO_H_ERR; /* program error */ /* */ ------------------ | | 28| 1|#define CT_ISO_H_ERR (CT_ERR_FIRST- 9) /*(-30009) */ | | ------------------ | | | | 18| 1|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2186| 1| } 2187| 212| } 2188| 509| } 2189| 428| num_iH = num_H - num_eH; /* number of implicit non-isotopic and isotopic H atoms */ 2190| 428| if (num_iH > 1) ------------------ | Branch (2190:13): [True: 1, False: 427] ------------------ 2191| 1| { 2192| | /* more than one implicit H: cannot reconstruct the geometry */ 2193| 1| bond_parity = -AB_PARITY_UNDF; ------------------ | | 222| 1|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2194| 1| goto exit_function; 2195| 1| } 2196| 428| } 2197| | /* djb-rwth: removing redundant code */ 2198| | /* at this point num_iH = number of implicit non-isotopic and isotopic H atoms */ 2199| 4.19k| if (at[cur_at].valence + num_eH < MIN_NUM_STEREO_BOND_NEIGH) ------------------ | | 875| 4.19k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (2199:9): [True: 26, False: 4.16k] ------------------ 2200| 26| { 2201| | /* =NH or =CHD when no explicit H is present */ 2202| 26| return num_H == 1 ? AB_PARITY_UNDF : -AB_PARITY_UNDF; ------------------ | | 222| 24|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ return num_H == 1 ? AB_PARITY_UNDF : -AB_PARITY_UNDF; ------------------ | | 222| 2|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2202:16): [True: 24, False: 2] ------------------ 2203| 26| } 2204| | 2205| 4.16k| bValence3 = bAtomHasValence3( at[cur_at].elname, at[cur_at].charge, at[cur_at].radical ); 2206| | /* 2207| | * Can one explicit hydrogen be added to make asymmetric configuration? 2208| | * For now we can add 1 H atom in case of an appropriate geometry if: 2209| | * (a) one non-isotopic H (even if explicit isotopic H atoms are present), or 2210| | * (b) one isotopic or non-isotopic H if NO explicit isotopic or non-isotopic H atom is present 2211| | * This makes sense only in case chem. valence = 4. In case of chem. valence = 3, do not check. 2212| | */ 2213| 4.16k| if (at[cur_at].valence + num_eH == MIN_NUM_STEREO_BOND_NEIGH && !bValence3 && ------------------ | | 875| 8.32k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (2213:9): [True: 3.54k, False: 616] | Branch (2213:69): [True: 87, False: 3.46k] ------------------ 2214| 87| !(/*(a)*/ (1 == num_nH && !num_iso_H[0]) || ------------------ | Branch (2214:21): [True: 77, False: 10] | Branch (2214:36): [True: 50, False: 27] ------------------ 2215| 37| /*(b)*/ (1 == num_H && !num_eH )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2215:23): [True: 30, False: 7] | Branch (2215:37): [True: 3, False: 27] ------------------ 2216| 4.16k| ) 2217| 34| { 2218| 34| goto exit_function; 2219| | /* return num_H == 1? AB_PARITY_UNDF : -AB_PARITY_UNDF; */ 2220| 34| } 2221| | 2222| | /* store neighbors coordinates */ 2223| 4.13k| num_z = num_either_single = 0; /* djb-rwth: ignoring LLVM warning: variable used for switch statement; removing redundant code */ 2224| 12.3k| for (k = nNumExplictAttachments = 0; k < 2; k++) ------------------ | Branch (2224:42): [True: 8.26k, False: 4.13k] ------------------ 2225| 8.26k| { 2226| 8.26k| switch (k) ------------------ | Branch (2226:17): [True: 8.26k, False: 0] ------------------ 2227| 8.26k| { 2228| 4.13k| case 0: ------------------ | Branch (2228:13): [True: 4.13k, False: 4.13k] ------------------ 2229| 4.31k| for (j = 0; j < num_eH; j++, nNumExplictAttachments++) ------------------ | Branch (2229:29): [True: 183, False: 4.13k] ------------------ 2230| 183| { 2231| 183| next = index_H[j]; 2232| 183| at_coord[nNumExplictAttachments][0] = at_removed_H[next].x - at[cur_at].x; 2233| 183| at_coord[nNumExplictAttachments][1] = at_removed_H[next].y - at[cur_at].y; 2234| 183| nSbNeighOrigAtNumb[nNumExplictAttachments] = at_removed_H[next].orig_at_number; 2235| | /* use the fact that (at_removed_H - at) = (number of atoms except removed explicit H) */ 2236| 183| z = -get_z_coord( at, (int) ( at_removed_H - at ) + next, 2237| 183| 0 /*neighbor #*/, 2238| 183| &nType, 2239| 183| -( bPointedEdgeStereo & PES_BIT_POINT_EDGE_STEREO ) ); ------------------ | | 44| 183|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ 2240| 183| switch (nType) ------------------ | Branch (2240:29): [True: 0, False: 183] ------------------ 2241| 183| { 2242| 0| case ZTYPE_EITHER: ------------------ | | 24| 0|#define ZTYPE_EITHER 9999 ------------------ | Branch (2242:25): [True: 0, False: 183] ------------------ 2243| 0| num_either_single++; /* bond in "Either" direction. */ 2244| 0| break; 2245| 0| case ZTYPE_UP: ------------------ | | 22| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (2245:25): [True: 0, False: 183] ------------------ 2246| 0| case ZTYPE_DOWN: ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (2246:25): [True: 0, False: 183] ------------------ 2247| 0| nType = -nType; /* at_removed_H[] contains bonds TO the center, not from */ 2248| 0| z = len2( at_coord[nNumExplictAttachments] ); 2249| | /* 2250| | z = sqrt( at_coord[nNumExplictAttachments][0]*at_coord[nNumExplictAttachments][0] 2251| | + at_coord[nNumExplictAttachments][1]*at_coord[nNumExplictAttachments][1] ); 2252| | */ 2253| 0| if (nType == ZTYPE_DOWN) ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (2253:33): [True: 0, False: 0] ------------------ 2254| 0| { 2255| 0| z = -z; 2256| 0| } 2257| | /* no break; here */ 2258| 0| case ZTYPE_3D: ------------------ | | 23| 0|#define ZTYPE_3D 3 ------------------ | Branch (2258:25): [True: 0, False: 183] ------------------ 2259| 0| num_z++; 2260| 183| } 2261| 183| at_coord[nNumExplictAttachments][2] = z; 2262| 183| } 2263| 4.13k| break; 2264| 4.13k| case 1: ------------------ | Branch (2264:13): [True: 4.13k, False: 4.13k] ------------------ 2265| 12.8k| for (j = 0; j < at[cur_at].valence; j++, nNumExplictAttachments++) ------------------ | Branch (2265:29): [True: 8.69k, False: 4.13k] ------------------ 2266| 8.69k| { 2267| 8.69k| next = at[cur_at].neighbor[j]; 2268| 8.69k| at_coord[nNumExplictAttachments][0] = at[next].x - at[cur_at].x; 2269| 8.69k| at_coord[nNumExplictAttachments][1] = at[next].y - at[cur_at].y; 2270| 8.69k| nSbNeighOrigAtNumb[nNumExplictAttachments] = at[next].orig_at_number; 2271| | 2272| 8.69k| z = get_z_coord( at, cur_at, j /*neighbor #*/, &nType, ( bPointedEdgeStereo & PES_BIT_POINT_EDGE_STEREO ) ); ------------------ | | 44| 8.69k|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ 2273| 8.69k| switch (nType) ------------------ | Branch (2273:29): [True: 0, False: 8.69k] ------------------ 2274| 8.69k| { 2275| 0| case ZTYPE_EITHER: ------------------ | | 24| 0|#define ZTYPE_EITHER 9999 ------------------ | Branch (2275:25): [True: 0, False: 8.69k] ------------------ 2276| 0| num_either_single++; /* bond in "Either" direction. */ 2277| 0| break; 2278| 0| case ZTYPE_UP: ------------------ | | 22| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (2278:25): [True: 0, False: 8.69k] ------------------ 2279| 0| case ZTYPE_DOWN: ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (2279:25): [True: 0, False: 8.69k] ------------------ 2280| 0| z = len2( at_coord[nNumExplictAttachments] ); 2281| | /* 2282| | z = sqrt( at_coord[nNumExplictAttachments][0]*at_coord[nNumExplictAttachments][0] 2283| | + at_coord[nNumExplictAttachments][1]*at_coord[nNumExplictAttachments][1] ); 2284| | */ 2285| 0| if (nType == ZTYPE_DOWN) ------------------ | | 20| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (2285:33): [True: 0, False: 0] ------------------ 2286| 0| { 2287| 0| z = -z; 2288| 0| } 2289| | /* no break; here */ 2290| 0| case ZTYPE_3D: ------------------ | | 23| 0|#define ZTYPE_3D 3 ------------------ | Branch (2290:25): [True: 0, False: 8.69k] ------------------ 2291| 0| num_z++; 2292| 8.69k| } 2293| 8.69k| at_coord[nNumExplictAttachments][2] = z; 2294| 8.69k| } 2295| 4.13k| break; 2296| 8.26k| } 2297| 8.26k| } 2298| | 2299| 4.13k| if (num_either_single) ------------------ | Branch (2299:9): [True: 0, False: 4.13k] ------------------ 2300| 0| { 2301| 0| bond_parity = vABParityUnknown /*AB_PARITY_UNKN*/; /* single bond is 'unknown' */ 2302| 0| goto exit_function; 2303| 0| } 2304| | 2305| | /* nNumExplictAttachments is a total number of attachments, including removed explicit terminal hydrogens */ 2306| 4.13k| if (nNumExplictAttachments == 2) ------------------ | Branch (2306:9): [True: 3.51k, False: 616] ------------------ 2307| 3.51k| { 2308| | /* create coordinates of the implicit hydrogen (or a fictitious atom in case of ==N-X ), */ 2309| | /* coord[2][], attached to the cur_at. */ 2310| 14.0k| for (j = 0; j < 3; j++) ------------------ | Branch (2310:21): [True: 10.5k, False: 3.51k] ------------------ 2311| 10.5k| { 2312| 10.5k| at_coord[2][j] = -( at_coord[0][j] + at_coord[1][j] ); 2313| 10.5k| } 2314| 3.51k| nSbNeighOrigAtNumb[nNumExplictAttachments] = 0; /* implicit H or lone pair */ 2315| 3.51k| } 2316| 16.5k| for (j = 0; j < 3; j++) ------------------ | Branch (2316:17): [True: 12.3k, False: 4.13k] ------------------ 2317| 12.3k| { 2318| 12.3k| tmp[j] = len3( at_coord[j] ); 2319| 12.3k| } 2320| 4.13k| min_tmp = inchi_min( tmp[0], inchi_min( tmp[1], tmp[2] ) ); ------------------ | | 139| 8.26k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 4.13k] | | | Branch (139:32): [True: 0, False: 4.13k] | | | Branch (139:41): [True: 0, False: 4.13k] | | ------------------ ------------------ 2321| 4.13k| max_tmp = inchi_max( tmp[0], inchi_max( tmp[1], tmp[2] ) ); ------------------ | | 138| 8.26k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 4.13k] | | | Branch (138:32): [True: 0, False: 4.13k] | | | Branch (138:41): [True: 0, False: 4.13k] | | ------------------ ------------------ 2322| 4.13k| if (min_tmp < MIN_BOND_LEN || min_tmp < MIN_SINE*max_tmp) ------------------ | | 39| 8.26k|#define MIN_BOND_LEN 0.000001 ------------------ if (min_tmp < MIN_BOND_LEN || min_tmp < MIN_SINE*max_tmp) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (2322:9): [True: 4.13k, False: 0] | Branch (2322:35): [True: 0, False: 0] ------------------ 2323| 4.13k| { 2324| | /* all bonds or some of bonds are too short */ 2325| 4.13k| if (at[cur_at].sb_parity[0]) ------------------ | Branch (2325:13): [True: 1.02k, False: 3.10k] ------------------ 2326| 1.02k| { 2327| | /* use bond psrity; the reconciliation in ReconcileAllCmlBondParities() 2328| | * has made all ways to calculate parity produce same result 2329| | */ 2330| 1.02k| bond_parity = GetHalfStereobond0DParity( at, cur_at, nSbNeighOrigAtNumb, 2331| 1.02k| nNumExplictAttachments, bond_parity, FlagSB_0D ); ------------------ | | 60| 1.02k|#define FlagSB_0D 2 /**< bUsed0DParity */ ------------------ 2332| 1.02k| } 2333| | 2334| 4.13k| goto exit_function; 2335| 4.13k| } 2336| | /* normalize lengths to 1 */ 2337| 0| for (j = 0; j < 3; j++) ------------------ | Branch (2337:17): [True: 0, False: 0] ------------------ 2338| 0| { 2339| 0| mult3( at_coord[j], 1.0 / tmp[j], at_coord[j] ); 2340| 0| } 2341| | 2342| | /* find projections of at_coord vector differences on the plane containing their arrowhead ends */ 2343| 0| for (j = 0; j < 3; j++) ------------------ | Branch (2343:17): [True: 0, False: 0] ------------------ 2344| 0| { 2345| | /* pnt[0..2] = {0-1, 1-2, 2-0} */ 2346| 0| tmp[j] = len3((double *)diff3( at_coord[j], at_coord[( j + 1 ) % 3], pnt[j] ) ); /* djb-rwth: cast operator added for compatibility */ 2347| 0| if (tmp[j] < MIN_SINE) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (2347:13): [True: 0, False: 0] ------------------ 2348| 0| { 2349| 0| goto exit_function; /* angle #i-cur_at-#j is too small */ 2350| 0| } 2351| 0| mult3( pnt[j], 1.0 / tmp[j], pnt[j] ); /* 2003-10-06 */ 2352| 0| } 2353| | /* find pnt[p2], a vector perpendicular to the plane, and its length tmp[p2] */ 2354| | /* replace previous pnt[p2], tmp[p2] with new values; the old values do not have any additional */ 2355| | /* information because pnt[p0]+pnt[p1]+pnt[p2]=0 */ 2356| | /* 10-6-2003: a cross-product of one pair pnt[j], pnt[(j+1)%3] can be very small. Find the larges one */ 2357| 0| tmp1 = len3((double *)cross_prod3( pnt[0], pnt[1], temp ) ); /* djb-rwth: cast operator added for compatibility */ 2358| 0| for (j = 1, k = 0; j < 3; j++) ------------------ | Branch (2358:24): [True: 0, False: 0] ------------------ 2359| 0| { 2360| 0| tmp2 = len3((double *)cross_prod3( pnt[j], pnt[( j + 1 ) % 3], temp ) ); /* djb-rwth: cast operator added for compatibility */ 2361| 0| if (tmp2 > tmp1) ------------------ | Branch (2361:13): [True: 0, False: 0] ------------------ 2362| 0| { 2363| 0| tmp1 = tmp2; 2364| 0| k = j; 2365| 0| } 2366| 0| } 2367| | /* previously p0=0, p1=1, p2=2 */ 2368| 0| p0 = k; 2369| 0| p1 = ( k + 1 ) % 3; 2370| 0| p2 = ( k + 2 ) % 3; 2371| 0| tmp[p2] = len3((double *)cross_prod3( pnt[p0], pnt[p1], pnt[p2] ) ); /* djb-rwth: cast operator added for compatibility */ 2372| 0| if (tmp[p2] < MIN_SINE*tmp[p0] * tmp[p1]) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (2372:9): [True: 0, False: 0] ------------------ 2373| 0| { 2374| 0| goto exit_function; /* pnt[p0] is almost colinear to pnt[p1] */ 2375| 0| } 2376| | /* new basis: pnt[p0], pnt[p1], pnt[p2]; set z-coord sign and make abs(pnt[p2]) = 1 */ 2377| 0| mult3( pnt[p2], ( pnt[p2][2] > 0.0 ? 1.0 : -1.0 ) / tmp[p2], pnt[p2] ); /* unit vector in the new z-axis direction */ ------------------ | Branch (2377:23): [True: 0, False: 0] ------------------ 2378| | 2379| 0| min_tmp = dot_prod3( at_coord[0], pnt[p2] ); /* non-planarity measure (sine): hight of at_coord[] pyramid */ 2380| 0| mult3( pnt[p2], min_tmp, pnt[p0] ); /* vector height of the pyramid, ideally 0 */ 2381| | /* find new pnt[p0] = projection of at_coord[p0] on plane orthogonal to pnt[p2] */ 2382| 0| tmp[p0] = len3((double *)diff3( at_coord[0], pnt[p0], pnt[p0] ) ); /* djb-rwth: cast operator added for compatibility */ 2383| 0| mult3( pnt[p0], 1.0 / tmp[p0], pnt[p0] ); /* new x axis basis vector */ 2384| 0| cross_prod3( pnt[p2], pnt[p0], pnt[p1] ); /* new y axis basis vector */ 2385| | /* find at_coord in the new basis of {pnt[p0], pnt[p1], pnt[p2]} */ 2386| 0| for (j = 0; j < 3; j++) ------------------ | Branch (2386:17): [True: 0, False: 0] ------------------ 2387| 0| { 2388| | /* copy3(at_coord[j], temp);-- djb-rwth: removing copy3 function */ 2389| 0| memcpy(temp, at_coord[j], sizeof(at_coord[j])); 2390| 0| for (k = 0; k < 3; k++) ------------------ | Branch (2390:21): [True: 0, False: 0] ------------------ 2391| 0| { 2392| 0| at_coord[j][k] = dot_prod3( temp, pnt[( k + p0 ) % 3] ); 2393| 0| } 2394| | /* new xy plane projection length */ 2395| 0| tmp[j] = sqrt( at_coord[j][0] * at_coord[j][0] + at_coord[j][1] * at_coord[j][1] ); 2396| | /* make new xy plane projection length = 1 */ 2397| 0| mult3( at_coord[j], 1.0 / tmp[j], at_coord[j] ); 2398| 0| } 2399| | 2400| 0| s = fabs( at_coord[1][0] * at_coord[2][1] - at_coord[1][1] * at_coord[2][0] ); /* 1-2 sine */ 2401| 0| c = at_coord[1][0] * at_coord[2][0] + at_coord[1][1] * at_coord[2][1]; /* 1-2 cosine */ 2402| 0| if (s < MIN_SINE && c > 0.5) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (2402:9): [True: 0, False: 0] | Branch (2402:25): [True: 0, False: 0] ------------------ 2403| 0| { 2404| 0| goto exit_function; /* bonds to neigh. 1 and 2 have almost same direction; relative angles are undefined */ 2405| 0| } 2406| 0| c = at_coord[0][0]; /* cosine of the angle between new Ox axis and a bond to the neighbor 0. Should be 1 */ 2407| 0| s = at_coord[0][1]; /* sine. Should be 0 */ 2408| | /* turn vectors so that vector #1 (at_coord[0]) becomes {1, 0} */ 2409| 0| for (j = 0; j < MAX_NUM_STEREO_BOND_NEIGH; j++) ------------------ | | 874| 0|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2409:17): [True: 0, False: 0] ------------------ 2410| 0| { 2411| 0| tmp1 = c*at_coord[j][0] + s*at_coord[j][1]; 2412| 0| tmp2 = -s*at_coord[j][0] + c*at_coord[j][1]; 2413| 0| at_coord[j][0] = tmp1; 2414| 0| at_coord[j][1] = tmp2; 2415| 0| } 2416| | /* counterclockwise angles from the direction to neigh 0 to to directions to neighbors 1 and 2: */ 2417| 0| tmp1 = atan2( at_coord[1][1], at_coord[1][0] ); /* range -pi and +pi */ 2418| 0| tmp2 = atan2( at_coord[2][1], at_coord[2][0] ); 2419| 0| if (tmp1 < 0.0) ------------------ | Branch (2419:9): [True: 0, False: 0] ------------------ 2420| 0| { 2421| 0| tmp1 += two_pi; /* range 0 to 2*pi */ 2422| 0| } 2423| 0| if (tmp2 < 0.0) ------------------ | Branch (2423:9): [True: 0, False: 0] ------------------ 2424| 0| { 2425| 0| tmp2 += two_pi; 2426| 0| } 2427| | /*----------------------------------- 2428| | Example 2429| | 1 \ case tmp1 < tmp2 2430| | \ parity is odd 2431| | \ (counterclockwise) 2432| | A------- 0 2433| | / 2434| | / 2435| | 2 / 2436| | 2437| | ------------------------------------*/ 2438| 0| bond_parity = 2 - ( tmp1 < tmp2 ); 2439| 0| for (j = 0; j < 3; j++) ------------------ | Branch (2439:17): [True: 0, False: 0] ------------------ 2440| 0| { 2441| 0| if (z_dir) ------------------ | Branch (2441:13): [True: 0, False: 0] ------------------ 2442| 0| z_dir[j] = (S_CHAR) ( pnt[p2][j] >= 0.0 ? floor( 0.5 + 100.0 * pnt[p2][j] ) : ------------------ | Branch (2442:35): [True: 0, False: 0] ------------------ 2443| 0| -floor( 0.5 - 100.0 * pnt[p2][j] ) ); /* abs(z_dir) = 100 */ 2444| 0| } 2445| | /* check for ambiguity */ 2446| 0| if (nNumExplictAttachments > 2) ------------------ | Branch (2446:9): [True: 0, False: 0] ------------------ 2447| 0| { 2448| 0| min_tmp = inchi_min( tmp1, tmp2 ); ------------------ | | 139| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 0] | | ------------------ ------------------ 2449| 0| max_tmp = inchi_max( tmp1, tmp2 ); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 2450| 0| if (min_tmp > one_pi - MIN_SINE || max_tmp < one_pi + MIN_SINE || max_tmp - min_tmp > one_pi - MIN_SINE) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ if (min_tmp > one_pi - MIN_SINE || max_tmp < one_pi + MIN_SINE || max_tmp - min_tmp > one_pi - MIN_SINE) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ if (min_tmp > one_pi - MIN_SINE || max_tmp < one_pi + MIN_SINE || max_tmp - min_tmp > one_pi - MIN_SINE) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (2450:13): [True: 0, False: 0] | Branch (2450:44): [True: 0, False: 0] | Branch (2450:75): [True: 0, False: 0] ------------------ 2451| 0| { 2452| 0| at[cur_at].bAmbiguousStereo |= AMBIGUOUS_STEREO; ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 2453| 0| } 2454| 0| else /* 3D ambiguity 8-28-2002 */ 2455| 0| { 2456| 0| if (fabs( at_coord[0][2] ) > MAX_SINE) ------------------ | | 38| 0|#define MAX_SINE 0.70710678118654752440084436210485 /* 1/sqrt(2)=sin(pi/4) */ ------------------ | Branch (2456:17): [True: 0, False: 0] ------------------ 2457| 0| { /* all fabs(at_coord[j][2] (j=0..2) must be equal */ 2458| 0| at[cur_at].bAmbiguousStereo |= AMBIGUOUS_STEREO; ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 2459| 0| } 2460| 0| } 2461| 0| } 2462| 0| else 2463| 0| { 2464| 0| if (nNumExplictAttachments == 2) ------------------ | Branch (2464:13): [True: 0, False: 0] ------------------ 2465| 0| { /* 10-6-2003: added */ 2466| 0| min_tmp = fabs( tmp1 - one_pi ); 2467| 0| if (min_tmp < MIN_SINE) ------------------ | | 30| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (2467:17): [True: 0, False: 0] ------------------ 2468| 0| { 2469| 0| bond_parity = AB_PARITY_UNDF; /* consider as undefined 10-6-2003 */ ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2470| 0| } 2471| 0| else 2472| 0| { 2473| 0| if (min_tmp < MIN_ANGLE_DBOND) ------------------ | | 33| 0|#define MIN_ANGLE_DBOND 0.087156 /* 5 degrees = max angle considered as too small for unambiguous double bond stereo */ ------------------ | Branch (2473:21): [True: 0, False: 0] ------------------ 2474| 0| { 2475| 0| at[cur_at].bAmbiguousStereo |= AMBIGUOUS_STEREO; ------------------ | | 245| 0|#define AMBIGUOUS_STEREO 1 ------------------ 2476| 0| } 2477| 0| } 2478| 0| } 2479| 0| } 2480| | 2481| | /* for 3 neighbors moving implicit H to the index=0 from index=2 position */ 2482| | /* can be done in 2 transpositions and does not change atom's parity */ 2483| | 2484| 4.16k|exit_function: 2485| | 2486| 4.16k| if (num_H > 1 && bond_parity > 0 && !( bond_parity & AB_PARITY_0D ) /*&& PARITY_WELL_DEF(bond_parity)*/) ------------------ | | 225| 9|#define AB_PARITY_0D 8 /* 8 => bit signifies 0D case -- not used */ ------------------ | Branch (2486:9): [True: 10, False: 4.15k] | Branch (2486:22): [True: 9, False: 1] | Branch (2486:41): [True: 9, False: 0] ------------------ 2487| 9| { 2488| | /* 2489| | * stereo only if isotopes are counted. Do not inverse 2490| | * Examples: sign for this: 2491| | * H D 2492| | * / / H 2493| | * ==C or ==CH / 2494| | * \ ==N (bValence3=1) 2495| | * D 2496| | * two explicit one explicit H isotope (D), 2497| | * isotopic H atoms one implicit H 2498| | */ 2499| 9| bond_parity = -bond_parity; /* refers to isotopically substituted structure only */ 2500| 9| } 2501| | 2502| 4.16k| return bond_parity; 2503| 0|} ichister.c:half_stereo_bond_action: 2870| 8.22k|{ 2871| 8.22k|#define AB_NEGATIVE 0x10 2872| 8.22k|#define AB_UNKNOWN 0x20 2873| 8.22k| int nAction; 2874| | 2875| 8.22k| if (nParity == AB_PARITY_NONE) ------------------ | | 218| 8.22k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (2875:9): [True: 0, False: 8.22k] ------------------ 2876| 0| { 2877| 0| return AB_PARITY_NONE; ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 2878| 0| } 2879| | 2880| | /* Unknown (type 1) in the parity value may come from the 'Either' single bond only */ 2881| | /* Treat it as a known single bond geometry and unknown (Either) double bond */ 2882| 8.22k| if (nParity == vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (2882:9): [True: 7.13k, False: 1.09k] ------------------ 2883| 7.13k| { 2884| 7.13k| nParity = AB_PARITY_ODD | AB_UNKNOWN; ------------------ | | 219| 7.13k|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ nParity = AB_PARITY_ODD | AB_UNKNOWN; ------------------ | | 2872| 7.13k|#define AB_UNKNOWN 0x20 ------------------ 2885| 7.13k| } 2886| 8.22k| if (nParity == -vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (2886:9): [True: 26, False: 8.19k] ------------------ 2887| 26| { 2888| 26| nParity = AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE; ------------------ | | 219| 26|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ nParity = AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE; ------------------ | | 2872| 26|#define AB_UNKNOWN 0x20 ------------------ nParity = AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE; ------------------ | | 2871| 26|#define AB_NEGATIVE 0x10 ------------------ 2889| 26| } 2890| | 2891| | /* make positive, replace AB_PARITY_EVEN with AB_PARITY_ODD */ 2892| 8.22k| if (nParity < 0) ------------------ | Branch (2892:9): [True: 14, False: 8.20k] ------------------ 2893| 14| { 2894| 14| nParity = ( ( nParity == -AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( -nParity ) ) | AB_NEGATIVE; ------------------ | | 220| 14|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ nParity = ( ( nParity == -AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( -nParity ) ) | AB_NEGATIVE; ------------------ | | 219| 8|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ nParity = ( ( nParity == -AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( -nParity ) ) | AB_NEGATIVE; ------------------ | | 2871| 14|#define AB_NEGATIVE 0x10 ------------------ | Branch (2894:21): [True: 8, False: 6] ------------------ 2895| 14| } 2896| 8.20k| else 2897| 8.20k| { 2898| 8.20k| if (nParity == AB_PARITY_EVEN) ------------------ | | 220| 8.20k|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (2898:13): [True: 686, False: 7.52k] ------------------ 2899| 686| { 2900| 686| nParity = AB_PARITY_ODD; ------------------ | | 219| 686|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ 2901| 686| } 2902| 8.20k| } 2903| | 2904| | /* Unknown (type 2): was detected in the double bond attribute */ 2905| | /* (this 'unknown' came from 'Either' double bond) */ 2906| | /* Treat both unknowns in the same way */ 2907| 8.22k| if (bUnknown) ------------------ | Branch (2907:9): [True: 24, False: 8.19k] ------------------ 2908| 24| { 2909| 24| nParity |= AB_UNKNOWN; ------------------ | | 2872| 24|#define AB_UNKNOWN 0x20 ------------------ 2910| 24| } 2911| | 2912| 8.22k| if (bIsotopic) ------------------ | Branch (2912:9): [True: 4.11k, False: 4.11k] ------------------ 2913| 4.11k| { 2914| 4.11k| switch (nParity) 2915| 4.11k| { 2916| 513| case AB_PARITY_ODD: ------------------ | | 219| 513|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (2916:13): [True: 513, False: 3.59k] ------------------ 2917| 520| case AB_PARITY_ODD | AB_NEGATIVE: ------------------ | | 219| 520|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ case AB_PARITY_ODD | AB_NEGATIVE: ------------------ | | 2871| 520|#define AB_NEGATIVE 0x10 ------------------ | Branch (2917:13): [True: 7, False: 4.10k] ------------------ 2918| 520| nAction = AB_PARITY_CALC; ------------------ | | 224| 520|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ 2919| 520| break; 2920| 3.56k| case AB_PARITY_ODD | AB_UNKNOWN: ------------------ | | 219| 3.56k|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ case AB_PARITY_ODD | AB_UNKNOWN: ------------------ | | 2872| 3.56k|#define AB_UNKNOWN 0x20 ------------------ | Branch (2920:13): [True: 3.56k, False: 545] ------------------ 2921| 3.56k| case AB_PARITY_UNDF | AB_UNKNOWN: ------------------ | | 222| 3.56k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ case AB_PARITY_UNDF | AB_UNKNOWN: ------------------ | | 2872| 3.56k|#define AB_UNKNOWN 0x20 ------------------ | Branch (2921:13): [True: 0, False: 4.11k] ------------------ 2922| 3.57k| case AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 219| 3.57k|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ case AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2872| 3.57k|#define AB_UNKNOWN 0x20 ------------------ case AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2871| 3.57k|#define AB_NEGATIVE 0x10 ------------------ | Branch (2922:13): [True: 13, False: 4.09k] ------------------ 2923| 3.57k| case AB_PARITY_UNDF | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 222| 3.57k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ case AB_PARITY_UNDF | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2872| 3.57k|#define AB_UNKNOWN 0x20 ------------------ case AB_PARITY_UNDF | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2871| 3.57k|#define AB_NEGATIVE 0x10 ------------------ | Branch (2923:13): [True: 0, False: 4.11k] ------------------ 2924| 3.57k| nAction = vABParityUnknown /*AB_PARITY_UNKN*/; 2925| 3.57k| break; 2926| 0| case AB_PARITY_IISO: ------------------ | | 223| 0|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ | Branch (2926:13): [True: 0, False: 4.11k] ------------------ 2927| 0| case AB_PARITY_IISO | AB_UNKNOWN: ------------------ | | 223| 0|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ case AB_PARITY_IISO | AB_UNKNOWN: ------------------ | | 2872| 0|#define AB_UNKNOWN 0x20 ------------------ | Branch (2927:13): [True: 0, False: 4.11k] ------------------ 2928| 0| nAction = AB_PARITY_NONE; ------------------ | | 218| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 2929| 0| break; 2930| 0| case AB_PARITY_UNDF: ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2930:13): [True: 0, False: 4.11k] ------------------ 2931| 0| case AB_PARITY_UNDF | AB_NEGATIVE: ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ case AB_PARITY_UNDF | AB_NEGATIVE: ------------------ | | 2871| 0|#define AB_NEGATIVE 0x10 ------------------ | Branch (2931:13): [True: 0, False: 4.11k] ------------------ 2932| 0| nAction = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2933| 0| break; 2934| 12| default: ------------------ | Branch (2934:13): [True: 12, False: 4.09k] ------------------ 2935| 12| nAction = -1; /* program error */ 2936| 4.11k| } 2937| 4.11k| } 2938| 4.11k| else 2939| 4.11k| { 2940| | /* Non-isotopic */ 2941| 4.11k| switch (nParity) 2942| 4.11k| { 2943| 513| case AB_PARITY_ODD: ------------------ | | 219| 513|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (2943:13): [True: 513, False: 3.59k] ------------------ 2944| 513| nAction = AB_PARITY_CALC; ------------------ | | 224| 513|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ 2945| 513| break; 2946| 3.56k| case AB_PARITY_ODD | AB_UNKNOWN: ------------------ | | 219| 3.56k|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ case AB_PARITY_ODD | AB_UNKNOWN: ------------------ | | 2872| 3.56k|#define AB_UNKNOWN 0x20 ------------------ | Branch (2946:13): [True: 3.56k, False: 545] ------------------ 2947| 3.56k| case AB_PARITY_UNDF | AB_UNKNOWN: ------------------ | | 222| 3.56k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ case AB_PARITY_UNDF | AB_UNKNOWN: ------------------ | | 2872| 3.56k|#define AB_UNKNOWN 0x20 ------------------ | Branch (2947:13): [True: 0, False: 4.11k] ------------------ 2948| 3.56k| nAction = vABParityUnknown /*AB_PARITY_UNKN*/; 2949| 3.56k| break; 2950| | /* case AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE: */ 2951| 0| case AB_PARITY_UNDF: ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2951:13): [True: 0, False: 4.11k] ------------------ 2952| 0| nAction = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2953| 0| break; 2954| 13| case AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 219| 13|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ case AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2872| 13|#define AB_UNKNOWN 0x20 ------------------ case AB_PARITY_ODD | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2871| 13|#define AB_NEGATIVE 0x10 ------------------ | Branch (2954:13): [True: 13, False: 4.09k] ------------------ 2955| 20| case AB_PARITY_ODD | AB_NEGATIVE: ------------------ | | 219| 20|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ case AB_PARITY_ODD | AB_NEGATIVE: ------------------ | | 2871| 20|#define AB_NEGATIVE 0x10 ------------------ | Branch (2955:13): [True: 7, False: 4.10k] ------------------ 2956| 20| case AB_PARITY_IISO: ------------------ | | 223| 20|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ | Branch (2956:13): [True: 0, False: 4.11k] ------------------ 2957| 20| case AB_PARITY_IISO | AB_UNKNOWN: ------------------ | | 223| 20|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ case AB_PARITY_IISO | AB_UNKNOWN: ------------------ | | 2872| 20|#define AB_UNKNOWN 0x20 ------------------ | Branch (2957:13): [True: 0, False: 4.11k] ------------------ 2958| 20| case AB_PARITY_UNDF | AB_NEGATIVE: ------------------ | | 222| 20|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ case AB_PARITY_UNDF | AB_NEGATIVE: ------------------ | | 2871| 20|#define AB_NEGATIVE 0x10 ------------------ | Branch (2958:13): [True: 0, False: 4.11k] ------------------ 2959| 20| case AB_PARITY_UNDF | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 222| 20|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ case AB_PARITY_UNDF | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2872| 20|#define AB_UNKNOWN 0x20 ------------------ case AB_PARITY_UNDF | AB_UNKNOWN | AB_NEGATIVE: ------------------ | | 2871| 20|#define AB_NEGATIVE 0x10 ------------------ | Branch (2959:13): [True: 0, False: 4.11k] ------------------ 2960| 20| nAction = AB_PARITY_NONE; ------------------ | | 218| 20|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 2961| 20| break; 2962| 12| default: ------------------ | Branch (2962:13): [True: 12, False: 4.09k] ------------------ 2963| 12| nAction = -1; /* program error */ 2964| 4.11k| } 2965| 4.11k| } 2966| | 2967| 8.22k| return nAction; 2968| 8.22k|#undef AB_NEGATIVE 2969| 8.22k|#undef AB_UNKNOWN 2970| 8.22k|} ichister.c:triple_prod_char: 1190| 10|{ 1191| 10| inp_ATOM *at1, *at2; 1192| 10| double pnt[3][3], len; 1193| 10| int i; 1194| 10| int ret = 0; 1195| | 1196| 10| at1 = at + at_1; 1197| 10| at2 = at + at[at_1].neighbor[i_next_at_1]; 1198| | 1199| 10| pnt[0][0] = at2->x - at1->x; 1200| 10| pnt[0][1] = at2->y - at1->y; 1201| 10| pnt[0][2] = at2->z - at1->z; 1202| | 1203| 10| at2 = at + at_2; 1204| 10| at1 = at + at[at_2].neighbor[i_next_at_2]; 1205| | 1206| 10| pnt[1][0] = at2->x - at1->x; 1207| 10| pnt[1][1] = at2->y - at1->y; 1208| 10| pnt[1][2] = at2->z - at1->z; 1209| | /* 1210| | * resultant pnt vector directions: 1211| | * 1212| | * pnt[0] pnt[1] 1213| | * 1214| | * [at_1]---->[...] [...]---->[at_2] 1215| | * 1216| | * 1217| | * add3 below: (pnt[0] + pnt[1]) -> pnt[1] 1218| | */ 1219| 10| add3( pnt[0], pnt[1], pnt[1] ); 1220| | 1221| 40| for (i = 0; i < 3; i++) ------------------ | Branch (1221:17): [True: 30, False: 10] ------------------ 1222| 30| { 1223| 30| pnt[0][i] = (double) z_dir1[i]; 1224| 30| pnt[2][i] = (double) z_dir2[i]; 1225| 30| } 1226| 40| for (i = 0; i < 3; i++) ------------------ | Branch (1226:17): [True: 30, False: 10] ------------------ 1227| 30| { 1228| 30| len = len3( pnt[i] ); 1229| 30| if (len < MIN_BOND_LEN) ------------------ | | 39| 30|#define MIN_BOND_LEN 0.000001 ------------------ | Branch (1229:13): [True: 10, False: 20] ------------------ 1230| 10| { 1231| 10| if (i == 1 && ( at[at_1].bUsed0DParity || at[at_2].bUsed0DParity )) ------------------ | Branch (1231:17): [True: 10, False: 0] | Branch (1231:29): [True: 10, False: 0] | Branch (1231:55): [True: 0, False: 0] ------------------ 1232| 10| { 1233| 10| pnt[i][0] = 0.0; 1234| 10| pnt[i][1] = 1.0; 1235| 10| pnt[i][2] = 0.0; 1236| 10| len = 1.0; /* standard at_1-->at_2 vector coordinates in case of 0D allene */ 1237| 10| } 1238| 0| else 1239| 0| { 1240| 0| goto exit_function; /* too short bond */ 1241| 0| } 1242| 10| } 1243| 30| mult3( pnt[i], 1.0 / len, pnt[i] ); 1244| 30| } 1245| | 1246| 10| len = 100.0*triple_prod( pnt[0], pnt[1], pnt[2], NULL ); 1247| | 1248| | /* 1249| | * ^ pnt[0] 1250| | * | The orientation on this diagram 1251| | * | produces len = -100 1252| | * [at_1]------>[at_2] 1253| | * pnt[1] / 1254| | * / 1255| | * / pnt[2] (up from the plane) 1256| | * v 1257| | * 1258| | * Note: len is invariant upon at_1 <--> at_2 transposition because 1259| | * triple product changes sign upon pnt[0]<-->pnt[2] transposition and 1260| | * triple product changes sign upon pnt[1]--> -pnt[1] change of direction: 1261| | * 1262| | * triple_prod(pnt[0], pnt[1], pnt[2], NULL ) = 1263| | * triple_prod(pnt[2], -pnt[1], pnt[0], NULL ) 1264| | * 1265| | */ 1266| | 1267| 10| ret = len >= 0.0 ? (int) ( floor( len + 0.5 ) ) : -(int) ( floor( 0.5 - len ) ); ------------------ | Branch (1267:11): [True: 10, False: 0] ------------------ 1268| | 1269| 10|exit_function: 1270| | 1271| 10| return ret; 1272| 10|} ichister.c:dot_prodchar3: 276| 247|{ 277| 247| int prod = ( (int)a[0]*(int)b[0] + (int)a[1]*(int)b[1] + (int)a[2]*(int)b[2] ) / 100; 278| 247| if (prod > 100) ------------------ | Branch (278:9): [True: 0, False: 247] ------------------ 279| 0| { 280| 0| prod = 100; 281| 0| } 282| 247| else 283| 247| { 284| 247| if (prod < -100) ------------------ | Branch (284:13): [True: 0, False: 247] ------------------ 285| 0| { 286| 0| prod = -100; 287| 0| } 288| 247| } 289| | 290| 247| return prod; 291| 247|} ichister.c:save_a_stereo_bond: 2521| 4.08k|{ 2522| 4.08k| int i1, i2; 2523| | 2524| 4.44k| for (i1 = 0; i1 < MAX_NUM_STEREO_BONDS && stereo_bond_neighbor1[i1]; i1++) ------------------ | | 873| 8.88k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2524:18): [True: 4.44k, False: 0] | Branch (2524:47): [True: 356, False: 4.08k] ------------------ 2525| 356| { 2526| 356| ; 2527| 356| } 2528| 5.68k| for (i2 = 0; i2 < MAX_NUM_STEREO_BONDS && stereo_bond_neighbor2[i2]; i2++) ------------------ | | 873| 11.3k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2528:18): [True: 5.68k, False: 0] | Branch (2528:47): [True: 1.59k, False: 4.08k] ------------------ 2529| 1.59k| { 2530| 1.59k| ; 2531| 1.59k| } 2532| | 2533| 4.08k| if (i1 == MAX_NUM_STEREO_BONDS || i2 == MAX_NUM_STEREO_BONDS) ------------------ | | 873| 8.17k|#define MAX_NUM_STEREO_BONDS 3 ------------------ if (i1 == MAX_NUM_STEREO_BONDS || i2 == MAX_NUM_STEREO_BONDS) ------------------ | | 873| 4.08k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2533:9): [True: 0, False: 4.08k] | Branch (2533:39): [True: 0, False: 4.08k] ------------------ 2534| 0| { 2535| 0| return 0; 2536| 0| } 2537| | 2538| 4.08k| stereo_bond_parity1[i1] = 2539| 4.08k| stereo_bond_parity2[i2] = result_action; 2540| | 2541| 4.08k| stereo_bond_neighbor1[i1] = (AT_NUMB) ( at2 + 1 ); 2542| 4.08k| stereo_bond_ord1[i1] = (S_CHAR) ord1; 2543| 4.08k| stereo_bond_neighbor2[i2] = (AT_NUMB) ( at1 + 1 ); 2544| 4.08k| stereo_bond_ord2[i2] = (S_CHAR) ord2; 2545| 4.08k| stereo_bond_z_prod1[i1] = 2546| 4.08k| stereo_bond_z_prod2[i2] = (S_CHAR) z_prod; 2547| | 2548| 4.08k| return 1; 2549| 4.08k|} is_centerpoint_elem: 123| 1.84M|{ 124| 1.84M| switch (el_number) { 125| 193k| case EL_NUMBER_C: ------------------ | | 13| 193k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (125:9): [True: 193k, False: 1.64M] ------------------ 126| 545k| case EL_NUMBER_N: ------------------ | | 14| 545k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (126:9): [True: 352k, False: 1.49M] ------------------ 127| 649k| case EL_NUMBER_P: ------------------ | | 18| 649k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (127:9): [True: 103k, False: 1.73M] ------------------ 128| 746k| case EL_NUMBER_S: ------------------ | | 19| 746k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (128:9): [True: 97.4k, False: 1.74M] ------------------ 129| 777k| case EL_NUMBER_I: ------------------ | | 27| 777k|#define EL_NUMBER_I ((U_CHAR)53) ------------------ | Branch (129:9): [True: 30.8k, False: 1.81M] ------------------ 130| 785k| case EL_NUMBER_AS: ------------------ | | 22| 785k|#define EL_NUMBER_AS ((U_CHAR)33) ------------------ | Branch (130:9): [True: 8.36k, False: 1.83M] ------------------ 131| 794k| case EL_NUMBER_SB: ------------------ | | 25| 794k|#define EL_NUMBER_SB ((U_CHAR)51) ------------------ | Branch (131:9): [True: 8.74k, False: 1.83M] ------------------ 132| 804k| case EL_NUMBER_SE: ------------------ | | 23| 804k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (132:9): [True: 10.2k, False: 1.83M] ------------------ 133| 830k| case EL_NUMBER_TE: ------------------ | | 26| 830k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (133:9): [True: 25.7k, False: 1.81M] ------------------ 134| 832k| case EL_NUMBER_CL: ------------------ | | 20| 832k|#define EL_NUMBER_CL ((U_CHAR)17) ------------------ | Branch (134:9): [True: 1.61k, False: 1.84M] ------------------ 135| 833k| case EL_NUMBER_BR: ------------------ | | 24| 833k|#define EL_NUMBER_BR ((U_CHAR)35) ------------------ | Branch (135:9): [True: 1.21k, False: 1.84M] ------------------ 136| 833k| return 1; 137| 1.00M| default: ------------------ | Branch (137:9): [True: 1.00M, False: 833k] ------------------ 138| 1.00M| return 0; 139| 1.84M| } 140| 1.84M|} is_centerpoint_elem_strict: 156| 62.2k|{ 157| 62.2k| switch (el_number) { 158| 6.48k| case EL_NUMBER_C: ------------------ | | 13| 6.48k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (158:9): [True: 6.48k, False: 55.7k] ------------------ 159| 56.0k| case EL_NUMBER_N: ------------------ | | 14| 56.0k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (159:9): [True: 49.5k, False: 12.6k] ------------------ 160| 56.5k| case EL_NUMBER_P: ------------------ | | 18| 56.5k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (160:9): [True: 584, False: 61.6k] ------------------ 161| 57.2k| case EL_NUMBER_AS: ------------------ | | 22| 57.2k|#define EL_NUMBER_AS ((U_CHAR)33) ------------------ | Branch (161:9): [True: 686, False: 61.5k] ------------------ 162| 57.2k| case EL_NUMBER_SB: ------------------ | | 25| 57.2k|#define EL_NUMBER_SB ((U_CHAR)51) ------------------ | Branch (162:9): [True: 16, False: 62.2k] ------------------ 163| 57.2k| return 1; 164| 4.92k| default: ------------------ | Branch (164:9): [True: 4.92k, False: 57.2k] ------------------ 165| 4.92k| return 0; 166| 62.2k| } 167| 62.2k|} AddAtom2num: 177| 144k|{ /* bSubtract: 0=> add, 1=>subtract, 2=> fill */ 178| 144k| inp_ATOM *at = atom + at_no; 179| 144k| int k; 180| 144k| int nMobile = ( at->charge == -1 ); 181| 144k| if (bSubtract == 1) ------------------ | Branch (181:9): [True: 0, False: 144k] ------------------ 182| 0| { 183| | /* 1: subtract */ 184| 0| num[1] -= nMobile; 185| 0| nMobile += at->num_H; 186| 0| num[0] -= nMobile; 187| 0| for (k = 0; k < T_NUM_ISOTOPIC; k++) ------------------ | | 70| 0|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 25| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (187:21): [True: 0, False: 0] ------------------ 188| 0| { 189| | /* T (3H isotope) first because it has higher weight */ 190| 0| num[T_NUM_NO_ISOTOPIC + k] -= at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 69| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ num[T_NUM_NO_ISOTOPIC + k] -= at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 25| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ 191| 0| } 192| 0| } 193| 144k| else 194| 144k| { 195| 144k| if (bSubtract == 2) ------------------ | Branch (195:13): [True: 144k, False: 0] ------------------ 196| 144k| { 197| | /* fill */ 198| 144k| memset( num, 0, ( T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC ) * sizeof( num[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 69| 144k|#define T_NUM_NO_ISOTOPIC 2 ------------------ memset( num, 0, ( T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC ) * sizeof( num[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 70| 144k|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 25| 144k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ 199| 144k| } 200| | /* else (0): add */ 201| 144k| num[1] += nMobile; 202| 144k| nMobile += at->num_H; 203| 144k| num[0] += nMobile; 204| 578k| for (k = 0; k < T_NUM_ISOTOPIC; k++) ------------------ | | 70| 578k|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 25| 578k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (204:21): [True: 433k, False: 144k] ------------------ 205| 433k| { 206| | /* T (3H isotope) first because it has higher weight */ 207| 433k| num[T_NUM_NO_ISOTOPIC + k] += at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 69| 433k|#define T_NUM_NO_ISOTOPIC 2 ------------------ num[T_NUM_NO_ISOTOPIC + k] += at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 25| 433k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ 208| 433k| } 209| 144k| } 210| 144k| return nMobile; 211| 144k|} AddAtom2DA: 216| 144k|{ /* bSubtract: 0=> add, 1=>subtract, 2=> fill */ 217| 144k| inp_ATOM *at = atom + at_no; 218| 144k| int nDelta, nAcidic_O; 219| | 220| 144k| if (at->charge < -1 || (at->charge == 1 && !at->c_point) || at->charge > 1) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (220:9): [True: 0, False: 144k] | Branch (220:29): [True: 1.45k, False: 143k] | Branch (220:48): [True: 0, False: 1.45k] | Branch (220:65): [True: 0, False: 144k] ------------------ 221| 0| { 222| 0| return; 223| 0| } 224| | 225| 144k| nDelta = ( bSubtract == 1 ) ? -1 : 1; ------------------ | Branch (225:14): [True: 0, False: 144k] ------------------ 226| | 227| | /* "Acidic" O, S, Se, Te recognition */ 228| 144k| if (at->at_type & ATT_ACIDIC_CO) ------------------ | | 31| 144k|#define ATT_ACIDIC_CO 0x0001 ------------------ | Branch (228:9): [True: 9.37k, False: 135k] ------------------ 229| 9.37k| { 230| 9.37k| nAcidic_O = nDelta; 231| 9.37k| } 232| 135k| else 233| 135k| { 234| 135k| nAcidic_O = 0; 235| 135k| } 236| | 237| 144k| if (bSubtract == 2) ------------------ | Branch (237:9): [True: 144k, False: 0] ------------------ 238| 144k| { 239| | /* 2: fill, otherwise add */ 240| 144k| memset( num_DA, 0, TG_NUM_DA * sizeof( num_DA[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 241| 144k| } 242| 144k| if ((at->charge <= 0 && at->valence == at->chem_bonds_valence) || ------------------ | Branch (242:10): [True: 143k, False: 1.45k] | Branch (242:29): [True: 44.8k, False: 98.3k] ------------------ 243| | /* neutral or negative donor */ 244| 99.8k| (at->charge > 0 && at->valence + 1 == at->chem_bonds_valence) ------------------ | Branch (244:11): [True: 1.45k, False: 98.3k] | Branch (244:29): [True: 353, False: 1.09k] ------------------ 245| | /* positively charged donor */ 246| 144k| ) /* djb-rwth: addressing LLVM warnings */ 247| 45.1k| { 248| 45.1k| if (at->charge < 0) ------------------ | Branch (248:13): [True: 21.9k, False: 23.2k] ------------------ 249| 21.9k| { 250| 21.9k| num_DA[TG_Num_dM] += nDelta; 251| 21.9k| num_DA[TG_Num_dO] += nAcidic_O; 252| 21.9k| } 253| 23.2k| else 254| 23.2k| { 255| 23.2k| if (at->num_H) ------------------ | Branch (255:17): [True: 23.2k, False: 0] ------------------ 256| 23.2k| { 257| 23.2k| num_DA[TG_Num_dH] += nDelta; 258| 23.2k| num_DA[TG_Num_dO] += nAcidic_O; 259| 23.2k| } 260| 23.2k| } 261| 45.1k| } 262| 99.4k| else 263| 99.4k| { 264| 99.4k| if ((at->charge <= 0 && at->valence + 1 == at->chem_bonds_valence) || ------------------ | Branch (264:14): [True: 98.3k, False: 1.09k] | Branch (264:33): [True: 98.3k, False: 1] ------------------ 265| 1.09k| (at->charge > 0 && at->valence + 2 == at->chem_bonds_valence)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (265:15): [True: 1.09k, False: 1] | Branch (265:34): [True: 1.09k, False: 0] ------------------ 266| 99.4k| { 267| | /* acceptor */ 268| 99.4k| if (at->charge < 0) ------------------ | Branch (268:17): [True: 13.6k, False: 85.8k] ------------------ 269| 13.6k| { 270| 13.6k| num_DA[TG_Num_aM] += nDelta; 271| 13.6k| } 272| 85.8k| else 273| 85.8k| { 274| 85.8k| if (at->num_H) ------------------ | Branch (274:21): [True: 3.10k, False: 82.7k] ------------------ 275| 3.10k| { 276| 3.10k| num_DA[TG_Num_aH] += nDelta; 277| 3.10k| } 278| 82.7k| else 279| 82.7k| { 280| 82.7k| num_DA[TG_Num_aO] += nAcidic_O; /* acidic O-acceptor has no H or charge */ 281| 82.7k| } 282| 85.8k| } 283| 99.4k| } 284| 99.4k| } 285| 144k| return; 286| 144k|} AddEndPoint: 296| 1.09k|{ 297| 1.09k| pEndPoint->nAtomNumber = iat; 298| 1.09k| pEndPoint->nEquNumber = 0; 299| 1.09k| pEndPoint->nGroupNumber = at[iat].endpoint; 300| 1.09k| if (at[iat].endpoint) ------------------ | Branch (300:9): [True: 509, False: 583] ------------------ 301| 509| { 302| | /* already an endpoint */ 303| 509| memset( pEndPoint->num, 0, sizeof( pEndPoint->num ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 304| 509| } 305| 583| else 306| 583| { 307| | /* not an endpoint yet, make it an endpoint */ 308| 583| AddAtom2num( pEndPoint->num, at, iat, 2 ); /* fill */ 309| 583| AddAtom2DA( pEndPoint->num_DA, at, iat, 2 ); 310| | /* 311| | nMobile = pEndPoint->num[1] = (at[iat].charge == -1); 312| | nMobile = pEndPoint->num[0] = at[iat].num_H + nMobile; 313| | for ( k = 0; k < T_NUM_ISOTOPIC; k ++ ) { 314| | pEndPoint->num[T_NUM_NO_ISOTOPIC+k] = at[iat].num_iso_H[NUM_H_ISOTOPES-k-1]; 315| | } 316| | */ 317| 583| } 318| | 319| 1.09k| return 0; 320| 1.09k|} nGetEndpointInfo: 325| 5.64M|{ 326| 5.64M| int nEndpointValence; 327| 5.64M| int nMobile; 328| 5.64M| S_CHAR cChargeSubtype; 329| | 330| 5.64M| if (atom[iat].radical && atom[iat].radical != RADICAL_SINGLET) ------------------ | | 75| 134k|#define RADICAL_SINGLET 1 ------------------ | Branch (330:9): [True: 134k, False: 5.50M] | Branch (330:30): [True: 134k, False: 0] ------------------ 331| 134k| { 332| 134k| return 0; /* a radical */ 333| 134k| } 334| 5.50M| if (!( nEndpointValence = get_endpoint_valence( atom[iat].el_number ) )) ------------------ | Branch (334:9): [True: 3.50M, False: 2.00M] ------------------ 335| 3.50M| { 336| 3.50M| return 0; /* not an endpoint */ 337| 3.50M| } 338| 2.00M| if (nEndpointValence <= atom[iat].valence) ------------------ | Branch (338:9): [True: 190k, False: 1.81M] ------------------ 339| 190k| { 340| 190k| return 0; /* not an endpoint, for example >N(+)< or >N< or >O(+)- or >O- or >N- or -O- */ 341| 190k| } 342| | 343| 1.81M| if (atom[iat].charge == -1 || atom[iat].charge == 0) ------------------ | Branch (343:9): [True: 152k, False: 1.66M] | Branch (343:35): [True: 1.62M, False: 33.5k] ------------------ 344| 1.78M| { 345| | /* not a positive charge-point */ 346| 1.78M| if (nEndpointValence < atom[iat].chem_bonds_valence) ------------------ | Branch (346:13): [True: 13.3k, False: 1.76M] ------------------ 347| 13.3k| { 348| 13.3k| return 0; /* abnormal valence > standard endpoint valence */ 349| 13.3k| } 350| 1.76M| nMobile = atom[iat].num_H + ( atom[iat].charge == -1 ); 351| 1.76M| if (nMobile + atom[iat].chem_bonds_valence != nEndpointValence) ------------------ | Branch (351:13): [True: 1.20M, False: 564k] ------------------ 352| 1.20M| { 353| 1.20M| return 0; /* non-standard endpoint valence */ 354| 1.20M| } 355| 564k| switch (atom[iat].chem_bonds_valence - atom[iat].valence) 356| 564k| { 357| 177k| case 0: ------------------ | Branch (357:13): [True: 177k, False: 387k] ------------------ 358| 177k| eif->cDonor = 1; 359| 177k| eif->cAcceptor = 0; 360| 177k| break; 361| 360k| case 1: ------------------ | Branch (361:13): [True: 360k, False: 203k] ------------------ 362| 360k| eif->cDonor = 0; 363| 360k| eif->cAcceptor = 1; 364| 360k| break; 365| 26.8k| default: ------------------ | Branch (365:13): [True: 26.8k, False: 537k] ------------------ 366| 26.8k| return 0; 367| 564k| } 368| 537k| eif->cMobile = nMobile; 369| 537k| eif->cNeutralBondsValence = nEndpointValence - nMobile; 370| 537k| eif->cMoveableCharge = 0; 371| 537k|#if ( KETO_ENOL_TAUT == 1 ) 372| 537k| eif->cKetoEnolCode = 0; 373| 537k|#endif 374| 537k| return nEndpointValence; 375| 564k| } 376| 33.5k| else 377| 33.5k| { 378| 33.5k| if (atom[iat].c_point && ------------------ | Branch (378:13): [True: 5.89k, False: 27.6k] ------------------ 379| 5.89k| 0 <= GetChargeType( atom, iat, &cChargeSubtype ) && ------------------ | Branch (379:14): [True: 5.89k, False: 0] ------------------ 380| 5.89k| ( (int) cChargeSubtype & ( C_SUBTYPE_H_ACCEPT | C_SUBTYPE_H_DONOR ) )) ------------------ | | 107| 5.89k|#define C_SUBTYPE_H_ACCEPT 4 ------------------ ( (int) cChargeSubtype & ( C_SUBTYPE_H_ACCEPT | C_SUBTYPE_H_DONOR ) )) ------------------ | | 108| 5.89k|#define C_SUBTYPE_H_DONOR 8 ------------------ | Branch (380:14): [True: 5.89k, False: 0] ------------------ 381| 5.89k| { 382| | /* charge-point */ 383| 5.89k| { 384| 5.89k| if (cChargeSubtype & C_SUBTYPE_H_ACCEPT) ------------------ | | 107| 5.89k|#define C_SUBTYPE_H_ACCEPT 4 ------------------ | Branch (384:21): [True: 4.74k, False: 1.15k] ------------------ 385| 4.74k| { 386| 4.74k| eif->cDonor = 0; 387| 4.74k| eif->cAcceptor = 1; 388| 4.74k| } 389| 1.15k| else 390| 1.15k| { 391| 1.15k| if (cChargeSubtype & C_SUBTYPE_H_DONOR) ------------------ | | 108| 1.15k|#define C_SUBTYPE_H_DONOR 8 ------------------ | Branch (391:25): [True: 1.15k, False: 0] ------------------ 392| 1.15k| { 393| 1.15k| eif->cDonor = 1; 394| 1.15k| eif->cAcceptor = 0; 395| 1.15k| } 396| 0| else 397| 0| { 398| 0| return 0; 399| 0| } 400| 1.15k| } 401| 5.89k| } 402| 5.89k| eif->cMobile = atom[iat].num_H; 403| 5.89k| eif->cNeutralBondsValence = nEndpointValence - atom[iat].num_H; 404| 5.89k| eif->cMoveableCharge = atom[iat].charge; 405| 5.89k|#if ( KETO_ENOL_TAUT == 1 ) 406| 5.89k| eif->cKetoEnolCode = 0; 407| 5.89k|#endif 408| 5.89k| return nEndpointValence; 409| 5.89k| } 410| 33.5k| } 411| | 412| 27.6k| return 0; 413| 1.81M|} RegisterEndPoints: 999| 7.11k|{ 1000| 7.11k| T_GROUP *t_group = t_group_info->t_group; 1001| 7.11k| int *pnum_t = &t_group_info->num_t_groups; 1002| 7.11k| int max_num_t = t_group_info->max_num_t_groups; 1003| 7.11k| int nNumZeroEqu, nNumNewTGroups; 1004| 7.11k| AT_NUMB group, prev_group, prev_eqnum, nNextGroupNumber, nLeastGroupNumber; 1005| 7.11k| int nNumGroups, num_t, difference; 1006| 7.11k| int i, j, k, ret; 1007| 7.11k| AT_NUMB nNewTgNumberStackArray[MAX_STACK_ARRAY_LEN + 1]; 1008| 7.11k| AT_NUMB nGroupNumberStackArray[MAX_STACK_ARRAY_LEN + 1]; 1009| 7.11k| AT_NUMB nGroupNewNumberStackArray[MAX_STACK_ARRAY_LEN + 1]; 1010| 7.11k| AT_NUMB *nNewTgNumber = nNewTgNumberStackArray; 1011| 7.11k| AT_NUMB *nGroupNumber = nGroupNumberStackArray; 1012| 7.11k| AT_NUMB *nGroupNewNumber = nGroupNewNumberStackArray; 1013| | 1014| 7.11k| if (nNumEndPoints <= 0) ------------------ | Branch (1014:9): [True: 0, False: 7.11k] ------------------ 1015| 0| { 1016| 0| return 0; /* nothing to do */ 1017| 0| } 1018| 7.11k| num_t = *pnum_t; 1019| 7.11k| difference = 0; 1020| 7.11k| nNextGroupNumber = 0; 1021| 7.11k| nNumZeroEqu = 0; 1022| | /* djb-rwth: removing redundant code */ 1023| | /* find max group number; increment it to obtain next available group number */ 1024| 9.04k| for (i = 0; i < num_t; i++) ------------------ | Branch (1024:17): [True: 1.93k, False: 7.11k] ------------------ 1025| 1.93k| { 1026| 1.93k| if (nNextGroupNumber < t_group[i].nGroupNumber) ------------------ | Branch (1026:13): [True: 1.93k, False: 0] ------------------ 1027| 1.93k| { 1028| 1.93k| nNextGroupNumber = t_group[i].nGroupNumber; 1029| 1.93k| } 1030| 1.93k| } 1031| 7.11k| nNextGroupNumber++; 1032| | 1033| | /* find min non-zero group number nLeastGroupNumber; 1034| | count zero EndPoint[i].nEquNumber 1035| | if all EndPoint[i].nGroupNumber are equal and non-zero then exit: nothing to do. 1036| | */ 1037| 7.11k| nLeastGroupNumber = nNextGroupNumber; 1038| 7.11k| prev_group = EndPoint[0].nGroupNumber; 1039| 7.11k| prev_eqnum = EndPoint[0].nEquNumber; 1040| 22.7k| for (i = j = k = 0; i < nNumEndPoints; i++) ------------------ | Branch (1040:25): [True: 15.6k, False: 7.11k] ------------------ 1041| 15.6k| { 1042| 15.6k| if ((group = EndPoint[i].nGroupNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1042:13): [True: 2.32k, False: 13.2k] ------------------ 1043| 2.32k| { 1044| 2.32k| if (group < nLeastGroupNumber) ------------------ | Branch (1044:17): [True: 1.46k, False: 861] ------------------ 1045| 1.46k| { 1046| 1.46k| nLeastGroupNumber = group; 1047| 1.46k| } 1048| 2.32k| } 1049| 15.6k| j += ( prev_group == EndPoint[i].nGroupNumber ); /* count endpoints that belong to the 1st group */ 1050| 15.6k| k += ( prev_eqnum == EndPoint[i].nEquNumber ); /* count endpoints that belongo to a group equivalent to the 1st group */ 1051| 15.6k| nNumZeroEqu += !EndPoint[i].nEquNumber; /* count endpoints that have been processed by FindAccessibleEndPoints() */ 1052| 15.6k| } 1053| 7.11k| if (j == nNumEndPoints && prev_group && k == nNumEndPoints) ------------------ | Branch (1053:9): [True: 6.28k, False: 827] | Branch (1053:31): [True: 565, False: 5.72k] | Branch (1053:45): [True: 565, False: 0] ------------------ 1054| 565| { 1055| | /* all endpoints already belong to one t-group; 1056| | the last comparison is not needed for now 1057| | because EndPoint[i].nEquNumber cannot make 1058| | endpont partitioning finer 1059| | */ 1060| 565| return 0; 1061| 565| } 1062| | 1063| 6.54k| nNumNewTGroups = 0; 1064| | 1065| 6.54k| if (!nNumZeroEqu) ------------------ | Branch (1065:9): [True: 6.05k, False: 496] ------------------ 1066| 6.05k| { 1067| | /* EndPoint[] has been processed by FindAccessibleEndPoints; 1068| | * equal EndPoint[i].nEquNumber mark endpoints belonging to 1069| | * the same t-group 1070| | * Since now the next available t-group number, nNextGroupNumber, 1071| | * is known,replace fict. IDs assigned by FindAccessibleEndPoints 1072| | * with correct new t-group numbers. 1073| | */ 1074| 19.2k| for (i = 0; i < nNumEndPoints; i++) ------------------ | Branch (1074:21): [True: 13.2k, False: 6.05k] ------------------ 1075| 13.2k| { 1076| 13.2k| if (( group = EndPoint[i].nEquNumber ) >= nNextGroupNumber) ------------------ | Branch (1076:17): [True: 12.0k, False: 1.24k] ------------------ 1077| 12.0k| { 1078| | /* replace fict. IDs assigned by FindAccessibleEndPoints() with new t-group numbers */ 1079| | /* these fict. IDs have values = (num_atoms+1), (num_atoms+2),...; they may be non-contiguous */ 1080| 12.0k| for (j = 0; j < nNumNewTGroups; j++) ------------------ | Branch (1080:29): [True: 6.51k, False: 5.49k] ------------------ 1081| 6.51k| { 1082| 6.51k| if (group == nGroupNewNumber[j]) ------------------ | Branch (1082:25): [True: 6.51k, False: 0] ------------------ 1083| 6.51k| { 1084| 6.51k| break; 1085| 6.51k| } 1086| 6.51k| } 1087| 12.0k| if (j == nNumNewTGroups) ------------------ | Branch (1087:21): [True: 5.49k, False: 6.51k] ------------------ 1088| 5.49k| { 1089| | /* found new fict. ID = group */ 1090| 5.49k| if (j == MAX_STACK_ARRAY_LEN && nGroupNewNumber == nGroupNewNumberStackArray) ------------------ | | 112| 10.9k|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (1090:25): [True: 0, False: 5.49k] | Branch (1090:53): [True: 0, False: 0] ------------------ 1091| 0| { 1092| | /* stack array overflow; allocate more memory than may be needed */ 1093| 0| nGroupNewNumber = (AT_NUMB *) inchi_malloc( nNumEndPoints * sizeof( nGroupNewNumber[0] ) ); ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 1094| 0| if (!nGroupNewNumber) ------------------ | Branch (1094:29): [True: 0, False: 0] ------------------ 1095| 0| { 1096| 0| ret = -1; 1097| 0| goto exit_function; 1098| 0| } 1099| 0| memcpy(nGroupNewNumber, nGroupNewNumberStackArray, nNumNewTGroups * sizeof(nGroupNewNumber[0])); 1100| 0| } 1101| | /* save newly found fict. t-group ID to compare to the next values of EndPoint[].nEquNumber */ 1102| 5.49k| nGroupNewNumber[j] = group; 1103| 5.49k| nNumNewTGroups++; 1104| 5.49k| } 1105| 12.0k| EndPoint[i].nEquNumber = nNextGroupNumber + j; 1106| 12.0k| } 1107| 13.2k| } /* after this point the values just stored in nGroupNewNumber[] will not 1108| | be used. However, the obtained nNumNewTGroups value will be used */ 1109| 6.05k| } 1110| 496| else 1111| 496| { 1112| 496| if (nNumZeroEqu == nNumEndPoints) ------------------ | Branch (1112:13): [True: 496, False: 0] ------------------ 1113| 496| { 1114| | /* EndPoint[] has NOT been processed by FindAccessibleEndPoints; 1115| | all atoms and t-groups to which endpoints belong should 1116| | be merged into a single t-group */ 1117| 496| if (nLeastGroupNumber == nNextGroupNumber) ------------------ | Branch (1117:17): [True: 230, False: 266] ------------------ 1118| 230| { 1119| | /* flag to create a new t-group: none of the found 1120| | endpoints belong to an already known t-group */ 1121| 230| nNumNewTGroups = 1; /* otherwise 0 */ 1122| 230| } 1123| | /* All EndPoint[*].nEquNumber are zeroes. All endpoints will 1124| | * belong to one new or old t-group; its ID is nLeastGroupNumber. 1125| | * Set EndPoint[i].nEquNumber = nLeastGroupNumber; */ 1126| 1.72k| for (i = 0; i < nNumEndPoints; i++) ------------------ | Branch (1126:25): [True: 1.22k, False: 496] ------------------ 1127| 1.22k| { 1128| 1.22k| EndPoint[i].nEquNumber = nLeastGroupNumber; 1129| 1.22k| } 1130| 496| } 1131| 0| else 1132| 0| { 1133| 0| ret = -1; /* program error: only some of EndPoint[i].nEquNumber are zero */ /* */ 1134| 0| goto exit_function; 1135| 0| } 1136| 496| } 1137| | 1138| 6.54k| if (nNumNewTGroups) ------------------ | Branch (1138:9): [True: 5.72k, False: 827] ------------------ 1139| 5.72k| { 1140| | /* create new nNumNewTGroups t-group(s) */ 1141| 5.72k| if (num_t + nNumNewTGroups > max_num_t) ------------------ | Branch (1141:13): [True: 0, False: 5.72k] ------------------ 1142| 0| { 1143| 0| ret = -1; /* found too many t-groups */ /* */ 1144| 0| goto exit_function; 1145| 0| } 1146| | /* initialize new t-group(s) */ 1147| 5.72k| memset( t_group + num_t, 0, nNumNewTGroups * sizeof( t_group[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1148| 11.4k| for (i = 0; i < nNumNewTGroups; i++) ------------------ | Branch (1148:21): [True: 5.72k, False: 5.72k] ------------------ 1149| 5.72k| { 1150| 5.72k| t_group[num_t + i].nGroupNumber = nNextGroupNumber + i; 1151| 5.72k| } 1152| 5.72k| } 1153| | 1154| | /* At this point: 1155| | * EndPoint[i].nGroupNumber == 0 => the endpoint atom does not belong to a t-group yet 1156| | * EndPoint[i].nGroupNumber > 0 => current t-group ID of the endpoint atom 1157| | * EndPoint[i].nEquNumber --> new ID of a tautomeric group of this endpoint atom 1158| | * EndPoint[i].nAtomNumber --> number of the endpoint atom 1159| | */ 1160| | 1161| 6.54k| nNumGroups = 0; /* counts the groups to be renumbered */ 1162| 21.0k| for (i = j = 0; i < nNumEndPoints; i++) ------------------ | Branch (1162:21): [True: 14.4k, False: 6.54k] ------------------ 1163| 14.4k| { 1164| 14.4k| if ((group = EndPoint[i].nGroupNumber)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1164:13): [True: 1.17k, False: 13.2k] ------------------ 1165| 1.17k| { 1166| 1.17k| if (group == EndPoint[i].nEquNumber) ------------------ | Branch (1166:17): [True: 940, False: 230] ------------------ 1167| 940| { 1168| 940| continue; /* ignore: the endpoint belongs to the same t-group as before */ 1169| 940| } 1170| | /* save information for renumbering of the existing t-groups */ 1171| 233| for (j = 0; j < nNumGroups; j++) ------------------ | Branch (1171:25): [True: 80, False: 153] ------------------ 1172| 80| { 1173| 80| if (group == nGroupNumber[j]) ------------------ | Branch (1173:21): [True: 77, False: 3] ------------------ 1174| 77| { 1175| 77| if (EndPoint[i].nEquNumber != nGroupNewNumber[j]) ------------------ | Branch (1175:25): [True: 0, False: 77] ------------------ 1176| 0| { 1177| 0| ret = -1; /* program error */ /* */ 1178| 0| goto exit_function; 1179| 0| } 1180| 77| break; 1181| 77| } 1182| 80| } 1183| 230| if (j == nNumGroups) ------------------ | Branch (1183:17): [True: 153, False: 77] ------------------ 1184| 153| { 1185| | /* discovered a new t-group number; store it together with its nEquNumber */ 1186| 153| if (j == MAX_STACK_ARRAY_LEN) ------------------ | | 112| 153|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (1186:21): [True: 0, False: 153] ------------------ 1187| 0| { 1188| 0| if (nGroupNewNumber == nGroupNewNumberStackArray) ------------------ | Branch (1188:25): [True: 0, False: 0] ------------------ 1189| 0| { 1190| 0| nGroupNewNumber = (AT_NUMB *) inchi_malloc( nNumEndPoints * sizeof( nGroupNewNumber[0] ) ); ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 1191| 0| if (!nGroupNewNumber) ------------------ | Branch (1191:29): [True: 0, False: 0] ------------------ 1192| 0| { 1193| 0| ret = -1; 1194| 0| goto exit_function; 1195| 0| } 1196| 0| memcpy(nGroupNewNumber, nGroupNewNumberStackArray, nNumGroups * sizeof(nGroupNewNumber[0])); 1197| 0| } 1198| 0| if (nGroupNumber == nGroupNumberStackArray) ------------------ | Branch (1198:25): [True: 0, False: 0] ------------------ 1199| 0| { 1200| 0| nGroupNumber = (AT_NUMB *) inchi_malloc( nNumEndPoints * sizeof( nGroupNumber[0] ) ); ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 1201| 0| if (!nGroupNumber) ------------------ | Branch (1201:29): [True: 0, False: 0] ------------------ 1202| 0| { 1203| 0| ret = -1; 1204| 0| goto exit_function; 1205| 0| } 1206| 0| memcpy(nGroupNumber, nGroupNumberStackArray, nNumGroups * sizeof(nGroupNumber[0])); 1207| 0| } 1208| 0| } 1209| | 1210| 153| nGroupNumber[j] = group; /* old t-group ID */ 1211| 153| nGroupNewNumber[j] = EndPoint[i].nEquNumber; /* new t-group ID */ 1212| 153| nNumGroups++; 1213| 153| } 1214| 230| } 1215| 13.2k| else 1216| 13.2k| { 1217| | /* add a new endpoint to the newly created or previously existing t-groups */ 1218| 13.2k| group = EndPoint[i].nEquNumber; 1219| 13.2k| if (group >= nNextGroupNumber) ------------------ | Branch (1219:17): [True: 12.5k, False: 784] ------------------ 1220| 12.5k| { 1221| | /* get index of a new t-group from equ number */ 1222| 12.5k| j = num_t + group - nNextGroupNumber; /* newly assigned IDs are contiguous */ 1223| 12.5k| } 1224| 784| else 1225| 784| { 1226| | /* old t-group */ 1227| 784| if (j >= num_t || group != t_group[j].nGroupNumber) ------------------ | Branch (1227:21): [True: 0, False: 784] | Branch (1227:35): [True: 56, False: 728] ------------------ 1228| 56| { 1229| | /* search only if j is not a needed group index */ 1230| 112| for (j = 0; j < num_t; j++) ------------------ | Branch (1230:33): [True: 112, False: 0] ------------------ 1231| 112| { 1232| 112| if (group == t_group[j].nGroupNumber) ------------------ | Branch (1232:29): [True: 56, False: 56] ------------------ 1233| 56| { 1234| 56| break; 1235| 56| } 1236| 112| } 1237| 56| if (j == num_t) ------------------ | Branch (1237:25): [True: 0, False: 56] ------------------ 1238| 0| { 1239| 0| ret = -1; /* program error: t-group not found */ /* */ 1240| 0| goto exit_function; 1241| 0| } 1242| 56| } 1243| 784| } 1244| | /* add aton to existing or new t-group */ 1245| 13.2k| t_group[j].nNumEndpoints++; 1246| 79.7k| for (k = 0; k < (int) ( sizeof( t_group->num ) / sizeof( t_group->num[0] ) ); k++) ------------------ | Branch (1246:25): [True: 66.4k, False: 13.2k] ------------------ 1247| 66.4k| { 1248| 66.4k| t_group[j].num[k] += EndPoint[i].num[k]; 1249| 66.4k| } 1250| 93.0k| for (k = 0; k < (int) ( sizeof( t_group->num_DA ) / sizeof( t_group->num_DA[0] ) ); k++) ------------------ | Branch (1250:25): [True: 79.7k, False: 13.2k] ------------------ 1251| 79.7k| { 1252| 79.7k| t_group[j].num_DA[k] += EndPoint[i].num_DA[k]; 1253| 79.7k| } 1254| | /* mark endpoint */ 1255| 13.2k| at[EndPoint[i].nAtomNumber].endpoint = group; 1256| 13.2k| difference++; 1257| 13.2k| } 1258| 14.4k| } 1259| | 1260| 6.54k| difference += nNumGroups; 1261| 6.54k| num_t += nNumNewTGroups; 1262| 6.54k| if (!difference) ------------------ | Branch (1262:9): [True: 0, False: 6.54k] ------------------ 1263| 0| { 1264| 0| ret = 0; /* nothing to do. Not necessarily a program error: happens if all EndPoint[i].nGroupNumber==EndPoint[i].nEquNumber */ 1265| 0| goto exit_function; 1266| 0| } 1267| | 1268| 6.54k| if (nNumGroups) ------------------ | Branch (1268:9): [True: 151, False: 6.39k] ------------------ 1269| 151| { 1270| | /* prepare for renumbering: find max t-group number */ 1271| 456| for (i = 0, nNextGroupNumber = 0; i < num_t; i++) ------------------ | Branch (1271:43): [True: 305, False: 151] ------------------ 1272| 305| { 1273| 305| if (nNextGroupNumber < t_group[i].nGroupNumber) ------------------ | Branch (1273:17): [True: 305, False: 0] ------------------ 1274| 305| { 1275| 305| nNextGroupNumber = t_group[i].nGroupNumber; 1276| 305| } 1277| 305| } 1278| 151| } 1279| | /* renumber and merge t-groups */ 1280| 6.70k| for (i = 0; i < nNumGroups; i++) ------------------ | Branch (1280:17): [True: 153, False: 6.54k] ------------------ 1281| 153| { 1282| 153| int i1, i2; 1283| 153| AT_NUMB group1 = nGroupNumber[i]; 1284| 153| AT_NUMB group2 = nGroupNewNumber[i]; 1285| | /* add group1 to group2, then delete group1. */ 1286| 461| for (j = 0, i1 = i2 = -1; j < num_t && ( i1 < 0 || i2 < 0 ); j++) ------------------ | Branch (1286:35): [True: 309, False: 152] | Branch (1286:50): [True: 308, False: 1] | Branch (1286:60): [True: 0, False: 1] ------------------ 1287| 308| { 1288| 308| if (i1 < 0 && group1 == t_group[j].nGroupNumber) ------------------ | Branch (1288:17): [True: 308, False: 0] | Branch (1288:27): [True: 153, False: 155] ------------------ 1289| 153| { 1290| 153| i1 = j; 1291| 153| } 1292| 308| if (i2 < 0 && group2 == t_group[j].nGroupNumber) ------------------ | Branch (1292:17): [True: 154, False: 154] | Branch (1292:27): [True: 153, False: 1] ------------------ 1293| 153| { 1294| 153| i2 = j; 1295| 153| } 1296| 308| } 1297| 153| if (i1 < 0 || i2 < 0) ------------------ | Branch (1297:13): [True: 0, False: 153] | Branch (1297:23): [True: 0, False: 153] ------------------ 1298| 0| { 1299| 0| ret = -1; /* program error */ /* */ 1300| 0| goto exit_function; 1301| 0| } 1302| | /* add t_group[i1] to t_group[i2] and remove t_group[i1] */ 1303| 918| for (k = 0; k < (int) ( sizeof( t_group->num ) / sizeof( t_group->num[0] ) ); k++) ------------------ | Branch (1303:21): [True: 765, False: 153] ------------------ 1304| 765| { 1305| 765| t_group[i2].num[k] += t_group[i1].num[k]; 1306| 765| } 1307| 1.07k| for (k = 0; k < (int) ( sizeof( t_group->num_DA ) / sizeof( t_group->num_DA[0] ) ); k++) ------------------ | Branch (1307:21): [True: 918, False: 153] ------------------ 1308| 918| { 1309| 918| t_group[i2].num_DA[k] += t_group[i1].num_DA[k]; 1310| 918| } 1311| 153| t_group[i2].nNumEndpoints += t_group[i1].nNumEndpoints; 1312| 153| num_t--; 1313| 153| if (num_t > i1) ------------------ | Branch (1313:13): [True: 1, False: 152] ------------------ 1314| 1| { 1315| 1| memmove(t_group + i1, t_group + i1 + 1, ((long long)num_t - (long long)i1) * sizeof(t_group[0])); /* djb-rwth: cast operators added */ 1316| 1| } 1317| 153| } 1318| | 1319| 6.54k| if (nNumGroups) ------------------ | Branch (1319:9): [True: 151, False: 6.39k] ------------------ 1320| 151| { 1321| | /* there are groups to merge */ 1322| 151| if (nNextGroupNumber >= MAX_STACK_ARRAY_LEN) ------------------ | | 112| 151|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (1322:13): [True: 0, False: 151] ------------------ 1323| 0| { 1324| 0| nNewTgNumber = (AT_NUMB *) inchi_malloc( ( (long long)nNextGroupNumber + 1 ) * sizeof( *nNewTgNumber ) ); /* djb-rwth: cast operator added */ ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 1325| 0| if (!nNewTgNumber) ------------------ | Branch (1325:17): [True: 0, False: 0] ------------------ 1326| 0| { 1327| 0| ret = -1; 1328| 0| goto exit_function; /* error: out of RAM */ 1329| 0| } 1330| 0| } 1331| 151| memset( nNewTgNumber, 0, ( (long long)nNextGroupNumber + 1 ) * sizeof( *nNewTgNumber ) ); /* djb-rwth: cast operator added; memset_s C11/Annex K variant? */ 1332| 303| for (i = 0; i < num_t; i++) ------------------ | Branch (1332:21): [True: 152, False: 151] ------------------ 1333| 152| { 1334| 152| nNewTgNumber[t_group[i].nGroupNumber] = i + 1; /* new t-group numbers */ 1335| 152| } 1336| 304| for (j = 0; j < nNumGroups; j++) ------------------ | Branch (1336:21): [True: 153, False: 151] ------------------ 1337| 153| { 1338| 153| if (!nNewTgNumber[nGroupNumber[j]] && nNewTgNumber[nGroupNewNumber[j]]) ------------------ | Branch (1338:17): [True: 153, False: 0] | Branch (1338:51): [True: 153, False: 0] ------------------ 1339| 153| { 1340| 153| nNewTgNumber[nGroupNumber[j]] = nNewTgNumber[nGroupNewNumber[j]]; 1341| 153| } 1342| 0| else 1343| 0| { 1344| 0| ret = -1; /* program error: all new numbers must have been marked */ 1345| 0| goto exit_function; 1346| 0| } 1347| 153| } 1348| | /* renumber t-groups */ 1349| 303| for (i = 0; i < num_t; i++) ------------------ | Branch (1349:21): [True: 152, False: 151] ------------------ 1350| 152| { 1351| 152| t_group[i].nGroupNumber = nNewTgNumber[t_group[i].nGroupNumber]; 1352| 152| } 1353| |#if ( bRELEASE_VERSION != 1 ) 1354| | /* Check: debug only */ 1355| | for (i = 1; i < num_t; i++) 1356| | { 1357| | if (1 != t_group[i].nGroupNumber - t_group[i - 1].nGroupNumber) 1358| | { 1359| | ret = -1; /* debug */ 1360| | goto exit_function; 1361| | } 1362| | } 1363| |#endif 1364| | /* renumber endpoints */ 1365| 1.32k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1365:21): [True: 1.17k, False: 151] ------------------ 1366| 1.17k| { 1367| 1.17k| if ((group = at[i].endpoint)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1367:17): [True: 738, False: 440] ------------------ 1368| 738| { 1369| 738| if (!( at[i].endpoint = nNewTgNumber[group] ) || nNextGroupNumber <= nNewTgNumber[group]) ------------------ | Branch (1369:21): [True: 0, False: 738] | Branch (1369:66): [True: 0, False: 738] ------------------ 1370| 0| { 1371| 0| ret = -1; /* program error */ 1372| 0| goto exit_function; 1373| 0| } 1374| 738| } 1375| 1.17k| } 1376| 151| } 1377| 6.54k| if (nNewTgNumber != nNewTgNumberStackArray) ------------------ | Branch (1377:9): [True: 0, False: 6.54k] ------------------ 1378| 0| { 1379| 0| inchi_free( nNewTgNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1380| 0| nNewTgNumber = nNewTgNumberStackArray; 1381| 0| } 1382| 6.54k| if (nGroupNumber != nGroupNumberStackArray) ------------------ | Branch (1382:9): [True: 0, False: 6.54k] ------------------ 1383| 0| { 1384| 0| inchi_free( nGroupNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1385| 0| nGroupNumber = nGroupNumberStackArray; 1386| 0| } 1387| 6.54k| if (nGroupNewNumber != nGroupNewNumberStackArray) ------------------ | Branch (1387:9): [True: 0, False: 6.54k] ------------------ 1388| 0| { 1389| 0| inchi_free( nGroupNewNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1390| 0| nGroupNewNumber = nGroupNewNumberStackArray; 1391| 0| } 1392| 6.54k| if (!t_group_info->tGroupNumber) ------------------ | Branch (1392:9): [True: 0, False: 6.54k] ------------------ 1393| 0| { 1394| 0| t_group_info->tGroupNumber = (AT_NUMB *) inchi_malloc( 2 * (long long)max_num_t * sizeof( t_group_info->tGroupNumber[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 1395| 0| if (!t_group_info->tGroupNumber) ------------------ | Branch (1395:13): [True: 0, False: 0] ------------------ 1396| 0| { 1397| 0| ret = -1; 1398| 0| goto exit_function; 1399| 0| } 1400| 0| } 1401| | /* fill out t-group index 2004-02-27 */ 1402| 6.54k| memset( t_group_info->tGroupNumber, 0, 2 * (long long)max_num_t * sizeof( t_group_info->tGroupNumber[0] ) ); /* djb-rwth: cast operator added; memset_s C11/Annex K variant? */ 1403| 13.4k| for (i = 0; i < num_t; i++) ------------------ | Branch (1403:17): [True: 6.92k, False: 6.54k] ------------------ 1404| 6.92k| { 1405| 6.92k| if (t_group[i].nNumEndpoints && t_group[i].nGroupNumber) ------------------ | Branch (1405:13): [True: 6.92k, False: 0] | Branch (1405:41): [True: 6.92k, False: 0] ------------------ 1406| 6.92k| { 1407| 6.92k| t_group_info->tGroupNumber[t_group[i].nGroupNumber] = i + 1; 1408| 6.92k| } 1409| 6.92k| } 1410| | 1411| 6.54k| if (pBNS && ( pBNS->tot_st_cap == pBNS->tot_st_flow || ALWAYS_ADD_TG_ON_THE_FLY )) ------------------ | | 539| 1.13k|#define ALWAYS_ADD_TG_ON_THE_FLY 1 /* 1 => disables radical calcellation by taut-charge movement */ | | ------------------ | | | Branch (539:37): [True: 1.13k, Folded] | | ------------------ ------------------ | Branch (1411:9): [True: 6.54k, False: 0] | Branch (1411:19): [True: 5.41k, False: 1.13k] ------------------ 1412| 6.54k| { 1413| 6.54k| T_GROUP_INFO tgi; 1414| 6.54k| int ret_bns; 1415| 6.54k| memset( &tgi, 0, sizeof( tgi ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 1416| 6.54k| tgi.num_t_groups = num_t; 1417| 6.54k| tgi.t_group = t_group; 1418| 6.54k|#if ( KETO_ENOL_TAUT == 1 ) 1419| 6.54k| tgi.bTautFlags |= ( t_group_info->bTautFlags & TG_FLAG_KETO_ENOL_TAUT ); /* needed in AddTGroups2BnStruct() */ ------------------ | | 946| 6.54k|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ 1420| 6.54k|#endif 1421| | 1422| 6.54k|#if ( TAUT_PT_22_00 == 1 ) 1423| 6.54k| tgi.bTautFlags |= (t_group_info->bTautFlags & TG_FLAG_PT_22_00); /* needed in AddTGroups2BnStruct() */ ------------------ | | 953| 6.54k|#define TG_FLAG_PT_22_00 0x00800000 ------------------ 1424| 6.54k|#endif 1425| 6.54k|#if ( TAUT_PT_16_00 == 1 ) 1426| 6.54k| tgi.bTautFlags |= (t_group_info->bTautFlags & TG_FLAG_PT_16_00); /* needed in AddTGroups2BnStruct() */ ------------------ | | 954| 6.54k|#define TG_FLAG_PT_16_00 0x01000000 ------------------ 1427| 6.54k|#endif 1428| 6.54k|#if ( TAUT_PT_06_00 == 1 ) 1429| 6.54k| tgi.bTautFlags |= (t_group_info->bTautFlags & TG_FLAG_PT_06_00); /* needed in AddTGroups2BnStruct() */ ------------------ | | 955| 6.54k|#define TG_FLAG_PT_06_00 0x02000000 ------------------ 1430| 6.54k|#endif 1431| 6.54k|#if ( TAUT_PT_39_00 == 1 ) 1432| 6.54k| tgi.bTautFlags |= (t_group_info->bTautFlags & TG_FLAG_PT_39_00); /* needed in AddTGroups2BnStruct() */ ------------------ | | 956| 6.54k|#define TG_FLAG_PT_39_00 0x04000000 ------------------ 1433| 6.54k|#endif 1434| 6.54k|#if ( TAUT_PT_13_00 == 1 ) 1435| 6.54k| tgi.bTautFlags |= (t_group_info->bTautFlags & TG_FLAG_PT_13_00); /* needed in AddTGroups2BnStruct() */ ------------------ | | 957| 6.54k|#define TG_FLAG_PT_13_00 0x08000000 ------------------ 1436| 6.54k|#endif 1437| 6.54k|#if ( TAUT_PT_18_00 == 1 ) 1438| 6.54k| tgi.bTautFlags |= (t_group_info->bTautFlags & TG_FLAG_PT_18_00); /* needed in AddTGroups2BnStruct() */ ------------------ | | 958| 6.54k|#define TG_FLAG_PT_18_00 0x10000000 ------------------ 1439| 6.54k|#endif 1440| | /* reinitialize BN Structure */ 1441| 6.54k| ret_bns = ReInitBnStruct( pBNS, at, num_atoms, 0 ); 1442| 6.54k| if (IS_BNS_ERROR( ret_bns )) ------------------ | | 67| 6.54k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 6.54k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 6.54k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 6.54k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 6.54k, False: 0] | | | Branch (67:44): [True: 0, False: 6.54k] | | ------------------ ------------------ 1443| 0| { 1444| 0| return ret_bns; 1445| 0| } 1446| 6.54k| if (*pBNS->pbTautFlags & TG_FLAG_MOVE_POS_CHARGES) ------------------ | | 921| 6.54k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (1446:13): [True: 6.54k, False: 0] ------------------ 1447| 6.54k| { 1448| | /* set new charge groups */ 1449| 6.54k| ret_bns = AddCGroups2BnStruct( pCG, pBNS, at, num_atoms, cgi ); 1450| 6.54k| if (IS_BNS_ERROR( ret_bns )) ------------------ | | 67| 6.54k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 6.54k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 6.54k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 6.54k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 6.54k, False: 0] | | | Branch (67:44): [True: 0, False: 6.54k] | | ------------------ ------------------ 1451| 0| { 1452| 0| return ret_bns; 1453| 0| } 1454| 6.54k| } 1455| | /* set new tautomeric groups */ 1456| 6.54k| ret_bns = AddTGroups2BnStruct( pCG, pBNS, at, num_atoms, &tgi ); 1457| 6.54k| if (IS_BNS_ERROR( ret_bns )) ------------------ | | 67| 6.54k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 6.54k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 6.54k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 6.54k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 6.54k, False: 0] | | | Branch (67:44): [True: 5, False: 6.54k] | | ------------------ ------------------ 1458| 5| { 1459| 5| return ret_bns; 1460| 5| } 1461| 6.54k| } 1462| | 1463| 6.54k| *pnum_t = num_t; 1464| 6.54k| return difference; 1465| | 1466| 0|exit_function: 1467| 0| if (nNewTgNumber != nNewTgNumberStackArray) ------------------ | Branch (1467:9): [True: 0, False: 0] ------------------ 1468| 0| { 1469| 0| inchi_free( nNewTgNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1470| 0| } 1471| 0| if (nGroupNumber != nGroupNumberStackArray) ------------------ | Branch (1471:9): [True: 0, False: 0] ------------------ 1472| 0| { 1473| 0| inchi_free( nGroupNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1474| 0| } 1475| 0| if (nGroupNewNumber != nGroupNewNumberStackArray) ------------------ | Branch (1475:9): [True: 0, False: 0] ------------------ 1476| 0| { 1477| 0| inchi_free( nGroupNewNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1478| 0| } 1479| | 1480| 0| return ret; 1481| 6.54k|} SetTautomericBonds: 1491| 39.2k|{ 1492| 39.2k| int k, n; 1493| 128k| for (k = n = 0; k < nNumBondPos; k++) ------------------ | Branch (1493:21): [True: 88.7k, False: 39.2k] ------------------ 1494| 88.7k| { 1495| 88.7k| int neighbor_index = BondPos[k].neighbor_index; 1496| 88.7k| int center = BondPos[k].nAtomNumber; 1497| 88.7k| int bond_mark = at[center].bond_type[neighbor_index]; 1498| 88.7k| int bond_type = bond_mark & ~BOND_MARK_ALL; ------------------ | | 191| 88.7k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 1499| 88.7k| int neighbor; 1500| 88.7k|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 1501| 88.7k| if (bond_type != BOND_TAUTOM) ------------------ | | 185| 88.7k|#define BOND_TAUTOM 8 ------------------ | Branch (1501:13): [True: 13.3k, False: 75.4k] ------------------ 1502| |#else 1503| | if (bond_type != BOND_ALTERN && bond_type != BOND_TAUTOM) 1504| |#endif 1505| 13.3k| { 1506| 13.3k| int ii; 1507| | /* change bond type to BOND_TAUTOM presering higher bits marks */ 1508| 13.3k| bond_type = ( bond_mark & BOND_MARK_ALL ) | BOND_TAUTOM; ------------------ | | 191| 13.3k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ bond_type = ( bond_mark & BOND_MARK_ALL ) | BOND_TAUTOM; ------------------ | | 185| 13.3k|#define BOND_TAUTOM 8 ------------------ 1509| | /* change center-neighbor bond */ 1510| 13.3k| at[center].bond_type[neighbor_index] = bond_type; 1511| 13.3k| neighbor = at[center].neighbor[neighbor_index]; 1512| 14.8k| for (ii = 0; ii < at[neighbor].valence; ii++) ------------------ | Branch (1512:26): [True: 14.8k, False: 0] ------------------ 1513| 14.8k| { 1514| 14.8k| if (at[neighbor].neighbor[ii] == center) ------------------ | Branch (1514:21): [True: 13.3k, False: 1.47k] ------------------ 1515| 13.3k| { 1516| | /* neighbor-center bond found */ 1517| 13.3k| at[neighbor].bond_type[ii] = bond_type; 1518| 13.3k| break; 1519| 13.3k| } 1520| 14.8k| } 1521| 13.3k| n++; 1522| 13.3k| } 1523| 88.7k| } 1524| | 1525| 39.2k| return n; 1526| 39.2k|} GetNeutralRepsIfNeeded: 1537| 8.03k|{ 1538| 8.03k| AT_NUMB ri = *pri; 1539| 8.03k| AT_NUMB rj = *prj; 1540| 8.03k| int i, k; 1541| 8.03k| AT_NUMB c_point, endpoint, r; 1542| | 1543| 8.03k| if (( c_point = at[ri].c_point ) && ------------------ | Branch (1543:9): [True: 383, False: 7.64k] ------------------ 1544| 383| ( at[rj].c_point == c_point ) && ------------------ | Branch (1544:9): [True: 341, False: 42] ------------------ 1545| 341| ( at[ri].charge == 1 || at[rj].charge == 1 ) && ------------------ | Branch (1545:12): [True: 101, False: 240] | Branch (1545:34): [True: 158, False: 82] ------------------ 1546| 259| cgi && ------------------ | Branch (1546:10): [True: 259, False: 0] ------------------ 1547| 259| cgi->num_c_groups > 0) ------------------ | Branch (1547:10): [True: 259, False: 0] ------------------ 1548| 259| { 1549| | /* at[ri] and at[rj] belong to the same charge group, at least one is charged */ 1550| 259| for (k = 0; k < cgi->num_c_groups; k++) /* MS VC++ 2008 reports unreachable code here ??? */ /* djb-rwth: addressing coverity ID #499559 -- read the previous comment; can cgi->num_c_groups only have values 0 and 1? */ ------------------ | Branch (1550:21): [True: 259, False: 0] ------------------ 1551| 259| { 1552| 259| if (cgi->c_group[k].nGroupNumber == c_point) ------------------ | Branch (1552:17): [True: 219, False: 40] ------------------ 1553| 219| { 1554| | /* cgi->c_group[k] is found to be this charge group */ 1555| 219| if (cgi->c_group[k].num_CPoints - cgi->c_group[k].num[0] < 2) ------------------ | Branch (1555:21): [True: 101, False: 118] ------------------ 1556| 101| { 1557| | /* Only one neutral in the c-group: we will not be able to neutralize both */ 1558| | /* when looking for the alt path to discover the tautomerism. */ 1559| | /* Therefore we need to find a neutral t-group representative at[rj] */ 1560| 101| if ((endpoint = at[rj].endpoint)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1560:25): [True: 5, False: 96] ------------------ 1561| 5| { 1562| 15| for (i = 0; i < nNumEndPoints; i++) ------------------ | Branch (1562:37): [True: 10, False: 5] ------------------ 1563| 10| { 1564| 10| if (( r = EndPoint[i].nAtomNumber ) == *prj) ------------------ | Branch (1564:33): [True: 5, False: 5] ------------------ 1565| 5| { 1566| 5| continue; /* ignore at[*prj] */ 1567| 5| } 1568| 5| if (at[r].endpoint != endpoint) ------------------ | Branch (1568:33): [True: 5, False: 0] ------------------ 1569| 5| { 1570| 5| continue; /* at[r] does not belong to the same t-group as at[*prj]; ignore the atom */ 1571| 5| } 1572| 0| if (!at[r].c_point) ------------------ | Branch (1572:33): [True: 0, False: 0] ------------------ 1573| 0| { 1574| 0| rj = r; /* found a neutral t-group representative */ 1575| 0| break; 1576| 0| } 1577| 0| if (at[r].c_point != c_point && c_point == at[rj].c_point) ------------------ | Branch (1577:33): [True: 0, False: 0] | Branch (1577:61): [True: 0, False: 0] ------------------ 1578| 0| { 1579| | /* replace only once because of (c_point == at[rj].c_point) condition */ 1580| 0| rj = r; 1581| 0| } 1582| 0| } 1583| 5| if (rj == *prj /*&& at[ri].endpoint*/) ------------------ | Branch (1583:29): [True: 5, False: 0] ------------------ 1584| 5| { 1585| | /* !!! "&& at[ri].endpoint": only between 2 t-groups 2004-02-27; 1586| | the change disabled due to undiscovered yet possibility of ambiguity*/ 1587| | /* no replacement has been found in EndPoint[]; try all atoms in the t-group */ 1588| 18| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1588:41): [True: 18, False: 0] ------------------ 1589| 18| { 1590| 18| if (at[i].endpoint != endpoint) ------------------ | Branch (1590:37): [True: 12, False: 6] ------------------ 1591| 12| { 1592| 12| continue; 1593| 12| } 1594| 6| if (i == (int) *prj) ------------------ | Branch (1594:37): [True: 1, False: 5] ------------------ 1595| 1| { 1596| 1| continue; 1597| 1| } 1598| 5| if (!at[i].c_point) ------------------ | Branch (1598:37): [True: 5, False: 0] ------------------ 1599| 5| { 1600| 5| rj = (AT_NUMB) i; /* found neutral t-group representative */ 1601| 5| break; 1602| 5| } 1603| 0| if (at[i].c_point != c_point && c_point == at[rj].c_point) ------------------ | Branch (1603:37): [True: 0, False: 0] | Branch (1603:65): [True: 0, False: 0] ------------------ 1604| 0| { 1605| | /* replace only once */ 1606| 0| rj = (AT_NUMB) i; 1607| 0| } 1608| 0| } 1609| 5| } 1610| 5| } 1611| | /* at[ri] */ 1612| 101| if ((endpoint = at[ri].endpoint)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1612:25): [True: 49, False: 52] ------------------ 1613| 49| { 1614| 155| for (i = 0; i < nNumEndPoints; i++) ------------------ | Branch (1614:37): [True: 132, False: 23] ------------------ 1615| 132| { 1616| 132| if (( r = EndPoint[i].nAtomNumber ) == *pri) ------------------ | Branch (1616:33): [True: 49, False: 83] ------------------ 1617| 49| { 1618| 49| continue; 1619| 49| } 1620| 83| if (at[r].endpoint != endpoint) ------------------ | Branch (1620:33): [True: 57, False: 26] ------------------ 1621| 57| { 1622| 57| continue; 1623| 57| } 1624| 26| if (!at[r].c_point) ------------------ | Branch (1624:33): [True: 26, False: 0] ------------------ 1625| 26| { 1626| 26| ri = r; /* found neutral t-group representative */ 1627| 26| break; 1628| 26| } 1629| 0| if (at[r].c_point != c_point && c_point == at[ri].c_point && ------------------ | Branch (1629:33): [True: 0, False: 0] | Branch (1629:61): [True: 0, False: 0] ------------------ 1630| 0| at[r].c_point != at[rj].c_point) ------------------ | Branch (1630:34): [True: 0, False: 0] ------------------ 1631| 0| { 1632| | /* replace only once */ 1633| 0| ri = r; 1634| 0| } 1635| 0| } 1636| 49| if (ri == *pri && at[rj].endpoint) ------------------ | Branch (1636:29): [True: 23, False: 26] | Branch (1636:43): [True: 5, False: 18] ------------------ 1637| 5| { 1638| | /* !!! "&& at[rj].endpoint": only between 2 t-groups 2004-02-27; 1639| | the change disabled due to undiscovered yet possibility of ambiguity */ 1640| 19| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1640:41): [True: 19, False: 0] ------------------ 1641| 19| { 1642| 19| if (at[i].endpoint != endpoint) ------------------ | Branch (1642:37): [True: 9, False: 10] ------------------ 1643| 9| { 1644| 9| continue; 1645| 9| } 1646| 10| if (i == (int) *pri) ------------------ | Branch (1646:37): [True: 5, False: 5] ------------------ 1647| 5| { 1648| 5| continue; 1649| 5| } 1650| 5| if (!at[i].c_point) ------------------ | Branch (1650:37): [True: 5, False: 0] ------------------ 1651| 5| { 1652| 5| ri = (AT_NUMB) i; /* found neutral t-group representative */ 1653| 5| break; 1654| 5| } 1655| 0| if (at[i].c_point != c_point && c_point == at[ri].c_point && ------------------ | Branch (1655:37): [True: 0, False: 0] | Branch (1655:65): [True: 0, False: 0] ------------------ 1656| 0| at[i].c_point != at[rj].c_point) ------------------ | Branch (1656:38): [True: 0, False: 0] ------------------ 1657| 0| { 1658| | /* replace only once */ 1659| 0| ri = (AT_NUMB) i; 1660| 0| } 1661| 0| } 1662| 5| } 1663| 49| } 1664| 101| } 1665| 219| } 1666| 259| break; 1667| 259| } 1668| 259| *prj = rj; 1669| 259| *pri = ri; 1670| 259| } 1671| | 1672| 8.03k| return 0; 1673| 8.03k|} FindAccessibleEndPoints: 1688| 39.3k|{ 1689| 39.3k| AT_NUMB nTGroupRepresenative[MAXVAL], nTGroupEqu[MAXVAL], nTGEndPointNo[MAXVAL], ri, rj; 1690| 39.3k| AT_NUMB nCurTGroupNumber, nMaxTGroupNumber, nNumTgroupNumbers, nMaxEquNumber; 1691| 39.3k| int i, j, k, nNumDiffTGroupNumbers = 0, nNumFoundEqu, nErr; 1692| | 1693| 39.3k| if (*nNumEndPoints != *nNumBondPos) ------------------ | Branch (1693:9): [True: 0, False: 39.3k] ------------------ 1694| 0| return 0; 1695| | /* collect all group numbers. Fill EndPoint[i].nEquNumber */ 1696| 128k| for (i = 0; i < *nNumEndPoints; i++) ------------------ | Branch (1696:17): [True: 88.8k, False: 39.3k] ------------------ 1697| 88.8k| { 1698| 88.8k| nCurTGroupNumber = EndPoint[i].nEquNumber = EndPoint[i].nGroupNumber; /* initial equivalence */ 1699| 88.8k| if (nCurTGroupNumber) ------------------ | Branch (1699:13): [True: 75.8k, False: 12.9k] ------------------ 1700| 75.8k| { 1701| | /* found endpoint that already belongs to a t-group */ 1702| 75.9k| for (j = 0; j < nNumDiffTGroupNumbers; j++) ------------------ | Branch (1702:25): [True: 42.1k, False: 33.7k] ------------------ 1703| 42.1k| { 1704| 42.1k| if (nTGroupEqu[j] == nCurTGroupNumber) ------------------ | Branch (1704:21): [True: 42.1k, False: 32] ------------------ 1705| 42.1k| { 1706| 42.1k| break; 1707| 42.1k| } 1708| 42.1k| } 1709| 75.8k| if (j == nNumDiffTGroupNumbers) ------------------ | Branch (1709:17): [True: 33.7k, False: 42.1k] ------------------ 1710| 33.7k| { 1711| 33.7k| nTGroupRepresenative[nNumDiffTGroupNumbers] = EndPoint[i].nAtomNumber; 1712| 33.7k| nTGroupEqu[nNumDiffTGroupNumbers] = EndPoint[i].nGroupNumber; 1713| 33.7k| nTGEndPointNo[nNumDiffTGroupNumbers] = i; 1714| 33.7k| nNumDiffTGroupNumbers++; 1715| 33.7k| } 1716| 75.8k| } 1717| 88.8k| } 1718| | 1719| | /* check whether each pair belongs to the same t-group and establish the equivalence(s) */ 1720| 73.0k| for (i = 0, nNumFoundEqu = 0; i < nNumDiffTGroupNumbers; i++) ------------------ | Branch (1720:35): [True: 33.7k, False: 39.3k] ------------------ 1721| 33.7k| { 1722| 33.8k| for (j = i + 1; j < nNumDiffTGroupNumbers; j++) ------------------ | Branch (1722:25): [True: 30, False: 33.7k] ------------------ 1723| 30| { 1724| 30| ri = nTGroupRepresenative[i]; 1725| 30| rj = nTGroupRepresenative[j]; 1726| | /* both at[ri] and at[rj] are known to belong to tautomeric groups */ 1727| 30| GetNeutralRepsIfNeeded( &ri, &rj, at, num_atoms, EndPoint, *nNumEndPoints, cgi ); 1728| 30| nErr = bExistsAnyAltPath( pCG, pBNS, pBD, at, num_atoms, ri, rj, taut_mode ); 1729| 30| if (IS_BNS_ERROR( nErr )) ------------------ | | 67| 30|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 30|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 30|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 30|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 30, False: 0] | | | Branch (67:44): [True: 0, False: 30] | | ------------------ ------------------ 1730| 0| { 1731| 0| return nErr; 1732| 0| } 1733| 30| if (0 == nErr) ------------------ | Branch (1733:17): [True: 1, False: 29] ------------------ 1734| 1| { 1735| 1| continue; /* alt path between at[ri] and at[rj] not found */ 1736| 1| } 1737| 29| nCurTGroupNumber = inchi_min( nTGroupEqu[i], nTGroupEqu[j] ); ------------------ | | 139| 29|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 21, False: 8] | | ------------------ ------------------ 1738| 29| nMaxTGroupNumber = inchi_max( nTGroupEqu[i], nTGroupEqu[j] ); ------------------ | | 138| 29|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 8, False: 21] | | ------------------ ------------------ 1739| 87| for (k = 0; k < nNumDiffTGroupNumbers; k++) ------------------ | Branch (1739:25): [True: 58, False: 29] ------------------ 1740| 58| { 1741| 58| if (nTGroupEqu[k] == nMaxTGroupNumber) ------------------ | Branch (1741:21): [True: 29, False: 29] ------------------ 1742| 29| { 1743| 29| nTGroupEqu[k] = nCurTGroupNumber; 1744| 29| nNumFoundEqu++; 1745| 29| } 1746| 58| } 1747| 101| for (k = 0; k < *nNumEndPoints; k++) ------------------ | Branch (1747:25): [True: 72, False: 29] ------------------ 1748| 72| { 1749| 72| if (EndPoint[k].nEquNumber == nMaxTGroupNumber) ------------------ | Branch (1749:21): [True: 31, False: 41] ------------------ 1750| 31| { 1751| 31| EndPoint[k].nEquNumber = nCurTGroupNumber; 1752| 31| } 1753| 72| } 1754| 29| } 1755| 33.7k| } 1756| | 1757| 39.3k| if (nNumFoundEqu) ------------------ | Branch (1757:9): [True: 29, False: 39.2k] ------------------ 1758| 29| { 1759| | /* leave in only non-equivalent representatives */ 1760| 58| for (i = 1; i < nNumDiffTGroupNumbers; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (1760:21): [True: 29, False: 29] ------------------ 1761| 29| { 1762| 29| for (j = 0; j < i; j++) ------------------ | Branch (1762:25): [True: 29, False: 0] ------------------ 1763| 29| { 1764| 29| if (nTGroupEqu[j] == nTGroupEqu[i]) ------------------ | Branch (1764:21): [True: 29, False: 0] ------------------ 1765| 29| { 1766| 29| nTGroupEqu[i] = 0; /* i > j; mark equivalent for removal*/ 1767| 29| break; 1768| 29| } 1769| 29| } 1770| 29| } 1771| 87| for (i = j = 0; i < nNumDiffTGroupNumbers; i++) ------------------ | Branch (1771:25): [True: 58, False: 29] ------------------ 1772| 58| { 1773| 58| if (nTGroupEqu[i]) ------------------ | Branch (1773:17): [True: 29, False: 29] ------------------ 1774| 29| { 1775| 29| if (i != j) ------------------ | Branch (1775:21): [True: 0, False: 29] ------------------ 1776| 0| { /* remove the marked */ 1777| 0| nTGroupEqu[j] = nTGroupEqu[i]; 1778| 0| nTGroupRepresenative[j] = nTGroupRepresenative[i]; 1779| 0| nTGEndPointNo[j] = nTGEndPointNo[i]; 1780| 0| } 1781| 29| j++; 1782| 29| } 1783| 58| } 1784| 29| nNumDiffTGroupNumbers = j; /* number of known t-group representatives */ 1785| 29| } 1786| | 1787| | /* collect endpoints that have not been assigned to t-groups */ 1788| 128k| for (i = 0, j = nNumDiffTGroupNumbers; i < *nNumEndPoints; i++) ------------------ | Branch (1788:44): [True: 88.8k, False: 39.3k] ------------------ 1789| 88.8k| { 1790| 88.8k| if (EndPoint[i].nEquNumber) ------------------ | Branch (1790:13): [True: 75.8k, False: 12.9k] ------------------ 1791| 75.8k| { 1792| 75.8k| continue; 1793| 75.8k| } 1794| 12.9k| nTGroupEqu[j] = 0; 1795| 12.9k| nTGroupRepresenative[j] = EndPoint[i].nAtomNumber; 1796| 12.9k| nTGEndPointNo[j] = i; 1797| 12.9k| j++; 1798| 12.9k| } 1799| 39.3k| nNumTgroupNumbers = j; 1800| 39.3k| nMaxEquNumber = num_atoms + 1; /* impossible atom or t-group number */ 1801| | 1802| | /* check whether each pair belongs to the same group and establish the equivalence(s) */ 1803| 85.9k| for (i = 0, nNumFoundEqu = 0; i < nNumTgroupNumbers; i++) ------------------ | Branch (1803:35): [True: 46.6k, False: 39.3k] ------------------ 1804| 46.6k| { 1805| 55.2k| for (j = i + 1; j < nNumTgroupNumbers; j++) ------------------ | Branch (1805:25): [True: 8.61k, False: 46.6k] ------------------ 1806| 8.61k| { 1807| 8.61k| if ((nTGroupEqu[i] != nTGroupEqu[j] && ( i >= nNumDiffTGroupNumbers || j >= nNumDiffTGroupNumbers )) || ------------------ | Branch (1807:18): [True: 1.94k, False: 6.66k] | Branch (1807:54): [True: 1.16k, False: 783] | Branch (1807:84): [True: 782, False: 1] ------------------ 1808| | /* equivalence of a t-group and a non-t-group atom */ 1809| 6.66k| (!nTGroupEqu[i] && !nTGroupEqu[j]) ------------------ | Branch (1809:19): [True: 6.05k, False: 610] | Branch (1809:37): [True: 6.05k, False: 0] ------------------ 1810| | /* equivalence of two non-t-group atoms */ 1811| 8.61k| ) /* djb-rwth: addressing LLVM warnings */ 1812| 8.00k| { 1813| 8.00k| ri = nTGroupRepresenative[i]; 1814| 8.00k| rj = nTGroupRepresenative[j]; 1815| | /*------------------------------!!!--------------------------------------------- 1816| | Explanation why GetNeutralRepsIfNeeded() may need to be changed 2004-02-27 1817| | The change has been disabled due to undiscovered yet possibility of ambiguity 1818| | to search for neutral only among EndPoint[] in case taut-not_taut pairs 1819| | 1820| | Counterexample: O=C-NH(+)=C-NH2 1821| | 1 2 3 1822| | 1823| | Has already been found: 2-3 (+)-charge exchange 1824| | 1-2 tautomerism (charge removed to 3) 1825| | Now testing: 2-3 tautomerism. If not commented out, 1826| | GetNeutralRepsIfNeeded() would replace 2-3 test with 1-3 test because: 1827| | o Charge group has only one neutral and both 2 and 3 belong to it, 1828| | therefore we cannot neutralize both; search for neutral representative; 1829| | o Since 1 and 2 belong to the same t-group and 1 is neutral, 1830| | test 1-3 instead of 2-3. 1831| | This breaks our condition: 1832| | Test tautomeric H movement only between neutral atoms. 1833| | -----------------------------------------------------------------------------*/ 1834| 8.00k| GetNeutralRepsIfNeeded( &ri, &rj, at, num_atoms, EndPoint, *nNumEndPoints, cgi ); 1835| | 1836| 8.00k| nErr = bExistsAnyAltPath( pCG, pBNS, pBD, at, num_atoms, ri, rj, taut_mode ); 1837| 8.00k| if (IS_BNS_ERROR( nErr )) ------------------ | | 67| 8.00k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 8.00k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 8.00k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 8.00k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 8.00k, False: 0] | | | Branch (67:44): [True: 3, False: 7.99k] | | ------------------ ------------------ 1838| 3| { 1839| 3| return nErr; 1840| 3| } 1841| 7.99k| if (nErr <= 0) ------------------ | Branch (1841:21): [True: 875, False: 7.12k] ------------------ 1842| 875| { 1843| 875| continue; 1844| 875| } 1845| 7.12k| if (nTGroupEqu[i] && nTGroupEqu[j]) ------------------ | Branch (1845:21): [True: 1.19k, False: 5.93k] | Branch (1845:38): [True: 1, False: 1.19k] ------------------ 1846| 1| { 1847| | /* found equivalence of two t-groups; at least one of them must be a new one */ 1848| 1| nCurTGroupNumber = inchi_min( nTGroupEqu[i], nTGroupEqu[j] ); ------------------ | | 139| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (139:26): [True: 0, False: 1] | | ------------------ ------------------ 1849| 1| nMaxTGroupNumber = inchi_max( nTGroupEqu[i], nTGroupEqu[j] ); ------------------ | | 138| 1|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 1, False: 0] | | ------------------ ------------------ 1850| 4| for (k = 0; k < nNumTgroupNumbers; k++) ------------------ | Branch (1850:33): [True: 3, False: 1] ------------------ 1851| 3| { 1852| 3| if (nTGroupEqu[k] == nMaxTGroupNumber) ------------------ | Branch (1852:29): [True: 1, False: 2] ------------------ 1853| 1| { 1854| 1| nTGroupEqu[k] = nCurTGroupNumber; 1855| 1| nNumFoundEqu++; 1856| 1| } 1857| 3| } 1858| 4| for (k = 0; k < *nNumEndPoints; k++) ------------------ | Branch (1858:33): [True: 3, False: 1] ------------------ 1859| 3| { 1860| 3| if (EndPoint[k].nEquNumber == nMaxTGroupNumber) ------------------ | Branch (1860:29): [True: 1, False: 2] ------------------ 1861| 1| { 1862| 1| EndPoint[k].nEquNumber = nCurTGroupNumber; 1863| 1| } 1864| 3| } 1865| 1| } 1866| 7.12k| else 1867| 7.12k| { 1868| 7.12k| if (nTGroupEqu[i]) ------------------ | Branch (1868:25): [True: 1.19k, False: 5.93k] ------------------ 1869| 1.19k| { /* extend existing t-group */ 1870| 1.19k| nTGroupEqu[j] = nTGroupEqu[i]; 1871| 1.19k| EndPoint[nTGEndPointNo[j]].nEquNumber = nTGroupEqu[i]; 1872| 1.19k| } 1873| 5.93k| else 1874| 5.93k| { 1875| 5.93k| if (nTGroupEqu[j]) ------------------ | Branch (1875:29): [True: 440, False: 5.49k] ------------------ 1876| 440| { /* extend existing t-group */ 1877| 440| nTGroupEqu[i] = nTGroupEqu[j]; 1878| 440| EndPoint[nTGEndPointNo[i]].nEquNumber = nTGroupEqu[j]; 1879| 440| } 1880| 5.49k| else 1881| 5.49k| { /* establis a new t-group */ 1882| 5.49k| nTGroupEqu[i] = 1883| 5.49k| nTGroupEqu[j] = nMaxEquNumber; /* assign a fict. ID to establish equivalence */ 1884| 5.49k| EndPoint[nTGEndPointNo[i]].nEquNumber = 1885| 5.49k| EndPoint[nTGEndPointNo[j]].nEquNumber = nMaxEquNumber; 1886| 5.49k| nMaxEquNumber++; 1887| 5.49k| } 1888| 5.93k| } 1889| 7.12k| } 1890| 7.12k| } 1891| 8.61k| } 1892| 46.6k| } 1893| | 1894| | /* eliminate endpoints and bonds that do not belong to t-group(s) 1895| | (they have not been found connected by an alt path to any other endpoint) 1896| | */ 1897| 128k| for (i = 0, j = 0; i < *nNumEndPoints; i++) ------------------ | Branch (1897:24): [True: 88.7k, False: 39.3k] ------------------ 1898| 88.7k| { 1899| 88.7k| if (EndPoint[i].nEquNumber) ------------------ | Branch (1899:13): [True: 88.4k, False: 300] ------------------ 1900| 88.4k| { 1901| 88.4k|#if ( IGNORE_SINGLE_ENDPOINTS == 1 ) /* 1-28-2003 */ 1902| 298k| for (k = 0, nNumFoundEqu = 0; k < *nNumEndPoints; k++) ------------------ | Branch (1902:43): [True: 209k, False: 88.4k] ------------------ 1903| 209k| { 1904| 209k| nNumFoundEqu += ( EndPoint[i].nEquNumber == EndPoint[k].nEquNumber ); 1905| 209k| } 1906| 88.4k| if (nNumFoundEqu <= 1) ------------------ | Branch (1906:17): [True: 66, False: 88.4k] ------------------ 1907| 66| { 1908| | /* one time it is equal to itself when i == k above */ 1909| | /* if EndPoint[i] is not "equivalent" to any other EndPoint then ignore it */ 1910| 66| continue; 1911| 66| } 1912| 88.4k|#endif 1913| 88.4k| if (i != j) ------------------ | Branch (1913:17): [True: 143, False: 88.2k] ------------------ 1914| 143| { 1915| | /* save endpoints that are found to be connected to other endpoints by alt paths */ 1916| 143| EndPoint[j] = EndPoint[i]; 1917| 143| BondPos[j] = BondPos[i]; 1918| 143| } 1919| 88.4k| j++; 1920| 88.4k| } 1921| 88.7k| } 1922| | 1923| |#if ( IGNORE_SINGLE_ENDPOINTS != 1 ) /* 1-28-2003 */ 1924| | /* Do not allow a centerpoint to have only one tautomeric bond */ 1925| | /* Hack: we may have only one centerpoint */ 1926| | /* BondPos[*].nAtomNumber are centerpoints */ 1927| | if (j == 1) 1928| | { 1929| | /* check if there exist other centerpoint neighbors 1930| | * connected to it by another tautomeric-bond 1931| | */ 1932| | for (i = 0, k = 0; i < at[BondPos[0].nAtomNumber].valence; i++) 1933| | { 1934| | k += ( i != BondPos[0].neighbor_index && 1935| | BOND_TAUTOM == ( at[BondPos[0].nAtomNumber].bond_type[i] & ~BOND_MARK_ALL ) ); 1936| | } 1937| | if (!k) 1938| | { 1939| | j = 0; 1940| | } 1941| | } 1942| |#endif 1943| | 1944| 39.3k| *nNumEndPoints = *nNumBondPos = j; 1945| | 1946| 39.3k| return j; 1947| 39.3k|} bCanBeACPoint: 2019| 135k|{ 2020| 135k| int nChangeValence; 2021| 135k| int nNumBonds; 2022| 135k| int nBondsValence; 2023| 135k| int bNegCharge = ( at->charge == -1 ); /* add fict. bonds to (-) 2004-02-24*/ 2024| | 2025| 135k| if (at->charge == cCharge && at->valence == at->chem_bonds_valence && at->num_H) ------------------ | Branch (2025:9): [True: 12.8k, False: 122k] | Branch (2025:34): [True: 222, False: 12.6k] | Branch (2025:75): [True: 71, False: 151] ------------------ 2026| 71| { 2027| | /* proton donors candidates >NH(+)-, >NH2(+), -NH3(+), >OH(+), -OH2(+) */ 2028| | /* charged, added p-transfer -- 01-28-2004 */ 2029| 71| nChangeValence = at->charge * cChangeValence; /* +1 or -1; currently only +1 */ 2030| 71| nBondsValence = at->chem_bonds_valence + at->num_H; 2031| 71| if (nBondsValence == neutral_bonds_valence + nChangeValence && nEndpointValence) ------------------ | Branch (2031:13): [True: 53, False: 18] | Branch (2031:72): [True: 49, False: 4] ------------------ 2032| 49| { 2033| 49| *cChargeSubtype = C_SUBTYPE_CHARGED_p_DONOR; /* ignore Phosphorus p-donors for now */ ------------------ | | 1998| 49|#define C_SUBTYPE_CHARGED_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1988| 49|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1989| 49|#define C_SUBTYPE_p_DONOR 1 /* new */ | | ------------------ ------------------ 2034| 49| } 2035| 71| return 0; 2036| 71| } 2037| | 2038| 135k| else 2039| 135k| { 2040| 135k| if (at->charge == cCharge && at->valence < at->chem_bonds_valence) ------------------ | Branch (2040:13): [True: 12.8k, False: 122k] | Branch (2040:38): [True: 12.6k, False: 151] ------------------ 2041| 12.6k| { 2042| | /* the requirement at->valence < at->chem_bonds_valence rejects 2043| | candidates >NH(+)-, >NH2(+), -NH3(+), >N(+)<, >OH(+), -OH2(+), >O(+)- 2044| | Moveable charge requires double bonds; these ions have no double bonds 2045| | */ 2046| | 2047| | /* charged */ 2048| 12.6k| nChangeValence = at->charge * cChangeValence; /* +1 or -1; currently only +1 */ 2049| 12.6k| nBondsValence = at->chem_bonds_valence + at->num_H; 2050| 12.6k| nNumBonds = at->valence + at->num_H; 2051| 12.6k| if (nBondsValence == neutral_bonds_valence + nChangeValence) ------------------ | Branch (2051:17): [True: 12.1k, False: 534] ------------------ 2052| 12.1k| { 2053| | /* known valence */ 2054| 12.1k| if (nNumBonds == neutral_valence) ------------------ | Branch (2054:21): [True: 2.58k, False: 9.53k] ------------------ 2055| 2.58k| { 2056| | /* non-tautomeric: >N(+)=, =O(+)- 2057| | possibly tautomeric donor: =NH(+)-, =NH2(+), =OH(+) */ 2058| 2.58k| if (at->valence == neutral_valence || !nEndpointValence) ------------------ | Branch (2058:25): [True: 1.05k, False: 1.52k] | Branch (2058:59): [True: 11, False: 1.51k] ------------------ 2059| 1.06k| { 2060| | /* non-tautomeric: >N(+)=, =O(+)-; any suitable P+: >P(+)=, =PH(+)-, =PH2(+) */ 2061| 1.06k| *cChargeSubtype = C_SUBTYPE_CHARGED_NON_TAUT; ------------------ | | 1997| 1.06k|#define C_SUBTYPE_CHARGED_NON_TAUT (C_SUBTYPE_CHARGED) | | ------------------ | | | | 1988| 1.06k|#define C_SUBTYPE_CHARGED 0 | | ------------------ ------------------ 2062| 1.06k| } 2063| 1.51k| else 2064| 1.51k| { 2065| | /* possibly tautomeric donor: =NH(+)-, =NH2(+), =OH(+) */ 2066| 1.51k| *cChargeSubtype = C_SUBTYPE_CHARGED_H_DONOR; ------------------ | | 2001| 1.51k|#define C_SUBTYPE_CHARGED_H_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_DONOR |C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1988| 1.51k|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_DONOR |C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1992| 1.51k|#define C_SUBTYPE_H_DONOR 8 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_DONOR |C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1989| 1.51k|#define C_SUBTYPE_p_DONOR 1 /* new */ | | ------------------ ------------------ 2067| 1.51k| } 2068| 2.58k| return 1; 2069| 2.58k| } 2070| 9.53k| if (nNumBonds == neutral_valence - 1) ------------------ | Branch (2070:21): [True: 9.53k, False: 0] ------------------ 2071| 9.53k| { 2072| | /* possibly tutomeric acceptor: =N(+)=, #N(+)-, #NH(+), #O(+) */ 2073| 9.53k| if (nEndpointValence) ------------------ | Branch (2073:25): [True: 8.63k, False: 904] ------------------ 2074| 8.63k| { 2075| 8.63k| *cChargeSubtype = at->num_H ? C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR : C_SUBTYPE_CHARGED_H_ACCEPT; ------------------ | | 2000| 23|#define C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1988| 23|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1991| 23|#define C_SUBTYPE_H_ACCEPT 4 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1989| 23|#define C_SUBTYPE_p_DONOR 1 /* new */ | | ------------------ ------------------ *cChargeSubtype = at->num_H ? C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR : C_SUBTYPE_CHARGED_H_ACCEPT; ------------------ | | 1999| 17.2k|#define C_SUBTYPE_CHARGED_H_ACCEPT (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1988| 8.61k|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_ACCEPT (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1991| 8.61k|#define C_SUBTYPE_H_ACCEPT 4 | | ------------------ ------------------ | Branch (2075:43): [True: 23, False: 8.61k] ------------------ 2076| 8.63k| } 2077| 904| else 2078| 904| { 2079| | /* =P(+)=, #P(+)-, #PH(+) */ 2080| 904| *cChargeSubtype = C_SUBTYPE_CHARGED_NON_TAUT; ------------------ | | 1997| 904|#define C_SUBTYPE_CHARGED_NON_TAUT (C_SUBTYPE_CHARGED) | | ------------------ | | | | 1988| 904|#define C_SUBTYPE_CHARGED 0 | | ------------------ ------------------ 2081| 904| } 2082| 9.53k| return 1; /* charge type, charged */ 2083| 9.53k| } 2084| 9.53k| } 2085| 12.6k| } 2086| 122k| else 2087| 122k| { 2088| 122k| if (at->charge == 0 || bNegCharge) ------------------ | Branch (2088:17): [True: 107k, False: 14.9k] | Branch (2088:36): [True: 14.7k, False: 151] ------------------ 2089| 122k| { 2090| | /* neutral atom or anion, all bonds are single */ 2091| 122k| nBondsValence = at->chem_bonds_valence + at->num_H + bNegCharge; /* add fict. bonds to (-) 2004-02-24*/ 2092| 122k| nNumBonds = at->valence + at->num_H + bNegCharge; /* add fict. bonds to (-) 2004-02-24*/ 2093| 122k| if (nBondsValence == neutral_bonds_valence) ------------------ | Branch (2093:21): [True: 51.4k, False: 71.1k] ------------------ 2094| 51.4k| { 2095| 51.4k| if (nNumBonds == neutral_valence) ------------------ | Branch (2095:25): [True: 10.8k, False: 40.5k] ------------------ 2096| 10.8k| { 2097| | /* only single bonds: >N-, >NH, -NH2, -O-, -OH, >P- >PH -PH2 */ 2098| | /* >N(-), -NH(-), -O(-). >P(-) -PH(-) */ 2099| 10.8k| { 2100| 10.8k| if (at->valence == neutral_valence || !nEndpointValence) ------------------ | Branch (2100:33): [True: 4.90k, False: 5.94k] | Branch (2100:67): [True: 521, False: 5.42k] ------------------ 2101| 5.42k| { 2102| | /* >N-, -O-, any P(3 single bonds): >P- >PH -PH2 */ 2103| 5.42k| *cChargeSubtype = C_SUBTYPE_NEUTRAL_NON_TAUT; ------------------ | | 2003| 5.42k|#define C_SUBTYPE_NEUTRAL_NON_TAUT (C_SUBTYPE_NEUTRAL) | | ------------------ | | | | 1993| 5.42k|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ ------------------ 2104| 5.42k| } 2105| 5.42k| else 2106| 5.42k| { 2107| 5.42k| if (at->valence < neutral_valence /*&& nEndpointValence */) ------------------ | Branch (2107:37): [True: 5.41k, False: 6] ------------------ 2108| 5.41k| { 2109| | /* num_H > 0: >NH -NH2 -OH */ 2110| | /* num_H = 0: none C_SUBTYPE_NEUTRAL_H_ACCEPT for now */ 2111| 5.41k| *cChargeSubtype = at->num_H ? C_SUBTYPE_NEUTRAL_H_DONOR : C_SUBTYPE_NEUTRAL_H_ACCEPT; ------------------ | | 2006| 2.80k|#define C_SUBTYPE_NEUTRAL_H_DONOR (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_DONOR) | | ------------------ | | | | 1993| 2.80k|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ | | #define C_SUBTYPE_NEUTRAL_H_DONOR (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_DONOR) | | ------------------ | | | | 1992| 2.80k|#define C_SUBTYPE_H_DONOR 8 | | ------------------ ------------------ *cChargeSubtype = at->num_H ? C_SUBTYPE_NEUTRAL_H_DONOR : C_SUBTYPE_NEUTRAL_H_ACCEPT; ------------------ | | 2004| 8.02k|#define C_SUBTYPE_NEUTRAL_H_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1993| 2.61k|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ | | #define C_SUBTYPE_NEUTRAL_H_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1991| 2.61k|#define C_SUBTYPE_H_ACCEPT 4 | | ------------------ ------------------ | Branch (2111:55): [True: 2.80k, False: 2.61k] ------------------ 2112| 5.41k| } 2113| 6| else 2114| 6| { 2115| 6| return 0; 2116| 6| } 2117| 5.42k| } 2118| 10.8k| } 2119| 10.8k| return 1; /* charge type, neutral */ 2120| 10.8k| } 2121| 40.5k| if (nNumBonds == neutral_valence - 1) ------------------ | Branch (2121:25): [True: 33.7k, False: 6.84k] ------------------ 2122| 33.7k| { 2123| | /* possibly tautomeric acceptor =N-, =NH, =O or non-taut =P-, =PH */ 2124| 33.7k| if (nEndpointValence) ------------------ | Branch (2124:29): [True: 30.9k, False: 2.74k] ------------------ 2125| 30.9k| { 2126| | /* =N-, =NH, =O */ 2127| 30.9k| *cChargeSubtype = C_SUBTYPE_NEUTRAL_H_ACCEPT_p_ACCEPT; ------------------ | | 2005| 30.9k|#define C_SUBTYPE_NEUTRAL_H_ACCEPT_p_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_ACCEPT) | | ------------------ | | | | 1993| 30.9k|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ | | #define C_SUBTYPE_NEUTRAL_H_ACCEPT_p_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_ACCEPT) | | ------------------ | | | | 1991| 30.9k|#define C_SUBTYPE_H_ACCEPT 4 | | ------------------ | | #define C_SUBTYPE_NEUTRAL_H_ACCEPT_p_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_ACCEPT) | | ------------------ | | | | 1990| 30.9k|#define C_SUBTYPE_p_ACCEPT 2 /* new */ | | ------------------ ------------------ 2128| 30.9k| } 2129| 2.74k| else 2130| 2.74k| { 2131| | /* =P-, =PH */ 2132| 2.74k| *cChargeSubtype = C_SUBTYPE_NEUTRAL_NON_TAUT; ------------------ | | 2003| 2.74k|#define C_SUBTYPE_NEUTRAL_NON_TAUT (C_SUBTYPE_NEUTRAL) | | ------------------ | | | | 1993| 2.74k|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ ------------------ 2133| 2.74k| } 2134| 33.7k| return 1; /* charge type, (+) => neutral */ 2135| 33.7k| } 2136| 40.5k| } 2137| 122k| } 2138| 122k| } 2139| 135k| } 2140| | 2141| 78.6k| return 0; 2142| 135k|} GetChargeType: 2147| 947k|{ 2148| 947k| int i, n; 2149| 947k| S_CHAR nEndpointValence; 2150| 947k| inp_ATOM *at = atom + iat; 2151| | 2152| 947k| *cChargeSubtype = 0; 2153| | /* ignore ion pairs and charges != 1 */ 2154| 947k| if (abs( at->charge ) == 1) ------------------ | Branch (2154:9): [True: 89.5k, False: 858k] ------------------ 2155| 89.5k| { 2156| 200k| for (i = 0; i < at->valence; i++) ------------------ | Branch (2156:21): [True: 131k, False: 68.7k] ------------------ 2157| 131k| { 2158| 131k| n = at->neighbor[i]; 2159| | /* allow negatively charged tautomeric neighbors 2004-02-26 */ 2160| 131k| if (abs( atom[n].charge + at->charge ) < abs( atom[n].charge - at->charge ) && !atom[n].endpoint) ------------------ | Branch (2160:17): [True: 21.9k, False: 109k] | Branch (2160:92): [True: 20.8k, False: 1.08k] ------------------ 2161| 20.8k| { 2162| 20.8k| return -1; /* charges have different signs */ 2163| 20.8k| } 2164| 131k| } 2165| 89.5k| } 2166| 858k| else 2167| 858k| { 2168| 858k| if (at->charge) ------------------ | Branch (2168:13): [True: 4.62k, False: 853k] ------------------ 2169| 4.62k| { 2170| 4.62k| return -1; /* abs(charge) != 1 */ 2171| 4.62k| } 2172| 858k| } 2173| | 2174| | /* find candidates */ 2175| 6.12M| for (i = 0; i < NUM_C_TYPES; i++) ------------------ | | 2008| 6.12M|#define NUM_C_TYPES (int)(sizeof( CType )/sizeof(CType[0])) ------------------ | Branch (2175:17): [True: 5.25M, False: 865k] ------------------ 2176| 5.25M| { 2177| 5.25M| if (!strcmp( at->elname, CType[i].elname ) && ------------------ | Branch (2177:13): [True: 372k, False: 4.88M] ------------------ 2178| 372k| ( !CType[i].num_bonds || (CType[i].num_bonds == at->valence && at->nNumAtInRingSystem >= 5) )) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2178:15): [True: 133k, False: 238k] | Branch (2178:39): [True: 13.8k, False: 225k] | Branch (2178:76): [True: 2.27k, False: 11.5k] ------------------ 2179| 135k| { 2180| 135k| nEndpointValence = (S_CHAR) get_endpoint_valence( at->el_number ); 2181| 135k| if (bCanBeACPoint( at, CType[i].charge, CType[i].cChangeValence, CType[i].neutral_bonds_valence, ------------------ | Branch (2181:17): [True: 56.6k, False: 78.7k] ------------------ 2182| 135k| CType[i].neutral_valence, nEndpointValence, cChargeSubtype )) 2183| 56.6k| { 2184| 56.6k| return CType[i].cChargeType; 2185| 56.6k| } 2186| 135k| } 2187| 5.25M| } 2188| | 2189| 865k| return -1; 2190| 922k|} CmpCCandidates: 2195| 36.7k|{ 2196| 36.7k| const C_CANDIDATE *c1 = (const C_CANDIDATE *) a1; 2197| 36.7k| const C_CANDIDATE *c2 = (const C_CANDIDATE *) a2; 2198| 36.7k| int ret; 2199| 36.7k| if ((ret = (int) c1->type - (int) c2->type)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2199:9): [True: 2.06k, False: 34.7k] ------------------ 2200| 2.06k| { 2201| 2.06k| return ret; 2202| 2.06k| } 2203| 34.7k| if ((ret = (int) c1->subtype - (int) c2->subtype)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2203:9): [True: 15.4k, False: 19.2k] ------------------ 2204| 15.4k| { 2205| 15.4k| return ret; 2206| 15.4k| } 2207| 19.2k| ret = (int) c1->atnumber - (int) c2->atnumber; 2208| | 2209| 19.2k| return ret; 2210| 34.7k|} RegisterCPoints: 2223| 1.28k|{ 2224| 1.28k| int num_c = *pnum_c, i, i1, i2; 2225| 1.28k| AT_NUMB nGroupNumber = 0, nNewGroupNumber; 2226| | 2227| 1.28k| if (at[point1].c_point == at[point2].c_point) ------------------ | Branch (2227:9): [True: 893, False: 387] ------------------ 2228| 893| { 2229| 893| if (at[point1].c_point) ------------------ | Branch (2229:13): [True: 0, False: 893] ------------------ 2230| 0| { 2231| 0| return 0; 2232| 0| } 2233| 893| memset( c_group + num_c, 0, sizeof( c_group[0] ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 2234| 893| if (num_c < max_num_c) ------------------ | Branch (2234:13): [True: 893, False: 0] ------------------ 2235| 893| { 2236| 893| c_group[num_c].num[0] = CHARGED_CPOINT( at, point1 ) + CHARGED_CPOINT( at, point2 ); ------------------ | | 253| 893|#define CHARGED_CPOINT(X,i) ((X)[i].charge==1) ------------------ c_group[num_c].num[0] = CHARGED_CPOINT( at, point1 ) + CHARGED_CPOINT( at, point2 ); ------------------ | | 253| 893|#define CHARGED_CPOINT(X,i) ((X)[i].charge==1) ------------------ 2237| 893| c_group[num_c].num_CPoints += 2; 2238| 893| c_group[num_c].cGroupType = ctype; 2239| | /* get next available c-group number */ 2240| 968| for (i = 0; i < num_c; i++) ------------------ | Branch (2240:25): [True: 75, False: 893] ------------------ 2241| 75| { 2242| 75| if (nGroupNumber < c_group[i].nGroupNumber) ------------------ | Branch (2242:21): [True: 75, False: 0] ------------------ 2243| 75| { 2244| 75| nGroupNumber = c_group[i].nGroupNumber; 2245| 75| } 2246| 75| } 2247| 893| nGroupNumber++; 2248| 893| c_group[num_c].nGroupNumber = 2249| 893| at[point1].c_point = 2250| 893| at[point2].c_point = nGroupNumber; 2251| 893| *pnum_c = num_c + 1; 2252| | /* count protons */ 2253| 893| if (at[point1].num_H) ------------------ | Branch (2253:17): [True: 153, False: 740] ------------------ 2254| 153| { 2255| 153| c_group[num_c].num[1] ++; 2256| 153| } 2257| 740| else 2258| 740| { 2259| 740| if (at[point2].num_H) ------------------ | Branch (2259:21): [True: 58, False: 682] ------------------ 2260| 58| { 2261| 58| c_group[num_c].num[1] ++; 2262| 58| } 2263| 682| else 2264| 682| { 2265| 682| if (( at[point1].endpoint || at[point2].endpoint ) && t_group_info && t_group_info->t_group && t_group_info->num_t_groups) ------------------ | Branch (2265:27): [True: 0, False: 682] | Branch (2265:50): [True: 8, False: 674] | Branch (2265:75): [True: 8, False: 0] | Branch (2265:91): [True: 8, False: 0] | Branch (2265:116): [True: 8, False: 0] ------------------ 2266| 8| { 2267| | /* !!! add later !!! */ 2268| 8| } 2269| 682| } 2270| 740| } 2271| 893| return 1; 2272| 893| } 2273| | 2274| 0| return BNS_CPOINT_ERR; /* overflow */ ------------------ | | 56| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2275| 893| } 2276| | 2277| 387| if (at[point1].c_point > at[point2].c_point) ------------------ | Branch (2277:9): [True: 274, False: 113] ------------------ 2278| 274| { 2279| | /* make sure at[point1].c_point < at[point2].c_point */ 2280| 274| i = point1; 2281| 274| point1 = point2; 2282| 274| point2 = i; 2283| 274| } 2284| | 2285| 387| if (!at[point1].c_point) ------------------ | Branch (2285:9): [True: 355, False: 32] ------------------ 2286| 355| { 2287| | /* add a new c-endpoint to an existing c-group */ 2288| 355| nGroupNumber = at[point2].c_point; 2289| 406| for (i = 0; i < num_c; i++) ------------------ | Branch (2289:21): [True: 406, False: 0] ------------------ 2290| 406| { 2291| 406| if (nGroupNumber == c_group[i].nGroupNumber) ------------------ | Branch (2291:17): [True: 355, False: 51] ------------------ 2292| 355| { 2293| 355| at[point1].c_point = at[point2].c_point; 2294| 355| c_group[i].num_CPoints++; 2295| 355| c_group[i].num[0] += CHARGED_CPOINT( at, point1 ); ------------------ | | 253| 355|#define CHARGED_CPOINT(X,i) ((X)[i].charge==1) ------------------ 2296| 355| return 1; 2297| 355| } 2298| 406| } 2299| 0| return BNS_CPOINT_ERR; /* program error: c-group not found */ ------------------ | | 56| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2300| 355| } 2301| 32| else 2302| 32| { 2303| | /* merge two c-groups */ 2304| 32| nNewGroupNumber = at[point1].c_point; 2305| 32| nGroupNumber = at[point2].c_point; 2306| 108| for (i = 0, i1 = i2 = -1; i < num_c && ( i1 < 0 || i2 < 0 ); i++) ------------------ | Branch (2306:35): [True: 77, False: 31] | Branch (2306:50): [True: 35, False: 42] | Branch (2306:60): [True: 41, False: 1] ------------------ 2307| 76| { 2308| 76| if (nNewGroupNumber == c_group[i].nGroupNumber) ------------------ | Branch (2308:17): [True: 32, False: 44] ------------------ 2309| 32| { 2310| 32| i1 = i; 2311| 32| continue; 2312| 32| } 2313| 44| if (nGroupNumber == c_group[i].nGroupNumber) ------------------ | Branch (2313:17): [True: 32, False: 12] ------------------ 2314| 32| { 2315| 32| i2 = i; 2316| 32| continue; 2317| 32| } 2318| 44| } 2319| 32| if (i1 < 0 || i2 < 0) ------------------ | Branch (2319:13): [True: 0, False: 32] | Branch (2319:23): [True: 0, False: 32] ------------------ 2320| 0| { 2321| 0| return BNS_CPOINT_ERR; /* at least one not found */ ------------------ | | 56| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2322| 0| } 2323| | 2324| 32| c_group[i1].num[0] += c_group[i2].num[0]; 2325| 32| c_group[i1].num_CPoints += c_group[i2].num_CPoints; 2326| 32| num_c--; 2327| 32| if (num_c > i2) ------------------ | Branch (2327:13): [True: 1, False: 31] ------------------ 2328| 1| { 2329| 1| memmove(c_group + i2, c_group + i2 + 1, ((long long)num_c - i2) * sizeof(c_group[0])); /* djb-rwth: cast operators added */ 2330| 1| } 2331| 32| *pnum_c = num_c; 2332| | /* renumber c-groups */ 2333| 77| for (i = 0; i < num_c; i++) ------------------ | Branch (2333:21): [True: 45, False: 32] ------------------ 2334| 45| { 2335| 45| if (c_group[i].nGroupNumber > nGroupNumber) ------------------ | Branch (2335:17): [True: 1, False: 44] ------------------ 2336| 1| { 2337| 1| c_group[i].nGroupNumber--; 2338| 1| } 2339| 45| } 2340| | /* renumber c-points */ 2341| 276| for (i = 0; i < num_atoms; i++) ------------------ | Branch (2341:21): [True: 244, False: 32] ------------------ 2342| 244| { 2343| 244| if (at[i].c_point > nGroupNumber) ------------------ | Branch (2343:17): [True: 3, False: 241] ------------------ 2344| 3| { 2345| 3| at[i].c_point--; 2346| 3| } 2347| 241| else 2348| 241| { 2349| 241| if (at[i].c_point == nGroupNumber) ------------------ | Branch (2349:21): [True: 81, False: 160] ------------------ 2350| 81| { 2351| 81| at[i].c_point = nNewGroupNumber; 2352| 81| } 2353| 241| } 2354| 244| } 2355| 32| return 1; 2356| 32| } 2357| | 2358| 387|} MarkChargeGroups: 2369| 294k|{ 2370| 294k| int nNumChanges = 0; 2371| | 2372| 294k| if (c_group_info && c_group_info->c_candidate && c_group_info->max_num_candidates > 0) ------------------ | Branch (2372:9): [True: 294k, False: 0] | Branch (2372:25): [True: 109k, False: 184k] | Branch (2372:54): [True: 109k, False: 0] ------------------ 2373| 109k| { 2374| 109k| int i, i1, i2, i3, j, num_tested; 2375| 109k| C_CANDIDATE *c_candidate = c_group_info->c_candidate; 2376| 109k| int nMaxNumCandidates = c_group_info->max_num_candidates; 2377| 109k| int nNumCandidates = c_group_info->num_candidates; 2378| 109k| S_CHAR c_type, c_subtype; 2379| 109k| int iat1, iat2, ret, nDelta; 2380| | 2381| 109k| if (nNumCandidates == -1) ------------------ | Branch (2381:13): [True: 5.26k, False: 104k] ------------------ 2382| 5.26k| { 2383| 5.26k| nNumCandidates = 0; /* 2004-02-26 they could appear after t-group discovery */ 2384| | /*return 0;*/ 2385| 5.26k| } 2386| 109k| if (nNumCandidates == 0) ------------------ | Branch (2386:13): [True: 108k, False: 1.14k] ------------------ 2387| 108k| { 2388| 1.05M| for (i = 0, nNumCandidates = 0; i < num_atoms; i++) ------------------ | Branch (2388:45): [True: 941k, False: 108k] ------------------ 2389| 941k| { 2390| 941k| if (0 <= ( c_type = GetChargeType( at, i, &c_subtype ) )) ------------------ | Branch (2390:21): [True: 50.7k, False: 890k] ------------------ 2391| 50.7k| { 2392| 50.7k| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (2392:25): [True: 0, False: 50.7k] ------------------ 2393| 0| { 2394| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2395| 0| } 2396| 50.7k| c_candidate[nNumCandidates].atnumber = i; 2397| 50.7k| c_candidate[nNumCandidates].type = c_type; 2398| 50.7k| c_candidate[nNumCandidates].subtype = c_subtype; 2399| 50.7k| nNumCandidates++; 2400| 50.7k| } 2401| 941k| } 2402| 108k| if (nNumCandidates <= 1) ------------------ | Branch (2402:17): [True: 95.3k, False: 13.4k] ------------------ 2403| 95.3k| { 2404| 95.3k| c_group_info->num_candidates = -1; /* no candidate exists */ 2405| 95.3k| return 0; 2406| 95.3k| } 2407| 108k| } 2408| | /* sorting keys: (1) atom type (N,P); (2) uncharged=16/charged=0; (3) other; 2409| | atom-charged-N .... i1 2410| | ... 2411| | atom-charged-N 2412| | atom-neutral-N .... i2 2413| | ... 2414| | atom-neutral-N 2415| | atom-charged-P .... i3 ... i1 2416| | ... 2417| | atom-charged-P 2418| | atom-neutral-P ........... i2 2419| | ... 2420| | atom-neutral-P 2421| | end. ........... i3 2422| | */ 2423| | 2424| 14.6k| qsort( c_candidate, nNumCandidates, sizeof( c_candidate[0] ), CmpCCandidates ); 2425| | 2426| 14.6k| i1 = 0; 2427| 14.6k| num_tested = 0; 2428| | /* djb-rwth: removing redundant code */ 2429| | 2430| 19.4k| while (i1 < nNumCandidates) ------------------ | Branch (2430:16): [True: 15.1k, False: 4.25k] ------------------ 2431| 15.1k| { 2432| | /* the the first charged candidate of a new atom type */ 2433| 42.3k| for (; i1 < nNumCandidates && ( c_candidate[i1].subtype & C_SUBTYPE_NEUTRAL ); i1++) ------------------ | | 1993| 32.5k|#define C_SUBTYPE_NEUTRAL 16 ------------------ | Branch (2433:20): [True: 32.5k, False: 9.78k] | Branch (2433:43): [True: 27.1k, False: 5.38k] ------------------ 2434| 27.1k| { 2435| 27.1k| ; 2436| 27.1k| } 2437| 15.1k| if (i1 == nNumCandidates) ------------------ | Branch (2437:17): [True: 9.78k, False: 5.38k] ------------------ 2438| 9.78k| { 2439| 9.78k| break; /* not found */ 2440| 9.78k| } 2441| | 2442| | /* bypass other charged candidates of the same atom type */ 2443| 6.55k| for (i2 = i1 + 1; i2 < nNumCandidates && ------------------ | Branch (2443:31): [True: 5.97k, False: 583] ------------------ 2444| 5.97k| c_candidate[i2].type == c_candidate[i1].type && ------------------ | Branch (2444:19): [True: 5.65k, False: 318] ------------------ 2445| 5.65k| !( c_candidate[i2].subtype & C_SUBTYPE_NEUTRAL ); ------------------ | | 1993| 5.65k|#define C_SUBTYPE_NEUTRAL 16 ------------------ | Branch (2445:19): [True: 1.17k, False: 4.48k] ------------------ 2446| 5.38k| i2++) 2447| 1.17k| { 2448| 1.17k| ; 2449| 1.17k| } 2450| 5.38k| if (i2 == nNumCandidates) ------------------ | Branch (2450:17): [True: 583, False: 4.80k] ------------------ 2451| 583| { 2452| 583| break; /* no neutral candidates */ 2453| 583| } 2454| | 2455| | /* find next to the last neutral candidate of the same atom type */ 2456| 13.3k| for (i3 = i2; i3 < nNumCandidates && ------------------ | Branch (2456:28): [True: 9.11k, False: 4.25k] ------------------ 2457| 9.11k| c_candidate[i3].type == c_candidate[i1].type; ------------------ | Branch (2457:19): [True: 8.56k, False: 550] ------------------ 2458| 8.56k| i3++) 2459| 8.56k| { 2460| 8.56k| ; 2461| 8.56k| } 2462| | 2463| 4.80k| if (i3 == i2) ------------------ | Branch (2463:17): [True: 318, False: 4.48k] ------------------ 2464| 318| { 2465| | /* no neutral candidates found */ 2466| 318| if (i2 < nNumCandidates) ------------------ | Branch (2466:21): [True: 318, False: 0] ------------------ 2467| 318| { 2468| 318| i1 = i3; 2469| 318| continue; /* move to the next atom type */ 2470| 318| } 2471| 0| break; /* nothing more to do */ 2472| 318| } 2473| | 2474| | /* found charged candidates: i1...i2-1; neutral candidates: i2...i3-1 */ 2475| 9.98k| for (i = i1; i < i2; i++) ------------------ | Branch (2475:26): [True: 5.50k, False: 4.48k] ------------------ 2476| 5.50k| { 2477| 5.50k| iat1 = c_candidate[i].atnumber; 2478| 16.4k| for (j = i2; j < i3; j++) ------------------ | Branch (2478:30): [True: 10.9k, False: 5.49k] ------------------ 2479| 10.9k| { 2480| | /* check alt path at[iat1]=-=-...-at[iat2]; at[iat1] is charged, at[iat2] is neutral */ 2481| 10.9k| num_tested++; 2482| 10.9k| iat2 = c_candidate[j].atnumber; 2483| 10.9k| if (at[iat1].c_point && at[iat1].c_point == at[iat2].c_point) ------------------ | Branch (2483:25): [True: 4.48k, False: 6.46k] | Branch (2483:45): [True: 2.22k, False: 2.25k] ------------------ 2484| 2.22k| { 2485| 2.22k| continue; 2486| 2.22k| } 2487| | 2488| 8.72k| ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, iat1, iat2, ALT_PATH_MODE_CHARGE ); ------------------ | | 311| 8.72k|#define ALT_PATH_MODE_CHARGE 2 ------------------ 2489| | 2490| 8.72k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 8.72k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 8.72k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 8.72k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 8.72k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 8.72k, False: 0] | | | Branch (67:44): [True: 1, False: 8.72k] | | ------------------ ------------------ 2491| 1| { 2492| 1| return ret; 2493| 1| } 2494| 8.72k| if (ret & 1) ------------------ | Branch (2494:25): [True: 1.28k, False: 7.44k] ------------------ 2495| 1.28k| { 2496| 1.28k| nDelta = ( ret & ~3 ) >> 2; 2497| 1.28k| nNumChanges += ( ret & 2 ); 2498| | 2499| 1.28k| ret = RegisterCPoints( c_group_info->c_group, &c_group_info->num_c_groups, 2500| 1.28k| c_group_info->max_num_c_groups, t_group_info, 2501| 1.28k| iat1, iat2, c_candidate[i1].type, at, num_atoms ); 2502| | 2503| 1.28k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 1.28k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.28k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.28k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.28k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.28k, False: 0] | | | Branch (67:44): [True: 0, False: 1.28k] | | ------------------ ------------------ 2504| 0| { 2505| 0| return ret; 2506| 0| } 2507| 1.28k| if (nDelta) ------------------ | Branch (2507:29): [True: 0, False: 1.28k] ------------------ 2508| 0| { 2509| 0| goto quick_exit; 2510| 0| } 2511| 1.28k| } 2512| 8.72k| } 2513| 5.50k| } 2514| 4.48k| i1 = i3; 2515| 4.48k| } 2516| | 2517| 14.6k| quick_exit: 2518| 14.6k| if (c_group_info->num_candidates == 0) ------------------ | Branch (2518:13): [True: 11.6k, False: 3.00k] ------------------ 2519| 11.6k| { 2520| | /* first time: initialize */ 2521| 11.6k| c_group_info->num_candidates = num_tested ? nNumCandidates : -1; /* no candidate exists */ ------------------ | Branch (2521:44): [True: 3.23k, False: 8.37k] ------------------ 2522| 11.6k| } 2523| 14.6k| } 2524| | 2525| 199k| return nNumChanges; 2526| 294k|} GetSaltChargeType: 2534| 3.15M|{ 2535| | /* 2536| | type (returned value): 2537| | -1 => ignore 2538| | 0 => oxygen 2539| | subtype: 2540| | 1 = SALT_DONOR_H => has H 2541| | 2 = SALT_DONOR_Neg => has (-) charge 2542| | 4 = SALT_ACCEPTOR => may be an acceptor of H or (-), but not necessarily 2543| | 2544| | O-atom should be: 2545| | - a terminal atom 2546| | - connected to unsaturated, uncharged, non-radical atom C that has chemical valence 4: 2547| | H-donors: =CH-OH, =C(-X)-OH 2548| | possible H-acceptors: -CH=O, >C=O 2549| | H-acceptors are true if O is tautomeric 2550| | */ 2551| | 2552| 3.15M| int iC, tg, i, type; 2553| | 2554| 3.15M| *s_subtype = 0; /* initialize the output */ 2555| | /* check whether it is a candidate */ 2556| 3.15M| if (at[at_no].valence != 1 || ------------------ | Branch (2556:9): [True: 2.83M, False: 321k] ------------------ 2557| 321k| (at[at_no].radical && at[at_no].radical != RADICAL_SINGLET) || ------------------ | | 75| 52.5k|#define RADICAL_SINGLET 1 ------------------ | Branch (2557:11): [True: 52.5k, False: 269k] | Branch (2557:32): [True: 52.5k, False: 0] ------------------ 2558| 269k| at[at_no].charge < -1 || ------------------ | Branch (2558:10): [True: 327, False: 268k] ------------------ 2559| 268k| (at[at_no].charge > 0 && !at[at_no].c_point)) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2559:11): [True: 28.8k, False: 239k] | Branch (2559:35): [True: 28.8k, False: 3] ------------------ 2560| 2.91M| { 2561| 2.91M| return -1; 2562| 2.91M| } 2563| | 2564| 239k| if (at[at_no].el_number == EL_NUMBER_O || ------------------ | | 15| 479k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2564:9): [True: 41.2k, False: 198k] ------------------ 2565| 198k| at[at_no].el_number == EL_NUMBER_S || ------------------ | | 19| 438k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2565:10): [True: 30.2k, False: 168k] ------------------ 2566| 168k| at[at_no].el_number == EL_NUMBER_SE || ------------------ | | 23| 408k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2566:10): [True: 3.61k, False: 164k] ------------------ 2567| 164k| at[at_no].el_number == EL_NUMBER_TE) ------------------ | | 26| 164k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2567:10): [True: 3.17k, False: 161k] ------------------ 2568| 78.2k| { 2569| 78.2k| type = 0; /* terminal oxygen atom, needs more to be checked... */ 2570| 78.2k| } 2571| 161k| else 2572| 161k| { 2573| 161k| type = -1; /* ignore this atom */ 2574| 161k| } 2575| | 2576| 239k| if (type < 0 || ------------------ | Branch (2576:9): [True: 161k, False: 78.2k] ------------------ 2577| 78.2k| at[at_no].chem_bonds_valence + at[at_no].num_H != ------------------ | Branch (2577:10): [True: 401, False: 77.8k] ------------------ 2578| 78.2k| get_el_valence( at[at_no].el_number, at[at_no].charge, 0 )) 2579| 161k| { 2580| 161k| return -1; /* non-standard valence or not an oxygen */ 2581| 161k| } 2582| | 2583| 77.8k| iC = at[at_no].neighbor[0]; 2584| | 2585| 77.8k|#if ( SALT_WITH_PROTONS == 1 ) 2586| 77.8k| if (at[iC].el_number != EL_NUMBER_C || ------------------ | | 13| 155k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (2586:9): [True: 66.5k, False: 11.3k] ------------------ 2587| 11.3k| at[iC].chem_bonds_valence + at[iC].num_H != 4 || /* allow =C(H)-OH or -C(H)=O */ ------------------ | Branch (2587:10): [True: 1.80k, False: 9.55k] ------------------ 2588| 9.55k| at[iC].charge || ------------------ | Branch (2588:10): [True: 27, False: 9.53k] ------------------ 2589| 9.53k| (at[iC].radical && at[iC].radical != RADICAL_SINGLET) || ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2589:11): [True: 0, False: 9.53k] | Branch (2589:29): [True: 0, False: 0] ------------------ 2590| 9.53k| at[iC].valence == at[iC].chem_bonds_valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2590:10): [True: 1.18k, False: 8.34k] ------------------ 2591| 69.5k| { 2592| 69.5k| return -1; /* oxigen is connected to a wrong atom */ 2593| 69.5k| } 2594| |#else 2595| | if (at[iC].el_number != EL_NUMBER_C || 2596| | at[iC].num_H || 2597| | at[iC].chem_bonds_valence != 4 || /* allow only no H on C */ 2598| | at[iC].charge || 2599| | at[iC].radical && at[iC].radical != RADICAL_SINGLET || 2600| | at[iC].valence == at[iC].chem_bonds_valence) 2601| | { 2602| | return -1; /* oxigen is connected to a wrong atom */ 2603| | } 2604| |#endif 2605| 8.34k| if (( tg = at[at_no].endpoint ) && t_group_info && t_group_info->t_group) ------------------ | Branch (2605:9): [True: 4.65k, False: 3.69k] | Branch (2605:40): [True: 4.65k, False: 0] | Branch (2605:56): [True: 4.65k, False: 0] ------------------ 2606| 4.65k| { 2607| | /* O-atom is in a tautomeric group */ 2608| 4.81k| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (2608:21): [True: 4.81k, False: 0] ------------------ 2609| 4.81k| { 2610| 4.81k| if (tg == t_group_info->t_group[i].nGroupNumber) ------------------ | Branch (2610:17): [True: 4.65k, False: 161] ------------------ 2611| 4.65k| { 2612| | /* 2613| | t_group_info->t_group[i].num[0] = number of attached H-atoms and negative charges 2614| | t_group_info->t_group[i].num[1] = number of attached negative charges 2615| | */ 2616| 4.65k| if (t_group_info->t_group[i].num[0] > t_group_info->t_group[i].num[1]) ------------------ | Branch (2616:21): [True: 3.67k, False: 974] ------------------ 2617| 3.67k| { 2618| 3.67k| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 62| 3.67k|#define SALT_DONOR_H 1 ------------------ 2619| 3.67k| } 2620| 4.65k| if (t_group_info->t_group[i].num[1]) ------------------ | Branch (2620:21): [True: 1.32k, False: 3.32k] ------------------ 2621| 1.32k| { 2622| 1.32k| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 63| 1.32k|#define SALT_DONOR_Neg 2 ------------------ 2623| 1.32k| } 2624| 4.65k| *s_subtype |= SALT_ACCEPTOR; /* there is always an acceptor in a t-group */ ------------------ | | 64| 4.65k|#define SALT_ACCEPTOR 4 ------------------ 2625| 4.65k| return type; 2626| 4.65k| } 2627| 4.81k| } 2628| 0| return -1; /* error: t-group not found */ 2629| 4.65k| } 2630| | 2631| | /* O is not not in a tautomeric group */ 2632| | /* assume valence(O-) < valence(O) < valence(O+) */ 2633| 3.69k| if (at[at_no].charge == -1) ------------------ | Branch (2633:9): [True: 351, False: 3.34k] ------------------ 2634| 351| { 2635| 351| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 63| 351|#define SALT_DONOR_Neg 2 ------------------ 2636| 351| } 2637| 3.69k| if (at[at_no].charge <= 0 && at[at_no].num_H) ------------------ | Branch (2637:9): [True: 3.69k, False: 0] | Branch (2637:34): [True: 1.91k, False: 1.78k] ------------------ 2638| 1.91k| { 2639| 1.91k| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 62| 1.91k|#define SALT_DONOR_H 1 ------------------ 2640| 1.91k| } 2641| 3.69k| if (at[at_no].charge == 0 && at[at_no].chem_bonds_valence == 2) ------------------ | Branch (2641:9): [True: 3.34k, False: 351] | Branch (2641:34): [True: 1.44k, False: 1.90k] ------------------ 2642| 1.44k| { 2643| 1.44k| *s_subtype |= SALT_ACCEPTOR; ------------------ | | 64| 1.44k|#define SALT_ACCEPTOR 4 ------------------ 2644| 1.44k| } 2645| | /* since O cannot be a charge point, the following cannot happen: */ 2646| 3.69k| if (at[at_no].charge == 1 && at[at_no].c_point && at[at_no].chem_bonds_valence == 2 && at[at_no].num_H) ------------------ | Branch (2646:9): [True: 0, False: 3.69k] | Branch (2646:34): [True: 0, False: 0] | Branch (2646:55): [True: 0, False: 0] | Branch (2646:92): [True: 0, False: 0] ------------------ 2647| 0| { 2648| 0| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 62| 0|#define SALT_DONOR_H 1 ------------------ 2649| 0| } 2650| | 2651| 3.69k| return type; 2652| 8.34k|} bDoNotMergeNonTautAtom: 2657| 32.3k|{ 2658| 32.3k| if (at[at_no].el_number == EL_NUMBER_N) ------------------ | | 14| 32.3k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2658:9): [True: 20.9k, False: 11.4k] ------------------ 2659| 20.9k| { 2660| 20.9k| return 1; 2661| 20.9k| } 2662| 11.4k| return 0; 2663| 32.3k|} GetOtherSaltChargeType: 2672| 3.14M|{ 2673| | /* 2674| | type (returned value): 2675| | -1 => ignore 2676| | 1 => not an oxygen 2677| | subtype: 2678| | 1 = SALT_DONOR_H => has H 2679| | 2 = SALT_DONOR_Neg => has (-) charge 2680| | 4 = SALT_ACCEPTOR => may be an acceptor of H or (-), but not necessarily 2681| | 2682| | the atom should be: 2683| | - a tautomeric endpoint atom 2684| | - connected to possible centerpoint atom 2685| | 2686| | another description of the atom searched here: 2687| | 2688| | any possibly tautomeric atom adjacent to a possibly centerpoint 2689| | that has at least one double bond (possibly if positively charged); 2690| | if eif.cAcceptor then the bond between the atom and the centerpoint must be possibly double 2691| | if eif.cAcceptor then the bond must be possibly single 2692| | Donors that belong to a t-group are also acceptors 2693| | */ 2694| | 2695| 3.14M| int tg, i, j, type, endpoint_valence, num_centerpoints, bond_type, centerpoint; 2696| 3.14M| ENDPOINT_INFO eif; 2697| | 2698| 3.14M| *s_subtype = 0; /* initialize the output */ 2699| 3.14M| if (!bAccept_O /* only N */ && ------------------ | Branch (2699:9): [True: 0, False: 3.14M] ------------------ 2700| 0| ( at[at_no].el_number == EL_NUMBER_O || ------------------ | | 15| 0|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2700:11): [True: 0, False: 0] ------------------ 2701| 0| at[at_no].el_number == EL_NUMBER_S || ------------------ | | 19| 0|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2701:11): [True: 0, False: 0] ------------------ 2702| 0| at[at_no].el_number == EL_NUMBER_SE || ------------------ | | 23| 0|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2702:11): [True: 0, False: 0] ------------------ 2703| 0| at[at_no].el_number == EL_NUMBER_TE )) ------------------ | | 26| 0|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2703:11): [True: 0, False: 0] ------------------ 2704| 0| { 2705| 0| return -1; /* we are not looking for oxygen here */ 2706| 0| } 2707| | 2708| 3.14M| type = 1; 2709| 3.14M| if (!( endpoint_valence = nGetEndpointInfo( at, at_no, &eif ) )) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (2709:9): [True: 2.98M, False: 160k] ------------------ 2710| 2.98M| { 2711| 2.98M| return -1; /* not a possible endpoint */ 2712| 2.98M| } 2713| 160k| else 2714| 160k| { 2715| | /* at[at_no] is not not in a tautomeric group; use eif previously filled out by nGetEndpointInfo */ 2716| | /* check whether there is adjacent atom-candidate for a centerpoint */ 2717| 160k| num_centerpoints = 0; 2718| 221k| for (j = 0; j < at[at_no].valence; j++) ------------------ | Branch (2718:21): [True: 181k, False: 40.3k] ------------------ 2719| 181k| { 2720| 181k| bond_type = (int) at[at_no].bond_type[j] & BOND_TYPE_MASK; ------------------ | | 189| 181k|#define BOND_TYPE_MASK 0x0f ------------------ 2721| 181k| centerpoint = (int) at[at_no].neighbor[j]; /* a centerpoint candidate */ 2722| 181k| if (( (eif.cAcceptor && ( bond_type == BOND_DOUBLE || ------------------ | | 178| 133k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 267k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (2722:20): [True: 133k, False: 47.5k] | Branch (2722:39): [True: 77.1k, False: 56.7k] ------------------ 2723| 56.7k| bond_type == BOND_ALTERN || /* possibly double */ ------------------ | | 180| 56.7k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 190k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2723:38): [True: 11.5k, False: 45.2k] ------------------ 2724| 45.2k| bond_type == BOND_ALT12NS || ------------------ | | 186| 179k|#define BOND_ALT12NS 9 ------------------ | Branch (2724:38): [True: 8.92k, False: 36.3k] ------------------ 2725| 36.3k| bond_type == BOND_TAUTOM )) || ------------------ | | 185| 36.3k|#define BOND_TAUTOM 8 ------------------ | Branch (2725:38): [True: 18.9k, False: 17.3k] ------------------ 2726| 64.9k| (eif.cDonor && ( bond_type == BOND_SINGLE || ------------------ | | 177| 47.5k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 95.0k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (2726:20): [True: 47.5k, False: 17.3k] | Branch (2726:36): [True: 30.4k, False: 17.0k] ------------------ 2727| 17.0k| bond_type == BOND_ALTERN || /* possibly single */ ------------------ | | 180| 17.0k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 64.6k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2727:35): [True: 227, False: 16.8k] ------------------ 2728| 16.8k| bond_type == BOND_ALT12NS || ------------------ | | 186| 64.3k|#define BOND_ALT12NS 9 ------------------ | Branch (2728:35): [True: 341, False: 16.4k] ------------------ 2729| 16.4k| bond_type == BOND_TAUTOM )) ) && ------------------ | | 185| 16.4k|#define BOND_TAUTOM 8 ------------------ | Branch (2729:35): [True: 16.4k, False: 3] ------------------ 2730| 164k| ( at[centerpoint].chem_bonds_valence > at[centerpoint].valence || ------------------ | Branch (2730:37): [True: 141k, False: 22.2k] ------------------ 2731| | /* check for possible endpoint added 2004-02-24 */ 2732| 22.2k| (at[centerpoint].chem_bonds_valence == at[centerpoint].valence && ------------------ | Branch (2732:38): [True: 22.2k, False: 0] ------------------ 2733| 22.2k| ( at[centerpoint].endpoint || at[centerpoint].c_point )) /* tautomerism or charge may increment at[centerpoint].chem_bonds_valence*/ ) && ------------------ | Branch (2733:39): [True: 1.08k, False: 21.1k] | Branch (2733:67): [True: 371, False: 20.7k] ------------------ 2734| 143k| is_centerpoint_elem( at[centerpoint].el_number )) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2734:18): [True: 119k, False: 23.4k] ------------------ 2735| 119k| { 2736| 119k| num_centerpoints++; 2737| 119k| break; /* at least one possibly centerpoint neighbor has been found */ 2738| 119k| } 2739| 181k| } 2740| 160k| if (!num_centerpoints) ------------------ | Branch (2740:13): [True: 40.3k, False: 119k] ------------------ 2741| 40.3k| { 2742| 40.3k| return -1; 2743| 40.3k| } 2744| | /* moved here from just after "type = 1;" line 2004-02-26 */ 2745| 119k| if (( tg = at[at_no].endpoint ) && t_group_info && t_group_info->t_group) ------------------ | Branch (2745:13): [True: 34.2k, False: 85.6k] | Branch (2745:44): [True: 34.2k, False: 0] | Branch (2745:60): [True: 34.2k, False: 0] ------------------ 2746| 34.2k| { 2747| | /* atom is in a tautomeric group */ 2748| 35.6k| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (2748:25): [True: 35.6k, False: 0] ------------------ 2749| 35.6k| { 2750| 35.6k| if (tg == t_group_info->t_group[i].nGroupNumber) ------------------ | Branch (2750:21): [True: 34.2k, False: 1.34k] ------------------ 2751| 34.2k| { 2752| | /* 2753| | t_group_info->t_group[i].num[0] = number of attached H-atoms and negative charges 2754| | t_group_info->t_group[i].num[1] = number of attached negative charges 2755| | */ 2756| 34.2k| if (t_group_info->t_group[i].num[0] > t_group_info->t_group[i].num[1]) ------------------ | Branch (2756:25): [True: 20.2k, False: 14.0k] ------------------ 2757| 20.2k| { 2758| 20.2k| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 62| 20.2k|#define SALT_DONOR_H 1 ------------------ 2759| 20.2k| } 2760| 34.2k| if (t_group_info->t_group[i].num[1]) ------------------ | Branch (2760:25): [True: 20.0k, False: 14.2k] ------------------ 2761| 20.0k| { 2762| 20.0k| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 63| 20.0k|#define SALT_DONOR_Neg 2 ------------------ 2763| 20.0k| } 2764| 34.2k| *s_subtype |= SALT_ACCEPTOR; /* there is always an acceptor in a t-group */ ------------------ | | 64| 34.2k|#define SALT_ACCEPTOR 4 ------------------ 2765| 34.2k| return type; 2766| 34.2k| } 2767| 35.6k| } 2768| 0| return -1; /* error: t-group not found */ 2769| 34.2k| } 2770| | 2771| 85.6k| if (eif.cAcceptor) ------------------ | Branch (2771:13): [True: 78.6k, False: 6.99k] ------------------ 2772| 78.6k| { 2773| 78.6k| *s_subtype |= SALT_ACCEPTOR; ------------------ | | 64| 78.6k|#define SALT_ACCEPTOR 4 ------------------ 2774| 78.6k| } 2775| 85.6k| if (eif.cDonor) ------------------ | Branch (2775:13): [True: 6.99k, False: 78.6k] ------------------ 2776| 6.99k| { 2777| 6.99k| if (at[at_no].charge == -1) ------------------ | Branch (2777:17): [True: 5.29k, False: 1.69k] ------------------ 2778| 5.29k| { 2779| 5.29k| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 63| 5.29k|#define SALT_DONOR_Neg 2 ------------------ 2780| 5.29k| } 2781| 6.99k| if (at[at_no].num_H) ------------------ | Branch (2781:17): [True: 1.98k, False: 5.01k] ------------------ 2782| 1.98k| { 2783| 1.98k| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 62| 1.98k|#define SALT_DONOR_H 1 ------------------ 2784| 1.98k| } 2785| 6.99k| } 2786| 85.6k| } 2787| | 2788| 85.6k| return type; 2789| 3.14M|} GetOtherSaltType: 2794| 3.02M|{ 2795| | /* 2796| | type (returned value): 2797| | -1 => ignore 2798| | 2 => found: SH 2799| | proton donor -CH2-SH, >CH-SH, >C< S(-) 2800| | proton acceptor -CH2-S(-), >CH-S(-), >C< 2801| | subtype: 2802| | 1 = SALT_DONOR_H => has H 2803| | 2 = SALT_DONOR_Neg => has (-) charge 2804| | 4 = SALT_ACCEPTOR => may be an acceptor of H or (-), but not necessarily 2805| | 2806| | non-O-atom should be: 2807| | - a tautomeric endpoint atom 2808| | - connected to possible middle point atom 2809| | */ 2810| | 2811| 3.02M| int type, endpoint_valence, centerpoint; /* djb-rwth: removing redundant variables */ 2812| 3.02M| ENDPOINT_INFO eif; 2813| | 2814| 3.02M| if (at[at_no].valence != 1 || at[at_no].chem_bonds_valence != 1 || ------------------ | Branch (2814:9): [True: 2.77M, False: 251k] | Branch (2814:35): [True: 101k, False: 150k] ------------------ 2815| 150k| 1 != ( at[at_no].num_H == 1 ) + ( at[at_no].charge == -1 )) ------------------ | Branch (2815:10): [True: 111k, False: 39.0k] ------------------ 2816| 2.98M| { 2817| 2.98M| return -1; 2818| 2.98M| } 2819| | 2820| 39.0k| *s_subtype = 0; /* initialize the output */ 2821| 39.0k| if (!( at[at_no].el_number == EL_NUMBER_S || ------------------ | | 19| 78.0k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (2821:12): [True: 6.44k, False: 32.5k] ------------------ 2822| 32.5k| at[at_no].el_number == EL_NUMBER_SE || ------------------ | | 23| 71.5k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (2822:12): [True: 810, False: 31.7k] ------------------ 2823| 31.7k| at[at_no].el_number == EL_NUMBER_TE )) ------------------ | | 26| 31.7k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (2823:12): [True: 902, False: 30.8k] ------------------ 2824| 30.8k| { 2825| 30.8k| return -1; /* we are not looking for oxygen here */ 2826| 30.8k| } 2827| | 2828| 8.15k| type = 2; /* non-tautomeric p-donor or acceptor: C-SH, C-S(-) */ 2829| | 2830| 8.15k| if (!( endpoint_valence = nGetEndpointInfo( at, at_no, &eif ) ) || ------------------ | Branch (2830:9): [True: 74, False: 8.07k] ------------------ 2831| 8.07k| (eif.cMoveableCharge && !at[at_no].c_point) || !eif.cDonor || eif.cAcceptor) /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (2831:11): [True: 0, False: 8.07k] | Branch (2831:34): [True: 0, False: 0] | Branch (2831:57): [True: 0, False: 8.07k] | Branch (2831:72): [True: 0, False: 8.07k] ------------------ 2832| 74| { 2833| 74| return -1; /* not a possible -SH or -S(-) */ 2834| 74| } 2835| 8.07k| else 2836| 8.07k| { 2837| | /* at[at_no] is not not in a tautomeric group; use eif previously filled out by nGetEndpointInfo */ 2838| | /* check whether there is adjacent atom-candidate for a centerpoint */ 2839| 8.07k| centerpoint = (int) at[at_no].neighbor[0]; 2840| | /* djb-rwth: removing redundant code */ 2841| 8.07k| if (at[centerpoint].el_number != EL_NUMBER_C || ------------------ | | 13| 16.1k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (2841:13): [True: 6.31k, False: 1.76k] ------------------ 2842| 1.76k| at[centerpoint].charge || ------------------ | Branch (2842:14): [True: 435, False: 1.33k] ------------------ 2843| 1.33k| (at[centerpoint].radical && at[centerpoint].radical != RADICAL_SINGLET) || ------------------ | | 75| 258|#define RADICAL_SINGLET 1 ------------------ | Branch (2843:15): [True: 258, False: 1.07k] | Branch (2843:42): [True: 258, False: 0] ------------------ 2844| 1.07k| at[centerpoint].valence != at[centerpoint].chem_bonds_valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2844:14): [True: 0, False: 1.07k] ------------------ 2845| 7.00k| { 2846| 7.00k| return -1; /* not a carbon with all single bonds */ 2847| 7.00k| } 2848| 1.07k| if (at[at_no].num_H == 1) ------------------ | Branch (2848:13): [True: 820, False: 255] ------------------ 2849| 820| { 2850| 820| *s_subtype |= SALT_p_DONOR; ------------------ | | 65| 820|#define SALT_p_DONOR 8 /* >C-SH */ ------------------ 2851| 820| } 2852| 255| else 2853| 255| { 2854| 255| if (at[at_no].charge == -1) ------------------ | Branch (2854:17): [True: 255, False: 0] ------------------ 2855| 255| { 2856| 255| *s_subtype |= SALT_p_ACCEPTOR; ------------------ | | 66| 255|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ ------------------ 2857| 255| } 2858| 0| else 2859| 0| { 2860| 0| return -1; 2861| 0| } 2862| 255| } 2863| 1.07k| } 2864| | 2865| 1.07k| return type; 2866| 8.15k|} comp_candidates: 2896| 1.55k|{ 2897| 1.55k| const S_CANDIDATE *s1 = (const S_CANDIDATE *) a1; 2898| 1.55k| const S_CANDIDATE *s2 = (const S_CANDIDATE *) a2; 2899| 1.55k| int ret; 2900| 1.55k| if (s1->type >= 0 /* enabled < */ && s2->type < 0 /* disabled */) ------------------ | Branch (2900:9): [True: 1.17k, False: 380] | Branch (2900:42): [True: 528, False: 649] ------------------ 2901| 528| { 2902| 528| return -1; /* enabled goes first */ 2903| 528| } 2904| 1.02k| if (s1->type < 0 /* disabled > */ && s2->type >= 0 /* enabled */) ------------------ | Branch (2904:9): [True: 380, False: 649] | Branch (2904:42): [True: 114, False: 266] ------------------ 2905| 114| { 2906| 114| return 1; 2907| 114| } 2908| 915| if (s1->endpoint && !s2->endpoint) ------------------ | Branch (2908:9): [True: 435, False: 480] | Branch (2908:25): [True: 124, False: 311] ------------------ 2909| 124| { 2910| 124| return -1; /* tautomeric goes first; only tautomeric may be disabled */ 2911| 124| } 2912| 791| if (!s1->endpoint && s2->endpoint) ------------------ | Branch (2912:9): [True: 480, False: 311] | Branch (2912:26): [True: 50, False: 430] ------------------ 2913| 50| { 2914| 50| return 1; /* tautomeric goes first; only tautomeric may be disabled */ 2915| 50| } 2916| 741| if (s1->endpoint && s2->endpoint && ( ret = (int) s1->endpoint - (int) s2->endpoint )) ------------------ | Branch (2916:9): [True: 311, False: 430] | Branch (2916:25): [True: 311, False: 0] | Branch (2916:41): [True: 99, False: 212] ------------------ 2917| 99| { 2918| 99| return ret; 2919| 99| } 2920| | 2921| 642| return (int) s1->atnumber - (int) s2->atnumber; 2922| 741|} MarkSaltChargeGroups2: 2934| 252k|{ 2935| | /* BNS_EDGE_FORBIDDEN_TEMP */ 2936| 252k|#define ALT_PATH_FOUND (MAX_ATOMS+1) 2937| 252k|#define NO_ENDPOINT (MAX_ATOMS+2) /* the two defines must be different */ 2938| 252k|#define DISABLE_CANDIDATE 10 2939| 252k|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] 2940| 252k|#define ACCEPTOR_PAIR 1 2941| 252k|#define DONOR_PAIR 2 2942| | 2943| 252k| int nNumOtherChanges = 0, nTotNumChanges = 0; /* djb-rwth: removing redundant variables */ 2944| 252k| S_CHAR *cPair = NULL; 2945| 252k| T_ENDPOINT *EndPoint = NULL; 2946| 252k| if (s_group_info && s_group_info->s_candidate && s_group_info->max_num_candidates > 0) ------------------ | Branch (2946:9): [True: 252k, False: 0] | Branch (2946:25): [True: 252k, False: 0] | Branch (2946:54): [True: 252k, False: 0] ------------------ 2947| 252k| { 2948| 252k| int i, j, i1, j1; 2949| 252k| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 2950| 252k| int nMaxNumCandidates = s_group_info->max_num_candidates; 2951| 252k| int nNumCandidates = s_group_info->num_candidates; 2952| 252k| int nNumOtherCandidates; /* djb-rwth: removing redundant code */ 2953| | /* djb-rwth: removing redundant variables */ 2954| 252k| int nNumLeftCandidates = 0; 2955| 252k| int nNumMarkedCandidates = 0; 2956| 252k| int s_type, s_subtype; 2957| 252k| int ret, nDelta; 2958| 252k| int bHardAddedRemovedProtons = t_group_info && ( t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT ); ------------------ | | 172| 252k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 252k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 173| 252k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 252k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 174| 252k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 151| 252k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (2958:49): [True: 252k, False: 0] | Branch (2958:65): [True: 176, False: 251k] ------------------ 2959| | 2960| 252k| int s_subtype_all = 0; 2961| 252k| int nDonorPairs, nAcceptorPairs, nCurDonorPairs, nCurAcceptorPairs, bAlreadyTested; 2962| | /* 2963| | ENDPOINT_INFO eif; 2964| | */ 2965| | 2966| 252k|#if ( IGNORE_TGROUP_WITHOUT_H == 1 ) 2967| 252k| int bTGroupHasNegativeChargesOnly = 1; 2968| 252k|#endif 2969| | /*return 0;*/ /* debug only */ 2970| | 2971| | /* djb-rwth: removing redundant code */ 2972| | 2973| 252k| if (nNumCandidates <= -2 || !t_group_info || !t_group_info->t_group) ------------------ | Branch (2973:13): [True: 0, False: 252k] | Branch (2973:37): [True: 0, False: 252k] | Branch (2973:54): [True: 0, False: 252k] ------------------ 2974| 0| { 2975| 0| return 0; 2976| 0| } 2977| | 2978| | /*************************************************************************/ 2979| | /* Find all candidates including those with differen s_type (other type) */ 2980| | /*************************************************************************/ 2981| 1.30M| for (i = 0, nNumCandidates = nNumOtherCandidates = 0; i < num_atoms; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (2981:63): [True: 1.05M, False: 252k] ------------------ 2982| 1.05M| { 2983| 1.05M| if (0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (2983:17): [True: 2.73k, False: 1.04M] ------------------ 2984| | /* -C=O or =C-OH, O = S, Se, Te */ 2985| 1.04M| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1/* bAccept_O*/ ) ) || ------------------ | Branch (2985:18): [True: 39.9k, False: 1.00M] ------------------ 2986| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above */ 2987| 1.00M| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) || ------------------ | Branch (2987:18): [True: 350, False: 1.00M] ------------------ 2988| 1.00M| ( bHardAddedRemovedProtons && 4 == ( s_type = bIsHardRemHCandidate( at, i, &s_subtype ) ) ) ------------------ | Branch (2988:20): [True: 565, False: 1.00M] | Branch (2988:48): [True: 99, False: 466] ------------------ 2989| | /* >C-SH, >C-S(-); S=S,Se,Te */ 2990| 1.05M| ) 2991| 43.0k| { 2992| | 2993| 43.0k| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (2993:21): [True: 0, False: 43.0k] ------------------ 2994| 0| { 2995| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2996| 0| } 2997| 43.0k| s_candidate[nNumCandidates].atnumber = i; 2998| 43.0k| s_candidate[nNumCandidates].type = s_type; 2999| 43.0k| s_candidate[nNumCandidates].subtype = s_subtype; 3000| 43.0k| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 3001| 43.0k| nNumCandidates++; 3002| 43.0k| nNumOtherCandidates += ( 1 == s_type ); 3003| 43.0k| s_subtype_all |= s_subtype; 3004| | /* djb-rwth: removing redundant code */ 3005| 43.0k| } 3006| 1.05M| } 3007| | 3008| 252k| if (nNumCandidates <= 1 || /* TG_FLAG_ALLOW_NO_NEGTV_O <=> CHARGED_SALTS_ONLY=0 */ ------------------ | Branch (3008:13): [True: 238k, False: 13.4k] ------------------ 3009| 13.4k| !( s_subtype_all & SALT_ACCEPTOR ) || ------------------ | | 64| 13.4k|#define SALT_ACCEPTOR 4 ------------------ | Branch (3009:14): [True: 136, False: 13.3k] ------------------ 3010| 13.3k| ( ( ( t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O ) || ------------------ | | 923| 13.3k|#define TG_FLAG_ALLOW_NO_NEGTV_O 0x00000020 /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */ ------------------ | Branch (3010:14): [True: 12.7k, False: 570] | Branch (3010:18): [True: 0, False: 13.3k] ------------------ 3011| 13.3k| ( t_group_info->bTautFlagsDone & TG_FLAG_FOUND_SALT_CHARGES_DONE ) || ------------------ | | 980| 13.3k|#define TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */ ------------------ | Branch (3011:14): [True: 0, False: 13.3k] ------------------ 3012| 13.3k| ( t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT ) ) ? ------------------ | | 172| 13.3k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 13.3k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 173| 13.3k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 13.3k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 174| 13.3k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 151| 13.3k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (3012:18): [True: 175, False: 13.1k] ------------------ 3013| 175| !( s_subtype_all & ( SALT_DONOR ) ) : ------------------ | | 70| 175|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 63| 175|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 62| 175|#define SALT_DONOR_H 1 | | ------------------ ------------------ 3014| 13.3k| ( !( s_subtype_all & SALT_DONOR_Neg ) || nNumOtherCandidates == nNumCandidates ) ) ------------------ | | 63| 13.1k|#define SALT_DONOR_Neg 2 ------------------ | Branch (3014:18): [True: 9.89k, False: 3.24k] | Branch (3014:57): [True: 2.80k, False: 436] ------------------ 3015| 252k| ) 3016| 251k| { 3017| 251k| s_group_info->num_candidates = 0; /* no candidate exists */ 3018| 251k| return 0; 3019| 251k| } 3020| | 3021| 570| if (!( s_subtype_all & ( SALT_DONOR_Neg ) )) ------------------ | | 63| 570|#define SALT_DONOR_Neg 2 ------------------ | Branch (3021:13): [True: 74, False: 496] ------------------ 3022| 74| { 3023| 74| t_group_info->bTautFlagsDone |= TG_FLAG_ALLOW_NO_NEGTV_O_DONE; ------------------ | | 968| 74|#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040 ------------------ 3024| 74| } 3025| | 3026| | /************************************************************************************/ 3027| | /* Mark redundant candidates so that only one candidate from one t-group is left in */ 3028| | /************************************************************************************/ 3029| 2.35k| for (i = 0; i < nNumCandidates; i++) ------------------ | Branch (3029:21): [True: 1.78k, False: 570] ------------------ 3030| 1.78k| { 3031| | /* djb-rwth: fixing oss-fuzz issue #45059 */ 3032| 1.78k| if ((nNumCandidates < nMaxNumCandidates) && (2 == s_candidate[nNumCandidates].type)) ------------------ | Branch (3032:17): [True: 1.77k, False: 11] | Branch (3032:57): [True: 0, False: 1.77k] ------------------ 3033| 0| { 3034| 0| s_candidate[i].type -= DISABLE_CANDIDATE; /* disable >C-SH candidates */ ------------------ | | 2938| 0|#define DISABLE_CANDIDATE 10 ------------------ 3035| 0| nNumLeftCandidates++; /* count rejected */ 3036| 0| continue; 3037| 0| } 3038| 1.78k| if (s_candidate[i].endpoint) ------------------ | Branch (3038:17): [True: 1.13k, False: 644] ------------------ 3039| 1.13k| { 3040| 1.46k| for (j = i - 1; 0 <= j; j--) ------------------ | Branch (3040:33): [True: 1.00k, False: 467] ------------------ 3041| 1.00k| { 3042| 1.00k| if (s_candidate[i].endpoint == s_candidate[j].endpoint) ------------------ | Branch (3042:25): [True: 670, False: 332] ------------------ 3043| 670| { 3044| 670| s_candidate[i].type -= DISABLE_CANDIDATE; /* disable subsequent redundant */ ------------------ | | 2938| 670|#define DISABLE_CANDIDATE 10 ------------------ 3045| 670| nNumLeftCandidates++; /* count rejected */ 3046| 670| break; 3047| 670| } 3048| 1.00k| } 3049| 1.13k| } 3050| 1.78k| } 3051| | 3052| 570| nNumLeftCandidates = nNumCandidates - nNumLeftCandidates; /* subtract num. rejected from the total */ 3053| 570| s_group_info->num_candidates = 0; /* reinit next time */ 3054| | /*********************************************************************/ 3055| | /* reorder so that all disabled are at the end, tautomeric are first */ 3056| | /*********************************************************************/ 3057| | 3058| 570| qsort( s_candidate, nNumCandidates, sizeof( s_candidate[0] ), comp_candidates ); 3059| | 3060| 570| if (nNumLeftCandidates) /* djb-rwth: avoiding zero-length allocation */ ------------------ | Branch (3060:13): [True: 570, False: 0] ------------------ 3061| 570| cPair = (S_CHAR *) inchi_calloc( (long long)nNumLeftCandidates * (long long)nNumLeftCandidates, sizeof( cPair[0] ) ); /* djb-rwth: cast operators added */ ------------------ | | 1146| 570|#define inchi_calloc calloc ------------------ 3062| 570| if (!cPair) ------------------ | Branch (3062:13): [True: 0, False: 570] ------------------ 3063| 0| { 3064| | /*printf("BNS_OUT_OF_RAM-6\n");*/ 3065| 0| nTotNumChanges = BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3066| 0| goto quick_exit; 3067| 0| } 3068| 570| nDonorPairs = nAcceptorPairs = 0; 3069| | 3070| | /**********************************************************************/ 3071| | /* Find whether we have at least one donor pair and one acceptor pair */ 3072| | /**********************************************************************/ 3073| 1.65k| for (i = 0; i < nNumLeftCandidates; i++) ------------------ | Branch (3073:21): [True: 1.10k, False: 553] ------------------ 3074| 1.10k| { 3075| 1.10k| nCurDonorPairs = nCurAcceptorPairs = 0; 3076| 3.04k| for (j = 0; j <= i; j++) ------------------ | Branch (3076:25): [True: 1.95k, False: 1.08k] ------------------ 3077| 1.95k| { 3078| 1.95k| if (i == j && !s_candidate[i].endpoint) ------------------ | Branch (3078:21): [True: 1.08k, False: 876] | Branch (3078:31): [True: 616, False: 467] ------------------ 3079| 616| { 3080| 616| continue; /* same non-taut atom. However, success for i==j means * 3081| | * that the whole tautomeric group may donate or accept 2H */ 3082| 616| } 3083| | /* check for acceptor pair */ 3084| 1.34k| if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 64| 1.34k|#define SALT_ACCEPTOR 4 ------------------ if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 64| 1.13k|#define SALT_ACCEPTOR 4 ------------------ | Branch (3084:21): [True: 1.13k, False: 208] | Branch (3084:67): [True: 1.00k, False: 132] ------------------ 3085| 1.00k| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (3085:21): [True: 239, False: 764] ------------------ 3086| 1.00k| s_candidate[j].atnumber, ALT_PATH_MODE_ADD2H_TST ) )) ------------------ | | 317| 1.00k|#define ALT_PATH_MODE_ADD2H_TST 8 /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */ ------------------ 3087| 239| { 3088| 239| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 239|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 239|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 239|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 239|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 239, False: 0] | | | Branch (67:44): [True: 0, False: 239] | | ------------------ ------------------ 3089| 0| { 3090| 0| nTotNumChanges = ret; 3091| 0| goto quick_exit; 3092| 0| } 3093| 239| if (ret & 1) ------------------ | Branch (3093:25): [True: 239, False: 0] ------------------ 3094| 239| { 3095| 239| nDelta = ( ret & ~3 ) >> 2; 3096| | /*nNumChanges += (ret & 2);*/ 3097| 239| if (nDelta) ------------------ | Branch (3097:29): [True: 0, False: 239] ------------------ 3098| 0| { 3099| | /* alt path unleashed previously localized radicals and they annihilated */ 3100| | /* djb-rwth: removing redundant code */ 3101| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3102| 0| goto quick_exit; 3103| 0| } 3104| 239| cPAIR( i, j ) |= ACCEPTOR_PAIR; /* the result: mark the pair */ ------------------ | | 2939| 239|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= ACCEPTOR_PAIR; /* the result: mark the pair */ ------------------ | | 2940| 239|#define ACCEPTOR_PAIR 1 ------------------ 3105| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 3106| 239| } 3107| 239| } 3108| | /* Check for donor pair */ 3109| 1.34k| if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 70| 1.34k|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 63| 1.34k|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 62| 1.34k|#define SALT_DONOR_H 1 | | ------------------ ------------------ if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 70| 769|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 63| 769|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 62| 769|#define SALT_DONOR_H 1 | | ------------------ ------------------ | Branch (3109:21): [True: 769, False: 574] | Branch (3109:64): [True: 611, False: 158] ------------------ 3110| 611| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (3110:21): [True: 70, False: 541] ------------------ 3111| 611| s_candidate[j].atnumber, ALT_PATH_MODE_REM2H_TST ) )) ------------------ | | 316| 611|#define ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */ ------------------ 3112| 70| { 3113| 70| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 70|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 70|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 70|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 70|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 70, False: 0] | | | Branch (67:44): [True: 0, False: 70] | | ------------------ ------------------ 3114| 0| { 3115| 0| nTotNumChanges = ret; 3116| 0| goto quick_exit; 3117| 0| } 3118| 70| if (ret & 1) ------------------ | Branch (3118:25): [True: 70, False: 0] ------------------ 3119| 70| { 3120| 70| nDelta = ( ret & ~3 ) >> 2; 3121| | /*nNumChanges += (ret & 2);*/ 3122| 70| if (nDelta) ------------------ | Branch (3122:29): [True: 0, False: 70] ------------------ 3123| 0| { 3124| | /* Alt path unleashed previously localized radicals and they annihilated */ 3125| | /* djb-rwth: removing redundant code */ 3126| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3127| 0| goto quick_exit; 3128| 0| } 3129| 70| cPAIR( i, j ) |= DONOR_PAIR; /* the result: mark the pair */ ------------------ | | 2939| 70|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= DONOR_PAIR; /* the result: mark the pair */ ------------------ | | 2941| 70|#define DONOR_PAIR 2 ------------------ 3130| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 3131| 70| } 3132| 70| } 3133| | /* Since the results will be used later to change bonds, check only now */ 3134| | /* when both results for (i,j) have been obtained. */ 3135| 1.34k| if (cPAIR( i, j ) & ACCEPTOR_PAIR) ------------------ | | 2939| 1.34k|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (cPAIR( i, j ) & ACCEPTOR_PAIR) ------------------ | | 2940| 1.34k|#define ACCEPTOR_PAIR 1 ------------------ | Branch (3135:21): [True: 239, False: 1.10k] ------------------ 3136| 239| { 3137| 239| nCurAcceptorPairs++; 3138| 239| if (nDonorPairs) ------------------ | Branch (3138:25): [True: 12, False: 227] ------------------ 3139| 12| { 3140| | /* Find donor pair (i1,j1) such that i!=i1, i!=j1, j!=i1, j!=j1 */ 3141| 34| for (i1 = 0; i1 < i; i1++) ------------------ | Branch (3141:38): [True: 31, False: 3] ------------------ 3142| 31| { 3143| 69| for (j1 = 0; j1 <= i1; j1++) ------------------ | Branch (3143:42): [True: 47, False: 22] ------------------ 3144| 47| { 3145| | /* Here always j1 < i && i1 < i therefore we do not compare i to i1 or j1 */ 3146| 47| if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & DONOR_PAIR )) ------------------ | | 2939| 35|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & DONOR_PAIR )) ------------------ | | 2941| 35|#define DONOR_PAIR 2 ------------------ | Branch (3146:37): [True: 36, False: 11] | Branch (3146:48): [True: 35, False: 1] | Branch (3146:59): [True: 9, False: 26] ------------------ 3147| 9| { 3148| | /* Both the donor and the acceptor pairs have been found */ 3149| 9| goto bFound2Pairs; 3150| 9| } 3151| 47| } 3152| 31| } 3153| 12| } 3154| 239| } 3155| 1.33k| if (cPAIR( i, j ) & DONOR_PAIR) ------------------ | | 2939| 1.33k|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (cPAIR( i, j ) & DONOR_PAIR) ------------------ | | 2941| 1.33k|#define DONOR_PAIR 2 ------------------ | Branch (3155:21): [True: 70, False: 1.26k] ------------------ 3156| 70| { 3157| 70| nCurDonorPairs++; 3158| 70| if (nAcceptorPairs) ------------------ | Branch (3158:25): [True: 8, False: 62] ------------------ 3159| 8| { 3160| | /* Find acceptor pair (i1,j1) such that i!=i1, i!=j1, j!=i1, j!=j1 */ 3161| 25| for (i1 = 0; i1 < i; i1++) ------------------ | Branch (3161:38): [True: 25, False: 0] ------------------ 3162| 25| { 3163| 57| for (j1 = 0; j1 <= i1; j1++) ------------------ | Branch (3163:42): [True: 40, False: 17] ------------------ 3164| 40| { 3165| | /* Here always j1 < i && i1 < i therefore we do not compare i to i1 or j1 */ 3166| 40| if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & ACCEPTOR_PAIR )) ------------------ | | 2939| 23|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & ACCEPTOR_PAIR )) ------------------ | | 2940| 23|#define ACCEPTOR_PAIR 1 ------------------ | Branch (3166:37): [True: 26, False: 14] | Branch (3166:48): [True: 23, False: 3] | Branch (3166:59): [True: 8, False: 15] ------------------ 3167| 8| { 3168| | /* Both the donor and the acceptor pairs have been found */ 3169| 8| goto bFound2Pairs; 3170| 8| } 3171| 40| } 3172| 25| } 3173| 8| } 3174| 70| } 3175| 1.33k| } 3176| 1.08k| nDonorPairs += nCurDonorPairs; 3177| 1.08k| nAcceptorPairs += nCurAcceptorPairs; 3178| 1.08k| } 3179| | 3180| | /* Nothing has been found */ 3181| | /* djb-rwth: removing redundant code */ 3182| 553| inchi_free( cPair ); ------------------ | | 1152| 553|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 553, False: 0] | | | Branch (1152:50): [Folded, False: 553] | | ------------------ ------------------ 3183| 553| cPair = NULL; 3184| 553| goto quick_exit; 3185| | 3186| | 3187| | /* Both the donor and the acceptor pairs have been found */ 3188| 17| bFound2Pairs: 3189| | /* first, try already found pairs */ 3190| 17| i1 = i; 3191| 17| j1 = j; 3192| | 3193| | /* Find all possible donor and acceptor pairs */ 3194| 17| nNumMarkedCandidates = 0; 3195| 105| for (i = 0; i < nNumLeftCandidates; i++) ------------------ | Branch (3195:21): [True: 88, False: 17] ------------------ 3196| 88| { 3197| 88| nCurDonorPairs = nCurAcceptorPairs = 0; 3198| 366| for (j = 0; j <= i; j++) ------------------ | Branch (3198:25): [True: 278, False: 88] ------------------ 3199| 278| { 3200| 278| bAlreadyTested = ( i < i1 || (i == i1 && j <= j1 )); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (3200:36): [True: 138, False: 140] | Branch (3200:47): [True: 77, False: 63] | Branch (3200:58): [True: 44, False: 33] ------------------ 3201| 278| if ((bAlreadyTested && ( cPAIR( i, j ) & ACCEPTOR_PAIR )) || !bAlreadyTested) /* djb-rwth: addressing LLVM warning */ ------------------ | | 2939| 182|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if ((bAlreadyTested && ( cPAIR( i, j ) & ACCEPTOR_PAIR )) || !bAlreadyTested) /* djb-rwth: addressing LLVM warning */ ------------------ | | 2940| 182|#define ACCEPTOR_PAIR 1 ------------------ | Branch (3201:22): [True: 182, False: 96] | Branch (3201:40): [True: 24, False: 158] | Branch (3201:78): [True: 96, False: 158] ------------------ 3202| 120| { 3203| | /* Checking for acceptor pair */ 3204| 120| if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 64| 120|#define SALT_ACCEPTOR 4 ------------------ if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 64| 92|#define SALT_ACCEPTOR 4 ------------------ | Branch (3204:25): [True: 92, False: 28] | Branch (3204:71): [True: 74, False: 18] ------------------ 3205| 74| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (3205:25): [True: 37, False: 37] ------------------ 3206| 74| s_candidate[j].atnumber, ALT_PATH_MODE_ADD2H_CHG ) )) ------------------ | | 315| 74|#define ALT_PATH_MODE_ADD2H_CHG 6 /* add 2 H along alt. path A=-=B => AH-=-BH and change bonds to alternating */ ------------------ 3207| 37| { 3208| 37| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 37|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 37|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 37|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 37|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 37, False: 0] | | | Branch (67:44): [True: 0, False: 37] | | ------------------ ------------------ 3209| 0| { 3210| 0| nTotNumChanges = ret; 3211| 0| goto quick_exit; 3212| 0| } 3213| 37| if (ret & 1) ------------------ | Branch (3213:29): [True: 37, False: 0] ------------------ 3214| 37| { 3215| 37| nDelta = ( ret & ~3 ) >> 2; 3216| | /* djb-rwth: removing redundant code */ 3217| 37| if (nDelta) ------------------ | Branch (3217:33): [True: 0, False: 37] ------------------ 3218| 0| { 3219| | /* Alt path unleashed previously localized radicals and they annihilated */ 3220| | /* djb-rwth: removing redundant code */ 3221| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3222| 0| goto quick_exit; 3223| 0| } 3224| 37| cPAIR( i, j ) |= ACCEPTOR_PAIR; ------------------ | | 2939| 37|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= ACCEPTOR_PAIR; ------------------ | | 2940| 37|#define ACCEPTOR_PAIR 1 ------------------ 3225| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 3226| 37| nCurAcceptorPairs += !bAlreadyTested; 3227| 37| if (!( s_candidate[i].subtype & SALT_SELECTED )) ------------------ | | 72| 37|#define SALT_SELECTED 32 ------------------ | Branch (3227:33): [True: 30, False: 7] ------------------ 3228| 30| { 3229| 30| s_candidate[i].subtype |= SALT_SELECTED; ------------------ | | 72| 30|#define SALT_SELECTED 32 ------------------ 3230| 30| nNumMarkedCandidates++; 3231| 30| if (!s_candidate[i].endpoint && s_candidate[i].type) ------------------ | Branch (3231:37): [True: 26, False: 4] | Branch (3231:65): [True: 26, False: 0] ------------------ 3232| 26| { 3233| 26| nNumOtherChanges++; 3234| 26| } 3235| | /* djb-rwth: removing redundant code */ 3236| 30| } 3237| 37| if (!( s_candidate[j].subtype & SALT_SELECTED )) ------------------ | | 72| 37|#define SALT_SELECTED 32 ------------------ | Branch (3237:33): [True: 27, False: 10] ------------------ 3238| 27| { 3239| 27| s_candidate[j].subtype |= SALT_SELECTED; ------------------ | | 72| 27|#define SALT_SELECTED 32 ------------------ 3240| 27| nNumMarkedCandidates++; 3241| 27| if (!s_candidate[j].endpoint && s_candidate[j].type) ------------------ | Branch (3241:37): [True: 22, False: 5] | Branch (3241:65): [True: 22, False: 0] ------------------ 3242| 22| { 3243| 22| nNumOtherChanges++; 3244| 22| } 3245| | /* djb-rwth: removing redundant code */ 3246| 27| } 3247| 37| } 3248| 37| } 3249| 120| } 3250| | 3251| 278| if ((bAlreadyTested && ( cPAIR( i, j ) & DONOR_PAIR )) || !bAlreadyTested) /* djb-rwth: addressing LLVM warning */ ------------------ | | 2939| 182|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if ((bAlreadyTested && ( cPAIR( i, j ) & DONOR_PAIR )) || !bAlreadyTested) /* djb-rwth: addressing LLVM warning */ ------------------ | | 2941| 182|#define DONOR_PAIR 2 ------------------ | Branch (3251:22): [True: 182, False: 96] | Branch (3251:40): [True: 18, False: 164] | Branch (3251:75): [True: 96, False: 164] ------------------ 3252| 114| { 3253| | /* Checking for donor pair */ 3254| 114| if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 70| 114|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 63| 114|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 62| 114|#define SALT_DONOR_H 1 | | ------------------ ------------------ if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 70| 87|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 63| 87|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 62| 87|#define SALT_DONOR_H 1 | | ------------------ ------------------ | Branch (3254:25): [True: 87, False: 27] | Branch (3254:68): [True: 52, False: 35] ------------------ 3255| 52| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (3255:25): [True: 20, False: 32] ------------------ 3256| 52| s_candidate[j].atnumber, ALT_PATH_MODE_REM2H_CHG ) )) ------------------ | | 314| 52|#define ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */ ------------------ 3257| 20| { 3258| 20| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 20|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 20|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 20|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 20|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 20, False: 0] | | | Branch (67:44): [True: 0, False: 20] | | ------------------ ------------------ 3259| 0| { 3260| 0| nTotNumChanges = ret; 3261| 0| goto quick_exit; 3262| 0| } 3263| 20| if (ret & 1) ------------------ | Branch (3263:29): [True: 20, False: 0] ------------------ 3264| 20| { 3265| 20| nDelta = ( ret & ~3 ) >> 2; 3266| | /* djb-rwth: removing redundant code */ 3267| 20| if (nDelta) ------------------ | Branch (3267:33): [True: 0, False: 20] ------------------ 3268| 0| { 3269| | /* Alt path unleashed previously localized radicals and they annihilated */ 3270| | /* djb-rwth: removing redundant code */ 3271| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3272| 0| goto quick_exit; 3273| 0| } 3274| 20| cPAIR( i, j ) |= DONOR_PAIR; ------------------ | | 2939| 20|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= DONOR_PAIR; ------------------ | | 2941| 20|#define DONOR_PAIR 2 ------------------ 3275| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 3276| 20| nCurDonorPairs += !bAlreadyTested; 3277| 20| if (!( s_candidate[i].subtype & SALT_SELECTED )) ------------------ | | 72| 20|#define SALT_SELECTED 32 ------------------ | Branch (3277:33): [True: 16, False: 4] ------------------ 3278| 16| { 3279| 16| s_candidate[i].subtype |= SALT_SELECTED; ------------------ | | 72| 16|#define SALT_SELECTED 32 ------------------ 3280| 16| nNumMarkedCandidates++; 3281| 16| if (!s_candidate[i].endpoint && s_candidate[i].type) ------------------ | Branch (3281:37): [True: 16, False: 0] | Branch (3281:65): [True: 16, False: 0] ------------------ 3282| 16| { 3283| 16| nNumOtherChanges++; 3284| 16| } 3285| | /* djb-rwth: removing redundant code */ 3286| 16| } 3287| 20| if (!( s_candidate[j].subtype & SALT_SELECTED )) ------------------ | | 72| 20|#define SALT_SELECTED 32 ------------------ | Branch (3287:33): [True: 13, False: 7] ------------------ 3288| 13| { 3289| 13| s_candidate[j].subtype |= SALT_SELECTED; ------------------ | | 72| 13|#define SALT_SELECTED 32 ------------------ 3290| 13| nNumMarkedCandidates++; 3291| 13| if (!s_candidate[j].endpoint && s_candidate[j].type) ------------------ | Branch (3291:37): [True: 10, False: 3] | Branch (3291:65): [True: 10, False: 0] ------------------ 3292| 10| { 3293| 10| nNumOtherChanges++; 3294| 10| } 3295| | /* djb-rwth: removing redundant code */ 3296| 13| } 3297| 20| } 3298| 20| } 3299| 114| } 3300| 278| } 3301| 88| nDonorPairs += nCurDonorPairs; 3302| 88| nAcceptorPairs += nCurAcceptorPairs; 3303| 88| } 3304| | 3305| 17| inchi_free( cPair ); ------------------ | | 1152| 17|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 17, False: 0] | | | Branch (1152:50): [Folded, False: 17] | | ------------------ ------------------ 3306| 17| cPair = NULL; 3307| | 3308| 17| if (nNumMarkedCandidates) ------------------ | Branch (3308:13): [True: 17, False: 0] ------------------ 3309| 17| { 3310| 17| EndPoint = (T_ENDPOINT *) inchi_calloc( nNumMarkedCandidates, sizeof( EndPoint[0] ) ); ------------------ | | 1146| 17|#define inchi_calloc calloc ------------------ 3311| 17| if (!EndPoint) ------------------ | Branch (3311:17): [True: 0, False: 17] ------------------ 3312| 0| { 3313| | /*printf("BNS_OUT_OF_RAM-7\n");*/ 3314| 0| nTotNumChanges = BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3315| 0| goto quick_exit; 3316| 0| } 3317| 105| for (i = 0, j = 0; i < nNumLeftCandidates; i++) ------------------ | Branch (3317:32): [True: 88, False: 17] ------------------ 3318| 88| { 3319| 88| if (s_candidate[i].subtype & SALT_SELECTED) ------------------ | | 72| 88|#define SALT_SELECTED 32 ------------------ | Branch (3319:21): [True: 86, False: 2] ------------------ 3320| 86| { 3321| 86| s_candidate[i].subtype ^= SALT_SELECTED; /* remove the flag */ ------------------ | | 72| 86|#define SALT_SELECTED 32 ------------------ 3322| 86| if (j < nNumMarkedCandidates) ------------------ | Branch (3322:25): [True: 86, False: 0] ------------------ 3323| 86| { 3324| 86| i1 = s_candidate[i].atnumber; /* save a representative of the t-group to be created */ 3325| 86| AddEndPoint( EndPoint + j, at, i1 ); 3326| 86| } 3327| 86| j++; 3328| 86| } 3329| 88| } 3330| 17| if (j != nNumMarkedCandidates) ------------------ | Branch (3330:17): [True: 0, False: 17] ------------------ 3331| 0| { 3332| 0| nTotNumChanges = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3333| 0| goto quick_exit; 3334| 0| } 3335| | 3336| | /* Merge all marked atoms and their t-groups into one t-group */ 3337| 17| ret = RegisterEndPoints( pCG, t_group_info, EndPoint, 3338| 17| nNumMarkedCandidates, at, 3339| 17| num_atoms, c_group_info, pBNS ); 3340| | 3341| 17| if (ret == -1) ------------------ | Branch (3341:17): [True: 0, False: 17] ------------------ 3342| 0| { 3343| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3344| 0| } 3345| 17| if (ret < 0) ------------------ | Branch (3345:17): [True: 0, False: 17] ------------------ 3346| 0| { 3347| 0| nTotNumChanges = ret; 3348| 0| goto quick_exit; 3349| 0| } 3350| 17| nTotNumChanges += ( ret > 0 ); 3351| 17| inchi_free( EndPoint ); ------------------ | | 1152| 17|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 17, False: 0] | | | Branch (1152:50): [Folded, False: 17] | | ------------------ ------------------ 3352| 17| EndPoint = NULL; 3353| | 3354| 17| if (nNumMarkedCandidates) ------------------ | Branch (3354:17): [True: 17, False: 0] ------------------ 3355| 17| { 3356| 30| for (i = nNumLeftCandidates; i < nNumCandidates; i++) ------------------ | Branch (3356:46): [True: 13, False: 17] ------------------ 3357| 13| { 3358| 13| s_candidate[i].type += DISABLE_CANDIDATE; ------------------ | | 2938| 13|#define DISABLE_CANDIDATE 10 ------------------ 3359| 13| j1 = s_candidate[i].atnumber; 3360| 13| if (at[j1].endpoint == at[i1].endpoint) ------------------ | Branch (3360:25): [True: 13, False: 0] ------------------ 3361| 13| { 3362| 13| if (!s_candidate[i].endpoint && s_candidate[i].type) ------------------ | Branch (3362:29): [True: 0, False: 13] | Branch (3362:57): [True: 0, False: 0] ------------------ 3363| 0| { 3364| 0| nNumOtherChanges++; 3365| 0| } 3366| | /* djb-rwth: removing redundant code */ 3367| 13| } 3368| 13| } 3369| 17| } 3370| 0| else 3371| 0| { 3372| 0| for (i = nNumLeftCandidates; i < nNumCandidates; i++) ------------------ | Branch (3372:46): [True: 0, False: 0] ------------------ 3373| 0| { 3374| 0| s_candidate[i].type += DISABLE_CANDIDATE; ------------------ | | 2938| 0|#define DISABLE_CANDIDATE 10 ------------------ 3375| 0| } 3376| 0| } 3377| | 3378| | /* Find whether the new t-group have any movable H */ 3379| 34| for (i = 0, bTGroupHasNegativeChargesOnly = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (3379:60): [True: 17, False: 17] ------------------ 3380| 17| { 3381| 17| if (t_group_info->t_group[i].nGroupNumber == at[i1].endpoint && ------------------ | Branch (3381:21): [True: 17, False: 0] ------------------ 3382| 17| t_group_info->t_group[i].num[0] == t_group_info->t_group[i].num[1]) ------------------ | Branch (3382:22): [True: 0, False: 17] ------------------ 3383| 0| { 3384| 0| bTGroupHasNegativeChargesOnly = 1; 3385| 0| break; 3386| 0| } 3387| 17| } 3388| 17| } 3389| 17| nTotNumChanges = ( nTotNumChanges > 0 ); 3390| | 3391| 17|#if ( IGNORE_TGROUP_WITHOUT_H == 1 ) 3392| 17| if (nTotNumChanges && bTGroupHasNegativeChargesOnly) ------------------ | Branch (3392:13): [True: 17, False: 0] | Branch (3392:31): [True: 0, False: 17] ------------------ 3393| 0| { 3394| 0| nTotNumChanges = 2; /* means no moveable H has been affected */ 3395| 0| } 3396| 17|#endif 3397| 17| } 3398| | 3399| 570|quick_exit: 3400| 570| if (nNumOtherChanges && nTotNumChanges == 1) ------------------ | Branch (3400:9): [True: 17, False: 553] | Branch (3400:29): [True: 17, False: 0] ------------------ 3401| 17| { 3402| 17| nTotNumChanges = 5; /* not only acidic atoms merged */ 3403| 17| } 3404| 570| if (cPair) ------------------ | Branch (3404:9): [True: 0, False: 570] ------------------ 3405| 0| { 3406| 0| inchi_free( cPair ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3407| | /*cPair = NULL;*/ 3408| 0| } 3409| 570| if (EndPoint) ------------------ | Branch (3409:9): [True: 0, False: 570] ------------------ 3410| 0| { 3411| 0| inchi_free( EndPoint ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3412| | /*EndPoint = NULL;*/ 3413| 0| } 3414| | 3415| 570| return nTotNumChanges; /* 0=>no changes, 1=>new salt tautomerism found, 2=>only new charge tautomerism found */ 3416| 252k|#undef ALT_PATH_FOUND 3417| 252k|#undef NO_ENDPOINT 3418| 252k|} MarkSaltChargeGroups: 3456| 252k|{ 3457| | 3458| 252k| int nNumChanges = 0, nTotNumChanges = 0; 3459| 252k| if (s_group_info && s_group_info->s_candidate && s_group_info->max_num_candidates > 0) ------------------ | Branch (3459:9): [True: 252k, False: 0] | Branch (3459:25): [True: 252k, False: 0] | Branch (3459:54): [True: 252k, False: 0] ------------------ 3460| 252k| { 3461| 252k| int i, i1, i2, j, j1, j2, jj, ii1, ii2, jj1, jj2, /*k,*/ num_tested; 3462| 252k| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 3463| 252k| int nMaxNumCandidates = s_group_info->max_num_candidates; 3464| 252k| int nNumCandidates = s_group_info->num_candidates; 3465| 252k| int nNumOtherCandidates; /* djb-rwth: removing redundant code */ 3466| 252k| int nNumPOnlyCandidates; /* djb-rwth: removing redundant code */ 3467| 252k| int s_type, s_subtype; 3468| 252k| int ret, nDelta, /*nMobile,*/ err = 0; 3469| 252k| int s_subtype_all = 0; 3470| 252k| int nGroupNumber; 3471| 252k| T_ENDPOINT EndPoint[2]; 3472| |#if ( MAX_LOCAL_TGNUM > 0 ) 3473| | TGroupData tgData[MAX_LOCAL_TGNUM]; 3474| | TGroupData *ptgData = tgData; 3475| |#endif 3476| 252k| int cond1 = 0, cond2a = 0, cond2b = 0, cond2c = 0, cond2 = 0; 3477| | 3478| 252k| if (nNumCandidates <= -1 || !t_group_info || !t_group_info->t_group) ------------------ | Branch (3478:13): [True: 0, False: 252k] | Branch (3478:37): [True: 0, False: 252k] | Branch (3478:54): [True: 0, False: 252k] ------------------ 3479| 0| { 3480| 0| return 0; 3481| 0| } 3482| | 3483| | /* count t-groups */ 3484| 257k| for (i = 0, nGroupNumber = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (3484:39): [True: 5.62k, False: 252k] ------------------ 3485| 5.62k| { 3486| 5.62k| if (nGroupNumber < t_group_info->t_group[i].nGroupNumber) ------------------ | Branch (3486:17): [True: 5.62k, False: 0] ------------------ 3487| 5.62k| { 3488| 5.62k| nGroupNumber = t_group_info->t_group[i].nGroupNumber; /* max. t-group number */ 3489| 5.62k| } 3490| 5.62k| } 3491| |#if ( MAX_LOCAL_TGNUM > 0 ) 3492| | /* prepare memory */ 3493| | if (nGroupNumber >= MAX_LOCAL_TGNUM) 3494| | { 3495| | if (!( ptgData = (TGroupData*) inchi_calloc( nGroupNumber + 1, sizeof( TGroupData ) ) )) 3496| | { 3497| | err = BNS_OUT_OF_RAM; 3498| | goto quick_exit; 3499| | } 3500| | } 3501| | else 3502| | { 3503| | memset( ptgData, 0, sizeof( tgData ) ); 3504| | } 3505| | ptgData[0].nGroupIndex = -1; /* data for non-tautomeric atoms */ 3506| | for (i = 0, nGroupNumber = 0; i < t_group_info->num_t_groups; i++) 3507| | { 3508| | if (nGroupNumber = t_group_info->t_group[i].nGroupNumber) 3509| | { 3510| | ptgData[nGroupNumber].nGroupIndex = i; 3511| | ptgData[i].nGroupNumber = nGroupNumber; 3512| | } 3513| | } 3514| |#endif 3515| 252k| nNumCandidates = 0; /* always recalculate 2004-03-22 */ 3516| 252k| num_tested = 0; 3517| | 3518| 252k| if (nNumCandidates == 0) ------------------ | Branch (3518:13): [True: 252k, False: 0] ------------------ 3519| 252k| { 3520| 1.30M| for (i = 0, nNumCandidates = nNumOtherCandidates = nNumPOnlyCandidates = 0; i < num_atoms; i++) ------------------ | Branch (3520:89): [True: 1.05M, False: 252k] ------------------ 3521| 1.05M| { 3522| 1.05M| if (0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (3522:21): [True: 2.87k, False: 1.04M] ------------------ 3523| | /* -C=O or =C-OH, O = S, Se, Te */ 3524| 1.04M|#if ( INCL_NON_SALT_CANDIDATATES == 1 ) 3525| 1.04M| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1 ) ) || ------------------ | Branch (3525:22): [True: 40.1k, False: 1.00M] ------------------ 3526| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above */ 3527| 1.00M|#endif 3528| 1.00M| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) ------------------ | Branch (3528:22): [True: 350, False: 1.00M] ------------------ 3529| | /* >C-SH, >C-S(-); S=S,Se,Te */ 3530| 1.05M| ) 3531| 43.3k| { 3532| | 3533| 43.3k| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (3533:25): [True: 0, False: 43.3k] ------------------ 3534| 0| { 3535| 0| err = BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3536| 0| goto quick_exit; 3537| 0| } 3538| 43.3k| s_candidate[nNumCandidates].atnumber = i; 3539| 43.3k| s_candidate[nNumCandidates].type = s_type; 3540| 43.3k| s_candidate[nNumCandidates].subtype = s_subtype; 3541| 43.3k| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 3542| 43.3k| nNumCandidates++; 3543| 43.3k| nNumOtherCandidates += ( 1 == s_type ); 3544| 43.3k| nNumPOnlyCandidates += ( 2 == s_type ); 3545| 43.3k| s_subtype_all |= s_subtype; 3546| | /*i1 = i;*/ /* save a representative of a tautomeric group */ 3547| 43.3k| } 3548| 1.05M| } /* for */ 3549| | 3550| | /* changes: TG_FLAG_ALLOW_NO_NEGTV_O replaced CHARGED_SALTS_ONLY==0 */ 3551| 252k| cond1 = s_subtype_all & SALT_ACCEPTOR; ------------------ | | 64| 252k|#define SALT_ACCEPTOR 4 ------------------ 3552| 252k| cond2a = t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O; ------------------ | | 923| 252k|#define TG_FLAG_ALLOW_NO_NEGTV_O 0x00000020 /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */ ------------------ 3553| 252k| cond2b = t_group_info->bTautFlagsDone & TG_FLAG_FOUND_SALT_CHARGES_DONE; ------------------ | | 980| 252k|#define TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */ ------------------ 3554| 252k| cond2c = t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT; ------------------ | | 172| 252k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 252k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 173| 252k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 252k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 174| 252k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 151| 252k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ 3555| 252k| if (cond2a || cond2b || cond2c) ------------------ | Branch (3555:17): [True: 0, False: 252k] | Branch (3555:27): [True: 0, False: 252k] | Branch (3555:37): [True: 211, False: 252k] ------------------ 3556| 211| { 3557| 211| cond2 = !( s_subtype_all & ( SALT_DONOR_Neg | SALT_DONOR_H ) ); ------------------ | | 63| 211|#define SALT_DONOR_Neg 2 ------------------ cond2 = !( s_subtype_all & ( SALT_DONOR_Neg | SALT_DONOR_H ) ); ------------------ | | 62| 211|#define SALT_DONOR_H 1 ------------------ 3558| 211| } 3559| 252k| else 3560| 252k| { 3561| 252k| cond2 = !( s_subtype_all & SALT_DONOR_Neg ) || nNumOtherCandidates == nNumCandidates; ------------------ | | 63| 252k|#define SALT_DONOR_Neg 2 ------------------ | Branch (3561:25): [True: 247k, False: 4.67k] | Branch (3561:64): [True: 4.11k, False: 561] ------------------ 3562| 252k| } 3563| 252k| if (nNumCandidates <= 1 || !cond1 || cond2 ------------------ | Branch (3563:17): [True: 238k, False: 13.5k] | Branch (3563:40): [True: 136, False: 13.4k] | Branch (3563:50): [True: 12.7k, False: 669] ------------------ 3564| | /*( 3565| | ( cond2a || cond2b || cond2c ) 3566| | ? !(s_subtype_all & (SALT_DONOR_Neg | SALT_DONOR_H)) 3567| | : ( !(s_subtype_all & SALT_DONOR_Neg) || nNumOtherCandidates==nNumCandidates) ) */ 3568| 252k| ) 3569| 251k| { 3570| 251k| s_group_info->num_candidates = -1; /* no candidate exists */ 3571| 251k| goto quick_exit; 3572| 251k| } 3573| 669| if (!( s_subtype_all & ( SALT_DONOR_Neg ) )) ------------------ | | 63| 669|#define SALT_DONOR_Neg 2 ------------------ | Branch (3573:17): [True: 83, False: 586] ------------------ 3574| 83| { 3575| 83| t_group_info->bTautFlagsDone |= TG_FLAG_ALLOW_NO_NEGTV_O_DONE; ------------------ | | 968| 83|#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040 ------------------ 3576| 83| } 3577| 669| } 3578| 0| else 3579| 0| { 3580| 0| for (i = 0; i < nNumCandidates; i++) ------------------ | Branch (3580:25): [True: 0, False: 0] ------------------ 3581| 0| { 3582| 0| i1 = s_candidate[i].atnumber; 3583| 0| if (0 <= ( s_type = GetSaltChargeType( at, i1, t_group_info, &s_subtype ) ) ------------------ | Branch (3583:21): [True: 0, False: 0] ------------------ 3584| 0|#if ( INCL_NON_SALT_CANDIDATATES == 1 ) 3585| 0| || 0 < ( s_type = GetOtherSaltChargeType( at, i1, t_group_info, &s_subtype, 1 /* bAccept_O*/ ) ) ------------------ | Branch (3585:25): [True: 0, False: 0] ------------------ 3586| 0|#endif 3587| 0| ) 3588| 0| { 3589| 0| s_candidate[nNumCandidates].type = s_type; 3590| 0| s_candidate[nNumCandidates].subtype = s_subtype; 3591| 0| s_candidate[nNumCandidates].endpoint = at[i1].endpoint; 3592| 0| } 3593| 0| } 3594| 0| } 3595| | 3596| | /* Look for alt paths connecting: 3597| | SALT_DONOR_Neg to SALT_ACCEPTOR : long distance migration of negative charges 3598| | SALT_DONOR_H to SALT_ACCEPTOR : long distance migration of H-atoms 3599| | */ 3600| 669| do 3601| 787| { 3602| 787| nNumChanges = 0; 3603| 3.15k| for (i1 = 0; i1 < nNumCandidates; i1++) ------------------ | Branch (3603:26): [True: 2.36k, False: 787] ------------------ 3604| 2.36k| { 3605| 2.36k| j1 = s_candidate[i1].atnumber; 3606| 5.25k| for (i2 = i1 + 1; i2 < nNumCandidates; i2++) ------------------ | Branch (3606:35): [True: 2.88k, False: 2.36k] ------------------ 3607| 2.88k| { 3608| | /* prev. approach: do not test if both candidates are not "salt-type". Disabled 2004-03-18 3609| | if ( s_candidate[i1].type && s_candidate[i2].type ) 3610| | continue; 3611| | */ 3612| 2.88k| j2 = s_candidate[i2].atnumber; 3613| 2.88k| if (at[j1].endpoint && at[j1].endpoint == at[j2].endpoint) ------------------ | Branch (3613:25): [True: 2.01k, False: 878] | Branch (3613:44): [True: 1.38k, False: 625] ------------------ 3614| 1.38k| { 3615| 1.38k| continue; 3616| 1.38k| } 3617| 4.29k| for (j = 0; j < 2; j++) ------------------ | Branch (3617:33): [True: 2.93k, False: 1.35k] ------------------ 3618| 2.93k| { 3619| 2.93k| if (j) ------------------ | Branch (3619:29): [True: 1.43k, False: 1.50k] ------------------ 3620| 1.43k| { 3621| 1.43k| ii1 = i2; /* candidate 1 (donor) ordering number */ 3622| 1.43k| ii2 = i1; /* candidate 2 (acceptor) ordering number */ 3623| 1.43k| jj1 = j2; /* candidate 1 (donor) atom number */ 3624| 1.43k| jj2 = j1; /* candidate 2 (acceptor) atom number */ 3625| 1.43k| } 3626| 1.50k| else 3627| 1.50k| { 3628| | /* transposition */ 3629| 1.50k| ii1 = i1; /* candidate 1 (donor) ordering number */ 3630| 1.50k| ii2 = i2; /* candidate 2 (acceptor) ordering number */ 3631| 1.50k| jj1 = j1; /* candidate 1 (donor) atom number */ 3632| 1.50k| jj2 = j2; /* candidate 2 (acceptor) atom number */ 3633| 1.50k| } 3634| | 3635| 2.93k| if (( s_candidate[ii1].subtype & ( SALT_DONOR_Neg | SALT_DONOR_H ) ) && ------------------ | | 63| 2.93k|#define SALT_DONOR_Neg 2 ------------------ if (( s_candidate[ii1].subtype & ( SALT_DONOR_Neg | SALT_DONOR_H ) ) && ------------------ | | 62| 2.93k|#define SALT_DONOR_H 1 ------------------ | Branch (3635:29): [True: 1.70k, False: 1.23k] ------------------ 3636| 1.70k| ( s_candidate[ii2].subtype & SALT_ACCEPTOR )) ------------------ | | 64| 1.70k|#define SALT_ACCEPTOR 4 ------------------ | Branch (3636:29): [True: 1.43k, False: 261] ------------------ 3637| 1.43k| { 3638| | /****printf("\nChkpt @ %-s:%-d ", __FILE__,__LINE__); fflush(stdout);*/ 3639| | 3640| 1.43k| ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, jj2, jj1, ALT_PATH_MODE_4_SALT ); ------------------ | | 312| 1.43k|#define ALT_PATH_MODE_4_SALT 3 /* mark alt bonds along the path */ ------------------ 3641| | 3642| 1.43k| num_tested++; 3643| 1.43k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 1.43k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 1.43k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 1.43k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 1.43k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 1.43k, False: 0] | | | Branch (67:44): [True: 0, False: 1.43k] | | ------------------ ------------------ 3644| 0| { 3645| 0| err = ret; 3646| 0| goto quick_exit; 3647| 0| } 3648| | 3649| 1.43k| if (ret & 1) ------------------ | Branch (3649:33): [True: 146, False: 1.29k] ------------------ 3650| 146| { 3651| 146| nDelta = ( ret & ~3 ) >> 2; 3652| 146| nNumChanges += ( ret & 2 ); 3653| 438| for (i = 0; i < 2; i++) ------------------ | Branch (3653:45): [True: 292, False: 146] ------------------ 3654| 292| { 3655| 292| jj = i ? jj2 : jj1; ------------------ | Branch (3655:42): [True: 146, False: 146] ------------------ 3656| 292| AddEndPoint( EndPoint + i, at, jj ); 3657| 292| } 3658| | 3659| | /* add/merge taut groups and reinit pBNS in the fly */ 3660| 146| ret = RegisterEndPoints( pCG, t_group_info, 3661| 146| EndPoint, 2, at, 3662| 146| num_atoms, c_group_info, 3663| 146| pBNS ); 3664| 146| if (ret == -1) ------------------ | Branch (3664:37): [True: 0, False: 146] ------------------ 3665| 0| { 3666| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3667| 0| } 3668| 146| if (ret < 0) ------------------ | Branch (3668:37): [True: 0, False: 146] ------------------ 3669| 0| { 3670| 0| err = ret; 3671| 0| goto quick_exit; 3672| 0| } 3673| 146| if (nDelta) ------------------ | Branch (3673:37): [True: 0, False: 146] ------------------ 3674| 0| { 3675| 0| err = BNS_RADICAL_ERR; ------------------ | | 59| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3676| 0| goto quick_exit; 3677| 0| } 3678| 146| nNumChanges += ( ret > 0 ); 3679| 146| break; /* avoid redundant repetition */ 3680| 146| } 3681| 1.43k| } 3682| 2.93k| } 3683| 1.50k| } 3684| 2.36k| } 3685| 787| nTotNumChanges += nNumChanges; 3686| 787| } while (num_tested && nNumChanges); ------------------ | Branch (3686:18): [True: 514, False: 273] | Branch (3686:32): [True: 118, False: 396] ------------------ 3687| | 3688| 252k| quick_exit: 3689| 252k| if (!err) ------------------ | Branch (3689:13): [True: 252k, False: 0] ------------------ 3690| 252k| { 3691| 252k| nTotNumChanges += nNumChanges; /* nNumChanges != 0 only in case of 'goto quick_exit' */ 3692| 252k| if (s_group_info->num_candidates == 0) ------------------ | Branch (3692:17): [True: 551, False: 251k] ------------------ 3693| 551| { 3694| | /* first time: initialize */ 3695| 551| s_group_info->num_candidates = num_tested ? nNumCandidates : -1; /* no candidate exists */ ------------------ | Branch (3695:48): [True: 370, False: 181] ------------------ 3696| 551| } 3697| 252k| } 3698| 0| else 3699| 0| { 3700| 0| nTotNumChanges = err; 3701| 0| } 3702| |#if ( MAX_LOCAL_TGNUM > 0 ) 3703| | if (ptgData != tgData) 3704| | { 3705| | inchi_free( ptgData ); 3706| | } 3707| |#endif 3708| 252k| } 3709| | 3710| 252k| return nTotNumChanges; 3711| 252k|} MergeSaltTautGroups: 3925| 252k|{ 3926| | /* Count candidates to be connected: exclude pure donors that do not belong to any t-group */ 3927| 252k| AT_NUMB nCurTGroupNumber; 3928| 252k| int i, j, /*k,*/ ret, iat, /*nMobile,*/ nMinNumEndpoints; 3929| 252k| int s_subtype_all, s_subtype_taut; 3930| 252k| int nMaxNumCandidates, nNumCandidates; /* djb-rwth: removing redundant variables */ 3931| 252k| T_ENDPOINT EndPointStackArray[MAX_STACK_ARRAY_LEN]; /* will be reallocated if too short */ 3932| 252k| T_ENDPOINT *EndPoint = EndPointStackArray; 3933| | 3934| | 3935| 252k| if (!s_group_info || !s_group_info->s_candidate || /*s_group_info->num_candidates <= 0 ||*/ ------------------ | Branch (3935:9): [True: 0, False: 252k] | Branch (3935:26): [True: 0, False: 252k] ------------------ 3936| 252k| !t_group_info || !t_group_info->t_group || !c_group_info) ------------------ | Branch (3936:10): [True: 0, False: 252k] | Branch (3936:27): [True: 0, False: 252k] | Branch (3936:53): [True: 0, False: 252k] ------------------ 3937| 0| { 3938| 0| return 0; 3939| 0| } 3940| 252k| nMinNumEndpoints = 0; 3941| 252k| nMaxNumCandidates = s_group_info->max_num_candidates; 3942| 252k| nCurTGroupNumber = MAX_ATOMS; /* impossible t-group number */ ------------------ | | 15| 252k|#define MAX_ATOMS 32766 ------------------ 3943| 252k| s_subtype_all = s_subtype_taut = 0; 3944| | 3945| | /* Collect tautomeric acidic O and previously non-tautomeric C-OH, C-SH, C-O(-), C-S(-) */ 3946| | /* find whether previously found tautomeric atoms have both mobile H and (-) */ 3947| 252k| if (1 || ( s_group_info->num_candidates < 0 )) ------------------ | Branch (3947:9): [True: 252k, Folded] | Branch (3947:14): [True: 0, False: 0] ------------------ 3948| 252k| { 3949| | /* Can be only -O(-) and -OH */ 3950| 252k| int s_type, s_subtype; 3951| 252k| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 3952| 1.30M| for (i = 0, nNumCandidates = 0; i < num_atoms; i++) /* djb-rwth: removing redundant code */ ------------------ | Branch (3952:41): [True: 1.05M, False: 252k] ------------------ 3953| 1.05M| { 3954| 1.05M| s_subtype = 0; 3955| 1.05M| if (0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (3955:17): [True: 2.73k, False: 1.04M] ------------------ 3956| | /* -C=O or =C-OH, O = S, Se, Te */ 3957| | 3958| | /*(t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT) &&*/ 3959| 1.04M| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1/* bAccept_O*/ ) ) || ------------------ | Branch (3959:18): [True: 39.9k, False: 1.00M] ------------------ 3960| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above. M may be N */ 3961| | 3962| 1.00M| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) || ------------------ | Branch (3962:18): [True: 350, False: 1.00M] ------------------ 3963| | /* >C-SH, >C-S(-); S=S,Se,Te */ 3964| | 3965| | /* other proton donor or acceptor */ 3966| 1.00M| (bHasAcidicHydrogen(at, i) && ((s_type = 3), (s_subtype = SALT_p_DONOR))) || ------------------ | | 65| 1.76k|#define SALT_p_DONOR 8 /* >C-SH */ ------------------ | Branch (3966:18): [True: 1.76k, False: 1.00M] | Branch (3966:47): [True: 1.76k, False: 0] ------------------ 3967| 1.00M| (bHasAcidicMinus(at, i) && ((s_type = 3), (s_subtype = SALT_p_ACCEPTOR))) ------------------ | | 66| 581|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ ------------------ | Branch (3967:18): [True: 581, False: 1.00M] | Branch (3967:44): [True: 581, False: 0] ------------------ 3968| 1.05M| ) 3969| 45.3k| { 3970| | 3971| 45.3k| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (3971:21): [True: 0, False: 45.3k] ------------------ 3972| 0| { 3973| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3974| 0| } 3975| 45.3k| if (at[i].endpoint) ------------------ | Branch (3975:21): [True: 12.9k, False: 32.3k] ------------------ 3976| 12.9k| { 3977| 12.9k| s_subtype_taut |= s_subtype; 3978| 12.9k| } 3979| 32.3k| else 3980| 32.3k| { 3981| 32.3k| if (bDoNotMergeNonTautAtom( at, i )) ------------------ | Branch (3981:25): [True: 20.9k, False: 11.4k] ------------------ 3982| 20.9k| { 3983| 20.9k| continue; /* ignore non-tautomeric N */ 3984| 20.9k| } 3985| 32.3k| } 3986| 24.4k| if (!( s_subtype & SALT_DONOR_ALL ) || ------------------ | | 67| 24.4k|#define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 63| 24.4k|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 62| 24.4k|#define SALT_DONOR_H 1 | | ------------------ | | #define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 66| 24.4k|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ | | #define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 65| 24.4k|#define SALT_p_DONOR 8 /* >C-SH */ | | ------------------ ------------------ | Branch (3986:21): [True: 6.55k, False: 17.8k] ------------------ 3987| 17.8k| (( s_subtype & SALT_ACCEPTOR ) && !at[i].endpoint)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 64| 17.8k|#define SALT_ACCEPTOR 4 ------------------ | Branch (3987:22): [True: 12.9k, False: 4.91k] | Branch (3987:55): [True: 0, False: 12.9k] ------------------ 3988| 6.55k| { 3989| 6.55k| continue; /* do not include non-taut acceptors like -C=O */ 3990| 6.55k| } 3991| 17.8k| s_candidate[nNumCandidates].atnumber = i; 3992| 17.8k| s_candidate[nNumCandidates].type = s_type; 3993| 17.8k| s_candidate[nNumCandidates].subtype = s_subtype; 3994| 17.8k| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 3995| 17.8k| nNumCandidates++; 3996| 17.8k| s_subtype_all |= s_subtype; 3997| 17.8k| } 3998| 1.05M| } 3999| | 4000| | /* 4001| | Forced merging occurs upon: 4002| | =========================== 4003| | (t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O) or 4004| | (t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT) 4005| | 4006| | 4007| | Allow forced merging in cases: 4008| | {t-groups} (H, (-)} {H, (-), t-groups} 4009| | 4010| | 4011| | Normal salt merging in cases: 4012| | (H, (-)} {H, (-), t-groups}, 4013| | 4014| | Cannot merge H into t-groups if no (-) is present 4015| | */ 4016| 252k| if (( t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O ) || ------------------ | | 923| 252k|#define TG_FLAG_ALLOW_NO_NEGTV_O 0x00000020 /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */ ------------------ | Branch (4016:13): [True: 0, False: 252k] ------------------ 4017| 252k| ( t_group_info->bTautFlagsDone & TG_FLAG_FOUND_SALT_CHARGES_DONE ) || ------------------ | | 980| 252k|#define TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */ ------------------ | Branch (4017:13): [True: 0, False: 252k] ------------------ 4018| 252k| ( t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT )) ------------------ | | 172| 252k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 252k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 173| 252k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 252k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 174| 252k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 151| 252k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (4018:14): [True: 172, False: 251k] ------------------ 4019| 172| { 4020| | /* Force merge even though no negative charges are present */ 4021| 172| if (nNumCandidates <= 1 || ------------------ | Branch (4021:17): [True: 53, False: 119] ------------------ 4022| 119| (( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) ) && ------------------ | | 68| 119|#define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 63| 119|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 66| 119|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ ------------------ (( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) ) && ------------------ | | 69| 52|#define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 62| 52|#define SALT_DONOR_H 1 | | ------------------ | | #define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 65| 52|#define SALT_p_DONOR 8 /* >C-SH */ | | ------------------ ------------------ | Branch (4022:20): [True: 67, False: 52] | Branch (4022:60): [True: 26, False: 26] ------------------ 4023| 93| !t_group_info->num_t_groups)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4023:18): [True: 0, False: 93] ------------------ 4024| 53| { 4025| 53| s_group_info->num_candidates = -1; /* no candidate exists */ 4026| 53| return 0; 4027| 53| } 4028| 172| } 4029| 251k| else 4030| 251k| { 4031| | /* normal salt mode: merge if both -XH and -X(-) are present */ 4032| 251k| if (nNumCandidates <= 1 || ------------------ | Branch (4032:17): [True: 246k, False: 5.49k] ------------------ 4033| 5.49k| ( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) )) ------------------ | | 68| 5.49k|#define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 63| 5.49k|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 66| 5.49k|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ ------------------ ( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) )) ------------------ | | 69| 3.03k|#define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 62| 3.03k|#define SALT_DONOR_H 1 | | ------------------ | | #define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 65| 3.03k|#define SALT_p_DONOR 8 /* >C-SH */ | | ------------------ ------------------ | Branch (4033:19): [True: 2.45k, False: 3.03k] | Branch (4033:59): [True: 2.01k, False: 1.02k] ------------------ 4034| 250k| { 4035| 250k| s_group_info->num_candidates = -1; /* no candidate exists */ 4036| 250k| return 0; 4037| 250k| } 4038| 251k| } 4039| | /* -- old code -- 4040| | if ( nNumCandidates <= 1 || 4041| | (((t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O) || 4042| | (t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT)) ? 4043| | !(s_subtype_all & SALT_DONOR_ALL): 4044| | !(s_subtype_all & SALT_DONOR_Neg2) 4045| | ) 4046| | ) { 4047| | s_group_info->num_candidates = -1; 4048| | return 0; 4049| | } 4050| | */ 4051| 1.14k| if (!( s_subtype_all & ( SALT_DONOR_Neg2 ) )) ------------------ | | 68| 1.14k|#define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 63| 1.14k|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 66| 1.14k|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ ------------------ | Branch (4051:13): [True: 67, False: 1.07k] ------------------ 4052| 67| { 4053| 67| t_group_info->bTautFlagsDone |= TG_FLAG_ALLOW_NO_NEGTV_O_DONE; ------------------ | | 968| 67|#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040 ------------------ 4054| 67| } 4055| 1.14k| s_group_info->num_candidates = nNumCandidates; 4056| 1.14k| } 4057| | 4058| 4.41k| for (i = 0; i < s_group_info->num_candidates; i++) ------------------ | Branch (4058:17): [True: 3.27k, False: 1.14k] ------------------ 4059| 3.27k| { 4060| 3.27k| iat = s_group_info->s_candidate[i].atnumber; 4061| 3.27k| if (( s_group_info->s_candidate[i].subtype & SALT_ACCEPTOR ) && !at[iat].endpoint) ------------------ | | 64| 3.27k|#define SALT_ACCEPTOR 4 ------------------ | Branch (4061:13): [True: 2.96k, False: 303] | Branch (4061:73): [True: 0, False: 2.96k] ------------------ 4062| 0| { 4063| 0| continue; /* should not happen */ 4064| 0| } 4065| 3.27k| s_subtype_all |= s_group_info->s_candidate[i].subtype; 4066| 3.27k| if (at[iat].endpoint != nCurTGroupNumber || !at[iat].endpoint) ------------------ | Branch (4066:13): [True: 1.45k, False: 1.82k] | Branch (4066:53): [True: 142, False: 1.67k] ------------------ 4067| 1.59k| { 4068| 1.59k| nMinNumEndpoints++; 4069| 1.59k| } 4070| 3.27k| nCurTGroupNumber = (int) at[iat].endpoint; 4071| 3.27k| } 4072| 1.14k| if (nMinNumEndpoints <= 1) ------------------ | Branch (4072:9): [True: 878, False: 267] ------------------ 4073| 878| { 4074| 878| return 0; /* too few endpoints */ 4075| 878| } 4076| | 4077| | /* Make sure we have enough memory */ 4078| 267| if (nMinNumEndpoints > MAX_STACK_ARRAY_LEN) ------------------ | | 112| 267|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (4078:9): [True: 0, False: 267] ------------------ 4079| 0| { 4080| 0| if (!( EndPoint = (T_ENDPOINT *) inchi_calloc( nMinNumEndpoints, sizeof( EndPoint[0] ) ) )) ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ | Branch (4080:13): [True: 0, False: 0] ------------------ 4081| 0| { 4082| | /*printf("BNS_OUT_OF_RAM-8\n");*/ 4083| 0| return BNS_OUT_OF_RAM; ------------------ | | 49| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4084| 0| } 4085| 0| } 4086| | 4087| 267| nCurTGroupNumber = MAX_ATOMS; /* impossible t-group number */ ------------------ | | 15| 267|#define MAX_ATOMS 32766 ------------------ 4088| 1.17k| for (i = j = 0; i < s_group_info->num_candidates; i++) ------------------ | Branch (4088:21): [True: 911, False: 267] ------------------ 4089| 911| { 4090| 911| iat = s_group_info->s_candidate[i].atnumber; 4091| 911| if (s_group_info->s_candidate[i].subtype == SALT_ACCEPTOR && !at[iat].endpoint) ------------------ | | 64| 1.82k|#define SALT_ACCEPTOR 4 ------------------ | Branch (4091:13): [True: 0, False: 911] | Branch (4091:70): [True: 0, False: 0] ------------------ 4092| 0| { 4093| 0| continue; 4094| 0| } 4095| 911| if (at[iat].endpoint != nCurTGroupNumber || !at[iat].endpoint) ------------------ | Branch (4095:13): [True: 572, False: 339] | Branch (4095:53): [True: 142, False: 197] ------------------ 4096| 714| { 4097| 714| AddEndPoint( EndPoint + j, at, iat ); 4098| 714| j++; 4099| 714| } 4100| 911| nCurTGroupNumber = (int) at[iat].endpoint; 4101| 911| } 4102| | 4103| 267| ret = RegisterEndPoints( pCG, t_group_info, EndPoint, j, at, 4104| 267| num_atoms, c_group_info, pBNS ); 4105| | 4106| 267| if (ret == -1) ------------------ | Branch (4106:9): [True: 0, False: 267] ------------------ 4107| 0| { 4108| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4109| 0| } 4110| | 4111| 267| if (EndPoint != EndPointStackArray) ------------------ | Branch (4111:9): [True: 0, False: 267] ------------------ 4112| 0| { 4113| 0| inchi_free( EndPoint ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 4114| 0| } 4115| | 4116| 267| return ret; 4117| 267|} MakeIsotopicHGroup: 4125| 4.89k|{ 4126| | /* All tautomeric atoms and all possible H+ donors and acceptors that have H */ 4127| 4.89k| int i, j, k, n, bHasH, tg, nError = 0; 4128| | /* djb-rwth: removing redundant variables */ 4129| 4.89k| int nMaxNumCandidates, nNumCandidates, nNumNonTautCandidates; 4130| | 4131| | 4132| 4.89k| if (!s_group_info || !s_group_info->s_candidate || /*s_group_info->num_candidates <= 0 ||*/ ------------------ | Branch (4132:9): [True: 0, False: 4.89k] | Branch (4132:26): [True: 0, False: 4.89k] ------------------ 4133| 4.89k| !t_group_info || !t_group_info->t_group) ------------------ | Branch (4133:10): [True: 0, False: 4.89k] | Branch (4133:27): [True: 0, False: 4.89k] ------------------ 4134| 0| { 4135| 0| return 0; 4136| 0| } 4137| 4.89k| nMaxNumCandidates = s_group_info->max_num_candidates; 4138| | /* djb-rwth: removing redundant code */ 4139| 4.89k| memset( t_group_info->num_iso_H, 0, sizeof( t_group_info->num_iso_H ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4140| 4.89k| if (1 || ( s_group_info->num_candidates < 0 )) ------------------ | Branch (4140:9): [True: 4.89k, Folded] | Branch (4140:14): [True: 0, False: 0] ------------------ 4141| 4.89k| { 4142| 4.89k| int s_type, s_subtype; 4143| 4.89k| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 4144| 19.7k| for (i = 0, nNumCandidates = nNumNonTautCandidates = 0; i < num_atoms; i++) ------------------ | Branch (4144:65): [True: 14.8k, False: 4.89k] ------------------ 4145| 14.8k| { 4146| 14.8k| s_subtype = 0; 4147| 14.8k| s_type = 0; 4148| 14.8k| if (at[i].endpoint) ------------------ | Branch (4148:17): [True: 350, False: 14.4k] ------------------ 4149| 350| { 4150| 350| if (( tg = t_group_info->tGroupNumber[at[i].endpoint] ) && ------------------ | Branch (4150:21): [True: 350, False: 0] ------------------ 4151| 350| at[i].endpoint == t_group_info->t_group[tg -= 1].nGroupNumber) ------------------ | Branch (4151:22): [True: 350, False: 0] ------------------ 4152| 350| { 4153| 350| bHasH = (int) t_group_info->t_group[tg].num[0] - (int) t_group_info->t_group[tg].num[1]; 4154| 350| } 4155| 0| else 4156| 0| { 4157| 0| nError = BNS_PROGRAM_ERR; ------------------ | | 50| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4158| 0| break; 4159| 0| } 4160| 350| } 4161| 14.4k| else 4162| 14.4k| { 4163| 14.4k| bHasH = (int) at[i].num_H; 4164| 14.4k| } 4165| 14.8k| if ((bHasH && at[i].endpoint) || /* tautomeric atoms */ ------------------ | Branch (4165:18): [True: 844, False: 13.9k] | Branch (4165:27): [True: 297, False: 547] ------------------ 4166| | /* non-tautomeric heteroatoms that 4167| | (a) have H and 4168| | (b) may be donors of H 4169| | therefore may exchange isotopic-non-isotopic H */ 4170| 14.5k| (bHasH && ------------------ | Branch (4170:19): [True: 547, False: 13.9k] ------------------ 4171| 547| ( 0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (4171:20): [True: 11, False: 536] ------------------ 4172| | /* -C=O or =C-OH, O = S, Se, Te */ 4173| | 4174| | /*(t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT) &&*/ 4175| 536| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1/* bAccept_O*/ ) ) || ------------------ | Branch (4175:20): [True: 23, False: 513] ------------------ 4176| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above. M may be N */ 4177| | 4178| 513| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) || ------------------ | Branch (4178:20): [True: 25, False: 488] ------------------ 4179| | /* >C-SH, >C-S(-); S=S,Se,Te */ 4180| | 4181| | /* other proton donor or acceptor */ 4182| 488| (bHasAcidicHydrogen(at, i) && ((s_type = 3), (s_subtype = SALT_p_DONOR))) || ------------------ | | 65| 165|#define SALT_p_DONOR 8 /* >C-SH */ ------------------ | Branch (4182:23): [True: 165, False: 323] | Branch (4182:52): [True: 165, False: 0] ------------------ 4183| 323| (bHasAcidicMinus(at, i) && ((s_type = 3), (s_subtype = SALT_p_ACCEPTOR))) || ------------------ | | 66| 11|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ ------------------ | Branch (4183:23): [True: 11, False: 312] | Branch (4183:49): [True: 11, False: 0] ------------------ 4184| 312| (bHasOtherExchangableH(at, i) && ((s_type = 3), (s_subtype = SALT_DONOR_H))))) ------------------ | | 62| 11|#define SALT_DONOR_H 1 ------------------ | Branch (4184:23): [True: 11, False: 301] | Branch (4184:55): [True: 11, False: 0] ------------------ 4185| | 4186| 14.8k| ) 4187| 543| { 4188| 543| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (4188:21): [True: 0, False: 543] ------------------ 4189| 0| { 4190| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 54| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4191| 0| } 4192| 543| s_candidate[nNumCandidates].atnumber = i; 4193| 543| s_candidate[nNumCandidates].type = s_type; 4194| 543| s_candidate[nNumCandidates].subtype = s_subtype; 4195| 543| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 4196| 543| nNumCandidates++; 4197| 543| nNumNonTautCandidates += !at[i].endpoint; 4198| | /* djb-rwth: removing redundant code */ 4199| 543| } 4200| 14.8k| } 4201| | 4202| 4.89k| if (nError) ------------------ | Branch (4202:13): [True: 0, False: 4.89k] ------------------ 4203| 0| { 4204| 0| return nError; 4205| 0| } 4206| | 4207| 4.89k| if (nNumCandidates > 0) ------------------ | Branch (4207:13): [True: 273, False: 4.62k] ------------------ 4208| 273| { 4209| 273| t_group_info->nIsotopicEndpointAtomNumber = (AT_NUMB *) inchi_calloc( (long long)nNumNonTautCandidates + 1, sizeof( t_group_info->nIsotopicEndpointAtomNumber[0] ) ); /* djb-rwth: cast operator added */ ------------------ | | 1146| 273|#define inchi_calloc calloc ------------------ 4210| 273| if (t_group_info->nIsotopicEndpointAtomNumber) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (4210:17): [True: 273, False: 0] ------------------ 4211| 273| { 4212| 273| t_group_info->nIsotopicEndpointAtomNumber[0] = nNumNonTautCandidates; 4213| 816| for (i = 0, n = 1; i < nNumCandidates; i++) ------------------ | Branch (4213:36): [True: 543, False: 273] ------------------ 4214| 543| { 4215| 543| k = s_candidate[i].atnumber; 4216| 543| if (!at[k].endpoint) ------------------ | Branch (4216:25): [True: 246, False: 297] ------------------ 4217| 246| { 4218| 246| t_group_info->nIsotopicEndpointAtomNumber[n++] = k; 4219| 246| } 4220| 2.17k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 25| 2.17k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (4220:33): [True: 1.62k, False: 543] ------------------ 4221| 1.62k| { 4222| 1.62k| t_group_info->num_iso_H[j] += at[k].num_iso_H[j]; 4223| 1.62k| } 4224| 543| at[k].cFlags |= AT_FLAG_ISO_H_POINT; ------------------ | | 50| 543|#define AT_FLAG_ISO_H_POINT 0x01 /**< may have isotopic H */ ------------------ 4225| 543| } 4226| 273| t_group_info->nNumIsotopicEndpoints = nNumNonTautCandidates + 1; 4227| 273| } 4228| 273| } 4229| 4.89k| } 4230| | 4231| 4.89k| return nNumCandidates; 4232| 4.89k|} MarkTautomerGroups: 4308| 299k|{ 4309| 299k| int i, j, k, m, endpoint_valence, centerpoint, endpoint, bond_type, nMobile, num_changes = 0, tot_changes = 0; 4310| 299k| T_ENDPOINT EndPoint[MAXVAL]; 4311| 299k| T_BONDPOS BondPos[MAXVAL]; 4312| 299k| AT_NUMB nGroupNumber; 4313| 299k| int bDiffGroups; 4314| 299k| int nNumEndPoints, nNumBondPos, nNumPossibleMobile; 4315| 299k| int bNonTautBond, bAltBond; /* djb-rwth: removing redundant variables */ 4316| 299k| int nNumDonor, nNumAcceptor, bPossiblyEndpoint; 4317| 299k| int bIgnoreIsotopic; /* djb-rwth: removing redundant variables */ 4318| 299k| ENDPOINT_INFO eif1, eif2; 4319| 299k| int nErr = 0; 4320| | 4321| 299k|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) 4322| 299k|#define ACTUAL_ORDER(PBNS, IAT,IBOND, BTYPE) ( ((PBNS) && (PBNS)->edge && (PBNS)->vert &&\ 4323| 299k| ((BTYPE)==BOND_ALT_123 || (BTYPE)==BOND_ALT_13 || (BTYPE)==BOND_ALT_23))? (PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].flow+BOND_TYPE_SINGLE:(BTYPE)) 4324| | 4325| | 4326| 299k| if (!t_group_info || !( t_group_info->bTautFlags & TG_FLAG_TEST_TAUT__ATOMS )) ------------------ | | 918| 263k|#define TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */ ------------------ | Branch (4326:9): [True: 36.3k, False: 263k] | Branch (4326:26): [True: 0, False: 263k] ------------------ 4327| 36.3k| { 4328| 36.3k| return 0; 4329| 36.3k| } 4330| | 4331| | /* Initial t_group allocation */ 4332| 263k| if (!t_group_info->t_group && !t_group_info->max_num_t_groups) ------------------ | Branch (4332:9): [True: 252k, False: 11.0k] | Branch (4332:35): [True: 252k, False: 0] ------------------ 4333| 252k| { 4334| 252k| INCHI_MODE bTautFlags = t_group_info->bTautFlags; /* save initial setting */ 4335| 252k| INCHI_MODE bTautFlagsDone = t_group_info->bTautFlagsDone; /* save previous findings, if any */ 4336| 252k| TNI tni = t_group_info->tni; 4337| 252k| AT_NUMB *tGroupNumber = t_group_info->tGroupNumber; 4338| 252k| T_GROUP* tgi_tgr = NULL; /* copied from below 2024-09-01 DT */ 4339| | 4340| 252k| bIgnoreIsotopic = t_group_info->bIgnoreIsotopic; 4341| 252k| memset( t_group_info, 0, sizeof( *t_group_info ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 4342| 252k| t_group_info->bIgnoreIsotopic = bIgnoreIsotopic; /* restore initial setting */ 4343| 252k| t_group_info->bTautFlags = bTautFlags; 4344| 252k| t_group_info->bTautFlagsDone = bTautFlagsDone; 4345| 252k| t_group_info->tni = tni; 4346| 252k| t_group_info->tGroupNumber = tGroupNumber; 4347| 252k| t_group_info->max_num_t_groups = num_atoms / 2 + 1; /* upper limit */ 4348| | /* djb-rwth: fixing oss-fuzz issue #52978 */ 4349| 252k| tgi_tgr = (T_GROUP*)inchi_calloc((long long)t_group_info->max_num_t_groups + 1, sizeof(t_group_info->t_group[0])); ------------------ | | 1146| 252k|#define inchi_calloc calloc ------------------ 4350| 252k| if (!tgi_tgr) ------------------ | Branch (4350:13): [True: 0, False: 252k] ------------------ 4351| 0| { 4352| 0| t_group_info->max_num_t_groups = -1; 4353| 0| t_group_info->t_group = NULL; 4354| 0| return (-1); /* failed, out of RAM */ 4355| 0| } 4356| 252k| else 4357| 252k| { 4358| 252k| t_group_info->t_group = tgi_tgr; 4359| 252k| } 4360| 252k| } 4361| | 4362| | /* Check if t_group_info exists */ 4363| 263k| if (!t_group_info->t_group || !t_group_info->max_num_t_groups) ------------------ | Branch (4363:9): [True: 0, False: 263k] | Branch (4363:35): [True: 0, False: 263k] ------------------ 4364| 0| { 4365| 0| return 0; 4366| 0| } 4367| | 4368| 263k| if (0 > t_group_info->max_num_t_groups) ------------------ | Branch (4368:9): [True: 0, False: 263k] ------------------ 4369| 0| { 4370| 0| return t_group_info->max_num_t_groups; 4371| 0| } 4372| | 4373| | /* djb-rwth: removing redundant code */ 4374| | 4375| | /* 1-3 tautomers */ 4376| 1.38M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4376:17): [True: 1.11M, False: 263k] ------------------ 4377| 1.11M| { 4378| | /* Find possible endpoint Z = at[i] */ 4379| 1.11M| if ((endpoint_valence = nGetEndpointInfo( at, i, &eif1 ))) /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4379:13): [True: 89.2k, False: 1.02M] ------------------ 4380| 89.2k| { 4381| | /* 1st endpoint candidate found. Find centerpoint candidate */ 4382| 212k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4382:25): [True: 123k, False: 89.2k] ------------------ 4383| 123k| { 4384| 123k| bond_type = (int) at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 123k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4385| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4386| | bond_type = ACTUAL_ORDER( pBNS, i, j, bond_type ); 4387| |#endif 4388| 123k| centerpoint = (int) at[i].neighbor[j]; /* a centerpoint candidate */ 4389| 123k| if (( bond_type == BOND_DOUBLE || ------------------ | | 178| 123k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 246k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4389:23): [True: 35.2k, False: 88.1k] ------------------ 4390| 88.1k| bond_type == BOND_ALTERN || ------------------ | | 180| 88.1k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 211k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4390:23): [True: 7.87k, False: 80.2k] ------------------ 4391| 80.2k| bond_type == BOND_ALT12NS || ------------------ | | 186| 203k|#define BOND_ALT12NS 9 ------------------ | Branch (4391:23): [True: 5.60k, False: 74.6k] ------------------ 4392| 86.2k| bond_type == BOND_TAUTOM ) && is_centerpoint_elem( at[centerpoint].el_number ) ------------------ | | 185| 74.6k|#define BOND_TAUTOM 8 ------------------ | Branch (4392:23): [True: 37.5k, False: 37.1k] | Branch (4392:53): [True: 77.7k, False: 8.45k] ------------------ 4393| 77.7k| && ALLOWED_EDGE( pBNS, i, j ) ------------------ | | 4321| 77.7k|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 77.7k] | | | Branch (4321:53): [True: 0, False: 77.7k] | | | Branch (4321:70): [True: 0, False: 77.7k] | | | Branch (4321:87): [True: 75.3k, False: 2.43k] | | ------------------ ------------------ 4394| 123k| ) 4395| 75.3k| { 4396| | /* Test a centerpoint candidate. */ 4397| | /* find all endpoints including at[i] and store them into EndPoint[] */ 4398| 75.3k| nNumPossibleMobile = 0; 4399| 75.3k| nGroupNumber = (AT_NUMB) num_atoms; /* greater than any tautomeric group number */ 4400| 75.3k| bDiffGroups = -1; /* ignore the first difference */ 4401| 75.3k| nNumDonor = nNumAcceptor = 0; 4402| 288k| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) ------------------ | Branch (4402:69): [True: 213k, False: 75.3k] ------------------ 4403| 213k| { 4404| 213k| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 4405| 213k| bond_type = (int) at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 213k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4406| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4407| | bond_type = ACTUAL_ORDER( pBNS, centerpoint, k, bond_type ); 4408| |#endif 4409| | /* djb-rwth: removing redundant code */ 4410| 213k| bNonTautBond = 4411| 213k| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 4412| 213k| bPossiblyEndpoint = 0; 4413| 213k| if (!ALLOWED_EDGE( pBNS, centerpoint, k )) ------------------ | | 4321| 213k|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 213k] | | | Branch (4321:53): [True: 0, False: 213k] | | | Branch (4321:70): [True: 0, False: 213k] | | | Branch (4321:87): [True: 207k, False: 5.78k] | | ------------------ ------------------ 4414| 5.78k| { 4415| 5.78k| continue; 4416| 5.78k| } 4417| 207k| else 4418| 207k| { 4419| 207k| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 180| 207k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 415k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 186| 401k|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 185| 179k|#define BOND_TAUTOM 8 ------------------ | Branch (4419:33): [True: 14.5k, False: 193k] | Branch (4419:61): [True: 13.2k, False: 179k] | Branch (4419:90): [True: 81.2k, False: 98.6k] ------------------ 4420| 109k| { 4421| | /* djb-rwth: removing redundant code */ 4422| 109k|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 4423| 109k| bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 109k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 218k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 94.5k|#define BOND_ALT12NS 9 ------------------ | Branch (4423:46): [True: 14.5k, False: 94.5k] | Branch (4423:74): [True: 13.2k, False: 81.2k] ------------------ 4424| 109k|#endif 4425| 109k| } 4426| 98.6k| else 4427| 98.6k| { 4428| 98.6k| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 177| 98.6k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 197k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 178| 43.5k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 43.5k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4428:37): [True: 55.1k, False: 43.5k] | Branch (4428:65): [True: 38.2k, False: 5.25k] ------------------ 4429| 93.4k| { 4430| 93.4k| bNonTautBond = 1; 4431| 93.4k| } 4432| 5.25k| else 4433| 5.25k| { 4434| 5.25k| continue; 4435| 5.25k| } 4436| 98.6k| } 4437| 207k| } 4438| | 4439| 202k| if (!( endpoint_valence = nGetEndpointInfo( at, endpoint, &eif1 ) )) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4439:29): [True: 58.6k, False: 143k] ------------------ 4440| 58.6k| continue; /* not an endpoint element or can't have mobile groups */ 4441| | /* save information about the found possible tautomeric endpoint */ 4442| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 4443| 143k| nMobile = 4444| 143k| AddAtom2num( EndPoint[nNumEndPoints].num, at, endpoint, 2 ); /* fill out */ 4445| 143k| AddAtom2DA( EndPoint[nNumEndPoints].num_DA, at, endpoint, 2 ); 4446| | /* --- why is isitopic info missing ? -- see below 4447| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 4448| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 4449| | */ 4450| 143k| if (bNonTautBond) ------------------ | Branch (4450:29): [True: 44.1k, False: 99.8k] ------------------ 4451| 44.1k| { 4452| 44.1k| m = ( bond_type == BOND_SINGLE && ( nMobile || at[endpoint].endpoint ) ); ------------------ | | 177| 44.1k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 88.2k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4452:35): [True: 10.8k, False: 33.2k] | Branch (4452:65): [True: 6.32k, False: 4.50k] | Branch (4452:76): [True: 224, False: 4.28k] ------------------ 4453| 44.1k| nNumDonor += m; 4454| 44.1k| bPossiblyEndpoint += m; 4455| 44.1k| m = ( bond_type == BOND_DOUBLE ); ------------------ | | 178| 44.1k|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 44.1k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 4456| 44.1k| nNumAcceptor += m; 4457| 44.1k| bPossiblyEndpoint += m; 4458| 44.1k| } 4459| 99.8k| else 4460| 99.8k| { 4461| | /* Tautomeric or alternating bond */ 4462| 99.8k| m = ( 0 != at[endpoint].endpoint || eif1.cDonor ); ------------------ | Branch (4462:35): [True: 77.4k, False: 22.4k] | Branch (4462:65): [True: 487, False: 21.9k] ------------------ 4463| 99.8k| nNumDonor += m; 4464| 99.8k| bPossiblyEndpoint += m; 4465| 99.8k| m = ( at[endpoint].endpoint || ------------------ | Branch (4465:35): [True: 77.4k, False: 22.4k] ------------------ 4466| 22.4k| eif1.cNeutralBondsValence > at[endpoint].valence ); ------------------ | Branch (4466:35): [True: 21.9k, False: 487] ------------------ 4467| 99.8k| nNumAcceptor += m; 4468| 99.8k| bPossiblyEndpoint += m; 4469| 99.8k| } 4470| 143k| if (!bPossiblyEndpoint) ------------------ | Branch (4470:29): [True: 4.28k, False: 139k] ------------------ 4471| 4.28k| { 4472| 4.28k| continue; 4473| 4.28k| } 4474| 139k| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 4475| 139k| EndPoint[nNumEndPoints].nEquNumber = 0; 4476| 139k| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB) endpoint; 4477| 139k| if (nGroupNumber != at[endpoint].endpoint) ------------------ | Branch (4477:29): [True: 76.0k, False: 63.5k] ------------------ 4478| 76.0k| { 4479| 76.0k| bDiffGroups++; 4480| 76.0k| nGroupNumber = at[endpoint].endpoint; 4481| 76.0k| } 4482| | 4483| | /* save positions of all, not only possibly tautomeric bonds */ 4484| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4485| | if (bNonTautBond || bAltBond) 4486| | { 4487| |#endif 4488| 139k| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB) centerpoint; 4489| 139k| BondPos[nNumBondPos].neighbor_index = (AT_NUMB) k; /* bond ordering number; used to change bonds to tautomeric only */ 4490| 139k| nNumBondPos++; 4491| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4492| | } 4493| |#endif 4494| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 4495| | /* (b) the centerpoint is adjacent to another endpoint */ 4496| 139k| nNumPossibleMobile += ( nMobile > 0 || at[endpoint].endpoint ); ------------------ | Branch (4496:49): [True: 60.5k, False: 79.0k] | Branch (4496:64): [True: 32.1k, False: 46.9k] ------------------ 4497| 139k| nNumEndPoints++; 4498| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 4499| 139k| } 4500| 75.3k| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor) ------------------ | Branch (4500:25): [True: 52.9k, False: 22.3k] | Branch (4500:46): [True: 41.7k, False: 11.2k] | Branch (4500:68): [True: 39.3k, False: 2.42k] | Branch (4500:81): [True: 39.3k, False: 40] ------------------ 4501| 39.3k| { 4502| | /* 4503| | * a tautomeric group has been found 4504| | * 4505| | * at this point: 4506| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 4507| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 4508| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 4509| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 4510| | */ 4511| | 4512| 39.3k| nErr = FindAccessibleEndPoints( pCG, EndPoint, 4513| 39.3k| &nNumEndPoints, 4514| 39.3k| BondPos, &nNumBondPos, 4515| 39.3k| pBNS, pBD, at, 4516| 39.3k| num_atoms, c_group_info, 4517| 39.3k| ALT_PATH_MODE_TAUTOM ); ------------------ | | 310| 39.3k|#define ALT_PATH_MODE_TAUTOM 1 ------------------ 4518| | 4519| 39.3k| if (IS_BNS_ERROR( nErr )) ------------------ | | 67| 39.3k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 39.3k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 39.3k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 39.3k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 39.3k, False: 0] | | | Branch (67:44): [True: 3, False: 39.3k] | | ------------------ ------------------ 4520| 3| { 4521| 3| return nErr; 4522| 3| } 4523| 39.3k| nErr = 0; 4524| 39.3k| if (nNumEndPoints > 0) { ------------------ | Branch (4524:29): [True: 39.1k, False: 126] ------------------ 4525| 39.1k| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (4525:33): [True: 5.82k, False: 33.3k] | Branch (4525:50): [True: 297, False: 33.0k] ------------------ 4526| | 4527| 6.12k| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 4528| 6.12k| if (num_changes == -1) { ------------------ | Branch (4528:37): [True: 0, False: 6.12k] ------------------ 4529| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4530| 0| } 4531| 6.12k| if (num_changes < 0) { ------------------ | Branch (4531:37): [True: 0, False: 6.12k] ------------------ 4532| 0| nErr = num_changes; 4533| 0| } 4534| 6.12k| if (nErr) ------------------ | Branch (4534:37): [True: 0, False: 6.12k] ------------------ 4535| 0| goto exit_function; 4536| 6.12k| tot_changes += (num_changes>0); 4537| 6.12k| } 4538| 39.1k| if (nNumBondPos > 0) { ------------------ | Branch (4538:33): [True: 39.1k, False: 0] ------------------ 4539| | /* some of the bonds have not been marked as tautomeric yet */ 4540| 39.1k| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 4541| 39.1k| tot_changes += (num_changes>0); 4542| 39.1k| } 4543| 39.1k| } 4544| 39.3k| } 4545| 75.3k| } 4546| 123k| } 4547| 89.2k| } 4548| 1.11M| } 4549| | 4550| | 4551| 263k|#if ( TAUT_PT_22_00 == 1 ) /******* BEGIN PT_22_00 ********/ 4552| 263k| if (t_group_info->bTautFlags & TG_FLAG_PT_22_00) { ------------------ | | 953| 263k|#define TG_FLAG_PT_22_00 0x00800000 ------------------ | Branch (4552:9): [True: 0, False: 263k] ------------------ 4553| | /*** [#1:1][CX4:2][NX2:3]=[CX3:4]>>[CX3:2]=[NX2:3][CX4:4][#1:1] ***/ 4554| | /*** Similar to the previous case of M=Q-ZH >> MH-Q=Z, with M,Z = "C" and Q = "N" ***/ 4555| 0| for (i = 0; i < num_atoms; i++) { ------------------ | Branch (4555:21): [True: 0, False: 0] ------------------ 4556| | /* find possible endpoint Z = at[i] */ 4557| 0| if ((endpoint_valence = nGetEndpointInfo_PT_22_00(at, i, &eif1))) { /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4557:17): [True: 0, False: 0] ------------------ 4558| | /* 1st endpoint candidate found. Find centerpoint candidate */ 4559| 0| for (j = 0; j < at[i].valence; j++) { ------------------ | Branch (4559:29): [True: 0, False: 0] ------------------ 4560| 0| bond_type = (int)at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4561| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4562| | bond_type = ACTUAL_ORDER(pBNS, i, j, bond_type); 4563| |#endif 4564| 0| centerpoint = (int)at[i].neighbor[j]; /* a centerpoint candidate */ 4565| 0| if ((bond_type == BOND_DOUBLE || ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4565:26): [True: 0, False: 0] ------------------ 4566| 0| bond_type == BOND_ALTERN || ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4566:25): [True: 0, False: 0] ------------------ 4567| 0| bond_type == BOND_ALT12NS || ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4567:25): [True: 0, False: 0] ------------------ 4568| 0| bond_type == BOND_TAUTOM) && at[centerpoint].el_number == EL_NUMBER_N ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ bond_type == BOND_TAUTOM) && at[centerpoint].el_number == EL_NUMBER_N ------------------ | | 14| 0|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (4568:25): [True: 0, False: 0] | Branch (4568:54): [True: 0, False: 0] ------------------ 4569| 0| && ALLOWED_EDGE(pBNS, i, j) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 4570| 0| ) { 4571| | /* test a centerpoint candidate. */ 4572| | /* find all endpoints including at[i] and store them into EndPoint[] */ 4573| 0| nNumPossibleMobile = 0; 4574| 0| nGroupNumber = (AT_NUMB)num_atoms; /* greater than any tautomeric group number */ 4575| 0| bDiffGroups = -1; /* ignore the first difference */ 4576| 0| nNumDonor = nNumAcceptor = 0; 4577| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) { ------------------ | Branch (4577:73): [True: 0, False: 0] ------------------ 4578| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 4579| 0| bond_type = (int)at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4580| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4581| | bond_type = ACTUAL_ORDER(pBNS, centerpoint, k, bond_type); 4582| |#endif 4583| | /* djb-rwth: removing redundant code */ 4584| 0| bNonTautBond = 4585| 0| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 4586| 0| bPossiblyEndpoint = 0; 4587| 0| if (!ALLOWED_EDGE(pBNS, centerpoint, k)) { ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 4588| 0| continue; 4589| 0| } 4590| 0| else 4591| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4591:37): [True: 0, False: 0] | Branch (4591:65): [True: 0, False: 0] | Branch (4591:94): [True: 0, False: 0] ------------------ 4592| | /* djb-rwth: removing redundant code */ 4593| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 4594| 0| bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4594:49): [True: 0, False: 0] | Branch (4594:77): [True: 0, False: 0] ------------------ 4595| 0|#endif 4596| 0| } 4597| 0| else 4598| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4598:41): [True: 0, False: 0] | Branch (4598:69): [True: 0, False: 0] ------------------ 4599| 0| bNonTautBond = 1; 4600| 0| else 4601| 0| continue; 4602| | 4603| 0| if (!(endpoint_valence = nGetEndpointInfo_PT_22_00(at, endpoint, &eif1))) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4603:33): [True: 0, False: 0] ------------------ 4604| 0| continue; /* not an endpoint element or can't have mobile groups */ 4605| | /* save information about the found possible tautomeric endpoint */ 4606| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 4607| 0| nMobile = 4608| 0| AddAtom2num(EndPoint[nNumEndPoints].num, at, endpoint, 2); /* fill out */ 4609| 0| AddAtom2DA(EndPoint[nNumEndPoints].num_DA, at, endpoint, 2); 4610| | /* --- why is isitopic info missing ? -- see below 4611| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 4612| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 4613| | */ 4614| 0| if (bNonTautBond) { ------------------ | Branch (4614:33): [True: 0, False: 0] ------------------ 4615| 0| m = (bond_type == BOND_SINGLE && (nMobile || at[endpoint].endpoint)); ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4615:38): [True: 0, False: 0] | Branch (4615:67): [True: 0, False: 0] | Branch (4615:78): [True: 0, False: 0] ------------------ 4616| 0| nNumDonor += m; 4617| 0| bPossiblyEndpoint += m; 4618| 0| m = (bond_type == BOND_DOUBLE); ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 4619| 0| nNumAcceptor += m; 4620| 0| bPossiblyEndpoint += m; 4621| 0| } 4622| 0| else { 4623| | /* tautomeric or alternating bond */ 4624| 0| m = (0 != at[endpoint].endpoint || eif1.cDonor); ------------------ | Branch (4624:38): [True: 0, False: 0] | Branch (4624:68): [True: 0, False: 0] ------------------ 4625| 0| nNumDonor += m; 4626| 0| bPossiblyEndpoint += m; 4627| 0| m = (at[endpoint].endpoint || ------------------ | Branch (4627:38): [True: 0, False: 0] ------------------ 4628| 0| eif1.cNeutralBondsValence > at[endpoint].valence); ------------------ | Branch (4628:37): [True: 0, False: 0] ------------------ 4629| 0| nNumAcceptor += m; 4630| 0| bPossiblyEndpoint += m; 4631| 0| } 4632| 0| if (!bPossiblyEndpoint) ------------------ | Branch (4632:33): [True: 0, False: 0] ------------------ 4633| 0| continue; 4634| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 4635| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 4636| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB)endpoint; 4637| 0| if (nGroupNumber != at[endpoint].endpoint) { ------------------ | Branch (4637:33): [True: 0, False: 0] ------------------ 4638| 0| bDiffGroups++; 4639| 0| nGroupNumber = at[endpoint].endpoint; 4640| 0| } 4641| | 4642| | /* save positions of all, not only possibly tautomeric bonds */ 4643| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4644| | if (bNonTautBond || bAltBond) { 4645| |#endif 4646| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB)centerpoint; 4647| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB)k; /* bond ordering number; used to change bonds to tautomeric only */ 4648| 0| nNumBondPos++; 4649| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4650| | } 4651| |#endif 4652| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 4653| | /* (b) the centerpoint is adjacent to another endpoint */ 4654| 0| nNumPossibleMobile += (nMobile>0 || at[endpoint].endpoint); ------------------ | Branch (4654:52): [True: 0, False: 0] | Branch (4654:65): [True: 0, False: 0] ------------------ 4655| 0| nNumEndPoints++; 4656| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 4657| 0| } 4658| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor) { ------------------ | Branch (4658:29): [True: 0, False: 0] | Branch (4658:50): [True: 0, False: 0] | Branch (4658:72): [True: 0, False: 0] | Branch (4658:85): [True: 0, False: 0] ------------------ 4659| | /* 4660| | * a tautomeric group has been found 4661| | * 4662| | * at this point: 4663| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 4664| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 4665| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 4666| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 4667| | */ 4668| | 4669| 0| nErr = FindAccessibleEndPoints(pCG, 4670| 0| EndPoint, &nNumEndPoints, 4671| 0| BondPos, &nNumBondPos, 4672| 0| pBNS, pBD, at, 4673| 0| num_atoms, c_group_info, 4674| 0| ALT_PATH_MODE_TAUTOM_PT_22_00); ------------------ | | 324| 0|#define ALT_PATH_MODE_TAUTOM_PT_22_00 11 ------------------ 4675| | 4676| 0| if (IS_BNS_ERROR(nErr)) { ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 4677| 0| return nErr; 4678| 0| } 4679| 0| nErr = 0; 4680| | 4681| 0| if (nNumEndPoints > 0) { ------------------ | Branch (4681:33): [True: 0, False: 0] ------------------ 4682| 0| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (4682:37): [True: 0, False: 0] | Branch (4682:54): [True: 0, False: 0] ------------------ 4683| | 4684| 0| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 4685| 0| if (num_changes == -1) { ------------------ | Branch (4685:41): [True: 0, False: 0] ------------------ 4686| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4687| 0| } 4688| 0| if (num_changes < 0) { ------------------ | Branch (4688:41): [True: 0, False: 0] ------------------ 4689| 0| nErr = num_changes; 4690| 0| } 4691| | 4692| 0| if (nErr) ------------------ | Branch (4692:41): [True: 0, False: 0] ------------------ 4693| 0| goto exit_function; 4694| 0| tot_changes += (num_changes>0); 4695| 0| } 4696| 0| if (nNumBondPos > 0) { ------------------ | Branch (4696:37): [True: 0, False: 0] ------------------ 4697| | /* some of the bonds have not been marked as tautomeric yet */ 4698| 0| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 4699| 0| tot_changes += (num_changes>0); 4700| 0| } 4701| 0| } 4702| 0| } 4703| 0| } 4704| 0| } 4705| 0| } 4706| 0| } 4707| 0| } 4708| 263k|#endif /********** END PT_22_00 ************/ 4709| | 4710| 263k|#if ( TAUT_PT_16_00 == 1 ) /******* BEGIN PT_16_00 ********/ 4711| 263k| if (t_group_info->bTautFlags & TG_FLAG_PT_16_00) { ------------------ | | 954| 263k|#define TG_FLAG_PT_16_00 0x01000000 ------------------ | Branch (4711:9): [True: 0, False: 263k] ------------------ 4712| | /*** [#1:1][O;!R:2][N+0z1:3]=[CX3:4]>>[O;!R:2]=[N+0z1:3][CX4:4][#1:1] ***/ 4713| | /*** Similar to the previous case of M=Q-ZH >> MH-Q=Z, with M,Z = "C, O" and Q = "N" ***/ 4714| 0| for (i = 0; i < num_atoms; i++) { ------------------ | Branch (4714:21): [True: 0, False: 0] ------------------ 4715| | /* find possible endpoint Z = at[i] */ 4716| 0| if ((endpoint_valence = nGetEndpointInfo_PT_16_00(at, i, &eif1))) { /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4716:17): [True: 0, False: 0] ------------------ 4717| | /* 1st endpoint candidate found. Find centerpoint candidate */ 4718| 0| for (j = 0; j < at[i].valence; j++) { ------------------ | Branch (4718:29): [True: 0, False: 0] ------------------ 4719| 0| bond_type = (int)at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4720| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4721| | bond_type = ACTUAL_ORDER(pBNS, i, j, bond_type); 4722| |#endif 4723| 0| centerpoint = (int)at[i].neighbor[j]; /* a centerpoint candidate */ 4724| 0| if ((bond_type == BOND_DOUBLE || ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4724:26): [True: 0, False: 0] ------------------ 4725| 0| bond_type == BOND_ALTERN || ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4725:25): [True: 0, False: 0] ------------------ 4726| 0| bond_type == BOND_ALT12NS || ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4726:25): [True: 0, False: 0] ------------------ 4727| 0| bond_type == BOND_TAUTOM) ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4727:25): [True: 0, False: 0] ------------------ 4728| 0| && at[centerpoint].el_number == EL_NUMBER_N ------------------ | | 14| 0|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (4728:28): [True: 0, False: 0] ------------------ 4729| 0| && at[centerpoint].valence == 2 ------------------ | Branch (4729:28): [True: 0, False: 0] ------------------ 4730| 0| && at[centerpoint].charge == 0 ------------------ | Branch (4730:28): [True: 0, False: 0] ------------------ 4731| 0| && ALLOWED_EDGE(pBNS, i, j) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 4732| 0| ) { 4733| | /* test a centerpoint candidate. */ 4734| | /* find all endpoints including at[i] and store them into EndPoint[] */ 4735| 0| nNumPossibleMobile = 0; 4736| 0| nGroupNumber = (AT_NUMB)num_atoms; /* greater than any tautomeric group number */ 4737| 0| bDiffGroups = -1; /* ignore the first difference */ 4738| 0| nNumDonor = nNumAcceptor = 0; 4739| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) { ------------------ | Branch (4739:73): [True: 0, False: 0] ------------------ 4740| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 4741| 0| bond_type = (int)at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4742| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4743| | bond_type = ACTUAL_ORDER(pBNS, centerpoint, k, bond_type); 4744| |#endif 4745| | /* djb-rwth: removing redundant code */ 4746| 0| bNonTautBond = 4747| 0| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 4748| 0| bPossiblyEndpoint = 0; 4749| 0| if (!ALLOWED_EDGE(pBNS, centerpoint, k)) { ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 4750| 0| continue; 4751| 0| } 4752| 0| else 4753| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4753:37): [True: 0, False: 0] | Branch (4753:65): [True: 0, False: 0] | Branch (4753:94): [True: 0, False: 0] ------------------ 4754| | /* djb-rwth: removing redundant code */ 4755| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 4756| 0| bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4756:49): [True: 0, False: 0] | Branch (4756:77): [True: 0, False: 0] ------------------ 4757| 0|#endif 4758| 0| } 4759| 0| else 4760| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4760:41): [True: 0, False: 0] | Branch (4760:69): [True: 0, False: 0] ------------------ 4761| 0| bNonTautBond = 1; 4762| 0| else 4763| 0| continue; 4764| | 4765| 0| if (!(endpoint_valence = nGetEndpointInfo_PT_16_00(at, endpoint, &eif1))) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4765:33): [True: 0, False: 0] ------------------ 4766| 0| continue; /* not an endpoint element or can't have mobile groups */ 4767| 0| if (at[endpoint].el_number == EL_NUMBER_O && ------------------ | | 15| 0|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (4767:33): [True: 0, False: 0] ------------------ 4768| 0| at[endpoint].nNumAtInRingSystem != 1) ------------------ | Branch (4768:33): [True: 0, False: 0] ------------------ 4769| 0| continue; 4770| 0| if (endpoint != i && at[endpoint].el_number == at[i].el_number) ------------------ | Branch (4770:33): [True: 0, False: 0] | Branch (4770:50): [True: 0, False: 0] ------------------ 4771| 0| continue; 4772| | /* save information about the found possible tautomeric endpoint */ 4773| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 4774| 0| nMobile = 4775| 0| AddAtom2num(EndPoint[nNumEndPoints].num, at, endpoint, 2); /* fill out */ 4776| 0| AddAtom2DA(EndPoint[nNumEndPoints].num_DA, at, endpoint, 2); 4777| | /* --- why is isitopic info missing ? -- see below 4778| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 4779| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 4780| | */ 4781| 0| if (bNonTautBond) { ------------------ | Branch (4781:33): [True: 0, False: 0] ------------------ 4782| 0| m = (bond_type == BOND_SINGLE && (nMobile || at[endpoint].endpoint)); ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4782:38): [True: 0, False: 0] | Branch (4782:67): [True: 0, False: 0] | Branch (4782:78): [True: 0, False: 0] ------------------ 4783| 0| nNumDonor += m; 4784| 0| bPossiblyEndpoint += m; 4785| 0| m = (bond_type == BOND_DOUBLE); ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 4786| 0| nNumAcceptor += m; 4787| 0| bPossiblyEndpoint += m; 4788| 0| } 4789| 0| else { 4790| | /* tautomeric or alternating bond */ 4791| 0| m = (0 != at[endpoint].endpoint || eif1.cDonor); ------------------ | Branch (4791:38): [True: 0, False: 0] | Branch (4791:68): [True: 0, False: 0] ------------------ 4792| 0| nNumDonor += m; 4793| 0| bPossiblyEndpoint += m; 4794| 0| m = (at[endpoint].endpoint || ------------------ | Branch (4794:38): [True: 0, False: 0] ------------------ 4795| 0| eif1.cNeutralBondsValence > at[endpoint].valence); ------------------ | Branch (4795:37): [True: 0, False: 0] ------------------ 4796| 0| nNumAcceptor += m; 4797| 0| bPossiblyEndpoint += m; 4798| 0| } 4799| 0| if (!bPossiblyEndpoint) ------------------ | Branch (4799:33): [True: 0, False: 0] ------------------ 4800| 0| continue; 4801| | 4802| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 4803| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 4804| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB)endpoint; 4805| 0| if (nGroupNumber != at[endpoint].endpoint) { ------------------ | Branch (4805:33): [True: 0, False: 0] ------------------ 4806| 0| bDiffGroups++; 4807| 0| nGroupNumber = at[endpoint].endpoint; 4808| 0| } 4809| | 4810| | /* save positions of all, not only possibly tautomeric bonds */ 4811| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4812| | if (bNonTautBond || bAltBond) { 4813| |#endif 4814| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB)centerpoint; 4815| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB)k; /* bond ordering number; used to change bonds to tautomeric only */ 4816| 0| nNumBondPos++; 4817| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4818| | } 4819| |#endif 4820| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 4821| | /* (b) the centerpoint is adjacent to another endpoint */ 4822| 0| nNumPossibleMobile += (nMobile>0 || at[endpoint].endpoint); ------------------ | Branch (4822:52): [True: 0, False: 0] | Branch (4822:65): [True: 0, False: 0] ------------------ 4823| 0| nNumEndPoints++; 4824| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 4825| 0| } 4826| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor) { ------------------ | Branch (4826:29): [True: 0, False: 0] | Branch (4826:50): [True: 0, False: 0] | Branch (4826:72): [True: 0, False: 0] | Branch (4826:85): [True: 0, False: 0] ------------------ 4827| | /* 4828| | * a tautomeric group has been found 4829| | * 4830| | * at this point: 4831| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 4832| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 4833| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 4834| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 4835| | */ 4836| 0| nErr = FindAccessibleEndPoints(pCG, 4837| 0| EndPoint, &nNumEndPoints, 4838| 0| BondPos, &nNumBondPos, 4839| 0| pBNS, pBD, at, 4840| 0| num_atoms, c_group_info, 4841| 0| ALT_PATH_MODE_TAUTOM_PT_16_00); ------------------ | | 327| 0|#define ALT_PATH_MODE_TAUTOM_PT_16_00 12 ------------------ 4842| | 4843| 0| if (IS_BNS_ERROR(nErr)) { ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 4844| 0| return nErr; 4845| 0| } 4846| 0| nErr = 0; 4847| | 4848| 0| if (nNumEndPoints > 0) { ------------------ | Branch (4848:33): [True: 0, False: 0] ------------------ 4849| 0| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (4849:37): [True: 0, False: 0] | Branch (4849:54): [True: 0, False: 0] ------------------ 4850| | 4851| 0| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 4852| 0| if (num_changes == -1) { ------------------ | Branch (4852:41): [True: 0, False: 0] ------------------ 4853| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4854| 0| } 4855| 0| if (num_changes < 0) { ------------------ | Branch (4855:41): [True: 0, False: 0] ------------------ 4856| 0| nErr = num_changes; 4857| 0| } 4858| | 4859| 0| if (nErr) ------------------ | Branch (4859:41): [True: 0, False: 0] ------------------ 4860| 0| goto exit_function; 4861| 0| tot_changes += (num_changes>0); 4862| 0| } 4863| 0| if (nNumBondPos > 0) { ------------------ | Branch (4863:37): [True: 0, False: 0] ------------------ 4864| | /* some of the bonds have not been marked as tautomeric yet */ 4865| 0| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 4866| 0| tot_changes += (num_changes>0); 4867| 0| } 4868| 0| } 4869| 0| } 4870| 0| } 4871| 0| } 4872| 0| } 4873| 0| } 4874| 0| } 4875| 263k|#endif /********** END PT_16_00 ************/ 4876| | 4877| 263k|#if ( TAUT_PT_06_00 == 1 ) /******* BEGIN PT_06_00 ********/ 4878| 263k| if (t_group_info->bTautFlags & TG_FLAG_PT_06_00) { ------------------ | | 955| 263k|#define TG_FLAG_PT_06_00 0x02000000 ------------------ | Branch (4878:9): [True: 0, False: 263k] ------------------ 4879| | /*** [CX{2-3}z{0-1},N,n,S,s,O,o,Se,Te:1]=[NX2,nX2,CX3,c,P,p:2][N,n,S,O,Se,Te:3][#1:4] >> [#1:4][CX4z{0-1},N,n,S,O,Se,Te:1][NX2,nX2,CX3z{0-1},c,P,p:2]=[N,n,S,s,O,o,Se,Te:3] ***/ 4880| | /*** Similar to the previous case of M=Q-ZH >> MH-Q=Z, with M = "C,N,S,O,Se,Te", Q = "N,C,P", and Z = "N,S,O,Se,Te" ***/ 4881| 0| for (i = 0; i < num_atoms; i++) { ------------------ | Branch (4881:21): [True: 0, False: 0] ------------------ 4882| | /* find possible endpoint Z = at[i] */ 4883| 0| if ((endpoint_valence = nGetEndpointInfo_PT_06_00(at, i, &eif1))) { /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4883:17): [True: 0, False: 0] ------------------ 4884| | /* 1st endpoint candidate found. Find centerpoint candidate */ 4885| 0| for (j = 0; j < at[i].valence; j++) { ------------------ | Branch (4885:29): [True: 0, False: 0] ------------------ 4886| 0| bond_type = (int)at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4887| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4888| | bond_type = ACTUAL_ORDER(pBNS, i, j, bond_type); 4889| |#endif 4890| 0| centerpoint = (int)at[i].neighbor[j]; /* a centerpoint candidate */ 4891| 0| if ((bond_type == BOND_DOUBLE || ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4891:26): [True: 0, False: 0] ------------------ 4892| 0| bond_type == BOND_ALTERN || ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4892:25): [True: 0, False: 0] ------------------ 4893| 0| bond_type == BOND_ALT12NS || ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4893:25): [True: 0, False: 0] ------------------ 4894| 0| bond_type == BOND_TAUTOM) && ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4894:25): [True: 0, False: 0] ------------------ 4895| 0| (at[centerpoint].el_number == EL_NUMBER_N || ------------------ | | 14| 0|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (4895:26): [True: 0, False: 0] ------------------ 4896| 0| at[centerpoint].el_number == EL_NUMBER_C || ------------------ | | 13| 0|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (4896:29): [True: 0, False: 0] ------------------ 4897| 0| at[centerpoint].el_number == EL_NUMBER_P) ------------------ | | 18| 0|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (4897:29): [True: 0, False: 0] ------------------ 4898| 0| && ALLOWED_EDGE(pBNS, i, j) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 4899| 0| ) { 4900| | /* test a centerpoint candidate. */ 4901| | /* find all endpoints including at[i] and store them into EndPoint[] */ 4902| 0| nNumPossibleMobile = 0; 4903| 0| nGroupNumber = (AT_NUMB)num_atoms; /* greater than any tautomeric group number */ 4904| 0| bDiffGroups = -1; /* ignore the first difference */ 4905| 0| nNumDonor = nNumAcceptor = 0; 4906| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) { ------------------ | Branch (4906:73): [True: 0, False: 0] ------------------ 4907| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 4908| 0| bond_type = (int)at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4909| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4910| | bond_type = ACTUAL_ORDER(pBNS, centerpoint, k, bond_type); 4911| |#endif 4912| | /* djb-rwth: removing redundant code */ 4913| 0| bNonTautBond = 4914| 0| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 4915| 0| bPossiblyEndpoint = 0; 4916| 0| if (!ALLOWED_EDGE(pBNS, centerpoint, k)) { ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 4917| 0| continue; 4918| 0| } 4919| 0| else 4920| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4920:37): [True: 0, False: 0] | Branch (4920:65): [True: 0, False: 0] | Branch (4920:94): [True: 0, False: 0] ------------------ 4921| | /* djb-rwth: removing redundant code */ 4922| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 4923| 0| bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4923:49): [True: 0, False: 0] | Branch (4923:77): [True: 0, False: 0] ------------------ 4924| 0|#endif 4925| 0| } 4926| 0| else 4927| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4927:41): [True: 0, False: 0] | Branch (4927:69): [True: 0, False: 0] ------------------ 4928| 0| bNonTautBond = 1; 4929| 0| else 4930| 0| continue; 4931| 0| if (!(endpoint_valence = nGetEndpointInfo_PT_06_00(at, endpoint, &eif1))) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (4931:33): [True: 0, False: 0] ------------------ 4932| 0| continue; /* not an endpoint element or can't have mobile groups */ 4933| 0| if (i != endpoint && ------------------ | Branch (4933:33): [True: 0, False: 0] ------------------ 4934| 0| at[endpoint].el_number == EL_NUMBER_C && ------------------ | | 13| 0|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (4934:33): [True: 0, False: 0] ------------------ 4935| 0| at[i].el_number == EL_NUMBER_C) ------------------ | | 13| 0|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (4935:33): [True: 0, False: 0] ------------------ 4936| 0| continue; 4937| | /* save information about the found possible tautomeric endpoint */ 4938| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 4939| 0| nMobile = 4940| 0| AddAtom2num(EndPoint[nNumEndPoints].num, at, endpoint, 2); /* fill out */ 4941| 0| AddAtom2DA(EndPoint[nNumEndPoints].num_DA, at, endpoint, 2); 4942| | /* --- why is isitopic info missing ? -- see below 4943| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 4944| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 4945| | */ 4946| 0| if (bNonTautBond) { ------------------ | Branch (4946:33): [True: 0, False: 0] ------------------ 4947| 0| m = (bond_type == BOND_SINGLE && (nMobile || at[endpoint].endpoint)); ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4947:38): [True: 0, False: 0] | Branch (4947:67): [True: 0, False: 0] | Branch (4947:78): [True: 0, False: 0] ------------------ 4948| 0| nNumDonor += m; 4949| 0| bPossiblyEndpoint += m; 4950| 0| m = (bond_type == BOND_DOUBLE); ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 4951| 0| nNumAcceptor += m; 4952| 0| bPossiblyEndpoint += m; 4953| 0| } 4954| 0| else { 4955| | /* tautomeric or alternating bond */ 4956| 0| m = (0 != at[endpoint].endpoint || eif1.cDonor); ------------------ | Branch (4956:38): [True: 0, False: 0] | Branch (4956:68): [True: 0, False: 0] ------------------ 4957| 0| nNumDonor += m; 4958| 0| bPossiblyEndpoint += m; 4959| 0| m = (at[endpoint].endpoint || ------------------ | Branch (4959:38): [True: 0, False: 0] ------------------ 4960| 0| eif1.cNeutralBondsValence > at[endpoint].valence); ------------------ | Branch (4960:37): [True: 0, False: 0] ------------------ 4961| 0| nNumAcceptor += m; 4962| 0| bPossiblyEndpoint += m; 4963| 0| } 4964| 0| if (!bPossiblyEndpoint) ------------------ | Branch (4964:33): [True: 0, False: 0] ------------------ 4965| 0| continue; 4966| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 4967| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 4968| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB)endpoint; 4969| 0| if (nGroupNumber != at[endpoint].endpoint) { ------------------ | Branch (4969:33): [True: 0, False: 0] ------------------ 4970| 0| bDiffGroups++; 4971| 0| nGroupNumber = at[endpoint].endpoint; 4972| 0| } 4973| | 4974| | /* save positions of all, not only possibly tautomeric bonds */ 4975| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4976| | if (bNonTautBond || bAltBond) { 4977| |#endif 4978| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB)centerpoint; 4979| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB)k; /* bond ordering number; used to change bonds to tautomeric only */ 4980| 0| nNumBondPos++; 4981| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4982| | } 4983| |#endif 4984| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 4985| | /* (b) the centerpoint is adjacent to another endpoint */ 4986| 0| nNumPossibleMobile += (nMobile>0 || at[endpoint].endpoint); ------------------ | Branch (4986:52): [True: 0, False: 0] | Branch (4986:65): [True: 0, False: 0] ------------------ 4987| 0| nNumEndPoints++; 4988| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 4989| 0| } 4990| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor) { ------------------ | Branch (4990:29): [True: 0, False: 0] | Branch (4990:50): [True: 0, False: 0] | Branch (4990:72): [True: 0, False: 0] | Branch (4990:85): [True: 0, False: 0] ------------------ 4991| | /*printf("Real %d\n", nNumEndPoints);*/ 4992| | /* 4993| | * a tautomeric group has been found 4994| | * 4995| | * at this point: 4996| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 4997| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 4998| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 4999| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 5000| | */ 5001| | 5002| 0| nErr = FindAccessibleEndPoints(pCG, 5003| 0| EndPoint, &nNumEndPoints, 5004| 0| BondPos, &nNumBondPos, 5005| 0| pBNS, pBD, at, 5006| 0| num_atoms, c_group_info, 5007| 0| ALT_PATH_MODE_TAUTOM_PT_06_00); ------------------ | | 330| 0|#define ALT_PATH_MODE_TAUTOM_PT_06_00 13 ------------------ 5008| | 5009| 0| if (IS_BNS_ERROR(nErr)) { ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 5010| 0| return nErr; 5011| 0| } 5012| 0| nErr = 0; 5013| | 5014| 0| if (nNumEndPoints > 0) { ------------------ | Branch (5014:33): [True: 0, False: 0] ------------------ 5015| 0| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (5015:37): [True: 0, False: 0] | Branch (5015:54): [True: 0, False: 0] ------------------ 5016| | 5017| 0| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 5018| 0| if (num_changes == -1) { ------------------ | Branch (5018:41): [True: 0, False: 0] ------------------ 5019| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5020| 0| } 5021| 0| if (num_changes < 0) { ------------------ | Branch (5021:41): [True: 0, False: 0] ------------------ 5022| 0| nErr = num_changes; 5023| 0| } 5024| | 5025| 0| if (nErr) ------------------ | Branch (5025:41): [True: 0, False: 0] ------------------ 5026| 0| goto exit_function; 5027| 0| tot_changes += (num_changes>0); 5028| 0| } 5029| 0| if (nNumBondPos > 0) { ------------------ | Branch (5029:37): [True: 0, False: 0] ------------------ 5030| | /* some of the bonds have not been marked as tautomeric yet */ 5031| 0| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 5032| 0| tot_changes += (num_changes>0); 5033| 0| } 5034| 0| } 5035| 0| } 5036| 0| } 5037| 0| } 5038| 0| } 5039| 0| } 5040| 0| } 5041| 263k|#endif /********** END PT_06_00 ************/ 5042| | 5043| 263k|#if ( TAUT_PT_39_00 == 1 ) /******* BEGIN PT_39_00 ********/ 5044| 263k| if (t_group_info->bTautFlags & TG_FLAG_PT_39_00) { ------------------ | | 956| 263k|#define TG_FLAG_PT_39_00 0x04000000 ------------------ | Branch (5044:9): [True: 0, False: 263k] ------------------ 5045| | /*** [CX3,NX2:1]=[NX3+:2]([O-:3])[CX4:4][#1:5]>>[#1:5][CX4,NX3:1][NX3+:2]([O-:3])=[CX3:4] ***/ 5046| | /*** Similar to the previous case of M=Q-ZH >> MH-Q=Z, with M,Z = "C, N" and Q = "N+" ***/ 5047| 0| for (i = 0; i < num_atoms; i++) { ------------------ | Branch (5047:21): [True: 0, False: 0] ------------------ 5048| | /* find possible endpoint Z = at[i] */ 5049| 0| if ((endpoint_valence = nGetEndpointInfo_PT_39_00(at, i, &eif1))) { /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (5049:17): [True: 0, False: 0] ------------------ 5050| | /* 1st endpoint candidate found. Find centerpoint candidate */ 5051| 0| for (j = 0; j < at[i].valence; j++) { ------------------ | Branch (5051:29): [True: 0, False: 0] ------------------ 5052| 0| bond_type = (int)at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5053| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5054| | bond_type = ACTUAL_ORDER(pBNS, i, j, bond_type); 5055| |#endif 5056| 0| centerpoint = (int)at[i].neighbor[j]; /* a centerpoint candidate */ 5057| 0| if ((bond_type == BOND_DOUBLE || ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (5057:26): [True: 0, False: 0] ------------------ 5058| 0| bond_type == BOND_ALTERN || ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (5058:25): [True: 0, False: 0] ------------------ 5059| 0| bond_type == BOND_ALT12NS || ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (5059:25): [True: 0, False: 0] ------------------ 5060| 0| bond_type == BOND_TAUTOM) ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5060:25): [True: 0, False: 0] ------------------ 5061| 0| && at[centerpoint].el_number == EL_NUMBER_N ------------------ | | 14| 0|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (5061:28): [True: 0, False: 0] ------------------ 5062| 0| && at[centerpoint].valence == 3 ------------------ | Branch (5062:28): [True: 0, False: 0] ------------------ 5063| 0| && ALLOWED_EDGE(pBNS, i, j) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5064| 0| ) { 5065| 0| int num_O = 0; 5066| 0| int num_N = 0; 5067| | /* test a centerpoint candidate. */ 5068| | /* find all endpoints including at[i] and store them into EndPoint[] */ 5069| 0| nNumPossibleMobile = 0; 5070| 0| nGroupNumber = (AT_NUMB)num_atoms; /* greater than any tautomeric group number */ 5071| 0| bDiffGroups = -1; /* ignore the first difference */ 5072| 0| nNumDonor = nNumAcceptor = 0; 5073| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) { ------------------ | Branch (5073:73): [True: 0, False: 0] ------------------ 5074| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 5075| 0| num_O += (at[endpoint].el_number == EL_NUMBER_O); ------------------ | | 15| 0|#define EL_NUMBER_O ((U_CHAR)8) ------------------ 5076| 0| num_N += (at[endpoint].el_number == EL_NUMBER_N); ------------------ | | 14| 0|#define EL_NUMBER_N ((U_CHAR)7) ------------------ 5077| 0| bond_type = (int)at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5078| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5079| | bond_type = ACTUAL_ORDER(pBNS, centerpoint, k, bond_type); 5080| |#endif 5081| | /* djb-rwth: removing redundant code */ 5082| 0| bNonTautBond = 5083| 0| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 5084| 0| bPossiblyEndpoint = 0; 5085| 0| if (!ALLOWED_EDGE(pBNS, centerpoint, k)) { ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5086| 0| continue; 5087| 0| } 5088| 0| else 5089| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) { ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5089:37): [True: 0, False: 0] | Branch (5089:65): [True: 0, False: 0] | Branch (5089:94): [True: 0, False: 0] ------------------ 5090| | /* djb-rwth: removing redundant code */ 5091| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 5092| 0| bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (5092:49): [True: 0, False: 0] | Branch (5092:77): [True: 0, False: 0] ------------------ 5093| 0|#endif 5094| 0| } 5095| 0| else 5096| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (5096:41): [True: 0, False: 0] | Branch (5096:69): [True: 0, False: 0] ------------------ 5097| 0| bNonTautBond = 1; 5098| 0| else 5099| 0| continue; 5100| | 5101| 0| if (!(endpoint_valence = nGetEndpointInfo_PT_39_00(at, endpoint, &eif1))) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (5101:33): [True: 0, False: 0] ------------------ 5102| 0| continue; /* not an endpoint element or can't have mobile groups */ 5103| | 5104| | 5105| | /* save information about the found possible tautomeric endpoint */ 5106| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 5107| 0| nMobile = 5108| 0| AddAtom2num(EndPoint[nNumEndPoints].num, at, endpoint, 2); /* fill out */ 5109| 0| AddAtom2DA(EndPoint[nNumEndPoints].num_DA, at, endpoint, 2); 5110| | /* --- why is isitopic info missing ? -- see below 5111| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 5112| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 5113| | */ 5114| 0| if (bNonTautBond) { ------------------ | Branch (5114:33): [True: 0, False: 0] ------------------ 5115| 0| m = (bond_type == BOND_SINGLE && (nMobile || at[endpoint].endpoint)); ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (5115:38): [True: 0, False: 0] | Branch (5115:67): [True: 0, False: 0] | Branch (5115:78): [True: 0, False: 0] ------------------ 5116| 0| nNumDonor += m; 5117| 0| bPossiblyEndpoint += m; 5118| 0| m = (bond_type == BOND_DOUBLE); ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 5119| 0| nNumAcceptor += m; 5120| 0| bPossiblyEndpoint += m; 5121| 0| } 5122| 0| else { 5123| | /* tautomeric or alternating bond */ 5124| 0| m = (0 != at[endpoint].endpoint || eif1.cDonor); ------------------ | Branch (5124:38): [True: 0, False: 0] | Branch (5124:68): [True: 0, False: 0] ------------------ 5125| 0| nNumDonor += m; 5126| 0| bPossiblyEndpoint += m; 5127| 0| m = (at[endpoint].endpoint || ------------------ | Branch (5127:38): [True: 0, False: 0] ------------------ 5128| 0| eif1.cNeutralBondsValence > at[endpoint].valence); ------------------ | Branch (5128:37): [True: 0, False: 0] ------------------ 5129| 0| nNumAcceptor += m; 5130| 0| bPossiblyEndpoint += m; 5131| 0| } 5132| 0| if (!bPossiblyEndpoint) ------------------ | Branch (5132:33): [True: 0, False: 0] ------------------ 5133| 0| continue; 5134| | 5135| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 5136| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 5137| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB)endpoint; 5138| 0| if (nGroupNumber != at[endpoint].endpoint) { ------------------ | Branch (5138:33): [True: 0, False: 0] ------------------ 5139| 0| bDiffGroups++; 5140| 0| nGroupNumber = at[endpoint].endpoint; 5141| 0| } 5142| | 5143| | /* save positions of all, not only possibly tautomeric bonds */ 5144| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5145| | if (bNonTautBond || bAltBond) { 5146| |#endif 5147| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB)centerpoint; 5148| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB)k; /* bond ordering number; used to change bonds to tautomeric only */ 5149| 0| nNumBondPos++; 5150| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5151| | } 5152| |#endif 5153| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 5154| | /* (b) the centerpoint is adjacent to another endpoint */ 5155| 0| nNumPossibleMobile += (nMobile>0 || at[endpoint].endpoint); ------------------ | Branch (5155:52): [True: 0, False: 0] | Branch (5155:65): [True: 0, False: 0] ------------------ 5156| 0| nNumEndPoints++; 5157| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 5158| 0| } 5159| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor && num_O == 1 && num_N < 2) { ------------------ | Branch (5159:29): [True: 0, False: 0] | Branch (5159:50): [True: 0, False: 0] | Branch (5159:72): [True: 0, False: 0] | Branch (5159:85): [True: 0, False: 0] | Branch (5159:101): [True: 0, False: 0] | Branch (5159:115): [True: 0, False: 0] ------------------ 5160| | /* 5161| | * a tautomeric group has been found 5162| | * 5163| | * at this point: 5164| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 5165| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 5166| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 5167| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 5168| | */ 5169| 0| nErr = FindAccessibleEndPoints(pCG, 5170| 0| EndPoint, &nNumEndPoints, 5171| 0| BondPos, &nNumBondPos, 5172| 0| pBNS, pBD, at, 5173| 0| num_atoms, c_group_info, 5174| 0| ALT_PATH_MODE_TAUTOM_PT_39_00); ------------------ | | 333| 0|#define ALT_PATH_MODE_TAUTOM_PT_39_00 14 ------------------ 5175| | 5176| 0| if (IS_BNS_ERROR(nErr)) { ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 5177| 0| return nErr; 5178| 0| } 5179| 0| nErr = 0; 5180| | 5181| 0| if (nNumEndPoints > 0) { ------------------ | Branch (5181:33): [True: 0, False: 0] ------------------ 5182| 0| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (5182:37): [True: 0, False: 0] | Branch (5182:54): [True: 0, False: 0] ------------------ 5183| | 5184| 0| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 5185| 0| if (num_changes == -1) { ------------------ | Branch (5185:41): [True: 0, False: 0] ------------------ 5186| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5187| 0| } 5188| 0| if (num_changes < 0) { ------------------ | Branch (5188:41): [True: 0, False: 0] ------------------ 5189| 0| nErr = num_changes; 5190| 0| } 5191| | 5192| 0| if (nErr) ------------------ | Branch (5192:41): [True: 0, False: 0] ------------------ 5193| 0| goto exit_function; 5194| 0| tot_changes += (num_changes>0); 5195| 0| } 5196| 0| if (nNumBondPos > 0) { ------------------ | Branch (5196:37): [True: 0, False: 0] ------------------ 5197| | /* some of the bonds have not been marked as tautomeric yet */ 5198| 0| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 5199| 0| tot_changes += (num_changes>0); 5200| 0| } 5201| 0| } 5202| 0| } 5203| 0| } 5204| 0| } 5205| 0| } 5206| 0| } 5207| 0| } 5208| 263k|#endif /********** END PT_39_00 ************/ 5209| | 5210| 263k|#if ( TAUT_PT_13_00 == 1 ) /******* BEGIN PT_13_00 ********/ 5211| 263k| if (t_group_info->bTautFlags & TG_FLAG_PT_13_00) { ------------------ | | 957| 263k|#define TG_FLAG_PT_13_00 0x08000000 ------------------ | Branch (5211:9): [True: 0, False: 263k] ------------------ 5212| | /*** [O,S,Se,Te;X1:1]=[C:2]=[C:3][#1:4]>>[#1:4][O,S,Se,Te;X2:1][C:2]#[C:3] ***/ 5213| | /*** Similar to the previous case of M=Q-ZH >> MH-Q=Z, with M = "S,O,Se,Te", Q = "C", and Z = "C" ***/ 5214| 0| for (i = 0; i < num_atoms; i++) { ------------------ | Branch (5214:21): [True: 0, False: 0] ------------------ 5215| | /* find possible endpoint Z = at[i] */ 5216| 0| if ((endpoint_valence = nGetEndpointInfo_PT_13_00(at, i, &eif1))) { /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (5216:17): [True: 0, False: 0] ------------------ 5217| | /* 1st endpoint candidate found. Find centerpoint candidate */ 5218| 0| for (j = 0; j < at[i].valence; j++) { ------------------ | Branch (5218:29): [True: 0, False: 0] ------------------ 5219| 0| bond_type = (int)at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5220| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5221| | bond_type = ACTUAL_ORDER(pBNS, i, j, bond_type); 5222| |#endif 5223| 0| centerpoint = (int)at[i].neighbor[j]; /* a centerpoint candidate */ 5224| 0| if ((bond_type == BOND_DOUBLE || ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (5224:26): [True: 0, False: 0] ------------------ 5225| 0| bond_type == BOND_SINGLE || ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (5225:25): [True: 0, False: 0] ------------------ 5226| 0| bond_type == BOND_ALTERN || ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (5226:25): [True: 0, False: 0] ------------------ 5227| 0| bond_type == BOND_ALT12NS || ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (5227:25): [True: 0, False: 0] ------------------ 5228| 0| bond_type == BOND_ALT_13 || ------------------ | | 183| 0|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (5228:25): [True: 0, False: 0] ------------------ 5229| 0| bond_type == BOND_TAUTOM) && ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5229:25): [True: 0, False: 0] ------------------ 5230| 0| at[centerpoint].el_number == EL_NUMBER_C && ------------------ | | 13| 0|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (5230:25): [True: 0, False: 0] ------------------ 5231| 0| at[centerpoint].valence == 2 && ------------------ | Branch (5231:25): [True: 0, False: 0] ------------------ 5232| 0| ALLOWED_EDGE(pBNS, i, j) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5233| 0| ) { 5234| | /* test a centerpoint candidate. */ 5235| | /* find all endpoints including at[i] and store them into EndPoint[] */ 5236| 0| int num_O = 0; 5237| 0| int num_C = 0; 5238| 0| nNumPossibleMobile = 0; 5239| 0| nGroupNumber = (AT_NUMB)num_atoms; /* greater than any tautomeric group number */ 5240| 0| bDiffGroups = -1; /* ignore the first difference */ 5241| 0| nNumDonor = nNumAcceptor = 0; 5242| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) { ------------------ | Branch (5242:73): [True: 0, False: 0] ------------------ 5243| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 5244| 0| bond_type = (int)at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5245| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5246| | bond_type = ACTUAL_ORDER(pBNS, centerpoint, k, bond_type); 5247| |#endif 5248| | /* djb-rwth: removing redundant code */ 5249| 0| bNonTautBond = 5250| 0| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 5251| 0| bPossiblyEndpoint = 0; 5252| 0| if (!ALLOWED_EDGE(pBNS, centerpoint, k)) { ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5253| 0| continue; 5254| 0| } 5255| 0| else 5256| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 183| 0|#define BOND_ALT_13 6 /* single/triple */ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5256:37): [True: 0, False: 0] | Branch (5256:65): [True: 0, False: 0] | Branch (5256:94): [True: 0, False: 0] | Branch (5256:122): [True: 0, False: 0] ------------------ 5257| | /* djb-rwth: removing redundant code */ 5258| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 5259| 0| bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 183| 0|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (5259:49): [True: 0, False: 0] | Branch (5259:77): [True: 0, False: 0] | Branch (5259:106): [True: 0, False: 0] ------------------ 5260| 0|#endif 5261| 0| } 5262| 0| else 5263| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE || bond_type == BOND_TRIPLE) ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE || bond_type == BOND_TRIPLE) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE || bond_type == BOND_TRIPLE) ------------------ | | 179| 0|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 0|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (5263:41): [True: 0, False: 0] | Branch (5263:69): [True: 0, False: 0] | Branch (5263:97): [True: 0, False: 0] ------------------ 5264| 0| bNonTautBond = 1; 5265| 0| else 5266| 0| continue; 5267| 0| if (!(endpoint_valence = nGetEndpointInfo_PT_13_00(at, endpoint, &eif1))) ------------------ | Branch (5267:33): [True: 0, False: 0] ------------------ 5268| 0| continue; /* not an endpoint element or can't have mobile groups */ 5269| | 5270| | /* save information about the found possible tautomeric endpoint */ 5271| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 5272| 0| nMobile = 5273| 0| AddAtom2num(EndPoint[nNumEndPoints].num, at, endpoint, 2); /* fill out */ 5274| 0| AddAtom2DA(EndPoint[nNumEndPoints].num_DA, at, endpoint, 2); 5275| | /* --- why is isitopic info missing ? -- see below 5276| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 5277| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 5278| | */ 5279| 0| if (bNonTautBond) { ------------------ | Branch (5279:33): [True: 0, False: 0] ------------------ 5280| 0| m = (nMobile || at[endpoint].endpoint); ------------------ | Branch (5280:38): [True: 0, False: 0] | Branch (5280:49): [True: 0, False: 0] ------------------ 5281| 0| nNumDonor += m; 5282| 0| bPossiblyEndpoint += m; 5283| 0| m = (nMobile == 0); 5284| 0| nNumAcceptor += m; 5285| 0| bPossiblyEndpoint += m; 5286| 0| } 5287| 0| else { 5288| | /* tautomeric or alternating bond */ 5289| 0| m = (eif1.cDonor != 0); 5290| 0| nNumDonor += m; 5291| 0| bPossiblyEndpoint += m; 5292| 0| m = (eif1.cNeutralBondsValence > at[endpoint].valence); 5293| 0| nNumAcceptor += m; 5294| 0| bPossiblyEndpoint += m; 5295| 0| } 5296| | 5297| | 5298| 0| if (!bPossiblyEndpoint) ------------------ | Branch (5298:33): [True: 0, False: 0] ------------------ 5299| 0| continue; 5300| | 5301| 0| num_O += (endpoint_valence == 2); 5302| 0| num_C += (endpoint_valence == 4); 5303| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 5304| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 5305| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB)endpoint; 5306| 0| if (nGroupNumber != at[endpoint].endpoint) { ------------------ | Branch (5306:33): [True: 0, False: 0] ------------------ 5307| 0| bDiffGroups++; 5308| 0| nGroupNumber = at[endpoint].endpoint; 5309| 0| } 5310| | 5311| | /* save positions of all, not only possibly tautomeric bonds */ 5312| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5313| | if (bNonTautBond || bAltBond) { 5314| |#endif 5315| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB)centerpoint; 5316| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB)k; /* bond ordering number; used to change bonds to tautomeric only */ 5317| 0| nNumBondPos++; 5318| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5319| | } 5320| |#endif 5321| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 5322| | /* (b) the centerpoint is adjacent to another endpoint */ 5323| 0| nNumPossibleMobile += (nMobile>0); 5324| 0| nNumEndPoints++; 5325| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 5326| 0| } 5327| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor && num_O == 1 && num_C == 1) { ------------------ | Branch (5327:29): [True: 0, False: 0] | Branch (5327:50): [True: 0, False: 0] | Branch (5327:72): [True: 0, False: 0] | Branch (5327:85): [True: 0, False: 0] | Branch (5327:101): [True: 0, False: 0] | Branch (5327:115): [True: 0, False: 0] ------------------ 5328| | /*printf("Real %d\n", nNumEndPoints);*/ 5329| | /* 5330| | * a tautomeric group has been found 5331| | * 5332| | * at this point: 5333| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 5334| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 5335| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 5336| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 5337| | */ 5338| | 5339| 0| nErr = FindAccessibleEndPoints(pCG, 5340| 0| EndPoint, &nNumEndPoints, 5341| 0| BondPos, &nNumBondPos, 5342| 0| pBNS, pBD, at, 5343| 0| num_atoms, c_group_info, 5344| 0| ALT_PATH_MODE_TAUTOM_PT_13_00); ------------------ | | 336| 0|#define ALT_PATH_MODE_TAUTOM_PT_13_00 15 ------------------ 5345| | 5346| 0| if (IS_BNS_ERROR(nErr)) { ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 5347| 0| return nErr; 5348| 0| } 5349| 0| nErr = 0; 5350| | 5351| 0| if (nNumEndPoints > 0) { ------------------ | Branch (5351:33): [True: 0, False: 0] ------------------ 5352| 0| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (5352:37): [True: 0, False: 0] | Branch (5352:54): [True: 0, False: 0] ------------------ 5353| | 5354| 0| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 5355| 0| if (num_changes == -1) { ------------------ | Branch (5355:41): [True: 0, False: 0] ------------------ 5356| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5357| 0| } 5358| 0| if (num_changes < 0) { ------------------ | Branch (5358:41): [True: 0, False: 0] ------------------ 5359| 0| nErr = num_changes; 5360| 0| } 5361| | 5362| 0| if (nErr) ------------------ | Branch (5362:41): [True: 0, False: 0] ------------------ 5363| 0| goto exit_function; 5364| 0| tot_changes += (num_changes>0); 5365| 0| } 5366| 0| if (nNumBondPos > 0) { ------------------ | Branch (5366:37): [True: 0, False: 0] ------------------ 5367| | /* some of the bonds have not been marked as tautomeric yet */ 5368| 0| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 5369| 0| tot_changes += (num_changes>0); 5370| 0| } 5371| 0| } 5372| 0| } 5373| 0| } 5374| 0| } 5375| 0| } 5376| 0| } 5377| 0| } 5378| 263k|#endif /********** END PT_13_00 ************/ 5379| | 5380| 263k|#if ( TAUT_PT_18_00 == 1 ) /******* BEGIN PT_18_00 ********/ 5381| 263k| if (t_group_info->bTautFlags & TG_FLAG_PT_18_00) { ------------------ | | 958| 263k|#define TG_FLAG_PT_18_00 0x10000000 ------------------ | Branch (5381:9): [True: 0, False: 263k] ------------------ 5382| | /*** [#1:1][O:2][C:3]#[N:4]>>[O:2]=[C:3]=[N:4][#1:1] ***/ 5383| | /*** Similar to the previous case of M=Q-ZH >> MH-Q=Z, with M = "O", Q = "C", and Z = "N" ***/ 5384| 0| for (i = 0; i < num_atoms; i++) { ------------------ | Branch (5384:21): [True: 0, False: 0] ------------------ 5385| | /* find possible endpoint Z = at[i] */ 5386| 0| if ((endpoint_valence = nGetEndpointInfo_PT_18_00(at, i, &eif1))) { /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (5386:17): [True: 0, False: 0] ------------------ 5387| | /* 1st endpoint candidate found. Find centerpoint candidate */ 5388| 0| for (j = 0; j < at[i].valence; j++) { ------------------ | Branch (5388:29): [True: 0, False: 0] ------------------ 5389| 0| bond_type = (int)at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5390| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5391| | bond_type = ACTUAL_ORDER(pBNS, i, j, bond_type); 5392| |#endif 5393| 0| centerpoint = (int)at[i].neighbor[j]; /* a centerpoint candidate */ 5394| | /*printf("Centerpoint: %d\n", centerpoint+1);*/ 5395| 0| if ((bond_type == BOND_DOUBLE || ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (5395:26): [True: 0, False: 0] ------------------ 5396| 0| bond_type == BOND_SINGLE || ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (5396:25): [True: 0, False: 0] ------------------ 5397| 0| bond_type == BOND_ALTERN || ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (5397:25): [True: 0, False: 0] ------------------ 5398| 0| bond_type == BOND_ALT12NS || ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (5398:25): [True: 0, False: 0] ------------------ 5399| 0| bond_type == BOND_ALT_13 || ------------------ | | 183| 0|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (5399:25): [True: 0, False: 0] ------------------ 5400| 0| bond_type == BOND_TAUTOM) && ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5400:25): [True: 0, False: 0] ------------------ 5401| 0| at[centerpoint].el_number == EL_NUMBER_C && ------------------ | | 13| 0|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (5401:25): [True: 0, False: 0] ------------------ 5402| 0| at[centerpoint].valence == 2 && ------------------ | Branch (5402:25): [True: 0, False: 0] ------------------ 5403| 0| ALLOWED_EDGE(pBNS, i, j) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5404| 0| ) { 5405| | /* test a centerpoint candidate. */ 5406| | /* find all endpoints including at[i] and store them into EndPoint[] */ 5407| 0| int num_O = 0; 5408| 0| int num_N = 0; 5409| 0| nNumPossibleMobile = 0; 5410| 0| nGroupNumber = (AT_NUMB)num_atoms; /* greater than any tautomeric group number */ 5411| 0| bDiffGroups = -1; /* ignore the first difference */ 5412| 0| nNumDonor = nNumAcceptor = 0; 5413| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) { ------------------ | Branch (5413:73): [True: 0, False: 0] ------------------ 5414| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 5415| | /*printf("Endpoint: %d\n", endpoint+1);*/ 5416| 0| bond_type = (int)at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5417| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5418| | bond_type = ACTUAL_ORDER(pBNS, centerpoint, k, bond_type); 5419| |#endif 5420| | 5421| | /* djb-rwth: removing redundant code */ 5422| 0| bNonTautBond = 5423| 0| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 5424| 0| bPossiblyEndpoint = 0; 5425| 0| if (!ALLOWED_EDGE(pBNS, centerpoint, k)) { ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5426| 0| continue; 5427| 0| } 5428| 0| else 5429| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 183| 0|#define BOND_ALT_13 6 /* single/triple */ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13 || bond_type == BOND_TAUTOM) { ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5429:37): [True: 0, False: 0] | Branch (5429:65): [True: 0, False: 0] | Branch (5429:94): [True: 0, False: 0] | Branch (5429:122): [True: 0, False: 0] ------------------ 5430| | /* djb-rwth: removing redundant code */ 5431| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 5432| 0| bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ bAltBond = (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_ALT_13); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 183| 0|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (5432:49): [True: 0, False: 0] | Branch (5432:77): [True: 0, False: 0] | Branch (5432:106): [True: 0, False: 0] ------------------ 5433| 0|#endif 5434| 0| } 5435| 0| else 5436| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE || bond_type == BOND_TRIPLE) ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE || bond_type == BOND_TRIPLE) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE || bond_type == BOND_TRIPLE) ------------------ | | 179| 0|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 34| 0|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (5436:41): [True: 0, False: 0] | Branch (5436:69): [True: 0, False: 0] | Branch (5436:97): [True: 0, False: 0] ------------------ 5437| 0| bNonTautBond = 1; 5438| 0| else 5439| 0| continue; 5440| 0| if (!(endpoint_valence = nGetEndpointInfo_PT_18_00(at, endpoint, &eif1))) ------------------ | Branch (5440:33): [True: 0, False: 0] ------------------ 5441| 0| continue; /* not an endpoint element or can't have mobile groups */ 5442| | 5443| | /* save information about the found possible tautomeric endpoint */ 5444| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 5445| 0| nMobile = eif1.cMobile; 5446| 0| AddAtom2num(EndPoint[nNumEndPoints].num, at, endpoint, 2); /* fill out */ 5447| 0| AddAtom2DA(EndPoint[nNumEndPoints].num_DA, at, endpoint, 2); 5448| | /* --- why is isitopic info missing ? -- see below 5449| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 5450| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 5451| | */ 5452| | 5453| 0| if (bond_type == BOND_DOUBLE && endpoint_valence == 3 && nMobile == 0) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (5453:33): [True: 0, False: 0] | Branch (5453:61): [True: 0, False: 0] | Branch (5453:86): [True: 0, False: 0] ------------------ 5454| 0| continue; 5455| | 5456| 0| if (bNonTautBond) { ------------------ | Branch (5456:33): [True: 0, False: 0] ------------------ 5457| | /*printf("AAA %d\n", nMobile);*/ 5458| 0| m = (nMobile || at[endpoint].endpoint); ------------------ | Branch (5458:38): [True: 0, False: 0] | Branch (5458:49): [True: 0, False: 0] ------------------ 5459| 0| nNumDonor += m; 5460| 0| bPossiblyEndpoint += m; 5461| 0| m = (nMobile == 0); 5462| 0| nNumAcceptor += m; 5463| 0| bPossiblyEndpoint += m; 5464| 0| } 5465| 0| else { 5466| | /* tautomeric or alternating bond */ 5467| | /*printf("BBB %d %d %d\n", eif1.cDonor, eif1.cNeutralBondsValence, at[endpoint].valence);*/ 5468| 0| m = (eif1.cDonor != 0); 5469| 0| nNumDonor += m; 5470| 0| bPossiblyEndpoint += m; 5471| 0| m = (eif1.cAcceptor != 0); 5472| 0| nNumAcceptor += m; 5473| 0| bPossiblyEndpoint += m; 5474| 0| } 5475| | 5476| | 5477| 0| if (!bPossiblyEndpoint) ------------------ | Branch (5477:33): [True: 0, False: 0] ------------------ 5478| 0| continue; 5479| | 5480| 0| num_O += (endpoint_valence == 2); 5481| 0| num_N += (endpoint_valence == 3); 5482| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 5483| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 5484| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB)endpoint; 5485| 0| if (nGroupNumber != at[endpoint].endpoint) { ------------------ | Branch (5485:33): [True: 0, False: 0] ------------------ 5486| 0| bDiffGroups++; 5487| 0| nGroupNumber = at[endpoint].endpoint; 5488| 0| } 5489| | 5490| | /* save positions of all, not only possibly tautomeric bonds */ 5491| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5492| | if (bNonTautBond || bAltBond) { 5493| |#endif 5494| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB)centerpoint; 5495| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB)k; /* bond ordering number; used to change bonds to tautomeric only */ 5496| 0| nNumBondPos++; 5497| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5498| | } 5499| |#endif 5500| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 5501| | /* (b) the centerpoint is adjacent to another endpoint */ 5502| 0| nNumPossibleMobile += (nMobile>0); 5503| 0| nNumEndPoints++; 5504| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 5505| 0| } 5506| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor && num_O == 1 && num_N == 1) { ------------------ | Branch (5506:29): [True: 0, False: 0] | Branch (5506:50): [True: 0, False: 0] | Branch (5506:72): [True: 0, False: 0] | Branch (5506:85): [True: 0, False: 0] | Branch (5506:101): [True: 0, False: 0] | Branch (5506:115): [True: 0, False: 0] ------------------ 5507| | /*printf("Real %d\n", nNumEndPoints);*/ 5508| | /* 5509| | * a tautomeric group has been found 5510| | * 5511| | * at this point: 5512| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 5513| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 5514| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 5515| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 5516| | */ 5517| | 5518| 0| nErr = FindAccessibleEndPoints(pCG, 5519| 0| EndPoint, &nNumEndPoints, 5520| 0| BondPos, &nNumBondPos, 5521| 0| pBNS, pBD, at, 5522| 0| num_atoms, c_group_info, 5523| 0| ALT_PATH_MODE_TAUTOM_PT_18_00); ------------------ | | 339| 0|#define ALT_PATH_MODE_TAUTOM_PT_18_00 16 ------------------ 5524| | 5525| 0| if (IS_BNS_ERROR(nErr)) { ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 5526| 0| return nErr; 5527| 0| } 5528| 0| nErr = 0; 5529| | 5530| 0| if (nNumEndPoints > 0) { ------------------ | Branch (5530:33): [True: 0, False: 0] ------------------ 5531| 0| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (5531:37): [True: 0, False: 0] | Branch (5531:54): [True: 0, False: 0] ------------------ 5532| | 5533| 0| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 5534| 0| if (num_changes == -1) { ------------------ | Branch (5534:41): [True: 0, False: 0] ------------------ 5535| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5536| 0| } 5537| 0| if (num_changes < 0) { ------------------ | Branch (5537:41): [True: 0, False: 0] ------------------ 5538| 0| nErr = num_changes; 5539| 0| } 5540| | 5541| 0| if (nErr) ------------------ | Branch (5541:41): [True: 0, False: 0] ------------------ 5542| 0| goto exit_function; 5543| 0| tot_changes += (num_changes>0); 5544| 0| } 5545| 0| if (nNumBondPos > 0) { ------------------ | Branch (5545:37): [True: 0, False: 0] ------------------ 5546| | /* some of the bonds have not been marked as tautomeric yet */ 5547| 0| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 5548| 0| tot_changes += (num_changes>0); 5549| 0| } 5550| 0| } 5551| 0| } 5552| 0| } 5553| 0| } 5554| 0| } 5555| 0| } 5556| 0| } 5557| 263k|#endif /********** END PT_18_00 ************/ 5558| | 5559| | 5560| 263k|#if ( KETO_ENOL_TAUT == 1 ) /***** post v.1 feature *****/ 5561| 263k| if (t_group_info->bTautFlags & TG_FLAG_KETO_ENOL_TAUT) ------------------ | | 946| 263k|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (5561:9): [True: 0, False: 263k] ------------------ 5562| 0| { 5563| | /* 1,3 keto-enol tautomerism */ 5564| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5564:21): [True: 0, False: 0] ------------------ 5565| 0| { 5566| | /* Find possible endpoint Z = at[i] */ 5567| 0| if ((endpoint_valence = nGetEndpointInfo_KET( at, i, &eif1 ))) /* djb-rwth: addressing LLVM warning; ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (5567:17): [True: 0, False: 0] ------------------ 5568| 0| { 5569| | /* 1st endpoint candidate found. Find centerpoint candidate */ 5570| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (5570:29): [True: 0, False: 0] ------------------ 5571| 0| { 5572| 0| bond_type = (int) at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5573| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5574| | bond_type = ACTUAL_ORDER( pBNS, i, j, bond_type ); 5575| |#endif 5576| 0| centerpoint = (int) at[i].neighbor[j]; /* a centerpoint candidate */ 5577| 0| if (( bond_type == BOND_DOUBLE || ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (5577:27): [True: 0, False: 0] ------------------ 5578| 0| bond_type == BOND_ALTERN || ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (5578:27): [True: 0, False: 0] ------------------ 5579| 0| bond_type == BOND_ALT12NS || ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (5579:27): [True: 0, False: 0] ------------------ 5580| 0| bond_type == BOND_TAUTOM ) && ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5580:27): [True: 0, False: 0] ------------------ 5581| 0| is_centerpoint_elem_KET( at[centerpoint].el_number ) && ------------------ | Branch (5581:26): [True: 0, False: 0] ------------------ 5582| 0| !at[centerpoint].charge && !at[centerpoint].radical && ------------------ | Branch (5582:26): [True: 0, False: 0] | Branch (5582:53): [True: 0, False: 0] ------------------ 5583| | /* only normal carbon is allowed */ 5584| 0| 4 == at[centerpoint].chem_bonds_valence + at[centerpoint].num_H ------------------ | Branch (5584:26): [True: 0, False: 0] ------------------ 5585| 0| && ALLOWED_EDGE( pBNS, i, j )) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5586| 0| { 5587| 0| int num_O = 0; 5588| 0| int num_C = 0; 5589| | /* Test a centerpoint candidate. */ 5590| | /* find all endpoints including at[i] and store them into EndPoint[] */ 5591| 0| nNumPossibleMobile = 0; 5592| 0| nGroupNumber = (AT_NUMB) num_atoms; /* greater than any tautomeric group number */ 5593| 0| bDiffGroups = -1; /* ignore the first difference */ 5594| 0| nNumDonor = nNumAcceptor = 0; 5595| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) ------------------ | Branch (5595:73): [True: 0, False: 0] ------------------ 5596| 0| { 5597| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 5598| 0| bond_type = (int) at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 191| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5599| |#if ( FIX_BOND23_IN_TAUT == 1 ) 5600| | bond_type = ACTUAL_ORDER( pBNS, centerpoint, k, bond_type ); 5601| |#endif 5602| | /* djb-rwth: removing redundant code */ 5603| 0| bNonTautBond = 5604| 0| bAltBond = /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 5605| 0| bPossiblyEndpoint = 0; 5606| 0| if (!ALLOWED_EDGE( pBNS, centerpoint, k )) ------------------ | | 4321| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 0] | | | Branch (4321:53): [True: 0, False: 0] | | | Branch (4321:70): [True: 0, False: 0] | | | Branch (4321:87): [True: 0, False: 0] | | ------------------ ------------------ 5607| 0| { 5608| 0| continue; 5609| 0| } 5610| 0| else 5611| 0| { 5612| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 185| 0|#define BOND_TAUTOM 8 ------------------ | Branch (5612:37): [True: 0, False: 0] | Branch (5612:65): [True: 0, False: 0] | Branch (5612:94): [True: 0, False: 0] ------------------ 5613| 0| { 5614| | /* djb-rwth: removing redundant code */ 5615| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 5616| 0| bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 180| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ ------------------ | | 186| 0|#define BOND_ALT12NS 9 ------------------ | Branch (5616:50): [True: 0, False: 0] | Branch (5616:78): [True: 0, False: 0] ------------------ 5617| 0|#endif 5618| 0| } 5619| 0| else 5620| 0| { 5621| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (5621:41): [True: 0, False: 0] | Branch (5621:69): [True: 0, False: 0] ------------------ 5622| 0| { 5623| 0| bNonTautBond = 1; 5624| 0| } 5625| 0| else 5626| 0| { 5627| 0| continue; 5628| 0| } 5629| 0| } 5630| 0| } 5631| | 5632| 0| if (!( endpoint_valence = nGetEndpointInfo_KET( at, endpoint, &eif2 ) )) ------------------ | Branch (5632:33): [True: 0, False: 0] ------------------ 5633| 0| { 5634| 0| continue; 5635| 0| } 5636| | /* 5637| | if ( 3 != eif1.cKetoEnolCode + eif2.cKetoEnolCode && endpoint != i ) 5638| | continue; 5639| | */ 5640| | /* save information about the found possible tautomeric endpoint */ 5641| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 5642| 0| nMobile = AddAtom2num( EndPoint[nNumEndPoints].num, at, endpoint, 2 ); /* fill out */ 5643| 0| AddAtom2DA( EndPoint[nNumEndPoints].num_DA, at, endpoint, 2 ); 5644| | /* --- why is isitopic info missing ? -- see below 5645| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 5646| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 5647| | */ 5648| 0| if (bNonTautBond) ------------------ | Branch (5648:33): [True: 0, False: 0] ------------------ 5649| 0| { 5650| 0| m = ( bond_type == BOND_SINGLE && ( nMobile || at[endpoint].endpoint ) ); ------------------ | | 177| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (5650:39): [True: 0, False: 0] | Branch (5650:69): [True: 0, False: 0] | Branch (5650:80): [True: 0, False: 0] ------------------ 5651| 0| nNumDonor += m; 5652| 0| bPossiblyEndpoint += m; 5653| 0| m = ( bond_type == BOND_DOUBLE ); ------------------ | | 178| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 5654| 0| nNumAcceptor += m; 5655| 0| bPossiblyEndpoint += m; 5656| 0| } 5657| 0| else 5658| 0| { 5659| | /* Tautomeric or alternating bond */ 5660| 0| m = ( 0 != at[endpoint].endpoint || eif1.cDonor ); ------------------ | Branch (5660:39): [True: 0, False: 0] | Branch (5660:69): [True: 0, False: 0] ------------------ 5661| 0| nNumDonor += m; 5662| 0| bPossiblyEndpoint += m; 5663| 0| m = ( at[endpoint].endpoint || ------------------ | Branch (5663:39): [True: 0, False: 0] ------------------ 5664| 0| eif1.cNeutralBondsValence > at[endpoint].valence ); ------------------ | Branch (5664:39): [True: 0, False: 0] ------------------ 5665| 0| nNumAcceptor += m; 5666| 0| bPossiblyEndpoint += m; 5667| 0| } 5668| 0| if (!bPossiblyEndpoint) ------------------ | Branch (5668:33): [True: 0, False: 0] ------------------ 5669| 0| { 5670| 0| continue; 5671| 0| } 5672| | 5673| 0| num_O += ( endpoint_valence == 2 ); 5674| 0| num_C += ( endpoint_valence == 4 ); 5675| | 5676| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 5677| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 5678| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB) endpoint; 5679| 0| if (nGroupNumber != at[endpoint].endpoint) ------------------ | Branch (5679:33): [True: 0, False: 0] ------------------ 5680| 0| { 5681| 0| bDiffGroups++; 5682| 0| nGroupNumber = at[endpoint].endpoint; 5683| 0| } 5684| | 5685| | /* Save positions of all, not only possibly tautomeric bonds */ 5686| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5687| | if (bNonTautBond || bAltBond) 5688| | { 5689| |#endif 5690| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB) centerpoint; 5691| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB) k; /* bond ordering number; used to change bonds to tautomeric only */ 5692| 0| nNumBondPos++; 5693| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 5694| | } 5695| |#endif 5696| | /* Mobile group is possible if (a) the endpoint has a mobile group or */ 5697| | /* (b) the centerpoint is adjacent to another endpoint */ 5698| 0| nNumPossibleMobile += ( nMobile > 0 || at[endpoint].endpoint ); ------------------ | Branch (5698:53): [True: 0, False: 0] | Branch (5698:68): [True: 0, False: 0] ------------------ 5699| 0| nNumEndPoints++; 5700| 0| } 5701| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && ------------------ | Branch (5701:29): [True: 0, False: 0] | Branch (5701:50): [True: 0, False: 0] ------------------ 5702| 0| nNumDonor && nNumAcceptor && ------------------ | Branch (5702:30): [True: 0, False: 0] | Branch (5702:43): [True: 0, False: 0] ------------------ 5703| 0| num_O == 1 && num_C) ------------------ | Branch (5703:30): [True: 0, False: 0] | Branch (5703:44): [True: 0, False: 0] ------------------ 5704| 0| { 5705| | /* 5706| | * A tautomeric group has been found 5707| | * 5708| | * at this point: 5709| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 5710| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 5711| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 5712| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 5713| | */ 5714| | 5715| 0| nErr = FindAccessibleEndPoints( pCG, EndPoint, &nNumEndPoints, BondPos, &nNumBondPos, 5716| 0| pBNS, pBD, at, num_atoms, c_group_info, ALT_PATH_MODE_TAUTOM_KET ); ------------------ | | 320| 0|#define ALT_PATH_MODE_TAUTOM_KET 10 /* same as ALT_PATH_MODE_TAUTOM, applies to C=-OH or CH-=O; H may be (-) */ ------------------ 5717| | 5718| 0| if (IS_BNS_ERROR( nErr )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 5719| 0| { 5720| 0| return nErr; 5721| 0| } 5722| 0| nErr = 0; 5723| | 5724| 0| if (nNumEndPoints > 0) ------------------ | Branch (5724:33): [True: 0, False: 0] ------------------ 5725| 0| { 5726| 0| if (!nGroupNumber || bDiffGroups > 0) ------------------ | Branch (5726:37): [True: 0, False: 0] | Branch (5726:54): [True: 0, False: 0] ------------------ 5727| 0| { 5728| | 5729| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 5730| 0| if (num_changes == -1) ------------------ | Branch (5730:41): [True: 0, False: 0] ------------------ 5731| 0| { 5732| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5733| 0| } 5734| 0| if (num_changes < 0) ------------------ | Branch (5734:41): [True: 0, False: 0] ------------------ 5735| 0| { 5736| 0| nErr = num_changes; 5737| 0| } 5738| 0| if (nErr) ------------------ | Branch (5738:41): [True: 0, False: 0] ------------------ 5739| 0| { 5740| 0| goto exit_function; 5741| 0| } 5742| 0| tot_changes += ( num_changes > 0 ); 5743| 0| } 5744| 0| if (nNumBondPos > 0) ------------------ | Branch (5744:37): [True: 0, False: 0] ------------------ 5745| 0| { 5746| | /* Some of the bonds have not been marked as tautomeric yet */ 5747| 0| num_changes = SetTautomericBonds( at, nNumBondPos, BondPos ); 5748| 0| tot_changes += ( num_changes > 0 ); 5749| 0| } 5750| 0| } 5751| 0| } 5752| 0| } 5753| 0| } 5754| 0| } 5755| 0| } 5756| 0| } 5757| 263k|#endif /* KETO_ENOL_TAUT */ 5758| | 5759| 263k|#if ( TAUT_OTHER == 1 ) /* { */ 5760| 263k| if (!tot_changes) ------------------ | Branch (5760:9): [True: 257k, False: 5.48k] ------------------ 5761| 257k| { 5762| 257k|#define MAX_ALT_PATH_LEN 8 5763| 257k| int nMaxLenDfsPath = MAX_ALT_PATH_LEN; ------------------ | | 5762| 257k|#define MAX_ALT_PATH_LEN 8 ------------------ 5764| 257k| int i1, i2; 5765| 257k| AT_RANK *nDfsPathPos = (AT_RANK *) inchi_calloc( num_atoms, sizeof( nDfsPathPos[0] ) ); ------------------ | | 1146| 257k|#define inchi_calloc calloc ------------------ 5766| 257k| DFS_PATH DfsPath[MAX_ALT_PATH_LEN]; 5767| 257k| int ret; 5768| | 5769| 257k| if (!nDfsPathPos) /* djb-rwth: removing redundant code as address of DfsPath will always evaluate to true */ ------------------ | Branch (5769:13): [True: 0, False: 257k] ------------------ 5770| 0| { 5771| 0| tot_changes = CT_OUT_OF_RAM; /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5772| 0| goto free_memory; 5773| 0| } 5774| | 5775| 257k|#if ( TAUT_15_NON_RING == 1 ) /***** post v.1 feature *****/ 5776| 257k| if (t_group_info->bTautFlags & TG_FLAG_1_5_TAUT) ------------------ | | 947| 257k|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (5776:13): [True: 0, False: 257k] ------------------ 5777| 0| { 5778| | /* 1,5 tautomerism; one of the endpoints should no be on a ring */ 5779| | /* 5780| | O OH O 5781| | || | || 5782| | A--pos- A--pos- A--pos- 5783| | / sib- // sib- ? / sib- 5784| | C ly C ly CH ly 5785| | \\ a <--> \ a <--> \ a 5786| | B--ring B--ring B--ring 5787| | | || || 5788| | NH N N 5789| | 5790| | Note: few recent modifications now allow the terminal N be in a ring, too 5791| | */ 5792| 0| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (5792:26): [True: 0, False: 0] ------------------ 5793| 0| { 5794| | /* Find possible endpoint Z = at[i1] */ 5795| 0| if (!( endpoint_valence = nGetEndpointInfo( at, i1, &eif1 ) ) /*|| ------------------ | Branch (5795:21): [True: 0, False: 0] ------------------ 5796| 0| at[i1].nNumAtInRingSystem > 1*/) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 5797| 0| { 5798| 0| continue; /* not a possibly endpoint */ 5799| 0| } 5800| | 5801| 0| if (1) ------------------ | Branch (5801:21): [True: 0, Folded] ------------------ 5802| 0| { 5803| 0| nNumEndPoints = 0; 5804| 0| nNumBondPos = 0; 5805| | 5806| 0| ret = nGet15TautInAltPath( pCG, at, i1, nDfsPathPos, 5807| 0| DfsPath, nMaxLenDfsPath, 5808| 0| EndPoint, sizeof( EndPoint ) / sizeof( EndPoint[0] ), 5809| 0| BondPos, sizeof( BondPos ) / sizeof( BondPos[0] ), 5810| 0| &nNumEndPoints, &nNumBondPos, 5811| 0| pBNS, pBD, num_atoms ); 5812| | 5813| 0| if (ret > 0) ------------------ | Branch (5813:25): [True: 0, False: 0] ------------------ 5814| 0| { 5815| 0| if (nNumEndPoints) ------------------ | Branch (5815:29): [True: 0, False: 0] ------------------ 5816| 0| { 5817| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 5818| 0| if (num_changes == -1) ------------------ | Branch (5818:33): [True: 0, False: 0] ------------------ 5819| 0| { 5820| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5821| 0| } 5822| 0| if (num_changes < 0) ------------------ | Branch (5822:33): [True: 0, False: 0] ------------------ 5823| 0| { 5824| 0| nErr = num_changes; 5825| 0| } 5826| 0| if (nErr) ------------------ | Branch (5826:33): [True: 0, False: 0] ------------------ 5827| 0| { 5828| 0| goto free_memory; 5829| 0| } 5830| 0| tot_changes += ( num_changes > 0 ); 5831| 0| } 5832| 0| if (nNumBondPos) ------------------ | Branch (5832:29): [True: 0, False: 0] ------------------ 5833| 0| { 5834| 0| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 5835| 0| } 5836| 0| } 5837| 0| else 5838| 0| { 5839| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 5840| 0| { 5841| 0| nErr = ret; 5842| 0| goto free_memory; 5843| 0| } 5844| 0| } 5845| 0| } 5846| 0| } 5847| 0| } 5848| 257k|#endif 5849| | 5850| 257k|#if ( TAUT_4PYRIDINOL_RINGS == 1 ) 5851| | /* 6-member rings */ 5852| | /* 5853| | O OH OH 5854| | || | | 5855| | / \ // \ / \\ 5856| | || || <--> | || <--> || | 5857| | \ / \\ / \ // 5858| | NH N N 5859| | */ 5860| 1.34M| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (5860:22): [True: 1.08M, False: 257k] ------------------ 5861| 1.08M| { 5862| | /* Find possible endpoint Z = at[i1] */ 5863| 1.08M| if (3 != ( endpoint_valence = nGetEndpointInfo( at, i1, &eif1 ) ) || ------------------ | Branch (5863:17): [True: 1.04M, False: 37.4k] ------------------ 5864| 37.4k| 2 != at[i1].valence) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (5864:18): [True: 9.35k, False: 28.0k] ------------------ 5865| 1.05M| { 5866| 1.05M| continue; /* not a nitrogen atom or a wrong valence */ 5867| 1.05M| } 5868| | 5869| 28.0k| if (at[i1].nNumAtInRingSystem >= 6) ------------------ | Branch (5869:17): [True: 6.09k, False: 22.0k] ------------------ 5870| 6.09k| { 5871| 6.09k| nNumEndPoints = 0; 5872| 6.09k| nNumBondPos = 0; 5873| | 5874| 6.09k| ret = nGet15TautIn6MembAltRing( pCG, at, i1, nDfsPathPos, 5875| 6.09k| DfsPath, nMaxLenDfsPath, EndPoint, 5876| 6.09k| sizeof( EndPoint ) / sizeof( EndPoint[0] ), 5877| 6.09k| BondPos, 5878| 6.09k| sizeof( BondPos ) / sizeof( BondPos[0] ), 5879| 6.09k| &nNumEndPoints, &nNumBondPos, 5880| 6.09k| pBNS, pBD, num_atoms ); 5881| 6.09k| if (ret > 0) ------------------ | Branch (5881:21): [True: 41, False: 6.05k] ------------------ 5882| 41| { 5883| 41| if (nNumEndPoints) ------------------ | Branch (5883:25): [True: 41, False: 0] ------------------ 5884| 41| { 5885| 41| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 5886| 41| if (num_changes == -1) ------------------ | Branch (5886:29): [True: 0, False: 41] ------------------ 5887| 0| { 5888| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5889| 0| } 5890| 41| if (num_changes < 0) ------------------ | Branch (5890:29): [True: 0, False: 41] ------------------ 5891| 0| { 5892| 0| nErr = num_changes; 5893| 0| } 5894| 41| if (nErr) ------------------ | Branch (5894:29): [True: 0, False: 41] ------------------ 5895| 0| { 5896| 0| goto free_memory; 5897| 0| } 5898| 41| tot_changes += ( num_changes > 0 ); 5899| 41| } 5900| 41| if (nNumBondPos) ------------------ | Branch (5900:25): [True: 11, False: 30] ------------------ 5901| 11| { 5902| 11| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 5903| 11| } 5904| 41| } 5905| 6.05k| else 5906| 6.05k| { 5907| 6.05k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 6.05k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 6.05k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 6.05k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 6.05k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 6.05k, False: 0] | | | Branch (67:44): [True: 0, False: 6.05k] | | ------------------ ------------------ 5908| 0| { 5909| 0| nErr = ret; 5910| 0| goto free_memory; 5911| 0| } 5912| 6.05k| } 5913| 6.09k| } 5914| 28.0k| } 5915| 257k|#endif /* TAUT_4PYRIDINOL_RINGS */ 5916| | 5917| 257k|#if ( TAUT_PYRAZOLE_RINGS == 1 ) 5918| | /* 5-member rings: 5919| | 5920| | Z Z 5921| | / \\ // \ 5922| | X Y <--> X Y 5923| | \\ / \ // 5924| | N--NH HN--N 5925| | 5926| | ^ ^ 5927| | search for these NH 5928| | */ 5929| | /* 5-member rings (pyrazole derivatives): look for the neighboring N */ 5930| 1.34M| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (5930:22): [True: 1.08M, False: 257k] ------------------ 5931| 1.08M| { 5932| 1.08M| if (2 == at[i1].valence && ------------------ | Branch (5932:17): [True: 109k, False: 975k] ------------------ 5933| 109k| at[i1].nNumAtInRingSystem >= 5 && ------------------ | Branch (5933:18): [True: 21.9k, False: 87.1k] ------------------ 5934| 21.9k| 3 == ( endpoint_valence = nGetEndpointInfo( at, i1, &eif1 ) ) ------------------ | Branch (5934:18): [True: 10.1k, False: 11.7k] ------------------ 5935| 1.08M| ) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 5936| 10.1k| { 5937| 10.1k| nMobile = at[i1].num_H + ( at[i1].charge == -1 ); 5938| 30.5k| for (j = 0; j < at[i1].valence; j++) ------------------ | Branch (5938:29): [True: 20.3k, False: 10.1k] ------------------ 5939| 20.3k| { 5940| 20.3k| int nMobile2, endpoint_valence2; 5941| 20.3k| i2 = at[i1].neighbor[j]; 5942| | 5943| | /* may be important */ 5944| 20.3k| if (i2 >= i1) ------------------ | Branch (5944:25): [True: 10.7k, False: 9.67k] ------------------ 5945| 10.7k| { 5946| 10.7k| continue; /* do not try same pair 2 times */ 5947| 10.7k| } 5948| | 5949| 9.67k| if (at[i2].nRingSystem != at[i1].nRingSystem) ------------------ | Branch (5949:25): [True: 0, False: 9.67k] ------------------ 5950| 0| { 5951| 0| continue; 5952| 0| } 5953| | 5954| 9.67k| bond_type = ( at[i1].bond_type[j] & ~BOND_MARK_ALL ); ------------------ | | 191| 9.67k|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 5955| 9.67k| if ((bond_type != BOND_SINGLE && ------------------ | | 177| 9.67k|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 19.3k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (5955:26): [True: 7.93k, False: 1.73k] ------------------ 5956| 7.93k| bond_type != BOND_TAUTOM && ------------------ | | 185| 17.6k|#define BOND_TAUTOM 8 ------------------ | Branch (5956:26): [True: 5.13k, False: 2.80k] ------------------ 5957| 5.13k| bond_type != BOND_ALT12NS && ------------------ | | 186| 14.8k|#define BOND_ALT12NS 9 ------------------ | Branch (5957:26): [True: 3.99k, False: 1.14k] ------------------ 5958| 3.99k| bond_type != BOND_ALTERN) || /* added 1-15-2002 */ ------------------ | | 180| 3.99k|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 3.99k|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (5958:26): [True: 2.00k, False: 1.99k] ------------------ 5959| 7.67k| 2 != at[i2].valence || ------------------ | Branch (5959:26): [True: 1.18k, False: 6.49k] ------------------ 5960| 6.49k| 3 != ( endpoint_valence2 = nGetEndpointInfo( at, i2, &eif2 ) )) /* djb-rwth: addressing LLVM warning; variable used to store function return value */ ------------------ | Branch (5960:26): [True: 1.28k, False: 5.20k] ------------------ 5961| 4.46k| { 5962| 4.46k| continue; /* not a nitrogen atom or a wrong valence or not a single bond */ 5963| 4.46k| } 5964| 5.20k| nMobile2 = at[i2].num_H + ( at[i2].charge == -1 ); /* number of mobile groups */ 5965| |#if ( TAUT_IGNORE_EQL_ENDPOINTS == 1 ) 5966| | if (at[i1].endpoint && at[i1].endpoint == at[i2].endpoint) 5967| | { 5968| | continue; /* atoms already belong to the same t-group */ 5969| | } 5970| |#endif 5971| 5.20k| if (!at[i1].endpoint && !at[i2].endpoint && 1 != nMobile + nMobile2) ------------------ | Branch (5971:25): [True: 3.47k, False: 1.72k] | Branch (5971:45): [True: 2.96k, False: 518] | Branch (5971:65): [True: 2.80k, False: 158] ------------------ 5972| 2.80k| { 5973| 2.80k| continue; 5974| 2.80k| } 5975| | 5976| 2.40k| ret = nGet12TautIn5MembAltRing( pCG, at, i1, j, nDfsPathPos, 5977| 2.40k| DfsPath, nMaxLenDfsPath, 5978| 2.40k| EndPoint, 5979| 2.40k| sizeof( EndPoint ) / sizeof( EndPoint[0] ), 5980| 2.40k| BondPos, 5981| 2.40k| sizeof( BondPos ) / sizeof( BondPos[0] ), 5982| 2.40k| &nNumEndPoints, &nNumBondPos, 5983| 2.40k| pBNS, pBD, num_atoms ); 5984| 2.40k| if (ret > 0) ------------------ | Branch (5984:25): [True: 245, False: 2.16k] ------------------ 5985| 245| { 5986| 245| if (nNumEndPoints) ------------------ | Branch (5986:29): [True: 245, False: 0] ------------------ 5987| 245| { 5988| 245| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 5989| 245| if (num_changes == -1) ------------------ | Branch (5989:33): [True: 0, False: 245] ------------------ 5990| 0| { 5991| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5992| 0| } 5993| 245| if (num_changes < 0) ------------------ | Branch (5993:33): [True: 0, False: 245] ------------------ 5994| 0| { 5995| 0| nErr = num_changes; 5996| 0| } 5997| 245| if (nErr) ------------------ | Branch (5997:33): [True: 0, False: 245] ------------------ 5998| 0| goto free_memory; 5999| 245| tot_changes += ( num_changes > 0 ); 6000| 245| } 6001| 245| if (nNumBondPos) ------------------ | Branch (6001:29): [True: 21, False: 224] ------------------ 6002| 21| { 6003| 21| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 6004| 21| } 6005| 245| } 6006| 2.16k| else 6007| 2.16k| { 6008| 2.16k| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 2.16k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 2.16k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 2.16k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 2.16k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 2.16k, False: 0] | | | Branch (67:44): [True: 0, False: 2.16k] | | ------------------ ------------------ 6009| 0| { 6010| 0| nErr = ret; 6011| 0| goto free_memory; 6012| 0| } 6013| 2.16k| } 6014| 2.40k| } 6015| 10.1k| } 6016| 1.08M| } 6017| 257k|#endif /* TAUT_PYRAZOLE_RINGS */ 6018| | 6019| 257k|#if ( TAUT_TROPOLONE_7 == 1 || TAUT_TROPOLONE_5 == 1 ) /* { */ 6020| | /******************************************************** 6021| | * A B 6022| | * | || 6023| | * 7-member rings (tropolones): look for M=Q--R--ZH, 6024| | * ^ ^ ^ ^ 6025| | * endpoint1 i1 i2 endpoint2 6026| | * where A-Q-R=B belong to a 7-member alt. (except Q-R bond) ring: ..=A-(Q-R)=B-.. 6027| | * Bond Q-R should be single or tautomeric or alternating 6028| | * M=Q and R-ZH should be chain (non-ring) bonds 6029| | * Same for 5-member rings 6030| | */ 6031| 1.34M| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (6031:22): [True: 1.08M, False: 257k] ------------------ 6032| 1.08M| { 6033| 1.08M| if (at[i1].nNumAtInRingSystem >= ------------------ | Branch (6033:17): [True: 30.8k, False: 1.05M] ------------------ 6034| 1.08M|#if ( TAUT_TROPOLONE_5 == 1 ) 6035| 1.08M| 5 6036| |#else 6037| | 7 6038| |#endif 6039| 30.8k| && 6040| 30.8k| bIsCenterPointStrict( at, i1 ) && ------------------ | Branch (6040:18): [True: 15.5k, False: 15.2k] ------------------ 6041| 15.5k|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 6042| 15.5k| at[i1].bCutVertex && ------------------ | Branch (6042:18): [True: 2.50k, False: 13.0k] ------------------ 6043| 2.50k|#endif 6044| 2.50k| at[i1].valence == 3 && !at[i1].endpoint) ------------------ | Branch (6044:18): [True: 1.65k, False: 854] | Branch (6044:41): [True: 1.65k, False: 0] ------------------ 6045| 1.65k| { 6046| 1.65k| int nMobile1, endpoint1, endpoint1_valence, bond_type1; 6047| 1.65k| int nMobile2, endpoint2, endpoint2_valence, bond_type2; 6048| 6.61k| for (j = 0; j < at[i1].valence; j++) ------------------ | Branch (6048:29): [True: 4.96k, False: 1.65k] ------------------ 6049| 4.96k| { 6050| 4.96k| i2 = at[i1].neighbor[j]; 6051| | /* may be important 6052| | if ( i2 > i1 ) 6053| | continue; 6054| | do not try same pair 2 times 6055| | */ 6056| 4.96k| if (at[i2].nRingSystem != at[i1].nRingSystem || ------------------ | Branch (6056:25): [True: 1.62k, False: 3.34k] ------------------ 6057| 3.34k| !bIsCenterPointStrict( at, i2 ) || ------------------ | Branch (6057:26): [True: 1.13k, False: 2.21k] ------------------ 6058| 2.21k|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 6059| 2.21k| !at[i2].bCutVertex || ------------------ | Branch (6059:26): [True: 1.35k, False: 857] ------------------ 6060| 857|#endif 6061| 857| at[i2].valence != 3 || at[i2].endpoint) ------------------ | Branch (6061:26): [True: 91, False: 766] | Branch (6061:49): [True: 0, False: 766] ------------------ 6062| 4.19k| { 6063| 4.19k| continue; 6064| 4.19k| } 6065| 766| bond_type = ( at[i1].bond_type[j] & ~BOND_MARK_ALL ); ------------------ | | 191| 766|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 6066| 766| if (bond_type != BOND_SINGLE && ------------------ | | 177| 766|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 1.53k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (6066:25): [True: 217, False: 549] ------------------ 6067| 217| bond_type != BOND_TAUTOM && ------------------ | | 185| 983|#define BOND_TAUTOM 8 ------------------ | Branch (6067:26): [True: 144, False: 73] ------------------ 6068| 144| bond_type != BOND_ALT12NS && ------------------ | | 186| 910|#define BOND_ALT12NS 9 ------------------ | Branch (6068:26): [True: 86, False: 58] ------------------ 6069| 86| bond_type != BOND_ALTERN) ------------------ | | 180| 86|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 86|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (6069:26): [True: 50, False: 36] ------------------ 6070| 50| { 6071| 50| continue; /* not a single bond between Q-R */ 6072| 50| } 6073| | 6074| | /* Find endpoints */ 6075| 2.86k| for (k = 0; k < at[i1].valence; k++) ------------------ | Branch (6075:33): [True: 2.14k, False: 716] ------------------ 6076| 2.14k| { 6077| 2.14k| endpoint1 = at[i1].neighbor[k]; 6078| 2.14k| if (endpoint1 == i2) ------------------ | Branch (6078:29): [True: 716, False: 1.43k] ------------------ 6079| 716| { 6080| 716| continue; /* j == k */ 6081| 716| } 6082| 1.43k| if (!( endpoint1_valence = nGetEndpointInfo( at, endpoint1, &eif1 ) )) ------------------ | Branch (6082:29): [True: 773, False: 659] ------------------ 6083| 773| { 6084| 773| continue; /* not an endpoint1 element or can't have mobile groups */ 6085| 773| } 6086| 659|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 6087| 659| if (at[endpoint1].nRingSystem == at[i1].nRingSystem) ------------------ | Branch (6087:29): [True: 101, False: 558] ------------------ 6088| 101| { 6089| 101| continue; 6090| 101| } 6091| 558|#endif 6092| 558| nMobile1 = at[endpoint1].num_H + ( at[endpoint1].charge == -1 ); /* number of mobile groups */ 6093| 558| if (nMobile1 + at[endpoint1].chem_bonds_valence != endpoint1_valence) ------------------ | Branch (6093:29): [True: 0, False: 558] ------------------ 6094| 0| continue; /* abnormal endpoint1 valence; ignore. */ 6095| 558| bond_type1 = ( at[i1].bond_type[k] & ~BOND_MARK_ALL ); ------------------ | | 191| 558|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 6096| | 6097| 558| if (bond_type1 != BOND_SINGLE && ------------------ | | 177| 558|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 1.11k|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (6097:29): [True: 486, False: 72] ------------------ 6098| 486| bond_type1 != BOND_DOUBLE && ------------------ | | 178| 486|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 1.04k|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (6098:30): [True: 348, False: 138] ------------------ 6099| 348| bond_type1 != BOND_TAUTOM && ------------------ | | 185| 906|#define BOND_TAUTOM 8 ------------------ | Branch (6099:30): [True: 71, False: 277] ------------------ 6100| 71| bond_type1 != BOND_ALT12NS && ------------------ | | 186| 629|#define BOND_ALT12NS 9 ------------------ | Branch (6100:30): [True: 28, False: 43] ------------------ 6101| 28| bond_type1 != BOND_ALTERN) ------------------ | | 180| 28|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 28|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (6101:30): [True: 0, False: 28] ------------------ 6102| 0| { 6103| 0| continue; 6104| 0| } 6105| 2.23k| for (m = 0; m < at[i2].valence; m++) ------------------ | Branch (6105:37): [True: 1.67k, False: 558] ------------------ 6106| 1.67k| { 6107| 1.67k| endpoint2 = at[i2].neighbor[m]; 6108| 1.67k| if (endpoint2 == i1) ------------------ | Branch (6108:33): [True: 558, False: 1.11k] ------------------ 6109| 558| { 6110| 558| continue; 6111| 558| } 6112| 1.11k| if (!( endpoint2_valence = nGetEndpointInfo( at, endpoint2, &eif2 ) )) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (6112:33): [True: 537, False: 579] ------------------ 6113| 537| { 6114| 537| continue; /* not an endpoint2 element or can't have mobile groups */ 6115| 537| } 6116| 579|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 6117| 579| if (at[endpoint2].nRingSystem == at[i2].nRingSystem) ------------------ | Branch (6117:33): [True: 93, False: 486] ------------------ 6118| 93| { 6119| 93| continue; 6120| 93| } 6121| 486|#endif 6122| 486| nMobile2 = at[endpoint2].num_H + ( at[endpoint2].charge == -1 ); /* number of mobile groups */ 6123| 486| bond_type2 = ( at[i2].bond_type[m] & ~BOND_MARK_ALL ); ------------------ | | 191| 486|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 6124| | 6125| 486| if (bond_type2 != BOND_SINGLE && ------------------ | | 177| 486|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 972|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (6125:33): [True: 425, False: 61] ------------------ 6126| 425| bond_type2 != BOND_DOUBLE && ------------------ | | 178| 425|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 911|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (6126:34): [True: 299, False: 126] ------------------ 6127| 299| bond_type2 != BOND_TAUTOM && ------------------ | | 185| 785|#define BOND_TAUTOM 8 ------------------ | Branch (6127:34): [True: 29, False: 270] ------------------ 6128| 29| bond_type2 != BOND_ALT12NS && ------------------ | | 186| 515|#define BOND_ALT12NS 9 ------------------ | Branch (6128:34): [True: 20, False: 9] ------------------ 6129| 20| bond_type2 != BOND_ALTERN) ------------------ | | 180| 20|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 35| 20|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (6129:34): [True: 0, False: 20] ------------------ 6130| 0| { 6131| 0| continue; 6132| 0| } 6133| | 6134| | /* Final test for possible tautomerism */ 6135| 486| nMobile = 0; 6136| | 6137| 486| if (ALLOWED_EDGE( pBNS, i1, k ) && ALLOWED_EDGE( pBNS, i2, m )) ------------------ | | 4321| 972|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 486] | | | Branch (4321:53): [True: 0, False: 486] | | | Branch (4321:70): [True: 0, False: 486] | | | Branch (4321:87): [True: 486, False: 0] | | ------------------ ------------------ if (ALLOWED_EDGE( pBNS, i1, k ) && ALLOWED_EDGE( pBNS, i2, m )) ------------------ | | 4321| 486|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (4321:42): [True: 0, False: 486] | | | Branch (4321:53): [True: 0, False: 486] | | | Branch (4321:70): [True: 0, False: 486] | | | Branch (4321:87): [True: 486, False: 0] | | ------------------ ------------------ 6138| 486| { 6139| | /* Can mobile group move from 1 to 2? */ 6140| 486| nMobile += ( at[endpoint1].endpoint || nMobile1 ) && /* from endpoint1 */ ------------------ | Branch (6140:46): [True: 292, False: 194] | Branch (6140:72): [True: 101, False: 93] ------------------ 6141| 393| ( bond_type1 != BOND_DOUBLE ) && ------------------ | | 178| 393|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 393|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (6141:37): [True: 364, False: 29] ------------------ 6142| | 6143| 364| ( at[endpoint2].endpoint || /* to endpoint2 */ ------------------ | Branch (6143:39): [True: 281, False: 83] ------------------ 6144| 83| eif2.cNeutralBondsValence > at[endpoint2].valence ) && ------------------ | Branch (6144:39): [True: 48, False: 35] ------------------ 6145| 329| ( bond_type2 != BOND_SINGLE ); ------------------ | | 177| 329|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 329|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (6145:39): [True: 329, False: 0] ------------------ 6146| | 6147| | /* Can mobile group move from 2 to 1? */ 6148| 486| nMobile += ( at[endpoint2].endpoint || nMobile2 ) && /* from endpoint2 */ ------------------ | Branch (6148:46): [True: 291, False: 195] | Branch (6148:72): [True: 94, False: 101] ------------------ 6149| 385| ( bond_type2 != BOND_DOUBLE ) && /*changed from BOND_SINGLE 2004-02-26 */ ------------------ | | 178| 385|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 385|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (6149:37): [True: 358, False: 27] ------------------ 6150| | 6151| 358| ( at[endpoint1].endpoint || /* to endpoint1 */ ------------------ | Branch (6151:39): [True: 280, False: 78] ------------------ 6152| 78| eif1.cNeutralBondsValence > at[endpoint1].valence ) && ------------------ | Branch (6152:39): [True: 42, False: 36] ------------------ 6153| 322| ( bond_type1 != BOND_SINGLE ); ------------------ | | 177| 322|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 322|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (6153:39): [True: 322, False: 0] ------------------ 6154| 486| } 6155| 486| if (!nMobile) ------------------ | Branch (6155:33): [True: 110, False: 376] ------------------ 6156| 110| { 6157| 110| continue; 6158| 110| } 6159| | 6160| 376| if (bond_type1 == bond_type2 && ------------------ | Branch (6160:33): [True: 263, False: 113] ------------------ 6161| 263| ( bond_type1 == BOND_SINGLE || bond_type1 == BOND_DOUBLE )) ------------------ | | 177| 263|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 32| 526|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ ( bond_type1 == BOND_SINGLE || bond_type1 == BOND_DOUBLE )) ------------------ | | 178| 263|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 33| 263|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (6161:35): [True: 0, False: 263] | Branch (6161:64): [True: 0, False: 263] ------------------ 6162| 0| { 6163| 0| continue; 6164| 0| } 6165| | 6166| | /* -- old -- 6167| | if ( !at[endpoint1].endpoint && !at[endpoint2].endpoint && 1 != nMobile1 + nMobile2 ) 6168| | continue; 6169| | */ 6170| | /* -- new -- 6171| | 6172| | if ( !at[endpoint1].endpoint && !at[endpoint2].endpoint ) { 6173| | if ( !(bond_type1 == BOND_SINGLE || bond_type1 == BOND_DOUBLE) || 6174| | !(bond_type2 == BOND_SINGLE || bond_type2 == BOND_DOUBLE) ) { 6175| | // at this point bond_type1 != bond_type2 6176| | continue; 6177| | } 6178| | if ( bond_type1 == BOND_SINGLE && !nMobile1 || 6179| | bond_type2 == BOND_SINGLE && !nMobile2 || 6180| | 0 == nMobile1 + nMobile2 ) { 6181| | continue; 6182| | } 6183| | } 6184| | */ 6185| | 6186| 376|#if ( TAUT_TROPOLONE_7 == 1 ) 6187| 376| if (at[i1].nNumAtInRingSystem >= 7) ------------------ | Branch (6187:33): [True: 0, False: 376] ------------------ 6188| 0| { 6189| | 6190| 0| ret = nGet14TautIn7MembAltRing( pCG, at, i1, 6191| 0| j, k, m, nDfsPathPos, 6192| 0| DfsPath, nMaxLenDfsPath, 6193| 0| EndPoint, 6194| 0| sizeof( EndPoint ) / sizeof( EndPoint[0] ), 6195| 0| BondPos, 6196| 0| sizeof( BondPos ) / sizeof( BondPos[0] ), 6197| 0| &nNumEndPoints, &nNumBondPos, 6198| 0| pBNS, pBD, num_atoms ); 6199| 0| if (ret > 0) ------------------ | Branch (6199:37): [True: 0, False: 0] ------------------ 6200| 0| { 6201| 0| if (nNumEndPoints) ------------------ | Branch (6201:41): [True: 0, False: 0] ------------------ 6202| 0| { 6203| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 6204| 0| if (num_changes == -1) ------------------ | Branch (6204:45): [True: 0, False: 0] ------------------ 6205| 0| { 6206| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6207| 0| } 6208| 0| if (num_changes < 0) ------------------ | Branch (6208:45): [True: 0, False: 0] ------------------ 6209| 0| { 6210| 0| nErr = num_changes; 6211| 0| } 6212| 0| if (nErr) ------------------ | Branch (6212:45): [True: 0, False: 0] ------------------ 6213| 0| { 6214| 0| goto free_memory; 6215| 0| } 6216| 0| tot_changes += ( num_changes > 0 ); 6217| 0| } 6218| 0| if (nNumBondPos) ------------------ | Branch (6218:41): [True: 0, False: 0] ------------------ 6219| 0| { 6220| 0| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 6221| 0| } 6222| 0| } 6223| 0| else 6224| 0| { 6225| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 0, False: 0] | | | Branch (67:44): [True: 0, False: 0] | | ------------------ ------------------ 6226| 0| { 6227| 0| nErr = ret; 6228| 0| goto free_memory; 6229| 0| } 6230| 0| } 6231| 0| } 6232| 376|#endif 6233| | 6234| 376|#if ( TAUT_TROPOLONE_5 == 1 ) 6235| 376| if (at[i1].nNumAtInRingSystem >= 5) ------------------ | Branch (6235:33): [True: 376, False: 0] ------------------ 6236| 376| { 6237| | 6238| 376| ret = nGet14TautIn5MembAltRing( pCG, at, i1, j, k, m, nDfsPathPos, 6239| 376| DfsPath, nMaxLenDfsPath, 6240| 376| EndPoint, sizeof( EndPoint ) / sizeof( EndPoint[0] ), 6241| 376| BondPos, sizeof( BondPos ) / sizeof( BondPos[0] ), 6242| 376| &nNumEndPoints, &nNumBondPos, 6243| 376| pBNS, pBD, num_atoms ); 6244| 376| if (ret > 0) ------------------ | Branch (6244:37): [True: 276, False: 100] ------------------ 6245| 276| { 6246| 276| if (nNumEndPoints) ------------------ | Branch (6246:41): [True: 276, False: 0] ------------------ 6247| 276| { 6248| 276| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 6249| 276| if (num_changes == -1) ------------------ | Branch (6249:45): [True: 0, False: 276] ------------------ 6250| 0| { 6251| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6252| 0| } 6253| 276| if (num_changes < 0) ------------------ | Branch (6253:45): [True: 0, False: 276] ------------------ 6254| 0| { 6255| 0| nErr = num_changes; 6256| 0| } 6257| 276| if (nErr) ------------------ | Branch (6257:45): [True: 0, False: 276] ------------------ 6258| 0| { 6259| 0| goto free_memory; 6260| 0| } 6261| 276| tot_changes += ( num_changes > 0 ); 6262| 276| } 6263| 276| if (nNumBondPos) ------------------ | Branch (6263:41): [True: 44, False: 232] ------------------ 6264| 44| { 6265| 44| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 6266| 44| } 6267| 276| } 6268| 100| else 6269| 100| { 6270| 100| if (IS_BNS_ERROR( ret )) ------------------ | | 67| 100|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 47| 100|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 65| 100|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 47| 100|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (67:26): [True: 100, False: 0] | | | Branch (67:44): [True: 0, False: 100] | | ------------------ ------------------ 6271| 0| { 6272| 0| nErr = ret; 6273| 0| goto free_memory; 6274| 0| } 6275| 100| } 6276| 376| } 6277| 376|#endif 6278| 376| } 6279| 558| } 6280| 716| } 6281| 1.65k| } 6282| 1.08M| } 6283| 257k|#endif /* } TAUT_TROPOLONE */ 6284| | 6285| 257k| free_memory: 6286| 257k| if (nDfsPathPos) ------------------ | Branch (6286:13): [True: 257k, False: 0] ------------------ 6287| 257k| { 6288| 257k| inchi_free( nDfsPathPos ); ------------------ | | 1152| 257k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 257k, False: 0] | | | Branch (1152:50): [Folded, False: 257k] | | ------------------ ------------------ 6289| 257k| } 6290| 257k|#undef MAX_ALT_PATH_LEN 6291| 257k| } 6292| 263k|#endif /* } FIND_RING_SYSTEMS */ 6293| | 6294| 263k|exit_function: 6295| | 6296| 263k| return nErr < 0 ? nErr : tot_changes; ------------------ | Branch (6296:12): [True: 0, False: 263k] ------------------ 6297| 263k|} free_t_group_info: 6302| 707k|{ 6303| 707k| if (t_group_info) ------------------ | Branch (6303:9): [True: 707k, False: 0] ------------------ 6304| 707k| { 6305| 707k| if (t_group_info->t_group) ------------------ | Branch (6305:13): [True: 131k, False: 576k] ------------------ 6306| 131k| { 6307| 131k| inchi_free( t_group_info->t_group ); ------------------ | | 1152| 131k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 131k, False: 0] | | | Branch (1152:50): [Folded, False: 131k] | | ------------------ ------------------ 6308| 131k| } 6309| 707k| if (t_group_info->nEndpointAtomNumber) ------------------ | Branch (6309:13): [True: 7.17k, False: 700k] ------------------ 6310| 7.17k| { 6311| 7.17k| inchi_free( t_group_info->nEndpointAtomNumber ); ------------------ | | 1152| 7.17k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 7.17k, False: 0] | | | Branch (1152:50): [Folded, False: 7.17k] | | ------------------ ------------------ 6312| 7.17k| } 6313| 707k| if (t_group_info->tGroupNumber) ------------------ | Branch (6313:13): [True: 7.17k, False: 700k] ------------------ 6314| 7.17k| { 6315| 7.17k| inchi_free( t_group_info->tGroupNumber ); ------------------ | | 1152| 7.17k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 7.17k, False: 0] | | | Branch (1152:50): [Folded, False: 7.17k] | | ------------------ ------------------ 6316| 7.17k| } 6317| 707k| if (t_group_info->nIsotopicEndpointAtomNumber) ------------------ | Branch (6317:13): [True: 462, False: 707k] ------------------ 6318| 462| { 6319| 462| inchi_free( t_group_info->nIsotopicEndpointAtomNumber ); ------------------ | | 1152| 462|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 462, False: 0] | | | Branch (1152:50): [Folded, False: 462] | | ------------------ ------------------ 6320| 462| } 6321| 707k| memset( t_group_info, 0, sizeof( *t_group_info ) ); /* djb-rwth: memset_s C11/Annex K variant? */ 6322| 707k| } 6323| | 6324| 707k| return 0; 6325| 707k|} make_a_copy_of_t_group_info: 6331| 40.8k|{ 6332| 40.8k| int err = 0, len; 6333| 40.8k| free_t_group_info( t_group_info ); 6334| 40.8k| if (t_group_info_orig && t_group_info) ------------------ | Branch (6334:9): [True: 40.8k, False: 0] | Branch (6334:30): [True: 40.8k, False: 0] ------------------ 6335| 40.8k| { 6336| 40.8k| if (( len = t_group_info_orig->max_num_t_groups ) > 0) ------------------ | Branch (6336:13): [True: 40.8k, False: 0] ------------------ 6337| 40.8k| { 6338| 40.8k| T_GROUP* tgi_tg = NULL; /* Copied from below 2024-09-01 DT */ 6339| | /* djb-rwth: fixing oss-fuzz issue #52978 */ 6340| 40.8k| tgi_tg = (T_GROUP*)inchi_malloc(((long long)len+1) * sizeof(t_group_info->t_group[0])); /* djb-rwth: cast operator added */ ------------------ | | 1143| 40.8k|#define inchi_malloc malloc ------------------ 6341| 40.8k| if (tgi_tg && t_group_info_orig->t_group) ------------------ | Branch (6341:17): [True: 40.8k, False: 0] | Branch (6341:27): [True: 40.8k, False: 0] ------------------ 6342| 40.8k| { 6343| 40.8k| t_group_info->t_group = tgi_tg; 6344| 40.8k| memcpy(tgi_tg, 6345| 40.8k| t_group_info_orig->t_group, 6346| 40.8k| len * sizeof(t_group_info->t_group[0])); /* djb-rwth: cast operator added */ 6347| 40.8k| } 6348| 0| else 6349| 0| { 6350| 0| if (tgi_tg) /* djb-rwth: avoiding memory leak */ ------------------ | Branch (6350:21): [True: 0, False: 0] ------------------ 6351| 0| { 6352| 0| inchi_free(tgi_tg); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6353| 0| } 6354| 0| err++; 6355| 0| } 6356| 40.8k| } 6357| 40.8k| if (( len = t_group_info_orig->nNumEndpoints ) > 0) ------------------ | Branch (6357:13): [True: 3.47k, False: 37.4k] ------------------ 6358| 3.47k| { 6359| 3.47k| if ((t_group_info->nEndpointAtomNumber = ------------------ | Branch (6359:17): [True: 3.47k, False: 0] ------------------ 6360| 3.47k| (AT_NUMB*) inchi_malloc( len * sizeof( t_group_info->nEndpointAtomNumber[0] ) ))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1143| 3.47k|#define inchi_malloc malloc ------------------ 6361| 3.47k| { 6362| 3.47k| memcpy(t_group_info->nEndpointAtomNumber, 6363| 3.47k| t_group_info_orig->nEndpointAtomNumber, 6364| 3.47k| len * sizeof(t_group_info->nEndpointAtomNumber[0])); 6365| 3.47k| } 6366| 0| else 6367| 0| { 6368| 0| err++; 6369| 0| } 6370| 3.47k| } 6371| 40.8k| if (( len = t_group_info_orig->num_t_groups ) > 0) ------------------ | Branch (6371:13): [True: 3.47k, False: 37.4k] ------------------ 6372| 3.47k| { 6373| 3.47k| if ((t_group_info->tGroupNumber = ------------------ | Branch (6373:17): [True: 3.47k, False: 0] ------------------ 6374| 3.47k| (AT_NUMB*) inchi_malloc( (long long)len * TGSO_TOTAL_LEN * sizeof( t_group_info->tGroupNumber[0] ) ))) /* djb-rwth: cast operator added; djb-rwth: addressing LLVM warning */ ------------------ | | 1143| 3.47k|#define inchi_malloc malloc ------------------ (AT_NUMB*) inchi_malloc( (long long)len * TGSO_TOTAL_LEN * sizeof( t_group_info->tGroupNumber[0] ) ))) /* djb-rwth: cast operator added; djb-rwth: addressing LLVM warning */ ------------------ | | 141| 3.47k|#define TGSO_TOTAL_LEN 4 ------------------ 6375| 3.47k| { 6376| 3.47k| memcpy(t_group_info->tGroupNumber, 6377| 3.47k| t_group_info_orig->tGroupNumber, 6378| 3.47k| (long long)len * TGSO_TOTAL_LEN * sizeof(t_group_info->tGroupNumber[0])); /* djb-rwth: cast operator added */ ------------------ | | 141| 3.47k|#define TGSO_TOTAL_LEN 4 ------------------ 6379| 3.47k| } 6380| 0| else 6381| 0| { 6382| 0| err++; 6383| 0| } 6384| 3.47k| } 6385| 40.8k| if (( len = t_group_info_orig->nNumIsotopicEndpoints ) > 0) ------------------ | Branch (6385:13): [True: 270, False: 40.6k] ------------------ 6386| 270| { 6387| | /* djb-rwth: fixing oss-fuzz issue #53519 */ 6388| 270| AT_NUMB* tgi_niean = (AT_NUMB*)inchi_malloc(len * sizeof(t_group_info->nIsotopicEndpointAtomNumber[0])); ------------------ | | 1143| 270|#define inchi_malloc malloc ------------------ 6389| 270| AT_NUMB* tgior_niean = (AT_NUMB*)inchi_realloc(t_group_info_orig->nIsotopicEndpointAtomNumber, len * sizeof(t_group_info_orig->nIsotopicEndpointAtomNumber[0])); ------------------ | | 1149| 270|#define inchi_realloc realloc ------------------ 6390| 270| if (tgi_niean && tgior_niean) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6390:17): [True: 270, False: 0] | Branch (6390:30): [True: 270, False: 0] ------------------ 6391| 270| { 6392| 270| t_group_info->nIsotopicEndpointAtomNumber = tgi_niean; 6393| 270| t_group_info_orig->nIsotopicEndpointAtomNumber = tgior_niean; 6394| 270| memcpy(tgi_niean, 6395| 270| tgior_niean, 6396| 270| len * sizeof(t_group_info->nIsotopicEndpointAtomNumber[0])); 6397| 270| } 6398| 0| else 6399| 0| { 6400| | /* djb-rwth: avoiding memory leaks */ 6401| 0| if (tgi_niean) ------------------ | Branch (6401:21): [True: 0, False: 0] ------------------ 6402| 0| { 6403| 0| inchi_free(tgi_niean); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6404| 0| } 6405| 0| if (tgior_niean) ------------------ | Branch (6405:21): [True: 0, False: 0] ------------------ 6406| 0| { 6407| 0| inchi_free(tgior_niean); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6408| 0| } 6409| 0| err++; 6410| 0| } 6411| 270| } 6412| 40.8k| if (!err) ------------------ | Branch (6412:13): [True: 40.8k, False: 0] ------------------ 6413| 40.8k| { 6414| 40.8k| t_group_info->nNumEndpoints = t_group_info_orig->nNumEndpoints; 6415| 40.8k| t_group_info->num_t_groups = t_group_info_orig->num_t_groups; 6416| 40.8k| t_group_info->max_num_t_groups = t_group_info_orig->max_num_t_groups; 6417| 40.8k| t_group_info->bIgnoreIsotopic = t_group_info_orig->bIgnoreIsotopic; 6418| 40.8k| t_group_info->nNumIsotopicEndpoints = t_group_info_orig->nNumIsotopicEndpoints; 6419| 40.8k| t_group_info->tni = t_group_info_orig->tni; 6420| | /* 6421| | t_group_info->nNumRemovedExplicitH = t_group_info_orig->nNumRemovedExplicitH; 6422| | t_group_info->nNumRemovedProtons = t_group_info_orig->nNumRemovedProtons; 6423| | t_group_info->bNormalizationFlags = t_group_info_orig->bNormalizationFlags; 6424| | */ 6425| | /* 6426| | t_group_info->bHardAddedRemovedProtons = t_group_info_orig->bHardAddedRemovedProtons; 6427| | t_group_info->bSimpleAddedRemovedProtons = t_group_info_orig->bSimpleAddedRemovedProtons; 6428| | t_group_info->nNumCanceledCharges = t_group_info_orig->nNumCanceledCharges; 6429| | */ 6430| 40.8k| } 6431| 40.8k| t_group_info->bTautFlags = t_group_info_orig->bTautFlags; 6432| 40.8k| t_group_info->bTautFlagsDone = t_group_info_orig->bTautFlagsDone; 6433| 40.8k| } 6434| | 6435| 40.8k| return err; 6436| 40.8k|} set_tautomer_iso_sort_keys: 6443| 40.8k|{ 6444| 40.8k| T_GROUP *t_group; 6445| 40.8k| T_GROUP_ISOWT Mult = 1; 6446| 40.8k| int i, j, num_t_groups, num_iso_t_groups = 0; 6447| | 6448| 40.8k| if (!t_group_info || !( t_group = t_group_info->t_group ) || ------------------ | Branch (6448:9): [True: 0, False: 40.8k] | Branch (6448:26): [True: 0, False: 40.8k] ------------------ 6449| 40.8k| 0 >= ( num_t_groups = t_group_info->num_t_groups ) || t_group_info->nNumIsotopicEndpoints) ------------------ | Branch (6449:10): [True: 37.4k, False: 3.47k] | Branch (6449:64): [True: 117, False: 3.36k] ------------------ 6450| 37.5k| { 6451| 37.5k| return 0; 6452| 37.5k| } 6453| | 6454| 6.79k| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (6454:17): [True: 3.43k, False: 3.36k] ------------------ 6455| 3.43k| { 6456| 3.43k| t_group[i].iWeight = 0; 6457| 3.43k| j = T_NUM_ISOTOPIC - 1; ------------------ | | 70| 3.43k|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 25| 3.43k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ 6458| 3.43k| Mult = 1; 6459| 3.43k| do 6460| 10.3k| { 6461| 10.3k| t_group[i].iWeight += Mult * (T_GROUP_ISOWT) t_group[i].num[T_NUM_NO_ISOTOPIC + j]; ------------------ | | 69| 10.3k|#define T_NUM_NO_ISOTOPIC 2 ------------------ 6462| 10.3k| } while (--j >= 0 && ( Mult *= T_GROUP_ISOWT_MULT )); ------------------ | | 81| 6.87k|#define T_GROUP_ISOWT_MULT 1024 /* (max. number of identical isotopic hydrogens in a taut. group) + 1 */ ------------------ | Branch (6462:18): [True: 6.87k, False: 3.43k] | Branch (6462:30): [True: 6.87k, False: 0] ------------------ 6463| | 6464| 3.43k| num_iso_t_groups += ( t_group[i].iWeight != 0 ); 6465| 3.43k| } 6466| | 6467| 3.36k| return num_iso_t_groups; 6468| 40.8k|} CountTautomerGroups: 6487| 252k|{ 6488| 252k| int i, j, ret = 0, nNumEndpoints, max_t_group, num_groups_noH; 6489| | 6490| 252k| AT_NUMB nGroupNumber, nNewGroupNumber, *nCurrEndpointAtNoPos = NULL; 6491| | 6492| 252k| T_GROUP *t_group; 6493| 252k| int num_t; 6494| | /* int bIgnoreIsotopic, max_num_t; */ 6495| 252k| AT_NUMB *nTautomerGroupNumber = NULL; 6496| 252k| AT_NUMB *nEndpointAtomNumber = NULL; 6497| 252k| AT_NUMB *tGroupNumber = NULL; 6498| | 6499| 252k| if (!t_group_info || !t_group_info->t_group || 0 >= t_group_info->max_num_t_groups) ------------------ | Branch (6499:9): [True: 0, False: 252k] | Branch (6499:26): [True: 0, False: 252k] | Branch (6499:52): [True: 0, False: 252k] ------------------ 6500| 0| { 6501| 0| return 0; /* empty t-groups */ 6502| 0| } 6503| 252k| num_t = t_group_info->num_t_groups; 6504| 252k| t_group = t_group_info->t_group; 6505| | /* 6506| | max_num_t = t_group_info->max_num_t_groups; 6507| | bIgnoreIsotopic = t_group_info->bIgnoreIsotopic; 6508| | */ 6509| 252k| num_groups_noH = 0; 6510| | 6511| | /* the following 2 arrays are to be rebuilt here */ 6512| | /* djb-rwth: fixing oss-fuzz issue #70006 */ 6513| 252k| if (t_group_info->nEndpointAtomNumber) ------------------ | Branch (6513:9): [True: 0, False: 252k] ------------------ 6514| 0| { 6515| | /* free( t_group_info->nEndpointAtomNumber ); */ 6516| 0| t_group_info->nEndpointAtomNumber = NULL; 6517| 0| } 6518| 252k| if (t_group_info->tGroupNumber) ------------------ | Branch (6518:9): [True: 0, False: 252k] ------------------ 6519| 0| { 6520| | /* inchi_free( t_group_info->tGroupNumber ); */ 6521| 0| t_group_info->tGroupNumber = NULL; 6522| 0| } 6523| | 6524| | /* Find max_t_group */ 6525| 257k| for (i = 0, max_t_group = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (6525:34): [True: 5.56k, False: 252k] ------------------ 6526| 5.56k| { 6527| 5.56k| if (max_t_group < t_group[i].nGroupNumber) ------------------ | Branch (6527:13): [True: 5.56k, False: 0] ------------------ 6528| 5.56k| max_t_group = t_group[i].nGroupNumber; 6529| 5.56k| } 6530| | /* Allocate memory for temp storage of numbers of endpoints */ 6531| 252k| if (max_t_group && ------------------ | Branch (6531:9): [True: 5.45k, False: 246k] ------------------ 6532| 5.45k| !( nTautomerGroupNumber = (AT_NUMB*) inchi_calloc( (long long)max_t_group + 1, sizeof( nTautomerGroupNumber[0] ) ) /*temp*/ )) /* djb-rwth: cast operator added */ ------------------ | | 1146| 5.45k|#define inchi_calloc calloc ------------------ | Branch (6532:10): [True: 0, False: 5.45k] ------------------ 6533| 0| { 6534| 0| goto err_exit_function; /* program error: out of RAM */ /* */ 6535| 0| } 6536| | 6537| | /* Count endpoints for each tautomer group */ 6538| 1.30M| for (i = 0, nNumEndpoints = 0; i < num_atoms; i++) ------------------ | Branch (6538:36): [True: 1.04M, False: 252k] ------------------ 6539| 1.04M| { 6540| 1.04M| if (( j = at[i].endpoint ) == 0) ------------------ | Branch (6540:13): [True: 1.03M, False: 13.2k] ------------------ 6541| 1.03M| { 6542| 1.03M| continue; 6543| 1.03M| } 6544| 13.2k| if (j > max_t_group) /* debug only */ ------------------ | Branch (6544:13): [True: 0, False: 13.2k] ------------------ 6545| 0| { 6546| 0| goto err_exit_function; /* program error */ /* */ 6547| 0| } 6548| 13.2k| if (nTautomerGroupNumber) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (6548:13): [True: 13.2k, False: 0] ------------------ 6549| 13.2k| nTautomerGroupNumber[j] ++; 6550| 13.2k| nNumEndpoints++; 6551| 13.2k| } 6552| | 6553| 252k| if (!nNumEndpoints) ------------------ | Branch (6553:9): [True: 246k, False: 5.45k] ------------------ 6554| 246k| { 6555| 246k| goto exit_function; /* not a tautomer */ 6556| 246k| } 6557| | 6558| | /* allocate temporary array */ 6559| 5.45k| if (!( nEndpointAtomNumber = (AT_NUMB*) inchi_calloc( nNumEndpoints, sizeof( nEndpointAtomNumber[0] ) ) ) || ------------------ | | 1146| 5.45k|#define inchi_calloc calloc ------------------ | Branch (6559:9): [True: 0, False: 5.45k] ------------------ 6560| 5.45k| !( nCurrEndpointAtNoPos = (AT_NUMB*) inchi_calloc( num_t, sizeof( nCurrEndpointAtNoPos[0] ) ) /*temp*/ )) ------------------ | | 1146| 5.45k|#define inchi_calloc calloc ------------------ | Branch (6560:10): [True: 0, False: 5.45k] ------------------ 6561| 0| { 6562| 0| goto err_exit_function; /* program error: out of RAM */ /* */ 6563| 0| } 6564| | 6565| | /* 6566| | * Remove missing endpoints from t_group. Since only one 6567| | * disconnected part is processed, some endpoints groups may have disappeared. 6568| | * Mark t_groups containing charges only for subsequent removal 6569| | */ 6570| 11.0k| for (i = 0, nNewGroupNumber = 0; i < num_t; /*i ++*/) ------------------ | Branch (6570:38): [True: 5.56k, False: 5.45k] ------------------ 6571| 5.56k| { 6572| 5.56k| int bNoH = 0, nNumH; 6573| 5.56k| nGroupNumber = t_group[i].nGroupNumber; 6574| 11.1k| for (j = 1, nNumH = t_group[i].num[0]; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 69| 11.1k|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (6574:48): [True: 5.56k, False: 5.56k] ------------------ 6575| 5.56k| { 6576| 5.56k| nNumH -= (int) t_group[i].num[j]; 6577| 5.56k| } 6578| 5.56k| if (nTautomerGroupNumber) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (6578:13): [True: 5.56k, False: 0] ------------------ 6579| 5.56k| { 6580| 5.56k| if (t_group[i].nNumEndpoints != nTautomerGroupNumber[(int)nGroupNumber] ------------------ | Branch (6580:17): [True: 0, False: 5.56k] ------------------ 6581| 5.56k|#if ( IGNORE_TGROUP_WITHOUT_H == 1 ) 6582| 5.56k| || (bNoH = (t_group[i].num[0] == t_group[i].num[1])) /* only for (H,-) t-groups; (+) t-groups are not removed */ ------------------ | Branch (6582:20): [True: 1.98k, False: 3.57k] ------------------ 6583| 5.56k|#endif 6584| 5.56k| ) /* djb-rwth: fixing a NULL pointer dereference */ 6585| 1.98k| { 6586| 1.98k| if (!nTautomerGroupNumber[(int)nGroupNumber] || bNoH) ------------------ | Branch (6586:21): [True: 0, False: 1.98k] | Branch (6586:65): [True: 1.98k, False: 0] ------------------ 6587| 1.98k| { 6588| | /* The group belongs to another disconnected part of the structure or has only charges */ 6589| | /* Remove the group */ 6590| 1.98k| num_t--; 6591| 1.98k| if (i < num_t) ------------------ | Branch (6591:25): [True: 8, False: 1.97k] ------------------ 6592| 8| memmove(t_group + i, t_group + i + 1, ((long long)num_t - (long long)i) * sizeof(t_group[0])); /* djb-rwth: cast operators added */ 6593| 1.98k| if (bNoH) ------------------ | Branch (6593:25): [True: 1.98k, False: 0] ------------------ 6594| 1.98k| { 6595| | /* Group contains no mobile hydrogen atoms, only charges. Prepare to remove it. */ 6596| 1.98k| nTautomerGroupNumber[(int)nGroupNumber] = 0; 6597| 1.98k| num_groups_noH++; 6598| 1.98k| } 6599| | /*i --;*/ 6600| 1.98k| } 6601| 0| else 6602| 0| { 6603| | /* Different number of endpoints */ 6604| 0| goto err_exit_function; /* program error */ /* */ 6605| 0| } 6606| 1.98k| } 6607| 3.57k| else 6608| 3.57k| { 6609| | /* Renumber t_group and prepare to renumber at[i].endpoint */ 6610| 3.57k| nTautomerGroupNumber[(int)nGroupNumber] = 6611| 3.57k| t_group[i].nGroupNumber = ++nNewGroupNumber; /* = i+1 */ 6612| | /* get first group atom orig. number position in the nEndpointAtomNumber[] */ 6613| | /* and in the tautomer endpoint canon numbers part of the connection table */ 6614| 3.57k| t_group[i].nFirstEndpointAtNoPos = nCurrEndpointAtNoPos[i] = 6615| 3.57k| i ? (t_group[i - 1].nFirstEndpointAtNoPos + t_group[i - 1].nNumEndpoints) : 0; ------------------ | Branch (6615:21): [True: 101, False: 3.47k] ------------------ 6616| 3.57k| t_group[i].num[0] = nNumH; 6617| |#if ( REMOVE_TGROUP_CHARGE == 1 ) 6618| | t_group[i].num[1] = 0; /* remove only (-) charges */ 6619| |#endif 6620| | /* -- wrong condition. Disabled. 6621| | if ( t_group[i].nGroupNumber != i + 1 ) { // for debug only 6622| | goto err_exit_function; // program error 6623| | } 6624| | */ 6625| 3.57k| i++; 6626| 3.57k| } 6627| 5.56k| } 6628| 5.56k| } 6629| 5.45k| if (num_t != nNewGroupNumber) ------------------ | Branch (6629:9): [True: 0, False: 5.45k] ------------------ 6630| 0| { 6631| | /* for debug only */ 6632| 0| goto err_exit_function; /* program error */ /* */ 6633| 0| } 6634| | 6635| | /* Check if any tautomer group was left */ 6636| 5.45k| if (!nNewGroupNumber) ------------------ | Branch (6636:9): [True: 1.97k, False: 3.47k] ------------------ 6637| 1.97k| { 6638| 1.97k| if (!num_groups_noH) ------------------ | Branch (6638:13): [True: 0, False: 1.97k] ------------------ 6639| 0| { 6640| 0| goto err_exit_function; /* program error: not a tautomer */ /* */ 6641| 0| } 6642| 1.97k| else 6643| 1.97k| { 6644| 1.97k| goto exit_function; 6645| 1.97k| } 6646| 1.97k| } 6647| | 6648| | /* 6649| | * An array for tautomer group sorting later, at the time of storing Connection Table 6650| | * Later the sorting consists out of 2 steps: 6651| | * 1) Sort t_group[i].nNumEndpoints endpoint atom ranks within each endpoint group 6652| | * starting from t_group[i].nFirstEndpointAtNoPos; i = 0..t_group_info->num_t_groups-1 6653| | * 2) Sort the groups indexes t_group_info->tGroupNumber[] 6654| | */ 6655| 3.47k| if (!( tGroupNumber = ------------------ | Branch (6655:9): [True: 0, False: 3.47k] ------------------ 6656| 3.47k| (AT_NUMB*) inchi_calloc( (long long)nNewGroupNumber * (long long)TGSO_TOTAL_LEN, sizeof( tGroupNumber[0] ) ) )) /* djb-rwth: cast operator added */ ------------------ | | 1146| 3.47k|#define inchi_calloc calloc ------------------ (AT_NUMB*) inchi_calloc( (long long)nNewGroupNumber * (long long)TGSO_TOTAL_LEN, sizeof( tGroupNumber[0] ) ) )) /* djb-rwth: cast operator added */ ------------------ | | 141| 3.47k|#define TGSO_TOTAL_LEN 4 ------------------ 6657| 0| { 6658| 0| goto err_exit_function; /* out of RAM */ 6659| 0| } 6660| 7.05k| for (i = 0; i < nNewGroupNumber; i++) ------------------ | Branch (6660:17): [True: 3.57k, False: 3.47k] ------------------ 6661| 3.57k| { 6662| 3.57k| tGroupNumber[i] = (AT_NUMB) i; /* initialization: original t_group number = (at[i]->endpoint-1) */ 6663| 3.57k| } 6664| | /* 6665| | * Renumber endpoint atoms and save their orig. atom 6666| | * numbers for filling out the tautomer part of the LinearCT. 6667| | * nCurrEndpointAtNoPos[j] is an index of the atom number in the nEndpointAtomNumber[] 6668| | */ 6669| 26.0k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6669:17): [True: 22.6k, False: 3.47k] ------------------ 6670| 22.6k| { 6671| 22.6k| if ((j = (int) at[i].endpoint)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (6671:13): [True: 8.61k, False: 14.0k] ------------------ 6672| 8.61k| { 6673| 8.61k| j = (int) ( at[i].endpoint = nTautomerGroupNumber[j] ) - 1; /* new t_group number */ 6674| 8.61k| if (j >= 0 && j < num_t) /* djb-rwth: fixing buffer overflow */ ------------------ | Branch (6674:17): [True: 8.61k, False: 0] | Branch (6674:27): [True: 8.61k, False: 0] ------------------ 6675| 8.61k| { 6676| | /* j=-1 in case of no mobile hydrogen atoms (charges only), group being removed */ 6677| 8.61k| if (nCurrEndpointAtNoPos[j] >= /* debug only */ ------------------ | Branch (6677:21): [True: 0, False: 8.61k] ------------------ 6678| 8.61k| t_group[j].nFirstEndpointAtNoPos + t_group[j].nNumEndpoints) 6679| 0| { 6680| 0| goto err_exit_function; /* program error */ /* */ 6681| 0| } 6682| 8.61k| nEndpointAtomNumber[(int) nCurrEndpointAtNoPos[j] ++] = (AT_NUMB) i; 6683| 8.61k| } 6684| 0| else 6685| 0| { 6686| 0| nNumEndpoints--; /* endpoint has been removed */ 6687| 0| } 6688| 8.61k| } 6689| 22.6k| } 6690| 3.47k| t_group_info->num_t_groups = nNewGroupNumber; 6691| 3.47k| t_group_info->nNumEndpoints = nNumEndpoints; 6692| 3.47k| t_group_info->nEndpointAtomNumber = nEndpointAtomNumber; 6693| 3.47k| t_group_info->tGroupNumber = tGroupNumber; /* only the 1st segment filled */ 6694| 3.47k| inchi_free( nTautomerGroupNumber ); ------------------ | | 1152| 3.47k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 3.47k, False: 0] | | | Branch (1152:50): [Folded, False: 3.47k] | | ------------------ ------------------ 6695| 3.47k| inchi_free( nCurrEndpointAtNoPos ); ------------------ | | 1152| 3.47k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 3.47k, False: 0] | | | Branch (1152:50): [Folded, False: 3.47k] | | ------------------ ------------------ 6696| 3.47k| return nNumEndpoints + T_GROUP_HDR_LEN * nNewGroupNumber + 1; /* nLenLinearCTTautomer */ ------------------ | | 72| 3.47k|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 69| 3.47k|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 6697| | 6698| 0|err_exit_function: 6699| 0| ret = CT_TAUCOUNT_ERR; ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6700| | 6701| 248k|exit_function: 6702| | 6703| | /* release allocated memory; set "no tautomeric group" */ 6704| 248k| if (nEndpointAtomNumber) ------------------ | Branch (6704:9): [True: 1.97k, False: 246k] ------------------ 6705| 1.97k| { 6706| 1.97k| inchi_free( nEndpointAtomNumber ); ------------------ | | 1152| 1.97k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.97k, False: 0] | | | Branch (1152:50): [Folded, False: 1.97k] | | ------------------ ------------------ 6707| 1.97k| } 6708| 248k| if (nTautomerGroupNumber) ------------------ | Branch (6708:9): [True: 1.97k, False: 246k] ------------------ 6709| 1.97k| { 6710| 1.97k| inchi_free( nTautomerGroupNumber ); ------------------ | | 1152| 1.97k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.97k, False: 0] | | | Branch (1152:50): [Folded, False: 1.97k] | | ------------------ ------------------ 6711| 1.97k| } 6712| 248k| if (tGroupNumber) ------------------ | Branch (6712:9): [True: 0, False: 248k] ------------------ 6713| 0| { 6714| 0| inchi_free( tGroupNumber ); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 6715| 0| } 6716| 248k| if (nCurrEndpointAtNoPos) ------------------ | Branch (6716:9): [True: 1.97k, False: 246k] ------------------ 6717| 1.97k| { 6718| 1.97k| inchi_free( nCurrEndpointAtNoPos ); ------------------ | | 1152| 1.97k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.97k, False: 0] | | | Branch (1152:50): [Folded, False: 1.97k] | | ------------------ ------------------ 6719| 1.97k| } 6720| 248k| t_group_info->nNumEndpoints = 0; 6721| 248k| t_group_info->num_t_groups = 0; 6722| 248k| if (!ret && ( ( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) || ------------------ | | 156| 248k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 146| 248k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 157| 248k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 147| 248k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 158| 248k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 148| 248k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 159| 248k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 149| 248k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 160| 248k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 150| 248k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 161| 248k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 151| 248k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 162| 248k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 153| 248k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 163| 248k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 152| 248k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (6722:9): [True: 248k, False: 0] | Branch (6722:19): [True: 37.2k, False: 211k] ------------------ 6723| 211k| (t_group_info->nNumIsotopicEndpoints > 1 && ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 981| 122|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ (t_group_info->nNumIsotopicEndpoints > 1 && ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) )) )) /* djb-rwth: addressing LLVM warning */ ------------------ | | 982| 122|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (6723:20): [True: 122, False: 211k] | Branch (6723:63): [True: 122, False: 0] ------------------ 6724| 37.4k| { 6725| 37.4k| ret = 1; /* only protons have been (re)moved or neitralization happened */ 6726| 37.4k| } 6727| | 6728| 248k| return ret; 6729| 0|} CompRankTautomer: 6974| 5.19k|{ 6975| 5.19k| AT_RANK *pn_tRankForSort = (AT_RANK *) p; 6976| 5.19k| int ret = (int) pn_tRankForSort[(int) ( *(const AT_RANK*) a1 )] - 6977| 5.19k| (int) pn_tRankForSort[(int) ( *(const AT_RANK*) a2 )]; 6978| | 6979| 5.19k| return ret; 6980| 5.19k|} SortTautomerGroupsAndEndpoints: 6989| 252k|{ 6990| 252k| int i, nFirstEndpointAtNoPos, nNumEndpoints; 6991| 252k| AT_RANK *pn_tRankForSort; 6992| 252k| AT_NUMB *nEndpointAtomNumber; 6993| 252k| int num_t_groups = num_at_tg - num_atoms; 6994| 252k| T_GROUP *t_group = NULL; 6995| | 6996| | /* Check if sorting is required */ 6997| 252k| if (num_t_groups <= 0 || t_group_info->nNumEndpoints < 2) ------------------ | Branch (6997:9): [True: 248k, False: 3.52k] | Branch (6997:30): [True: 0, False: 3.52k] ------------------ 6998| 248k| { 6999| 248k| return 0; /* no tautomer data */ 7000| 248k| } 7001| | 7002| 3.52k| t_group = t_group_info->t_group; 7003| | 7004| | /* Sort endpoints within the groups */ 7005| 7.15k| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (7005:17): [True: 3.63k, False: 3.52k] ------------------ 7006| 3.63k| { 7007| 3.63k| if (t_group[i].nNumEndpoints < 2) ------------------ | Branch (7007:13): [True: 0, False: 3.63k] ------------------ 7008| 0| { 7009| 0| continue; /* program error; should not happen */ /* */ 7010| 0| } 7011| | 7012| | /* Set globals for sorting */ 7013| 3.63k| nFirstEndpointAtNoPos = t_group[i].nFirstEndpointAtNoPos; 7014| 3.63k| nNumEndpoints = t_group[i].nNumEndpoints; 7015| 3.63k| if (nNumEndpoints + nFirstEndpointAtNoPos > t_group_info->nNumEndpoints) ------------------ | Branch (7015:13): [True: 0, False: 3.63k] ------------------ 7016| 0| { 7017| | /* for debug only */ 7018| 0| return CT_TAUCOUNT_ERR; /* program error */ /* */ ------------------ | | 24| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 7019| 0| } 7020| 3.63k| nEndpointAtomNumber = t_group_info->nEndpointAtomNumber + (int) nFirstEndpointAtNoPos; 7021| 3.63k| pn_tRankForSort = nRank; 7022| | 7023| 3.63k| insertions_sort( pn_tRankForSort, nEndpointAtomNumber, nNumEndpoints, 7024| 3.63k| sizeof( nEndpointAtomNumber[0] ), CompRankTautomer ); 7025| 3.63k| } 7026| | 7027| | /* Sort the tautomeric groups according to their ranks only 7028| | (that is, ignoring the isotopic composition of the mobile groups and ranks of the endpoints) */ 7029| 3.52k| if (t_group_info->num_t_groups > 1) ------------------ | Branch (7029:9): [True: 115, False: 3.40k] ------------------ 7030| 115| { 7031| | /* Set globals for sorting */ 7032| | /* a hack: the ranks of all tautomeric groups are */ 7033| | /* located at nRank[num_atoms..num_at_tg-1] */ 7034| 115| pn_tRankForSort = nRank + num_atoms; 7035| | /* Sort */ 7036| | /* ordering numbers to sort : t_group_info->tGroupNumber; */ 7037| | 7038| 115| insertions_sort( pn_tRankForSort, t_group_info->tGroupNumber, 7039| 115| num_t_groups, sizeof( t_group_info->tGroupNumber[0] ), 7040| 115| CompRankTautomer ); 7041| 115| } 7042| | 7043| 3.52k| return t_group_info->num_t_groups; 7044| 3.52k|} base26_triplet_1: 1139| 12.6k|{ 1140| 12.6k| UINT32 b0, b1, h; 1141| 12.6k| b0 = (UINT32) a[0]; /* 1111 1111 */ 1142| 12.6k|#ifndef FIX_BASE26_ENC_BUG 1143| 12.6k| b1 = (UINT32) ( a[1] & 0x3f ); /* 0011 1111 */ 1144| 12.6k| h = (UINT32) ( b0 | b1 << 8 ); 1145| |#else 1146| | b1 = (UINT32) ( a[1] & 0xfc ); /* 1111 1100 */ 1147| | h = (UINT32) ( b0 << 8 | b1 ) >> 2; 1148| |#endif 1149| 12.6k| return t26[h]; 1150| 12.6k|} base26_triplet_2: 1157| 12.6k|{ 1158| 12.6k| UINT32 b0, b1, b2, h; 1159| 12.6k|#ifndef FIX_BASE26_ENC_BUG 1160| 12.6k| b0 = (UINT32) ( a[1] & 0xc0 ); /* 1100 0000 */ 1161| 12.6k| b1 = (UINT32) ( a[2] ); /* 1111 1111 */ 1162| 12.6k| b2 = (UINT32) ( a[3] & 0x0f ); /* 0000 1111 */ 1163| 12.6k| h = (UINT32) ( b0 | b1 << 8 | b2 << 16 ) >> 6; 1164| |#else 1165| | b0 = (UINT32) ( a[1] & 0x03 ); /* 0000 0011 */ 1166| | b1 = (UINT32) ( a[2] ); /* 1111 1111 */ 1167| | b2 = (UINT32) ( a[3] & 0xf0 ); /* 1111 0000 */ 1168| | h = (UINT32) ( b0 << 16 | b1 << 8 | b2 ) >> 4; 1169| |#endif 1170| 12.6k| return t26[h]; 1171| 12.6k|} base26_triplet_3: 1178| 6.32k|{ 1179| 6.32k| UINT32 b0, b1, b2, h; 1180| 6.32k|#ifndef FIX_BASE26_ENC_BUG 1181| 6.32k| b0 = (UINT32) ( a[3] & 0xf0 ); /* 1111 0000 */ 1182| 6.32k| b1 = (UINT32) ( a[4] ); /* 1111 1111 */ 1183| 6.32k| b2 = (UINT32) ( a[5] & 0x03 ); /* 0000 0011 */ 1184| 6.32k| h = (UINT32) ( b0 | b1 << 8 | b2 << 16 ) >> 4; 1185| |#else 1186| | b0 = (UINT32) ( a[3] & 0x0f ); /* 0000 1111 */ 1187| | b1 = (UINT32) ( a[4] ); /* 1111 1111 */ 1188| | b2 = (UINT32) ( a[5] & 0xc0 ); /* 1100 0000 */ 1189| | h = (UINT32) ( b0 << 16 | b1 << 8 | b2 ) >> 6; 1190| |#endif 1191| 6.32k| return t26[h]; 1192| 6.32k|} base26_triplet_4: 1199| 6.32k|{ 1200| 6.32k| UINT32 b0, b1, h; 1201| 6.32k|#ifndef FIX_BASE26_ENC_BUG 1202| 6.32k| b0 = (UINT32) ( a[5] & 0xfc ); /* 1111 1100 */ 1203| 6.32k| b1 = (UINT32) ( a[6] ); /* 1111 1111 */ 1204| 6.32k| h = (UINT32) ( b0 | b1 << 8 ) >> 2; 1205| |#else 1206| | b0 = (UINT32) ( a[5] & 0x3f ); /* 0011 1111 */ 1207| | b1 = (UINT32) ( a[6] ); /* 1111 1111 */ 1208| | h = (UINT32) ( b0 << 8 | b1 ); 1209| |#endif 1210| 6.32k| return t26[h]; 1211| 6.32k|} base26_dublet_for_bits_28_to_36: 1228| 6.32k|{ 1229| 6.32k| UINT32 b0, b1, h; 1230| 6.32k|#ifndef FIX_BASE26_ENC_BUG 1231| 6.32k| b0 = (UINT32) ( a[3] & 0xf0 ); /* 1111 0000 */ 1232| 6.32k| b1 = (UINT32) ( a[4] & 0x1f ); /* 0001 1111 */ 1233| 6.32k| h = (UINT32) ( b0 | b1 << 8 ) >> 4; 1234| |#else 1235| | b0 = (UINT32) ( a[3] & 0x0f ); /* 0000 1111 */ 1236| | b1 = (UINT32) ( a[4] & 0xf8 ); /* 1111 1000 */ 1237| | h = (UINT32) ( b0 << 8 | b1 ) >> 3; 1238| |#endif 1239| 6.32k| return d26[h]; 1240| 6.32k|} base26_dublet_for_bits_56_to_64: 1253| 6.32k|{ 1254| 6.32k| UINT32 b0, b1, h; 1255| 6.32k|#ifndef FIX_BASE26_ENC_BUG 1256| 6.32k| b0 = (UINT32) ( a[7] ); /* 1111 1111 */ 1257| 6.32k| b1 = (UINT32) ( a[8] & 0x01 ); /* 0000 0001 */ 1258| 6.32k| h = (UINT32) ( b0 | b1 << 8 ); 1259| |#else 1260| | b0 = (UINT32) ( a[7] ); /* 1111 1111 */ 1261| | b1 = (UINT32) ( a[8] & 0x80 ); /* 1000 0000 */ 1262| | h = (UINT32) ( b0 << 8 | b1 ) >> 7; 1263| |#endif 1264| 6.32k| return d26[h]; 1265| 6.32k|} GetINCHIKeyFromINCHI: 77| 6.37k|{ 78| 6.37k| int ret = INCHIKEY_OK; ------------------ | | 1015| 6.37k|#define INCHIKEY_OK 0 ------------------ 79| 6.37k| int ret1 = INCHIKEY_OK; ------------------ | | 1015| 6.37k|#define INCHIKEY_OK 0 ------------------ 80| 6.37k| int cn; 81| 6.37k| size_t slen, i, j, jproto = 0, ncp, pos_slash1 = 0; 82| 6.37k| char *str = NULL, *smajor = NULL, *sminor = NULL, 83| 6.37k| *sproto = NULL, *stmp = NULL, tmp[MINOUTLENGTH]; 84| 6.37k| unsigned char 85| 6.37k| digest_major[32], digest_minor[32]; 86| | 87| 6.37k| char flagstd = 'S', /* standard key */ 88| 6.37k| flagnonstd = 'N', /* non-standard key */ 89| 6.37k| flagexptl = 'B', /* experimental ('beta') key */ 90| 6.37k| flagsubver = 'A', /* base InChI subversion */ 91| 6.37k| flagproto = 'N'; /* no [de]protonization , by default */ 92| 6.37k| int nprotons; 93| | /* 94| | Protonization encoding: 95| | N 0 96| | O +1 P +2 Q +3 R +4 S +5 T +6 U +7 V +8 W +9 X +10 Y +11 Z +12 97| | M -1 L-2 K -3 J -4 I -5 H -6 G -7 F -8 E -9 D -10 C -11 B -12 98| | A < -12 or > +12 99| | */ 100| 6.37k| static const char *pplus = "OPQRSTUVWXYZ"; 101| 6.37k| static const char *pminus = "MLKJIHGFEDCB"; 102| 6.37k| int is_stdinchi = 0; /* 0 - non-standard, 103| | 1 standard 104| | -1 experimental ('beta') */ 105| | 106| 6.37k| int is_molecular_inorganic = 0; 107| | 108| | 109| | 110| 6.37k| if (NULL != szXtra1) /* Software version 1.06 added check to fix bug with NULL szXtra, thanks to WDI */ ------------------ | Branch (110:9): [True: 6.37k, False: 0] ------------------ 111| 6.37k| { 112| 6.37k| szXtra1[0] = '\0'; 113| 6.37k| } 114| 6.37k| if (NULL != szXtra2) ------------------ | Branch (114:9): [True: 6.37k, False: 0] ------------------ 115| 6.37k| { 116| 6.37k| szXtra2[0] = '\0'; 117| 6.37k| } 118| | 119| | /* Check if input is a valid InChI string */ 120| | 121| | /* .. non-empty */ 122| 6.37k| if (szINCHISource == NULL) ------------------ | Branch (122:9): [True: 0, False: 6.37k] ------------------ 123| 0| { 124| 0| return INCHIKEY_EMPTY_INPUT; ------------------ | | 1017| 0|#define INCHIKEY_EMPTY_INPUT 2 ------------------ 125| 0| } 126| | 127| 6.37k| slen = strlen( szINCHISource ); 128| | 129| | /* .. has valid prefix */ 130| 6.37k| if (slen < LEN_INCHI_STRING_PREFIX + 3) ------------------ | | 739| 6.37k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (130:9): [True: 1, False: 6.36k] ------------------ 131| 1| { 132| 1| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1018| 1|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 133| 1| } 134| 6.36k| if (memcmp( szINCHISource, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 738| 6.36k|#define INCHI_STRING_PREFIX "InChI=" ------------------ if (memcmp( szINCHISource, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 739| 6.36k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (134:9): [True: 13, False: 6.35k] ------------------ 135| 13| { 136| 13| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1018| 13|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 137| 13| } 138| | 139| | /* .. has InChI version 1 */ 140| | /* if (!isdigit(szINCHISource[LEN_INCHI_STRING_PREFIX]) ) */ 141| 6.35k| if (szINCHISource[LEN_INCHI_STRING_PREFIX] != '1') ------------------ | | 739| 6.35k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (141:9): [True: 0, False: 6.35k] ------------------ 142| 0| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1018| 0|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 143| | 144| | /* Determine the InChI calculation-class designator. 145| | * Historical InChI=1/... remains accepted as non-standard input. 146| | */ 147| 6.35k| pos_slash1 = LEN_INCHI_STRING_PREFIX + 1; ------------------ | | 739| 6.35k|#define LEN_INCHI_STRING_PREFIX 6 ------------------ 148| | 149| 6.35k| if (szINCHISource[pos_slash1] == 'S') ------------------ | Branch (149:9): [True: 36, False: 6.32k] ------------------ 150| 36| { 151| | /* Standard InChI */ 152| 36| is_stdinchi = 1; 153| 36| pos_slash1++; 154| 36| } 155| 6.32k| else if (szINCHISource[pos_slash1] == 'B') ------------------ | Branch (155:14): [True: 24, False: 6.29k] ------------------ 156| 24| { 157| | /* Experimental ('beta') InChI */ 158| 24| is_stdinchi = -1; 159| 24| pos_slash1++; 160| 24| } 161| 6.29k| else if (szINCHISource[pos_slash1] == 'N') ------------------ | Branch (161:14): [True: 0, False: 6.29k] ------------------ 162| 0| { 163| | /* Explicitly marked non-standard InChI */ 164| 0| is_stdinchi = 0; 165| 0| pos_slash1++; 166| 0| } 167| | 168| | /* Molecular Inorganics subversion designator */ 169| 6.35k| if (szINCHISource[pos_slash1] == 'B') ------------------ | Branch (169:9): [True: 0, False: 6.35k] ------------------ 170| 0| { 171| 0| is_molecular_inorganic = 1; 172| 0| pos_slash1++; 173| 0| } 174| | 175| | /* .. has trailing slash in the right place */ 176| 6.35k| if (szINCHISource[pos_slash1] != '/') ------------------ | Branch (176:9): [True: 0, False: 6.35k] ------------------ 177| 0| { 178| 0| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1018| 0|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 179| 0| } 180| | 181| | /* .. the rest of source string contains at least one a..Z0.9 or slash */ 182| 6.35k| if (!isalnum( szINCHISource[pos_slash1 + 1] )) ------------------ | Branch (182:9): [True: 38, False: 6.31k] ------------------ 183| 38| { 184| 38| int valid_empty_inchi = szINCHISource[pos_slash1 + 1] == '/'; 185| 38| int allowed_and_valid_err_inchi = 0; 186| 38| if (!valid_empty_inchi) ------------------ | Branch (186:13): [True: 4, False: 34] ------------------ 187| 4| { 188| 4| allowed_and_valid_err_inchi = szINCHISource[pos_slash1 + 1] == '?'; 189| 4| if (!allowed_and_valid_err_inchi) ------------------ | Branch (189:17): [True: 2, False: 2] ------------------ 190| 2| { 191| 2| return INCHIKEY_INVALID_INCHI; ------------------ | | 1020| 2|#define INCHIKEY_INVALID_INCHI 20 ------------------ 192| 2| } 193| 4| } 194| 38| } 195| | 196| | /* Ok. Will use a local copy of the source. */ 197| | 198| 6.35k| extract_inchi_substring( &str, szINCHISource, slen ); 199| 6.35k| if (NULL == str) ------------------ | Branch (199:9): [True: 0, False: 6.35k] ------------------ 200| 0| { 201| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; ------------------ | | 1019| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 202| 0| goto fin; 203| 0| } 204| 6.35k| slen = strlen( str ); 205| | 206| | 207| | /* Make buffers. */ 208| 6.35k| smajor = (char*) inchi_calloc( slen + 1, sizeof( char ) ); ------------------ | | 1146| 6.35k|#define inchi_calloc calloc ------------------ 209| 6.35k| if (NULL == smajor) ------------------ | Branch (209:9): [True: 0, False: 6.35k] ------------------ 210| 0| { 211| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1019| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 212| 0| } 213| 6.35k| sminor = (char*) inchi_calloc( 2 * slen + 2, sizeof( char ) ); /* we may double the length ... */ ------------------ | | 1146| 6.35k|#define inchi_calloc calloc ------------------ 214| 6.35k| if (NULL == sminor) ------------------ | Branch (214:9): [True: 0, False: 6.35k] ------------------ 215| 0| { 216| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1019| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 217| 0| } 218| 6.35k| stmp = (char*) inchi_calloc( slen + 1, sizeof( char ) ); ------------------ | | 1146| 6.35k|#define inchi_calloc calloc ------------------ 219| 6.35k| if (NULL == stmp) ------------------ | Branch (219:9): [True: 0, False: 6.35k] ------------------ 220| 0| { 221| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1019| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 222| 0| } 223| 6.35k| sproto = (char*) inchi_calloc( slen + 1, sizeof( char ) ); ------------------ | | 1146| 6.35k|#define inchi_calloc calloc ------------------ 224| 6.35k| if (NULL == sproto) ------------------ | Branch (224:9): [True: 0, False: 6.35k] ------------------ 225| 0| { 226| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1019| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 227| 0| } 228| | 229| 6.35k| szINCHIKey[0] = '\0'; 230| | 231| | /* Extract the major block */ 232| 6.35k| smajor[0] = '\0'; 233| 1.39M| for (j = pos_slash1 + 1; j < slen - 1; j++) ------------------ | Branch (233:30): [True: 1.39M, False: 2.76k] ------------------ 234| 1.39M| { 235| 1.39M| if (str[j] == '/') ------------------ | Branch (235:13): [True: 11.6k, False: 1.38M] ------------------ 236| 11.6k| { 237| 11.6k| cn = str[j + 1]; 238| 11.6k| switch (cn) 239| 11.6k| { 240| | /* anything allowed from a major part */ 241| 4.89k| case 'c': ------------------ | Branch (241:17): [True: 4.89k, False: 6.71k] ------------------ 242| 7.22k| case 'h': ------------------ | Branch (242:17): [True: 2.33k, False: 9.27k] ------------------ 243| 7.59k| case 'q': continue; ------------------ | Branch (243:17): [True: 373, False: 11.2k] ------------------ 244| | 245| | /* "/p"; protons now go to to special string, not to minor hash */ 246| 416| case 'p': ------------------ | Branch (246:17): [True: 416, False: 11.1k] ------------------ 247| 416| jproto = j; 248| 416| continue; 249| | 250| | /* "/f", "/r" : may not occur in stdInChI */ 251| 1.22k| case 'f': ------------------ | Branch (251:17): [True: 1.22k, False: 10.3k] ------------------ 252| 1.43k| case 'r': ------------------ | Branch (252:17): [True: 205, False: 11.3k] ------------------ 253| 1.43k| if (is_stdinchi==1) ------------------ | Branch (253:25): [True: 18, False: 1.41k] ------------------ 254| 18| { 255| 18| ret = INCHIKEY_INVALID_STD_INCHI; ------------------ | | 1021| 18|#define INCHIKEY_INVALID_STD_INCHI 21 ------------------ 256| 18| goto fin; 257| 18| } 258| 1.41k| break; 259| | 260| | /* anything allowed from a minor part */ 261| 2.16k| default: ------------------ | Branch (261:17): [True: 2.16k, False: 9.44k] ------------------ 262| 2.16k| break; 263| 11.6k| } 264| 3.57k| break; 265| 11.6k| } 266| 1.39M| } 267| 6.33k| j++; 268| 6.33k| if (j == slen) ------------------ | Branch (268:9): [True: 2.76k, False: 3.57k] ------------------ 269| 2.76k| { 270| 2.76k| j++; 271| 2.76k| } 272| 3.57k| else 273| 3.57k| { 274| 3.57k| j--; 275| 3.57k| } 276| | 277| 6.33k| if (jproto) ------------------ | Branch (277:9): [True: 179, False: 6.15k] ------------------ 278| 179| { 279| 179| ncp = jproto - pos_slash1 - 1; 280| 179| } 281| 6.15k| else 282| 6.15k| { 283| 6.15k| ncp = j - pos_slash1 - 1; 284| 6.15k| } 285| | 286| | 287| | /* Hash only the InChI layers following the parsed version prefix. */ 288| 6.33k| memcpy(smajor, str + pos_slash1 + 1, ncp * sizeof(str[0])); 289| 6.33k| smajor[ncp] = '\0'; 290| | 291| | 292| | /* Treat protonization */ 293| 6.33k| if (jproto) ------------------ | Branch (293:9): [True: 179, False: 6.15k] ------------------ 294| 179| { 295| | /* 2009-01-07 fix bug/typo: assigned incorrect length to the protonation segment of 296| | source string ( was sproto[ncp]='\0'; should be sproto[lenproto]='\0'; ) */ 297| 179| int lenproto = j - (int) jproto; 298| 179| if (lenproto < 3) ------------------ | Branch (298:13): [True: 4, False: 175] ------------------ 299| 4| { 300| | /* empty "/p", should not occur */ 301| 4| ret = INCHIKEY_INVALID_INCHI; ------------------ | | 1020| 4|#define INCHIKEY_INVALID_INCHI 20 ------------------ 302| 4| goto fin; 303| 4| } 304| | 305| 175| memcpy(sproto, str + pos_slash1 + ncp + 1, lenproto * sizeof(str[0])); 306| 175| sproto[lenproto] = '\0'; 307| | 308| 175| nprotons = strtol( sproto + 2, NULL, 10 ); 309| | 310| 175| if (nprotons > 0) ------------------ | Branch (310:13): [True: 105, False: 70] ------------------ 311| 105| { 312| 105| if (nprotons > 12) ------------------ | Branch (312:17): [True: 24, False: 81] ------------------ 313| 24| { 314| 24| flagproto = 'A'; 315| 24| } 316| 81| else 317| 81| { 318| 81| flagproto = pplus[nprotons - 1]; 319| 81| } 320| 105| } 321| 70| else if (nprotons < 0) ------------------ | Branch (321:18): [True: 66, False: 4] ------------------ 322| 66| { 323| 66| if (nprotons < -12) ------------------ | Branch (323:17): [True: 23, False: 43] ------------------ 324| 23| { 325| 23| flagproto = 'A'; 326| 23| } 327| 43| else 328| 43| { 329| 43| flagproto = pminus[-nprotons - 1]; 330| 43| } 331| 66| } 332| 4| else 333| 4| { 334| | /* should never occur */ 335| 4| ret = INCHIKEY_INVALID_STD_INCHI; ------------------ | | 1021| 4|#define INCHIKEY_INVALID_STD_INCHI 21 ------------------ 336| 4| goto fin; 337| 4| } 338| 175| } 339| | 340| | /* Extract the minor block. */ 341| | 342| 6.32k| if (j != slen + 1) /* check that something exists at right.*/ ------------------ | Branch (342:9): [True: 3.56k, False: 2.75k] ------------------ 343| 3.56k| { 344| 3.56k| ncp = slen - j; 345| 3.56k| memcpy(sminor, str + j, (ncp) * sizeof(str[0])); 346| 3.56k| sminor[ncp] = '\0'; 347| 3.56k| } 348| 2.75k| else 349| 2.75k| { 350| 2.75k| sminor[0] = '\0'; 351| 2.75k| } 352| | 353| | 354| |#if INCHIKEY_DEBUG 355| | ITRACE_( "Source: {%-s}\n", str ); 356| | ITRACE_( "SMajor: {%-s}\n", smajor ); 357| | ITRACE_( "SMinor: {%-s}\n", sminor ); 358| | ITRACE_( "SProto: {%-s}\n", sproto ); 359| |#endif 360| | 361| | /* Compute and compose the InChIKey string. */ 362| | 363| | /* Major hash sub-string. */ 364| 208k| for (i = 0; i < 32; i++) ------------------ | Branch (364:17): [True: 202k, False: 6.32k] ------------------ 365| 202k| { 366| 202k| digest_major[i] = 0; 367| 202k| } 368| | 369| 6.32k| sha2_csum( (unsigned char *) smajor, (int) strlen( smajor ), digest_major ); 370| | 371| 6.32k| sprintf(tmp, "%-.3s%-.3s%-.3s%-.3s%-.2s", 372| 6.32k| base26_triplet_1(digest_major), base26_triplet_2(digest_major), 373| 6.32k| base26_triplet_3(digest_major), base26_triplet_4(digest_major), 374| 6.32k| base26_dublet_for_bits_56_to_64(digest_major)); 375| 6.32k| strcat(szINCHIKey, tmp); 376| |#if (INCHIKEY_DEBUG>1) 377| | fprint_digest( stderr, "Major hash, full SHA-256", digest_major ); 378| |#endif 379| | 380| | 381| | /* Minor hash sub-string. */ 382| 208k| for (i = 0; i < 32; i++) ------------------ | Branch (382:17): [True: 202k, False: 6.32k] ------------------ 383| 202k| { 384| 202k| digest_minor[i] = 0; 385| 202k| } 386| 6.32k| slen = strlen( sminor ); 387| 6.32k| if (( slen > 0 ) && ( slen < 255 )) ------------------ | Branch (387:9): [True: 3.56k, False: 2.75k] | Branch (387:25): [True: 3.42k, False: 146] ------------------ 388| 3.42k| { 389| 3.42k| strcpy(stmp, sminor); 390| 3.42k| strcpy(sminor + slen, stmp); 391| 3.42k| } 392| | 393| 6.32k| sha2_csum( (unsigned char *) sminor, (int) strlen( sminor ), digest_minor ); 394| | 395| |#if (INCHIKEY_DEBUG>1) 396| | fprint_digest( stderr, "Minor hash, full SHA-256", digest_minor ); 397| |#endif 398| | 399| 6.32k| strcat(szINCHIKey, "-"); 400| 6.32k| sprintf(tmp, "%-.3s%-.3s%-.2s", 401| 6.32k| base26_triplet_1(digest_minor), 402| 6.32k| base26_triplet_2(digest_minor), 403| 6.32k| base26_dublet_for_bits_28_to_36(digest_minor)); 404| 6.32k| strcat(szINCHIKey, tmp); 405| | /* Append calculation-class flag */ 406| 6.32k| slen = strlen(szINCHIKey); 407| 6.32k| if (is_stdinchi == 1) ------------------ | Branch (407:9): [True: 18, False: 6.31k] ------------------ 408| 18| { 409| 18| szINCHIKey[slen] = flagstd; 410| 18| } 411| 6.31k| else if (is_stdinchi == -1) ------------------ | Branch (411:14): [True: 24, False: 6.28k] ------------------ 412| 24| { 413| 24| szINCHIKey[slen] = flagexptl; 414| 24| } 415| 6.28k| else 416| 6.28k| { 417| 6.28k| szINCHIKey[slen] = flagnonstd; 418| 6.28k| } 419| | 420| | /* Append InChI subversion flag */ 421| 6.32k| szINCHIKey[slen + 1] = is_molecular_inorganic ? 'B' : flagsubver; ------------------ | Branch (421:28): [True: 0, False: 6.32k] ------------------ 422| | 423| | /* Append dash */ 424| 6.32k| szINCHIKey[slen + 2] = '-'; 425| | 426| | /* Append protonization flag */ 427| 6.32k| szINCHIKey[slen + 3] = flagproto; 428| 6.32k| szINCHIKey[slen + 4] = '\0'; 429| | 430| | 431| |#if INCHIKEY_DEBUG 432| | ITRACE_( "szINCHIKey: {%-s}\n", szINCHIKey ); 433| |#endif 434| | 435| | /* Hash extensions */ 436| 6.32k| if (xtra1 && szXtra1) ------------------ | Branch (436:9): [True: 0, False: 6.32k] | Branch (436:18): [True: 0, False: 0] ------------------ 437| 0| { 438| 0| get_xtra_hash_major_hex( digest_major, szXtra1 ); 439| |#if INCHIKEY_DEBUG 440| | fprintf( stderr, "XHash1=%-s\n", szXtra1 ); 441| | fprintf( stderr, "j=%-d\n", j ); 442| |#endif 443| 0| } 444| 6.32k| if (xtra2 && szXtra2) ------------------ | Branch (444:9): [True: 0, False: 6.32k] | Branch (444:18): [True: 0, False: 0] ------------------ 445| 0| { 446| 0| get_xtra_hash_minor_hex( digest_minor, szXtra2 ); 447| |#if INCHIKEY_DEBUG 448| | fprintf( stderr, "XHash2=%-s\n", szXtra2 ); 449| | fprintf( stderr, "j=%-d\n", j ); 450| |#endif 451| 0| } 452| | 453| | 454| 6.35k|fin: 455| | /* djb-rwth: fixing GH issue #87 (thanks to Ricardo Rodriguez) and oss-fuzz issue #66746 */ 456| 6.35k| if (NULL != str) ------------------ | Branch (456:9): [True: 6.35k, False: 0] ------------------ 457| 6.35k| { 458| 6.35k| inchi_free( str ); ------------------ | | 1152| 6.35k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.35k, False: 0] | | | Branch (1152:50): [Folded, False: 6.35k] | | ------------------ ------------------ 459| 6.35k| } 460| 6.35k| if (NULL != smajor) ------------------ | Branch (460:9): [True: 6.35k, False: 0] ------------------ 461| 6.35k| { 462| 6.35k| inchi_free( smajor ); ------------------ | | 1152| 6.35k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.35k, False: 0] | | | Branch (1152:50): [Folded, False: 6.35k] | | ------------------ ------------------ 463| 6.35k| } 464| 6.35k| if (NULL != sminor) ------------------ | Branch (464:9): [True: 6.35k, False: 0] ------------------ 465| 6.35k| { 466| 6.35k| inchi_free( sminor ); ------------------ | | 1152| 6.35k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.35k, False: 0] | | | Branch (1152:50): [Folded, False: 6.35k] | | ------------------ ------------------ 467| 6.35k| sminor = NULL; 468| 6.35k| } 469| 6.35k| if (NULL != stmp) ------------------ | Branch (469:9): [True: 6.35k, False: 0] ------------------ 470| 6.35k| { 471| 6.35k| inchi_free( stmp ); ------------------ | | 1152| 6.35k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.35k, False: 0] | | | Branch (1152:50): [Folded, False: 6.35k] | | ------------------ ------------------ 472| 6.35k| } 473| 6.35k| if (NULL != sproto) ------------------ | Branch (473:9): [True: 6.35k, False: 0] ------------------ 474| 6.35k| { 475| 6.35k| inchi_free( sproto ); ------------------ | | 1152| 6.35k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 6.35k, False: 0] | | | Branch (1152:50): [Folded, False: 6.35k] | | ------------------ ------------------ 476| 6.35k| } 477| 6.35k| if (( ret == INCHIKEY_OK ) && ( ret1 != INCHIKEY_OK )) ------------------ | | 1015| 6.35k|#define INCHIKEY_OK 0 ------------------ if (( ret == INCHIKEY_OK ) && ( ret1 != INCHIKEY_OK )) ------------------ | | 1015| 6.32k|#define INCHIKEY_OK 0 ------------------ | Branch (477:9): [True: 6.32k, False: 26] | Branch (477:35): [True: 0, False: 6.32k] ------------------ 478| 0| { 479| 0| ret = ret1; 480| 0| } 481| | 482| 6.35k| return ret; 483| 6.32k|} CreateInpAtom: 1121| 648k|{ 1122| 648k| void *p = NULL; 1123| 648k| if (num_atoms >= 0) ------------------ | Branch (1123:9): [True: 648k, False: 0] ------------------ 1124| 648k| { 1125| 648k| p = inchi_calloc(num_atoms, sizeof(inp_ATOM)); ------------------ | | 1146| 648k|#define inchi_calloc calloc ------------------ 1126| 648k| } 1127| | 1128| | // void *p = inchi_calloc(num_atoms, sizeof(inp_ATOM)); 1129| 648k| return (inp_ATOM *)p; 1130| 648k|} FreeInpAtom: 1134| 3.33M|{ 1135| 3.33M| if (at && *at) ------------------ | Branch (1135:9): [True: 3.33M, False: 0] | Branch (1135:15): [True: 790k, False: 2.54M] ------------------ 1136| 790k| { 1137| 790k| inchi_free(*at); ------------------ | | 1152| 790k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 790k, False: 0] | | | Branch (1152:50): [Folded, False: 790k] | | ------------------ ------------------ 1138| 790k| *at = NULL; 1139| 790k| } 1140| | 1141| 3.33M| return; 1142| 3.33M|} FreeInpAtomData: 1146| 1.47M|{ 1147| 1.47M| if (inp_at_data) ------------------ | Branch (1147:9): [True: 1.33M, False: 144k] ------------------ 1148| 1.33M| { 1149| 1.33M| FreeInpAtom(&inp_at_data->at); 1150| 1.33M| FreeInpAtom(&inp_at_data->at_fixed_bonds); 1151| | 1152| | /*@nnuk*/ 1153| 1.33M| if (inp_at_data->keep_explicit_HDT) ------------------ | Branch (1153:13): [True: 0, False: 1.33M] ------------------ 1154| 0| { 1155| 0| inchi_free(inp_at_data->keep_explicit_HDT); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1156| 0| inp_at_data->keep_explicit_HDT = NULL; 1157| 0| } 1158| | 1159| 1.33M| memset(inp_at_data, 0, sizeof(*inp_at_data)); /* djb-rwth: memset_s C11/Annex K variant? */ 1160| 1.33M| } 1161| | 1162| 1.47M| return; 1163| 1.47M|} CreateInpAtomData: 1169| 395k|{ 1170| 395k| FreeInpAtomData(inp_at_data); 1171| | 1172| 395k| if ((inp_at_data->at = CreateInpAtom(num_atoms)) && ------------------ | Branch (1172:9): [True: 395k, False: 0] ------------------ 1173| 395k| (!create_at_fixed_bonds || (inp_at_data->at_fixed_bonds = CreateInpAtom(num_atoms)))) ------------------ | Branch (1173:10): [True: 143k, False: 252k] | Branch (1173:36): [True: 252k, False: 0] ------------------ 1174| 395k| { 1175| 395k| inp_at_data->num_at = num_atoms; 1176| 395k| return 1; 1177| 395k| } 1178| | 1179| 0| FreeInpAtomData(inp_at_data); 1180| | 1181| 0| return 0; 1182| 395k|} FreeCompAtomData: 1186| 423k|{ 1187| 423k| FreeInpAtom(&inp_at_data->at); 1188| | 1189| 423k| if (inp_at_data->nOffsetAtAndH) ------------------ | Branch (1189:9): [True: 820, False: 422k] ------------------ 1190| 820| { 1191| 820| inchi_free(inp_at_data->nOffsetAtAndH); ------------------ | | 1152| 820|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 820, False: 0] | | | Branch (1152:50): [Folded, False: 820] | | ------------------ ------------------ 1192| 820| } 1193| 423k| memset(inp_at_data, 0, sizeof(*inp_at_data)); /* djb-rwth: memset_s C11/Annex K variant? */ 1194| 423k|} FreeOrigAtData: 1320| 211k|{ 1321| 211k| if (!orig_at_data) ------------------ | Branch (1321:9): [True: 0, False: 211k] ------------------ 1322| 0| { 1323| 0| return; 1324| 0| } 1325| | 1326| 211k| FreeInpAtom(&orig_at_data->at); 1327| | 1328| 211k| if (orig_at_data->nCurAtLen) ------------------ | Branch (1328:9): [True: 70.4k, False: 140k] ------------------ 1329| 70.4k| { 1330| 70.4k| inchi_free(orig_at_data->nCurAtLen); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 1331| 70.4k| } 1332| | 1333| 211k| if (orig_at_data->nOldCompNumber) ------------------ | Branch (1333:9): [True: 70.4k, False: 140k] ------------------ 1334| 70.4k| { 1335| 70.4k| inchi_free(orig_at_data->nOldCompNumber); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 1336| 70.4k| } 1337| | 1338| 211k| if (orig_at_data->szCoord) ------------------ | Branch (1338:9): [True: 0, False: 211k] ------------------ 1339| 0| { 1340| 0| inchi_free(orig_at_data->szCoord); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1341| 0| } 1342| | 1343| 211k| if (orig_at_data->nEquLabels) ------------------ | Branch (1343:9): [True: 0, False: 211k] ------------------ 1344| 0| { 1345| 0| inchi_free(orig_at_data->nEquLabels); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1346| 0| } 1347| | 1348| 211k| if (orig_at_data->nSortedOrder) ------------------ | Branch (1348:9): [True: 0, False: 211k] ------------------ 1349| 0| { 1350| 0| inchi_free(orig_at_data->nSortedOrder); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1351| 0| } 1352| | 1353| | /* v 1.05 */ 1354| 211k| FreeExtOrigAtData(orig_at_data->polymer, orig_at_data->v3000); 1355| | 1356| 211k| memset(orig_at_data, 0, sizeof(*orig_at_data)); /* djb-rwth: memset_s C11/Annex K variant? */ 1357| | 1358| 211k| return; 1359| 211k|} FreeExtOrigAtData: 1365| 231k|{ 1366| 231k| int k; 1367| | 1368| 231k| OAD_Polymer_Free(pd); 1369| 231k| pd = NULL; 1370| | 1371| 231k| if (v3k) ------------------ | Branch (1371:9): [True: 0, False: 231k] ------------------ 1372| 0| { 1373| 0| if (v3k->atom_index_orig) ------------------ | Branch (1373:13): [True: 0, False: 0] ------------------ 1374| 0| { 1375| 0| inchi_free(v3k->atom_index_orig); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1376| 0| v3k->atom_index_orig = NULL; 1377| 0| } 1378| 0| if (v3k->atom_index_fin) ------------------ | Branch (1378:13): [True: 0, False: 0] ------------------ 1379| 0| { 1380| 0| inchi_free(v3k->atom_index_fin); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1381| 0| v3k->atom_index_fin = NULL; 1382| 0| } 1383| 0| if (v3k->n_haptic_bonds && v3k->lists_haptic_bonds) ------------------ | Branch (1383:13): [True: 0, False: 0] | Branch (1383:36): [True: 0, False: 0] ------------------ 1384| 0| { 1385| 0| for (k = 0; k < v3k->n_haptic_bonds; k++) ------------------ | Branch (1385:25): [True: 0, False: 0] ------------------ 1386| 0| if (v3k->lists_haptic_bonds[k]) ------------------ | Branch (1386:21): [True: 0, False: 0] ------------------ 1387| 0| { 1388| 0| inchi_free(v3k->lists_haptic_bonds[k]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1389| 0| v3k->lists_haptic_bonds[k] = NULL; 1390| 0| } 1391| 0| inchi_free(v3k->lists_haptic_bonds); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1392| 0| v3k->lists_haptic_bonds = NULL; 1393| 0| } 1394| 0| if (v3k->n_steabs && v3k->lists_steabs) ------------------ | Branch (1394:13): [True: 0, False: 0] | Branch (1394:30): [True: 0, False: 0] ------------------ 1395| 0| { 1396| 0| for (k = 0; k < v3k->n_steabs; k++) ------------------ | Branch (1396:25): [True: 0, False: 0] ------------------ 1397| 0| if (v3k->lists_steabs[k]) ------------------ | Branch (1397:21): [True: 0, False: 0] ------------------ 1398| 0| { 1399| 0| inchi_free(v3k->lists_steabs[k]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1400| 0| v3k->lists_steabs[k] = NULL; 1401| 0| } 1402| 0| inchi_free(v3k->lists_steabs); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1403| 0| v3k->lists_steabs = NULL; 1404| 0| } 1405| 0| if (v3k->n_sterel && v3k->lists_sterel) ------------------ | Branch (1405:13): [True: 0, False: 0] | Branch (1405:30): [True: 0, False: 0] ------------------ 1406| 0| { 1407| 0| for (k = 0; k < v3k->n_sterel; k++) ------------------ | Branch (1407:25): [True: 0, False: 0] ------------------ 1408| 0| if (v3k->lists_sterel[k]) ------------------ | Branch (1408:21): [True: 0, False: 0] ------------------ 1409| 0| { 1410| 0| inchi_free(v3k->lists_sterel[k]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1411| 0| v3k->lists_sterel[k] = NULL; 1412| 0| } 1413| 0| inchi_free(v3k->lists_sterel); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1414| 0| v3k->lists_sterel = NULL; 1415| 0| } 1416| 0| if (v3k->n_sterac && v3k->lists_sterac) ------------------ | Branch (1416:13): [True: 0, False: 0] | Branch (1416:30): [True: 0, False: 0] ------------------ 1417| 0| { 1418| 0| for (k = 0; k < v3k->n_sterac; k++) ------------------ | Branch (1418:25): [True: 0, False: 0] ------------------ 1419| 0| if (v3k->lists_sterac[k]) ------------------ | Branch (1419:21): [True: 0, False: 0] ------------------ 1420| 0| { 1421| 0| inchi_free(v3k->lists_sterac[k]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1422| 0| v3k->lists_sterac[k] = NULL; 1423| 0| } 1424| 0| inchi_free(v3k->lists_sterac); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1425| 0| v3k->lists_sterac = NULL; 1426| 0| } 1427| 0| memset(v3k, 0, sizeof(*v3k)); /* djb-rwth: memset_s C11/Annex K variant? */ 1428| 0| inchi_free(v3k); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1429| 0| } 1430| | 1431| 231k| return; 1432| 231k|} IntArray_Alloc: 476| 1.78k|{ 477| 1.78k| if ((items->item = (int *)inchi_calloc(nitems, sizeof(int)))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 1146| 1.78k|#define inchi_calloc calloc ------------------ | Branch (477:9): [True: 1.78k, False: 0] ------------------ 478| 1.78k| { 479| 1.78k| items->increment = items->allocated = nitems; 480| 1.78k| items->used = 0; 481| 1.78k| return 0; 482| 1.78k| } 483| | 484| 0| return -1; 485| 1.78k|} IntArray_ReAlloc: 491| 762|{ 492| 762| if (items) ------------------ | Branch (492:9): [True: 762, False: 0] ------------------ 493| 762| { 494| 762| if (items->item && items->allocated > 0 && items->increment > 0) ------------------ | Branch (494:13): [True: 762, False: 0] | Branch (494:28): [True: 762, False: 0] | Branch (494:52): [True: 762, False: 0] ------------------ 495| 762| { 496| 762| void *p = items->item; 497| 762| if ((items->item = ------------------ | Branch (497:17): [True: 762, False: 0] ------------------ 498| 762| (int *)inchi_calloc((long long)items->allocated + (long long)items->increment, sizeof(items->item[0])))) /* djb-rwth: cast operators added; addressing LLVM warning */ ------------------ | | 1146| 762|#define inchi_calloc calloc ------------------ 499| 762| { 500| 762| memcpy(items->item, p, items->used * sizeof(items->item[0])); 501| 762| inchi_free(p); ------------------ | | 1152| 762|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 762, False: 0] | | | Branch (1152:50): [Folded, False: 762] | | ------------------ ------------------ 502| 762| items->allocated += items->increment; 503| 762| return 0; 504| 762| } 505| 0| inchi_free(p); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 506| 0| } 507| 762| } 508| | 509| 0| return -1; 510| 762|} IntArray_Append: 516| 7.83k|{ 517| 7.83k| if (items) ------------------ | Branch (517:9): [True: 7.83k, False: 0] ------------------ 518| 7.83k| { 519| 7.83k| if (items->used + 1 > items->allocated) ------------------ | Branch (519:13): [True: 762, False: 7.06k] ------------------ 520| 762| { 521| | /* need to expand buffer */ 522| 762| if (IntArray_ReAlloc(items)) ------------------ | Branch (522:17): [True: 0, False: 762] ------------------ 523| 0| { 524| 0| return -1; 525| 0| } 526| 762| } 527| 7.83k| items->item[items->used++] = new_item; 528| 7.83k| return 0; 529| 7.83k| } 530| | 531| 0| return -1; 532| 7.83k|} IntArray_Reset: 569| 1.29k|{ 570| 1.29k| items->used = 0; 571| 1.29k| return; 572| 1.29k|} IntArray_Free: 576| 1.78k|{ 577| 1.78k| if (items) ------------------ | Branch (577:9): [True: 1.78k, False: 0] ------------------ 578| 1.78k| { 579| 1.78k| if (items->item) ------------------ | Branch (579:13): [True: 1.78k, False: 0] ------------------ 580| 1.78k| { 581| 1.78k| inchi_free(items->item); ------------------ | | 1152| 1.78k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.78k, False: 0] | | | Branch (1152:50): [Folded, False: 1.78k] | | ------------------ ------------------ 582| 1.78k| } 583| 1.78k| memset(items, 0, sizeof(*items)); /* djb-rwth: memset_s C11/Annex K variant? */ 584| 1.78k| } 585| 1.78k| return; 586| 1.78k|} ProcessOneStructure: 199| 70.4k|{ 200| 70.4k| int nRet = 0, 201| 70.4k| nRet1, i, k, 202| 70.4k| maxINChI = 0, 203| 70.4k| bSortPrintINChIFlags = 0; 204| 70.4k| COMP_ATOM_DATA 205| 70.4k| composite_norm_data[INCHI_NUM][TAUT_NUM + 1]; /* [0]:non-taut, 206| | [1]:taut, 207| | [2]:intermediate taut struct */ 208| 70.4k| NORM_CANON_FLAGS ncFlags; 209| 70.4k| NORM_CANON_FLAGS* pncFlags = &ncFlags; 210| 70.4k| ORIG_STRUCT OrigStruct; 211| 70.4k| ORIG_STRUCT* pOrigStruct = NULL; 212| 70.4k| int err, ret1 = 0; 213| | 214| | /* djb-rwth: removing redundant code */ 215| |#ifdef GHI100_FIX 216| |#if ((SPRINTF_FLAG != 1) && (SPRINTF_FLAG != 2)) 217| | setlocale(LC_ALL, "en-US"); /* djb-rwth: setting all locales to "en-US" */ 218| |#endif 219| |#endif 220| | 221| | /* 1. Preliminary work */ 222| | 223| | /* djb-rwth: fixing coverity ID #499508 */ 224| 70.4k| if (!orig_inp_data) ------------------ | Branch (224:9): [True: 0, False: 70.4k] ------------------ 225| 0| { 226| 0| goto exit_function; 227| 0| } 228| | 229| 70.4k| int is_polymer = orig_inp_data->valid_polymer ------------------ | Branch (229:22): [True: 0, False: 70.4k] ------------------ 230| 0| && orig_inp_data->polymer ------------------ | Branch (230:25): [True: 0, False: 0] ------------------ 231| 0| && orig_inp_data->polymer->n ; ------------------ | Branch (231:25): [True: 0, False: 0] ------------------ 232| | 233| 70.4k| int is_polymer2inchi = is_polymer && (ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE); ------------------ | Branch (233:28): [True: 0, False: 70.4k] | Branch (233:43): [True: 0, False: 0] | Branch (233:78): [True: 0, False: 0] ------------------ 234| | 235| 70.4k| sd->bUserQuitComponent = 0; 236| 70.4k| sd->bUserQuitComponentDisplay = 0; 237| 70.4k| memset(composite_norm_data, 0, sizeof(composite_norm_data)); /* djb-rwth: memset_s C11/Annex K variant? */ 238| 70.4k| memset(pncFlags, 0, sizeof(*pncFlags)); /* djb-rwth: memset_s C11/Annex K variant? */ 239| | 240| | 241| | 242| | /* For experimental purposes only */ 243| | /*ret1 = DoOneStructureEarlyPreprocessing( num_inp, sd, ip, inp_file, 244| | log_file, out_file, prb_file, 245| | orig_inp_data, prep_inp_data ); 246| | */ 247| 70.4k| ret1 = DoOneStructureEarlyPreprocessing(ic, pCG, num_inp, sd, ip, 248| 70.4k| inp_file, log_file, out_file, prb_file, 249| 70.4k| orig_inp_data, prep_inp_data); 250| 70.4k| switch ( ret1 ) ------------------ | Branch (250:14): [True: 0, False: 70.4k] ------------------ 251| 70.4k| { 252| 0| case _IS_SKIP: ------------------ | | 16| 0|#define _IS_SKIP -2 ------------------ | Branch (252:5): [True: 0, False: 70.4k] ------------------ 253| 0| case _IS_ERROR: ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (253:5): [True: 0, False: 70.4k] ------------------ 254| 0| case _IS_FATAL: ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ | Branch (254:5): [True: 0, False: 70.4k] ------------------ 255| 0| nRet = ret1; 256| 70.4k| } 257| | 258| 70.4k| if ( ret1 ) ------------------ | Branch (258:10): [True: 0, False: 70.4k] ------------------ 259| 0| { 260| 0| goto exit_function; 261| 0| } 262| | 263| | /*(@nnuk : Nauman Ullah Khan) 264| | *invoking Molecular Inorganics preprocessing (if flag is active) 265| | */ 266| 70.4k| if ( ip->bMolecularInorganics && nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 13| 140k|#define _IS_FATAL 3 ------------------ if ( ip->bMolecularInorganics && nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 12| 70.4k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (266:10): [True: 70.4k, False: 0] | Branch (266:38): [True: 70.4k, False: 0] | Branch (266:59): [True: 70.4k, False: 0] ------------------ 267| 70.4k| { 268| | /* Capture the native input as OrigStruct before MolecularInorganicsPreprocessing() 269| | * disconnects bonds in orig_inp_data. This mirrors the standard path (where 270| | * orig_inp_data stays pristine because preprocessing works on a copy) so the 271| | * AuxInfo reversibility layers (/rA, /rB, /rC), including atom coordinates, 272| | * describe the original drawn structure. */ 273| 70.4k| pOrigStruct = &OrigStruct; 274| 70.4k| memset(pOrigStruct, 0, sizeof(*pOrigStruct)); 275| 70.4k| OrigAtData_StoreNativeInput(pCG, &nRet, sd, ip, orig_inp_data, pOrigStruct); 276| 70.4k| if ( nRet == _IS_FATAL || nRet == _IS_ERROR ) ------------------ | | 13| 140k|#define _IS_FATAL 3 ------------------ if ( nRet == _IS_FATAL || nRet == _IS_ERROR ) ------------------ | | 12| 70.4k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (276:14): [True: 0, False: 70.4k] | Branch (276:35): [True: 0, False: 70.4k] ------------------ 277| 0| { 278| | /* Route to the shared cleanup so OrigStruct_Free() releases pOrigStruct */ 279| 0| goto after_structure_generation; 280| 0| } 281| | 282| | /* Call the MolecularInorganicsPreprocessing function to handle specific inorganics-related tasks */ 283| 70.4k| ret1 = MolecularInorganicsPreprocessing(orig_inp_data, ip); 284| | 285| | /* Check for errors during preprocessing */ 286| 70.4k| if ( ret1 < 0 ) ------------------ | Branch (286:14): [True: 0, False: 70.4k] ------------------ 287| 0| { 288| | /* Log and handle fatal error in molecular inorganics preprocessing */ 289| 0| fprintf(stderr, "Error during Molecular Inorganics preprocessing\n"); 290| 0| AddErrorMessage(sd->pStrErrStruct, "Molecular Inorganics preprocessing failed"); 291| 0| nRet = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 292| 0| goto exit_function; 293| 0| } 294| | 295| | /* Preserve SDF output in Molecular Inorganics mode if requested */ 296| 70.4k| ret1 = OrigAtData_SaveMolfile(orig_inp_data, sd, ip, num_inp, out_file); 297| 70.4k| if (ret1) ------------------ | Branch (297:13): [True: 0, False: 70.4k] ------------------ 298| 0| { 299| 0| goto exit_function; 300| 0| } 301| | 302| 70.4k| nRet1 = CreateOneStructureINChI(pCG, ic, sd, ip, szTitle, 303| 70.4k| pINChI, pINChI_Aux, INCHI_BAS, ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 304| 70.4k| inp_file, log_file, out_file, prb_file, 305| 70.4k| orig_inp_data, prep_inp_data, 306| 70.4k| composite_norm_data, 307| 70.4k| num_inp, strbuf, pncFlags); 308| 70.4k| nRet = inchi_max(nRet, nRet1); ------------------ | | 138| 70.4k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 70.4k] | | ------------------ ------------------ 309| | 310| | /* If preprocessing indicates we need a reconnected InChI, create it here */ 311| 70.4k| if ( ip->bMolecularInorganicsReconnectedInChI && nRet != _IS_FATAL && ------------------ | | 13| 76.8k|#define _IS_FATAL 3 ------------------ | Branch (311:14): [True: 6.41k, False: 64.0k] | Branch (311:58): [True: 6.41k, False: 2] ------------------ 312| 6.41k| nRet != _IS_ERROR && ------------------ | | 12| 76.8k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (312:13): [True: 6.41k, False: 0] ------------------ 313| 6.41k| (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 570| 6.41k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 975| 6.41k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (313:13): [True: 0, False: 6.41k] ------------------ 314| 0| (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) ) ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (314:13): [True: 0, False: 0] ------------------ 315| 0| { 316| | 317| 0| nRet1 = CreateOneStructureINChI(pCG, ic, sd, ip, szTitle, 318| 0| pINChI, pINChI_Aux, INCHI_REC, ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 319| 0| inp_file, log_file, out_file, prb_file, 320| 0| orig_inp_data, prep_inp_data, 321| 0| composite_norm_data, 322| 0| num_inp, strbuf, pncFlags); 323| 0| nRet = inchi_max(nRet, nRet1); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 324| | 325| 0| if ( nRet1 == _IS_FATAL || nRet1 == _IS_ERROR ) ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ if ( nRet1 == _IS_FATAL || nRet1 == _IS_ERROR ) ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (325:18): [True: 0, False: 0] | Branch (325:40): [True: 0, False: 0] ------------------ 326| 0| { 327| 0| fprintf(stderr, "Error during reconnected InChI generation.\n"); 328| 0| goto exit_function; 329| 0| } 330| | 331| 0| if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (331:18): [True: 0, False: 0] | Branch (331:39): [True: 0, False: 0] ------------------ 332| 0| { 333| 0| maxINChI = 2; /* Update to indicate reconnected InChI has been generated */ 334| 0| } 335| 0| } 336| | 337| 70.4k| else if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 13| 140k|#define _IS_FATAL 3 ------------------ else if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 12| 70.4k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (337:18): [True: 70.4k, False: 2] | Branch (337:39): [True: 70.4k, False: 2] ------------------ 338| 70.4k| { 339| 70.4k| maxINChI = 1; 340| 70.4k| } 341| | 342| | /* 343| | * InChI is already generated via the Molecular Inorganics-specific path. 344| | * Skip the standard structure-generation path to prevent duplicate 345| | * CreateOneStructureINChI() calls and redundant allocations. 346| | * 347| | * pOrigStruct and OrigStruct were populated above from the native input, so the shared 348| | * cleanup path (SortAndPrintINChI + OrigStruct_Free) emits the AuxInfo 349| | * reversibility layers (/rA, /rB, /rC), including atom coordinates, and 350| | * releases it. 351| | */ 352| 70.4k| goto after_structure_generation; 353| 70.4k| } 354| | 355| | 356| 0| if ( is_polymer ) ------------------ | Branch (356:10): [True: 0, False: 0] ------------------ 357| 0| { 358| | /* Polymer house-keeping related to possible CRU frame shift(s) */ 359| | 360| 0| orig_inp_data->polymer->frame_shift_scheme = ip->bFrameShiftScheme; 361| 0| orig_inp_data->polymer->treat = ip->bPolymers; 362| | 363| 0| if ( !is_polymer2inchi ) ------------------ | Branch (363:14): [True: 0, False: 0] ------------------ 364| 0| { 365| | /* Polymer structure is being restored from InChI string */ 366| | /* If CRUs were pre-cyclized, re-open them in preferred forms here */ 367| 0| if ( orig_inp_data->polymer->frame_shift_scheme == FSS_STARS_CYCLED ) ------------------ | Branch (367:18): [True: 0, False: 0] ------------------ 368| 0| { 369| 0| OAD_Polymer_SmartReopenCyclizedUnits(orig_inp_data->polymer, 370| 0| orig_inp_data->at, 371| 0| orig_inp_data->num_inp_atoms, 372| 0| &orig_inp_data->num_inp_bonds); 373| 0| } 374| 0| } 375| 0| } 376| | 377| | 378| 0| ret1 = OrigAtData_SaveMolfile(orig_inp_data, sd, ip, num_inp, out_file); 379| 0| if ( ret1 ) ------------------ | Branch (379:10): [True: 0, False: 0] ------------------ 380| 0| { 381| 0| goto exit_function; 382| 0| } 383| | 384| | 385| 0| pOrigStruct = &OrigStruct; 386| 0| memset(pOrigStruct, 0, sizeof(*pOrigStruct)); /* djb-rwth: memset_s C11/Annex K variant? */ 387| | 388| 0| OrigAtData_StoreNativeInput(pCG, &nRet, sd, ip, orig_inp_data, pOrigStruct); 389| | 390| | /* 2. Create INChI for the whole disconnected or original structure */ 391| | 392| 0| if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (392:10): [True: 0, False: 0] | Branch (392:31): [True: 0, False: 0] ------------------ 393| 0| { 394| 0| nRet1 = CreateOneStructureINChI(pCG, ic, sd, ip, szTitle, 395| 0| pINChI, pINChI_Aux, INCHI_BAS, ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 396| 0| inp_file, log_file, out_file, prb_file, 397| 0| orig_inp_data, prep_inp_data, 398| 0| composite_norm_data, 399| 0| num_inp, strbuf, pncFlags); 400| 0| nRet = inchi_max(nRet, nRet1); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 401| | 402| | /* If we create InChI from polymer-containing structure */ 403| 0| if ( is_polymer2inchi ) ------------------ | Branch (403:14): [True: 0, False: 0] ------------------ 404| 0| { 405| 0| int polymer_repr_type = OAD_Polymer_GetRepresentation(orig_inp_data->polymer); 406| | 407| 0|#ifdef ALLOW_MIXED_SRU_AND_MON 408| 0| if ( polymer_repr_type == POLYMER_REPRESENTATION_STRUCTURE_BASED || ------------------ | | 173| 0|#define POLYMER_REPRESENTATION_STRUCTURE_BASED 2 ------------------ | Branch (408:18): [True: 0, False: 0] ------------------ 409| 0| polymer_repr_type == POLYMER_REPRESENTATION_MIXED ) ------------------ | | 174| 0|#define POLYMER_REPRESENTATION_MIXED 3 ------------------ | Branch (409:17): [True: 0, False: 0] ------------------ 410| |#else 411| | if ( polymer_repr_type == POLYMER_REPRESENTATION_STRUCTURE_BASED ) 412| |#endif 413| 0| { 414| | /* Temporarily copy ptr to polymer data to prep_inp_data */ 415| 0| OAD_Polymer* prep_polymer = prep_inp_data->polymer; /* may be NULL */ 416| 0| prep_inp_data->polymer = orig_inp_data->polymer; 417| | 418| 0| OAD_Polymer_FindBackbones(prep_inp_data, /* NB: not orig_inp_data! */ 419| 0| &(composite_norm_data[INCHI_BAS][TAUT_YES]), ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ &(composite_norm_data[INCHI_BAS][TAUT_YES]), ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 420| 0| &err, sd->pStrErrStruct); 421| 0| if ( err ) ------------------ | Branch (421:22): [True: 0, False: 0] ------------------ 422| 0| { 423| 0| ret1 = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 424| 0| } 425| 0| nRet = inchi_max(nRet, ret1); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 426| 0| prep_inp_data->polymer = prep_polymer; /* restore temp copied*/ 427| 0| } 428| 0| } 429| 0| } 430| | 431| 0| if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (431:10): [True: 0, False: 0] | Branch (431:31): [True: 0, False: 0] ------------------ 432| 0| { 433| 0| maxINChI = 1; 434| 0| } 435| | 436| | 437| | /* 3. Create INChI for the whole metal-reconnected structure */ 438| | 439| 0| if ( nRet != _IS_FATAL && ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ | Branch (439:10): [True: 0, False: 0] ------------------ 440| 0| nRet != _IS_ERROR && ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (440:9): [True: 0, False: 0] ------------------ 441| 0| (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 975| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (441:9): [True: 0, False: 0] ------------------ 442| 0| (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) ) ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (442:9): [True: 0, False: 0] ------------------ 443| 0| { 444| | 445| 0| nRet1 = CreateOneStructureINChI(pCG, ic, sd, ip, szTitle, 446| 0| pINChI, pINChI_Aux, INCHI_REC, inp_file, ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 447| 0| log_file, out_file, prb_file, 448| 0| orig_inp_data, prep_inp_data, 449| 0| composite_norm_data, 450| 0| num_inp, strbuf, pncFlags); 451| 0| nRet = inchi_max(nRet, nRet1); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 452| | 453| 0| if ( is_polymer2inchi ) ------------------ | Branch (453:14): [True: 0, False: 0] ------------------ 454| 0| { 455| 0| ret1 = 0; 456| | /* temporarily copy ptr to polymer data to prep_inp_data */ 457| 0| prep_inp_data->polymer = orig_inp_data->polymer; 458| | 459| 0| OAD_Polymer_FindBackbones(prep_inp_data, /* NB: not orig_inp_data! */ 460| 0| &(composite_norm_data[INCHI_REC][TAUT_YES]), ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ &(composite_norm_data[INCHI_REC][TAUT_YES]), ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 461| 0| &err, sd->pStrErrStruct); 462| 0| if ( err ) ------------------ | Branch (462:18): [True: 0, False: 0] ------------------ 463| 0| { 464| 0| ret1 = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 465| 0| } 466| 0| nRet = inchi_max(nRet, ret1); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 467| 0| prep_inp_data->polymer = NULL; /* remove temp copied */ 468| 0| } 469| 0| if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (469:14): [True: 0, False: 0] | Branch (469:35): [True: 0, False: 0] ------------------ 470| 0| { 471| 0| maxINChI = 2; 472| 0| } 473| 0| } 474| | 475| 70.4k|after_structure_generation: 476| | 477| 70.4k| if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 13| 140k|#define _IS_FATAL 3 ------------------ if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 12| 70.4k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (477:10): [True: 70.4k, False: 2] | Branch (477:31): [True: 70.4k, False: 2] ------------------ 478| 70.4k| { 479| 70.4k| if ( (sd->bChiralFlag & FLAG_INP_AT_CHIRAL) && ------------------ | | 669| 70.4k|#define FLAG_INP_AT_CHIRAL 1 ------------------ | Branch (479:14): [True: 0, False: 70.4k] ------------------ 480| 0| (ip->nMode & REQ_MODE_STEREO) && ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (480:13): [True: 0, False: 0] ------------------ 481| 0| !(ip->nMode & (REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO)) && ------------------ | | 26| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ !(ip->nMode & (REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO)) && ------------------ | | 28| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (481:13): [True: 0, False: 0] ------------------ 482| 0| !bIsStructChiral(pINChI, sd->num_components) ) ------------------ | Branch (482:13): [True: 0, False: 0] ------------------ 483| 0| { 484| 0| if ( !ip->bNoWarnings ) ------------------ | Branch (484:18): [True: 0, False: 0] ------------------ 485| 0| { 486| 0| WarningMessage(sd->pStrErrStruct, "Not chiral"); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 487| 0| } 488| 0| } 489| 70.4k| if ( !sd->bUserQuitComponent && !sd->bUserQuit ) ------------------ | Branch (489:14): [True: 70.4k, False: 0] | Branch (489:41): [True: 70.4k, False: 0] ------------------ 490| 70.4k| { 491| 70.4k| nRet1 = TreatCreateINChIWarning(sd, ip, prep_inp_data, num_inp, 492| 70.4k| inp_file, log_file, out_file, prb_file); 493| 70.4k| nRet = inchi_max(nRet, nRet1); ------------------ | | 138| 70.4k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 70.4k] | | ------------------ ------------------ 494| 70.4k| } 495| 70.4k| } 496| | 497| | 498| | /* 4. Sort and print INChI for the whole structure */ 499| | 500| 70.4k| PrepareSaveOptBits(&save_opt_bits, ip); 501| 70.4k| if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 13| 140k|#define _IS_FATAL 3 ------------------ if ( nRet != _IS_FATAL && nRet != _IS_ERROR ) ------------------ | | 12| 70.4k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (501:10): [True: 70.4k, False: 2] | Branch (501:31): [True: 70.4k, False: 2] ------------------ 502| 70.4k| { 503| 70.4k| nRet1 = SortAndPrintINChI(pCG, out_file, strbuf, log_file, ip, 504| 70.4k| orig_inp_data, prep_inp_data, 505| 70.4k| composite_norm_data, 506| 70.4k| pOrigStruct, sd->num_components, 507| 70.4k| sd->num_non_taut, sd->num_taut, 508| 70.4k| sd->bTautFlags, sd->bTautFlagsDone, 509| 70.4k| pncFlags, num_inp, 510| 70.4k| pINChI, pINChI_Aux, 511| 70.4k| &bSortPrintINChIFlags, save_opt_bits); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 512| 70.4k| } 513| | 514| | 515| | /* 5. Post-process */ 516| | 517| 70.4k| DisplayOrigAndResultStructuresAndComponents(nRet, ic, pCG, sd, ip, szTitle, 518| 70.4k| pINChI, pINChI_Aux, 519| 70.4k| inp_file, log_file, out_file, 520| 70.4k| orig_inp_data, prep_inp_data, 521| 70.4k| num_inp, maxINChI, 522| 70.4k| composite_norm_data); 523| | 524| | 525| 70.4k| SaveOkProcessedMolfile(nRet, sd, ip, prb_file, inp_file); 526| | 527| | 528| | /* Cleanup */ 529| | 530| 211k| for ( i = 0; i < INCHI_NUM; i++ ) ------------------ | | 569| 211k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (530:18): [True: 140k, False: 70.4k] ------------------ 531| 140k| { 532| 563k| for ( k = 0; k < TAUT_NUM + 1; k++ ) ------------------ | | 573| 563k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (532:22): [True: 422k, False: 140k] ------------------ 533| 422k| { 534| 422k| FreeCompAtomData(&composite_norm_data[i][k]); 535| 422k| } 536| 140k| } 537| | 538| 70.4k| OrigStruct_Free(pOrigStruct); 539| | 540| 70.4k|exit_function: 541| | 542| 70.4k| return nRet; 543| 70.4k|} OrigAtData_SaveMolfile: 629| 70.4k|{ 630| 70.4k| int ret = 0; 631| | 632| 70.4k| if ( !(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) ) ------------------ | | 133| 70.4k|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (632:10): [True: 70.4k, False: 0] ------------------ 633| 70.4k| { 634| 70.4k| return _IS_OKAY; ------------------ | | 10| 70.4k|#define _IS_OKAY 0 ------------------ 635| 70.4k| } 636| 0| else 637| 0| { 638| 0| char szNumber[256]; 639| 0| sprintf(szNumber, "Structure #%ld. %s%s%s%s", num_inp, SDF_LBL_VAL(ip->pSdfLabel, ip->pSdfValue)); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ 640| 0| ret = OrigAtData_WriteToSDfile(orig_inp_data, out_file, szNumber, NULL, 641| 0| (sd->bChiralFlag & FLAG_INP_AT_CHIRAL) ? 1 : 0, ------------------ | | 669| 0|#define FLAG_INP_AT_CHIRAL 1 ------------------ | Branch (641:13): [True: 0, False: 0] ------------------ 642| 0| (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ATOMS_DT) ? 1 : 0, ------------------ | | 140| 0|#define INCHI_OUT_SDFILE_ATOMS_DT 0x0800 /* SDfile output H isotopes as D and T */ ------------------ | Branch (642:13): [True: 0, False: 0] ------------------ 643| 0| ip->pSdfLabel, ip->pSdfValue); 644| 0| } 645| | 646| 0| return ret; 647| 70.4k|} CreateOneStructureINChI: 887| 70.4k|{ 888| 70.4k| int i, j, k, nRet = 0, n = 0l; 889| |#if defined (TARGET_EXE_STANDALONE) && defined(_WIN32) 890| | int err_display; 891| |#endif 892| | 893| |#ifdef GHI100_FIX 894| |#if ((SPRINTF_FLAG != 1) && (SPRINTF_FLAG != 2)) 895| | setlocale(LC_ALL, "en-US"); /* djb-rwth: setting all locales to "en-US" */ 896| |#endif 897| |#endif 898| | 899| 70.4k| PINChI2 *pINChI = NULL; 900| 70.4k| PINChI_Aux2 *pINChI_Aux = NULL; 901| | 902| 70.4k| INP_ATOM_DATA InpCurAtData; 903| 70.4k| INP_ATOM_DATA* inp_cur_data; 904| | 905| 70.4k| INP_ATOM_DATA InpNormAtData, InpNormTautData; 906| 70.4k| INP_ATOM_DATA* inp_norm_data[TAUT_NUM]; /* = { &InpNormAtData, &InpNormTautData }; */ 907| 70.4k| ORIG_ATOM_DATA* cur_prep_inp_data = prep_inp_data + iINChI; 908| 70.4k| inchiTime ulTStart; 909| | 910| | /* Always create info data structures (but do not display them always ) 911| | #ifndef COMPILE_ANSI_ONLY 912| | */ 913| 70.4k| int bShowStructure = 0; 914| 70.4k| int bStructurePreprocessed = 0; /* All changes except disconnection */ 915| 70.4k| int bStructureDisconnected = 0; 916| 70.4k| int bAlsoOutputReconnected = 0, bINCHI_LIB_Flag = 0; 917| 70.4k| COMP_ATOM_DATA* composite_norm_data = composite_norm_data2[iINChI]; 918| 70.4k| INP_ATOM_DATA2* all_inp_norm_data = NULL; 919| | /*#endif*/ 920| | 921| | /* Order of actions: 922| | 923| | if ( orig_inp_data is NOT empty AND 924| | prep_inp_data[0] IS empty ) then do 925| | in PreprocessOneStructure() : 926| | 927| | 1. copy orig_inp_data --> prep_inp_data[0] 928| | 2. fix odd things in prep_inp_data[0] 929| | 3. if( orig_inp_data->bDisconnectSalts ) then 930| | -- disconnect salts in prep_inp_data[0] 931| | 4. move protons to neutralize charges on heteroatoms 932| | 5. if( orig_inp_data->bDisconnectCoord ) then 933| | -- copy prep_inp_data[0] --> prep_inp_data[1] 934| | -- disconnect metals in prep_inp_data[0] 935| | 936| | iINChI = 0 937| | ========= 938| | (normal/disconnected layer) 939| | 940| | 1. normalize prep_inp_data[0] in inp_norm_data[0,1] 941| | 2. create INChI[ iINChI ] out of inp_norm_data[0,1] 942| | 943| | 944| | iINChI = 1 AND orig_inp_data->bDisconnectCoord > 0 945| | ================================================= 946| | (reconnected layer) 947| | 948| | 1. normalize prep_inp_data[1] in inp_norm_data[0,1] 949| | 2. create INChI[ iINChI ] out of inp_norm_data[0,1] 950| | 951| | */ 952| | 953| 70.4k| ip->msec_LeftTime = ip->msec_MaxTime; /* start timeout countdown for each component */ 954| | 955| 70.4k| inp_cur_data = &InpCurAtData; 956| 70.4k| inp_norm_data[TAUT_NON] = &InpNormAtData; ------------------ | | 574| 70.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 957| 70.4k| inp_norm_data[TAUT_YES] = &InpNormTautData; ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 958| | 959| 70.4k| memset(inp_cur_data, 0, sizeof(*inp_cur_data)); /* djb-rwth: memset_s C11/Annex K variant? */ 960| 70.4k| memset(inp_norm_data[TAUT_NON], 0, sizeof(*inp_norm_data[0])); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 574| 70.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 961| 70.4k| memset(inp_norm_data[TAUT_YES], 0, sizeof(*inp_norm_data[0])); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 962| | 963| 70.4k| { 964| | /*#ifndef COMPILE_ANSI_ONLY*/ 965| 70.4k| memset(composite_norm_data + TAUT_NON, 0, sizeof(composite_norm_data[0])); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 574| 70.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 966| 70.4k| memset(composite_norm_data + TAUT_YES, 0, sizeof(composite_norm_data[0])); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 967| 70.4k| memset(composite_norm_data + TAUT_INI, 0, sizeof(composite_norm_data[0])); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 576| 70.4k|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ 968| 70.4k| } /*#endif*/ 969| | 970| 70.4k| if ( ip->bAllowEmptyStructure && !orig_inp_data->at && !orig_inp_data->num_inp_atoms ) ------------------ | Branch (970:10): [True: 0, False: 70.4k] | Branch (970:38): [True: 0, False: 0] | Branch (970:60): [True: 0, False: 0] ------------------ 971| 0| { 972| 0| ; 973| 0| } 974| 70.4k| else if ( !orig_inp_data->at || !orig_inp_data->num_inp_atoms ) ------------------ | Branch (974:15): [True: 0, False: 70.4k] | Branch (974:37): [True: 0, False: 70.4k] ------------------ 975| 0| { 976| 0| return 0; /* nothing to do */ 977| 0| } 978| 70.4k| if ( iINChI == 1 && orig_inp_data->bDisconnectCoord <= 0 ) ------------------ | Branch (978:10): [True: 0, False: 70.4k] | Branch (978:25): [True: 0, False: 0] ------------------ 979| 0| { 980| 0| return 0; 981| 0| } 982| | 983| | /* m = iINChI; */ /* orig_inp_data index */ 984| 70.4k| if ( iINChI != INCHI_BAS && iINChI != INCHI_REC ) ------------------ | | 570| 140k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ( iINChI != INCHI_BAS && iINChI != INCHI_REC ) ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (984:10): [True: 0, False: 70.4k] | Branch (984:33): [True: 0, False: 0] ------------------ 985| 0| { 986| 0| AddErrorMessage(sd->pStrErrStruct, "Fatal undetermined program error"); 987| 0| sd->nStructReadError = 97; 988| 0| nRet = sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 989| 0| inchi_free(all_inp_norm_data); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 990| 0| goto exit_function; 991| 0| } 992| | 993| | /******************************************************************* 994| | * * 995| | * * 996| | * Whole structure preprocessing: 1st step of the normalization * 997| | * * 998| | * Happen only on the first call to CreateOneStructureINChI() * 999| | * * 1000| | * * 1001| | *******************************************************************/ 1002| | 1003| 70.4k| if ( (!prep_inp_data->at || !prep_inp_data->num_inp_atoms) && ------------------ | Branch (1003:11): [True: 70.4k, False: 0] | Branch (1003:33): [True: 0, False: 0] ------------------ 1004| 70.4k| orig_inp_data->num_inp_atoms > 0 ) ------------------ | Branch (1004:9): [True: 70.4k, False: 0] ------------------ 1005| 70.4k| { 1006| | /* The structure has not been preprocessed */ 1007| 70.4k| if ( ip->msec_MaxTime ) ------------------ | Branch (1007:14): [True: 0, False: 70.4k] ------------------ 1008| 0| { 1009| 0| InchiTimeGet(&ulTStart); 1010| 0| } 1011| | 1012| 70.4k| PreprocessOneStructure(ic, sd, ip, orig_inp_data, prep_inp_data); 1013| | 1014| 70.4k| pncFlags->bTautFlags[iINChI][TAUT_YES] = ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1015| 70.4k| pncFlags->bTautFlags[iINChI][TAUT_NON] = ------------------ | | 574| 70.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1016| 70.4k| sd->bTautFlags[INCHI_BAS] | ip->bTautFlags; ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1017| | 1018| 70.4k| pncFlags->bTautFlagsDone[iINChI][TAUT_YES] = ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1019| 70.4k| pncFlags->bTautFlagsDone[iINChI][TAUT_NON] = ------------------ | | 574| 70.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1020| 70.4k| sd->bTautFlagsDone[INCHI_BAS] | ip->bTautFlagsDone; ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1021| | 1022| 70.4k| { 1023| | /*#ifndef COMPILE_ANSI_ONLY*/ 1024| | /* in this location the call happens once for each input structure, before preprocessing */ 1025| 70.4k| bStructurePreprocessed = (0 != (sd->bTautFlagsDone[INCHI_BAS] & ( ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1026| 70.4k| TG_FLAG_MOVE_HPLUS2NEUTR_DONE | ------------------ | | 962| 70.4k|#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */ ------------------ 1027| 70.4k| TG_FLAG_DISCONNECT_SALTS_DONE | ------------------ | | 964| 70.4k|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 1028| 70.4k| TG_FLAG_MOVE_POS_CHARGES_DONE | ------------------ | | 966| 70.4k|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 1029| 70.4k| TG_FLAG_FIX_ODD_THINGS_DONE))); ------------------ | | 978| 70.4k|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 1030| | 1031| 70.4k| bStructureDisconnected = (0 != (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE)); ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ bStructureDisconnected = (0 != (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE)); ------------------ | | 975| 70.4k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 1032| | 1033| 70.4k| bShowStructure = (bStructurePreprocessed || ------------------ | Branch (1033:31): [True: 783, False: 69.6k] ------------------ 1034| 69.6k| bStructureDisconnected || ------------------ | Branch (1034:17): [True: 0, False: 69.6k] ------------------ 1035| 69.6k| prep_inp_data[0].num_components > 1); ------------------ | Branch (1035:17): [True: 790, False: 68.8k] ------------------ 1036| | 1037| | /* sd->bTautFlags[] contains output flags 1038| | ip->bTautFlags contains input flags 1039| | */ 1040| 70.4k| bAlsoOutputReconnected = (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ bAlsoOutputReconnected = (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 975| 70.4k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (1040:38): [True: 0, False: 70.4k] ------------------ 1041| 0| (ip->bTautFlags & TG_FLAG_RECONNECT_COORD); ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1041:17): [True: 0, False: 0] ------------------ 1042| 70.4k| bINCHI_LIB_Flag = 0; 1043| | 1044| | /*************** output structures to TARGET_LIB_FOR_WINCHI conditions ********************* 1045| | * 1046| | * Send to TARGET_LIB_FOR_WINCHI: 1047| | * 1048| | * type component conditions 1049| | * 1050| | * COMPONENT_ORIGINAL #0: (num_components > 1) 1051| | * COMPONENT_ORIGINAL_PREPROCESSED #0: (num_components > 1) && (preprocessed) 1052| | * COMPONENT_ORIGINAL #1: (num_components = 1) && (preprocessed) 1053| | * 1054| | * Flags explanation: 1055| | * MAIN => iINChI=0, RECN => iINChI=1 (Reconnected) 1056| | * ORIG => Original, PREP => Preprocessed 1057| | * 1058| | * Possible flags: k 1059| | * 1060| | * COMP_ORIG_0_MAIN 0x0001 0 COMPONENT_ORIGINAL, bMain, component #0 1061| | * COMP_ORIG_0_RECN 0x0002 1 COMPONENT_ORIGINAL, bRecn, component #0 1062| | * 1063| | * COMP_PREP_0_MAIN 0x0004 2 COMPONENT_ORIGINAL_PREPROCESSED, bMain, component #0 1064| | * COMP_PREP_0_RECN 0x0008 3 COMPONENT_ORIGINAL_PREPROCESSED, bRecn, component #0 1065| | * 1066| | * COMP_ORIG_1_MAIN 0x0010 4 COMPONENT_ORIGINAL, bMain, component #1 1067| | * COMP_ORIG_1_RECN 0x0020 5 COMPONENT_ORIGINAL, bRecn, component #1 1068| | * 1069| | * bReconnected = k%2 (0 or 1) 1070| | * nComponent = k/4 (0 or 1) 1071| | * bPreprocessed = (k/2)%2 (0 or 1) 1072| | * 1073| | ******************************************************************************/ 1074| | 1075| | /* Original -> Main, component #0, Original */ 1076| 70.4k| if ( prep_inp_data[INCHI_BAS].num_components > 1 ) ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1076:18): [True: 811, False: 69.6k] ------------------ 1077| 811| { 1078| 811| bINCHI_LIB_Flag |= COMP_ORIG_0_MAIN; ------------------ | | 25| 811|#define COMP_ORIG_0_MAIN 0x0001 ------------------ 1079| 811| } 1080| 69.6k| else 1081| 69.6k| { 1082| | /* Original -> Main, component #1, Original */ 1083| 69.6k| if ( prep_inp_data[INCHI_BAS].num_components == 1 && bStructurePreprocessed ) ------------------ | | 570| 69.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1083:22): [True: 69.6k, False: 0] | Branch (1083:70): [True: 762, False: 68.8k] ------------------ 1084| 762| { 1085| 762| bINCHI_LIB_Flag |= COMP_ORIG_1_MAIN; ------------------ | | 29| 762|#define COMP_ORIG_1_MAIN 0x0010 ------------------ 1086| | /* preprocessed will be added when output canonicalization results */ 1087| 762| } 1088| 69.6k| } 1089| | 1090| 70.4k| if ( bAlsoOutputReconnected ) ------------------ | Branch (1090:18): [True: 0, False: 70.4k] ------------------ 1091| 0| { 1092| | /* Original -> Reconnected, component #0, Original */ 1093| 0| if ( prep_inp_data[INCHI_REC].num_components > 1 ) ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1093:22): [True: 0, False: 0] ------------------ 1094| 0| { 1095| 0| bINCHI_LIB_Flag |= COMP_ORIG_0_RECN; ------------------ | | 26| 0|#define COMP_ORIG_0_RECN 0x0002 ------------------ 1096| 0| } 1097| 0| else if ( prep_inp_data[INCHI_BAS].num_components == 1 && bStructurePreprocessed ) ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1097:27): [True: 0, False: 0] | Branch (1097:75): [True: 0, False: 0] ------------------ 1098| 0| { 1099| | /* Original -> Reconnected, component #1, Original */ 1100| 0| bINCHI_LIB_Flag |= COMP_ORIG_1_RECN; ------------------ | | 30| 0|#define COMP_ORIG_1_RECN 0x0020 ------------------ 1101| | /* preprocessed will be added when output canonicalization results */ 1102| 0| } 1103| 0| } 1104| 70.4k| if ( ip->msec_MaxTime ) ------------------ | Branch (1104:18): [True: 0, False: 70.4k] ------------------ 1105| 0| { 1106| 0| ip->msec_LeftTime -= InchiTimeElapsed(ic, &ulTStart); 1107| 0| } 1108| | 1109| | /* display the ORIGINAL, UN-PREPROCESSED structure */ 1110| | 1111| 70.4k| if ( ip->bDisplay ) ------------------ | Branch (1111:18): [True: 0, False: 70.4k] ------------------ 1112| 0| { 1113| 0| if ( DisplayTheWholeStructure(pCG, ic, sd, ip, szTitle, ------------------ | Branch (1113:22): [True: 0, False: 0] ------------------ 1114| 0| inp_file, log_file, orig_inp_data, num_inp, 1115| 0| -1, bShowStructure, bINCHI_LIB_Flag) ) 1116| 0| { 1117| 0| inchi_free(all_inp_norm_data); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1118| 0| goto exit_function; 1119| 0| } 1120| 0| } 1121| 70.4k| } /*#endif */ 1122| | 1123| 70.4k| switch ( sd->nErrorType ) ------------------ | Branch (1123:18): [True: 0, False: 70.4k] ------------------ 1124| 70.4k| { 1125| 0| case _IS_ERROR: ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1125:9): [True: 0, False: 70.4k] ------------------ 1126| 0| case _IS_FATAL: ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ | Branch (1126:9): [True: 0, False: 70.4k] ------------------ 1127| | /* error message */ 1128| 0| nRet = TreatErrorsInReadTheStructure(sd, ip, 1129| 0| LOG_MASK_ALL, ------------------ | | 98| 0|#define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 94| 0|#define LOG_MASK_WARN 1 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 95| 0|#define LOG_MASK_ERR 2 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 96| 0|#define LOG_MASK_FATAL 4 | | ------------------ ------------------ 1130| 0| inp_file, log_file, out_file, prb_file, 1131| 0| prep_inp_data, &num_inp); 1132| 0| goto exit_cycle; 1133| 70.4k| } 1134| 70.4k| } 1135| | /* tranfer flags from INChI_Aux to sd */ 1136| | 1137| | 1138| 70.4k| { 1139| | /*#ifndef COMPILE_ANSI_ONLY */ /* { */ 1140| | 1141| | /******************************************/ 1142| | /* Displaying the structures */ 1143| | /* Only under WIN32 */ 1144| | /******************************************/ 1145| 70.4k| if ( /* ip->bDisplayCompositeResults && !sd->bUserQuitComponentDisplay && */ 1146| 70.4k| prep_inp_data[iINChI].num_components > 1 ------------------ | Branch (1146:13): [True: 811, False: 69.6k] ------------------ 1147| 70.4k| ) 1148| 811| { 1149| 811| all_inp_norm_data = (INP_ATOM_DATA2*)inchi_calloc(prep_inp_data[iINChI].num_components, sizeof(all_inp_norm_data[0])); ------------------ | | 1146| 811|#define inchi_calloc calloc ------------------ 1150| 811| } 1151| | 1152| | /* Display the input structure AFTER PREPROCESSING */ 1153| 70.4k| switch ( iINChI ) 1154| 70.4k| { 1155| 70.4k| case INCHI_BAS: ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1155:9): [True: 70.4k, False: 0] ------------------ 1156| | /*------------ Possibly disconnected structure -------------------*/ 1157| 70.4k| bStructurePreprocessed = 0 != (sd->bTautFlagsDone[iINChI] & ( 1158| 70.4k| TG_FLAG_MOVE_HPLUS2NEUTR_DONE | ------------------ | | 962| 70.4k|#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */ ------------------ 1159| 70.4k| TG_FLAG_DISCONNECT_SALTS_DONE | ------------------ | | 964| 70.4k|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 1160| 70.4k| TG_FLAG_MOVE_POS_CHARGES_DONE | ------------------ | | 966| 70.4k|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 1161| 70.4k| TG_FLAG_MOVE_CHARGE_COORD_DONE | ------------------ | | 977| 70.4k|#define TG_FLAG_MOVE_CHARGE_COORD_DONE 0x00000400 /* changed charge of a disconnected ligand to fit its valence */ ------------------ 1162| 70.4k| TG_FLAG_DISCONNECT_COORD_DONE | ------------------ | | 975| 70.4k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 1163| 70.4k| TG_FLAG_FIX_ODD_THINGS_DONE)); ------------------ | | 978| 70.4k|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 1164| 70.4k| bINCHI_LIB_Flag = 0; 1165| | /* Preprocessed/Main -> Main, component #0, Preprocessed */ 1166| 70.4k| if ( prep_inp_data[iINChI].num_components > 1 && ------------------ | Branch (1166:18): [True: 811, False: 69.6k] ------------------ 1167| 811| bStructurePreprocessed ) ------------------ | Branch (1167:17): [True: 21, False: 790] ------------------ 1168| 21| { 1169| 21| bINCHI_LIB_Flag |= COMP_PREP_0_MAIN; ------------------ | | 27| 21|#define COMP_PREP_0_MAIN 0x0004 ------------------ 1170| 21| } 1171| 70.4k| bShowStructure = (bStructurePreprocessed && ------------------ | Branch (1171:31): [True: 783, False: 69.6k] ------------------ 1172| 783| prep_inp_data[iINChI].num_components > 1); ------------------ | Branch (1172:17): [True: 21, False: 762] ------------------ 1173| 70.4k| break; 1174| | 1175| 0| case INCHI_REC: ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1175:9): [True: 0, False: 70.4k] ------------------ 1176| | /*------------ Reconnected structure ------------------------------*/ 1177| 0| bAlsoOutputReconnected = 1178| 0| (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 975| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (1178:17): [True: 0, False: 0] ------------------ 1179| 0| (ip->bTautFlags & TG_FLAG_RECONNECT_COORD); ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1179:17): [True: 0, False: 0] ------------------ 1180| | 1181| 0| if ( !bAlsoOutputReconnected ) ------------------ | Branch (1181:18): [True: 0, False: 0] ------------------ 1182| 0| { 1183| 0| break; 1184| 0| } 1185| | 1186| 0| bStructurePreprocessed = 0 != (sd->bTautFlagsDone[iINChI] & ( 1187| 0| TG_FLAG_MOVE_HPLUS2NEUTR_DONE | ------------------ | | 962| 0|#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */ ------------------ 1188| 0| TG_FLAG_DISCONNECT_SALTS_DONE | ------------------ | | 964| 0|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 1189| 0| TG_FLAG_MOVE_POS_CHARGES_DONE | ------------------ | | 966| 0|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 1190| 0| TG_FLAG_FIX_ODD_THINGS_DONE)); ------------------ | | 978| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 1191| 0| bINCHI_LIB_Flag = 0; 1192| | /* Preprocessed/Reconnected -> Reconnected, component #0, Preprocessed */ 1193| 0| if ( prep_inp_data[iINChI].num_components > 1 && bStructurePreprocessed ) ------------------ | Branch (1193:18): [True: 0, False: 0] | Branch (1193:62): [True: 0, False: 0] ------------------ 1194| 0| { 1195| 0| bINCHI_LIB_Flag |= COMP_PREP_0_RECN; ------------------ | | 28| 0|#define COMP_PREP_0_RECN 0x0008 ------------------ 1196| 0| } 1197| 0| bShowStructure = (bStructurePreprocessed && ------------------ | Branch (1197:31): [True: 0, False: 0] ------------------ 1198| 0| prep_inp_data[iINChI].num_components > 1); ------------------ | Branch (1198:17): [True: 0, False: 0] ------------------ 1199| 0| break; 1200| | 1201| 0| default: ------------------ | Branch (1201:9): [True: 0, False: 70.4k] ------------------ 1202| 0| bShowStructure = 0; 1203| 70.4k| } 1204| | 1205| | 1206| 70.4k| if ( ip->bDisplay && prep_inp_data[iINChI].num_inp_atoms > 0 ) ------------------ | Branch (1206:14): [True: 0, False: 70.4k] | Branch (1206:30): [True: 0, False: 0] ------------------ 1207| 0| { 1208| 0| if ( DisplayTheWholeStructure(pCG, ic, sd, ip, szTitle, ------------------ | Branch (1208:18): [True: 0, False: 0] ------------------ 1209| 0| inp_file, log_file, 1210| 0| prep_inp_data + iINChI, 1211| 0| num_inp, 1212| 0| iINChI, 1213| 0| bShowStructure, 1214| 0| bINCHI_LIB_Flag) ) 1215| 0| { 1216| 0| inchi_free(all_inp_norm_data); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1217| 0| goto exit_function; 1218| 0| } 1219| 0| } 1220| 70.4k| } /* #endif */ /* } ifndef COMPILE_ANSI_ONLY */ 1221| | 1222| | 1223| | /* allocate pINChI[iINChI] and pINChI_Aux2[iINChI] -- arrays of pointers to INChI and INChI_Aux */ 1224| | /* assign values to sd->num_components[] */ 1225| | 1226| | /* djb-rwth: MYREALLOC2 has been replaced and the whole block rewritten to address memory leaks and reading from freed memory locations */ 1227| 70.4k| do { 1228| 70.4k| if ( (sd->num_components[iINChI]) <= ((long long)cur_prep_inp_data->num_components) ) { ------------------ | Branch (1228:14): [True: 70.4k, False: 0] ------------------ 1229| 70.4k| PINChI2* newPTR1 = (PINChI2*)inchi_calloc(((long long)cur_prep_inp_data->num_components) + 1, sizeof(PINChI2)); ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 1230| 70.4k| PINChI_Aux2* newPTR2 = (PINChI_Aux2*)inchi_calloc(((long long)cur_prep_inp_data->num_components) + 1, sizeof(PINChI_Aux2)); ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 1231| 70.4k| if ( newPTR1 && newPTR2 ) { ------------------ | Branch (1231:18): [True: 70.4k, False: 0] | Branch (1231:29): [True: 70.4k, False: 0] ------------------ 1232| 70.4k| if ( (pINChI2[iINChI]) && (sd->num_components[iINChI]) > 0 ) ------------------ | Branch (1232:22): [True: 0, False: 70.4k] | Branch (1232:43): [True: 0, False: 0] ------------------ 1233| 0| memcpy(newPTR1, pINChI2[iINChI], (sd->num_components[iINChI]) * sizeof(PINChI2)); 1234| 70.4k| if ( (pINChI_Aux2[iINChI]) && (sd->num_components[iINChI]) > 0 ) ------------------ | Branch (1234:22): [True: 0, False: 70.4k] | Branch (1234:47): [True: 0, False: 0] ------------------ 1235| 0| memcpy(newPTR2, pINChI_Aux2[iINChI], (sd->num_components[iINChI]) * sizeof(PINChI_Aux2)); 1236| 70.4k| if ( pINChI2[iINChI] ) ------------------ | Branch (1236:22): [True: 0, False: 70.4k] ------------------ 1237| 0| inchi_free(pINChI2[iINChI]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1238| 70.4k| if ( pINChI_Aux2[iINChI] ) ------------------ | Branch (1238:22): [True: 0, False: 70.4k] ------------------ 1239| 0| inchi_free(pINChI_Aux2[iINChI]); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1240| 70.4k| pINChI2[iINChI] = newPTR1; 1241| 70.4k| pINChI_Aux2[iINChI] = newPTR2; 1242| 70.4k| sd->num_components[iINChI] = cur_prep_inp_data->num_components; 1243| 70.4k| k = 0; 1244| 70.4k| } 1245| 0| else { 1246| 0| inchi_free(newPTR1); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1247| 0| inchi_free(newPTR2); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1248| 0| k = 1; 1249| 0| } 1250| 70.4k| } 1251| 0| else { k = 0; } 1252| 70.4k| } while ( 0 ); ------------------ | Branch (1252:15): [Folded, False: 70.4k] ------------------ 1253| | 1254| 70.4k| if ( k ) ------------------ | Branch (1254:10): [True: 0, False: 70.4k] ------------------ 1255| 0| { 1256| 0| AddErrorMessage(sd->pStrErrStruct, "Cannot allocate output data. Terminating"); 1257| 0| sd->nStructReadError = 99; 1258| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 1259| 0| inchi_free(all_inp_norm_data); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1260| 0| goto exit_function; 1261| 0| } 1262| | 1263| 70.4k| pINChI = pINChI2[iINChI]; 1264| 70.4k| pINChI_Aux = pINChI_Aux2[iINChI]; 1265| | 1266| | /**************************************************************************/ 1267| | /* */ 1268| | /* */ 1269| | /* M A I N C Y C L E: P R O C E S S C O M P O N E N T S */ 1270| | /* */ 1271| | /* */ 1272| | /* O N E B Y O N E */ 1273| | /* */ 1274| | /* */ 1275| | /**************************************************************************/ 1276| | 1277| 70.4k| for ( i = 0, nRet = 0; 1278| 176k| !sd->bUserQuitComponent && i < cur_prep_inp_data->num_components; ------------------ | Branch (1278:9): [True: 176k, False: 0] | Branch (1278:36): [True: 106k, False: 70.4k] ------------------ 1279| 106k| i++ ) 1280| 106k| { 1281| 106k| if ( ip->msec_MaxTime ) ------------------ | Branch (1281:14): [True: 0, False: 106k] ------------------ 1282| 0| { 1283| 0| InchiTimeGet(&ulTStart); 1284| 0| } 1285| | 1286| 106k|#ifndef TARGET_LIB_FOR_WINCHI /* { */ 1287| 106k|#if ( bREUSE_INCHI == 1 ) 1288| | 1289| 106k| if ( (iINChI == INCHI_REC && ------------------ | | 571| 212k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1289:15): [True: 0, False: 106k] ------------------ 1290| | /*( !ip->bDisplay && 1291| | !ip->bDisplayCompositeResults && */ 1292| 0| !(ip->bCompareComponents & CMP_COMPONENTS)) || ------------------ | | 54| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ | Branch (1292:13): [True: 0, False: 0] ------------------ 1293| 106k| sd->bUserQuitComponentDisplay ) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1293:13): [True: 0, False: 106k] ------------------ 1294| 0| { 1295| | /* Reconnected structure (06-20-2005: added "&& !ip->bDisplayCompositeResults" to display composite structure) */ 1296| 0| int m = iINChI - 1; 1297| | 1298| | /* Find whether we have already calculated this INChI in basic (disconnected) layer */ 1299| 0| for ( j = n = 0; j < prep_inp_data[m].num_components; j++ ) ------------------ | Branch (1299:30): [True: 0, False: 0] ------------------ 1300| 0| { 1301| 0| if ( i + 1 == prep_inp_data[m].nOldCompNumber[j] && ------------------ | Branch (1301:22): [True: 0, False: 0] ------------------ 1302| 0| (pINChI2[m][j][TAUT_NON] || pINChI2[m][j][TAUT_YES]) ) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ (pINChI2[m][j][TAUT_NON] || pINChI2[m][j][TAUT_YES]) ) ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1302:22): [True: 0, False: 0] | Branch (1302:49): [True: 0, False: 0] ------------------ 1303| 0| { 1304| | /* Yes, we have already done this */ 1305| 0| if ( !n++ ) ------------------ | Branch (1305:26): [True: 0, False: 0] ------------------ 1306| 0| { 1307| 0| memcpy(pINChI + i, pINChI2[m] + j, sizeof(pINChI[0])); 1308| 0| memcpy(pINChI_Aux + i, pINChI_Aux2[m] + j, sizeof(pINChI_Aux[0])); 1309| 0| for ( k = 0; k < TAUT_NUM; k++ ) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1309:38): [True: 0, False: 0] ------------------ 1310| 0| { 1311| 0| if ( pINChI[i][k] ) ------------------ | Branch (1311:34): [True: 0, False: 0] ------------------ 1312| 0| { 1313| 0| pINChI[i][k]->nRefCount++; 1314| 0| if ( pINChI[i][k]->nNumberOfAtoms > 0 ) ------------------ | Branch (1314:38): [True: 0, False: 0] ------------------ 1315| 0| { 1316| 0| switch ( k ) ------------------ | Branch (1316:46): [True: 0, False: 0] ------------------ 1317| 0| { 1318| 0| case TAUT_NON: ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1318:37): [True: 0, False: 0] ------------------ 1319| 0| sd->num_non_taut[iINChI]++; 1320| 0| break; 1321| 0| case TAUT_YES: ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1321:37): [True: 0, False: 0] ------------------ 1322| 0| if ( pINChI[i][k]->lenTautomer > 0 ) ------------------ | Branch (1322:46): [True: 0, False: 0] ------------------ 1323| 0| { 1324| 0| sd->num_taut[iINChI]++; 1325| 0| } 1326| 0| else 1327| 0| if ( !pINChI[i][TAUT_NON] || ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1327:50): [True: 0, False: 0] ------------------ 1328| 0| !pINChI[i][TAUT_NON]->nNumberOfAtoms ) ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1328:49): [True: 0, False: 0] ------------------ 1329| 0| { 1330| 0| sd->num_non_taut[iINChI]++; 1331| 0| } 1332| 0| break; 1333| 0| } 1334| 0| } 1335| 0| } 1336| 0| if ( pINChI_Aux[i][k] ) ------------------ | Branch (1336:34): [True: 0, False: 0] ------------------ 1337| 0| { 1338| 0| pINChI_Aux[i][k]->nRefCount++; 1339| 0| } 1340| 0| } 1341| 0| } 1342| 0| } 1343| 0| } 1344| | 1345| 0| if ( n == 1 ) ------------------ | Branch (1345:18): [True: 0, False: 0] ------------------ 1346| 0| { 1347| 0| continue; 1348| 0| } 1349| 0| if ( n > 1 ) ------------------ | Branch (1349:18): [True: 0, False: 0] ------------------ 1350| 0| { 1351| | /* ith component is equivalent to more than one another component */ 1352| 0| AddErrorMessage(sd->pStrErrStruct, "Cannot distinguish components"); 1353| 0| sd->nStructReadError = 99; 1354| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 1355| 0| inchi_free(all_inp_norm_data); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 1356| 0| goto exit_function; 1357| 0| } 1358| 0| } 1359| | 1360| 106k|#endif 1361| 106k|#endif /* } TARGET_LIB_FOR_WINCHI */ 1362| | 1363| | /*****************************************************/ 1364| | /* a) Allocate memory and extract current component */ 1365| | /*****************************************************/ 1366| | 1367| 106k| nRet = GetOneComponent(ic, sd, ip, 1368| 106k| log_file, out_file, 1369| 106k| inp_cur_data, cur_prep_inp_data, 1370| 106k| i, num_inp); 1371| | 1372| 106k| if ( ip->msec_MaxTime ) ------------------ | Branch (1372:14): [True: 0, False: 106k] ------------------ 1373| 0| { 1374| 0| ip->msec_LeftTime -= InchiTimeElapsed(ic, &ulTStart); 1375| 0| } 1376| | 1377| 106k| switch ( nRet ) ------------------ | Branch (1377:18): [True: 0, False: 106k] ------------------ 1378| 106k| { 1379| 0| case _IS_ERROR: ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1379:9): [True: 0, False: 106k] ------------------ 1380| 0| case _IS_FATAL: ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ | Branch (1380:9): [True: 0, False: 106k] ------------------ 1381| 0| goto exit_cycle; 1382| 106k| } 1383| | 1384| |#if !defined(TARGET_API_LIB) && !defined(COMPILE_ANSI_ONLY) 1385| | /* console request: Display the component? */ 1386| | if ( ip->bDisplay && inp_file->f != stdin ) 1387| | { 1388| | if ( user_quit(ic, "Enter=Display Component, Esc=Stop ?", ip->ulDisplTime) ) 1389| | { 1390| | sd->bUserQuitComponent = 1; 1391| | break; 1392| | } 1393| | } 1394| |#endif 1395| | 1396| | /*#ifndef COMPILE_ANSI_ONLY 1397| | { */ 1398| | 1399| | /* b) Display the extracted original component structure */ 1400| 106k| if ( ip->bDisplay && inp_cur_data->at && !sd->bUserQuitComponentDisplay ) ------------------ | Branch (1400:14): [True: 0, False: 106k] | Branch (1400:30): [True: 0, False: 0] | Branch (1400:50): [True: 0, False: 0] ------------------ 1401| 0| { 1402| 0| if ( cur_prep_inp_data->num_components == 1 ) ------------------ | Branch (1402:18): [True: 0, False: 0] ------------------ 1403| 0| { 1404| 0| sprintf(szTitle, "%sInput Structure #%ld.%s%s%s%s%s", 1405| 0| bStructurePreprocessed ? "Preprocessed " : "", ------------------ | Branch (1405:21): [True: 0, False: 0] ------------------ 1406| 0| num_inp, SDF_LBL_VAL(ip->pSdfLabel, ip->pSdfValue), iINChI ? " (Reconnected)" : ""); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ | Branch (1406:73): [True: 0, False: 0] ------------------ 1407| 0| } 1408| 0| else 1409| 0| { 1410| 0| sprintf(szTitle, "Component #%d of %d, Input Structure #%ld.%s%s%s%s%s", 1411| 0| i + 1, cur_prep_inp_data->num_components, 1412| 0| num_inp, SDF_LBL_VAL(ip->pSdfLabel, ip->pSdfValue), iINChI ? " (Reconnected)" : ""); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ | Branch (1412:73): [True: 0, False: 0] ------------------ 1413| 0| } 1414| | 1415| |#if defined (TARGET_EXE_STANDALONE) && defined(_WIN32) 1416| | err_display = DisplayStructure(pCG, 1417| | inp_cur_data->at, 1418| | inp_cur_data->num_at, 1419| | NULL, /* OAD_Polymer *polymer, */ 1420| | 0, 1421| | 1, 1422| | 0, 1423| | NULL, 1424| | 1 /*isotopic*/, 1425| | 0 /*taut*/, 1426| | NULL, 1427| | NULL, 1428| | ip->bAbcNumbers, 1429| | &ip->dp, 1430| | ip->nMode, 1431| | szTitle); 1432| | 1433| | sd->bUserQuitComponentDisplay = (err_display == ESC_KEY); 1434| | 1435| | if ( !err_display ) 1436| | { 1437| | inchi_fprintf(stderr, "Cannot display the structure\n"); 1438| | } 1439| |#endif 1440| |#ifdef TARGET_LIB_FOR_WINCHI 1441| | if ( DRAWDATA && DRAWDATA_EXISTS ) 1442| | { 1443| | struct DrawData vDrawData; 1444| | int nType = COMPONENT_ORIGINAL; 1445| | vDrawData.pWindowData = CreateWinData_(pCG, 1446| | inp_cur_data->at, 1447| | inp_cur_data->num_at, 1448| | 0, 1449| | 1 /* bAdd_DT_to_num_H */, 1450| | 0, 1451| | NULL, 1452| | 1 /* display isotopic if present */, 1453| | 0, 1454| | NULL, 1455| | NULL, 1456| | ip->bAbcNumbers, 1457| | &ip->dp, 1458| | ip->nMode); 1459| | if ( vDrawData.pWindowData != NULL ) 1460| | { 1461| | if ( DRAWDATA_EXISTS(i + 1, nType, iINChI) ) 1462| | { 1463| | /* i = component number */ 1464| | nType = COMPONENT_ORIGINAL_PREPROCESSED; 1465| | } 1466| | vDrawData.nComponent = i + 1; 1467| | vDrawData.nType = nType; 1468| | vDrawData.bReconnected = iINChI; /* 0=>main; 1=>reconnected */ 1469| | vDrawData.szTitle = inchi__strdup(szTitle); 1470| | vDrawData.pWindowData->szTitle = inchi__strdup(szTitle); 1471| | DRAWDATA(&vDrawData); 1472| | } 1473| | } 1474| |#endif 1475| 0| } 1476| | /*#endif */ /* } COMPILE_ANSI_ONLY */ 1477| | 1478| | 1479| | /*******************************************************************************/ 1480| | /* */ 1481| | /* N O R M A L I Z A T I O N a n d C A N O N I C A L I Z A T I O N */ 1482| | /* */ 1483| | /* (both tautomeric and non-tautomeric if requested) */ 1484| | /* */ 1485| | /*******************************************************************************/ 1486| | /* c) Create the component's INChI ( copies ip->bTautFlags into sd->bTautFlags)*/ 1487| | /*******************************************************************************/ 1488| | 1489| 106k| nRet = CreateOneComponentINChI(pCG, ic, sd, ip, 1490| 106k| inp_cur_data, orig_inp_data, 1491| 106k| pINChI/*2[iINChI]*/, 1492| 106k| pINChI_Aux/*2[iINChI]*/, 1493| 106k| iINChI, i, num_inp, 1494| 106k| inp_norm_data, pncFlags, log_file); 1495| | 1496| | 1497| | 1498| | /* d) Display one component structure and/or INChI results only if there was no error */ 1499| | 1500| | /* #ifndef COMPILE_ANSI_ONLY */ /* { */ 1501| 106k| if ( !nRet ) ------------------ | Branch (1501:14): [True: 106k, False: 4] ------------------ 1502| 106k| { 1503| | /* output one component INChI to the stdout if requested */ 1504| | /* 1505| | if ( ip->bDisplayEachComponentINChI ) { 1506| | int cur_num_non_taut = (pINChI[i][TAUT_NON] && pINChI[i][TAUT_NON]->nNumberOfAtoms>0); 1507| | int cur_num_taut = (pINChI[i][TAUT_YES] && pINChI[i][TAUT_YES]->nNumberOfAtoms>0); 1508| | if ( ip->bDisplayEachComponentINChI && cur_num_non_taut + cur_num_taut ) { 1509| | SortAndPrintINChI( pCG, stdout, pStr, nStrLen, NULL, 1510| | ip, 1, cur_num_non_taut, cur_num_taut, 1511| | num_inp, pINChI+i, pINChI_Aux+i, 1512| | save_opt_bits); 1513| | } 1514| | } 1515| | */ 1516| | /************************************************************************** 1517| | * display from one up to 4 structure pictures-results for each component * 1518| | * Enable buttons: * 1519| | * BN (non-tautomeric non-isotopic): inp_norm_data[0]->bExists * 1520| | * TN (tautomeric non-isotopic): inp_norm_data[1]->bExists * 1521| | * BI (non-tautomeric isotopic): inp_norm_data[0]->bExists && * 1522| | * inp_norm_data[0]->bHasIsotopicLayer * 1523| | * TI (tautomeric isotopic): inp_norm_data[1]->bExists && * 1524| | * inp_norm_data[1]->bHasIsotopicLayer * 1525| | **************************************************************************/ 1526| | 1527| 106k| int bIsotopic, bTautomeric, bDisplayTaut, bHasIsotopicLayer, bFixedBondsTaut, m_max, m, nNumDisplayedFixedBondTaut = 0; /* djb-rwth: ignoring LLVM warning: variable used */ 1528| | 1529| 106k| for ( j = 0; 1530| 106k| ip->bDisplay && !sd->bUserQuitComponentDisplay && j < TAUT_NUM; ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1530:17): [True: 0, False: 106k] | Branch (1530:33): [True: 0, False: 0] | Branch (1530:67): [True: 0, False: 0] ------------------ 1531| 106k| j++ ) 1532| 0| { 1533| 0| if ( inp_norm_data[j]->bExists && !inp_norm_data[j]->bDeleted ) ------------------ | Branch (1533:22): [True: 0, False: 0] | Branch (1533:51): [True: 0, False: 0] ------------------ 1534| 0| { 1535| 0| bTautomeric = (pINChI[i][j]->lenTautomer > 0); 1536| | /* same as (inp_norm_data[j]->bTautomeric > 0) */ 1537| | 1538| | /* If requested tautomeric and no tautmerism found then do not say mobile or fixed H. 2004-10-27 */ 1539| 0| bDisplayTaut = (!(ip->nMode & REQ_MODE_BASIC) && !bTautomeric) ? -1 : bTautomeric; ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (1539:37): [True: 0, False: 0] | Branch (1539:70): [True: 0, False: 0] ------------------ 1540| 0| bHasIsotopicLayer = (inp_norm_data[j]->bHasIsotopicLayer > 0); 1541| | 1542| 0| for ( k = 0; k <= bHasIsotopicLayer; k++ ) ------------------ | Branch (1542:34): [True: 0, False: 0] ------------------ 1543| 0| { 1544| 0| bIsotopic = (k > 0); 1545| 0| m_max = inp_norm_data[j]->at_fixed_bonds && inp_norm_data[j]->bTautPreprocessed ? 1 : 0; ------------------ | Branch (1545:33): [True: 0, False: 0] | Branch (1545:69): [True: 0, False: 0] ------------------ 1546| 0| for ( m = m_max; 0 <= m; m-- ) ------------------ | Branch (1546:42): [True: 0, False: 0] ------------------ 1547| 0| { 1548| 0| bFixedBondsTaut = (m > 0); 1549| 0| nNumDisplayedFixedBondTaut += bFixedBondsTaut; 1550| | /* display only one time */ 1551| | 1552| | /* Added number of components, added another format for a single component case - DCh */ 1553| 0| if ( cur_prep_inp_data->num_components > 1 ) ------------------ | Branch (1553:34): [True: 0, False: 0] ------------------ 1554| 0| { 1555| 0| sprintf(szTitle, "%s Component #%d of %d, Structure #%ld%s%s.%s%s%s%s%s", 1556| 0| bFixedBondsTaut ? "Preprocessed" : "Result for", ------------------ | Branch (1556:37): [True: 0, False: 0] ------------------ 1557| 0| i + 1, cur_prep_inp_data->num_components, num_inp, 1558| 0| bDisplayTaut == 1 ? ", mobile H" : bDisplayTaut == 0 ? ", fixed H" : "", ------------------ | Branch (1558:37): [True: 0, False: 0] | Branch (1558:72): [True: 0, False: 0] ------------------ 1559| 0| bIsotopic ? ", isotopic" : "", ------------------ | Branch (1559:37): [True: 0, False: 0] ------------------ 1560| 0| SDF_LBL_VAL(ip->pSdfLabel, ip->pSdfValue), iINChI ? " (Reconnected)" : ""); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ | Branch (1560:80): [True: 0, False: 0] ------------------ 1561| 0| } 1562| 0| else 1563| 0| { 1564| 0| sprintf(szTitle, "%s Structure #%ld%s%s.%s%s%s%s%s", 1565| 0| bFixedBondsTaut ? "Preprocessed" : "Result for", ------------------ | Branch (1565:37): [True: 0, False: 0] ------------------ 1566| 0| num_inp, 1567| 0| bDisplayTaut == 1 ? ", mobile H" : bDisplayTaut == 0 ? ", fixed H" : "", ------------------ | Branch (1567:37): [True: 0, False: 0] | Branch (1567:72): [True: 0, False: 0] ------------------ 1568| 0| bIsotopic ? ", isotopic" : "", ------------------ | Branch (1568:37): [True: 0, False: 0] ------------------ 1569| 0| SDF_LBL_VAL(ip->pSdfLabel, ip->pSdfValue), iINChI ? " (Reconnected)" : ""); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ | Branch (1569:80): [True: 0, False: 0] ------------------ 1570| 0| } 1571| | 1572| |#if defined (TARGET_EXE_STANDALONE) && defined(_WIN32) 1573| | if ( bFixedBondsTaut && nNumDisplayedFixedBondTaut != 1 ) 1574| | { 1575| | continue; 1576| | } 1577| | if ( ip->bDisplay ) 1578| | { 1579| | if ( bFixedBondsTaut ) 1580| | { 1581| | err_display = DisplayStructure(pCG, 1582| | inp_norm_data[j]->at_fixed_bonds, 1583| | inp_norm_data[j]->num_at, 1584| | NULL, /* OAD_Polymer *polymer, */ 1585| | inp_norm_data[j]->num_removed_H, 1586| | 0 /*bAdd_DT_to_num_H*/, 1587| | inp_norm_data[j]->nNumRemovedProtons, 1588| | inp_norm_data[j]->nNumRemovedProtonsIsotopic, 1589| | bHasIsotopicLayer, 1590| | j, 1591| | NULL, 1592| | NULL, 1593| | ip->bAbcNumbers, 1594| | &ip->dp, 1595| | ip->nMode, 1596| | szTitle); 1597| | } 1598| | else 1599| | { 1600| | err_display = DisplayStructure(pCG, 1601| | inp_norm_data[j]->at, 1602| | inp_norm_data[j]->num_at, 1603| | NULL, /* OAD_Polymer *polymer, */ 1604| | 0, 1605| | 0 /*bAdd_DT_to_num_H*/, 1606| | 0, 1607| | NULL, 1608| | k, 1609| | j, 1610| | pINChI[i], 1611| | pINChI_Aux[i], 1612| | ip->bAbcNumbers, 1613| | &ip->dp, 1614| | ip->nMode, szTitle); 1615| | } 1616| | if ( (sd->bUserQuitComponentDisplay = (err_display == ESC_KEY)) ) /* djb-rwth: addressing LLVM warning */ 1617| | { 1618| | break; 1619| | } 1620| | } 1621| |#endif 1622| |#ifdef TARGET_LIB_FOR_WINCHI 1623| | 1624| | if ( DRAWDATA && !bFixedBondsTaut ) 1625| | { 1626| | struct DrawData vDrawData; 1627| | vDrawData.pWindowData = 1628| | CreateWinData_(pCG, 1629| | inp_norm_data[j]->at, 1630| | inp_norm_data[j]->num_at, 1631| | 0, 1632| | 0 /* bAdd_DT_to_num_H */, 1633| | 0, 1634| | NULL, 1635| | k, 1636| | j, 1637| | pINChI[i], 1638| | pINChI_Aux[i], 1639| | ip->bAbcNumbers, 1640| | &ip->dp, 1641| | ip->nMode); 1642| | 1643| | if ( vDrawData.pWindowData != NULL ) 1644| | { 1645| | int nType; 1646| | vDrawData.nComponent = i + 1; 1647| | if ( bTautomeric == 0 ) 1648| | nType = (bIsotopic == 0) ? COMPONENT_BN 1649| | : COMPONENT_BI; 1650| | else 1651| | nType = (bIsotopic == 0) ? COMPONENT_TN 1652| | : COMPONENT_TI; 1653| | vDrawData.nType = nType; 1654| | 1655| | vDrawData.bReconnected = iINChI; /* 0=>main; 1=>reconnected */ 1656| | vDrawData.szTitle = inchi__strdup(szTitle); 1657| | vDrawData.pWindowData->szTitle = inchi__strdup(szTitle); 1658| | DRAWDATA(&vDrawData); 1659| | } 1660| | } 1661| | else if ( DRAWDATA && bFixedBondsTaut ) 1662| | { 1663| | struct DrawData vDrawData; 1664| | if ( (ip->bCompareComponents & CMP_COMPONENTS) && 1665| | !(ip->bCompareComponents & CMP_COMPONENTS_NONTAUT) && 1666| | !bIsotopic == !inp_norm_data[j]->bHasIsotopicLayer ) 1667| | { 1668| | 1669| | vDrawData.pWindowData = 1670| | CreateWinData_(pCG, 1671| | inp_norm_data[j]->at_fixed_bonds, 1672| | inp_norm_data[j]->num_at, 1673| | inp_norm_data[j]->num_removed_H, 1674| | 0 /* bAdd_DT_to_num_H */, 1675| | inp_norm_data[j]->nNumRemovedProtons, 1676| | inp_norm_data[j]->nNumRemovedProtonsIsotopic, 1677| | k, 1678| | j, 1679| | NULL, 1680| | NULL, 1681| | ip->bAbcNumbers, 1682| | &ip->dp, 1683| | ip->nMode); 1684| | } 1685| | else 1686| | { 1687| | continue; 1688| | } 1689| | if ( vDrawData.pWindowData != NULL ) 1690| | { 1691| | vDrawData.nComponent = i + 1; 1692| | vDrawData.nType = COMPONENT_ORIGINAL_PREPROCESSED; 1693| | vDrawData.bReconnected = iINChI; /* 0=>main; 1=>reconnected */ 1694| | vDrawData.szTitle = inchi__strdup(szTitle); 1695| | vDrawData.pWindowData->szTitle = inchi__strdup(szTitle); 1696| | DRAWDATA(&vDrawData); 1697| | } 1698| | } 1699| |#endif 1700| 0| } 1701| 0| } 1702| 0| } 1703| 0| } 1704| | 1705| | /* Save normalized components for composite display */ 1706| 106k| if ( /*ip->bDisplayCompositeResults && */ 1707| 106k| all_inp_norm_data ------------------ | Branch (1707:17): [True: 36.4k, False: 69.6k] ------------------ 1708| 106k| ) 1709| 36.4k| { 1710| 109k| for ( j = 0; j < TAUT_NUM; j++ ) ------------------ | | 573| 109k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1710:30): [True: 72.8k, False: 36.4k] ------------------ 1711| 72.8k| { 1712| 72.8k| if ( inp_norm_data[j]->bExists ) ------------------ | Branch (1712:26): [True: 71.4k, False: 1.40k] ------------------ 1713| 71.4k| { 1714| 71.4k| all_inp_norm_data[i][j] = *inp_norm_data[j]; 1715| 71.4k| memset(inp_norm_data[j], 0, sizeof(*inp_norm_data[0])); /* djb-rwth: memset_s C11/Annex K variant? */ 1716| 71.4k| } 1717| 72.8k| } 1718| 36.4k| } 1719| 106k| } 1720| | 1721| | /* #endif */ /* } COMPILE_ANSI_ONLY */ 1722| | 1723| | 1724| 106k| if ( nRet ) ------------------ | Branch (1724:14): [True: 4, False: 106k] ------------------ 1725| 4| { 1726| 4| nRet = TreatErrorsInCreateOneComponentINChI(sd, ip, 1727| 4| cur_prep_inp_data, 1728| 4| i, num_inp, inp_file, 1729| 4| log_file, out_file, prb_file); 1730| 4| break; 1731| 4| } 1732| 106k| } 1733| | /**************************************************************************/ 1734| | /* */ 1735| | /* */ 1736| | /* E N D O F T H E M A I N C Y C L E P R O C E S S I N G */ 1737| | /* */ 1738| | /* C O M P O N E N T S O N E B Y O N E */ 1739| | /* */ 1740| | /* */ 1741| | /**************************************************************************/ 1742| | 1743| 70.4k|exit_cycle: 1744| 70.4k| switch ( nRet ) 1745| 70.4k| { 1746| 2| case _IS_FATAL: ------------------ | | 13| 2|#define _IS_FATAL 3 ------------------ | Branch (1746:5): [True: 2, False: 70.4k] ------------------ 1747| 4| case _IS_ERROR: ------------------ | | 12| 4|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1747:5): [True: 2, False: 70.4k] ------------------ 1748| 4| break; 1749| 70.4k| default: ------------------ | Branch (1749:5): [True: 70.4k, False: 4] ------------------ 1750| | 1751| | /* #ifndef COMPILE_ANSI_ONLY *//* { */ 1752| | /* composite results picture(s) */ 1753| 70.4k| if ( all_inp_norm_data ) ------------------ | Branch (1753:14): [True: 811, False: 69.6k] ------------------ 1754| 811| { 1755| 811| CreateCompositeNormAtom(composite_norm_data, 1756| 811| all_inp_norm_data, 1757| 811| prep_inp_data[iINChI].num_components); 1758| | /* 1759| | for ( i = 0; i < prep_inp_data[iINChI].num_components; i ++ ) { 1760| | for ( k = 0; k < TAUT_NUM; k ++ ) { 1761| | FreeInpAtomData( &all_inp_norm_data[i][k] ); 1762| | } 1763| | } 1764| | inchi_free( all_inp_norm_data ); 1765| | all_inp_norm_data = NULL; 1766| | */ 1767| 811| } 1768| | /* #endif */ /* } COMPILE_ANSI_ONLY */ 1769| | 1770| 70.4k| break; 1771| 70.4k| } 1772| | 1773| | /*#ifndef COMPILE_ANSI_ONLY*/ /* { */ 1774| | 1775| | /* avoid memory leaks in case of error */ 1776| 70.4k| if ( all_inp_norm_data ) ------------------ | Branch (1776:10): [True: 811, False: 69.6k] ------------------ 1777| 811| { 1778| 37.2k| for ( i = 0; i < prep_inp_data[iINChI].num_components; i++ ) ------------------ | Branch (1778:22): [True: 36.4k, False: 811] ------------------ 1779| 36.4k| { 1780| 109k| for ( k = 0; k < TAUT_NUM; k++ ) ------------------ | | 573| 109k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1780:26): [True: 72.8k, False: 36.4k] ------------------ 1781| 72.8k| { 1782| 72.8k| FreeInpAtomData(&all_inp_norm_data[i][k]); 1783| 72.8k| } 1784| 36.4k| } 1785| 811| inchi_free(all_inp_norm_data); ------------------ | | 1152| 811|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 811, False: 0] | | | Branch (1152:50): [Folded, False: 811] | | ------------------ ------------------ 1786| 811| all_inp_norm_data = NULL; 1787| 811| } 1788| | /*#endif */ /* } COMPILE_ANSI_ONLY */ 1789| | 1790| 70.4k| FreeInpAtomData(inp_cur_data); 1791| 211k| for ( i = 0; i < TAUT_NUM; i++ ) ------------------ | | 573| 211k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1791:18): [True: 140k, False: 70.4k] ------------------ 1792| 140k| { 1793| 140k| FreeInpAtomData(inp_norm_data[i]); 1794| 140k| } 1795| | 1796| | 1797| 70.4k|exit_function: 1798| | 1799| 70.4k| return nRet; 1800| 70.4k|} CreateOneComponentINChI: 1821| 106k|{ 1822| 106k| inchiTime ulTStart, ulTEnd, * pulTEnd = NULL; 1823| 106k| int k, num_at, ret = 0; 1824| 106k| int bOrigCoord; 1825| 106k| INCHI_MODE bTautFlags = ip->bTautFlags; 1826| 106k| INCHI_MODE bTautFlagsDone = (ip->bTautFlagsDone | sd->bTautFlagsDone[INCHI_BAS]); ------------------ | | 570| 106k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1827| 106k| INChI* cur_INChI[TAUT_NUM]; 1828| 106k| INChI_Aux* cur_INChI_Aux[TAUT_NUM]; 1829| 106k| long lElapsedTime; 1830| | 1831| 106k| int nAllocMode = 0; /* moved from below 2024-09-01 DT */ 1832| | 1833| |#ifdef GHI100_FIX 1834| |#if ((SPRINTF_FLAG != 1) && (SPRINTF_FLAG != 2)) 1835| | setlocale(LC_ALL, "en-US"); /* djb-rwth: setting all locales to "en-US" */ 1836| |#endif 1837| |#endif 1838| | 1839| 106k| InchiTimeGet( &ulTStart ); 1840| | 1841| 106k| bOrigCoord = 1842| 106k| !(ip->bINChIOutputOptions & (INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO)); ------------------ | | 129| 106k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ !(ip->bINChIOutputOptions & (INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO)); ------------------ | | 130| 106k|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1843| | 1844| 318k| for ( k = 0; k < TAUT_NUM; k++ ) ------------------ | | 573| 318k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1844:18): [True: 212k, False: 106k] ------------------ 1845| 212k| { 1846| 212k| cur_INChI[k] = NULL; 1847| 212k| cur_INChI_Aux[k] = NULL; 1848| 212k| } 1849| | 1850| | /* Allocate memory for non-tautomeric (k=0) and tautomeric (k=1) results */ 1851| 318k| for ( k = 0; k < TAUT_NUM; k++ ) ------------------ | | 573| 318k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1851:18): [True: 212k, False: 106k] ------------------ 1852| 212k| { 1853| | /* djb-rwth: introducing variables for correct nAllocMode expression */ 1854| 212k| int nAM1 = 0, nAM2 = 0; 1855| | 1856| 212k| if ( k == TAUT_YES ) ------------------ | | 575| 212k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1856:14): [True: 106k, False: 106k] ------------------ 1857| 106k| nAM1 = REQ_MODE_TAUT; ------------------ | | 16| 106k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1858| | 1859| 212k| if ( bTautFlagsDone & (TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE) ) ------------------ | | 981| 212k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ if ( bTautFlagsDone & (TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE) ) ------------------ | | 982| 212k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (1859:14): [True: 8.43k, False: 203k] ------------------ 1860| 8.43k| nAM2 = ip->nMode & REQ_MODE_ISO; ------------------ | | 17| 8.43k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1861| | 1862| 212k| nAllocMode = nAM1 | nAM2; /* djb-rwth: original sequence of bit-wise operations had to be rewritten */ 1863| | 1864| | 1865| 212k| if ( (k == TAUT_NON && (ip->nMode & REQ_MODE_BASIC)) || ------------------ | | 574| 424k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if ( (k == TAUT_NON && (ip->nMode & REQ_MODE_BASIC)) || ------------------ | | 15| 106k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (1865:15): [True: 106k, False: 106k] | Branch (1865:32): [True: 35.6k, False: 70.4k] ------------------ 1866| 176k| (k == TAUT_YES && (ip->nMode & REQ_MODE_TAUT)) ) /* djb-rwth: addressing LLVM warning */ ------------------ | | 575| 352k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ (k == TAUT_YES && (ip->nMode & REQ_MODE_TAUT)) ) /* djb-rwth: addressing LLVM warning */ ------------------ | | 16| 106k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (1866:14): [True: 106k, False: 70.4k] | Branch (1866:31): [True: 106k, False: 0] ------------------ 1867| 141k| { 1868| | /* alloc INChI and INChI_Aux */ 1869| 141k| cur_INChI[k] = Alloc_INChI(inp_cur_data->at, 1870| 141k| inp_cur_data->num_at, 1871| 141k| &inp_cur_data->num_bonds, 1872| 141k| &inp_cur_data->num_isotopic, 1873| 141k| nAllocMode); 1874| | 1875| 141k| cur_INChI_Aux[k] = Alloc_INChI_Aux(inp_cur_data->num_at, 1876| 141k| inp_cur_data->num_isotopic, 1877| 141k| nAllocMode, 1878| 141k| bOrigCoord); 1879| 141k| if ( cur_INChI_Aux[k] ) ------------------ | Branch (1879:18): [True: 141k, False: 0] ------------------ 1880| 141k| { 1881| 141k| cur_INChI_Aux[k]->bIsIsotopic = inp_cur_data->num_isotopic; 1882| 141k| } 1883| | /* alloc memory for the output structure: non-tautomeric and tautomeric (for displaying) */ 1884| | 1885| 141k| CreateInpAtomData(inp_norm_data[k], inp_cur_data->num_at, k); 1886| 141k| } 1887| 70.4k| else 1888| 70.4k| { 1889| 70.4k| FreeInpAtomData(inp_norm_data[k]); 1890| 70.4k| } 1891| 212k| } 1892| | 1893| 106k| lElapsedTime = InchiTimeElapsed(ic, &ulTStart); 1894| 106k| if ( ip->msec_MaxTime ) ------------------ | Branch (1894:10): [True: 0, False: 106k] ------------------ 1895| 0| { 1896| 0| ip->msec_LeftTime -= lElapsedTime; 1897| 0| } 1898| 106k| sd->ulStructTime += lElapsedTime; 1899| | 1900| | /*^^^#if ( !defined( TARGET_LIB_FOR_WINCHI ) && !defined( TARGET_API_LIB ) ) */ 1901| |#if ( !defined( TARGET_LIB_FOR_WINCHI ) && !defined( TARGET_API_LIB ) && !defined(TARGET_EXE_STANDALONE) ) 1902| |#endif 1903| | 1904| |/****************************************************** 1905| | * 1906| | * Get one component canonical numberings, etc. 1907| | * 1908| | ******************************************************/ 1909| | 1910| | /* Create_INChI() return value: 1911| | * num_at <= 0: error code 1912| | * num_at > 0: number of atoms (excluding terminal hydrogen atoms) 1913| | * inp_norm_data[0] => non-tautomeric, inp_norm_data[1] => tautomeric */ 1914| | 1915| 106k| InchiTimeGet(&ulTStart); 1916| | 1917| 106k| if ( ip->msec_MaxTime ) ------------------ | Branch (1917:10): [True: 0, False: 106k] ------------------ 1918| 0| { 1919| 0| ulTEnd = ulTStart; 1920| 0| pulTEnd = &ulTEnd; 1921| 0| if ( ip->msec_LeftTime > 0 ) ------------------ | Branch (1921:14): [True: 0, False: 0] ------------------ 1922| 0| { 1923| 0| InchiTimeAddMsec(ic, pulTEnd, ip->msec_LeftTime); 1924| 0| } 1925| 0| } 1926| | 1927| 106k| num_at = Create_INChI(pCG, ic, ip, 1928| 106k| cur_INChI, cur_INChI_Aux, 1929| 106k| orig_inp_data/* not used */, 1930| 106k| inp_cur_data->at, inp_norm_data, inp_cur_data->num_at, 1931| 106k| inp_cur_data->keep_explicit_HDT, 1932| 106k| ip->nMode, 1933| 106k| &bTautFlags, &bTautFlagsDone, 1934| 106k| pulTEnd, NULL, sd->pStrErrStruct); 1935| | 1936| 106k| SetConnectedComponentNumber(inp_cur_data->at, inp_cur_data->num_at, i + 1); 1937| | /* NB: normalization alters structure component number */ 1938| | 1939| 318k| for ( k = 0; k < TAUT_NUM; k++ ) ------------------ | | 573| 318k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1939:18): [True: 212k, False: 106k] ------------------ 1940| 212k| { 1941| 212k| if ( cur_INChI_Aux[k] && cur_INChI_Aux[k]->nNumberOfAtoms > 0 ) ------------------ | Branch (1941:14): [True: 141k, False: 70.4k] | Branch (1941:34): [True: 141k, False: 208] ------------------ 1942| 141k| { 1943| 141k| pncFlags->bNormalizationFlags[iINChI][k] |= 1944| 141k| cur_INChI_Aux[k]->bNormalizationFlags; 1945| 141k| pncFlags->bTautFlags[iINChI][k] |= 1946| 141k| cur_INChI_Aux[k]->bTautFlags; 1947| 141k| pncFlags->bTautFlagsDone[iINChI][k] |= 1948| 141k| cur_INChI_Aux[k]->bTautFlagsDone; 1949| 141k| pncFlags->nCanonFlags[iINChI][k] |= 1950| 141k| cur_INChI_Aux[k]->nCanonFlags; 1951| 141k| } 1952| 212k| } 1953| | 1954| | /* Detect errors */ 1955| 106k| if ( num_at < 0 ) ------------------ | Branch (1955:10): [True: 4, False: 106k] ------------------ 1956| 4| { 1957| 4| sd->nErrorCode = num_at; 1958| 4| } 1959| 106k| else if ( num_at == 0 ) ------------------ | Branch (1959:15): [True: 0, False: 106k] ------------------ 1960| 0| { 1961| 0| sd->nErrorCode = -1; 1962| 0| } 1963| 106k| else if ( cur_INChI[TAUT_NON] && cur_INChI[TAUT_NON]->nErrorCode ) ------------------ | | 574| 106k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ else if ( cur_INChI[TAUT_NON] && cur_INChI[TAUT_NON]->nErrorCode ) ------------------ | | 574| 35.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1963:15): [True: 35.6k, False: 70.4k] | Branch (1963:38): [True: 0, False: 35.6k] ------------------ 1964| 0| { /* non-tautomeric error */ 1965| 0| sd->nErrorCode = cur_INChI[TAUT_NON]->nErrorCode; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1966| 0| } 1967| 106k| else if ( cur_INChI[TAUT_YES] && cur_INChI[TAUT_YES]->nErrorCode ) ------------------ | | 575| 106k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ else if ( cur_INChI[TAUT_YES] && cur_INChI[TAUT_YES]->nErrorCode ) ------------------ | | 575| 106k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1967:15): [True: 106k, False: 0] | Branch (1967:38): [True: 0, False: 106k] ------------------ 1968| 0| { /* tautomeric error */ 1969| 0| sd->nErrorCode = cur_INChI[TAUT_YES]->nErrorCode; ------------------ | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1970| 0| } 1971| | 1972| | 1973| |#if ( bRELEASE_VERSION == 0 ) 1974| | if ( cur_INChI[TAUT_NON] ) sd->bExtract |= cur_INChI[TAUT_NON]->bExtract; 1975| | if ( cur_INChI[TAUT_YES] ) sd->bExtract |= cur_INChI[TAUT_YES]->bExtract; 1976| | if ( (TG_FLAG_TEST_TAUT3_SALTS_DONE & bTautFlagsDone) ) 1977| | { 1978| | sd->bExtract |= EXTR_TEST_TAUT3_SALTS_DONE; 1979| | } 1980| |#endif 1981| | 1982| | /* Detect and store stereo warnings */ 1983| 106k| if ( !sd->nErrorCode ) ------------------ | Branch (1983:10): [True: 106k, False: 4] ------------------ 1984| 106k| GetProcessingWarningsOneComponentInChI(cur_INChI, inp_norm_data, sd, ip->bNoWarnings); 1985| | 1986| 106k| lElapsedTime = InchiTimeElapsed(ic, &ulTStart); 1987| 106k| if ( ip->msec_MaxTime ) ------------------ | Branch (1987:10): [True: 0, False: 106k] ------------------ 1988| 0| { 1989| 0| ip->msec_LeftTime -= lElapsedTime; 1990| 0| } 1991| 106k| sd->ulStructTime += lElapsedTime; 1992| | 1993| |#if !defined(TARGET_API_LIB) && !defined(COMPILE_ANSI_ONLY) 1994| | /* Display the results */ 1995| | if ( ip->bDisplay ) 1996| | { 1997| | eat_keyboard_input(); 1998| | } 1999| |#endif 2000| | 2001| | /* a) No matter what happened save the allocated INChI pointers */ 2002| | /* save the INChI of the current component */ 2003| | 2004| 106k| InchiTimeGet(&ulTStart); 2005| 318k| for ( k = 0; k < TAUT_NUM; k++ ) ------------------ | | 573| 318k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2005:18): [True: 212k, False: 106k] ------------------ 2006| 212k| { 2007| 212k| pINChI[i][k] = cur_INChI[k]; 2008| 212k| pINChI_Aux[i][k] = cur_INChI_Aux[k]; 2009| 212k| cur_INChI[k] = NULL; 2010| 212k| cur_INChI_Aux[k] = NULL; 2011| 212k| } 2012| | 2013| | /* b) Count one component structure and/or INChI results only 2014| | if there was no error 2015| | Set inp_norm_data[j]->num_removed_H = number of removed explicit H 2016| | */ 2017| | 2018| 106k| if ( !sd->nErrorCode ) ------------------ | Branch (2018:10): [True: 106k, False: 4] ------------------ 2019| 106k| { 2020| | /* find where the current processed structure is located */ 2021| 106k| int cur_is_in_non_taut = (pINChI[i][TAUT_NON] && ------------------ | | 574| 106k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2021:35): [True: 35.6k, False: 70.4k] ------------------ 2022| 35.6k| pINChI[i][TAUT_NON]->nNumberOfAtoms > 0); ------------------ | | 574| 35.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2022:13): [True: 35.4k, False: 204] ------------------ 2023| 106k| int cur_is_in_taut = (pINChI[i][TAUT_YES] && ------------------ | | 575| 106k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2023:31): [True: 106k, False: 0] ------------------ 2024| 106k| pINChI[i][TAUT_YES]->nNumberOfAtoms > 0); ------------------ | | 575| 106k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2024:13): [True: 106k, False: 0] ------------------ 2025| | 2026| 106k| int cur_is_non_taut = (cur_is_in_non_taut && 0 == pINChI[i][TAUT_NON]->lenTautomer) || ------------------ | | 574| 35.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2026:32): [True: 35.4k, False: 70.6k] | Branch (2026:54): [True: 35.4k, False: 0] ------------------ 2027| 70.6k| (cur_is_in_taut && 0 == pINChI[i][TAUT_YES]->lenTautomer); /* djb-rwth: addressing LLVM warnings */ ------------------ | | 575| 70.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2027:14): [True: 70.6k, False: 0] | Branch (2027:32): [True: 69.1k, False: 1.44k] ------------------ 2028| 106k| int cur_is_taut = cur_is_in_taut && 0 < pINChI[i][TAUT_YES]->lenTautomer; ------------------ | | 575| 106k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2028:27): [True: 106k, False: 0] | Branch (2028:45): [True: 36.9k, False: 69.1k] ------------------ 2029| | 2030| | /* 2031| | sd->bTautFlags[iINChI] |= bTautFlags; 2032| | sd->bTautFlagsDone[iINChI] |= bTautFlagsDone; 2033| | */ 2034| | 2035| 106k| if ( cur_is_non_taut + cur_is_taut ) ------------------ | Branch (2035:14): [True: 106k, False: 0] ------------------ 2036| 106k| { 2037| | /* count tautomeric and non-tautomeric components of the structures */ 2038| 106k| int j1 = cur_is_in_non_taut ? TAUT_NON : TAUT_YES; ------------------ | | 574| 35.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ int j1 = cur_is_in_non_taut ? TAUT_NON : TAUT_YES; ------------------ | | 575| 70.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2038:22): [True: 35.4k, False: 70.6k] ------------------ 2039| 106k| int j2 = cur_is_in_taut ? TAUT_YES : TAUT_NON; ------------------ | | 575| 106k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int j2 = cur_is_in_taut ? TAUT_YES : TAUT_NON; ------------------ | | 574| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2039:22): [True: 106k, False: 0] ------------------ 2040| 106k| int j; 2041| 106k| sd->num_non_taut[iINChI] += cur_is_non_taut; 2042| 106k| sd->num_taut[iINChI] += cur_is_taut; 2043| 247k| for ( j = j1; j <= j2; j++ ) ------------------ | Branch (2043:27): [True: 141k, False: 106k] ------------------ 2044| 141k| { 2045| 141k| int bIsotopic = (pINChI[i][j]->nNumberOfIsotopicAtoms || ------------------ | Branch (2045:34): [True: 1.37k, False: 140k] ------------------ 2046| 140k| pINChI[i][j]->nNumberOfIsotopicTGroups || ------------------ | Branch (2046:21): [True: 0, False: 140k] ------------------ 2047| 140k| (pINChI[i][j]->nPossibleLocationsOfIsotopicH && pINChI[i][j]->nPossibleLocationsOfIsotopicH[0] > 1)); /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2047:22): [True: 6.86k, False: 133k] | Branch (2047:69): [True: 40, False: 6.82k] ------------------ 2048| 141k| if ( pINChI_Aux[i][j] && (j == TAUT_YES) ) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | | 575| 141k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2048:22): [True: 141k, False: 0] | Branch (2048:42): [True: 106k, False: 35.4k] ------------------ 2049| 106k| { 2050| 106k| bIsotopic |= (0 < pINChI_Aux[i][j]->nNumRemovedIsotopicH[0] + 2051| 106k| pINChI_Aux[i][j]->nNumRemovedIsotopicH[1] + 2052| 106k| pINChI_Aux[i][j]->nNumRemovedIsotopicH[2]); 2053| 106k| } 2054| | 2055| 141k| inp_norm_data[j]->bExists = 1; /* j=0: non-taut exists, j=1: taut exists */ 2056| 141k| inp_norm_data[j]->bHasIsotopicLayer = bIsotopic; 2057| | /*inp_norm_data[j]->num_removed_H = inp_norm_data[j]->num_at - num_at;*/ 2058| 141k| } 2059| 106k| } 2060| 106k| } 2061| | 2062| | /* return (sd->nErrorCode==CT_OUT_OF_RAM || sd->nErrorCode==CT_USER_QUIT_ERR)? _IS_FATAL : 2063| | sd->nErrorCode? _IS_ERROR : 0; */ 2064| | 2065| 106k| if ( sd->nErrorCode == CT_OUT_OF_RAM || sd->nErrorCode == CT_USER_QUIT_ERR ) ------------------ | | 21| 212k|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 106k|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ if ( sd->nErrorCode == CT_OUT_OF_RAM || sd->nErrorCode == CT_USER_QUIT_ERR ) ------------------ | | 32| 106k|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 18| 106k|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (2065:10): [True: 2, False: 106k] | Branch (2065:45): [True: 0, False: 106k] ------------------ 2066| 2| { 2067| 2| ret = _IS_FATAL; ------------------ | | 13| 2|#define _IS_FATAL 3 ------------------ 2068| 2| } 2069| 106k| else if ( sd->nErrorCode ) ------------------ | Branch (2069:15): [True: 2, False: 106k] ------------------ 2070| 2| { 2071| 2| ret = _IS_ERROR; ------------------ | | 12| 2|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2072| 2| } 2073| | 2074| 106k| lElapsedTime = InchiTimeElapsed(ic, &ulTStart); 2075| 106k| if ( ip->msec_MaxTime ) ------------------ | Branch (2075:10): [True: 0, False: 106k] ------------------ 2076| 0| { 2077| 0| ip->msec_LeftTime -= lElapsedTime; 2078| 0| } 2079| 106k| sd->ulStructTime += lElapsedTime; 2080| | 2081| 106k| return ret; 2082| 106k|} runichi.c:DoOneStructureEarlyPreprocessing: 564| 70.4k|{ 565| | 566| 70.4k|#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) 567| 70.4k| int ret1 = 0, ret2 = 0; /* djb-rwth: removing redundant variables */ 568| 70.4k|#endif 569| | 570| |#if ( REMOVE_ION_PAIRS_ORIG_STRU == 1 ) 571| | fix_odd_things(orig_inp_data->num_inp_atoms, orig_inp_data->at, 0, ip->bFixNonUniformDraw); 572| |#endif 573| | 574| 70.4k|#if ( UNDERIVATIZE == 1 ) 575| 70.4k| if ( ip->bUnderivatize ) ------------------ | Branch (575:10): [True: 0, False: 70.4k] ------------------ 576| 0| { 577| 0| if ( 0 > (ret2 = OAD_Edit_Underivatize(ic, pCG, orig_inp_data, (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY), ip->bUnderivatize & 2, ip->pSdfValue)) ) ------------------ | | 133| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (577:14): [True: 0, False: 0] ------------------ 578| 0| { 579| 0| long num_inp2 = num_inp; 580| 0| AddErrorMessage(sd->pStrErrStruct, "Underivatization error"); 581| 0| sd->nStructReadError = 99; 582| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 583| 0| TreatErrorsInReadTheStructure(sd, ip, LOG_MASK_ALL, inp_file, log_file, out_file, prb_file, ------------------ | | 98| 0|#define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 94| 0|#define LOG_MASK_WARN 1 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 95| 0|#define LOG_MASK_ERR 2 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 96| 0|#define LOG_MASK_FATAL 4 | | ------------------ ------------------ 584| 0| prep_inp_data, &num_inp2); 585| 0| return _IS_ERROR; /* output only if derivatives found */ ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 586| 0| } 587| 0| else if ( 0 < ret2 ) ------------------ | Branch (587:19): [True: 0, False: 0] ------------------ 588| 0| { 589| 0| if ( !ip->bNoWarnings ) ------------------ | Branch (589:18): [True: 0, False: 0] ------------------ 590| 0| { 591| 0| WarningMessage(sd->pStrErrStruct, "Input structure underivatized"); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 592| 0| } 593| 0| } 594| 0| } 595| 70.4k|#endif /* UNDERIVATIZE == 1 */ 596| | 597| 70.4k|#if ( RING2CHAIN == 1 ) 598| 70.4k| if ( ip->bRing2Chain && 0 > (ret1 = Ring2Chain(ic, pCG, orig_inp_data)) ) ------------------ | Branch (598:10): [True: 0, False: 70.4k] | Branch (598:29): [True: 0, False: 0] ------------------ 599| 0| { 600| 0| long num_inp2 = num_inp; 601| 0| AddErrorMessage(sd->pStrErrStruct, "Ring to chain error"); 602| 0| sd->nStructReadError = 99; 603| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 604| | /* djb-rwth: removing redundant code */ 605| 0| TreatErrorsInReadTheStructure(sd, ip, LOG_MASK_ALL, ------------------ | | 98| 0|#define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 94| 0|#define LOG_MASK_WARN 1 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 95| 0|#define LOG_MASK_ERR 2 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 96| 0|#define LOG_MASK_FATAL 4 | | ------------------ ------------------ 606| 0| inp_file, log_file, 607| 0| out_file, prb_file, 608| 0| prep_inp_data, &num_inp2); 609| 0| return _IS_ERROR; /* output only if derivatives found */ ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 610| 0| } 611| 70.4k|#endif /* RING2CHAIN == 1 */ 612| 70.4k|#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) /***** post v.1 feature *****/ 613| 70.4k| if ( ip->bIgnoreUnchanged && !ret1 && !ret2 ) ------------------ | Branch (613:10): [True: 0, False: 70.4k] | Branch (613:34): [True: 0, False: 0] | Branch (613:43): [True: 0, False: 0] ------------------ 614| 0| { 615| 0| return _IS_SKIP; /* output only if derivatives or ring/chain found */ ------------------ | | 16| 0|#define _IS_SKIP -2 ------------------ 616| 0| } 617| 70.4k|#endif /* RING2CHAIN == 1 || UNDERIVATIZE == 1 */ 618| 70.4k| return 0; 619| 70.4k|} runichi.c:OrigAtData_StoreNativeInput: 659| 70.4k|{ 660| | 661| | /* v. 1.05 always create and fill OrigStruc as it may be used to store e.g. polymer info */ 662| | /* If normal AuxInfo is requested, create full reversibility information from native inp data 663| | if ( ip->bINChIOutputOptions & (INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO)) 664| | return NULL; */ 665| | 666| 70.4k| if ( OrigStruct_FillOut(pCG, orig_inp_data, pOrigStruct, sd) ) ------------------ | Branch (666:10): [True: 0, False: 70.4k] ------------------ 667| 0| { 668| 0| AddErrorMessage(sd->pStrErrStruct, "Cannot interpret reversibility information"); 669| 0| sd->nStructReadError = 99; 670| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 671| 0| *nRet = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 672| 0| } 673| | 674| 70.4k| return pOrigStruct; 675| 70.4k|} runichi.c:PrepareSaveOptBits: 682| 70.4k|{ 683| 70.4k| if ( ip->nInputType != INPUT_INCHI ) ------------------ | Branch (683:10): [True: 0, False: 70.4k] ------------------ 684| 0| { 685| 0| *save_opt_bits = 0; 686| 0| if ( ip->bINChIOutputOptions & INCHI_OUT_SAVEOPT ) ------------------ | | 146| 0|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (686:14): [True: 0, False: 0] ------------------ 687| 0| { 688| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) ) ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (688:18): [True: 0, False: 0] ------------------ 689| 0| { 690| 0| (*save_opt_bits) |= SAVE_OPT_RECMET; ------------------ | | 158| 0|#define SAVE_OPT_RECMET 0x0008 ------------------ 691| 0| } 692| 0| if ( 0 != (ip->nMode & REQ_MODE_BASIC) ) ------------------ | | 15| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (692:18): [True: 0, False: 0] ------------------ 693| 0| { 694| 0| (*save_opt_bits) |= SAVE_OPT_FIXEDH; ------------------ | | 157| 0|#define SAVE_OPT_FIXEDH 0x0004 ------------------ 695| 0| } 696| 0| if ( 0 != (ip->nMode & REQ_MODE_DIFF_UU_STEREO) ) ------------------ | | 40| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (696:18): [True: 0, False: 0] ------------------ 697| 0| { 698| 0| (*save_opt_bits) |= SAVE_OPT_SLUUD; ------------------ | | 155| 0|#define SAVE_OPT_SLUUD 0x0001 ------------------ 699| 0| } 700| 0| if ( 0 == (ip->nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 32| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ if ( 0 == (ip->nMode & (REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU)) ) ------------------ | | 30| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (700:18): [True: 0, False: 0] ------------------ 701| 0| { 702| 0| (*save_opt_bits) |= SAVE_OPT_SUU; ------------------ | | 156| 0|#define SAVE_OPT_SUU 0x0002 ------------------ 703| 0| } 704| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_KETO_ENOL_TAUT) ) ------------------ | | 946| 0|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (704:18): [True: 0, False: 0] ------------------ 705| 0| { 706| 0| (*save_opt_bits) |= SAVE_OPT_KET; ------------------ | | 159| 0|#define SAVE_OPT_KET 0x0010 ------------------ 707| 0| } 708| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_1_5_TAUT) ) ------------------ | | 947| 0|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (708:18): [True: 0, False: 0] ------------------ 709| 0| { 710| 0| (*save_opt_bits) |= SAVE_OPT_15T; ------------------ | | 160| 0|#define SAVE_OPT_15T 0x0020 ------------------ 711| 0| } 712| | /* djb-rwth: addressing coverity ID #499536 -- despite different bit-sizes, works properly */ 713| 0| if (0 != (ip->bTautFlags & TG_FLAG_PT_22_00)) ------------------ | | 953| 0|#define TG_FLAG_PT_22_00 0x00800000 ------------------ | Branch (713:17): [True: 0, False: 0] ------------------ 714| 0| (*save_opt_bits) |= SAVE_OPT_PT_22_00; ------------------ | | 161| 0|#define SAVE_OPT_PT_22_00 0x0040 ------------------ 715| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_PT_16_00) ) ------------------ | | 954| 0|#define TG_FLAG_PT_16_00 0x01000000 ------------------ | Branch (715:18): [True: 0, False: 0] ------------------ 716| 0| (*save_opt_bits) |= SAVE_OPT_PT_16_00; ------------------ | | 162| 0|#define SAVE_OPT_PT_16_00 0x0080 ------------------ 717| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_PT_06_00) ) ------------------ | | 955| 0|#define TG_FLAG_PT_06_00 0x02000000 ------------------ | Branch (717:18): [True: 0, False: 0] ------------------ 718| 0| (*save_opt_bits) |= SAVE_OPT_PT_06_00; ------------------ | | 163| 0|#define SAVE_OPT_PT_06_00 0x0100 ------------------ 719| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_PT_39_00) ) ------------------ | | 956| 0|#define TG_FLAG_PT_39_00 0x04000000 ------------------ | Branch (719:18): [True: 0, False: 0] ------------------ 720| 0| (*save_opt_bits) |= SAVE_OPT_PT_39_00; ------------------ | | 164| 0|#define SAVE_OPT_PT_39_00 0x0200 ------------------ 721| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_PT_13_00) ) ------------------ | | 957| 0|#define TG_FLAG_PT_13_00 0x08000000 ------------------ | Branch (721:18): [True: 0, False: 0] ------------------ 722| 0| (*save_opt_bits) |= SAVE_OPT_PT_13_00; ------------------ | | 165| 0|#define SAVE_OPT_PT_13_00 0x0400 ------------------ 723| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_PT_18_00) ) ------------------ | | 958| 0|#define TG_FLAG_PT_18_00 0x10000000 ------------------ | Branch (723:18): [True: 0, False: 0] ------------------ 724| 0| (*save_opt_bits) |= SAVE_OPT_PT_18_00; ------------------ | | 166| 0|#define SAVE_OPT_PT_18_00 0x0800 ------------------ 725| | /* Check if /SNon requested and turn OFF stereo bits if so */ 726| 0| if ( !(ip->nMode & REQ_MODE_STEREO) ) ------------------ | | 19| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (726:18): [True: 0, False: 0] ------------------ 727| 0| { 728| 0| (*save_opt_bits) &= ~SAVE_OPT_SUU; ------------------ | | 156| 0|#define SAVE_OPT_SUU 0x0002 ------------------ 729| 0| (*save_opt_bits) &= ~SAVE_OPT_SLUUD; ------------------ | | 155| 0|#define SAVE_OPT_SLUUD 0x0001 ------------------ 730| 0| } 731| 0| } 732| 0| } 733| 70.4k|} runichi.c:DisplayOrigAndResultStructuresAndComponents: 755| 70.4k|{ 756| | 757| | 758| 70.4k| if ( ip->bDisplay ) ip->bDisplayCompositeResults = 1; /* v. 1.05 */ ------------------ | Branch (758:10): [True: 0, False: 70.4k] ------------------ 759| | 760| |#ifndef COMPILE_ANSI_ONLY /* { */ 761| | 762| | /* Display equivalent components on original or preprocessed structure(s) */ 763| |#ifndef TARGET_LIB_FOR_WINCHI 764| | if ( nRet != _IS_FATAL && nRet != _IS_ERROR && /*ip->bDisplay &&*/ 765| | (ip->bCompareComponents & CMP_COMPONENTS) && !sd->bUserQuit && !sd->bUserQuitComponent ) 766| | { 767| | int j, ret, ord; 768| | int bDisplaySaved = ip->bDisplay; 769| | ORIG_ATOM_DATA* inp_data; 770| | AT_NUMB nEquSet; 771| | for ( ord = -1; ord < INCHI_NUM; ord++ ) 772| | { 773| | switch ( ord ) 774| | { 775| | case -1: 776| | j = INCHI_BAS; /* preprocessed non-tautomeric */ 777| | break; 778| | case 0: 779| | j = INCHI_REC; /* preprocessed tautomeric */ 780| | break; 781| | case 1: 782| | j = -1; /* original input */ 783| | break; 784| | default: 785| | continue; 786| | } 787| | inp_data = j < 0 ? orig_inp_data : prep_inp_data + j; 788| | if ( inp_data && inp_data->num_inp_atoms && inp_data->at && 789| | inp_data->nEquLabels && 790| | inp_data->nNumEquSets ) 791| | { 792| | for ( nEquSet = 1; nEquSet <= inp_data->nNumEquSets; nEquSet++ ) 793| | { 794| | ip->dp.nEquLabels = inp_data->nEquLabels; 795| | ip->dp.nCurEquLabel = nEquSet; 796| | ip->dp.nNumEquSets = inp_data->nNumEquSets; 797| | ip->bDisplay = 1; /* force display if it was not requested */ 798| | ret = DisplayTheWholeStructure(pCG, ic, sd, ip, szTitle, 799| | inp_file, log_file, inp_data, 800| | num_inp, j, 1 /*bShowStructure*/, 0); 801| | ip->dp.nEquLabels = NULL; 802| | ip->dp.nCurEquLabel = 0; 803| | ip->dp.nNumEquSets = 0; 804| | ip->bDisplay = bDisplaySaved; /* restore display option */ 805| | if ( ret ) 806| | { 807| | /* user pressed Esc */ 808| | goto exit_loop; 809| | } 810| | } 811| | } 812| | } 813| | exit_loop:; 814| | } 815| |#endif 816| | 817| | /* Display composite results and equivalent components on composite results */ 818| | if ( nRet != _IS_FATAL && nRet != _IS_ERROR && /*ip->bDisplay &&*/ ip->bDisplayCompositeResults ) 819| | { 820| | int iINChI; 821| | for ( iINChI = 0; iINChI < maxINChI && !sd->bUserQuitComponentDisplay; iINChI++ ) 822| | { 823| | DisplayTheWholeCompositeStructure(pCG, ic, ip, sd, num_inp, 824| | iINChI, pINChI[iINChI], pINChI_Aux[iINChI], 825| | orig_inp_data, prep_inp_data, composite_norm_data[iINChI]); 826| | } 827| |#ifndef TARGET_LIB_FOR_WINCHI 828| | if ( !ip->bDisplay && sd->bUserQuitComponentDisplay ) 829| | { 830| | sd->bUserQuit = 1; 831| | } 832| |#endif 833| | } 834| | 835| |#endif /* } COMPILE_ANSI_ONLY */ 836| | 837| 70.4k| return; 838| 70.4k|} runichi.c:SaveOkProcessedMolfile: 850| 70.4k|{ 851| 70.4k| if ( ip->bSaveAllGoodStructsAsProblem && ------------------ | Branch (851:10): [True: 0, False: 70.4k] ------------------ 852| 0| nRet != _IS_FATAL && ------------------ | | 13| 70.4k|#define _IS_FATAL 3 ------------------ | Branch (852:9): [True: 0, False: 0] ------------------ 853| 0| nRet != _IS_ERROR && ------------------ | | 12| 70.4k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (853:9): [True: 0, False: 0] ------------------ 854| 0| prb_file && ------------------ | Branch (854:9): [True: 0, False: 0] ------------------ 855| 0| prb_file->f && ------------------ | Branch (855:9): [True: 0, False: 0] ------------------ 856| 0| 0L <= sd->fPtrStart && ------------------ | Branch (856:9): [True: 0, False: 0] ------------------ 857| 0| sd->fPtrStart < sd->fPtrEnd ) ------------------ | Branch (857:9): [True: 0, False: 0] ------------------ 858| 0| { 859| 0| MolfileSaveCopy( inp_file, sd->fPtrStart, sd->fPtrEnd, prb_file->f, 0 ); /* djb-rwth: addressing coverity ID #499510 -- return values handled properly */ 860| 0| } 861| | 862| 70.4k| return; 863| 70.4k|} GetOneComponent: 436| 106k|{ 437| 106k| inchiTime ulTStart; 438| | 439| 106k| InchiTimeGet( &ulTStart ); 440| | 441| 106k| CreateInpAtomData( inp_cur_data, orig_inp_data->nCurAtLen[i], 0 ); 442| | 443| 106k| inp_cur_data->num_at = ExtractConnectedComponent( orig_inp_data->at, orig_inp_data->num_inp_atoms, i + 1, inp_cur_data->at ); 444| | 445| 106k| if (BuildPolymerCrossingBondEndpointMask(inp_cur_data, orig_inp_data, ip, i + 1) < 0) ------------------ | Branch (445:9): [True: 0, False: 106k] ------------------ 446| 0| { 447| 0| AddErrorMessage(sd->pStrErrStruct, "Out of memory while processing polymer data"); 448| | 449| 0| sd->nErrorCode = CT_OUT_OF_RAM; ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 450| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 451| | 452| 0| sd->ulStructTime += InchiTimeElapsed(ic, &ulTStart); 453| | 454| 0| return sd->nErrorType; 455| 0| } 456| | 457| 106k| sd->ulStructTime += InchiTimeElapsed( ic, &ulTStart ); 458| | 459| | 460| | /* Error processing */ 461| 106k| if (inp_cur_data->num_at <= 0 || orig_inp_data->nCurAtLen[i] != inp_cur_data->num_at) ------------------ | Branch (461:9): [True: 0, False: 106k] | Branch (461:38): [True: 0, False: 106k] ------------------ 462| 0| { 463| | /* Log error message */ 464| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot extract Component" ); 465| 0| inchi_ios_eprint( log_file, "%s #%d structure #%ld.%s%s%s%s\n", sd->pStrErrStruct, i + 1, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ) ); ------------------ | | 830| 0|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 0] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 0] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 0] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 0] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 0] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 0| : gsEmpty ------------------ 466| 0| sd->nErrorCode = inp_cur_data->num_at < 0 ? inp_cur_data->num_at : ( orig_inp_data->nCurAtLen[i] != inp_cur_data->num_at ) ? CT_ATOMCOUNT_ERR : CT_UNKNOWN_ERR; ------------------ | | 30| 0|#define CT_ATOMCOUNT_ERR (CT_ERR_FIRST-11) /*(-30011) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ sd->nErrorCode = inp_cur_data->num_at < 0 ? inp_cur_data->num_at : ( orig_inp_data->nCurAtLen[i] != inp_cur_data->num_at ) ? CT_ATOMCOUNT_ERR : CT_UNKNOWN_ERR; ------------------ | | 38| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (466:26): [True: 0, False: 0] | Branch (466:76): [True: 0, False: 0] ------------------ 467| | /* num_err ++; */ 468| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 469| |#ifdef TARGET_LIB_FOR_WINCHI 470| | if (( ip->bINChIOutputOptions & INCHI_OUT_WINCHI_WINDOW ) && 471| | ( ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT )) 472| | { 473| | sd->nErrorType = ProcessStructError( out_file, 474| | log_file, 475| | sd->pStrErrStruct, 476| | sd->nErrorType, 477| | num_inp, 478| | ip ); 479| | } 480| |#endif 481| 0| } 482| | 483| 106k| return sd->nErrorType; 484| 106k|} runichi2.c:BuildPolymerCrossingBondEndpointMask: 331| 106k|{ 332| 106k| int orig_idx; 333| 106k| int local_idx = 0; 334| 106k| int unit_idx; 335| 106k| int endpoint_idx; 336| | 337| 106k| if (inp_cur_data->num_at <= 0 || ip->bPolymers == POLYMERS_NO || ------------------ | | 1215| 212k|#define POLYMERS_NO 0 /* ignore polymers */ ------------------ | Branch (337:9): [True: 0, False: 106k] | Branch (337:38): [True: 106k, False: 0] ------------------ 338| 0| !orig_inp_data->valid_polymer || !orig_inp_data->polymer || ------------------ | Branch (338:9): [True: 0, False: 0] | Branch (338:42): [True: 0, False: 0] ------------------ 339| 0| orig_inp_data->polymer->n <= 0) ------------------ | Branch (339:9): [True: 0, False: 0] ------------------ 340| 106k| { 341| 106k| return 0; 342| 106k| } 343| | 344| | /* No mask is needed if this component contains no explicit H/D/T atoms. */ 345| 0| for (local_idx = 0; local_idx < inp_cur_data->num_at; local_idx++) ------------------ | Branch (345:25): [True: 0, False: 0] ------------------ 346| 0| { 347| 0| const char *elname = inp_cur_data->at[local_idx].elname; 348| | 349| 0| if (elname[1] == '\0' && (elname[0] == 'H' || elname[0] == 'D' || elname[0] == 'T')) ------------------ | Branch (349:13): [True: 0, False: 0] | Branch (349:35): [True: 0, False: 0] | Branch (349:55): [True: 0, False: 0] | Branch (349:75): [True: 0, False: 0] ------------------ 350| 0| { 351| 0| break; 352| 0| } 353| 0| } 354| | 355| 0| if (local_idx == inp_cur_data->num_at) ------------------ | Branch (355:9): [True: 0, False: 0] ------------------ 356| 0| { 357| 0| return 0; 358| 0| } 359| | 360| 0| local_idx = 0; 361| | 362| 0| inp_cur_data->keep_explicit_HDT = (unsigned char *)inchi_calloc((long long)inp_cur_data->num_at, sizeof(inp_cur_data->keep_explicit_HDT[0])); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 363| | 364| 0| if (!inp_cur_data->keep_explicit_HDT) ------------------ | Branch (364:9): [True: 0, False: 0] ------------------ 365| 0| { 366| 0| return -1; 367| 0| } 368| | 369| 0| for (orig_idx = 0; orig_idx < orig_inp_data->num_inp_atoms; orig_idx++) ------------------ | Branch (369:24): [True: 0, False: 0] ------------------ 370| 0| { 371| 0| if (orig_inp_data->at[orig_idx].component != component_number) ------------------ | Branch (371:13): [True: 0, False: 0] ------------------ 372| 0| { 373| 0| continue; 374| 0| } 375| | 376| | /* 377| | * The mask is consulted only for explicit H/D/T atoms by 378| | * remove_terminal_HDT(), so heavy-atom and pseudoatom endpoints 379| | * do not need to be marked. 380| | */ 381| 0| if (!(orig_inp_data->at[orig_idx].elname[1] == '\0' && ------------------ | Branch (381:15): [True: 0, False: 0] ------------------ 382| 0| (orig_inp_data->at[orig_idx].elname[0] == 'H' || ------------------ | Branch (382:16): [True: 0, False: 0] ------------------ 383| 0| orig_inp_data->at[orig_idx].elname[0] == 'D' || ------------------ | Branch (383:16): [True: 0, False: 0] ------------------ 384| 0| orig_inp_data->at[orig_idx].elname[0] == 'T'))) ------------------ | Branch (384:16): [True: 0, False: 0] ------------------ 385| 0| { 386| 0| local_idx++; 387| 0| continue; 388| 0| } 389| | 390| 0| for (unit_idx = 0; unit_idx < orig_inp_data->polymer->n; unit_idx++) ------------------ | Branch (390:28): [True: 0, False: 0] ------------------ 391| 0| { 392| 0| const OAD_PolymerUnit *u = orig_inp_data->polymer->units[unit_idx]; 393| | 394| 0| if (!u || !u->blist) ------------------ | Branch (394:17): [True: 0, False: 0] | Branch (394:23): [True: 0, False: 0] ------------------ 395| 0| { 396| 0| continue; 397| 0| } 398| | 399| | /* 400| | * Each crossing bond contributes two atom numbers to blist. 401| | * blist uses whole-structure, 1-based atom numbering. 402| | */ 403| 0| for (endpoint_idx = 0; endpoint_idx < 2 * u->nb; endpoint_idx++) ------------------ | Branch (403:36): [True: 0, False: 0] ------------------ 404| 0| { 405| 0| if (u->blist[endpoint_idx] == orig_idx + 1) ------------------ | Branch (405:21): [True: 0, False: 0] ------------------ 406| 0| { 407| 0| inp_cur_data->keep_explicit_HDT[local_idx] = 1; 408| 0| break; 409| 0| } 410| 0| } 411| | 412| 0| if (inp_cur_data->keep_explicit_HDT[local_idx]) ------------------ | Branch (412:17): [True: 0, False: 0] ------------------ 413| 0| { 414| 0| break; 415| 0| } 416| 0| } 417| | 418| 0| local_idx++; 419| 0| } 420| | 421| 0| return 0; 422| 0|} OrigAtData_Duplicate: 115| 70.4k|{ 116| 70.4k| inp_ATOM* at = NULL; 117| 70.4k| AT_NUMB* nCurAtLen = NULL; 118| 70.4k| AT_NUMB* nOldCompNumber = NULL; 119| 70.4k| int k, m, nn; 120| 70.4k| int orig_nat = orig_atom->num_inp_atoms; 121| | 122| 70.4k| int ret = -1; /* fail; 0 - OK */ 123| | 124| 70.4k| if ( new_orig_atom->at && ------------------ | Branch (124:10): [True: 0, False: 70.4k] ------------------ 125| 0| new_orig_atom->num_inp_atoms >= orig_nat ) ------------------ | Branch (125:9): [True: 0, False: 0] ------------------ 126| 0| { 127| 0| at = new_orig_atom->at; 128| 0| } 129| 70.4k| else 130| 70.4k| { 131| 70.4k| at = (inp_ATOM*)inchi_calloc((long long)orig_nat + 1, sizeof(at[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 132| 70.4k| if ( !at ) ------------------ | Branch (132:14): [True: 0, False: 70.4k] ------------------ 133| 0| { 134| 0| goto exit_function; 135| 0| } 136| 70.4k| } 137| | 138| 70.4k| if ( new_orig_atom->nOldCompNumber && ------------------ | Branch (138:10): [True: 0, False: 70.4k] ------------------ 139| 0| new_orig_atom->num_components >= orig_atom->num_components ) ------------------ | Branch (139:9): [True: 0, False: 0] ------------------ 140| 0| { 141| 0| nCurAtLen = new_orig_atom->nCurAtLen; 142| 0| } 143| 70.4k| else 144| 70.4k| { 145| 70.4k| nCurAtLen = (AT_NUMB*)inchi_calloc((long long)orig_atom->num_components + 1, sizeof(nCurAtLen[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 146| 70.4k| if ( !nCurAtLen ) ------------------ | Branch (146:14): [True: 0, False: 70.4k] ------------------ 147| 0| { 148| 0| goto exit_function; 149| 0| } 150| 70.4k| } 151| | 152| 70.4k| if ( new_orig_atom->nCurAtLen && ------------------ | Branch (152:10): [True: 0, False: 70.4k] ------------------ 153| 0| new_orig_atom->num_components >= orig_atom->num_components ) ------------------ | Branch (153:9): [True: 0, False: 0] ------------------ 154| 0| { 155| 0| nOldCompNumber = new_orig_atom->nOldCompNumber; 156| 0| } 157| 70.4k| else 158| 70.4k| { 159| 70.4k| nOldCompNumber = (AT_NUMB*)inchi_calloc((long long)orig_atom->num_components + 1, ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 160| 70.4k| sizeof(nOldCompNumber[0])); /* djb-rwth: cast operator added */ 161| 70.4k| if ( !nOldCompNumber ) ------------------ | Branch (161:14): [True: 0, False: 70.4k] ------------------ 162| 0| { 163| 0| goto exit_function; 164| 0| } 165| 70.4k| } 166| | 167| 70.4k| if ( at && nCurAtLen && nOldCompNumber ) ------------------ | Branch (167:10): [True: 70.4k, False: 0] | Branch (167:16): [True: 70.4k, False: 0] | Branch (167:29): [True: 70.4k, False: 0] ------------------ 168| 70.4k| { 169| | /* Copy */ 170| 70.4k| if ( orig_atom->at ) ------------------ | Branch (170:14): [True: 70.4k, False: 0] ------------------ 171| 70.4k| { 172| 70.4k| memcpy(at, orig_atom->at, 173| 70.4k| orig_nat * sizeof(new_orig_atom->at[0])); 174| 70.4k| } 175| 70.4k| if ( orig_atom->nCurAtLen ) ------------------ | Branch (175:14): [True: 0, False: 70.4k] ------------------ 176| 0| { 177| 0| memcpy(nCurAtLen, orig_atom->nCurAtLen, 178| 0| orig_atom->num_components * sizeof(nCurAtLen[0])); 179| 0| } 180| 70.4k| if ( orig_atom->nOldCompNumber ) ------------------ | Branch (180:14): [True: 0, False: 70.4k] ------------------ 181| 0| { 182| 0| memcpy(nOldCompNumber, orig_atom->nOldCompNumber, 183| 0| orig_atom->num_components * sizeof(nOldCompNumber[0])); 184| 0| } 185| | 186| | /* Deallocate */ 187| 70.4k| if ( new_orig_atom->at && new_orig_atom->at != at ) ------------------ | Branch (187:14): [True: 0, False: 70.4k] | Branch (187:35): [True: 0, False: 0] ------------------ 188| 0| { 189| 0| inchi_free(new_orig_atom->at); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 190| 0| } 191| 70.4k| if ( new_orig_atom->nCurAtLen && new_orig_atom->nCurAtLen != nCurAtLen ) ------------------ | Branch (191:14): [True: 0, False: 70.4k] | Branch (191:42): [True: 0, False: 0] ------------------ 192| 0| { 193| 0| inchi_free(new_orig_atom->nCurAtLen); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 194| 0| } 195| 70.4k| if ( new_orig_atom->nOldCompNumber && ------------------ | Branch (195:14): [True: 0, False: 70.4k] ------------------ 196| 0| new_orig_atom->nOldCompNumber != nOldCompNumber ) ------------------ | Branch (196:13): [True: 0, False: 0] ------------------ 197| 0| { 198| 0| inchi_free(new_orig_atom->nOldCompNumber); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 199| 0| } 200| | 201| 70.4k| *new_orig_atom = *orig_atom; 202| 70.4k| new_orig_atom->at = at; 203| 70.4k| new_orig_atom->nCurAtLen = nCurAtLen; 204| 70.4k| new_orig_atom->nOldCompNumber = nOldCompNumber; 205| | 206| | /* Data that are not to be copied */ 207| 70.4k| new_orig_atom->nNumEquSets = 0; 208| 70.4k| memset(new_orig_atom->bSavedInINCHI_LIB, 0, sizeof(new_orig_atom->bSavedInINCHI_LIB)); /* djb-rwth: memset_s C11/Annex K variant? */ 209| 70.4k| memset(new_orig_atom->bPreprocessed, 0, sizeof(new_orig_atom->bPreprocessed)); /* djb-rwth: memset_s C11/Annex K variant? */ 210| | 211| | 212| | 213| 70.4k| new_orig_atom->szCoord = NULL; 214| 70.4k| if ( orig_atom->szCoord ) ------------------ | Branch (214:14): [True: 0, False: 70.4k] ------------------ 215| 0| { 216| 0| new_orig_atom->szCoord = (MOL_COORD*)inchi_calloc(orig_nat, sizeof(new_orig_atom->szCoord[0])); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 217| 0| if ( !new_orig_atom->szCoord ) ------------------ | Branch (217:18): [True: 0, False: 0] ------------------ 218| 0| { 219| 0| goto exit_function; 220| 0| } 221| 0| memcpy(new_orig_atom->szCoord, orig_atom->szCoord, orig_nat * sizeof(new_orig_atom->szCoord[0])); 222| 0| } 223| | 224| | 225| | /* Arrays that are not to be copied */ 226| | 227| 70.4k| new_orig_atom->nEquLabels = NULL; 228| 70.4k| new_orig_atom->nSortedOrder = NULL; 229| | 230| 70.4k| new_orig_atom->polymer = NULL; 231| 70.4k| if ( orig_atom->polymer ) ------------------ | Branch (231:14): [True: 0, False: 70.4k] ------------------ 232| 0| { 233| | /* Polymer stuff -- deep copy */ 234| 0| OAD_Polymer* oldp = orig_atom->polymer; 235| 0| OAD_Polymer* newp = NULL; 236| | 237| 0| newp = (OAD_Polymer*)inchi_calloc(1, sizeof(OAD_Polymer)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 238| 0| if ( !newp ) ------------------ | Branch (238:18): [True: 0, False: 0] ------------------ 239| 0| { 240| 0| inchi_free(newp); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 241| 0| goto exit_function; 242| 0| } 243| 0| memcpy(newp, orig_atom->polymer, sizeof(OAD_Polymer)); 244| 0| newp->units = (OAD_PolymerUnit**)inchi_calloc(newp->n, sizeof(OAD_PolymerUnit*)); /* djb-rwth: inchi_calloc must return OAD_PolymerUnit** */ ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 245| 0| if ( !newp->units ) ------------------ | Branch (245:18): [True: 0, False: 0] ------------------ 246| 0| { 247| 0| inchi_free(newp); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 248| 0| goto exit_function; 249| 0| } 250| 0| for ( k = 0; k < orig_atom->polymer->n; k++ ) ------------------ | Branch (250:26): [True: 0, False: 0] ------------------ 251| 0| { 252| 0| newp->units[k] = OAD_PolymerUnit_CreateCopy(orig_atom->polymer->units[k]); 253| 0| } 254| 0| if ( oldp->n_pzz > 0 ) ------------------ | Branch (254:18): [True: 0, False: 0] ------------------ 255| 0| { 256| 0| newp->n_pzz = oldp->n_pzz; 257| 0| newp->pzz = (int*)inchi_calloc(newp->n_pzz, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 258| 0| if ( !newp->pzz ) ------------------ | Branch (258:22): [True: 0, False: 0] ------------------ 259| 0| { 260| 0| inchi_free(newp->units); /* djb-rwth: fixing coverity ID #499546 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 261| 0| inchi_free(newp); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 262| 0| goto exit_function; 263| 0| } 264| 0| memcpy(newp->pzz, oldp->pzz, newp->n_pzz * sizeof(oldp->pzz[0])); 265| 0| } 266| 0| new_orig_atom->polymer = newp; 267| 0| } 268| | 269| 70.4k| new_orig_atom->v3000 = NULL; 270| 70.4k| if ( orig_atom->v3000 ) ------------------ | Branch (270:14): [True: 0, False: 70.4k] ------------------ 271| 0| { 272| | /* V3000 features -- deep copy */ 273| 0| OAD_V3000* new_v3000 = NULL; 274| 0| new_v3000 = (OAD_V3000*)inchi_calloc(1, sizeof(OAD_V3000)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 275| 0| if ( !new_v3000 ) ------------------ | Branch (275:18): [True: 0, False: 0] ------------------ 276| 0| { 277| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 278| 0| goto exit_function; 279| 0| } 280| 0| memcpy(new_v3000, orig_atom->v3000, sizeof(OAD_V3000)); 281| 0| if ( orig_atom->v3000->atom_index_orig ) ------------------ | Branch (281:18): [True: 0, False: 0] ------------------ 282| 0| { 283| 0| new_v3000->atom_index_orig = (int*)inchi_calloc(orig_nat, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 284| | /* if ( NULL==new_v3000->atom_index_orig ) {TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; } */ 285| 0| if ( !new_v3000->atom_index_orig ) ------------------ | Branch (285:22): [True: 0, False: 0] ------------------ 286| 0| { 287| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 288| 0| goto exit_function; 289| 0| } 290| 0| memcpy(new_v3000->atom_index_orig, orig_atom->v3000->atom_index_orig, orig_nat * sizeof(int)); 291| 0| } 292| 0| if ( orig_atom->v3000->atom_index_fin ) ------------------ | Branch (292:18): [True: 0, False: 0] ------------------ 293| 0| { 294| 0| new_v3000->atom_index_fin = (int*)inchi_calloc(orig_nat, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 295| | /* if ( NULL==new_v3000->atom_index_fin ) {TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; } */ 296| 0| if ( !new_v3000->atom_index_fin ) ------------------ | Branch (296:22): [True: 0, False: 0] ------------------ 297| 0| { 298| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 299| 0| goto exit_function; 300| 0| } 301| 0| memcpy(new_v3000->atom_index_fin, orig_atom->v3000->atom_index_fin, orig_nat * sizeof(int)); 302| 0| } 303| 0| if ( orig_atom->v3000->n_haptic_bonds && orig_atom->v3000->lists_haptic_bonds ) ------------------ | Branch (303:18): [True: 0, False: 0] | Branch (303:54): [True: 0, False: 0] ------------------ 304| 0| { 305| 0| new_v3000->lists_haptic_bonds = (int**)inchi_calloc(orig_atom->v3000->n_haptic_bonds, sizeof(int*)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 306| | /* if ( NULL==new_v3000->lists_haptic_bonds ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 307| 0| for ( m = 0; m < orig_atom->v3000->n_haptic_bonds; m++ ) ------------------ | Branch (307:30): [True: 0, False: 0] ------------------ 308| 0| { 309| 0| int* lst = NULL; 310| 0| int* old_lst = orig_atom->v3000->lists_haptic_bonds[m]; 311| 0| nn = old_lst[2] + 3; 312| 0| lst = new_v3000->lists_haptic_bonds[m] = (int*)inchi_calloc(nn, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 313| 0| if ( !lst ) ------------------ | Branch (313:26): [True: 0, False: 0] ------------------ 314| 0| { 315| 0| inchi_free(new_v3000->lists_haptic_bonds); /* djb-rwth: fixing coverity ID #499504 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 316| 0| inchi_free(new_v3000->atom_index_orig); /* djb-rwth: fixing coverity ID #499540 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 317| 0| inchi_free(new_v3000->atom_index_fin); /* djb-rwth: fixing coverity ID #499613 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 318| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 319| 0| goto exit_function; 320| 0| } 321| 0| memcpy(lst, old_lst, nn * sizeof(int)); 322| 0| } 323| 0| } 324| 0| if ( orig_atom->v3000->n_steabs && orig_atom->v3000->lists_steabs ) ------------------ | Branch (324:18): [True: 0, False: 0] | Branch (324:48): [True: 0, False: 0] ------------------ 325| 0| { 326| 0| new_v3000->lists_steabs = (int**)inchi_calloc(orig_atom->v3000->n_steabs, sizeof(int*)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 327| | /* if ( NULL==new_v3000->lists_steabs ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 328| 0| for ( m = 0; m < orig_atom->v3000->n_steabs; m++ ) ------------------ | Branch (328:30): [True: 0, False: 0] ------------------ 329| 0| { 330| 0| int* lst = NULL; 331| 0| int* old_lst = orig_atom->v3000->lists_steabs[m]; 332| 0| nn = old_lst[1] + 2; 333| 0| lst = new_v3000->lists_steabs[m] = (int*)inchi_calloc(nn, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 334| 0| if ( !lst ) ------------------ | Branch (334:26): [True: 0, False: 0] ------------------ 335| 0| { 336| 0| inchi_free(new_v3000->lists_haptic_bonds); /* djb-rwth: fixing coverity ID #499504 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 337| 0| inchi_free(new_v3000->lists_steabs); /* djb-rwth: fixing coverity ID #499543 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 338| 0| inchi_free(new_v3000->atom_index_orig); /* djb-rwth: fixing coverity ID #499540 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 339| 0| inchi_free(new_v3000->atom_index_fin); /* djb-rwth: fixing coverity ID #499613 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 340| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 341| 0| goto exit_function; 342| 0| } 343| 0| memcpy(lst, old_lst, nn * sizeof(int)); 344| 0| } 345| 0| } 346| 0| if ( orig_atom->v3000->n_sterel && orig_atom->v3000->lists_sterel ) ------------------ | Branch (346:18): [True: 0, False: 0] | Branch (346:48): [True: 0, False: 0] ------------------ 347| 0| { 348| 0| new_v3000->lists_sterel = (int**)inchi_calloc(orig_atom->v3000->n_sterel, sizeof(int*)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 349| 0| if ( !new_v3000 ) ------------------ | Branch (349:22): [True: 0, False: 0] ------------------ 350| 0| { 351| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 352| 0| goto exit_function; 353| 0| } 354| | /* if ( NULL==new_v3000->lists_sterel ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 355| 0| for ( m = 0; m < orig_atom->v3000->n_sterel; m++ ) ------------------ | Branch (355:30): [True: 0, False: 0] ------------------ 356| 0| { 357| 0| int* lst = NULL; 358| 0| int* old_lst = orig_atom->v3000->lists_sterel[m]; 359| 0| nn = old_lst[1] + 2; 360| 0| if ( new_v3000->lists_sterel ) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (360:26): [True: 0, False: 0] ------------------ 361| 0| lst = new_v3000->lists_sterel[m] = (int*)inchi_calloc(nn, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 362| 0| if ( !lst ) ------------------ | Branch (362:26): [True: 0, False: 0] ------------------ 363| 0| { 364| 0| inchi_free(new_v3000->lists_haptic_bonds); /* djb-rwth: fixing coverity ID #499504 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 365| 0| inchi_free(new_v3000->lists_steabs); /* djb-rwth: fixing coverity ID #499543 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 366| 0| inchi_free(new_v3000->lists_sterel); /* djb-rwth: fixing coverity ID #499504 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 367| 0| inchi_free(new_v3000->atom_index_orig); /* djb-rwth: fixing coverity ID #499540 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 368| 0| inchi_free(new_v3000->atom_index_fin); /* djb-rwth: fixing coverity ID #499613 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 369| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 370| 0| goto exit_function; 371| 0| } 372| 0| memcpy(lst, old_lst, nn * sizeof(int)); 373| 0| } 374| 0| } 375| 0| if ( orig_atom->v3000->n_sterac && orig_atom->v3000->lists_sterac ) ------------------ | Branch (375:18): [True: 0, False: 0] | Branch (375:48): [True: 0, False: 0] ------------------ 376| 0| { 377| 0| new_v3000->lists_sterac = (int**)inchi_calloc(orig_atom->v3000->n_sterac, sizeof(int*)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 378| | /* if ( NULL==new_v3000->lists_sterac ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 379| 0| if ( new_v3000->lists_sterac ) /* djb-rwth: fixing a NULL pointer dereference */ ------------------ | Branch (379:22): [True: 0, False: 0] ------------------ 380| 0| { 381| 0| for ( m = 0; m < orig_atom->v3000->n_sterac; m++ ) ------------------ | Branch (381:34): [True: 0, False: 0] ------------------ 382| 0| { 383| 0| int* lst = NULL; 384| 0| int* old_lst = orig_atom->v3000->lists_sterac[m]; 385| 0| nn = old_lst[1] + 2; 386| 0| lst = new_v3000->lists_sterac[m] = (int*)inchi_calloc(nn, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 387| 0| if ( !lst ) ------------------ | Branch (387:30): [True: 0, False: 0] ------------------ 388| 0| { 389| 0| inchi_free(new_v3000->lists_haptic_bonds); /* djb-rwth: fixing coverity ID #499504 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 390| 0| inchi_free(new_v3000->lists_steabs); /* djb-rwth: fixing coverity ID #499543 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 391| 0| inchi_free(new_v3000->lists_sterel); /* djb-rwth: fixing coverity ID #499504 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 392| 0| inchi_free(new_v3000->lists_sterac); /* djb-rwth: fixing coverity ID #499575 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 393| 0| inchi_free(new_v3000->atom_index_orig); /* djb-rwth: fixing coverity ID #499540 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 394| 0| inchi_free(new_v3000->atom_index_fin); /* djb-rwth: fixing coverity ID #499613 */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 395| 0| inchi_free(new_v3000); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 396| 0| goto exit_function; 397| 0| } 398| 0| memcpy(lst, old_lst, nn * sizeof(int)); 399| 0| } 400| 0| } 401| 0| } 402| | 403| 0| new_orig_atom->v3000 = new_v3000; 404| 0| } 405| | 406| | /* Success */ 407| 70.4k| ret = 0; 408| 70.4k| } 409| | 410| 70.4k|exit_function: 411| | 412| 70.4k| if ( ret != 0 ) ------------------ | Branch (412:10): [True: 0, False: 70.4k] ------------------ 413| 0| { 414| 0| if ( at && new_orig_atom->at != at ) ------------------ | Branch (414:14): [True: 0, False: 0] | Branch (414:20): [True: 0, False: 0] ------------------ 415| 0| inchi_free(at); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 416| 0| if ( nCurAtLen && new_orig_atom->nCurAtLen != nCurAtLen ) ------------------ | Branch (416:14): [True: 0, False: 0] | Branch (416:27): [True: 0, False: 0] ------------------ 417| 0| inchi_free(nCurAtLen); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 418| 0| if ( nOldCompNumber && new_orig_atom->nOldCompNumber != nOldCompNumber ) ------------------ | Branch (418:14): [True: 0, False: 0] | Branch (418:32): [True: 0, False: 0] ------------------ 419| 0| inchi_free(nOldCompNumber); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 420| 0| } 421| | 422| 70.4k| return ret; 423| 70.4k|} PreprocessOneStructure: 458| 70.4k|{ 459| 70.4k| int i; 460| 70.4k| INCHI_MODE bTautFlags = 0; 461| 70.4k| INCHI_MODE bTautFlagsDone = 0; 462| | 463| | /* 1. Copy orig_inp_data --> prep_inp_data */ 464| | 465| 70.4k| if ( 0 > OrigAtData_Duplicate(prep_inp_data, orig_inp_data) ) ------------------ | Branch (465:10): [True: 0, False: 70.4k] ------------------ 466| 0| { 467| 0| AddErrorMessage(sd->pStrErrStruct, "Out of RAM"); 468| 0| sd->nStructReadError = 99; 469| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 470| 0| goto exit_function; 471| 0| } 472| | 473| |#if ( bRELEASE_VERSION == 0 && (EXTR_HAS_METAL_ATOM & (EXTR_MASK | EXTR_FLAG) ) ) 474| | if ( bHasMetalAtom(orig_inp_data) ) 475| | { 476| | sd->bExtract |= EXTR_HAS_METAL_ATOM; 477| | } 478| |#endif 479| | 480| | /* 2. Fix odd things in prep_inp_data */ 481| | 482| 70.4k| if ( 0 < fix_odd_things(prep_inp_data->num_inp_atoms, prep_inp_data->at, /*0*/ip->bTautFlags & TG_FLAG_FIX_SP3_BUG, ip->bFixNonUniformDraw) ) ------------------ | | 944| 70.4k|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ | Branch (482:10): [True: 783, False: 69.6k] ------------------ 483| 783| { 484| | /* changed 2010-03-17 DT */ 485| 783| if ( !ip->bNoWarnings ) ------------------ | Branch (485:14): [True: 783, False: 0] ------------------ 486| 783| { 487| 783| WarningMessage(sd->pStrErrStruct, "Charges were rearranged"); ------------------ | | 132| 783|#define WarningMessage AddErrorMessage ------------------ 488| 783| } 489| 783| if ( sd->nErrorType < _IS_WARNING ) ------------------ | | 11| 783|#define _IS_WARNING 1 ------------------ | Branch (489:14): [True: 783, False: 0] ------------------ 490| 783| { 491| 783| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 783|#define _IS_WARNING 1 ------------------ 492| 783| } 493| 783| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 570| 783|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 978| 783|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 494| 783| } 495| | 496| |#if ( FIX_ADJ_RAD == 1 ) 497| | if ( ip->bTautFlags & TG_FLAG_FIX_ADJ_RADICALS ) 498| | { 499| | if ( 0 < FixAdjacentRadicals(prep_inp_data->num_inp_atoms, prep_inp_data->at) ) 500| | { 501| | sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ADJ_RADICALS_DONE; 502| | } 503| | } 504| |#endif 505| | 506| |#if ( bRELEASE_VERSION == 0 && (EXTR_FLAGS & EXTR_HAS_FEATURE) ) 507| | if ( bFoundFeature(prep_inp_data->at, prep_inp_data->num_inp_atoms) ) 508| | { 509| | sd->bExtract |= EXTR_HAS_FEATURE; 510| | } 511| |#endif 512| | 513| | 514| | /* Find whether the structure can be disconnected or is a salt */ 515| | 516| | 517| | /* Needs salt disconnection? */ 518| | 519| | /* (@nnuk -> Nauman Ullah Khan) :: In case of Metal Salts with MolecularInorganics parameter we need to skip this pre-processing of Salts */ 520| 70.4k| if ( ip->bMolecularInorganics ) ------------------ | Branch (520:10): [True: 70.4k, False: 0] ------------------ 521| 70.4k| { 522| 70.4k| ; 523| 70.4k| } 524| 0| else if ( ip->bTautFlags & TG_FLAG_DISCONNECT_SALTS ) ------------------ | | 919| 0|#define TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */ ------------------ | Branch (524:15): [True: 0, False: 0] ------------------ 525| 0| { 526| 0| prep_inp_data->bDisconnectSalts = (0 < DisconnectSalts(prep_inp_data, 0)); 527| 0| } 528| 0| else 529| 0| { 530| 0| prep_inp_data->bDisconnectSalts = 0; 531| 0| } 532| | 533| | /* Needs metal disconnection? */ 534| | 535| 70.4k| if ( ip->bTautFlags & TG_FLAG_DISCONNECT_COORD ) ------------------ | | 931| 70.4k|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (535:10): [True: 70.4k, False: 0] ------------------ 536| 70.4k| { 537| 70.4k| i = (0 != (ip->bTautFlags & TG_FLAG_CHECK_VALENCE_COORD)); ------------------ | | 933| 70.4k|#define TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */ ------------------ 538| 70.4k| bMayDisconnectMetals(prep_inp_data, i, &bTautFlagsDone); /* changes prep_inp_data->bDisconnectCoord */ 539| 70.4k| sd->bTautFlagsDone[INCHI_BAS] |= bTautFlagsDone; /* whether any disconnection has been rejected because of the metal proper valence */ ------------------ | | 570| 70.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 540| | 541| |#if ( bRELEASE_VERSION == 0 ) 542| | if ( i && (bTautFlagsDone & TG_FLAG_CHECK_VALENCE_COORD_DONE) ) 543| | { 544| | sd->bExtract |= EXTR_METAL_WAS_NOT_DISCONNECTED; 545| | } 546| |#endif 547| 70.4k| } 548| 0| else 549| 0| { 550| 0| prep_inp_data->bDisconnectCoord = 0; 551| 0| } 552| 70.4k| orig_inp_data->bDisconnectSalts = prep_inp_data->bDisconnectSalts; 553| 70.4k| orig_inp_data->bDisconnectCoord = prep_inp_data->bDisconnectCoord; 554| | 555| | /* 3. if( orig_inp_data->bDisconnectSalts ) then 556| | disconnect salts in prep_inp_data */ 557| | 558| 70.4k| if ( (ip->bTautFlags & TG_FLAG_DISCONNECT_SALTS) && prep_inp_data->bDisconnectSalts && ------------------ | | 919| 70.4k|#define TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */ ------------------ | Branch (558:10): [True: 0, False: 70.4k] | Branch (558:57): [True: 0, False: 0] ------------------ 559| 0| 0 < (i = DisconnectSalts(prep_inp_data, 1)) ) /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ ------------------ | Branch (559:9): [True: 0, False: 0] ------------------ 560| 0| { 561| 0| if ( !ip->bNoWarnings ) ------------------ | Branch (561:14): [True: 0, False: 0] ------------------ 562| 0| { 563| 0| WarningMessage(sd->pStrErrStruct, "Salt was disconnected"); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 564| 0| } 565| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_SALTS_DONE; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_SALTS_DONE; ------------------ | | 964| 0|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 566| 0| if ( sd->nErrorType < _IS_WARNING ) ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ | Branch (566:14): [True: 0, False: 0] ------------------ 567| 0| { 568| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ 569| 0| } 570| 0| if ( (i = ReconcileAllCmlBondParities(prep_inp_data->at, prep_inp_data->num_inp_atoms, 0)) ) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (570:14): [True: 0, False: 0] ------------------ 571| 0| { 572| 0| char szErrCode[16]; 573| 0| sprintf(szErrCode, "%d", i); 574| 0| AddErrorMessage(sd->pStrErrStruct, "0D Parities Reconciliation failed:"); 575| 0| AddErrorMessage(sd->pStrErrStruct, szErrCode); 576| 0| } 577| | 578| |#if ( bRELEASE_VERSION == 0 ) 579| | sd->bExtract |= EXTR_SALT_WAS_DISCONNECTED; 580| |#endif 581| 0| } 582| 70.4k| else 583| 70.4k| { 584| 70.4k| prep_inp_data->bDisconnectSalts = 0; 585| 70.4k| } 586| | 587| | /* Mark the (disconnected) components in prep_inp_data */ 588| | 589| 70.4k| prep_inp_data->num_components = MarkDisconnectedComponents(prep_inp_data, 0); 590| | 591| 70.4k| if ( prep_inp_data->num_components < 0 ) ------------------ | Branch (591:10): [True: 0, False: 70.4k] ------------------ 592| 0| { 593| 0| AddErrorMessage(sd->pStrErrStruct, "Out of RAM"); 594| 0| sd->nStructReadError = 99; 595| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 596| 0| goto exit_function; 597| 0| } 598| | 599| | /* Detect isotopic H on heteroatoms -- necessary condition 600| | for global isotopic tautomerism */ 601| | 602| 70.4k| if ( (i = bNumHeterAtomHasIsotopicH(prep_inp_data->at, prep_inp_data->num_inp_atoms)) ) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (602:10): [True: 244, False: 70.2k] ------------------ 603| 244| { 604| 244| if ( i & 1 ) ------------------ | Branch (604:14): [True: 120, False: 124] ------------------ 605| 120| { 606| 120| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_H_DONE; ------------------ | | 570| 120|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_H_DONE; ------------------ | | 981| 120|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 607| 120| } 608| 244| if ( i & 2 ) ------------------ | Branch (608:14): [True: 207, False: 37] ------------------ 609| 207| { 610| 207| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE; ------------------ | | 570| 207|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE; ------------------ | | 982| 207|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 611| 207| } 612| 244| } 613| | 614| | /* 4a. Detect unusual valences */ 615| | 616| 70.4k| if ( OrigAtData_bCheckUnusualValences(prep_inp_data, 1, sd->pStrErrStruct, ip->bNoWarnings) ) ------------------ | Branch (616:10): [True: 8.55k, False: 61.8k] ------------------ 617| 8.55k| { 618| |#if ( bRELEASE_VERSION == 0 ) 619| | sd->bExtract |= EXTR_UNUSUAL_VALENCES; 620| |#else 621| 8.55k| ; 622| 8.55k|#endif 623| 8.55k| } 624| | 625| | 626| | /* 5. if( orig_inp_data->bDisconnectCoord ) then 627| | -- copy prep_inp_data --> prep_inp_data+1 628| | -- disconnect metals in prep_inp_data */ 629| | 630| | /* (@nnuk -> Nauman Ullah Khan) :: In case of Metals with MolecularInorganics parameter we need to skip this pre-processing of Metals */ 631| 70.4k| if ( ip->bMolecularInorganics ) ------------------ | Branch (631:10): [True: 70.4k, False: 0] ------------------ 632| 70.4k| { 633| 70.4k| return 0; /* Skipping over current functionality */ 634| 70.4k| } 635| 0| else if ( prep_inp_data->bDisconnectCoord ) ------------------ | Branch (635:15): [True: 0, False: 0] ------------------ 636| 0| { 637| | 638| 0| prep_inp_data->num_components = MarkDisconnectedComponents(prep_inp_data, 0); 639| 0| if ( prep_inp_data->num_components < 0 ) ------------------ | Branch (639:14): [True: 0, False: 0] ------------------ 640| 0| { 641| 0| AddErrorMessage(sd->pStrErrStruct, "Out of RAM"); 642| 0| sd->nStructReadError = 99; 643| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 644| 0| goto exit_function; 645| 0| } 646| | 647| | /* Save reconnected structure in prep_inp_data+1 if requested */ 648| 0| if ( 0 != (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) ) ------------------ | | 932| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (648:14): [True: 0, False: 0] ------------------ 649| 0| { 650| 0| if ( 0 > OrigAtData_Duplicate(prep_inp_data + 1, prep_inp_data) ) ------------------ | Branch (650:18): [True: 0, False: 0] ------------------ 651| 0| { 652| 0| AddErrorMessage(sd->pStrErrStruct, "Out of RAM"); 653| 0| sd->nStructReadError = 99; 654| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 655| 0| goto exit_function; 656| 0| } 657| 0| sd->bTautFlags[INCHI_REC] = sd->bTautFlags[INCHI_BAS]; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlags[INCHI_REC] = sd->bTautFlags[INCHI_BAS]; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 658| 0| sd->bTautFlagsDone[INCHI_REC] = sd->bTautFlagsDone[INCHI_BAS]; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlagsDone[INCHI_REC] = sd->bTautFlagsDone[INCHI_BAS]; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 659| 0| { 660| | /* Remove "parity undefined in disconnected structure" flag from reconnected structure */ 661| 0| int k, m; /* djb-rwth: removing redundant variables */ 662| 0| inp_ATOM* at = (prep_inp_data + 1)->at; 663| 0| int num_at = (prep_inp_data + 1)->num_inp_atoms; 664| 0| for ( k = 0; k < num_at; k++ ) ------------------ | Branch (664:30): [True: 0, False: 0] ------------------ 665| 0| { 666| 0| for ( m = 0; m < MAX_NUM_STEREO_BONDS && at[k].sb_parity[m]; m++ ) /* djb-rwth: removing redundant code */ ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (666:34): [True: 0, False: 0] | Branch (666:62): [True: 0, False: 0] ------------------ 667| 0| { 668| 0| at[k].sb_parity[m] &= SB_PARITY_MASK; ------------------ | | 64| 0|#define SB_PARITY_MASK 0x07 ------------------ 669| 0| } 670| 0| } 671| 0| } 672| 0| } 673| | 674| | /* Make disconnected structure in prep_inp_data */ 675| 0| i = (0 != (ip->bTautFlags & TG_FLAG_CHECK_VALENCE_COORD)); ------------------ | | 933| 0|#define TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */ ------------------ 676| | 677| | /* prep_inp_data->bDisconnectCoord > 1 means add 678| | prep_inp_data->bDisconnectCoord-1 explicit H atoms */ 679| 0| if ( 0 < (i = DisconnectMetals(prep_inp_data, i, &bTautFlagsDone)) ) ------------------ | Branch (679:14): [True: 0, False: 0] ------------------ 680| 0| { 681| 0| if ( !ip->bNoWarnings ) ------------------ | Branch (681:18): [True: 0, False: 0] ------------------ 682| 0| { 683| 0| WarningMessage(sd->pStrErrStruct, "Metal was disconnected"); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 684| 0| } 685| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 975| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 686| 0| if ( sd->nErrorType < _IS_WARNING ) ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ | Branch (686:18): [True: 0, False: 0] ------------------ 687| 0| { 688| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ 689| 0| } 690| | 691| |#if ( bRELEASE_VERSION == 0 ) 692| | sd->bExtract |= EXTR_METAL_WAS_DISCONNECTED; 693| |#endif 694| | 695| | /* last parm=1 means find link between unchanged by Metal Disconnection components */ 696| 0| prep_inp_data->num_components = MarkDisconnectedComponents(prep_inp_data, 1); 697| | 698| 0| if ( prep_inp_data->num_components < 0 ) ------------------ | Branch (698:18): [True: 0, False: 0] ------------------ 699| 0| { 700| 0| AddErrorMessage(sd->pStrErrStruct, "Out of RAM"); 701| 0| sd->nStructReadError = 99; 702| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 13| 0|#define _IS_FATAL 3 ------------------ 703| 0| goto exit_function; 704| 0| } 705| | 706| 0| { 707| | /* Set parities for the disconnected structure */ 708| 0| int k, m, p; 709| 0| inp_ATOM* at = (prep_inp_data)->at; 710| 0| int num_at = (prep_inp_data)->num_inp_atoms; 711| 0| for ( k = 0; k < num_at; k++ ) ------------------ | Branch (711:30): [True: 0, False: 0] ------------------ 712| 0| { 713| 0| for ( m = 0; m < MAX_NUM_STEREO_BONDS && (p = at[k].sb_parity[m]); m++ ) ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (713:34): [True: 0, False: 0] | Branch (713:62): [True: 0, False: 0] ------------------ 714| 0| { 715| 0| if ( p & SB_PARITY_FLAG ) ------------------ | | 62| 0|#define SB_PARITY_FLAG 0x38 /**< mask for disconnected metal parity if it is different */ ------------------ | Branch (715:30): [True: 0, False: 0] ------------------ 716| 0| { 717| 0| at[k].sb_parity[m] = (p >> SB_PARITY_SHFT) & SB_PARITY_MASK; ------------------ | | 63| 0|#define SB_PARITY_SHFT 3 /**< number of right shift bits to get disconnected metal parity */ ------------------ at[k].sb_parity[m] = (p >> SB_PARITY_SHFT) & SB_PARITY_MASK; ------------------ | | 64| 0|#define SB_PARITY_MASK 0x07 ------------------ 718| 0| } 719| 0| } 720| 0| } 721| 0| } 722| | 723| 0| if ( (i = ReconcileAllCmlBondParities(prep_inp_data->at, prep_inp_data->num_inp_atoms, 1)) ) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (723:18): [True: 0, False: 0] ------------------ 724| 0| { 725| 0| char szErrCode[16]; 726| 0| sprintf(szErrCode, "%d", i); 727| 0| AddErrorMessage(sd->pStrErrStruct, "0D Parities Reconciliation failed:"); 728| 0| AddErrorMessage(sd->pStrErrStruct, szErrCode); 729| 0| } 730| | 731| 0|#if ( REMOVE_ION_PAIRS_DISC_STRU == 1 ) 732| 0| if ( 0 < remove_ion_pairs(prep_inp_data->num_inp_atoms, prep_inp_data->at) ) ------------------ | Branch (732:18): [True: 0, False: 0] ------------------ 733| 0| { 734| 0| if ( !ip->bNoWarnings ) ------------------ | Branch (734:22): [True: 0, False: 0] ------------------ 735| 0| { 736| 0| WarningMessage(sd->pStrErrStruct, "Charges were rearranged"); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 737| 0| } 738| 0| if ( sd->nErrorType < _IS_WARNING ) ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ | Branch (738:22): [True: 0, False: 0] ------------------ 739| 0| { 740| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ 741| 0| } 742| 0| sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 978| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 743| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 978| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 744| 0| } 745| 0|#endif 746| | 747| | /* 748| | if prep_inp_data->nOldCompNumber[i] = iINChI+1 > 0 then 749| | component #(i+1) in prep_inp_data is identical to component #(iINChI+1) in prep_inp_data+1 750| | */ 751| 0| } 752| 0| else if ( i < 0 ) ------------------ | Branch (752:19): [True: 0, False: 0] ------------------ 753| 0| { 754| 0| AddErrorMessage(sd->pStrErrStruct, "Cannot disconnect metal error"); 755| 0| sd->nStructReadError = i; 756| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 757| 0| goto exit_function; 758| 0| } 759| 0| } 760| 0| else 761| 0| { 762| | /* Remove "disconnected structure parities" from the structure */ 763| 0| int k, m; /* djb-rwth: removing redundant variables */ 764| 0| inp_ATOM* at = (prep_inp_data)->at; 765| 0| int num_at = (prep_inp_data)->num_inp_atoms; 766| 0| for ( k = 0; k < num_at; k++ ) ------------------ | Branch (766:22): [True: 0, False: 0] ------------------ 767| 0| { 768| 0| for ( m = 0; m < MAX_NUM_STEREO_BONDS && at[k].sb_parity[m]; m++ ) /* djb-rwth: removing redundant code */ ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (768:26): [True: 0, False: 0] | Branch (768:54): [True: 0, False: 0] ------------------ 769| 0| { 770| 0| at[k].sb_parity[m] &= SB_PARITY_MASK; ------------------ | | 64| 0|#define SB_PARITY_MASK 0x07 ------------------ 771| 0| } 772| 0| } 773| 0| } 774| | 775| 0|exit_function: 776| | 777| 0| if ( sd->nErrorType < _IS_ERROR && prep_inp_data ) ------------------ | | 12| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (777:10): [True: 0, False: 0] | Branch (777:40): [True: 0, False: 0] ------------------ 778| 0| { 779| 0| if ( 0 < post_fix_odd_things(prep_inp_data->num_inp_atoms, prep_inp_data->at) ) ------------------ | Branch (779:14): [True: 0, False: 0] ------------------ 780| 0| { 781| 0| if ( !ip->bNoWarnings ) ------------------ | Branch (781:18): [True: 0, False: 0] ------------------ 782| 0| { 783| 0| WarningMessage(sd->pStrErrStruct, "Charges were rearranged"); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 784| 0| } 785| 0| if ( sd->nErrorType < _IS_WARNING ) ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ | Branch (785:18): [True: 0, False: 0] ------------------ 786| 0| { 787| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ 788| 0| } 789| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 978| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 790| 0| } 791| 0| if ( (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if ( (sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE) && ------------------ | | 975| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (791:14): [True: 0, False: 0] ------------------ 792| 0| (prep_inp_data + 1)->at && (prep_inp_data + 1)->num_inp_atoms > 0 ) ------------------ | Branch (792:13): [True: 0, False: 0] | Branch (792:40): [True: 0, False: 0] ------------------ 793| 0| { 794| 0| if ( 0 < post_fix_odd_things((prep_inp_data + 1)->num_inp_atoms, (prep_inp_data + 1)->at) ) ------------------ | Branch (794:18): [True: 0, False: 0] ------------------ 795| 0| { 796| 0| if ( !ip->bNoWarnings ) ------------------ | Branch (796:22): [True: 0, False: 0] ------------------ 797| 0| { 798| 0| WarningMessage(sd->pStrErrStruct, "Charges were rearranged"); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 799| 0| } 800| 0| if ( sd->nErrorType < _IS_WARNING ) ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ | Branch (800:22): [True: 0, False: 0] ------------------ 801| 0| { 802| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 0|#define _IS_WARNING 1 ------------------ 803| 0| } 804| 0| sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 571| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 978| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 805| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 978| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 806| 0| } 807| 0| } 808| 0| } 809| | 810| 0| sd->bTautFlags[INCHI_BAS] |= bTautFlags; /* TG_FLAG_CHECK_VALENCE_COORD_DONE, TG_FLAG_MOVE_CHARGE_COORD_DONE */ ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 811| 0| sd->bTautFlagsDone[INCHI_BAS] |= bTautFlagsDone; /* TG_FLAG_CHECK_VALENCE_COORD_DONE, TG_FLAG_MOVE_CHARGE_COORD_DONE */ ------------------ | | 570| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 812| | 813| 0| return sd->nErrorType; 814| 70.4k|} OAD_PolymerUnit_New: 1151| 1.16k|{ 1152| 1.16k| int k, err = 0; 1153| 1.16k| OAD_PolymerUnit* u2 = NULL; 1154| | 1155| 1.16k| u2 = (OAD_PolymerUnit*)inchi_calloc(1, sizeof(OAD_PolymerUnit)); ------------------ | | 1146| 1.16k|#define inchi_calloc calloc ------------------ 1156| 1.16k| if ( NULL == u2 ) ------------------ | Branch (1156:10): [True: 0, False: 1.16k] ------------------ 1157| 0| { 1158| 0| err = 1; 1159| 0| goto exit_function; 1160| 0| } 1161| | 1162| 1.16k| u2->id = id; 1163| 1.16k| u2->label = label; 1164| 1.16k| u2->type = type; 1165| 1.16k| u2->subtype = subtype; 1166| 1.16k| u2->conn = conn; 1167| 1.16k| u2->na = na; 1168| 1.16k| u2->nb = nb; 1169| 1.16k| u2->cyclizable = CLOSING_SRU_NOT_APPLICABLE; ------------------ | | 19| 1.16k|#define CLOSING_SRU_NOT_APPLICABLE 0 ------------------ 1170| 1.16k| u2->cyclized = 0; 1171| 5.82k| for ( k = 0; k < 4; k++ ) ------------------ | Branch (1171:18): [True: 4.66k, False: 1.16k] ------------------ 1172| 4.66k| { 1173| 4.66k| u2->xbr1[k] = 0.0; 1174| 4.66k| u2->xbr2[k] = 0.0; 1175| 4.66k| } 1176| 1.16k| strcpy(u2->smt, smt); 1177| 1.16k| u2->cap1 = -1; 1178| 1.16k| u2->end_atom1 = -1; 1179| 1.16k| u2->cap2 = -1; 1180| 1.16k| u2->end_atom2 = -1; 1181| 1.16k| u2->maxbkbonds = maxbonds; 1182| 1.16k| u2->nbkbonds = nbkbonds; 1183| 1.16k| u2->cap1_is_undef = 0; 1184| 1.16k| u2->cap2_is_undef = 0; 1185| | 1186| 1.16k| u2->alist = NULL; 1187| 1.16k| if ( na > 0 || maxatoms > 0 ) ------------------ | Branch (1187:10): [True: 1.16k, False: 0] | Branch (1187:20): [True: 0, False: 0] ------------------ 1188| 1.16k| { 1189| 1.16k| u2->alist = (int*)inchi_calloc(na > 0 ? na : maxatoms, sizeof(int)); ------------------ | | 1146| 1.16k|#define inchi_calloc calloc ------------------ | Branch (1189:40): [True: 1.16k, False: 0] ------------------ 1190| 1.16k| if ( !u2->alist ) ------------------ | Branch (1190:14): [True: 0, False: 1.16k] ------------------ 1191| 0| { 1192| 0| err = 2; 1193| 0| goto exit_function; 1194| 0| } 1195| 6.10k| for ( k = 0; k < na; k++ ) ------------------ | Branch (1195:22): [True: 4.93k, False: 1.16k] ------------------ 1196| 4.93k| { 1197| 4.93k| u2->alist[k] = alist->item[k]; 1198| 4.93k| } 1199| 1.16k| } 1200| 1.16k| u2->blist = NULL; 1201| 1.16k| if ( nb > 0 || maxbonds > 0 ) ------------------ | Branch (1201:10): [True: 0, False: 1.16k] | Branch (1201:20): [True: 0, False: 1.16k] ------------------ 1202| 0| { 1203| 0| u2->blist = (int*)inchi_calloc(nb > 0 ? 2 * nb : 2 * maxbonds, sizeof(int)); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ | Branch (1203:40): [True: 0, False: 0] ------------------ 1204| 0| if ( !u2->blist ) ------------------ | Branch (1204:14): [True: 0, False: 0] ------------------ 1205| 0| { 1206| 0| err = 3; 1207| 0| goto exit_function; 1208| 0| } 1209| 0| if ( blist ) ------------------ | Branch (1209:14): [True: 0, False: 0] ------------------ 1210| 0| { 1211| 0| for ( k = 0; k < 2 * nb; k++ ) ------------------ | Branch (1211:26): [True: 0, False: 0] ------------------ 1212| 0| { 1213| 0| u2->blist[k] = blist->item[k]; 1214| 0| } 1215| 0| } 1216| | 1217| 0| } 1218| 1.16k| u2->bkbonds = NULL; 1219| | 1220| 1.16k|exit_function: 1221| | 1222| 1.16k| if ( err ) ------------------ | Branch (1222:10): [True: 0, False: 1.16k] ------------------ 1223| 0| { 1224| 0| OAD_PolymerUnit_Free(u2); 1225| 0| return NULL; 1226| 0| } 1227| | 1228| 1.16k| return u2; 1229| 1.16k|} OAD_PolymerUnit_Free: 1318| 2.30k|{ 1319| | 1320| 2.30k| ITRACE_("\n************** About to free OAD_PolymerUnit @ %-p\n", unit); ------------------ | | 98| 2.30k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 2.30k] | | ------------------ ------------------ | Branch (1320:5): [True: 0, False: 0] ------------------ 1321| 2.30k| OAD_PolymerUnit_DebugTrace(unit); 1322| | 1323| 2.30k| if ( unit ) ------------------ | Branch (1323:10): [True: 1.16k, False: 1.14k] ------------------ 1324| 1.16k| { 1325| 1.16k| if ( unit->alist ) ------------------ | Branch (1325:14): [True: 1.16k, False: 0] ------------------ 1326| 1.16k| { 1327| 1.16k| inchi_free(unit->alist); ------------------ | | 1152| 1.16k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.16k, False: 0] | | | Branch (1152:50): [Folded, False: 1.16k] | | ------------------ ------------------ 1328| 1.16k| unit->alist = NULL; 1329| 1.16k| } 1330| 1.16k| if ( unit->blist ) ------------------ | Branch (1330:14): [True: 120, False: 1.04k] ------------------ 1331| 120| { 1332| 120| inchi_free(unit->blist); ------------------ | | 1152| 120|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 120, False: 0] | | | Branch (1152:50): [Folded, False: 120] | | ------------------ ------------------ 1333| 120| unit->blist = NULL; 1334| 120| } 1335| 1.16k| if ( unit->bkbonds ) ------------------ | Branch (1335:14): [True: 120, False: 1.04k] ------------------ 1336| 120| { 1337| 120| imat_free(unit->maxbkbonds, unit->bkbonds); 1338| 120| unit->bkbonds = NULL; 1339| 120| } 1340| 1.16k| } 1341| | 1342| 2.30k| inchi_free(unit); ------------------ | | 1152| 2.30k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 1.16k, False: 1.14k] | | | Branch (1152:50): [Folded, False: 2.30k] | | ------------------ ------------------ 1343| | 1344| 2.30k| return; 1345| 2.30k|} UnMarkRingSystemsInp: 1932| 143|{ 1933| 143| int i; 1934| 17.7k| for ( i = 0; i < num_atoms; i++ ) ------------------ | Branch (1934:18): [True: 17.5k, False: 143] ------------------ 1935| 17.5k| { 1936| 17.5k| at[i].bCutVertex = 0; 1937| 17.5k| at[i].nRingSystem = 0; 1938| 17.5k| at[i].nNumAtInRingSystem = 0; 1939| 17.5k| at[i].nBlockSystem = 0; 1940| 17.5k| } 1941| | 1942| 143| return 0; 1943| 143|} OAD_Polymer_Free: 2042| 231k|{ 2043| 231k| if ( pd ) ------------------ | Branch (2043:10): [True: 837, False: 230k] ------------------ 2044| 837| { 2045| 837| if ( pd->pzz ) ------------------ | Branch (2045:14): [True: 0, False: 837] ------------------ 2046| 0| { 2047| 0| inchi_free(pd->pzz); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 2048| 0| pd->pzz = NULL; 2049| 0| pd->n_pzz = 0; 2050| 0| } 2051| 837| if ( pd->n && pd->units ) ------------------ | Branch (2051:14): [True: 421, False: 416] | Branch (2051:23): [True: 421, False: 0] ------------------ 2052| 421| { 2053| 421| int k; 2054| 2.72k| for ( k = 0; k < pd->n; k++ ) ------------------ | Branch (2054:26): [True: 2.30k, False: 421] ------------------ 2055| 2.30k| { 2056| 2.30k| OAD_PolymerUnit_Free(pd->units[k]); 2057| 2.30k| } 2058| 421| inchi_free(pd->units); ------------------ | | 1152| 421|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 421, False: 0] | | | Branch (1152:50): [Folded, False: 421] | | ------------------ ------------------ 2059| 421| pd->units = NULL; 2060| 421| pd->n = 0; 2061| 421| } 2062| 837| inchi_free(pd); ------------------ | | 1152| 837|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 837, False: 0] | | | Branch (1152:50): [Folded, False: 837] | | ------------------ ------------------ 2063| 837| pd = NULL; 2064| 837| } 2065| | 2066| 231k| return; 2067| 231k|} OrigAtData_RemoveHalfBond: 2492| 202|{ 2493| 202| int k, kk; 2494| | /* djb-rwth: fixing oss-fuzz issues #68286, #30342 */ 2495| 202| if ( at && (this_atom >= 0) && (other_atom >= 0) ) ------------------ | Branch (2495:10): [True: 202, False: 0] | Branch (2495:16): [True: 202, False: 0] | Branch (2495:36): [True: 202, False: 0] ------------------ 2496| 202| { 2497| 202| inp_ATOM* a = &(at[this_atom]); 2498| 202| if ( a ) ------------------ | Branch (2498:14): [True: 202, False: 0] ------------------ 2499| 202| { 2500| 270| for ( k = 0; k < a->valence; k++ ) ------------------ | Branch (2500:26): [True: 101, False: 169] ------------------ 2501| 101| { 2502| 101| if ( a->neighbor[k] != other_atom ) ------------------ | Branch (2502:22): [True: 68, False: 33] ------------------ 2503| 68| { 2504| 68| continue; 2505| 68| } 2506| | 2507| 33| *bond_type = a->bond_type[k]; 2508| 33| *bond_stereo = a->bond_stereo[k]; 2509| | 2510| 33| a->neighbor[k] = a->bond_type[k] = a->bond_stereo[k] = 0; 2511| | 2512| 83| for ( kk = k + 1; kk < a->valence; kk++ ) ------------------ | Branch (2512:35): [True: 50, False: 33] ------------------ 2513| 50| { 2514| 50| a->neighbor[kk - 1] = a->neighbor[kk]; 2515| 50| a->bond_type[kk - 1] = a->bond_type[kk]; 2516| 50| a->bond_stereo[kk - 1] = a->bond_stereo[kk]; 2517| 50| } 2518| 1.60k| for ( kk = a->valence - 1; kk < MAXVAL; kk++ ) ------------------ | | 70| 1.60k|#define MAXVAL 50 /* max number of bonds per atom */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (2518:44): [True: 1.57k, False: 33] ------------------ 2519| 1.57k| { 2520| 1.57k| a->neighbor[kk] = 0; 2521| 1.57k| a->bond_type[kk] = (U_CHAR)0; 2522| 1.57k| a->bond_stereo[kk] = (S_CHAR)0; 2523| 1.57k| } 2524| 33| return 1; 2525| 101| } /* k */ 2526| 202| } 2527| 202| } 2528| | 2529| 169| return 0; 2530| 202|} OrigAtData_RemoveBond: 2553| 102|{ 2554| 102| int del = 0; 2555| | 2556| 102| if ( at && (this_atom >= 0) && (other_atom >= 0) ) /* djb-rwth: fixing oss-fuzz issue #68329, #68286 */ ------------------ | Branch (2556:10): [True: 102, False: 0] | Branch (2556:16): [True: 102, False: 0] | Branch (2556:36): [True: 101, False: 1] ------------------ 2557| 101| { 2558| 101| del = OrigAtData_RemoveHalfBond(this_atom, other_atom, at, bond_type, bond_stereo); 2559| 101| del += OrigAtData_RemoveHalfBond(other_atom, this_atom, at, bond_type, bond_stereo); 2560| | 2561| 101| if ( del == 2 ) ------------------ | Branch (2561:14): [True: 15, False: 86] ------------------ 2562| 15| { 2563| 15| (*num_inp_bonds)--; 2564| 15| at[this_atom].valence--; 2565| 15| at[this_atom].chem_bonds_valence -= *bond_type; 2566| 15| at[other_atom].valence--; 2567| 15| at[other_atom].chem_bonds_valence -= *bond_type; 2568| 15| return 1; 2569| 15| } 2570| 101| } 2571| | 2572| 87| return 0; 2573| 102|} OrigAtData_AddBond: 2583| 223|{ 2584| 223| if ( at ) ------------------ | Branch (2584:10): [True: 223, False: 0] ------------------ 2585| 223| { 2586| | /* djb-rwth: fixing oss-fuzz issue #68286 */ 2587| 223| int i, k, already_here; 2588| 223| inp_ATOM* a = &(at[this_atom]); 2589| | 2590| 223| if ( at[this_atom].valence >= MAXVAL || ------------------ | | 70| 446|#define MAXVAL 50 /* max number of bonds per atom */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (2590:14): [True: 0, False: 223] ------------------ 2591| 223| at[other_atom].valence >= MAXVAL ) ------------------ | | 70| 223|#define MAXVAL 50 /* max number of bonds per atom */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (2591:13): [True: 0, False: 223] ------------------ 2592| 0| { 2593| 0| return 0; 2594| 0| } 2595| | 2596| 223| if ( bond_type != INCHI_BOND_TYPE_DOUBLE && bond_type != INCHI_BOND_TYPE_TRIPLE ) ------------------ | Branch (2596:14): [True: 222, False: 1] | Branch (2596:53): [True: 220, False: 2] ------------------ 2597| 220| { 2598| 220| bond_type = INCHI_BOND_TYPE_SINGLE; 2599| 220| } 2600| | 2601| 223| k = a->valence; 2602| 223| already_here = 0; 2603| 321| for ( i = 0; i < k; i++ ) ------------------ | Branch (2603:22): [True: 114, False: 207] ------------------ 2604| 114| { 2605| 114| if ( a->neighbor[i] == other_atom ) ------------------ | Branch (2605:18): [True: 16, False: 98] ------------------ 2606| 16| { 2607| 16| already_here = 1; break; 2608| 16| } 2609| 114| } 2610| | 2611| 223| if ( !already_here ) ------------------ | Branch (2611:14): [True: 207, False: 16] ------------------ 2612| 207| { 2613| 207| a->neighbor[k] = other_atom; 2614| 207| a->bond_type[k] = (U_CHAR)bond_type; 2615| 207| a->bond_stereo[k] = (S_CHAR)bond_stereo; 2616| 207| a->chem_bonds_valence += bond_type; 2617| 207| a->valence++; 2618| 207| } 2619| | 2620| 223| a = &(at[other_atom]); 2621| 223| k = a->valence; 2622| 223| already_here = 0; 2623| 383| for ( i = 0; i < k; i++ ) ------------------ | Branch (2623:22): [True: 195, False: 188] ------------------ 2624| 195| { 2625| 195| if ( a->neighbor[i] == this_atom ) ------------------ | Branch (2625:18): [True: 35, False: 160] ------------------ 2626| 35| { 2627| 35| already_here = 1; break; 2628| 35| } 2629| 195| } 2630| | 2631| 223| if ( !already_here && (k < MAXVAL) ) /* djb-rwth: condition added to prevent buffer overrun */ ------------------ | | 70| 188|#define MAXVAL 50 /* max number of bonds per atom */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (2631:14): [True: 188, False: 35] | Branch (2631:31): [True: 188, False: 0] ------------------ 2632| 188| { 2633| 188| a->neighbor[k] = this_atom; 2634| 188| a->bond_type[k] = (U_CHAR)bond_type; 2635| 188| a->bond_stereo[k] = (S_CHAR)bond_stereo; 2636| 188| a->chem_bonds_valence += bond_type; 2637| 188| a->valence++; 2638| 188| } 2639| | 2640| 223| (*num_bonds)++; 2641| | 2642| 223| return 1; 2643| 223| } 2644| 0| else 2645| 0| { 2646| 0| return 0; 2647| 0| } 2648| 223|} OrigAtData_AddSingleStereolessBond: 2656| 208|{ 2657| 208| return OrigAtData_AddBond(this_atom, other_atom, at, INCHI_BOND_TYPE_SINGLE, 0, num_bonds); 2658| 208|} OrigAtData_DecreaseBondOrder: 2723| 9|{ 2724| 9| int i, k, n_dn = 0; 2725| 9| inp_ATOM* a; 2726| | 2727| 9| a = &(at[this_atom]); 2728| 9| if ( a->chem_bonds_valence > MAXVAL - 1 ) ------------------ | | 70| 9|#define MAXVAL 50 /* max number of bonds per atom */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (2728:10): [True: 0, False: 9] ------------------ 2729| 0| { 2730| 0| return 0; 2731| 0| } 2732| | 2733| 9| k = a->valence; 2734| 25| for ( i = 0; i < k; i++ ) ------------------ | Branch (2734:18): [True: 22, False: 3] ------------------ 2735| 22| { 2736| 22| if ( a->neighbor[i] != other_atom ) ------------------ | Branch (2736:14): [True: 16, False: 6] ------------------ 2737| 16| { 2738| 16| continue; 2739| 16| } 2740| 6| if ( a->bond_type[i] < 2 ) ------------------ | Branch (2740:14): [True: 1, False: 5] ------------------ 2741| 1| { 2742| 1| return 0; 2743| 1| } 2744| 5| a->bond_type[i]--; 2745| 5| a->chem_bonds_valence--; 2746| 5| n_dn++; 2747| 5| break; 2748| 6| } 2749| | 2750| 8| a = &(at[other_atom]); 2751| 8| k = a->valence; 2752| 15| for ( i = 0; i < k; i++ ) ------------------ | Branch (2752:18): [True: 12, False: 3] ------------------ 2753| 12| { 2754| 12| if ( a->neighbor[i] != this_atom ) ------------------ | Branch (2754:14): [True: 7, False: 5] ------------------ 2755| 7| { 2756| 7| continue; 2757| 7| } 2758| 5| if ( a->bond_type[i] < 2 ) ------------------ | Branch (2758:14): [True: 0, False: 5] ------------------ 2759| 0| { 2760| 0| return 0; 2761| 0| } 2762| 5| a->bond_type[i]--; 2763| 5| a->chem_bonds_valence--; 2764| 5| n_dn++; 2765| 5| break; 2766| 5| } 2767| | 2768| 8| return n_dn; 2769| 8|} OAD_Polymer_FindRingSystems: 3213| 143|{ 3214| 143| int i, j, nrings = 0, bond_type, bond_stereo; 3215| | 3216| 143| if ( NULL == num_ring_sys ) ------------------ | Branch (3216:10): [True: 0, False: 143] ------------------ 3217| 0| { 3218| 0| return 0; 3219| 0| } 3220| | 3221| | /* Remove polymer SRU 'cyclizing' bonds if any */ 3222| 598| for ( j = 0; j < pd->n; j++ ) ------------------ | Branch (3222:18): [True: 455, False: 143] ------------------ 3223| 455| { 3224| 455| if ( pd->units[j]->cyclized ) ------------------ | Branch (3224:14): [True: 0, False: 455] ------------------ 3225| 0| { 3226| 0| OrigAtData_RemoveBond(pd->units[j]->end_atom1 - 1, 3227| 0| pd->units[j]->end_atom2 - 1, 3228| 0| at, &bond_type, &bond_stereo, 3229| 0| num_inp_bonds); 3230| 0| } 3231| 455| } 3232| | 3233| 143| MarkRingSystemsInp(at, nat, start); /*0 );*/ 3234| | 3235| 17.8k| for ( i = 0; i <= nat; i++ ) ------------------ | Branch (3235:18): [True: 17.7k, False: 143] ------------------ 3236| 17.7k| { 3237| 17.7k| num_ring_sys[i] = -1; 3238| 17.7k| } 3239| 17.7k| for ( i = 0; i < nat; i++ ) ------------------ | Branch (3239:18): [True: 17.5k, False: 143] ------------------ 3240| 17.5k| { 3241| 17.5k| if ( at[i].nNumAtInRingSystem > 2 ) ------------------ | Branch (3241:14): [True: 54, False: 17.5k] ------------------ 3242| 54| { 3243| 54| int atnum = at[i].orig_at_number; 3244| 54| num_ring_sys[atnum] = at[i].nRingSystem; 3245| 54| if ( NULL != size_ring_sys ) ------------------ | Branch (3245:18): [True: 54, False: 0] ------------------ 3246| 54| { 3247| 54| size_ring_sys[atnum] = at[i].nNumAtInRingSystem; 3248| 54| } 3249| 54| } 3250| 17.5k| } 3251| | 3252| 143| UnMarkRingSystemsInp(at, nat); 3253| | 3254| 17.7k| for ( i = 0; i < nat; i++ ) ------------------ | Branch (3254:18): [True: 17.5k, False: 143] ------------------ 3255| 17.5k| { 3256| 17.5k| if ( num_ring_sys[i] > -1 ) ------------------ | Branch (3256:14): [True: 47, False: 17.5k] ------------------ 3257| 47| { 3258| 47| nrings++; 3259| 47| } 3260| 17.5k| } 3261| | 3262| | /* Restore polymer SRU 'cyclizing' bonds if applicable */ 3263| 598| for ( j = 0; j < pd->n; j++ ) ------------------ | Branch (3263:18): [True: 455, False: 143] ------------------ 3264| 455| { 3265| 455| if ( pd->units[j]->cyclized ) ------------------ | Branch (3265:14): [True: 0, False: 455] ------------------ 3266| 0| { 3267| 0| OrigAtData_AddSingleStereolessBond(pd->units[j]->end_atom1 - 1, 3268| 0| pd->units[j]->end_atom2 - 1, 3269| 0| at, 3270| 0| num_inp_bonds); 3271| 0| } 3272| 455| } 3273| | 3274| 143| return nrings; 3275| 143|} OAD_Polymer_SetAtProps: 3288| 143|{ 3289| | /* Max rank for in-ring atom is 216 which is achieved for N (element number 7 in Periodic system & erank_rule2[] ),*/ 3290| | /* then goes O with rank 215 (element number 8), and so on... lowest rank is 1 for H . */ 3291| | /* */ 3292| | /* This follows to IUPAC rule 2 [Pure Appl. Chem., Vol. 74, No. 10, 2002, p. 1926] which states: */ 3293| | /* a. a ring or ring system containing nitrogen; */ 3294| | /* b. a ring or ring system containing the heteroatom occurring earliest in the order given in Rule 4; */ 3295| | /* ( which is O > S > Se > Te > N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Hg ) */ 3296| | /* ... */ 3297| | 3298| 143| int erank_rule2[] = { 0,1,198,197,196,202,2,216,215,191,190,189,188,187,206,210,214,183,182,181,180,179,178,177,176, 3299| 143| 175,174,173,172,171,170,169,205,209,213,165,164,163,162,161,160,159,158,157,156,155,154,153,152, 3300| 143| 151,204,208,212,147,146,145,144,143,142,141,140,139,138,137,136,135,134,133,132,131,130,129,128, 3301| 143| 127,126,125,124,123,122,121,201,119,203,207,116,115,114,113,112,111,110,109,108,107,106,105,104, 3302| 143| 103,102,101,100,99,98,97,96,95,94,93,92,91,90,89,88,87,86,85,84,83,82,81 }; 3303| | 3304| | 3305| | 3306| | /* Max rank for chain atom is 215 which is achieved for O (element number 8 in Periodic system & erank_rule4[] ), */ 3307| | /* then goes N with rank 212 (element number 8), and so on... lowest rank is 1 for H . */ 3308| | /* */ 3309| | /* This follows to IUPAC rule 4 [Pure Appl. Chem., Vol. 74, No. 10, 2002, p. 1927] which states: */ 3310| | /* O > S > Se > Te > N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Hg */ 3311| | /* Note: Other heteroatoms may be placed within this order as indicated by their positions in the */ 3312| | /* periodic table [5]. */ 3313| | 3314| 143| int erank_rule4[] = { 0,1,198,197,196,202,2,211,215,191,190,189,188,187,206,210,214,183,182,181,180,179,178,177,176, 3315| 143| 175,174,173,172,171,170,169,205,209,213,165,164,163,162,161,160,159,158,157,156,155,154,153,152, 3316| 143| 151,204,208,212,147,146,145,144,143,142,141,140,139,138,137,136,135,134,133,132,131,130,129,128, 3317| 143| 127,126,125,124,123,122,121,201,119,203,207,116,115,114,113,112,111,110,109,108,107,106,105,104, 3318| 143| 103,102,101,100,99,98,97,96,95,94,93,92,91,90,89,88,87,86,85,84,83,82,81 }; 3319| | 3320| | 3321| 143| int i, j, k, nrings = 0; 3322| 143| int a1, a2, dummy = 0, bond_type = -1, bond_stereo = -1; 3323| 143| int* num_ring_sys = NULL, * size_ring_sys = NULL; 3324| | /* djb-rwth: fixing oss-fuzz issue #68112 */ 3325| 143| int err2_len = sizeof(erank_rule2) / sizeof(erank_rule2[0]); 3326| 143| int err4_len = sizeof(erank_rule4) / sizeof(erank_rule4[0]); 3327| | 3328| 143| if ( (NULL == aprops) || !at || !pd ) /* djb-rwth: fixing oss-fuzz issue #68329, #68286 */ ------------------ | Branch (3328:10): [True: 0, False: 143] | Branch (3328:30): [True: 0, False: 143] | Branch (3328:37): [True: 0, False: 143] ------------------ 3329| 0| { 3330| 0| return; 3331| 0| } 3332| | 3333| | /* Establish element ranks for atoms */ 3334| 17.7k| for ( k = 0; k < nat; k++ ) ------------------ | Branch (3334:18): [True: 17.5k, False: 143] ------------------ 3335| 17.5k| { 3336| 17.5k| int atnum = at[k].orig_at_number, index = k; 3337| 17.5k| U_CHAR err4_ind = at[k].el_number; 3338| 17.5k| if ( cano_nums ) ------------------ | Branch (3338:14): [True: 0, False: 17.5k] ------------------ 3339| 0| { 3340| 0| index = cano_nums[atnum]; 3341| 0| } 3342| 17.5k| if ( index >= 0 && err4_ind < err4_len ) ------------------ | Branch (3342:14): [True: 17.5k, False: 0] | Branch (3342:28): [True: 17.3k, False: 196] ------------------ 3343| 17.3k| { 3344| 17.3k| aprops[index].erank = erank_rule4[err4_ind]; 3345| 17.3k| aprops[index].ring_erank = 0; 3346| 17.3k| aprops[index].ring_size = 0; 3347| 17.3k| aprops[index].ring_num = -1; 3348| 17.3k| } 3349| 196| else 3350| 196| { 3351| | /* deleted H's go here */ 3352| 196| ; 3353| 196| } 3354| | 3355| 17.5k| } 3356| | 3357| | /* Establish ring systems assignments for atoms */ 3358| 143| num_ring_sys = (int*)inchi_calloc((long long)nat + 1, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 143|#define inchi_calloc calloc ------------------ 3359| 143| if ( NULL == num_ring_sys ) ------------------ | Branch (3359:10): [True: 0, False: 143] ------------------ 3360| 0| { 3361| 0| goto exit_function; 3362| 0| } 3363| 143| size_ring_sys = (int*)inchi_calloc((long long)nat + 1, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 143|#define inchi_calloc calloc ------------------ 3364| 143| if ( NULL == size_ring_sys ) ------------------ | Branch (3364:10): [True: 0, False: 143] ------------------ 3365| 0| { 3366| 0| goto exit_function; 3367| 0| } 3368| | 3369| | /* Note that we get here on the way of InChI2Struct conversion. */ 3370| | /* Break temporarily any of (actually, the first) SRU 'cyclizing' bonds */ 3371| 598| for ( j = 0; j < pd->n; j++ ) ------------------ | Branch (3371:18): [True: 455, False: 143] ------------------ 3372| 455| { 3373| 455| if ( pd->units[j]->na > 2 && pd->units[j]->nbkbonds > 0 && ------------------ | Branch (3373:14): [True: 134, False: 321] | Branch (3373:38): [True: 15, False: 119] ------------------ 3374| 15| pd->units[j]->cyclized == 0 && ------------------ | Branch (3374:13): [True: 15, False: 0] ------------------ 3375| 15| pd->units[j]->cyclizable == CLOSING_SRU_RING ) ------------------ | | 20| 15|#define CLOSING_SRU_RING 1 ------------------ | Branch (3375:13): [True: 15, False: 0] ------------------ 3376| 15| { 3377| 15| a1 = pd->units[j]->bkbonds[0][0] - 1; 3378| 15| a2 = pd->units[j]->bkbonds[0][1] - 1; 3379| 15| OrigAtData_RemoveBond(a1, a2, at, &bond_type, &bond_stereo, &dummy); 3380| 15| } 3381| 455| } 3382| | 3383| 143| nrings = OAD_Polymer_FindRingSystems(pd, at, nat, num_inp_bonds, num_ring_sys, size_ring_sys, 0); 3384| | 3385| | /* Immediately restore just broken bond(s) */ 3386| 598| for ( j = 0; j < pd->n; j++ ) ------------------ | Branch (3386:18): [True: 455, False: 143] ------------------ 3387| 455| { 3388| 455| if ( pd->units[j]->na > 2 && ------------------ | Branch (3388:14): [True: 134, False: 321] ------------------ 3389| 134| pd->units[j]->nbkbonds > 0 && ------------------ | Branch (3389:13): [True: 15, False: 119] ------------------ 3390| 15| pd->units[j]->cyclized == 0 && ------------------ | Branch (3390:13): [True: 15, False: 0] ------------------ 3391| 15| pd->units[j]->cyclizable == CLOSING_SRU_RING ) ------------------ | | 20| 15|#define CLOSING_SRU_RING 1 ------------------ | Branch (3391:13): [True: 15, False: 0] ------------------ 3392| 15| { 3393| 15| a1 = pd->units[j]->bkbonds[0][0] - 1; 3394| 15| a2 = pd->units[j]->bkbonds[0][1] - 1; 3395| | /* OrigAtData_AddSingleStereolessBond( a1, a2, at, &dummy ); */ 3396| 15| OrigAtData_AddBond(a1, a2, at, bond_type, bond_stereo, &dummy); 3397| 15| } 3398| 455| } 3399| | 3400| 143| if ( nrings ) ------------------ | Branch (3400:10): [True: 14, False: 129] ------------------ 3401| 14| { 3402| 14| int max_ring_num = 0; 3403| | /* SRU contains ring[s], proceed with them following (not totally) the IUPAC guidelines */ 3404| 6.85k| for ( k = 0; k < nat; k++ ) ------------------ | Branch (3404:22): [True: 6.83k, False: 14] ------------------ 3405| 6.83k| { 3406| | /* Browse 0-based original atoms, go to 1-based cano nums domain if cano_nums mapping is suppied */ 3407| 6.83k| int atnum = at[k].orig_at_number, index = k; 3408| 6.83k| if ( cano_nums ) ------------------ | Branch (3408:18): [True: 0, False: 6.83k] ------------------ 3409| 0| { 3410| 0| index = cano_nums[atnum] + 1; 3411| 0| } 3412| 6.83k| if ( num_ring_sys[atnum] >= 0 ) ------------------ | Branch (3412:18): [True: 54, False: 6.78k] ------------------ 3413| 54| { 3414| 54| aprops[index].ring_num = num_ring_sys[atnum]; /* temporarily */ 3415| | 3416| 54| if ( max_ring_num < aprops[index].ring_num ) ------------------ | Branch (3416:22): [True: 14, False: 40] ------------------ 3417| 14| max_ring_num = aprops[index].ring_num; /* NB: OAD_Polymer_FindRingSystems may return num_ring_sys[] */ 3418| | /* which is not a list of consecutive numbers */ 3419| | 3420| 54| aprops[index].ring_size = size_ring_sys[atnum]; /* Size of ring system which includes the atom k . */ 3421| | /* It is used as an additional score for in-ring */ 3422| | /* atoms' prioritizing (instead of criteria in */ 3423| | /* 2c-2h of IUPAC rule 2 which deal with ring sizes). */ 3424| 54| } 3425| 6.83k| } 3426| | 3427| 76| for ( i = 0; i <= max_ring_num; i++ ) ------------------ | Branch (3427:22): [True: 62, False: 14] ------------------ 3428| 62| { 3429| 62| int erank, max_erank = 0; 3430| 20.7k| for ( k = 0; k < nat; k++ ) ------------------ | Branch (3430:26): [True: 20.6k, False: 62] ------------------ 3431| 20.6k| { 3432| 20.6k| int atnum = at[k].orig_at_number, index = k; 3433| 20.6k| if ( cano_nums ) ------------------ | Branch (3433:22): [True: 0, False: 20.6k] ------------------ 3434| 0| { 3435| 0| index = cano_nums[atnum] + 1; 3436| 0| } 3437| 20.6k| if ( aprops[index].ring_num == i ) ------------------ | Branch (3437:22): [True: 54, False: 20.6k] ------------------ 3438| 54| { 3439| 54| erank = erank_rule2[at[k].el_number]; 3440| 54| if ( erank > max_erank ) ------------------ | Branch (3440:26): [True: 24, False: 30] ------------------ 3441| 24| max_erank = erank; 3442| 54| } 3443| 20.6k| } 3444| 20.7k| for ( k = 0; k < nat; k++ ) ------------------ | Branch (3444:26): [True: 20.6k, False: 62] ------------------ 3445| 20.6k| { 3446| 20.6k| int atnum = at[k].orig_at_number, index = k; 3447| 20.6k| if ( cano_nums ) ------------------ | Branch (3447:22): [True: 0, False: 20.6k] ------------------ 3448| 0| { 3449| 0| index = cano_nums[atnum] + 1; 3450| 0| } 3451| 20.6k| if ( aprops[index].ring_num == i ) ------------------ | Branch (3451:22): [True: 54, False: 20.6k] ------------------ 3452| 54| { 3453| 54| if ( aprops[index].ring_size > 2 ) ------------------ | Branch (3453:26): [True: 54, False: 0] ------------------ 3454| 54| { 3455| 54| aprops[index].ring_erank = max_erank; 3456| 54| } 3457| 54| } 3458| 20.6k| } 3459| 62| } 3460| 14| } 3461| | 3462| 143|exit_function: 3463| 143| if ( num_ring_sys ) ------------------ | Branch (3463:10): [True: 143, False: 0] ------------------ 3464| 143| { 3465| 143| inchi_free(num_ring_sys); ------------------ | | 1152| 143|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 143, False: 0] | | | Branch (1152:50): [Folded, False: 143] | | ------------------ ------------------ 3466| 143| } 3467| 143| if ( size_ring_sys ) ------------------ | Branch (3467:10): [True: 143, False: 0] ------------------ 3468| 143| { 3469| 143| inchi_free(size_ring_sys); ------------------ | | 1152| 143|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 143, False: 0] | | | Branch (1152:50): [Folded, False: 143] | | ------------------ ------------------ 3470| 143| } 3471| | 3472| 143| return; 3473| 143|} OAD_PolymerUnit_DebugTrace: 3613| 2.30k|{ 3614| 2.30k| char* conn = "ABSENT", * typ = "ABSENT", * styp = "ABSENT"; 3615| | 3616| 2.30k| if ( !u ) ------------------ | Branch (3616:10): [True: 1.14k, False: 1.16k] ------------------ 3617| 1.14k| { 3618| 1.14k| return; 3619| 1.14k| } 3620| | 3621| 1.16k| if ( u->conn == 1 ) ------------------ | Branch (3621:10): [True: 495, False: 669] ------------------ 3622| 495| { 3623| 495| conn = "HT"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3624| 495| } 3625| 669| else if ( u->conn == 2 ) ------------------ | Branch (3625:15): [True: 529, False: 140] ------------------ 3626| 529| { 3627| 529| conn = "HH"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3628| 529| } 3629| 140| else if ( u->conn == 3 ) ------------------ | Branch (3629:15): [True: 48, False: 92] ------------------ 3630| 48| { 3631| 48| conn = "EU"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3632| 48| } 3633| | 3634| 1.16k| if ( u->type == 0 ) ------------------ | Branch (3634:10): [True: 0, False: 1.16k] ------------------ 3635| 0| { 3636| 0| typ = "NONE"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3637| 0| } 3638| 1.16k| else if ( u->type == 1 ) ------------------ | Branch (3638:15): [True: 12, False: 1.15k] ------------------ 3639| 12| { 3640| 12| typ = "SRU"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3641| 12| } 3642| 1.15k| else if ( u->type == 2 ) ------------------ | Branch (3642:15): [True: 2, False: 1.15k] ------------------ 3643| 2| { 3644| 2| typ = "MON"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3645| 2| } 3646| 1.15k| else if ( u->type == 3 ) ------------------ | Branch (3646:15): [True: 123, False: 1.02k] ------------------ 3647| 123| { 3648| 123| typ = "COP"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3649| 123| } 3650| 1.02k| else if ( u->type == 4 ) ------------------ | Branch (3650:15): [True: 25, False: 1.00k] ------------------ 3651| 25| { 3652| 25| typ = "MOD"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3653| 25| } 3654| 1.00k| else if ( u->type == 5 ) ------------------ | Branch (3654:15): [True: 965, False: 37] ------------------ 3655| 965| { 3656| 965| typ = "MER"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3657| 965| } 3658| | 3659| 1.16k| if ( u->subtype == 1 ) ------------------ | Branch (3659:10): [True: 366, False: 798] ------------------ 3660| 366| { 3661| 366| styp = "ALT"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3662| 366| } 3663| 798| else if ( u->subtype == 2 ) ------------------ | Branch (3663:15): [True: 143, False: 655] ------------------ 3664| 143| { 3665| 143| styp = "RAN"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3666| 143| } 3667| 655| else if ( u->subtype == 3 ) ------------------ | Branch (3667:15): [True: 30, False: 625] ------------------ 3668| 30| { 3669| 30| styp = "BLK"; /* djb-rwth: ignoring LLVM warning: possible presence of global variables */ 3670| 30| } 3671| | 3672| 1.16k| { 3673| 1.16k| int i, k; 3674| 1.16k| int na, nb; 3675| | 3676| 1.16k| ITRACE_("\n\nPOLYMER UNIT @ %-p", u); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3676:9): [True: 0, False: 0] ------------------ 3677| | 3678| 1.16k| ITRACE_("\n\tid=%-d label=%-d type=%-s subtype=%-s conn=%-s subscr='%-s'\n", ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3678:9): [True: 0, False: 0] ------------------ 3679| 0| u->id, u->label, typ, styp, conn, u->smt); 3680| | 3681| 1.16k| ITRACE_("\tBracket1 coords: %-f, %-f, %-f, %-f\n", u->xbr1[0], u->xbr1[1], u->xbr1[2], u->xbr1[3]); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3681:9): [True: 0, False: 0] ------------------ 3682| 1.16k| ITRACE_("\tBracket2 coords: %-f, %-f, %-f, %-f\n", u->xbr2[0], u->xbr2[1], u->xbr2[2], u->xbr2[3]); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3682:9): [True: 0, False: 0] ------------------ 3683| | 3684| 1.16k| na = u->na; 3685| 1.16k| ITRACE_("\t%-d atoms { ", na); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3685:9): [True: 0, False: 0] ------------------ 3686| 4.93k| for ( k = 0; k < na - 1; k++ ) ------------------ | Branch (3686:22): [True: 3.77k, False: 1.16k] ------------------ 3687| 3.77k| { 3688| 3.77k| ITRACE_(" %-d, ", u->alist[k]); ------------------ | | 98| 3.77k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 3.77k] | | ------------------ ------------------ | Branch (3688:13): [True: 0, False: 0] ------------------ 3689| 3.77k| } 3690| 1.16k| ITRACE_(" %-d }\n", u->alist[na - 1]); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3690:9): [True: 0, False: 0] ------------------ 3691| | 3692| 1.16k| nb = u->nb; 3693| 1.16k| ITRACE_("\t%-d bonds crossing unit borders { ", nb); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3693:9): [True: 0, False: 0] ------------------ 3694| | 3695| 1.40k| for ( k = 0; k < nb; k++ ) ------------------ | Branch (3695:22): [True: 240, False: 1.16k] ------------------ 3696| 240| { 3697| 240| ITRACE_(" %-d-%-d ", u->blist[2 * k], u->blist[2 * k + 1]); ------------------ | | 98| 240|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 240] | | ------------------ ------------------ | Branch (3697:13): [True: 0, False: 0] ------------------ 3698| 240| } 3699| 1.16k| ITRACE_("}\n"); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3699:9): [True: 0, False: 0] ------------------ 3700| | 3701| 1.16k| ITRACE_("\tCRU caps and end atoms { "); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3701:9): [True: 0, False: 0] ------------------ 3702| | 3703| 1.16k| ITRACE_("*%-d-[-%-d(end1) ... ", u->cap1, u->end_atom1); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3703:9): [True: 0, False: 0] ------------------ 3704| 1.16k| ITRACE_("%-d(end2)-]-*%-d", u->end_atom2, u->cap2); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3704:9): [True: 0, False: 0] ------------------ 3705| 1.16k| ITRACE_(" }\n"); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3705:9): [True: 0, False: 0] ------------------ 3706| | 3707| 1.16k| ITRACE_("\tBackbone bonds (may include 'artificially cyclizing' one) : %-d bonds ", u->nbkbonds); ------------------ | | 98| 1.16k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 1.16k] | | ------------------ ------------------ | Branch (3707:9): [True: 0, False: 0] ------------------ 3708| 1.16k| if ( u->nbkbonds ) ------------------ | Branch (3708:14): [True: 16, False: 1.14k] ------------------ 3709| 16| { 3710| 16| ITRACE_(" { "); ------------------ | | 98| 16|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 16] | | ------------------ ------------------ | Branch (3710:13): [True: 0, False: 0] ------------------ 3711| 43| for ( i = 0; i < u->nbkbonds; i++ ) ------------------ | Branch (3711:26): [True: 27, False: 16] ------------------ 3712| 27| { 3713| 27| ITRACE_("(%-d, %-d) ", u->bkbonds[i][0], u->bkbonds[i][1]); ------------------ | | 98| 27|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 27] | | ------------------ ------------------ | Branch (3713:17): [True: 0, False: 0] ------------------ 3714| 27| } 3715| 16| ITRACE_("}\n"); ------------------ | | 98| 16|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 16] | | ------------------ ------------------ | Branch (3715:13): [True: 0, False: 0] ------------------ 3716| 16| } 3717| 1.16k| } 3718| | 3719| | 3720| 1.16k| return; 3721| 2.30k|} OAD_Polymer_SmartReopenCyclizedUnits: 3852| 143|{ 3853| 143| int i; 3854| | /* djb-rwth: fixing oss-fuzz issue #68329 */ 3855| 143| OAD_AtProps* aprops = (OAD_AtProps*)inchi_calloc((long long)nat + 1, sizeof(OAD_AtProps)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 143|#define inchi_calloc calloc ------------------ 3856| | /* nat + 1: add extra element for possibe 1-based indexing */ 3857| | 3858| 143| if ( !p ) ------------------ | Branch (3858:10): [True: 0, False: 143] ------------------ 3859| 0| { 3860| 0| inchi_free(aprops); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3861| 0| return; 3862| 0| } 3863| 143| if ( p->n < 1 ) ------------------ | Branch (3863:10): [True: 0, False: 143] ------------------ 3864| 0| { 3865| 0| inchi_free(aprops); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3866| 0| return; 3867| 0| } 3868| 143| if ( !p->really_do_frame_shift ) ------------------ | Branch (3868:10): [True: 0, False: 143] ------------------ 3869| 0| { 3870| 0| inchi_free(aprops); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3871| 0| return; 3872| 0| } 3873| | /* djb-rwth: fixing oss-fuzz issue #68329 */ 3874| 143| if ( nat <= 0 ) ------------------ | Branch (3874:10): [True: 0, False: 143] ------------------ 3875| 0| { 3876| 0| inchi_free(aprops); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3877| 0| return; 3878| 0| } 3879| | 3880| | /*ITRACE_( "\n\n*********************************************************************\n* ENTERING OAD_Polymer_SmartReopenCyclizedUnits()" ); 3881| | OAD_Polymer_DebugTrace( p );*/ 3882| | 3883| | /* Set atom properties for sorting */ 3884| 143| if ( !aprops || !at ) /* djb-rwth: fixing oss-fuzz issue #68329, #68286 */ ------------------ | Branch (3884:10): [True: 0, False: 143] | Branch (3884:21): [True: 0, False: 143] ------------------ 3885| 0| { 3886| 0| inchi_free(aprops); /* djb-rwth: avoiding memory leak */ ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 3887| 0| return; 3888| 0| } 3889| 143| OAD_Polymer_SetAtProps(p, at, nat, num_inp_bonds, aprops, NULL); /* NULL as we alredy are in 1-based cano_nums while at i2s/i2i*/ 3890| 598| for ( i = 0; i < p->n; i++ ) ------------------ | Branch (3890:18): [True: 455, False: 143] ------------------ 3891| 455| { 3892| 455| if ( p->units[i] ) /* djb-rwth: fixing oss-fuzz issue #68329 */ ------------------ | Branch (3892:14): [True: 455, False: 0] ------------------ 3893| 455| { 3894| 455| OAD_PolymerUnit* u = p->units[i]; 3895| 455| if ( p->frame_shift_scheme == FSS_NONE ) ------------------ | Branch (3895:18): [True: 0, False: 455] ------------------ 3896| 0| { 3897| 0| continue; 3898| 0| } 3899| 455| if ( /* !u->cyclizable || u->cyclized || */ 3900| 455| u->nbkbonds < 1 || ------------------ | Branch (3900:17): [True: 346, False: 109] ------------------ 3901| 109| u->cap1 < 1 || u->cap2 < 1 || ------------------ | Branch (3901:17): [True: 2, False: 107] | Branch (3901:32): [True: 1, False: 106] ------------------ 3902| 106| u->cap1 > nat || u->cap2 > nat ) ------------------ | Branch (3902:17): [True: 1, False: 105] | Branch (3902:34): [True: 1, False: 104] ------------------ 3903| 351| { 3904| 351| continue; 3905| 351| } 3906| 104| if ( OAD_PolymerUnit_SetReopeningDetails(u, at) ) ------------------ | Branch (3906:18): [True: 104, False: 0] ------------------ 3907| 104| { 3908| 104| int senior_bond; 3909| 104| OAD_PolymerUnit_SortBackboneBondsAndSetSeniors(u, at, aprops, &senior_bond); 3910| 104| } 3911| 104| OAD_PolymerUnit_ReopenCyclized(u, at, aprops, nat, num_inp_bonds); 3912| 104| } 3913| 455| } 3914| | 3915| 143| p->really_do_frame_shift = 0; 3916| 143| inchi_free(aprops); ------------------ | | 1152| 143|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 143, False: 0] | | | Branch (1152:50): [Folded, False: 143] | | ------------------ ------------------ 3917| | 3918| 143| return; 3919| 143|} OAD_PolymerUnit_ReopenCyclized: 3928| 104|{ 3929| 104| int bond_type, bond_stereo; 3930| | 3931| 104| if ( u->cyclizable == CLOSING_SRU_RING ) ------------------ | | 20| 104|#define CLOSING_SRU_RING 1 ------------------ | Branch (3931:10): [True: 87, False: 17] ------------------ 3932| 87| { 3933| | /* Decyclize artificially introduced bond */ 3934| 87| OrigAtData_RemoveBond(u->end_atom1 - 1, u->end_atom2 - 1, 3935| 87| at, &bond_type, &bond_stereo, num_inp_bonds); 3936| 87| } 3937| 17| else if ( u->cyclizable == CLOSING_SRU_HIGHER_ORDER_BOND ) ------------------ | | 21| 17|#define CLOSING_SRU_HIGHER_ORDER_BOND 2 ------------------ | Branch (3937:15): [True: 9, False: 8] ------------------ 3938| 9| { 3939| 9| OrigAtData_DecreaseBondOrder(u->end_atom1 - 1, u->end_atom2 - 1, at); 3940| 9| } 3941| 8| else if ( u->cyclizable == CLOSING_SRU_DIRADICAL ) ------------------ | | 22| 8|#define CLOSING_SRU_DIRADICAL 3 ------------------ | Branch (3941:15): [True: 8, False: 0] ------------------ 3942| 8| { 3943| 8| if ( at[u->end_atom1 - 1].radical == RADICAL_TRIPLET ) ------------------ | | 77| 8|#define RADICAL_TRIPLET 3 ------------------ | Branch (3943:14): [True: 0, False: 8] ------------------ 3944| 0| { 3945| 0| at[u->end_atom1 - 1].radical = 0; 3946| 0| } 3947| 8| } 3948| | 3949| | /* Add explicitly connections to star atoms */ 3950| 104| OrigAtData_AddSingleStereolessBond(u->cap1 - 1, u->end_atom1 - 1, 3951| 104| at, num_inp_bonds); 3952| 104| OrigAtData_AddSingleStereolessBond(u->cap2 - 1, u->end_atom2 - 1, 3953| 104| at, num_inp_bonds); 3954| | 3955| | /* Create crossing bonds */ 3956| 104| u->nb = 2; 3957| 104| u->nbkbonds = 0; 3958| 104| if ( !u->blist ) ------------------ | Branch (3958:10): [True: 104, False: 0] ------------------ 3959| 104| { 3960| 104| u->blist = (int*)inchi_calloc(2 * (long long)u->nb, sizeof(int)); /* djb-rwth: cast operator added */ ------------------ | | 1146| 104|#define inchi_calloc calloc ------------------ 3961| 104| } 3962| 104| if ( !u->blist ) ------------------ | Branch (3962:10): [True: 0, False: 104] ------------------ 3963| 0| { 3964| 0| return; 3965| 0| } 3966| | 3967| 104| u->blist[0] = u->cap1; 3968| 104| u->blist[1] = u->end_atom1; 3969| 104| u->blist[2] = u->cap2; 3970| 104| u->blist[3] = u->end_atom2; 3971| | 3972| 104| return; 3973| 104|} OAD_PolymerUnit_SetReopeningDetails: 3978| 104|{ 3979| 104| int k; 3980| | 3981| | /* Check reopening type */ 3982| | 3983| | /* Caps are separated by one atom - that's not error but do nothing */ 3984| 104| if ( u->nbkbonds == 0 ) ------------------ | Branch (3984:10): [True: 0, False: 104] ------------------ 3985| 0| { 3986| 0| ; 3987| 0| } 3988| 104| else if ( u->nbkbonds == 1 ) ------------------ | Branch (3988:15): [True: 28, False: 76] ------------------ 3989| 28| { 3990| 28| u->end_atom1 = u->bkbonds[0][0]; 3991| 28| u->end_atom2 = u->bkbonds[0][1]; 3992| | 3993| 28| if ( u->end_atom1 == u->end_atom2 ) ------------------ | Branch (3993:14): [True: 8, False: 20] ------------------ 3994| 8| { 3995| 8|#ifdef ALLOW_CLOSING_SRU_VIA_DIRADICAL 3996| 8| u->cyclizable = CLOSING_SRU_DIRADICAL; ------------------ | | 22| 8|#define CLOSING_SRU_DIRADICAL 3 ------------------ 3997| |#else 3998| | u->cyclizable = CLOSING_SRU_NOT_APPLICABLE; 3999| |#endif 4000| 8| } 4001| 20| else 4002| 20| { 4003| | /* If caps are separated by two atoms - that's not error but do nothing */ 4004| 37| for ( k = 0; k < at[u->end_atom1 - 1].valence; k++ ) ------------------ | Branch (4004:26): [True: 30, False: 7] ------------------ 4005| 30| { 4006| 30| if ( at[u->end_atom1 - 1].neighbor[k] == u->end_atom2 - 1 ) ------------------ | Branch (4006:22): [True: 13, False: 17] ------------------ 4007| 13| { 4008| 13| if ( at[u->end_atom1 - 1].bond_type[k] > 1 ) ------------------ | Branch (4008:26): [True: 5, False: 8] ------------------ 4009| 5|#ifdef ALLOW_CLOSING_SRU_VIA_HIGHER_ORDER_BOND 4010| 5| u->cyclizable = CLOSING_SRU_HIGHER_ORDER_BOND; ------------------ | | 21| 5|#define CLOSING_SRU_HIGHER_ORDER_BOND 2 ------------------ 4011| |#else 4012| | /* u->cyclizable = CLOSING_SRU_NOT_APPLICABLE;*/ 4013| |#endif 4014| 13| break; 4015| 13| } 4016| 30| } 4017| 20| } 4018| 28| } /* */ 4019| | 4020| 104| return u->nbkbonds; 4021| 104|} OAD_PolymerUnit_SortBackboneBondsAndSetSeniors: 4030| 104|{ 4031| 104| int j, * bnum = NULL; 4032| | 4033| 104| *senior_bond = 0; 4034| | 4035| | /* Sort backbone (== frame shiftable) bonds if necessary */ 4036| 104| if ( u->nbkbonds > 1 ) ------------------ | Branch (4036:10): [True: 76, False: 28] ------------------ 4037| 76| { 4038| 76| bnum = (int*)inchi_calloc(u->nbkbonds, sizeof(int)); ------------------ | | 1146| 76|#define inchi_calloc calloc ------------------ 4039| 76| if ( bnum ) ------------------ | Branch (4039:14): [True: 76, False: 0] ------------------ 4040| 76| { 4041| 838| for ( j = 0; j < u->nbkbonds; j++ ) ------------------ | Branch (4041:26): [True: 762, False: 76] ------------------ 4042| 762| { 4043| 762| bnum[j] = j; 4044| 762| } 4045| 76| OAD_PolymerUnit_SortBackboneBonds(u, aprops, bnum); 4046| 76| *senior_bond = bnum[0]; 4047| 76| inchi_free(bnum); ------------------ | | 1152| 76|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 76, False: 0] | | | Branch (1152:50): [Folded, False: 76] | | ------------------ ------------------ 4048| 76| } 4049| 76| } 4050| | 4051| | /* v. 1.05+ : place senior atom the first ("left") in the senior bond */ 4052| 104| if ( OAD_Polymer_IsFirstAtomRankLower(u->bkbonds[*senior_bond][0], u->bkbonds[*senior_bond][1], aprops) == 1 ) ------------------ | Branch (4052:10): [True: 53, False: 51] ------------------ 4053| 53| { 4054| 53| int tmp = u->bkbonds[*senior_bond][0]; 4055| 53| u->bkbonds[*senior_bond][0] = u->bkbonds[*senior_bond][1]; 4056| 53| u->bkbonds[*senior_bond][1] = tmp; 4057| 53| } 4058| | 4059| 104| u->end_atom1 = u->bkbonds[*senior_bond][0]; 4060| 104| u->end_atom2 = u->bkbonds[*senior_bond][1]; 4061| | 4062| 104| return; 4063| 104|} OAD_PolymerUnit_SortBackboneBonds: 4070| 76|{ 4071| 76| int i, j, tmp; 4072| 76| int n = u->nbkbonds; 4073| 76| if ( NULL == bnum ) ------------------ | Branch (4073:10): [True: 0, False: 76] ------------------ 4074| 0| { 4075| 0| return; 4076| 0| } 4077| 762| for ( i = 1; i < n; i++ ) ------------------ | Branch (4077:18): [True: 686, False: 76] ------------------ 4078| 686| { 4079| 686| tmp = bnum[i]; 4080| 686| j = i - 1; 4081| 3.12k| while ( j >= 0 && OAD_Polymer_CompareBackboneBondsSeniority(u->bkbonds[bnum[j]], u->bkbonds[tmp], aprops) > 0 ) ------------------ | Branch (4081:17): [True: 3.03k, False: 86] | Branch (4081:27): [True: 2.43k, False: 600] ------------------ 4082| 2.43k| { 4083| 2.43k| bnum[j + 1] = bnum[j]; 4084| 2.43k| j--; 4085| 2.43k| } 4086| 686| bnum[j + 1] = tmp; 4087| 686| } 4088| | 4089| 76| return; 4090| 76|} OAD_Polymer_CompareBackboneBondsSeniority: 4099| 3.03k|{ 4100| 3.03k| int b1min, b1max, b2min, b2max, tmp, cmp = 0; 4101| | 4102| | /* Find min and max ext-ranked ends of the both bonds */ 4103| 3.03k| b1max = b1[0]; b1min = b1[1]; 4104| 3.03k| b2max = b2[0]; b2min = b2[1]; 4105| 3.03k| if ( OAD_Polymer_IsFirstAtomRankLower(b1min, b1max, aprops) == -1 ) ------------------ | Branch (4105:10): [True: 551, False: 2.48k] ------------------ 4106| 551| { 4107| 551| tmp = b1max; 4108| 551| b1max = b1min; 4109| 551| b1min = tmp; 4110| 551| } 4111| 3.03k| if ( OAD_Polymer_IsFirstAtomRankLower(b2min, b2max, aprops) == -1 ) ------------------ | Branch (4111:10): [True: 1.27k, False: 1.76k] ------------------ 4112| 1.27k| { 4113| 1.27k| tmp = b2max; 4114| 1.27k| b2max = b2min; 4115| 1.27k| b2min = tmp; 4116| 1.27k| } 4117| | 4118| | /* Compare bonds' seniority */ 4119| | 4120| | /* First, favor the bond which has greater ext-rank end 4121| | NB: the result may be 0, that is, equal max ext. ranks */ 4122| | 4123| 3.03k| cmp = OAD_Polymer_CompareRanksOfTwoAtoms(b1max, b2max, aprops); 4124| 3.03k| if ( cmp == 1 ) ------------------ | Branch (4124:10): [True: 276, False: 2.76k] ------------------ 4125| 276| { 4126| 276| return 1; /* rank(b1max) < rank(b2max), so bond2 is senior */ 4127| 276| } 4128| 2.76k| else if ( cmp == -1 ) ------------------ | Branch (4128:15): [True: 31, False: 2.73k] ------------------ 4129| 31| { 4130| 31| return -1; /* rank(b1max) > rank(b2max), so bond1 is senior */ 4131| 31| } 4132| | 4133| | /* Max ends are of the same rank, so favor the bond with lesser min-rank end 4134| | NB: the result may NOT be 0, that is, the case is always resolved */ 4135| | 4136| 2.73k| cmp = OAD_Polymer_CompareRanksOfTwoAtoms(b1min, b2min, aprops); /*OAD_Polymer_IsFirstAtomRankLower( b1min, b2min, aprops );*/ 4137| | 4138| 2.73k| if ( cmp == 1 ) ------------------ | Branch (4138:10): [True: 17, False: 2.71k] ------------------ 4139| 17| { 4140| 17| return -1; /* rank(b1min) < rank(b2min), so bond1 is senior */ 4141| 17| } 4142| 2.71k| else if ( cmp == -1 ) ------------------ | Branch (4142:15): [True: 225, False: 2.49k] ------------------ 4143| 225| { 4144| 225| return 1; /* rank(b1min) > rank(b2min), so bond2 is senior */ 4145| 225| } 4146| | 4147| | /* Min ends are of the same rank. Here is the time to compare directly 4148| | which canonical number is larger of max-ends ... */ 4149| | 4150| 2.49k| if ( b1max < b2max ) ------------------ | Branch (4150:10): [True: 1.80k, False: 685] ------------------ 4151| 1.80k| { 4152| 1.80k| return 1; 4153| 1.80k| } 4154| 685| if ( b1max > b2max ) ------------------ | Branch (4154:10): [True: 99, False: 586] ------------------ 4155| 99| { 4156| 99| return -1; 4157| 99| } 4158| | 4159| | /* ... they are the same, so compare which canonical number is larger for min-ends ... */ 4160| | 4161| 586| if ( b1min < b2min ) ------------------ | Branch (4161:10): [True: 18, False: 568] ------------------ 4162| 18| { 4163| 18| return -1; /* b1min < b2min, so bond1 is senior */ 4164| 18| } 4165| 568| if ( b1min > b2min ) ------------------ | Branch (4165:10): [True: 133, False: 435] ------------------ 4166| 133| { 4167| 133| return 1; /* b1min > b2min, so bond2 is senior */ 4168| 133| } 4169| | 4170| 435| return 0; /* we should not reach there */ 4171| 568|} OAD_Polymer_CompareRanksOfTwoAtoms: 4180| 11.9k|{ 4181| 11.9k| const int HETEROCYC = 3, HETEROAT = 2, CARBOCYC = 1, CARBOAT = 0; 4182| | /* NB: Carbon's rank is always 2, next to the lowest */ 4183| | 4184| 11.9k| int a1 = atom1 - 1; 4185| 11.9k| int a2 = atom2 - 1; 4186| 11.9k| int a1typ = CARBOAT; 4187| 11.9k| int a2typ = CARBOAT; 4188| | 4189| | /* djb-rwth: fixing oss-fuzz issue #69501, #68277 */ 4190| 11.9k| if ( (a1 < 0) || (a2 < 0) ) ------------------ | Branch (4190:10): [True: 5.21k, False: 6.73k] | Branch (4190:22): [True: 637, False: 6.09k] ------------------ 4191| 5.85k| { 4192| 5.85k| return 0; 4193| 5.85k| } 4194| | 4195| 6.09k| if ( aprops[a1].ring_size > 2 ) ------------------ | Branch (4195:10): [True: 1, False: 6.09k] ------------------ 4196| 1| { 4197| 1| if ( aprops[a1].ring_erank <= 2 ) ------------------ | Branch (4197:14): [True: 0, False: 1] ------------------ 4198| 0| { 4199| 0| a1typ = CARBOCYC; 4200| 0| } 4201| 1| else 4202| 1| { 4203| 1| a1typ = HETEROCYC; 4204| 1| } 4205| 1| } 4206| 6.09k| else 4207| 6.09k| { 4208| 6.09k| if ( aprops[a1].erank == 2 ) ------------------ | Branch (4208:14): [True: 451, False: 5.64k] ------------------ 4209| 451| { 4210| 451| a1typ = CARBOAT; 4211| 451| } 4212| 5.64k| else 4213| 5.64k| { 4214| 5.64k| a1typ = HETEROAT; 4215| 5.64k| } 4216| 6.09k| } 4217| | 4218| 6.09k| if ( aprops[a2].ring_size > 2 ) ------------------ | Branch (4218:10): [True: 4, False: 6.09k] ------------------ 4219| 4| { 4220| 4| if ( aprops[a2].ring_erank <= 2 ) ------------------ | Branch (4220:14): [True: 0, False: 4] ------------------ 4221| 0| { 4222| 0| a2typ = CARBOCYC; 4223| 0| } 4224| 4| else 4225| 4| { 4226| 4| a2typ = HETEROCYC; 4227| 4| } 4228| 4| } 4229| 6.09k| else 4230| 6.09k| { 4231| 6.09k| if ( aprops[a2].erank == 2 ) ------------------ | Branch (4231:14): [True: 355, False: 5.73k] ------------------ 4232| 355| { 4233| 355| a2typ = CARBOAT; 4234| 355| } 4235| 5.73k| else 4236| 5.73k| { 4237| 5.73k| a2typ = HETEROAT; 4238| 5.73k| } 4239| 6.09k| } 4240| | 4241| | /* Compare */ 4242| | 4243| | /* 4244| | Follow IUPAC Rule 1 4245| | 'The basic order of seniority of subunits is: 4246| | heterocyclic rings and ring systems > heteroatom chains > 4247| | > carbocyclic rings and ring systems > acyclic carbon chains' 4248| | */ 4249| | 4250| 6.09k| if ( a1typ == HETEROCYC && a2typ == HETEROCYC ) /* a1 and a2 are HETEROCYC */ ------------------ | Branch (4250:10): [True: 1, False: 6.09k] | Branch (4250:32): [True: 1, False: 0] ------------------ 4251| 1| { 4252| | /* Try resolving by senior-heteroatom ring */ 4253| 1| if ( aprops[a1].ring_erank < aprops[a2].ring_erank ) ------------------ | Branch (4253:14): [True: 0, False: 1] ------------------ 4254| 0| { 4255| 0| return 1; 4256| 0| } 4257| 1| if ( aprops[a1].ring_erank > aprops[a2].ring_erank ) ------------------ | Branch (4257:14): [True: 0, False: 1] ------------------ 4258| 0| { 4259| 0| return -1; 4260| 0| } 4261| | /* Same senior-heteroatom rings, try resolving by total ring size */ 4262| 1| if ( aprops[a1].ring_size < aprops[a2].ring_size ) ------------------ | Branch (4262:14): [True: 0, False: 1] ------------------ 4263| 0| { 4264| 0| return 1; 4265| 0| } 4266| 1| if ( aprops[a1].ring_size > aprops[a2].ring_size ) ------------------ | Branch (4266:14): [True: 0, False: 1] ------------------ 4267| 0| { 4268| 0| return -1; 4269| 0| } 4270| | /* Could not resolve... */ 4271| 1| return 0; 4272| 1| } 4273| 6.09k| else if ( a1typ == HETEROCYC ) ------------------ | Branch (4273:15): [True: 0, False: 6.09k] ------------------ 4274| 0| { 4275| 0| return -1; /* a1 is HETEROCYC, a2 is any other (==junior) */ 4276| 0| } 4277| 6.09k| else if ( a2typ == HETEROCYC ) ------------------ | Branch (4277:15): [True: 3, False: 6.09k] ------------------ 4278| 3| { 4279| 3| return 1; /* a2 is HETEROCYC, a1 is any other (==junior) */ 4280| 3| } 4281| | 4282| | /* HETEROCYC left out */ 4283| | 4284| 6.09k| if ( a1typ == HETEROAT && a2typ == HETEROAT ) /* a1 and a2 are HETEROAT */ ------------------ | Branch (4284:10): [True: 5.64k, False: 451] | Branch (4284:31): [True: 5.41k, False: 226] ------------------ 4285| 5.41k| { 4286| 5.41k| if ( aprops[a1].erank < aprops[a2].erank ) ------------------ | Branch (4286:14): [True: 775, False: 4.64k] ------------------ 4287| 775| { 4288| 775| return 1; 4289| 775| } 4290| 4.64k| if ( aprops[a1].erank > aprops[a2].erank ) ------------------ | Branch (4290:14): [True: 1.02k, False: 3.61k] ------------------ 4291| 1.02k| { 4292| 1.02k| return -1; 4293| 1.02k| } 4294| | /* Could not resolve... */ 4295| 3.61k| return 0; 4296| 4.64k| } 4297| 677| else if ( a1typ == HETEROAT ) ------------------ | Branch (4297:15): [True: 226, False: 451] ------------------ 4298| 226| { 4299| 226| return -1; /* a1 is HETEROAT, a2 is any other (==junior) */ 4300| 226| } 4301| 451| else if ( a2typ == HETEROAT ) ------------------ | Branch (4301:15): [True: 322, False: 129] ------------------ 4302| 322| { 4303| 322| return 1; /* a2 is HETEROAT, a1 is any other (==junior) */ 4304| 322| } 4305| | 4306| | /* HETEROAT left out */ 4307| 129| if ( a1typ == CARBOCYC && a2typ == CARBOCYC ) /* a1 and a2 are CARBOCYC */ ------------------ | Branch (4307:10): [True: 0, False: 129] | Branch (4307:31): [True: 0, False: 0] ------------------ 4308| 0| { 4309| | /* Same senior-atom (C) ring, try resolving by total ring size */ 4310| 0| if ( aprops[a1].ring_size < aprops[a2].ring_size ) ------------------ | Branch (4310:14): [True: 0, False: 0] ------------------ 4311| 0| { 4312| 0| return 1; 4313| 0| } 4314| 0| if ( aprops[a1].ring_size > aprops[a2].ring_size ) ------------------ | Branch (4314:14): [True: 0, False: 0] ------------------ 4315| 0| { 4316| 0| return -1; 4317| 0| } 4318| | /* Could not resolve... */ 4319| 0| return 0; 4320| 0| } 4321| 129| else if ( a1typ == CARBOCYC ) ------------------ | Branch (4321:15): [True: 0, False: 129] ------------------ 4322| 0| { 4323| 0| return -1; 4324| 0| } 4325| 129| else if ( a2typ == CARBOCYC ) ------------------ | Branch (4325:15): [True: 0, False: 129] ------------------ 4326| 0| { 4327| 0| return 1; 4328| 0| } 4329| | 4330| 129| return 0; /* 0 means unresolved. It is legal here */ 4331| 129|} OAD_Polymer_IsFirstAtomRankLower: 4340| 6.18k|{ 4341| | /* Compare ext-ranks */ 4342| 6.18k| int result = OAD_Polymer_CompareRanksOfTwoAtoms(atom1, atom2, aprops); 4343| | 4344| 6.18k| if ( result ) ------------------ | Branch (4344:10): [True: 1.80k, False: 4.38k] ------------------ 4345| 1.80k| { 4346| 1.80k| return result; 4347| 1.80k| } 4348| | 4349| | /* Could not resolve who is junior by extended-ranks... */ 4350| | /* As a last resort, simply check which canonical number is lesser */ 4351| 4.38k| if ( atom1 < atom2 ) ------------------ | Branch (4351:10): [True: 1.62k, False: 2.75k] ------------------ 4352| 1.62k| { 4353| 1.62k| return 1; 4354| 1.62k| } 4355| 2.75k| if ( atom1 > atom2 ) ------------------ | Branch (4355:10): [True: 867, False: 1.88k] ------------------ 4356| 867| { 4357| 867| return -1; 4358| 867| } 4359| | 4360| | /* should not reach there */ 4361| 1.88k| return 0; 4362| 2.75k|} runichi3.c:OrigAtData_bCheckUnusualValences: 58| 70.4k|{ 59| 70.4k| int i, val, num_found = 0; 60| 70.4k| char msg[32]; 61| 70.4k| int len, num_H; 62| | 63| 70.4k| int already_here = (orig_at_data && orig_at_data->num_inp_atoms > 0); ------------------ | Branch (63:25): [True: 70.4k, False: 0] | Branch (63:41): [True: 70.4k, False: 0] ------------------ 64| | 65| 70.4k| inp_ATOM* at = already_here ? orig_at_data->at : NULL; ------------------ | Branch (65:20): [True: 70.4k, False: 0] ------------------ 66| | 67| 70.4k| if ( at ) ------------------ | Branch (67:10): [True: 70.4k, False: 0] ------------------ 68| 70.4k| { 69| 229k| for ( i = 0, num_found = 0; i < orig_at_data->num_inp_atoms; i++ ) ------------------ | Branch (69:37): [True: 159k, False: 70.4k] ------------------ 70| 159k| { 71| 159k| num_H = bAddIsoH ? NUMH(at, i) : at[i].num_H; ------------------ | | 56| 159k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 159k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (71:21): [True: 159k, False: 0] ------------------ 72| | 73| 159k| val = detect_unusual_el_valence(at[i].el_number, 74| 159k| at[i].charge, 75| 159k| at[i].radical, 76| 159k| at[i].chem_bonds_valence, 77| 159k| num_H, 78| 159k| at[i].valence); 79| 159k| if ( val ) ------------------ | Branch (79:18): [True: 13.3k, False: 145k] ------------------ 80| 13.3k| { 81| 13.3k| num_found++; 82| 13.3k| if ( !bNoWarnings ) ------------------ | Branch (82:22): [True: 13.3k, False: 0] ------------------ 83| 13.3k| { 84| 13.3k| WarningMessage(pStrErrStruct, "Accepted unusual valence(s):"); ------------------ | | 132| 13.3k|#define WarningMessage AddErrorMessage ------------------ 85| 13.3k| } 86| 13.3k| len = sprintf(msg, "%s", at[i].elname); 87| 13.3k| if ( at[i].charge ) ------------------ | Branch (87:22): [True: 1.93k, False: 11.4k] ------------------ 88| 1.93k| { 89| 1.93k| len += sprintf(msg + len, "%+d", at[i].charge); 90| 1.93k| } 91| 13.3k| if ( at[i].radical ) ------------------ | Branch (91:22): [True: 193, False: 13.1k] ------------------ 92| 193| { 93| 193| len += sprintf(msg + len, ",%s", at[i].radical == RADICAL_SINGLET ? "s" : ------------------ | | 75| 193|#define RADICAL_SINGLET 1 ------------------ | Branch (93:54): [True: 0, False: 193] ------------------ 94| 193| at[i].radical == RADICAL_DOUBLET ? "d" : ------------------ | | 76| 193|#define RADICAL_DOUBLET 2 ------------------ | Branch (94:25): [True: 37, False: 156] ------------------ 95| 193| at[i].radical == RADICAL_TRIPLET ? "t" : "?"); ------------------ | | 77| 156|#define RADICAL_TRIPLET 3 ------------------ | Branch (95:25): [True: 17, False: 139] ------------------ 96| 193| } 97| 13.3k| len += sprintf(msg + len, "(%d)", val); 98| 13.3k| if ( !bNoWarnings ) ------------------ | Branch (98:22): [True: 13.3k, False: 0] ------------------ 99| 13.3k| { 100| 13.3k| WarningMessage(pStrErrStruct, msg); ------------------ | | 132| 13.3k|#define WarningMessage AddErrorMessage ------------------ 101| 13.3k| } 102| 13.3k| } 103| 159k| } 104| 70.4k| } 105| | 106| 70.4k| return num_found; 107| 70.4k|} SortAndPrintINChI: 87| 75.4k|{ 88| 75.4k| INCHI_SORT *pINChISort[INCHI_NUM][TAUT_NUM]; 89| 75.4k| int j, i, k, k1, ret, ret2, iINChI, max_num_components; /* djb-rwth: ignoring LLVM warning: variable used */ 90| 75.4k| int INCHI_basic_or_INCHI_reconnected; 91| | /* djb-rwth: removing redundant variables */ 92| 75.4k| int bDisconnectedCoord = ( 0 != ( bTautFlagsDone[0] & TG_FLAG_DISCONNECT_COORD_DONE ) ); ------------------ | | 975| 75.4k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 93| 75.4k| int bINChIOutputOptions0, bCurOption, bINChIOutputOptionsCur, bEmbedReconnected; 94| 75.4k| static const char szAnnHdr[] = "InChI ANNOTATED CONTENTS"; 95| |#ifdef TARGET_LIB_FOR_WINCHI 96| | int ikflag = 0; 97| | out_file->type = INCHI_IOS_TYPE_STRING; 98| |#endif 99| | 100| | /* 101| | Note: 102| | 103| | pINChI[INCHI_BAS] refers to either disconnected or original structure; 104| | num_components[INCHI_BAS] > 0 if there was input structure 105| | pINChI[INCHI_REC] refers to the reconnected structure, 106| | and only if the input structure has been disconnected, that is, 107| | num_components[INCHI_REC] > 0 108| | */ 109| | 110| 75.4k| ret = 1; 111| | 112| 226k| for (i = 0; i < INCHI_NUM; i++) ------------------ | | 569| 226k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (112:17): [True: 150k, False: 75.4k] ------------------ 113| 150k| { 114| 452k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 452k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (114:21): [True: 301k, False: 150k] ------------------ 115| 301k| { 116| 301k| bTautFlags[i] |= pncFlags->bTautFlags[i][k]; 117| 301k| bTautFlagsDone[i] |= pncFlags->bTautFlagsDone[i][k]; 118| 301k| } 119| 150k| } 120| | 121| | /* djb-rwth: removing redundant code */ 122| | 123| 75.4k| max_num_components = 0; 124| 226k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 569| 226k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (124:17): [True: 150k, False: 75.4k] ------------------ 125| 150k| { 126| 150k| if (max_num_components < num_components[j]) ------------------ | Branch (126:13): [True: 75.4k, False: 75.4k] ------------------ 127| 75.4k| { 128| 75.4k| max_num_components = num_components[j]; 129| 75.4k| } 130| 150k| } 131| 75.4k| if (max_num_components <= 0) ------------------ | Branch (131:9): [True: 0, False: 75.4k] ------------------ 132| 0| { 133| 0| max_num_components = 1; 134| 0| } 135| | 136| 226k| for (j = 0, i = 0; j < INCHI_NUM; j++) ------------------ | | 569| 226k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (136:24): [True: 150k, False: 75.4k] ------------------ 137| 150k| { 138| 150k| if (num_components[j]) ------------------ | Branch (138:13): [True: 75.4k, False: 75.4k] ------------------ 139| 75.4k| { 140| 226k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 573| 226k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (140:26): [True: 150k, False: 75.4k] ------------------ 141| 150k| { 142| 150k| pINChISort[j][k1] = 143| 150k| (INCHI_SORT *) inchi_calloc( max_num_components, ------------------ | | 1146| 150k|#define inchi_calloc calloc ------------------ 144| 150k| sizeof( pINChISort[0][0][0] ) ); 145| 150k| i += !pINChISort[j][k1]; /* number of failed allocatons */ 146| 150k| } 147| 75.4k| } 148| 75.4k| else 149| 75.4k| { 150| 226k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 573| 226k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (150:26): [True: 150k, False: 75.4k] ------------------ 151| 150k| { 152| 150k| pINChISort[j][k1] = NULL; /* keep BC happy */ 153| 150k| } 154| 75.4k| } 155| 150k| } 156| | 157| 75.4k| if (i) ------------------ | Branch (157:9): [True: 0, False: 75.4k] ------------------ 158| 0| { 159| 0| ret = CT_OUT_OF_RAM; ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 160| 0| goto exit_function; 161| 0| } 162| | 163| 226k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 569| 226k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (163:17): [True: 150k, False: 75.4k] ------------------ 164| 150k| { 165| 150k| if (!num_components[j]) ------------------ | Branch (165:13): [True: 75.4k, False: 75.4k] ------------------ 166| 75.4k| { 167| 75.4k| continue; 168| 75.4k| } 169| 75.4k| iINChI = j; 170| | 171| |#if ( OUTPUT_CONNECTED_METAL_ONLY == 1 ) /* test: output connected as the only one INChI */ 172| | if (INCHI_BAS == j && num_components[INCHI_REC]) 173| | { 174| | j = INCHI_REC; 175| | } 176| |#endif 177| | 178| | /* j = INCHI_BAS; <- for debug only */ 179| | /* for only normal or disconnected coord compounds */ 180| | /* (j=0=INCHI_BAS => normal or disconnected, j=1=INCHI_REC => reconnected */ 181| | 182| 226k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 573| 226k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (182:22): [True: 150k, False: 75.4k] ------------------ 183| 150k| { 184| 558k| for (i = 0; i < num_components[j]; i++) ------------------ | Branch (184:25): [True: 407k, False: 150k] ------------------ 185| 407k| { 186| 1.22M| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 1.22M|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (186:29): [True: 814k, False: 407k] ------------------ 187| 814k| { 188| 814k| pINChISort[j][k1][i].pINChI[k] = pINChI[j][i][k]; 189| 814k| pINChISort[j][k1][i].pINChI_Aux[k] = pINChI_Aux[j][i][k]; 190| 814k| } 191| 407k| pINChISort[j][k1][i].ord_number = i; 192| 407k| } 193| 150k| } 194| | 195| | /* Sort component INChIs */ 196| 226k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 573| 226k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (196:22): [True: 150k, False: 75.4k] ------------------ 197| 150k| { 198| 150k| switch (k1) ------------------ | Branch (198:21): [True: 150k, False: 0] ------------------ 199| 150k| { 200| 75.4k| case TAUT_NON: ------------------ | | 574| 75.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (200:17): [True: 75.4k, False: 75.4k] ------------------ 201| 75.4k| qsort( pINChISort[j][k1], 202| 75.4k| num_components[j], 203| 75.4k| sizeof( pINChISort[0][0][0] ), 204| 75.4k| CompINChINonTaut2 ); 205| 75.4k| break; 206| 75.4k| case TAUT_YES: ------------------ | | 575| 75.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (206:17): [True: 75.4k, False: 75.4k] ------------------ 207| 75.4k| qsort( pINChISort[j][k1], 208| 75.4k| num_components[j], 209| 75.4k| sizeof( pINChISort[0][0][0] ), 210| 75.4k| CompINChITaut2 ); 211| 75.4k| break; 212| 150k| } 213| 150k| } 214| | 215| |#ifndef COMPILE_ANSI_ONLY 216| | /* Find equivalent and wINChI display order; 217| | use requested in ip->bCompareComponents comparison */ 218| | 219| | ret = SaveEquComponentsInfoAndSortOrder( iINChI, pINChISort[j], 220| | num_components, 221| | orig_inp_data, prep_inp_data, 222| |#if ( FIX_DALKE_BUGS == 1 ) 223| | composite_norm_data ? composite_norm_data[j] : NULL, 224| |#else 225| | composite_norm_data[j], 226| |#endif 227| | ip->bCompareComponents ); 228| | if (RETURNED_ERROR( ret )) 229| | { 230| | ret = 0; 231| | goto exit_function; 232| | } 233| | else 234| | { 235| | ret = 1; 236| | } 237| |#endif 238| 75.4k| } /* j */ 239| | 240| 75.4k| if (!( ip->bINChIOutputOptions & INCHI_OUT_PRINT_OPTIONS )) ------------------ | | 168| 75.4k|#define INCHI_OUT_PRINT_OPTIONS (INCHI_OUT_EMBED_REC | \ | | ------------------ | | | | 132| 75.4k|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ | | ------------------ | | 169| 75.4k| INCHI_OUT_PLAIN_TEXT | \ | | ------------------ | | | | 135| 75.4k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ | | ------------------ | | 170| 75.4k| INCHI_OUT_PLAIN_TEXT_COMMENTS) | | ------------------ | | | | 136| 75.4k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ | | ------------------ ------------------ | Branch (240:9): [True: 70.4k, False: 5.02k] ------------------ 241| 70.4k| { 242| | /* Prepare InChI from the structures obtained by 243| | reversing InChI for returning to the caller */ 244| 211k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 569| 211k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (244:21): [True: 140k, False: 70.4k] ------------------ 245| 140k| { 246| 140k| if (!num_components[j]) ------------------ | Branch (246:17): [True: 70.4k, False: 70.4k] ------------------ 247| 70.4k| { 248| 70.4k| continue; 249| 70.4k| } 250| | 251| | /* pINChI[iINCHI][iComponent][bTaut] */ 252| | /* j = disconnected/connected */ 253| | /* k1 = sort order for Mobile or Fixed H */ 254| | 255| 70.4k| k1 = TAUT_YES; /* in Mobile H order */ ------------------ | | 575| 70.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 256| | /* store components in Mobile H order */ 257| | 258| 176k| for (i = 0; i < num_components[j] && i < max_num_components; i++) /* djb-rwth: fixing undefined index value / buffer overflow */ ------------------ | Branch (258:25): [True: 106k, False: 70.4k] | Branch (258:50): [True: 106k, False: 0] ------------------ 259| 106k| { 260| | 261| 106k| if (pINChISort[j][k1][i].pINChI[TAUT_NON] && ------------------ | | 574| 106k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (261:21): [True: 35.6k, False: 70.4k] ------------------ 262| 35.6k| !pINChISort[j][k1][i].pINChI[TAUT_YES]) ------------------ | | 575| 35.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (262:21): [True: 0, False: 35.6k] ------------------ 263| 0| { 264| | /* make sure Mobile-H is always present */ 265| 0| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (265:33): [True: 0, False: 0] ------------------ 266| 0| { 267| 0| pINChI[j][i][k] = pINChISort[j][k1][i].pINChI[ALT_TAUT( k )]; ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 268| 0| pINChI_Aux[j][i][k] = pINChISort[j][k1][i].pINChI_Aux[ALT_TAUT( k )]; ------------------ | | 577| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 575| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (577:29): [True: 0, False: 0] | | ------------------ ------------------ 269| 0| } 270| 0| } 271| 106k| else 272| 106k| { 273| 318k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 318k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (273:33): [True: 212k, False: 106k] ------------------ 274| 212k| { 275| 212k| pINChI[j][i][k] = pINChISort[j][k1][i].pINChI[k]; 276| 212k| pINChI_Aux[j][i][k] = pINChISort[j][k1][i].pINChI_Aux[k]; 277| 212k| } 278| 106k| } 279| 106k| } 280| 70.4k| } 281| 70.4k| } 282| 5.02k| else 283| 5.02k| { 284| | /* Print InChI string(s) */ 285| 5.02k| bINChIOutputOptions0 = ip->bINChIOutputOptions & ~INCHI_OUT_PRINT_OPTIONS; ------------------ | | 168| 5.02k|#define INCHI_OUT_PRINT_OPTIONS (INCHI_OUT_EMBED_REC | \ | | ------------------ | | | | 132| 5.02k|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ | | ------------------ | | 169| 5.02k| INCHI_OUT_PLAIN_TEXT | \ | | ------------------ | | | | 135| 5.02k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ | | ------------------ | | 170| 5.02k| INCHI_OUT_PLAIN_TEXT_COMMENTS) | | ------------------ | | | | 136| 5.02k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ | | ------------------ ------------------ 286| 5.02k| bEmbedReconnected = ip->bINChIOutputOptions & INCHI_OUT_EMBED_REC; ------------------ | | 132| 5.02k|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ 287| | 288| 15.0k| for (i = 1; i <= 2; i++) ------------------ | Branch (288:21): [True: 10.0k, False: 5.02k] ------------------ 289| 10.0k| { 290| 10.0k| bCurOption = INCHI_OUT_PLAIN_TEXT; ------------------ | | 135| 10.0k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 291| 10.0k| if (i == 2) ------------------ | Branch (291:17): [True: 5.02k, False: 5.02k] ------------------ 292| 5.02k| { 293| 5.02k| bCurOption = INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 136| 5.02k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 294| | /* continue; */ 295| 5.02k| } 296| 10.0k| if (!( ip->bINChIOutputOptions & bCurOption )) ------------------ | Branch (296:17): [True: 5.02k, False: 5.02k] ------------------ 297| 5.02k| { 298| 5.02k| continue; 299| 5.02k| } 300| | 301| 5.02k| bINChIOutputOptionsCur = bINChIOutputOptions0 | bCurOption; 302| 5.02k| if (i == 1) ------------------ | Branch (302:17): [True: 5.02k, False: 0] ------------------ 303| 5.02k| { 304| | /* output INChI */ 305| 5.02k| bINChIOutputOptionsCur |= bEmbedReconnected; 306| 5.02k| } 307| 0| else if (i == 2) ------------------ | Branch (307:22): [True: 0, False: 0] ------------------ 308| 0| { 309| | /* output annotation */ 310| 0| inchi_ios_print( out_file, "\n==== %s ====\n", szAnnHdr ); 311| 0| ITRACE_( "\n==== %s ====\n", szAnnHdr ); ------------------ | | 98| 0|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (98:17): [Folded, False: 0] | | ------------------ ------------------ | Branch (311:17): [True: 0, False: 0] ------------------ 312| 0| bINChIOutputOptionsCur |= bEmbedReconnected; 313| 0| bINChIOutputOptionsCur &= ~INCHI_OUT_TABBED_OUTPUT; ------------------ | | 139| 0|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 314| 0| } 315| 0| else 316| 0| { 317| 0| continue; 318| 0| } 319| | 320| |#if 0 /*^^^#ifdef TARGET_LIB_FOR_WINCHI*/ 321| | inchi_ios_free_str( out_file ); 322| |#endif 323| | 324| 5.02k| INCHI_basic_or_INCHI_reconnected = INCHI_BAS; ------------------ | | 570| 5.02k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 325| | 326| 5.02k| ret2 = OutputINChI2( pCG, 327| 5.02k| strbuf, 328| 5.02k| pINChISort, 329| 5.02k| INCHI_basic_or_INCHI_reconnected, 330| 5.02k| orig_inp_data, 331| 5.02k| pOrigStruct, 332| 5.02k| ip, 333| 5.02k| bDisconnectedCoord, 334| 5.02k| OUT_TN, ------------------ | | 583| 5.02k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ 335| 5.02k| bINChIOutputOptionsCur, 336| 5.02k| num_components, 337| 5.02k| num_non_taut, 338| 5.02k| num_taut, 339| 5.02k| out_file, 340| 5.02k| log_file, 341| 5.02k| num_inp, 342| 5.02k| pSortPrintINChIFlags, 343| 5.02k| save_opt_bits ); 344| | 345| 5.02k| ret &= ret2; 346| | 347| |#ifdef TARGET_LIB_FOR_WINCHI 348| | /* always calculate InChIKey */ 349| | winchi_calc_inchikey( ret, &ikflag, ip, out_file, log_file ); 350| | /*push_to_winchi_text_window( out_file ); 351| | inchi_ios_flush( out_file );*/ 352| | 353| |#endif 354| | 355| 5.02k| if (!ret) ------------------ | Branch (355:17): [True: 0, False: 5.02k] ------------------ 356| 0| { 357| 0| break; 358| 0| } 359| 5.02k| } /* i */ 360| 5.02k| } 361| | 362| | 363| 75.4k|exit_function: 364| | 365| 226k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 569| 226k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (365:17): [True: 150k, False: 75.4k] ------------------ 366| 150k| { 367| 452k| for (k1 = 0; k1 < TAUT_NUM; k1++) /* djb-rwth: removing redundant code */ ------------------ | | 573| 452k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (367:22): [True: 301k, False: 150k] ------------------ 368| 301k| { 369| 301k| if (pINChISort[j][k1]) ------------------ | Branch (369:17): [True: 150k, False: 150k] ------------------ 370| 150k| { 371| 150k| inchi_free( pINChISort[j][k1] ); ------------------ | | 1152| 150k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 150k, False: 0] | | | Branch (1152:50): [Folded, False: 150k] | | ------------------ ------------------ 372| 150k| } 373| 301k| } 374| 150k| } 375| | 376| | 377| 75.4k| ret = ret ? 0 : _IS_FATAL; ------------------ | | 13| 75.4k|#define _IS_FATAL 3 ------------------ | Branch (377:11): [True: 75.4k, False: 0] ------------------ 378| | 379| 75.4k| return ret; 380| 75.4k|} FreeAllINChIArrays: 1290| 186k|{ 1291| 186k| int k; 1292| 559k| for (k = 0; k < INCHI_NUM; k++) ------------------ | | 569| 559k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1292:17): [True: 372k, False: 186k] ------------------ 1293| 372k| { 1294| 372k| int nk = num_components[k]; 1295| | 1296| 372k| FreeINChIArrays( pINChI[k], pINChI_Aux[k], num_components[k] ); 1297| | 1298| 372k| num_components[k] = 0; 1299| | 1300| 372k| if (nk && /* added check for nk: 2013-12-15 IPl */ ------------------ | Branch (1300:13): [True: 75.4k, False: 297k] ------------------ 1301| 75.4k| pINChI[k]) ------------------ | Branch (1301:14): [True: 75.4k, False: 0] ------------------ 1302| 75.4k| { 1303| 75.4k| inchi_free( pINChI[k] ); ------------------ | | 1152| 75.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 75.4k, False: 0] | | | Branch (1152:50): [Folded, False: 75.4k] | | ------------------ ------------------ 1304| 75.4k| pINChI[k] = NULL; 1305| 75.4k| } 1306| | 1307| 372k| if (nk && /* added check for nk: 2013-12-15 IPl */ ------------------ | Branch (1307:13): [True: 75.4k, False: 297k] ------------------ 1308| 75.4k| pINChI_Aux[k]) ------------------ | Branch (1308:14): [True: 75.4k, False: 0] ------------------ 1309| 75.4k| { 1310| 75.4k| inchi_free( pINChI_Aux[k] ); ------------------ | | 1152| 75.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 75.4k, False: 0] | | | Branch (1152:50): [Folded, False: 75.4k] | | ------------------ ------------------ 1311| 75.4k| pINChI_Aux[k] = NULL; 1312| 75.4k| } 1313| 372k| } 1314| | 1315| 186k| return; 1316| 186k|} FreeINChIArrays: 1323| 372k|{ 1324| 372k| int i, k; 1325| | /* Release allocated memory */ 1326| 372k| if (pINChI) ------------------ | Branch (1326:9): [True: 75.4k, False: 297k] ------------------ 1327| 75.4k| { 1328| 279k| for (i = 0; i < num_components; i++) ------------------ | Branch (1328:21): [True: 203k, False: 75.4k] ------------------ 1329| 203k| { 1330| 610k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 610k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1330:25): [True: 407k, False: 203k] ------------------ 1331| 407k| { 1332| 407k| Free_INChI( &pINChI[i][k] ); 1333| 407k| } 1334| 203k| } 1335| 75.4k| } 1336| 372k| if (pINChI_Aux) ------------------ | Branch (1336:9): [True: 75.4k, False: 297k] ------------------ 1337| 75.4k| { 1338| 279k| for (i = 0; i < num_components; i++) ------------------ | Branch (1338:21): [True: 203k, False: 75.4k] ------------------ 1339| 203k| { 1340| 610k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 573| 610k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1340:25): [True: 407k, False: 203k] ------------------ 1341| 407k| { 1342| 407k| Free_INChI_Aux( &pINChI_Aux[i][k] ); 1343| 407k| } 1344| 203k| } 1345| 75.4k| } 1346| 372k|} TreatErrorsInCreateOneComponentINChI: 1360| 4|{ 1361| 4| if (sd->nErrorCode) ------------------ | Branch (1361:9): [True: 4, False: 0] ------------------ 1362| 4| { 1363| 4| AddErrorMessage( sd->pStrErrStruct, ErrMsg( sd->nErrorCode ) ); 1364| 4| inchi_ios_eprint( log_file, 1365| 4| "Error %d (%s) structure #%ld component %d.%s%s%s%s\n", 1366| 4| sd->nErrorCode, sd->pStrErrStruct, 1367| 4| num_inp, i + 1, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ) ); ------------------ | | 830| 4|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 4] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 4] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 4] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 4] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 4] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 4| : gsEmpty ------------------ 1368| 4| sd->nErrorType = ( sd->nErrorCode == CT_OUT_OF_RAM || sd->nErrorCode == CT_USER_QUIT_ERR ) ------------------ | | 21| 8|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 4|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ sd->nErrorType = ( sd->nErrorCode == CT_OUT_OF_RAM || sd->nErrorCode == CT_USER_QUIT_ERR ) ------------------ | | 32| 2|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 18| 2|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1368:28): [True: 2, False: 2] | Branch (1368:63): [True: 0, False: 2] ------------------ 1369| 4| ? _IS_FATAL ------------------ | | 13| 2|#define _IS_FATAL 3 ------------------ 1370| 4| : _IS_ERROR; ------------------ | | 12| 6|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 1371| | 1372| |#ifdef TARGET_LIB_FOR_WINCHI 1373| | if (( ip->bINChIOutputOptions & INCHI_OUT_WINCHI_WINDOW ) && 1374| | ( ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT )) 1375| | { 1376| | sd->nErrorType = ProcessStructError( out_file, log_file, 1377| | sd->pStrErrStruct, sd->nErrorType, 1378| | num_inp, ip ); 1379| | /* Save the problem structure */ 1380| | if (prb_file->f && 1381| | 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && 1382| | !ip->bSaveAllGoodStructsAsProblem) 1383| | { 1384| | MolfileSaveCopy( inp_file, sd->fPtrStart, sd->fPtrEnd, prb_file->f, num_inp ); 1385| | } 1386| | } 1387| | else 1388| | { 1389| | /* Save the problem structure */ 1390| | if (sd->nErrorCode && 1391| | prb_file->f && 1392| | 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd && 1393| | !ip->bSaveAllGoodStructsAsProblem) 1394| | { 1395| | MolfileSaveCopy( inp_file, sd->fPtrStart, sd->fPtrEnd, prb_file->f, num_inp ); 1396| | } 1397| | } 1398| |#endif 1399| 4| } 1400| | 1401| |/* #ifndef TARGET_API_LIB */ 1402| |#if ( !defined( TARGET_API_LIB ) && !defined(TARGET_EXE_STANDALONE) ) 1403| | /* print the logfile record */ 1404| | if (log_file->f && log_file->f != stderr && ( sd->ulStructTime >= 1000 || sd->nErrorCode )) 1405| | { 1406| | fprintf( log_file->f, "%10lu msec structure #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n", 1407| | sd->ulStructTime, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), 1408| | orig_inp_data->num_components, orig_inp_data->num_components == 1 ? "" : "s", 1409| | orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms == 1 ? "" : "s", sd->nErrorCode ); 1410| | } 1411| |#endif 1412| | 1413| 4| return sd->nErrorType; 1414| 4|} TreatCreateINChIWarning: 1426| 70.4k|{ 1427| | 1428| |#if ( bRELEASE_VERSION == 0 && (EXTR_FLAGS || EXTR_MASK) ) 1429| | if (EXTR_MASK ? ( ( sd->bExtract & EXTR_MASK ) == EXTR_FLAGS ) 1430| | : ( sd->bExtract & EXTR_FLAGS ) 1431| | ) 1432| | { 1433| | char szMsg[64]; 1434| | sprintf( szMsg, "ExtractStruct.code=0x%X", sd->bExtract ); 1435| | if (!ip->bNoWarnings) 1436| | { 1437| | WarningMessage( sd->pStrErrStruct, szMsg ); 1438| | } 1439| | } 1440| |#endif 1441| | 1442| 70.4k| if (!sd->nErrorCode && sd->pStrErrStruct[0]) ------------------ | Branch (1442:9): [True: 70.4k, False: 0] | Branch (1442:28): [True: 9.45k, False: 60.9k] ------------------ 1443| 9.45k| { 1444| 9.45k| inchi_ios_eprint( log_file, "Warning (%s) structure #%ld.%s%s%s%s\n", 1445| 9.45k| sd->pStrErrStruct, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ) ); ------------------ | | 830| 9.45k|#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \ | | ------------------ | | | Branch (830:28): [True: 0, False: 9.45k] | | | Branch (830:35): [True: 0, False: 0] | | | Branch (830:65): [True: 0, False: 9.45k] | | | Branch (830:72): [True: 0, False: 0] | | | Branch (830:96): [True: 0, False: 9.45k] | | | Branch (830:103): [True: 0, False: 0] | | | Branch (830:115): [True: 0, False: 0] | | | Branch (830:122): [True: 0, False: 0] | | | Branch (830:163): [True: 0, False: 9.45k] | | | Branch (830:170): [True: 0, False: 0] | | | Branch (830:185): [True: 0, False: 9.45k] | | | Branch (830:192): [True: 0, False: 0] | | ------------------ | | 831| 9.45k| : gsEmpty ------------------ 1446| 9.45k| sd->nErrorType = _IS_WARNING; ------------------ | | 11| 9.45k|#define _IS_WARNING 1 ------------------ 1447| | 1448| |#ifdef TARGET_LIB_FOR_WINCHI 1449| | if (( ip->bINChIOutputOptions & INCHI_OUT_WINCHI_WINDOW ) && 1450| | ( ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT )) 1451| | { 1452| | sd->nErrorType = ProcessStructError( out_file, 1453| | log_file, 1454| | sd->pStrErrStruct, 1455| | sd->nErrorType, 1456| | num_inp, 1457| | ip ); 1458| | } 1459| |#endif 1460| | /* save the structure as a problem structure if requested */ 1461| 9.45k| if (ip->bSaveWarningStructsAsProblem && !ip->bSaveAllGoodStructsAsProblem && ------------------ | Branch (1461:13): [True: 0, False: 9.45k] | Branch (1461:49): [True: 0, False: 0] ------------------ 1462| 0| prb_file->f && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd) ------------------ | Branch (1462:14): [True: 0, False: 0] | Branch (1462:29): [True: 0, False: 0] | Branch (1462:52): [True: 0, False: 0] ------------------ 1463| 0| { /* djb-rwth: addressing coverity ID #499545 -- return values handled properly */ 1464| 0| MolfileSaveCopy( inp_file, 1465| 0| sd->fPtrStart, 1466| 0| sd->fPtrEnd, 1467| 0| prb_file->f, 1468| 0| num_inp ); 1469| 0| } 1470| | 1471| |#if ( bRELEASE_VERSION == 0 ) 1472| | /* otherwise extract the structure as a problem structure if requested */ 1473| | else 1474| | if (( EXTR_MASK ? ( ( sd->bExtract & EXTR_MASK ) == EXTR_FLAGS ) : ( sd->bExtract & EXTR_FLAGS ) ) 1475| | && !ip->bSaveAllGoodStructsAsProblem && 1476| | prb_file->f && 1477| | 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd) 1478| | { 1479| | MolfileSaveCopy( inp_file->f, 1480| | sd->fPtrStart, 1481| | sd->fPtrEnd, 1482| | prb_file->f, 1483| | num_inp ); 1484| | } 1485| |#endif 1486| 9.45k| } 1487| | 1488| |#if ( bRELEASE_VERSION != 1 && bOUTPUT_ONE_STRUCT_TIME == 1 ) 1489| |#ifndef TARGET_API_LIB 1490| | if (log_file && log_file != stderr) 1491| | { 1492| | fprintf( log_file, "%10lu msec structure %1dD #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n", 1493| | sd->ulStructTime, orig_inp_data->num_dimensions, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), 1494| | orig_inp_data->num_components, orig_inp_data->num_components == 1 ? "" : "s", 1495| | orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms == 1 ? "" : "s", sd->nErrorCode ); 1496| | } 1497| |#else 1498| | if (log_file) 1499| | { 1500| | inchi_ios_eprint( log_file, "%10lu msec structure %1dD #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n", 1501| | sd->ulStructTime, orig_inp_data->num_dimensions, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), 1502| | orig_inp_data->num_components, orig_inp_data->num_components == 1 ? "" : "s", 1503| | orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms == 1 ? "" : "s", sd->nErrorCode ); 1504| | } 1505| |#endif 1506| |#endif 1507| | 1508| 70.4k| return sd->nErrorType; 1509| 70.4k|} GetProcessingWarningsOneComponentInChI: 1519| 106k|{ 1520| 106k| int i, ret = 0; 1521| 318k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 573| 318k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1521:17): [True: 212k, False: 106k] ------------------ 1522| 212k| { 1523| 212k| if (cur_INChI[i] && cur_INChI[i]->nNumberOfAtoms > 0) ------------------ | Branch (1523:13): [True: 141k, False: 70.4k] | Branch (1523:29): [True: 141k, False: 204] ------------------ 1524| 141k| { 1525| 141k| ret |= GetProcessingWarningsOneInChI( cur_INChI[i], 1526| 141k| inp_norm_data[i], 1527| 141k| sd->pStrErrStruct, 1528| 141k| bNoWarnings ); 1529| 141k| } 1530| 212k| } 1531| | 1532| 106k| return ret; 1533| 106k|} GetProcessingWarningsOneInChI: 1543| 141k|{ 1544| 141k| int j; 1545| 141k| int nAmbiguousStereoAtoms, nAmbiguousStereoBonds; 1546| 141k| nAmbiguousStereoAtoms = 0; 1547| 141k| nAmbiguousStereoBonds = 0; 1548| | 1549| 141k| if (inp_norm_data->at) ------------------ | Branch (1549:9): [True: 141k, False: 0] ------------------ 1550| 141k| { 1551| 331k| for (j = 0; j < pINChI->nNumberOfAtoms; j++) ------------------ | Branch (1551:21): [True: 189k, False: 141k] ------------------ 1552| 189k| { 1553| 189k| if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_ATOM | AMBIGUOUS_STEREO_ATOM_ISO )) ------------------ | | 246| 189k|#define AMBIGUOUS_STEREO_ATOM 2 ------------------ if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_ATOM | AMBIGUOUS_STEREO_ATOM_ISO )) ------------------ | | 248| 189k|#define AMBIGUOUS_STEREO_ATOM_ISO 8 ------------------ | Branch (1553:17): [True: 0, False: 189k] ------------------ 1554| 0| { 1555| 0| nAmbiguousStereoAtoms++; 1556| 0| } 1557| 189k| if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_BOND | AMBIGUOUS_STEREO_BOND_ISO )) ------------------ | | 247| 189k|#define AMBIGUOUS_STEREO_BOND 4 ------------------ if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_BOND | AMBIGUOUS_STEREO_BOND_ISO )) ------------------ | | 249| 189k|#define AMBIGUOUS_STEREO_BOND_ISO 16 ------------------ | Branch (1557:17): [True: 0, False: 189k] ------------------ 1558| 0| { 1559| 0| nAmbiguousStereoBonds++; 1560| 0| } 1561| 189k| } 1562| 141k| if (nAmbiguousStereoAtoms) ------------------ | Branch (1562:13): [True: 0, False: 141k] ------------------ 1563| 0| { 1564| 0| if (!bNoWarnings) ------------------ | Branch (1564:17): [True: 0, False: 0] ------------------ 1565| 0| { 1566| 0| WarningMessage( pStrErrStruct, "Ambiguous stereo:" ); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 1567| 0| WarningMessage( pStrErrStruct, "center(s)" ); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 1568| 0| } 1569| 0| } 1570| 141k| if (nAmbiguousStereoBonds) ------------------ | Branch (1570:13): [True: 0, False: 141k] ------------------ 1571| 0| { 1572| 0| if (!bNoWarnings) ------------------ | Branch (1572:17): [True: 0, False: 0] ------------------ 1573| 0| { 1574| 0| WarningMessage( pStrErrStruct, "Ambiguous stereo:" ); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 1575| 0| WarningMessage( pStrErrStruct, "bond(s)" ); ------------------ | | 132| 0|#define WarningMessage AddErrorMessage ------------------ 1576| 0| } 1577| 0| } 1578| 141k| } 1579| | 1580| 141k| return ( nAmbiguousStereoAtoms || nAmbiguousStereoBonds ); ------------------ | Branch (1580:14): [True: 0, False: 141k] | Branch (1580:39): [True: 0, False: 141k] ------------------ 1581| 141k|} sha2_starts: 58| 12.6k|{ 59| 12.6k| ctx->total[0] = 0; 60| 12.6k| ctx->total[1] = 0; 61| | 62| 12.6k| ctx->state[0] = 0x6A09E667; 63| 12.6k| ctx->state[1] = 0xBB67AE85; 64| 12.6k| ctx->state[2] = 0x3C6EF372; 65| 12.6k| ctx->state[3] = 0xA54FF53A; 66| 12.6k| ctx->state[4] = 0x510E527F; 67| 12.6k| ctx->state[5] = 0x9B05688C; 68| 12.6k| ctx->state[6] = 0x1F83D9AB; 69| 12.6k| ctx->state[7] = 0x5BE0CD19; 70| 12.6k|} sha2_update: 207| 37.9k|{ 208| 37.9k| int fill; 209| 37.9k| unsigned long left; 210| | 211| 37.9k| if (ilen <= 0) ------------------ | Branch (211:9): [True: 2.78k, False: 35.1k] ------------------ 212| 2.78k| return; 213| | 214| 35.1k| left = ctx->total[0] & 0x3F; 215| 35.1k| fill = 64 - left; 216| | 217| 35.1k| ctx->total[0] += ilen; 218| 35.1k| ctx->total[0] &= 0xFFFFFFFF; 219| | 220| 35.1k| if (ctx->total[0] < (unsigned long)ilen) ------------------ | Branch (220:9): [True: 0, False: 35.1k] ------------------ 221| 0| ctx->total[1]++; 222| | 223| 35.1k| if (left && ilen >= fill) ------------------ | Branch (223:9): [True: 22.4k, False: 12.6k] | Branch (223:17): [True: 12.8k, False: 9.64k] ------------------ 224| 12.8k| { 225| 12.8k| memcpy((void *)(ctx->buffer + left), 226| 12.8k| (void *)input, fill); 227| 12.8k| sha2_process(ctx, ctx->buffer); 228| 12.8k| input += fill; 229| 12.8k| ilen -= fill; 230| 12.8k| left = 0; 231| 12.8k| } 232| | 233| 94.6k| while (ilen >= 64) ------------------ | Branch (233:12): [True: 59.4k, False: 35.1k] ------------------ 234| 59.4k| { 235| 59.4k| sha2_process(ctx, input); /* djb-rwth: ignoring LLVM warning as ilen >= 64 just in test case */ 236| 59.4k| input += 64; 237| 59.4k| ilen -= 64; 238| 59.4k| } 239| | 240| 35.1k| if (ilen > 0) ------------------ | Branch (240:9): [True: 22.4k, False: 12.6k] ------------------ 241| 22.4k| { 242| 22.4k| memcpy((void *)(ctx->buffer + left), 243| 22.4k| (void *)input, ilen); 244| 22.4k| } 245| 35.1k|} sha2_finish: 258| 12.6k|{ 259| 12.6k| unsigned long last, padn; 260| 12.6k| unsigned long high, low; 261| 12.6k| unsigned char msglen[8]; 262| | 263| 12.6k| high = (ctx->total[0] >> 29) | (ctx->total[1] << 3); 264| 12.6k| low = (ctx->total[0] << 3); 265| | 266| 12.6k| PUT_UINT32_BE(high, msglen, 0); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 267| 12.6k| PUT_UINT32_BE(low, msglen, 4); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 268| | 269| 12.6k| last = ctx->total[0] & 0x3F; 270| 12.6k| padn = (last < 56) ? (56 - last) : (120 - last); ------------------ | Branch (270:12): [True: 12.4k, False: 187] ------------------ 271| | 272| 12.6k| sha2_update(ctx, (unsigned char *)sha2_padding, padn); 273| 12.6k| sha2_update(ctx, msglen, 8); 274| | 275| 12.6k| PUT_UINT32_BE(ctx->state[0], output, 0); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 276| 12.6k| PUT_UINT32_BE(ctx->state[1], output, 4); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 277| 12.6k| PUT_UINT32_BE(ctx->state[2], output, 8); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 278| 12.6k| PUT_UINT32_BE(ctx->state[3], output, 12); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 279| 12.6k| PUT_UINT32_BE(ctx->state[4], output, 16); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 280| 12.6k| PUT_UINT32_BE(ctx->state[5], output, 20); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 281| 12.6k| PUT_UINT32_BE(ctx->state[6], output, 24); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 282| 12.6k| PUT_UINT32_BE(ctx->state[7], output, 28); ------------------ | | 46| 12.6k| { \ | | 47| 12.6k| (b)[(i)] = (unsigned char)((n) >> 24); \ | | 48| 12.6k| (b)[(i) + 1] = (unsigned char)((n) >> 16); \ | | 49| 12.6k| (b)[(i) + 2] = (unsigned char)((n) >> 8); \ | | 50| 12.6k| (b)[(i) + 3] = (unsigned char)((n)); \ | | 51| 12.6k| } ------------------ 283| 12.6k|} sha2_csum: 314| 12.6k|{ 315| 12.6k| sha2_context ctx; 316| | 317| 12.6k| sha2_starts(&ctx); 318| 12.6k| sha2_update(&ctx, input, ilen); 319| 12.6k| sha2_finish(&ctx, output); 320| 12.6k|} sha2.c:sha2_process: 73| 72.3k|{ 74| 72.3k| unsigned long temp1, temp2, W[64]; 75| 72.3k| unsigned long A, B, C, D, E, F, G, H; 76| | 77| 72.3k| GET_UINT32_BE(W[0], data, 0); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 78| 72.3k| GET_UINT32_BE(W[1], data, 4); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 79| 72.3k| GET_UINT32_BE(W[2], data, 8); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 80| 72.3k| GET_UINT32_BE(W[3], data, 12); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 81| 72.3k| GET_UINT32_BE(W[4], data, 16); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 82| 72.3k| GET_UINT32_BE(W[5], data, 20); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 83| 72.3k| GET_UINT32_BE(W[6], data, 24); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 84| 72.3k| GET_UINT32_BE(W[7], data, 28); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 85| 72.3k| GET_UINT32_BE(W[8], data, 32); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 86| 72.3k| GET_UINT32_BE(W[9], data, 36); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 87| 72.3k| GET_UINT32_BE(W[10], data, 40); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 88| 72.3k| GET_UINT32_BE(W[11], data, 44); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 89| 72.3k| GET_UINT32_BE(W[12], data, 48); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 90| 72.3k| GET_UINT32_BE(W[13], data, 52); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 91| 72.3k| GET_UINT32_BE(W[14], data, 56); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 92| 72.3k| GET_UINT32_BE(W[15], data, 60); ------------------ | | 40| 72.3k| { \ | | 41| 72.3k| (n) = ((unsigned long)(b)[(i)] << 24) | ((unsigned long)(b)[(i) + 1] << 16) | ((unsigned long)(b)[(i) + 2] << 8) | ((unsigned long)(b)[(i) + 3]); \ | | 42| 72.3k| } ------------------ 93| | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) 96| | 97| 72.3k|#define S0(x) (ROTR(x, 7) ^ ROTR(x, 18) ^ SHR(x, 3)) 98| 72.3k|#define S1(x) (ROTR(x, 17) ^ ROTR(x, 19) ^ SHR(x, 10)) 99| | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) 102| | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) 105| | 106| 72.3k|#define R(t) \ 107| 72.3k| ( \ 108| 72.3k| W[t] = S1(W[t - 2]) + W[t - 7] + \ 109| 72.3k| S0(W[t - 15]) + W[t - 16]) 110| | 111| 72.3k|#define P(a, b, c, d, e, f, g, h, x, K) \ 112| 72.3k| { \ 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ 115| 72.3k| d += temp1; \ 116| 72.3k| h = temp1 + temp2; \ 117| 72.3k| } 118| | 119| 72.3k| A = ctx->state[0]; 120| 72.3k| B = ctx->state[1]; 121| 72.3k| C = ctx->state[2]; 122| 72.3k| D = ctx->state[3]; 123| 72.3k| E = ctx->state[4]; 124| 72.3k| F = ctx->state[5]; 125| 72.3k| G = ctx->state[6]; 126| 72.3k| H = ctx->state[7]; 127| | 128| 72.3k| P(A, B, C, D, E, F, G, H, W[0], 0x428A2F98); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 129| 72.3k| P(H, A, B, C, D, E, F, G, W[1], 0x71374491); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 130| 72.3k| P(G, H, A, B, C, D, E, F, W[2], 0xB5C0FBCF); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 131| 72.3k| P(F, G, H, A, B, C, D, E, W[3], 0xE9B5DBA5); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 132| 72.3k| P(E, F, G, H, A, B, C, D, W[4], 0x3956C25B); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 133| 72.3k| P(D, E, F, G, H, A, B, C, W[5], 0x59F111F1); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 134| 72.3k| P(C, D, E, F, G, H, A, B, W[6], 0x923F82A4); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 135| 72.3k| P(B, C, D, E, F, G, H, A, W[7], 0xAB1C5ED5); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 136| 72.3k| P(A, B, C, D, E, F, G, H, W[8], 0xD807AA98); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 137| 72.3k| P(H, A, B, C, D, E, F, G, W[9], 0x12835B01); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 138| 72.3k| P(G, H, A, B, C, D, E, F, W[10], 0x243185BE); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 139| 72.3k| P(F, G, H, A, B, C, D, E, W[11], 0x550C7DC3); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 140| 72.3k| P(E, F, G, H, A, B, C, D, W[12], 0x72BE5D74); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 141| 72.3k| P(D, E, F, G, H, A, B, C, W[13], 0x80DEB1FE); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 142| 72.3k| P(C, D, E, F, G, H, A, B, W[14], 0x9BDC06A7); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 143| 72.3k| P(B, C, D, E, F, G, H, A, W[15], 0xC19BF174); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 144| 72.3k| P(A, B, C, D, E, F, G, H, R(16), 0xE49B69C1); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 145| 72.3k| P(H, A, B, C, D, E, F, G, R(17), 0xEFBE4786); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 146| 72.3k| P(G, H, A, B, C, D, E, F, R(18), 0x0FC19DC6); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 147| 72.3k| P(F, G, H, A, B, C, D, E, R(19), 0x240CA1CC); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 148| 72.3k| P(E, F, G, H, A, B, C, D, R(20), 0x2DE92C6F); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 149| 72.3k| P(D, E, F, G, H, A, B, C, R(21), 0x4A7484AA); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 150| 72.3k| P(C, D, E, F, G, H, A, B, R(22), 0x5CB0A9DC); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 151| 72.3k| P(B, C, D, E, F, G, H, A, R(23), 0x76F988DA); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 152| 72.3k| P(A, B, C, D, E, F, G, H, R(24), 0x983E5152); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 153| 72.3k| P(H, A, B, C, D, E, F, G, R(25), 0xA831C66D); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 154| 72.3k| P(G, H, A, B, C, D, E, F, R(26), 0xB00327C8); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 155| 72.3k| P(F, G, H, A, B, C, D, E, R(27), 0xBF597FC7); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 156| 72.3k| P(E, F, G, H, A, B, C, D, R(28), 0xC6E00BF3); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 157| 72.3k| P(D, E, F, G, H, A, B, C, R(29), 0xD5A79147); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 158| 72.3k| P(C, D, E, F, G, H, A, B, R(30), 0x06CA6351); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 159| 72.3k| P(B, C, D, E, F, G, H, A, R(31), 0x14292967); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 160| 72.3k| P(A, B, C, D, E, F, G, H, R(32), 0x27B70A85); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 161| 72.3k| P(H, A, B, C, D, E, F, G, R(33), 0x2E1B2138); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 162| 72.3k| P(G, H, A, B, C, D, E, F, R(34), 0x4D2C6DFC); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 163| 72.3k| P(F, G, H, A, B, C, D, E, R(35), 0x53380D13); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 164| 72.3k| P(E, F, G, H, A, B, C, D, R(36), 0x650A7354); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 165| 72.3k| P(D, E, F, G, H, A, B, C, R(37), 0x766A0ABB); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 166| 72.3k| P(C, D, E, F, G, H, A, B, R(38), 0x81C2C92E); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 167| 72.3k| P(B, C, D, E, F, G, H, A, R(39), 0x92722C85); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 168| 72.3k| P(A, B, C, D, E, F, G, H, R(40), 0xA2BFE8A1); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 169| 72.3k| P(H, A, B, C, D, E, F, G, R(41), 0xA81A664B); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 170| 72.3k| P(G, H, A, B, C, D, E, F, R(42), 0xC24B8B70); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 171| 72.3k| P(F, G, H, A, B, C, D, E, R(43), 0xC76C51A3); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 172| 72.3k| P(E, F, G, H, A, B, C, D, R(44), 0xD192E819); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 173| 72.3k| P(D, E, F, G, H, A, B, C, R(45), 0xD6990624); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 174| 72.3k| P(C, D, E, F, G, H, A, B, R(46), 0xF40E3585); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 175| 72.3k| P(B, C, D, E, F, G, H, A, R(47), 0x106AA070); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 176| 72.3k| P(A, B, C, D, E, F, G, H, R(48), 0x19A4C116); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 177| 72.3k| P(H, A, B, C, D, E, F, G, R(49), 0x1E376C08); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 178| 72.3k| P(G, H, A, B, C, D, E, F, R(50), 0x2748774C); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 179| 72.3k| P(F, G, H, A, B, C, D, E, R(51), 0x34B0BCB5); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 180| 72.3k| P(E, F, G, H, A, B, C, D, R(52), 0x391C0CB3); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 181| 72.3k| P(D, E, F, G, H, A, B, C, R(53), 0x4ED8AA4A); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 182| 72.3k| P(C, D, E, F, G, H, A, B, R(54), 0x5B9CCA4F); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 183| 72.3k| P(B, C, D, E, F, G, H, A, R(55), 0x682E6FF3); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 184| 72.3k| P(A, B, C, D, E, F, G, H, R(56), 0x748F82EE); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 185| 72.3k| P(H, A, B, C, D, E, F, G, R(57), 0x78A5636F); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 186| 72.3k| P(G, H, A, B, C, D, E, F, R(58), 0x84C87814); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 187| 72.3k| P(F, G, H, A, B, C, D, E, R(59), 0x8CC70208); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 188| 72.3k| P(E, F, G, H, A, B, C, D, R(60), 0x90BEFFFA); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 189| 72.3k| P(D, E, F, G, H, A, B, C, R(61), 0xA4506CEB); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 190| 72.3k| P(C, D, E, F, G, H, A, B, R(62), 0xBEF9A3F7); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 191| 72.3k| P(B, C, D, E, F, G, H, A, R(63), 0xC67178F2); ------------------ | | 112| 72.3k| { \ | | 113| 72.3k| temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 101| 72.3k|#define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x, 11) ^ ROTR(x, 25)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e, f, g) + K + x; \ | | ------------------ | | | | 104| 72.3k|#define F1(x, y, z) (z ^ (x & (y ^ z))) | | ------------------ | | 114| 72.3k| temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 100| 72.3k|#define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x, 13) ^ ROTR(x, 22)) | | | | ------------------ | | | | | | 95| 72.3k|#define ROTR(x, n) (SHR(x, n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 94| 72.3k|#define SHR(x, n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a, b, c); \ | | ------------------ | | | | 103| 72.3k|#define F0(x, y, z) ((x & y) | (z & (x | y))) | | ------------------ | | 115| 72.3k| d += temp1; \ | | 116| 72.3k| h = temp1 + temp2; \ | | 117| 72.3k| } ------------------ 192| | 193| 72.3k| ctx->state[0] += A; 194| 72.3k| ctx->state[1] += B; 195| 72.3k| ctx->state[2] += C; 196| 72.3k| ctx->state[3] += D; 197| 72.3k| ctx->state[4] += E; 198| 72.3k| ctx->state[5] += F; 199| 72.3k| ctx->state[6] += G; 200| 72.3k| ctx->state[7] += H; 201| 72.3k|} cmp_iso_atw_diff_component_no: 135| 1.62k|{ 136| 1.62k| int ret = (int)((const inp_ATOM *)a1)->iso_atw_diff - (int)((const inp_ATOM *)a2)->iso_atw_diff; 137| 1.62k| if (!ret) /* make the sort stable */ ------------------ | Branch (137:9): [True: 1.57k, False: 44] ------------------ 138| 1.57k| { 139| 1.57k| ret = (int)((const inp_ATOM *)a1)->component - (int)((const inp_ATOM *)a2)->component; 140| 1.57k| } 141| | 142| 1.62k| return ret; 143| 1.62k|} the_only_doublet_neigh: 150| 17.3k|{ 151| 17.3k| int i, neigh1, num_rad1 = 0, num_rad2 = 0; 152| | 153| 17.3k| inp_ATOM *a = at + i1, *b; 154| 17.3k| if (RADICAL_DOUBLET != a->radical) ------------------ | | 76| 17.3k|#define RADICAL_DOUBLET 2 ------------------ | Branch (154:9): [True: 0, False: 17.3k] ------------------ 155| 0| { 156| 0| return -1; 157| 0| } 158| 39.9k| for (i = 0; i < a->valence; i++) ------------------ | Branch (158:17): [True: 22.5k, False: 17.3k] ------------------ 159| 22.5k| { 160| 22.5k| b = at + ((int)a->neighbor[i]); /* djb-rwth: removing redundant code */ 161| 22.5k| if (RADICAL_DOUBLET == b->radical) ------------------ | | 76| 22.5k|#define RADICAL_DOUBLET 2 ------------------ | Branch (161:13): [True: 159, False: 22.3k] ------------------ 162| 159| { 163| 159| num_rad1++; 164| 159| *ineigh1 = i; 165| 159| } 166| 22.5k| } 167| | 168| 17.3k| if (1 == num_rad1) ------------------ | Branch (168:9): [True: 63, False: 17.3k] ------------------ 169| 63| { 170| 63| a = at + (neigh1 = (int)a->neighbor[*ineigh1]); 171| 265| for (i = 0; i < a->valence; i++) ------------------ | Branch (171:21): [True: 202, False: 63] ------------------ 172| 202| { 173| 202| b = at + (int)a->neighbor[i]; 174| 202| if (RADICAL_DOUBLET == b->radical) ------------------ | | 76| 202|#define RADICAL_DOUBLET 2 ------------------ | Branch (174:17): [True: 151, False: 51] ------------------ 175| 151| { 176| 151| num_rad2++; 177| 151| *ineigh2 = i; 178| 151| } 179| 202| } 180| | 181| 63| if (1 == num_rad2) ------------------ | Branch (181:13): [True: 13, False: 50] ------------------ 182| 13| { 183| 13| return neigh1; 184| 13| } 185| 63| } 186| | 187| 17.3k| return -1; 188| 17.3k|} fix_non_uniform_drawn_oxoanions: 196| 216k|{ 197| | /* For central halogen, apply the following 198| | correction rules: 199| | 200| | O O(-) 201| | || | 202| | O=Hal(-)=O ===> O=Hal=O 203| | || || 204| | O O 205| | 206| | (perchlorate, etc.) 207| | 208| | 209| | O O(-) 210| | || | 211| | Hal(-)=O ===> Hal=O 212| | || || 213| | O O 214| | 215| | (chlorate, etc.) 216| | 217| | O O(-) 218| | || | 219| | Hal(-)=O ===> Hal=O 220| | 221| | 222| | (chlorite, etc.) 223| | 224| | Hal(-)=O ===> Hal-O(-) 225| | 226| | 227| | (hypochlorite, etc.) 228| | 229| | 230| | 231| | For halcogenes (S, Se, Te) 232| | Y Y(-) 233| | || | 234| | RnX(-) ===> RnX 235| | 236| | if: 237| | 1) (X = S, Y = O) || (X = Se, Y = S, O) || (X = Te, Y = O, S, Se) 238| | 2) valence of X exceeds 6, in initially drawn form 239| | 240| | 241| | So the following is corrected: 242| | 243| | O O(-) 244| | || | 245| | O=S(-)-R ===> O=S-R 246| | || || 247| | O O 248| | 249| | Or 250| | 251| | O O- 252| | || | 253| | F5Te(-) ===> F5Te 254| | 255| | but the following remains unchanged: 256| | 257| | 258| | O 259| | || 260| | O=S(-)-R 261| | 262| | 263| | The central atom (of IUPAC Group 16-17) is shown as negative but it contains double bond(s) 264| | to terminal atom of greater electronegativity (of Group 16). 265| | The central atom is halcogen (S,Se,Te) in highest oxidation state or halogen. 266| | 267| | Fix: 268| | move negative charge to terminal atom and change double bond to a single one. 269| | 270| | Eligible central atom Eligible terminal atom at double bond's end 271| | Cl O 272| | Br O 273| | I O 274| | [At S,Se,Te] 275| | S O 276| | Se O,S 277| | Te O, S, Se 278| | 279| | Comments: 280| | 1. Central atoms of Groups 13-15 are not considered. 281| | 2. Pauling electronegativities are: 282| | F(3.98) > O(3.44) > Cl (3.16) > N (3.04) > Br(2.96) > I(2.66) > S(2.58) > Se(2.55) > At (2.2) > Te(2.1) 283| | 284| | 285| | */ 286| | 287| | /* constants for element numbers */ 288| 216k| enum elems 289| 216k| { 290| 216k| dNone, 291| 216k| dCl = 17, 292| 216k| dBr = 35, 293| 216k| dI = 53, 294| 216k| dAt = 85, 295| 216k| dO = 8, 296| 216k| dS = 16, 297| 216k| dSe = 34, 298| 216k| dTe = 52, 299| 216k| dP = 15, 300| 216k| dC = 6, 301| 216k| dN = 7 302| 216k| }; 303| | 304| 216k| static U_CHAR allowed_elnums_center_halogen[] = {dCl, dBr, dI, dAt}; 305| 216k| static U_CHAR allowed_elnums_center_halcogen[] = {dS, dSe, dTe}; 306| | 307| 216k| int en_center; 308| 216k| int i, j, k; 309| | 310| 1.27M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (310:17): [True: 1.05M, False: 216k] ------------------ 311| 1.05M| { 312| | /* Find appropriate central atom. This center should be: ...*/ 313| | 314| | /* charged exactly (-1) ... */ 315| 1.05M| if (at[i].charge != -1) ------------------ | Branch (315:13): [True: 1.01M, False: 44.2k] ------------------ 316| 1.01M| { 317| 1.01M| continue; 318| 1.01M| } 319| 44.2k| en_center = at[i].el_number; 320| | /* from eligible element list ... */ 321| 44.2k| if (!memchr(allowed_elnums_center_halogen, en_center, sizeof(allowed_elnums_center_halogen))) ------------------ | Branch (321:13): [True: 44.0k, False: 191] ------------------ 322| 44.0k| { 323| | /* central atom is not not halogen; check if it is halcogen */ 324| 44.0k| if (memchr(allowed_elnums_center_halcogen, en_center, sizeof(allowed_elnums_center_halcogen))) ------------------ | Branch (324:17): [True: 5.66k, False: 38.3k] ------------------ 325| 5.66k| { 326| 5.66k| if (at[i].chem_bonds_valence < 7) ------------------ | Branch (326:21): [True: 5.33k, False: 327] ------------------ 327| 5.33k| { 328| | /* central atom is anionic halcogen, but not in the highest oxidation state */ 329| 5.33k| continue; 330| 5.33k| } 331| 5.66k| } 332| 38.3k| else 333| 38.3k| { 334| 38.3k| continue; 335| 38.3k| } 336| 44.0k| } 337| | 338| | /* OK, found central halogen or eligible central halcogen. */ 339| | 340| | /* non-radical... */ 341| 518| if (at[i].radical && (at[i].radical != RADICAL_SINGLET)) ------------------ | | 75| 175|#define RADICAL_SINGLET 1 ------------------ | Branch (341:13): [True: 175, False: 343] | Branch (341:30): [True: 175, False: 0] ------------------ 342| 175| { 343| 175| continue; 344| 175| } 345| | 346| | /* Center found, now examine the adjacent terminals... */ 347| 343| { 348| 343| int en_term, kk = 0, jj = 0, min_en = 999, iso = 0, min_iso = 999; 349| 343| jj = -1; 350| 1.92k| for (k = 0; k < at[i].valence; k++) ------------------ | Branch (350:25): [True: 1.58k, False: 343] ------------------ 351| 1.58k| { 352| 1.58k| j = at[i].neighbor[k]; 353| | 354| | /* Terminal should be: ... */ 355| | 356| | /* terminal... */ 357| 1.58k| if (at[j].valence != 1) ------------------ | Branch (357:21): [True: 425, False: 1.16k] ------------------ 358| 425| { 359| 425| continue; 360| 425| } 361| | /* double-bonded ... */ 362| 1.16k| if (at[i].bond_type[k] != BOND_TYPE_DOUBLE) ------------------ | | 33| 1.16k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (362:21): [True: 461, False: 700] ------------------ 363| 461| { 364| 461| continue; 365| 461| } 366| | /* zero-charged ... */ 367| 700| if (at[j].charge != 0) ------------------ | Branch (367:21): [True: 172, False: 528] ------------------ 368| 172| { 369| 172| continue; 370| 172| } 371| | /* non-radical */ 372| 528| if (at[j].radical && (at[j].radical != RADICAL_SINGLET)) ------------------ | | 75| 67|#define RADICAL_SINGLET 1 ------------------ | Branch (372:21): [True: 67, False: 461] | Branch (372:38): [True: 67, False: 0] ------------------ 373| 67| { 374| 67| continue; 375| 67| } 376| | /* of eligible elements list ... */ 377| 461| en_term = at[j].el_number; 378| 461| switch (en_term) 379| 461| { 380| 216| case dO: ------------------ | Branch (380:17): [True: 216, False: 245] ------------------ 381| 216| break; 382| 162| case dS: ------------------ | Branch (382:17): [True: 162, False: 299] ------------------ 383| 162| if ((en_center == dSe) || (en_center == dAt) || (en_center == dTe)) ------------------ | Branch (383:25): [True: 51, False: 111] | Branch (383:47): [True: 0, False: 111] | Branch (383:69): [True: 19, False: 92] ------------------ 384| 70| break; 385| 92| continue; 386| 92| case dSe: ------------------ | Branch (386:17): [True: 46, False: 415] ------------------ 387| 46| if ((en_center == dAt) || (en_center == dTe)) ------------------ | Branch (387:25): [True: 0, False: 46] | Branch (387:47): [True: 0, False: 46] ------------------ 388| 0| break; 389| 46| continue; 390| 46| case dTe: ------------------ | Branch (390:17): [True: 36, False: 425] ------------------ 391| 36| if (en_center == dAt) ------------------ | Branch (391:25): [True: 0, False: 36] ------------------ 392| 0| break; 393| 36| continue; 394| 36| default: ------------------ | Branch (394:17): [True: 1, False: 460] ------------------ 395| 1| continue; 396| 461| } 397| | 398| | /* From several candidates, select one with less el. number (==more electronegative). */ 399| 286| if (en_term < min_en) ------------------ | Branch (399:21): [True: 156, False: 130] ------------------ 400| 156| { 401| 156| min_en = en_term; 402| 156| kk = k; 403| 156| jj = j; 404| 156| min_iso = at[j].iso_atw_diff > 0 ? at[i].iso_atw_diff - 1 : at[i].iso_atw_diff; ------------------ | Branch (404:31): [True: 0, False: 156] ------------------ 405| 156| continue; 406| 156| } 407| | /* From same-element candidates, select one with less isotopic mass (arbitrary choice). */ 408| 130| else if (en_term == min_en) ------------------ | Branch (408:26): [True: 129, False: 1] ------------------ 409| 129| { 410| 129| iso = at[j].iso_atw_diff > 0 ? at[i].iso_atw_diff - 1 : at[i].iso_atw_diff; ------------------ | Branch (410:27): [True: 0, False: 129] ------------------ 411| 129| if (iso < min_iso) ------------------ | Branch (411:25): [True: 0, False: 129] ------------------ 412| 0| { 413| 0| min_iso = iso; 414| 0| kk = k; 415| 0| jj = j; 416| 0| continue; 417| 0| } 418| 129| } 419| 286| } /* end of checking nbrs. */ 420| | 421| | /* If OK, apply changes. */ 422| 343| if (jj >= 0) ------------------ | Branch (422:17): [True: 156, False: 187] ------------------ 423| 156| { 424| 156| at[i].charge = 0; 425| 156| at[jj].charge = -1; 426| 156| at[i].bond_type[kk] = BOND_TYPE_SINGLE; ------------------ | | 32| 156|#define BOND_TYPE_SINGLE 1 ------------------ 427| 156| at[jj].bond_type[0] = BOND_TYPE_SINGLE; ------------------ | | 32| 156|#define BOND_TYPE_SINGLE 1 ------------------ 428| 156| at[i].bond_stereo[kk] = at[jj].bond_stereo[0] = 0; 429| 156| at[i].chem_bonds_valence--; 430| 156| at[jj].chem_bonds_valence--; 431| 156| (*num_changes)++; 432| 156| } 433| 343| } 434| 343| } /* end of search for candidate centers. */ 435| | 436| 216k| return 0; 437| 216k|} fix_non_uniform_drawn_amidiniums: 446| 216k|{ 447| | /* Amidines include carboxamidines RC(=NR)NR2, 448| | sulfinamidines RS(=NR)NR2 and phosphinamidines, R2P(=NR)NR2. 449| | 450| | 451| | NR NR 452| | | | 453| | R"-Y-NHR' ===> R"-Y=N(+)HR' 454| | (+) 455| | 456| | 457| | Y = C, S, P 458| | 459| | 460| | Fix: 461| | move positive charge to nitrogen and change single bond to a double one. 462| | 463| | 464| | Comment: 465| | Fix is applied only if at least one of R's at N is hydrogen 466| | (otherwise we have just a '+' delocalization which is already recognized). 467| | 468| | 469| | */ 470| | 471| | /* constants for element numbers */ 472| 216k| enum elems 473| 216k| { 474| 216k| dNone, 475| 216k| dCl = 17, 476| 216k| dBr = 35, 477| 216k| dI = 53, 478| 216k| dAt = 85, 479| 216k| dO = 8, 480| 216k| dS = 16, 481| 216k| dSe = 34, 482| 216k| dTe = 52, 483| 216k| dP = 15, 484| 216k| dC = 6, 485| 216k| dN = 7 486| 216k| }; 487| | 488| 216k| static U_CHAR allowed_elnums_center[] = {dC, dS, dP}; 489| 216k| int en_center; 490| 216k| int i, j, k, jj, kk, k1; 491| 216k| int mismatch = 0, nuH = 0, nuN = 0, nitrogens[MAXVAL]; 492| | 493| 1.27M| for (i = 0; i < num_atoms; i++) ------------------ | Branch (493:17): [True: 1.05M, False: 216k] ------------------ 494| 1.05M| { 495| | /* Find appropriate central atom. This center should be: ...*/ 496| | 497| | /* charged exactly (+1) ... */ 498| 1.05M| if (at[i].charge != 1) ------------------ | Branch (498:13): [True: 981k, False: 75.8k] ------------------ 499| 981k| { 500| 981k| continue; 501| 981k| } 502| 75.8k| en_center = at[i].el_number; 503| | /* from eligible element list ... */ 504| 75.8k| if (!memchr(allowed_elnums_center, en_center, sizeof(allowed_elnums_center))) ------------------ | Branch (504:13): [True: 64.3k, False: 11.5k] ------------------ 505| 64.3k| { 506| 64.3k| continue; 507| 64.3k| } 508| | /* has exactly 3 neighbours connected by single bonds*/ 509| 11.5k| if (at[i].valence != 3) ------------------ | Branch (509:13): [True: 10.2k, False: 1.32k] ------------------ 510| 10.2k| { 511| 10.2k| continue; 512| 10.2k| } 513| 1.32k| if (at[i].chem_bonds_valence != 3) ------------------ | Branch (513:13): [True: 511, False: 812] ------------------ 514| 511| { 515| 511| continue; 516| 511| } 517| | 518| | /* non-radical. */ 519| 812| if (at[i].radical && (at[i].radical != RADICAL_SINGLET)) ------------------ | | 75| 22|#define RADICAL_SINGLET 1 ------------------ | Branch (519:13): [True: 22, False: 790] | Branch (519:30): [True: 22, False: 0] ------------------ 520| 22| { 521| 22| continue; 522| 22| } 523| | 524| | /* NB: center must have neutral neighbours, two of them are aliphatic N's of which at least one bears H. */ 525| 790| mismatch = nuH = nuN = kk = 0; /* djb-rwth: removing redundant code */ 526| 790| memset(nitrogens, 0, sizeof(nitrogens)); /* djb-rwth: memset_s C11/Annex K variant? */ 527| 790| jj = -1; 528| 2.31k| for (k = 0; k < at[i].valence; k++) ------------------ | Branch (528:21): [True: 1.82k, False: 490] ------------------ 529| 1.82k| { 530| 1.82k| j = at[i].neighbor[k]; 531| | 532| 1.82k| if (at[j].charge != 0) ------------------ | Branch (532:17): [True: 118, False: 1.70k] ------------------ 533| 118| { 534| 118| mismatch = 1; 535| 118| break; 536| 118| } 537| 1.70k| if (at[j].el_number == dN) ------------------ | Branch (537:17): [True: 248, False: 1.45k] ------------------ 538| 248| { 539| 248| if ((at[j].valence > 3) || (at[j].chem_bonds_valence > 3)) ------------------ | Branch (539:21): [True: 39, False: 209] | Branch (539:44): [True: 143, False: 66] ------------------ 540| 182| { 541| 182| mismatch = 1; 542| 182| break; 543| 182| } 544| 66| nuH += NUMH(at, j); ------------------ | | 56| 66|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 66|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 545| 66| nuN++; 546| 66| if (jj < 0) ------------------ | Branch (546:21): [True: 41, False: 25] ------------------ 547| 41| { 548| 41| jj = j; 549| 41| kk = k; 550| 41| } 551| 66| } 552| 1.70k| } 553| | 554| | /* If OK, apply changes. */ 555| 790| if (mismatch) ------------------ | Branch (555:13): [True: 300, False: 490] ------------------ 556| 300| { 557| 300| continue; 558| 300| } 559| 490| if (nuN != 2) ------------------ | Branch (559:13): [True: 467, False: 23] ------------------ 560| 467| { 561| 467| continue; 562| 467| } 563| 23| if (nuH < 1) ------------------ | Branch (563:13): [True: 20, False: 3] ------------------ 564| 20| { 565| 20| continue; 566| 20| } 567| 3| if (jj >= 0) ------------------ | Branch (567:13): [True: 3, False: 0] ------------------ 568| 3| { 569| 3| at[i].charge = 0; 570| 3| at[jj].charge = 1; 571| 3| at[i].bond_type[kk] = BOND_TYPE_DOUBLE; ------------------ | | 33| 3|#define BOND_TYPE_DOUBLE 2 ------------------ 572| 6| for (k1 = 0; k1 < at[jj].valence && i != at[jj].neighbor[k1]; k1++) ------------------ | Branch (572:26): [True: 6, False: 0] | Branch (572:49): [True: 3, False: 3] ------------------ 573| 3| ; 574| 3| at[jj].bond_type[k1] = BOND_TYPE_DOUBLE; ------------------ | | 33| 3|#define BOND_TYPE_DOUBLE 2 ------------------ 575| 3| at[i].chem_bonds_valence++; 576| 3| at[jj].chem_bonds_valence++; 577| | /* NB: do nothing with wedge stereo bonds (retain wedge) */ 578| | 579| 3| (*num_changes)++; 580| 3| } 581| 3| } /* end of search for candidate centers. */ 582| | 583| 216k| return 0; 584| 216k|} fix_odd_things: 591| 216k|{ 592| | /* N;P;As;Sb;O;S;Se;Te;C;Si */ 593| 216k| static const U_CHAR en[] = { 594| 216k| EL_NUMBER_N, ------------------ | | 14| 216k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ 595| 216k| EL_NUMBER_P, ------------------ | | 18| 216k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ 596| 216k| EL_NUMBER_AS, ------------------ | | 22| 216k|#define EL_NUMBER_AS ((U_CHAR)33) ------------------ 597| 216k| EL_NUMBER_SB, ------------------ | | 25| 216k|#define EL_NUMBER_SB ((U_CHAR)51) ------------------ 598| 216k| EL_NUMBER_O, ------------------ | | 15| 216k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ 599| 216k| EL_NUMBER_S, ------------------ | | 19| 216k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ 600| 216k| EL_NUMBER_SE, ------------------ | | 23| 216k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ 601| 216k| EL_NUMBER_TE}; ------------------ | | 26| 216k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ 602| 216k| static int ne = sizeof(en) / sizeof(en[0]); 603| | 604| 216k|#define FIRST_NEIGHB2 4 605| 216k|#define FIRST_CENTER2 5 606| | 607| 216k| int i1, i2, k1, k2, c = -1, num_changes = 0; 608| | /* djb-rwth: removing redundant variables */ 609| | 610| 216k| if (bFixNonUniformDraw) ------------------ | Branch (610:9): [True: 216k, False: 0] ------------------ 611| 216k| { 612| 216k| int ret1; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 613| 216k| ret1 = fix_non_uniform_drawn_oxoanions(num_atoms, at, &num_changes); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 614| 216k| ret1 = fix_non_uniform_drawn_amidiniums(num_atoms, at, &num_changes); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 615| 216k| } 616| | 617| | /* H(-)-X -> H-X(-); H(+)-X -> H-X(+) */ 618| 1.27M| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (618:18): [True: 1.05M, False: 216k] ------------------ 619| 1.05M| { 620| 1.05M| if (1 == at[i1].valence && ------------------ | Branch (620:13): [True: 110k, False: 947k] ------------------ 621| 110k| 1 == abs(at[i1].charge) && ------------------ | Branch (621:13): [True: 44.4k, False: 65.5k] ------------------ 622| 44.4k| (0 == at[i1].radical || RADICAL_SINGLET == at[i1].radical) && ------------------ | | 75| 7.91k|#define RADICAL_SINGLET 1 ------------------ | Branch (622:14): [True: 36.5k, False: 7.91k] | Branch (622:37): [True: 0, False: 7.91k] ------------------ 623| 36.5k| BOND_TYPE_SINGLE == at[i1].bond_type[0] && ------------------ | | 32| 36.5k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (623:13): [True: 16.4k, False: 20.0k] ------------------ 624| 16.4k| EL_NUMBER_H == at[i1].el_number && EL_NUMBER_H != at[i2 = (int)at[i1].neighbor[0]].el_number && ------------------ | | 11| 16.4k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ EL_NUMBER_H == at[i1].el_number && EL_NUMBER_H != at[i2 = (int)at[i1].neighbor[0]].el_number && ------------------ | | 11| 0|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (624:13): [True: 0, False: 16.4k] | Branch (624:48): [True: 0, False: 0] ------------------ 625| 0| !NUMH(at, i1) && !NUMH(at, i2)) ------------------ | | 56| 1.05M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 0|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ !NUMH(at, i1) && !NUMH(at, i2)) ------------------ | | 56| 0|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 0|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (625:13): [True: 0, False: 0] | Branch (625:30): [True: 0, False: 0] ------------------ 626| 0| { 627| 0| at[i2].charge += at[i1].charge; 628| 0| at[i1].charge = 0; 629| 0| } 630| 1.05M| } 631| | 632| | /* replace XHm(-)--Y==XHn(+) with XHm==Y--XHn, (n>=0 ,m>=0, X=N,P,As,Sb,O,S,Se,Te) */ 633| 1.27M| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (633:18): [True: 1.05M, False: 216k] ------------------ 634| 1.05M| { 635| 1.05M| if (1 != at[i1].charge || ------------------ | Branch (635:13): [True: 981k, False: 75.8k] ------------------ 636| 75.8k| (at[i1].radical && RADICAL_SINGLET != at[i1].radical) || ------------------ | | 75| 4.10k|#define RADICAL_SINGLET 1 ------------------ | Branch (636:14): [True: 4.10k, False: 71.7k] | Branch (636:32): [True: 4.10k, False: 0] ------------------ 637| 71.7k| at[i1].chem_bonds_valence == at[i1].valence || ------------------ | Branch (637:13): [True: 44.4k, False: 27.3k] ------------------ 638| 27.3k| !memchr(en, at[i1].el_number, ne) || ------------------ | Branch (638:13): [True: 9.66k, False: 17.7k] ------------------ 639| 17.7k| get_el_valence(at[i1].el_number, at[i1].charge, 0) != at[i1].chem_bonds_valence + NUMH(at, i1)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 56| 17.7k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 17.7k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (639:13): [True: 3.02k, False: 14.6k] ------------------ 640| 1.04M| { 641| 1.04M| continue; 642| 1.04M| } 643| | 644| | /* found a candidate at[i1] for X in XHn(+) */ 645| 14.6k| if (1 == at[i1].valence && ------------------ | Branch (645:13): [True: 707, False: 13.9k] ------------------ 646| 707| BOND_TYPE_DOUBLE == at[i1].bond_type[0]) ------------------ | | 33| 707|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (646:13): [True: 378, False: 329] ------------------ 647| 378| { 648| 378| c = (int)at[i1].neighbor[0]; 649| 1.43k| for (k2 = 0; k2 < at[c].valence; k2++) ------------------ | Branch (649:26): [True: 1.06k, False: 367] ------------------ 650| 1.06k| { 651| 1.06k| i2 = at[c].neighbor[k2]; 652| 1.06k| if (1 == at[i2].valence && ------------------ | Branch (652:21): [True: 632, False: 432] ------------------ 653| 632| -1 == at[i2].charge && ------------------ | Branch (653:21): [True: 93, False: 539] ------------------ 654| 93| at[i2].el_number == at[i1].el_number && /* exact match */ ------------------ | Branch (654:21): [True: 33, False: 60] ------------------ 655| 33| (0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical) && ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (655:22): [True: 33, False: 0] | Branch (655:45): [True: 0, False: 0] ------------------ 656| 33| BOND_TYPE_SINGLE == at[i2].bond_type[0] && ------------------ | | 32| 33|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (656:21): [True: 12, False: 21] ------------------ 657| | /*memchr(en, at[i2].el_number, ne) &&*/ 658| 12| get_el_valence(at[i2].el_number, at[i2].charge, 0) == at[i2].chem_bonds_valence + NUMH(at, i2)) ------------------ | | 56| 12|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 12|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (658:21): [True: 11, False: 1] ------------------ 659| 11| { 660| | /* found both X(-) and X(+); change bonds and remove charges */ 661| 30| for (k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1++) ------------------ | Branch (661:34): [True: 30, False: 0] | Branch (661:56): [True: 19, False: 11] ------------------ 662| 19| ; 663| 11| at[i1].charge = at[i2].charge = 0; 664| 11| at[i1].bond_type[0] = at[c].bond_type[k1] = BOND_TYPE_SINGLE; ------------------ | | 32| 11|#define BOND_TYPE_SINGLE 1 ------------------ 665| 11| at[i1].chem_bonds_valence--; 666| 11| at[i2].bond_type[0] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; ------------------ | | 33| 11|#define BOND_TYPE_DOUBLE 2 ------------------ 667| 11| at[i2].chem_bonds_valence++; 668| 11| num_changes++; 669| 11| break; 670| 11| } 671| 1.06k| } 672| 378| } 673| 14.3k| else 674| 14.3k| { 675| | /* explicit H case: detect H-neighbors and Y */ 676| 14.3k| int ineigh, neigh, i1_c, i2_c, num_H_i1, num_H_i2; 677| 42.8k| for (ineigh = 0, num_H_i1 = 0, i1_c = -1; ineigh < at[i1].valence; ineigh++) ------------------ | Branch (677:55): [True: 29.8k, False: 12.9k] ------------------ 678| 29.8k| { 679| 29.8k| neigh = at[i1].neighbor[ineigh]; 680| 29.8k| if (at[neigh].el_number == EL_NUMBER_H) ------------------ | | 11| 29.8k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (680:21): [True: 2.50k, False: 27.3k] ------------------ 681| 2.50k| { 682| 2.50k| if (at[neigh].chem_bonds_valence == 1 && ------------------ | Branch (682:25): [True: 1.14k, False: 1.36k] ------------------ 683| 1.14k| (0 == at[neigh].radical || RADICAL_SINGLET == at[neigh].radical)) ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (683:26): [True: 1.14k, False: 0] | Branch (683:52): [True: 0, False: 0] ------------------ 684| 1.14k| { 685| 1.14k| num_H_i1++; /* found H-neighbor */ 686| 1.14k| } 687| 1.36k| else 688| 1.36k| { 689| 1.36k| break; /* wrong neighbor */ 690| 1.36k| } 691| 2.50k| } 692| 27.3k| else if (at[i1].bond_type[ineigh] == BOND_TYPE_DOUBLE) ------------------ | | 33| 27.3k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (692:26): [True: 11.4k, False: 15.9k] ------------------ 693| 11.4k| { 694| | /* found a candidate for Y; bond must be double */ 695| 11.4k| i1_c = ineigh; 696| 11.4k| c = neigh; 697| 11.4k| } 698| 29.8k| } 699| 14.3k| if (i1_c < 0 || num_H_i1 + 1 != at[i1].valence) ------------------ | Branch (699:17): [True: 5.46k, False: 8.84k] | Branch (699:29): [True: 8.47k, False: 372] ------------------ 700| 13.9k| { 701| 13.9k| continue; 702| 13.9k| } 703| 1.13k| for (k2 = 0; k2 < at[c].valence; k2++) ------------------ | Branch (703:26): [True: 814, False: 324] ------------------ 704| 814| { 705| 814| i2 = at[c].neighbor[k2]; 706| 814| if (-1 == at[i2].charge && ------------------ | Branch (706:21): [True: 92, False: 722] ------------------ 707| 92| at[i2].el_number == at[i1].el_number && /* exact match */ ------------------ | Branch (707:21): [True: 76, False: 16] ------------------ 708| 76| (0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical) && ------------------ | | 75| 1|#define RADICAL_SINGLET 1 ------------------ | Branch (708:22): [True: 75, False: 1] | Branch (708:45): [True: 0, False: 1] ------------------ 709| 75| get_el_valence(at[i2].el_number, at[i2].charge, 0) == at[i2].chem_bonds_valence + NUMH(at, i2)) ------------------ | | 56| 75|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 75|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (709:21): [True: 75, False: 0] ------------------ 710| 75| { 711| 194| for (ineigh = 0, num_H_i2 = 0, i2_c = -1; ineigh < at[i2].valence; ineigh++) ------------------ | Branch (711:63): [True: 146, False: 48] ------------------ 712| 146| { 713| 146| neigh = at[i2].neighbor[ineigh]; 714| 146| if (at[neigh].el_number == EL_NUMBER_H) ------------------ | | 11| 146|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (714:29): [True: 70, False: 76] ------------------ 715| 70| { 716| 70| if (at[neigh].chem_bonds_valence == 1 && ------------------ | Branch (716:33): [True: 48, False: 22] ------------------ 717| 48| (0 == at[neigh].radical || RADICAL_SINGLET == at[neigh].radical)) ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (717:34): [True: 48, False: 0] | Branch (717:60): [True: 0, False: 0] ------------------ 718| 48| { 719| 48| num_H_i2++; /* found H-neighbor */ 720| 48| } 721| 22| else 722| 22| { 723| 22| break; /* wrong neighbor */ 724| 22| } 725| 70| } 726| 76| else 727| 76| { 728| 76| if (c == neigh && at[i2].bond_type[ineigh] == BOND_TYPE_SINGLE) ------------------ | | 32| 75|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (728:33): [True: 75, False: 1] | Branch (728:47): [True: 71, False: 4] ------------------ 729| 71| { 730| 71| i2_c = ineigh; /* position of Y neighbor; bond must be single */ 731| 71| } 732| 5| else 733| 5| { 734| 5| break; 735| 5| } 736| 76| } 737| 146| } 738| 75| if (num_H_i2 + (i2_c >= 0) != at[i2].valence) ------------------ | Branch (738:25): [True: 27, False: 48] ------------------ 739| 27| { 740| 27| continue; 741| 27| } 742| | /* found both X(-) and X(+); change bonds and remove charges */ 743| 94| for (k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1++) ------------------ | Branch (743:34): [True: 94, False: 0] | Branch (743:56): [True: 46, False: 48] ------------------ 744| 46| ; 745| 48| if ((i1_c >= 0) && (i2_c >= 0)) /* djb-rwth: fixing coverity ID #499537 */ ------------------ | Branch (745:25): [True: 48, False: 0] | Branch (745:40): [True: 48, False: 0] ------------------ 746| 48| { 747| 48| at[i1].charge = at[i2].charge = 0; 748| 48| at[i1].bond_type[i1_c] = at[c].bond_type[k1] = BOND_TYPE_SINGLE; ------------------ | | 32| 48|#define BOND_TYPE_SINGLE 1 ------------------ 749| 48| at[i1].chem_bonds_valence--; 750| 48| at[i2].bond_type[i2_c] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; ------------------ | | 33| 48|#define BOND_TYPE_DOUBLE 2 ------------------ 751| 48| at[i2].chem_bonds_valence++; 752| 48| num_changes++; 753| 48| break; 754| 48| } 755| 0| else 756| 0| { 757| 0| continue; 758| 0| } 759| 48| } 760| 814| } /* k2 */ 761| 372| } 762| 14.6k| } 763| | 764| | /* Replace 765| | 766| | X- X X=O,S,Se,Te -- terminal atoms (NEIGHB2) 767| | \ | \ || 768| | >Y++ with >Y Y=S,Se,Te -- central cation (CENTER2) 769| | / | / || 770| | X- X Y valence=4, original Y bond valence = 4 771| | 772| | 773| | --- the following case of P is processed separately in remove_ion_pairs() 774| | --- therefire, it has been disabled here, see #ifndef FIX_P_IV_Plus_O_Minus -- 2010-03-17 DT 775| | 776| | X- X X=O,S,Se,Te -- terminal atoms (NEIGHB2) 777| | \ | \ || 778| | >P+ with >P 779| | / | / | 780| | X- X- Y valence=4, original Y bond valence = 4 781| | 782| | */ 783| | 784| 1.27M| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (784:18): [True: 1.05M, False: 216k] ------------------ 785| 1.05M| { 786| 1.05M| if (1 == at[i1].valence && ------------------ | Branch (786:13): [True: 110k, False: 947k] ------------------ 787| 110k| -1 == at[i1].charge && ------------------ | Branch (787:13): [True: 33.7k, False: 76.2k] ------------------ 788| 33.7k| (0 == at[i1].radical || RADICAL_SINGLET == at[i1].radical) && ------------------ | | 75| 5.09k|#define RADICAL_SINGLET 1 ------------------ | Branch (788:14): [True: 28.6k, False: 5.09k] | Branch (788:37): [True: 0, False: 5.09k] ------------------ 789| 28.6k| !NUMH(at, i1) && ------------------ | | 56| 1.08M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 28.6k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (789:13): [True: 28.3k, False: 324] ------------------ 790| 28.3k| BOND_TYPE_SINGLE == at[i1].bond_type[0] && ------------------ | | 32| 28.3k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (790:13): [True: 13.8k, False: 14.4k] ------------------ 791| 13.8k| memchr(en + FIRST_NEIGHB2, at[i1].el_number, (long long)ne - FIRST_NEIGHB2)) /* djb-rwth: cast operator added */ ------------------ | | 604| 13.8k|#define FIRST_NEIGHB2 4 ------------------ memchr(en + FIRST_NEIGHB2, at[i1].el_number, (long long)ne - FIRST_NEIGHB2)) /* djb-rwth: cast operator added */ ------------------ | | 604| 13.8k|#define FIRST_NEIGHB2 4 ------------------ | Branch (791:13): [True: 12.2k, False: 1.65k] ------------------ 792| 12.2k| { 793| 12.2k| int charge, i; 794| | /* found a candidate for X */ 795| 12.2k| c = (int)at[i1].neighbor[0]; /* candidate for Y */ 796| 12.2k| if (((charge = 2) == at[c].charge && memchr(en + FIRST_CENTER2, at[c].el_number, (long long)ne - FIRST_CENTER2) /* djb-rwth: cast operator added */ ------------------ | | 605| 12|#define FIRST_CENTER2 5 ------------------ if (((charge = 2) == at[c].charge && memchr(en + FIRST_CENTER2, at[c].el_number, (long long)ne - FIRST_CENTER2) /* djb-rwth: cast operator added */ ------------------ | | 605| 12|#define FIRST_CENTER2 5 ------------------ | Branch (796:18): [True: 12, False: 12.2k] | Branch (796:50): [True: 0, False: 12] ------------------ 797| | 798| |#ifndef FIX_P_IV_Plus_O_Minus 799| | || (charge = 1) == at[c].charge && EL_NUMBER_P == at[c].el_number 800| |#endif 801| 12.2k| ) && 802| 0| 4 == at[c].valence && ------------------ | Branch (802:17): [True: 0, False: 0] ------------------ 803| 0| (0 == at[c].radical || RADICAL_SINGLET == at[c].radical) && ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (803:18): [True: 0, False: 0] | Branch (803:40): [True: 0, False: 0] ------------------ 804| 0| at[c].valence == at[c].chem_bonds_valence && ------------------ | Branch (804:17): [True: 0, False: 0] ------------------ 805| 0| !NUMH(at, c)) ------------------ | | 56| 0|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 0|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (805:17): [True: 0, False: 0] ------------------ 806| 0| { 807| 0| ; /* accept */ 808| 0| } 809| 12.2k| else 810| 12.2k| { 811| 12.2k| continue; /* ignore at[i1] */ 812| 12.2k| } 813| 0| for (k2 = 0; k2 < at[c].valence; k2++) ------------------ | Branch (813:26): [True: 0, False: 0] ------------------ 814| 0| { 815| 0| i2 = at[c].neighbor[k2]; 816| 0| if (i2 == i1) ------------------ | Branch (816:21): [True: 0, False: 0] ------------------ 817| 0| { 818| 0| continue; 819| 0| } 820| 0| if (1 == at[i2].valence && ------------------ | Branch (820:21): [True: 0, False: 0] ------------------ 821| 0| -1 == at[i2].charge && ------------------ | Branch (821:21): [True: 0, False: 0] ------------------ 822| 0| memchr(en + FIRST_NEIGHB2, at[i2].el_number, (long long)ne - FIRST_NEIGHB2) && /* djb-rwth: cast operator added */ ------------------ | | 604| 0|#define FIRST_NEIGHB2 4 ------------------ memchr(en + FIRST_NEIGHB2, at[i2].el_number, (long long)ne - FIRST_NEIGHB2) && /* djb-rwth: cast operator added */ ------------------ | | 604| 0|#define FIRST_NEIGHB2 4 ------------------ | Branch (822:21): [True: 0, False: 0] ------------------ 823| | /*at[i2].el_number == at[i1].el_number &&*/ /* exact match */ 824| 0| (0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical) && ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (824:22): [True: 0, False: 0] | Branch (824:45): [True: 0, False: 0] ------------------ 825| 0| !NUMH(at, i2) && ------------------ | | 56| 0|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 0|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (825:21): [True: 0, False: 0] ------------------ 826| 0| BOND_TYPE_SINGLE == at[i2].bond_type[0]) ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (826:21): [True: 0, False: 0] ------------------ 827| 0| { 828| | /* found both X(-) and X(-); change bonds and remove charges */ 829| 0| for (k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1++) ------------------ | Branch (829:34): [True: 0, False: 0] | Branch (829:56): [True: 0, False: 0] ------------------ 830| 0| { 831| 0| ; 832| 0| } 833| 0| for (i = 0; i < charge; i++) ------------------ | Branch (833:33): [True: 0, False: 0] ------------------ 834| 0| { 835| | /* in case of P it does not matter which X atom is neutralized 836| | because of tautomerism. However, neutral central atom is important 837| | for the neutralization of the components */ 838| 0| switch (i) ------------------ | Branch (838:33): [True: 0, False: 0] ------------------ 839| 0| { 840| 0| case 0: ------------------ | Branch (840:25): [True: 0, False: 0] ------------------ 841| 0| at[i1].charge++; /* = 0; changed 2010-03-17 DT*/ 842| 0| at[i1].bond_type[0] = at[c].bond_type[k1] = BOND_TYPE_DOUBLE; ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 843| 0| at[i1].bond_stereo[0] = at[c].bond_stereo[k1] = 0; 844| 0| at[i1].chem_bonds_valence++; 845| 0| at[c].chem_bonds_valence++; 846| 0| if (bFixBug) ------------------ | Branch (846:33): [True: 0, False: 0] ------------------ 847| 0| at[c].charge--; /* added 2010-03-17 DT*/ 848| 0| num_changes++; 849| 0| break; 850| 0| case 1: ------------------ | Branch (850:25): [True: 0, False: 0] ------------------ 851| 0| at[i2].charge++; /*= 0; changed 2010-03-17 DT*/ 852| 0| at[i2].bond_type[0] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; ------------------ | | 33| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 853| 0| at[i2].bond_stereo[0] = at[c].bond_stereo[k2] = 0; 854| 0| at[i2].chem_bonds_valence++; 855| 0| at[c].chem_bonds_valence++; 856| 0| if (bFixBug) ------------------ | Branch (856:33): [True: 0, False: 0] ------------------ 857| 0| at[c].charge--; /* added 2010-03-17 DT */ 858| 0| num_changes++; 859| 0| break; 860| 0| } 861| 0| } 862| | 863| | /* -- removed -- 2010-03-17 DT 864| | #if ( FIX_ODD_THINGS_REM_Plus_BUG == 1 ) 865| | at[c].charge -= charge; 866| | #else 867| | if ( bFixBug ) 868| | { 869| | at[c].charge -= charge; 870| | } 871| | #endif 872| | */ 873| 0| break; 874| 0| } 875| 0| } 876| 0| } 877| 1.05M| } 878| | 879| | /* A(doublet)-B(doublet) -> A=B (A and B have no other doublet neighbors) */ 880| | /* A(doublet)=B(doublet) -> A#B (A and B have no other doublet neighbors) */ 881| 1.27M| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (881:18): [True: 1.05M, False: 216k] ------------------ 882| 1.05M| { 883| 1.05M| if (RADICAL_DOUBLET == at[i1].radical && ------------------ | | 76| 1.05M|#define RADICAL_DOUBLET 2 ------------------ | Branch (883:13): [True: 17.3k, False: 1.03M] ------------------ 884| 17.3k| 0 <= (i2 = the_only_doublet_neigh(at, i1, &k1, &k2))) ------------------ | Branch (884:13): [True: 13, False: 17.3k] ------------------ 885| 13| { 886| 13| if (at[i1].bond_type[k1] <= BOND_TYPE_DOUBLE) ------------------ | | 33| 13|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (886:17): [True: 7, False: 6] ------------------ 887| 7| { 888| 7| at[i1].bond_type[k1]++; 889| 7| at[i1].chem_bonds_valence++; 890| 7| at[i2].bond_type[k2]++; 891| 7| at[i2].chem_bonds_valence++; 892| 7| at[i1].radical = 0; 893| 7| at[i2].radical = 0; 894| 7| } 895| 13| } 896| 1.05M| } 897| | 898| 216k|#if (REMOVE_ION_PAIRS_EARLY == 1) 899| 216k| num_changes += remove_ion_pairs(num_atoms, at); 900| 216k|#endif 901| | 902| 216k| return num_changes; 903| 216k|} nFindOneOM: 915| 147|{ 916| 147| int i, n_OM, best_value, cur_value, diff; /* djb-rwth: removing redundant variables */ 917| 147| int num_best; 918| | 919| 147| if (1 == num_OM) ------------------ | Branch (919:9): [True: 93, False: 54] ------------------ 920| 93| { 921| 93| return ord_OM[0]; 922| 93| } 923| 54| if (1 > num_OM) ------------------ | Branch (923:9): [True: 0, False: 54] ------------------ 924| 0| { 925| 0| return -1; 926| 0| } 927| | 928| | /* select neighbors with min. number of bonds */ 929| 54| num_best = 1; 930| 54| n_OM = (int)at[at_no].neighbor[ord_OM[0]]; 931| 54| best_value = (int)at[n_OM].valence; 932| | /* compare number of bonds; move indexes of the best neighbors to the first elements of ord_OM[] */ 933| 108| for (i = 1; i < num_OM; i++) ------------------ | Branch (933:17): [True: 54, False: 54] ------------------ 934| 54| { 935| 54| n_OM = at[at_no].neighbor[ord_OM[i]]; 936| 54| cur_value = (int)at[n_OM].valence; 937| 54| diff = cur_value - best_value; 938| 54| if (diff < 0) ------------------ | Branch (938:13): [True: 0, False: 54] ------------------ 939| 0| { 940| | /* djb-rwth: removing redundant code */ 941| 0| best_value = cur_value; 942| 0| ord_OM[0] = ord_OM[i]; 943| 0| num_best = 1; 944| 0| } 945| 54| else if (diff == 0) ------------------ | Branch (945:18): [True: 54, False: 0] ------------------ 946| 54| { /* was '=', pointed by WDI */ 947| 54| ord_OM[num_best++] = ord_OM[i]; 948| 54| } 949| 54| } 950| 54| num_OM = num_best; 951| 54| if (1 == num_OM) ------------------ | Branch (951:9): [True: 0, False: 54] ------------------ 952| 0| { 953| 0| return ord_OM[0]; 954| 0| } 955| | 956| | /* select neighbors with min. periodic numbers */ 957| 54| num_best = 1; 958| 54| n_OM = (int)at[at_no].neighbor[ord_OM[0]]; 959| 54| best_value = (int)at[n_OM].el_number; 960| | 961| | /* compare periodic numbers; move indexes of the best neighbors to the first elements of ord_OM[] */ 962| 108| for (i = 1; i < num_OM; i++) ------------------ | Branch (962:17): [True: 54, False: 54] ------------------ 963| 54| { 964| 54| n_OM = at[at_no].neighbor[ord_OM[i]]; 965| 54| cur_value = (int)at[n_OM].el_number; 966| 54| diff = cur_value - best_value; 967| 54| if (diff < 0) ------------------ | Branch (967:13): [True: 0, False: 54] ------------------ 968| 0| { 969| | /* djb-rwth: removing redundant code */ 970| 0| best_value = cur_value; 971| 0| ord_OM[0] = ord_OM[i]; 972| 0| num_best = 1; 973| 0| } 974| 54| else if (diff == 0) ------------------ | Branch (974:18): [True: 4, False: 50] ------------------ 975| 4| { /* was '=', pointed by WDI */ 976| 4| ord_OM[num_best++] = ord_OM[i]; 977| 4| } 978| 54| } 979| 54| num_OM = num_best; 980| 54| if (1 == num_OM) ------------------ | Branch (980:9): [True: 50, False: 4] ------------------ 981| 50| { 982| 50| return ord_OM[0]; 983| 50| } 984| | 985| | /* if neighbors are not terminal atoms then reject */ 986| 4| if (1 < at[n_OM].valence) ------------------ | Branch (986:9): [True: 0, False: 4] ------------------ 987| 0| { 988| 0| return -1; 989| 0| } 990| | 991| | /* if neighbors are terminal atoms then the one without isotope or with lightest isotope */ 992| 4| num_best = 1; 993| 4| n_OM = (int)at[at_no].neighbor[ord_OM[0]]; 994| 4| best_value = (int)at[n_OM].iso_atw_diff; 995| | 996| | /* compare periodic numbers; move indexes of the best neighbors to the first elements of ord_OM[] */ 997| 8| for (i = 1; i < num_OM; i++) ------------------ | Branch (997:17): [True: 4, False: 4] ------------------ 998| 4| { 999| 4| n_OM = at[at_no].neighbor[ord_OM[i]]; 1000| 4| cur_value = (int)at[n_OM].el_number; 1001| 4| diff = cur_value - best_value; 1002| 4| if ((!cur_value && best_value) || diff < 0) ------------------ | Branch (1002:14): [True: 0, False: 4] | Branch (1002:28): [True: 0, False: 0] | Branch (1002:43): [True: 0, False: 4] ------------------ 1003| 0| { 1004| | /* djb-rwth: removing redundant code */ 1005| 0| best_value = cur_value; 1006| 0| ord_OM[0] = ord_OM[i]; 1007| 0| num_best = 1; 1008| 0| } 1009| 4| else if (diff == 0) ------------------ | Branch (1009:18): [True: 0, False: 4] ------------------ 1010| 0| { 1011| | /* was '=', pointed by WDI */ 1012| 0| ord_OM[num_best++] = ord_OM[i]; 1013| 0| } 1014| 4| } 1015| | 1016| 4| num_OM = num_best; 1017| 4| if (1 == num_OM) ------------------ | Branch (1017:9): [True: 4, False: 0] ------------------ 1018| 4| { 1019| 4| return ord_OM[0]; 1020| 4| } 1021| | 1022| | /* return any */ 1023| 0| return ord_OM[0]; 1024| 4|} remove_ion_pairs: 1031| 216k|{ 1032| 216k| int num_changes = 0; 1033| 216k|#define MAX_NEIGH 6 1034| | 1035| 216k| int i, n, n2, i1, i2, i3, i4, type, chrg; 1036| 216k| int num_C_II = 0, num_C_plus = 0, num_C_minus = 0, num_N_plus = 0, num_N_minus = 0, num_O_plus = 0, num_O_minus = 0, num_All; 1037| | 1038| 216k|#ifdef FIX_P_IV_Plus_O_Minus 1039| 216k| int num_P_IV_plus = 0; /* added 2010-03-17 DT */ 1040| 216k|#endif 1041| | 1042| 216k| inp_ATOM *a; 1043| | /****** count candidates ********/ 1044| 1.27M| for (i = 0, a = at; i < num_atoms; i++, a++) ------------------ | Branch (1044:25): [True: 1.05M, False: 216k] ------------------ 1045| 1.05M| { 1046| 1.05M| if (1 == (chrg = a->charge) || -1 == chrg) ------------------ | Branch (1046:13): [True: 75.8k, False: 981k] | Branch (1046:40): [True: 44.1k, False: 937k] ------------------ 1047| 119k| { 1048| 119k| switch (ion_el_group(a->el_number)) ------------------ | Branch (1048:21): [True: 68.3k, False: 51.6k] ------------------ 1049| 119k| { 1050| 16.1k| case EL_NUMBER_C: ------------------ | | 13| 16.1k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1050:13): [True: 16.1k, False: 103k] ------------------ 1051| 16.1k| if (chrg > 0) ------------------ | Branch (1051:21): [True: 7.97k, False: 8.17k] ------------------ 1052| 7.97k| { 1053| 7.97k| num_C_plus++; 1054| 7.97k| } 1055| 8.17k| else 1056| 8.17k| { 1057| 8.17k| num_C_minus++; 1058| 8.17k| } 1059| 16.1k| break; 1060| 22.2k| case EL_NUMBER_O: ------------------ | | 15| 22.2k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1060:13): [True: 22.2k, False: 97.6k] ------------------ 1061| 22.2k| if (chrg > 0) ------------------ | Branch (1061:21): [True: 9.52k, False: 12.7k] ------------------ 1062| 9.52k| { 1063| 9.52k| num_O_plus++; 1064| 9.52k| } 1065| 12.7k| else 1066| 12.7k| { 1067| 12.7k| num_O_minus++; 1068| 12.7k| } 1069| 22.2k| break; 1070| 29.9k| case EL_NUMBER_N: ------------------ | | 14| 29.9k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1070:13): [True: 29.9k, False: 90.0k] ------------------ 1071| 29.9k| if (chrg > 0) ------------------ | Branch (1071:21): [True: 11.1k, False: 18.7k] ------------------ 1072| 11.1k| { 1073| 11.1k| num_N_plus++; 1074| 11.1k| } 1075| 18.7k| else 1076| 18.7k| { 1077| 18.7k| num_N_minus++; 1078| 18.7k| } 1079| 29.9k|#ifdef FIX_P_IV_Plus_O_Minus 1080| 29.9k| num_P_IV_plus += a->el_number != EL_NUMBER_N && ------------------ | | 14| 59.8k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1080:38): [True: 7.62k, False: 22.3k] ------------------ 1081| 7.62k| chrg == 1 && ------------------ | Branch (1081:38): [True: 2.66k, False: 4.95k] ------------------ 1082| 2.66k| a->valence == 4 && ------------------ | Branch (1082:38): [True: 142, False: 2.52k] ------------------ 1083| 142| a->chem_bonds_valence == 4; /* added 2010-03-17 DT */ ------------------ | Branch (1083:38): [True: 104, False: 38] ------------------ 1084| 29.9k|#endif 1085| 29.9k| break; 1086| 119k| } 1087| 119k| } 1088| 937k| else if (!chrg && a->chem_bonds_valence + NUMH(a, 0) == 2 && ------------------ | | 56| 933k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 933k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1088:18): [True: 933k, False: 3.80k] | Branch (1088:27): [True: 46.0k, False: 887k] ------------------ 1089| 46.0k| get_el_valence(a->el_number, 0, 0) == 4 && ------------------ | Branch (1089:18): [True: 1.84k, False: 44.2k] ------------------ 1090| 1.84k| ion_el_group(a->el_number) == EL_NUMBER_C) ------------------ | | 13| 1.84k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1090:18): [True: 1.60k, False: 239] ------------------ 1091| 1.60k| { 1092| 1.60k| num_C_II++; 1093| 1.60k| } 1094| 1.05M| } 1095| | 1096| 216k| num_All = num_C_II + num_C_plus + num_C_minus + num_N_plus + num_N_minus + num_O_plus + num_O_minus; 1097| | 1098| | /* do not add num_P_IV_plus ! -- 2010-03-17 DT */ 1099| 216k| if (!num_All) ------------------ | Branch (1099:9): [True: 183k, False: 32.7k] ------------------ 1100| 183k| { 1101| 183k| return 0; 1102| 183k| } 1103| | 1104| | /**************************************************************************/ 1105| | /*************************** Terminal ion pairs ***************************/ 1106| | /**************************************************************************/ 1107| | 1108| | /*------------------------------------------------------------------------- 1109| | Pair type 1 N=N,P,As,Sb; O=O,S,Se,Te 1110| | =========== 1111| | 1112| | X X if X is another -O(-) then neutralize O(-) 1113| | | | that has the smallest periodic table number 1114| | O=N(+)-O(-) => O=N=O 1115| | i n 1116| | --------------------------------------------------------------------------*/ 1117| | 1118| 621k| for (type = 1; type <= 18; type++) ------------------ | Branch (1118:20): [True: 589k, False: 32.7k] ------------------ 1119| 589k| { 1120| 589k| if ((!type || 1 == type)) ------------------ | Branch (1120:14): [True: 0, False: 589k] | Branch (1120:23): [True: 32.7k, False: 556k] ------------------ 1121| 32.7k| { 1122| 44.2k| for (i = 0; i < num_atoms && 0 < num_N_plus && 0 < num_O_minus; i++) ------------------ | Branch (1122:25): [True: 42.4k, False: 1.80k] | Branch (1122:42): [True: 19.6k, False: 22.8k] | Branch (1122:60): [True: 11.5k, False: 8.07k] ------------------ 1123| 11.5k| { 1124| 11.5k| if (1 == at[i].charge && 3 == nNoMetalNumBonds(at, i) && ------------------ | Branch (1124:21): [True: 3.36k, False: 8.15k] | Branch (1124:42): [True: 718, False: 2.65k] ------------------ 1125| 718| 4 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1125:21): [True: 532, False: 186] ------------------ 1126| 532| ion_el_group(at[i].el_number) == EL_NUMBER_N) ------------------ | | 14| 532|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1126:21): [True: 504, False: 28] ------------------ 1127| 504| { 1128| 504| int num_OM = 0, ord_OM[3]; /* -O(-) */ 1129| 504| int num_O = 0; /* =O */ 1130| 504| int num_O_other = 0; 1131| 2.01k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1131:34): [True: 1.51k, False: 504] ------------------ 1132| 1.51k| { 1133| 1.51k| n = at[i].neighbor[i1]; 1134| 1.51k| if (1 == nNoMetalNumBonds(at, n) && 0 == num_of_H(at, n) && ------------------ | Branch (1134:29): [True: 638, False: 875] | Branch (1134:61): [True: 604, False: 34] ------------------ 1135| 604| ion_el_group(at[n].el_number) == EL_NUMBER_O) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | | 15| 604|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1135:29): [True: 458, False: 146] ------------------ 1136| 458| { 1137| 458| if (BOND_TYPE_SINGLE == at[i].bond_type[i1] && ------------------ | | 32| 458|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1137:33): [True: 229, False: 229] ------------------ 1138| 229| -1 == at[n].charge) ------------------ | Branch (1138:33): [True: 223, False: 6] ------------------ 1139| 223| { 1140| 223| ord_OM[num_OM++] = i1; 1141| 223| } 1142| 235| else if (BOND_TYPE_DOUBLE == at[n].bond_type[0] && ------------------ | | 33| 235|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1142:38): [True: 229, False: 6] ------------------ 1143| 229| 0 == at[n].charge) ------------------ | Branch (1143:38): [True: 225, False: 4] ------------------ 1144| 225| { 1145| 225| num_O++; 1146| 225| } 1147| 10| else 1148| 10| { 1149| 10| num_O_other++; 1150| 10| } 1151| 458| } 1152| 1.51k| } 1153| 504| if (num_OM > 0 && num_O > 0 && !num_O_other && ------------------ | Branch (1153:25): [True: 206, False: 298] | Branch (1153:39): [True: 78, False: 128] | Branch (1153:52): [True: 78, False: 0] ------------------ 1154| 78| 0 <= (i1 = nFindOneOM(at, i, ord_OM, num_OM))) ------------------ | Branch (1154:25): [True: 78, False: 0] ------------------ 1155| 78| { 1156| | /* remove charges and increase bond order */ 1157| 78| n = at[i].neighbor[i1]; 1158| 78| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1159| 78| at[i].bond_type[i1]++; 1160| 78| at[n].bond_type[i2]++; 1161| 78| at[i].chem_bonds_valence++; 1162| 78| at[n].chem_bonds_valence++; 1163| 78| at[i].charge--; 1164| 78| at[n].charge++; 1165| 78| at[i].radical = 0; 1166| 78| at[n].radical = 0; 1167| 78| num_changes++; 1168| 78| num_N_plus--; 1169| 78| num_O_minus--; 1170| 78| num_All -= 2; 1171| 78| } 1172| 504| } 1173| 11.5k| } 1174| | 1175| 32.7k|#ifdef FIX_P_IV_Plus_O_Minus 1176| | 1177| | /*------------------------------------------------------------------------- 1178| | Pair type 1a P=P,As,Sb; O=O,S,Se,Te -- added 2010-03-17 1179| | ============= 1180| | 1181| | X X if X, Y, or Z is another -O(-) then neutralize O(-) 1182| | | | that has the smallest periodic table number 1183| | Y-P(+)-O(-) => Y-P=O 1184| | |i n | 1185| | Z Z 1186| | 1187| | --------------------------------------------------------------------------*/ 1188| | 1189| 33.1k| for (i = 0; i < num_atoms && 0 < num_P_IV_plus /*&& 0 < num_N_plus*/ && 0 < num_O_minus; i++) ------------------ | Branch (1189:25): [True: 33.1k, False: 30] | Branch (1189:42): [True: 472, False: 32.6k] | Branch (1189:85): [True: 467, False: 5] ------------------ 1190| 467| { 1191| 467| if (1 == at[i].charge && 4 == nNoMetalNumBonds(at, i) && ------------------ | Branch (1191:21): [True: 186, False: 281] | Branch (1191:42): [True: 112, False: 74] ------------------ 1192| 112| 4 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1192:21): [True: 105, False: 7] ------------------ 1193| 105| at[i].el_number != EL_NUMBER_N && ion_el_group(at[i].el_number) == EL_NUMBER_N) ------------------ | | 14| 572|#define EL_NUMBER_N ((U_CHAR)7) ------------------ at[i].el_number != EL_NUMBER_N && ion_el_group(at[i].el_number) == EL_NUMBER_N) ------------------ | | 14| 102|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1193:21): [True: 102, False: 3] | Branch (1193:55): [True: 99, False: 3] ------------------ 1194| 99| { 1195| 99| int num_OM = 0, ord_OM[4]; /* -O(-) */ 1196| | /*int num_O = 0;*/ /* =O */ 1197| | /* djb-rwth: removing redundant variables */ 1198| 495| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1198:34): [True: 396, False: 99] ------------------ 1199| 396| { 1200| 396| n = at[i].neighbor[i1]; 1201| 396| if (1 == nNoMetalNumBonds(at, n) && 0 == num_of_H(at, n) && ------------------ | Branch (1201:29): [True: 186, False: 210] | Branch (1201:61): [True: 168, False: 18] ------------------ 1202| 168| ion_el_group(at[n].el_number) == EL_NUMBER_O) /* djb-rwth: ignoring LLVM warning: variable used */ ------------------ | | 15| 168|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1202:29): [True: 128, False: 40] ------------------ 1203| 128| { 1204| 128| if (BOND_TYPE_SINGLE == at[i].bond_type[i1] && ------------------ | | 32| 128|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1204:33): [True: 128, False: 0] ------------------ 1205| 128| -1 == at[n].charge) ------------------ | Branch (1205:33): [True: 123, False: 5] ------------------ 1206| 123| { 1207| 123| ord_OM[num_OM++] = i1; 1208| | /* 1209| | } 1210| | if ( BOND_TYPE_DOUBLE == at[n].bond_type[0] && 1211| | 0 == at[n].charge ) { 1212| | num_O ++; 1213| | */ 1214| 123| } 1215| | /* djb-rwth: removing redundant code */ 1216| 128| } 1217| 396| } 1218| 99| if (num_OM > 0 /*&& num_O > 0 && !num_O_other*/ && ------------------ | Branch (1218:25): [True: 69, False: 30] ------------------ 1219| 69| 0 <= (i1 = nFindOneOM(at, i, ord_OM, num_OM))) ------------------ | Branch (1219:25): [True: 69, False: 0] ------------------ 1220| 69| { 1221| | /* remove charges and increase bond order */ 1222| 69| n = at[i].neighbor[i1]; 1223| 69| i2 = is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor; 1224| 69| at[i].bond_type[i1]++; 1225| 69| at[n].bond_type[i2]++; 1226| 69| at[i].chem_bonds_valence++; 1227| 69| at[n].chem_bonds_valence++; 1228| 69| at[i].charge--; 1229| 69| at[n].charge++; 1230| 69| at[i].radical = 0; 1231| 69| at[n].radical = 0; 1232| 69| num_changes++; 1233| 69| num_N_plus--; 1234| 69| num_O_minus--; 1235| 69| num_P_IV_plus--; 1236| 69| num_All -= 2; 1237| 69| } 1238| 99| } 1239| 467| } 1240| 32.7k|#endif /* FIX_P_IV_Plus_O_Minus */ 1241| 32.7k| } 1242| | 1243| | /*------------------------------------------------------------------------- 1244| | Terminal pair types: 2,3,4,5,6,7,8,9 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1245| | ==================================== 1246| | type # 1247| | 2 2: O=N-C(II)- => O=N#C- N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1248| | 3 9: O=O(+)-C(-)(III) => O=O=C(IV) 1249| | 4 3: O(-)-N(+)(IV) => O=N(V) (input structure has at least 1 double bond) 1250| | 5 4: O(-)-O(+)(III) => O=O(IV) 1251| | 6 8: O(-)-O-C(+)(III) => O=O=C(IV) 1252| | 7 5: N(-)=N(+)(IV) => N#N(V) allow terminal H on N(-) 1253| | 8 6: N(-)=O(+)(III) => N#O- 1254| | 9 7: N(-)=C(+)(III) => N#C- 1255| | --------------------------------------------------------------------------*/ 1256| | 1257| 589k| if (!type || (2 <= type && type <= 9)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1257:13): [True: 0, False: 589k] | Branch (1257:23): [True: 556k, False: 32.7k] | Branch (1257:36): [True: 261k, False: 294k] ------------------ 1258| 261k| { 1259| 1.73M| for (i = 0; i < num_atoms && 0 < num_All; i++) ------------------ | Branch (1259:25): [True: 1.47M, False: 257k] | Branch (1259:42): [True: 1.47M, False: 4.34k] ------------------ 1260| 1.47M| { 1261| 1.47M| if (0 == at[i].charge && 1 == nNoMetalNumBonds(at, i) && 2 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1261:21): [True: 826k, False: 647k] | Branch (1261:42): [True: 326k, False: 499k] | Branch (1261:74): [True: 91.6k, False: 235k] ------------------ 1262| 91.6k| 0 == num_of_H(at, i) && ------------------ | Branch (1262:21): [True: 90.8k, False: 790] ------------------ 1263| 90.8k| ion_el_group(at[i].el_number) == EL_NUMBER_O && ------------------ | | 15| 1.56M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1263:21): [True: 72.3k, False: 18.5k] ------------------ 1264| 72.3k| 0 <= (i1 = nNoMetalNeighIndex(at, i)) && ------------------ | Branch (1264:21): [True: 65.7k, False: 6.59k] ------------------ 1265| 65.7k| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE) ------------------ | | 34| 65.7k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1265:21): [True: 65.7k, False: 0] ------------------ 1266| 65.7k| { 1267| | /* terminal O= */ 1268| 65.7k| n = at[i].neighbor[i1]; 1269| 65.7k| if ((!type || type == 2) && 0 < num_C_II) ------------------ | Branch (1269:26): [True: 0, False: 65.7k] | Branch (1269:35): [True: 7.89k, False: 57.8k] | Branch (1269:49): [True: 383, False: 7.51k] ------------------ 1270| 383| { 1271| | /* avoid alternating bonds */ 1272| 383| if (0 == at[n].charge && ------------------ | Branch (1272:29): [True: 258, False: 125] ------------------ 1273| 258| 2 == nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && ------------------ | Branch (1273:29): [True: 198, False: 60] | Branch (1273:61): [True: 179, False: 19] ------------------ 1274| 179| 0 == num_of_H(at, n) && ------------------ | Branch (1274:29): [True: 177, False: 2] ------------------ 1275| 177| ion_el_group(at[n].el_number) == EL_NUMBER_N && ------------------ | | 14| 560|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1275:29): [True: 171, False: 6] ------------------ 1276| 171| 0 <= (i2 = nNoMetalOtherNeighIndex(at, n, i)) && ------------------ | Branch (1276:29): [True: 143, False: 28] ------------------ 1277| 143| at[n].bond_type[i2] <= BOND_TYPE_TRIPLE) ------------------ | | 34| 143|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1277:29): [True: 143, False: 0] ------------------ 1278| 143| { 1279| | /* i2 = index of opposite to at[i] neighbor of at[n] */ 1280| | /*i2 = (at[n].neighbor[0] == i);*/ 1281| 143| n2 = at[n].neighbor[i2]; 1282| 143| if (0 == at[n2].charge && ------------------ | Branch (1282:33): [True: 136, False: 7] ------------------ 1283| 136| 2 == at[n2].valence && 2 == at[n2].chem_bonds_valence && ------------------ | Branch (1283:33): [True: 93, False: 43] | Branch (1283:56): [True: 89, False: 4] ------------------ 1284| 89| 0 == num_of_H(at, n2) && ------------------ | Branch (1284:33): [True: 89, False: 0] ------------------ 1285| 89| ion_el_group(at[n2].el_number) == EL_NUMBER_C) ------------------ | | 13| 89|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1285:33): [True: 0, False: 89] ------------------ 1286| 0| { 1287| | /* i n n2 */ 1288| | /* found O=N-C(II)- */ 1289| | /* convert O=N-C(II)- => O=N#C- */ 1290| | 1291| 0| i3 = (at[n2].neighbor[0] != n); /* index of at[n] neighbor of n2 */ 1292| 0| at[n].chem_bonds_valence = 5; /* N */ 1293| 0| at[n2].chem_bonds_valence = 4; /* C */ 1294| 0| at[n].bond_type[i2] = BOND_TYPE_TRIPLE; ------------------ | | 34| 0|#define BOND_TYPE_TRIPLE 3 ------------------ 1295| 0| at[n2].bond_type[i3] = BOND_TYPE_TRIPLE; ------------------ | | 34| 0|#define BOND_TYPE_TRIPLE 3 ------------------ 1296| 0| at[n2].radical = 0; 1297| 0| num_changes++; 1298| 0| num_C_II--; 1299| 0| num_All--; 1300| 0| continue; 1301| 0| } 1302| 143| } 1303| 383| } 1304| | 1305| 65.7k| if ((!type || type == 3) && 0 < num_O_plus && 0 < num_C_minus) ------------------ | Branch (1305:26): [True: 0, False: 65.7k] | Branch (1305:35): [True: 7.89k, False: 57.8k] | Branch (1305:49): [True: 2.73k, False: 5.16k] | Branch (1305:67): [True: 834, False: 1.90k] ------------------ 1306| 834| { 1307| 834| if (1 == at[n].charge && 2 == nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && ------------------ | Branch (1307:29): [True: 578, False: 256] | Branch (1307:50): [True: 563, False: 15] | Branch (1307:82): [True: 562, False: 1] ------------------ 1308| 562| 0 == num_of_H(at, n) && ------------------ | Branch (1308:29): [True: 545, False: 17] ------------------ 1309| 545| ion_el_group(at[n].el_number) == EL_NUMBER_O && ------------------ | | 15| 1.37k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1309:29): [True: 288, False: 257] ------------------ 1310| 288| 0 <= (i2 = nNoMetalOtherNeighIndex(at, n, i)) && ------------------ | Branch (1310:29): [True: 288, False: 0] ------------------ 1311| 288| at[n].bond_type[i2] <= BOND_TYPE_TRIPLE) ------------------ | | 34| 288|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1311:29): [True: 288, False: 0] ------------------ 1312| 288| { 1313| | /* found O=O(+)- */ 1314| | /* i2 = index of opposite to at[i] neighbor of at[n] */ 1315| | /*i2 = (at[n].neighbor[0] == i);*/ 1316| 288| n2 = at[n].neighbor[i2]; 1317| 288| if (-1 == at[n2].charge && 3 >= nNoMetalNumBonds(at, n2) && 3 == nNoMetalBondsValence(at, n2) + NUMH(at, n2) && ------------------ | | 56| 296|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 8|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1317:33): [True: 27, False: 261] | Branch (1317:56): [True: 8, False: 19] | Branch (1317:89): [True: 7, False: 1] ------------------ 1318| 7| ion_el_group(at[n2].el_number) == EL_NUMBER_C) ------------------ | | 13| 7|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1318:33): [True: 7, False: 0] ------------------ 1319| 7| { 1320| | /* i n n2 */ 1321| | /* found found O=O(+)-C(-)(III) */ 1322| | /* convert O=O(+)-C(-)(III) => O=O=C(IV) */ 1323| 7| i3 = (at[n2].neighbor[0] != n); /* index of at[n] neighbor of n2 */ 1324| 7| at[n].charge--; 1325| 7| at[n2].charge++; 1326| 7| at[n].chem_bonds_valence += 1; /* =O- => =O= */ 1327| 7| at[n2].chem_bonds_valence += 1; /* -C => =C */ 1328| 7| at[n].bond_type[i2] = BOND_TYPE_DOUBLE; ------------------ | | 33| 7|#define BOND_TYPE_DOUBLE 2 ------------------ 1329| 7| at[n2].bond_type[i3] = BOND_TYPE_DOUBLE; ------------------ | | 33| 7|#define BOND_TYPE_DOUBLE 2 ------------------ 1330| 7| num_changes++; 1331| 7| num_O_plus--; 1332| 7| num_C_minus--; 1333| 7| num_All -= 2; 1334| 7| continue; 1335| 7| } 1336| 288| } 1337| 834| } 1338| 65.7k| } 1339| | 1340| 1.40M| else if (-1 == at[i].charge && ------------------ | Branch (1340:26): [True: 332k, False: 1.07M] ------------------ 1341| 332k| 0 < num_O_minus + num_N_minus && ------------------ | Branch (1341:26): [True: 259k, False: 72.7k] ------------------ 1342| 259k| 0 < num_N_plus + num_O_plus + num_C_plus && ------------------ | Branch (1342:26): [True: 170k, False: 88.8k] ------------------ 1343| 170k| 1 == nNoMetalNumBonds(at, i) && 1 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1343:26): [True: 134k, False: 36.8k] | Branch (1343:58): [True: 86.5k, False: 47.4k] ------------------ 1344| 86.5k| 0 == num_of_H(at, i) && ------------------ | Branch (1344:26): [True: 85.4k, False: 1.06k] ------------------ 1345| 85.4k| ion_el_group(at[i].el_number) == EL_NUMBER_O && ------------------ | | 15| 1.49M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1345:26): [True: 56.5k, False: 28.9k] ------------------ 1346| 56.5k| 0 <= (i1 = nNoMetalNeighIndex(at, i)) && ------------------ | Branch (1346:26): [True: 55.6k, False: 843] ------------------ 1347| 55.6k| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE) ------------------ | | 34| 55.6k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1347:26): [True: 55.6k, False: 0] ------------------ 1348| 55.6k| { 1349| | /* terminal O(-)- */ 1350| 55.6k| n = at[i].neighbor[i1]; 1351| | 1352| 55.6k| if ((!type || type == 4) && 0 < num_O_minus && 0 < num_N_plus && /* O(-)-N(+)(IV) */ ------------------ | Branch (1352:26): [True: 0, False: 55.6k] | Branch (1352:35): [True: 7.49k, False: 48.1k] | Branch (1352:49): [True: 7.49k, False: 0] | Branch (1352:68): [True: 1.81k, False: 5.68k] ------------------ 1353| 1.81k| 1 == at[n].charge && 3 >= nNoMetalNumBonds(at, n) && 4 == nNoMetalBondsValence(at, n) && ------------------ | Branch (1353:25): [True: 812, False: 1.00k] | Branch (1353:46): [True: 255, False: 557] | Branch (1353:78): [True: 142, False: 113] ------------------ 1354| 142| 0 == num_of_H(at, n) && ------------------ | Branch (1354:25): [True: 136, False: 6] ------------------ 1355| 136| ion_el_group(at[n].el_number) == EL_NUMBER_N /* except >O(+)- */ ------------------ | | 14| 136|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1355:25): [True: 129, False: 7] ------------------ 1356| 55.6k| ) 1357| 129| { 1358| | /* found O(-)-N(+)(IV) */ 1359| | /* convert O(-)-N(+)(IV) => O=N(V) */ 1360| | 1361| 129| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); /* index of at[i] neighbor of at[n] */ 1362| 129| at[i].charge++; 1363| 129| at[n].charge--; 1364| 129| at[i].chem_bonds_valence++; 1365| 129| at[n].chem_bonds_valence++; 1366| 129| at[i].bond_type[i1]++; 1367| 129| at[n].bond_type[i2]++; 1368| 129| num_changes++; 1369| 129| num_O_minus--; 1370| 129| num_N_plus--; 1371| 129| num_All -= 2; 1372| 129| continue; 1373| 129| } 1374| | 1375| 55.5k| if ((!type || type == 5) && 0 < num_O_minus && 0 < num_O_plus && /* O(-)-O(+)(III) */ ------------------ | Branch (1375:26): [True: 0, False: 55.5k] | Branch (1375:35): [True: 7.26k, False: 48.2k] | Branch (1375:49): [True: 7.26k, False: 0] | Branch (1375:68): [True: 3.72k, False: 3.53k] ------------------ 1376| 3.72k| 1 == at[n].charge && 3 >= nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && ------------------ | Branch (1376:25): [True: 1.78k, False: 1.94k] | Branch (1376:46): [True: 996, False: 791] | Branch (1376:78): [True: 897, False: 99] ------------------ 1377| 897| 0 == num_of_H(at, n) && ------------------ | Branch (1377:25): [True: 811, False: 86] ------------------ 1378| 811| ion_el_group(at[n].el_number) == EL_NUMBER_O /* except >O(+)- */ ------------------ | | 15| 811|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1378:25): [True: 785, False: 26] ------------------ 1379| 55.5k| ) 1380| 785| { 1381| | /* found O(+)(III) */ 1382| | /* convert O(-)-O(+)(III) => O=O(IV) */ 1383| | 1384| 785| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); /* index of at[i] neighbor of at[n] */ 1385| 785| at[i].charge++; 1386| 785| at[n].charge--; 1387| 785| at[i].chem_bonds_valence++; 1388| 785| at[n].chem_bonds_valence++; 1389| 785| at[i].bond_type[i1]++; 1390| 785| at[n].bond_type[i2]++; 1391| 785| num_changes++; 1392| 785| num_O_minus--; 1393| 785| num_O_plus--; 1394| 785| num_All -= 2; 1395| 785| continue; 1396| 785| } 1397| | 1398| | /* i n n2 */ 1399| 54.7k| if ((!type || type == 6) && /* O(-)-O-C(+)(III) */ ------------------ | Branch (1399:26): [True: 0, False: 54.7k] | Branch (1399:35): [True: 6.48k, False: 48.2k] ------------------ 1400| 6.48k| 0 < num_O_minus && 0 < num_C_plus && ------------------ | Branch (1400:25): [True: 6.48k, False: 0] | Branch (1400:44): [True: 3.25k, False: 3.22k] ------------------ 1401| 3.25k| 0 == at[n].charge && 2 == nNoMetalNumBonds(at, n) && 2 == nNoMetalBondsValence(at, n) && ------------------ | Branch (1401:25): [True: 2.48k, False: 766] | Branch (1401:46): [True: 989, False: 1.49k] | Branch (1401:78): [True: 797, False: 192] ------------------ 1402| 797| 0 == num_of_H(at, n) && ------------------ | Branch (1402:25): [True: 794, False: 3] ------------------ 1403| 794| ion_el_group(at[n].el_number) == EL_NUMBER_O && ------------------ | | 15| 55.5k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1403:25): [True: 717, False: 77] ------------------ 1404| 717| 0 <= (i2 = nNoMetalOtherNeighIndex(at, n, i)) && ------------------ | Branch (1404:25): [True: 381, False: 336] ------------------ 1405| 381| at[n].bond_type[i2] <= BOND_TYPE_TRIPLE) ------------------ | | 34| 381|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1405:25): [True: 381, False: 0] ------------------ 1406| 381| { 1407| | /* found O(-)-O- */ 1408| | /* i2 = index of opposite to at[i] neighbor of at[n] */ 1409| | /*i2 = (at[n].neighbor[0] == i);*/ 1410| 381| n2 = at[n].neighbor[i2]; 1411| 381| if (1 == at[n2].charge && 3 >= nNoMetalNumBonds(at, n2) && ------------------ | Branch (1411:29): [True: 116, False: 265] | Branch (1411:51): [True: 108, False: 8] ------------------ 1412| 108| 3 == nNoMetalBondsValence(at, n2) + NUMH(at, n2) && ------------------ | | 56| 489|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 108|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1412:29): [True: 91, False: 17] ------------------ 1413| 91| ion_el_group(at[n2].el_number) == EL_NUMBER_C) ------------------ | | 13| 91|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1413:29): [True: 1, False: 90] ------------------ 1414| 1| { 1415| | /* i n n2 */ 1416| | /* found O(-)-O-C(+)(III) */ 1417| | /* convert O(-)-O-C(+)(III) => O=O=C(IV) */ 1418| | /*i3 = (at[n2].neighbor[0] != n);*/ /* i3 = index of at[n] neighbor of at[n2] */ 1419| 1| i3 = (int)(is_in_the_list(at[n2].neighbor, (AT_NUMB)n, at[n2].valence) - at[n2].neighbor); 1420| | /*i4 = index of at[i] in the adjacency list of at[n] */ 1421| 1| i4 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1422| 1| at[i].charge++; 1423| 1| at[n2].charge--; 1424| 1| at[i].chem_bonds_valence += 1; /* O- => O= */ 1425| 1| at[n].chem_bonds_valence += 2; /* -O- => =O= */ 1426| 1| at[n2].chem_bonds_valence += 1; /* -C => =C */ 1427| 1| at[i].bond_type[i1] = BOND_TYPE_DOUBLE; ------------------ | | 33| 1|#define BOND_TYPE_DOUBLE 2 ------------------ 1428| 1| at[n].bond_type[i4] = BOND_TYPE_DOUBLE; ------------------ | | 33| 1|#define BOND_TYPE_DOUBLE 2 ------------------ 1429| 1| at[n].bond_type[i2] = BOND_TYPE_DOUBLE; ------------------ | | 33| 1|#define BOND_TYPE_DOUBLE 2 ------------------ 1430| 1| at[n2].bond_type[i3] = BOND_TYPE_DOUBLE; ------------------ | | 33| 1|#define BOND_TYPE_DOUBLE 2 ------------------ 1431| 1| num_changes++; 1432| 1| num_O_minus--; 1433| 1| num_C_plus--; 1434| 1| num_All -= 2; 1435| 1| continue; 1436| 1| } 1437| 381| } 1438| 54.7k| } 1439| 1.35M| else if (-1 == at[i].charge && 0 < num_N_minus && 0 < num_N_plus + num_O_plus + num_C_plus && ------------------ | Branch (1439:26): [True: 276k, False: 1.07M] | Branch (1439:48): [True: 165k, False: 111k] | Branch (1439:67): [True: 106k, False: 58.8k] ------------------ 1440| 106k| 1 == nNoMetalNumBonds(at, i) && 2 == nNoMetalBondsValence(at, i) + NUMH(at, i) && ------------------ | | 56| 1.42M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 74.2k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1440:26): [True: 74.2k, False: 32.1k] | Branch (1440:58): [True: 42.4k, False: 31.8k] ------------------ 1441| | /*0 == num_of_H( at, i ) &&*/ 1442| 42.4k| ion_el_group(at[i].el_number) == EL_NUMBER_N && ------------------ | | 14| 1.39M|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1442:26): [True: 40.9k, False: 1.42k] ------------------ 1443| 40.9k| 0 <= (i1 = nNoMetalNeighIndex(at, i)) && ------------------ | Branch (1443:26): [True: 40.4k, False: 570] ------------------ 1444| 40.4k| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE) ------------------ | | 34| 40.4k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1444:26): [True: 40.4k, False: 0] ------------------ 1445| 40.4k| { 1446| | /* terminal N(-)= */ 1447| 40.4k| n = at[i].neighbor[i1 = 0]; 1448| 40.4k| if ((!type || type == 7) && 0 < num_N_plus && /* N(-)=N(+)(IV) */ ------------------ | Branch (1448:26): [True: 0, False: 40.4k] | Branch (1448:35): [True: 5.48k, False: 34.9k] | Branch (1448:49): [True: 4.26k, False: 1.21k] ------------------ 1449| 4.26k| 1 == at[n].charge && 3 >= nNoMetalNumBonds(at, n) && 4 == nNoMetalBondsValence(at, n) && ------------------ | Branch (1449:25): [True: 2.42k, False: 1.84k] | Branch (1449:46): [True: 1.88k, False: 545] | Branch (1449:78): [True: 1.50k, False: 379] ------------------ 1450| 1.50k| 0 == num_of_H(at, n) && ------------------ | Branch (1450:25): [True: 1.49k, False: 7] ------------------ 1451| 1.49k| ion_el_group(at[n].el_number) == EL_NUMBER_N) ------------------ | | 14| 1.49k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1451:25): [True: 1.49k, False: 1] ------------------ 1452| 1.49k| { 1453| | /* found N(-)-N(+)(IV) */ 1454| | /* convert N(-)=N(+)(IV) => N#N(V) */ 1455| | 1456| 1.49k| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); /* index of at[i] neighbor of at[n] */ 1457| 1.49k| at[i].charge++; 1458| 1.49k| at[n].charge--; 1459| 1.49k| at[i].chem_bonds_valence++; 1460| 1.49k| at[n].chem_bonds_valence++; 1461| 1.49k| at[i].bond_type[i1]++; 1462| 1.49k| at[n].bond_type[i2]++; 1463| 1.49k| num_changes++; 1464| 1.49k| num_N_minus--; 1465| 1.49k| num_N_plus--; 1466| 1.49k| num_All -= 2; 1467| 1.49k| continue; 1468| 1.49k| } 1469| 38.9k| if ((!type || type == 8) && 0 < num_O_plus && /* N(-)=O(+)(III) */ ------------------ | Branch (1469:26): [True: 0, False: 38.9k] | Branch (1469:35): [True: 3.98k, False: 34.9k] | Branch (1469:49): [True: 1.45k, False: 2.52k] ------------------ 1470| 1.45k| 1 == at[n].charge && 2 == nNoMetalNumBonds(at, n) && 3 == nNoMetalBondsValence(at, n) && ------------------ | Branch (1470:25): [True: 1.13k, False: 323] | Branch (1470:46): [True: 539, False: 594] | Branch (1470:78): [True: 539, False: 0] ------------------ 1471| 539| 0 == num_of_H(at, n) && ------------------ | Branch (1471:25): [True: 537, False: 2] ------------------ 1472| 537| ion_el_group(at[n].el_number) == EL_NUMBER_O) ------------------ | | 15| 537|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1472:25): [True: 534, False: 3] ------------------ 1473| 534| { 1474| | /* found N(-)-O(+)(III) */ 1475| | /* convert N(-)=O(+)(III) => N#O(IV)- */ 1476| 534| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); /* index of at[i] neighbor of at[n] */ 1477| 534| at[i].charge++; 1478| 534| at[n].charge--; 1479| 534| at[i].chem_bonds_valence++; 1480| 534| at[n].chem_bonds_valence++; 1481| 534| at[i].bond_type[i1]++; 1482| 534| at[n].bond_type[i2]++; 1483| 534| num_changes++; 1484| 534| num_N_minus--; 1485| 534| num_O_plus--; 1486| 534| num_All -= 2; 1487| 534| continue; 1488| 534| } 1489| 38.3k| if ((!type || type == 9) && 0 < num_C_plus && /* N(-)=C(+)(III) */ ------------------ | Branch (1489:26): [True: 0, False: 38.3k] | Branch (1489:35): [True: 3.45k, False: 34.9k] | Branch (1489:49): [True: 983, False: 2.46k] ------------------ 1490| 983| 1 == at[n].charge && 2 == at[n].valence && 3 == at[n].chem_bonds_valence && ------------------ | Branch (1490:25): [True: 276, False: 707] | Branch (1490:46): [True: 8, False: 268] | Branch (1490:68): [True: 5, False: 3] ------------------ 1491| 5| 0 == num_of_H(at, n) && ------------------ | Branch (1491:25): [True: 4, False: 1] ------------------ 1492| 4| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 4|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1492:25): [True: 3, False: 1] ------------------ 1493| 3| { 1494| | /* found N(-)=C(+)(III) */ 1495| | /* convert N(-)=C(+)(III) => N#C(IV)- */ 1496| | 1497| 3| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); /* index of at[i] neighbor of at[n] */ 1498| 3| at[i].charge++; 1499| 3| at[n].charge--; 1500| 3| at[i].chem_bonds_valence++; 1501| 3| at[n].chem_bonds_valence++; 1502| 3| at[i].bond_type[i1]++; 1503| 3| at[n].bond_type[i2]++; 1504| 3| num_changes++; 1505| 3| num_N_minus--; 1506| 3| num_C_plus--; 1507| 3| num_All -= 2; 1508| 3| continue; 1509| 3| } 1510| 38.3k| } 1511| 1.47M| } 1512| 261k| } 1513| | 1514| | /**************************************************************************/ 1515| | /*********************** NON-Terminal ion pairs ***************************/ 1516| | /**************************************************************************/ 1517| | /*------------------------------------------------------------------------- 1518| | Non-Terminal pair types: 10,11,12,13,14 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1519| | ======================================== 1520| | 1521| | 10: N(+)(IV)-C(-)(III) => N(V)=C(IV) (N has 3 or 2 bonds) 1522| | 11: N(+)(IV)=C(-)(III) => N(V)#C(IV) (N has 3 or 2 bonds) 1523| | 12: N(+)(IV)-N(-)(II) => N(V)=N(III) (allow terminal H on N(-)) 1524| | 13: -O(+)-C(-)(III) => -O=C- 1525| | 14: -O(+)=C(-)(III) => -O#C- 1526| | 15: O(+)(III)-N(-)(II) => O(IV)=N(III) (allow terminal H on N(-)) 1527| | --------------------------------------------------------------------------*/ 1528| | 1529| 589k| if (!type || (10 <= type && type <= 15)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1529:13): [True: 0, False: 589k] | Branch (1529:23): [True: 294k, False: 294k] | Branch (1529:37): [True: 196k, False: 98.1k] ------------------ 1530| 196k| { 1531| 1.26M| for (i = 0; i < num_atoms && 0 < num_All; i++) ------------------ | Branch (1531:25): [True: 1.07M, False: 186k] | Branch (1531:42): [True: 1.06M, False: 10.1k] ------------------ 1532| 1.06M| { 1533| 1.06M| if (1 == at[i].charge && ------------------ | Branch (1533:21): [True: 206k, False: 860k] ------------------ 1534| 206k| 0 < num_N_plus + num_O_plus && 0 < num_C_minus + num_N_minus && ------------------ | Branch (1534:21): [True: 117k, False: 89.4k] | Branch (1534:52): [True: 79.0k, False: 38.1k] ------------------ 1535| 79.0k| 4 >= nNoMetalNumBonds(at, i) && 4 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1535:21): [True: 78.9k, False: 186] | Branch (1535:53): [True: 40.0k, False: 38.8k] ------------------ 1536| 40.0k| 0 == num_of_H(at, i) && ------------------ | Branch (1536:21): [True: 35.1k, False: 4.88k] ------------------ 1537| 35.1k| ion_el_group(at[i].el_number) == EL_NUMBER_N) ------------------ | | 14| 35.1k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1537:21): [True: 32.9k, False: 2.20k] ------------------ 1538| 32.9k| { 1539| | /* found non-terminal N(+)(IV) */ 1540| 32.9k| if ((!type || 10 == type) && 0 < num_N_plus && 0 < num_C_minus) ------------------ | Branch (1540:26): [True: 0, False: 32.9k] | Branch (1540:35): [True: 5.69k, False: 27.2k] | Branch (1540:50): [True: 5.69k, False: 0] | Branch (1540:68): [True: 1.19k, False: 4.50k] ------------------ 1541| 1.19k| { 1542| 1.19k| int num_neigh = 0, pos_neigh = -1; 1543| 3.98k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1543:38): [True: 2.79k, False: 1.19k] ------------------ 1544| 2.79k| { 1545| 2.79k| n = at[i].neighbor[i1]; 1546| 2.79k| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH(at, n) && ------------------ | | 56| 3.55k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 765|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1546:33): [True: 789, False: 2.00k] | Branch (1546:55): [True: 765, False: 24] | Branch (1546:77): [True: 636, False: 129] ------------------ 1547| | /*0 == at[n].num_H &&*/ 1548| 636| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 32| 3.42k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1548:33): [True: 19, False: 617] ------------------ 1549| 19| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 19|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1549:33): [True: 18, False: 1] ------------------ 1550| 18| { 1551| | /* found N(+)(IV)-C(-)(III); prepare conversion to N(V)=C(IV) */ 1552| 18| num_neigh++; 1553| 18| pos_neigh = i1; 1554| 18| } 1555| 2.79k| } 1556| 1.19k| i1 = pos_neigh; 1557| 1.19k| if (1 == num_neigh && ------------------ | Branch (1557:29): [True: 18, False: 1.17k] ------------------ 1558| 18| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE && ------------------ | | 34| 1.20k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1558:29): [True: 18, False: 0] ------------------ 1559| 18| !has_other_ion_neigh(at, i, n = at[i].neighbor[i1]) && ------------------ | Branch (1559:29): [True: 15, False: 3] ------------------ 1560| 15| !has_other_ion_neigh(at, n, i)) ------------------ | Branch (1560:29): [True: 12, False: 3] ------------------ 1561| 12| { 1562| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1563| 12| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1564| 12| at[i].charge--; 1565| 12| at[n].charge++; 1566| 12| at[i].chem_bonds_valence++; 1567| 12| at[n].chem_bonds_valence++; 1568| 12| at[i].bond_type[i1]++; 1569| 12| at[n].bond_type[i2]++; 1570| 12| num_changes++; 1571| 12| num_C_minus--; 1572| 12| num_N_plus--; 1573| 12| num_All -= 2; 1574| 12| continue; 1575| 12| } 1576| 1.19k| } 1577| 32.9k| if ((!type || 11 == type) && 0 < num_N_plus && 0 < num_C_minus) ------------------ | Branch (1577:26): [True: 0, False: 32.9k] | Branch (1577:35): [True: 5.68k, False: 27.2k] | Branch (1577:50): [True: 5.68k, False: 0] | Branch (1577:68): [True: 1.17k, False: 4.50k] ------------------ 1578| 1.17k| { 1579| 1.17k| int num_neigh = 0, pos_neigh = -1; 1580| 3.94k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1580:38): [True: 2.76k, False: 1.17k] ------------------ 1581| 2.76k| { 1582| 2.76k| n = at[i].neighbor[i1]; 1583| 2.76k| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH(at, n) && ------------------ | | 56| 3.51k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 753|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1583:33): [True: 777, False: 1.98k] | Branch (1583:55): [True: 753, False: 24] | Branch (1583:77): [True: 624, False: 129] ------------------ 1584| | /*0 == at[n].num_H &&*/ 1585| 624| at[i].bond_type[i1] == BOND_TYPE_DOUBLE && ------------------ | | 33| 3.38k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1585:33): [True: 53, False: 571] ------------------ 1586| 53| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 53|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1586:33): [True: 52, False: 1] ------------------ 1587| 52| { 1588| | /* found N(+)(IV)=C(-)(III); prepare conversion to N(V)#C(IV) */ 1589| 52| num_neigh++; 1590| 52| pos_neigh = i1; 1591| 52| } 1592| 2.76k| } 1593| 1.17k| if (1 == num_neigh && ------------------ | Branch (1593:29): [True: 52, False: 1.12k] ------------------ 1594| 52| !has_other_ion_neigh(at, i, n = at[i].neighbor[i1 = pos_neigh]) && ------------------ | Branch (1594:29): [True: 39, False: 13] ------------------ 1595| 39| !has_other_ion_neigh(at, n, i)) ------------------ | Branch (1595:29): [True: 35, False: 4] ------------------ 1596| 35| { 1597| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1598| 35| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1599| 35| at[i].charge--; 1600| 35| at[n].charge++; 1601| 35| at[i].chem_bonds_valence++; 1602| 35| at[n].chem_bonds_valence++; 1603| 35| at[i].bond_type[i1]++; 1604| 35| at[n].bond_type[i2]++; 1605| 35| num_changes++; 1606| 35| num_C_minus--; 1607| 35| num_N_plus--; 1608| 35| num_All -= 2; 1609| 35| continue; 1610| 35| } 1611| 1.17k| } 1612| 32.9k| if (!type || (12 == type && 0 < num_N_plus && 0 < num_N_minus)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1612:25): [True: 0, False: 32.9k] | Branch (1612:35): [True: 5.64k, False: 27.2k] | Branch (1612:49): [True: 5.64k, False: 0] | Branch (1612:67): [True: 4.57k, False: 1.07k] ------------------ 1613| 4.57k| { 1614| 4.57k| int num_neigh = 0, pos_neigh = -1; 1615| 14.0k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1615:38): [True: 9.46k, False: 4.57k] ------------------ 1616| 9.46k| { 1617| 9.46k| n = at[i].neighbor[i1]; 1618| 9.46k| if (-1 == at[n].charge && 2 >= nNoMetalNumBonds(at, n) && ------------------ | Branch (1618:33): [True: 1.02k, False: 8.44k] | Branch (1618:55): [True: 700, False: 324] ------------------ 1619| 700| 2 == nNoMetalBondsValence(at, n) + NUMH(at, n) && ------------------ | | 56| 10.1k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 700|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1619:33): [True: 409, False: 291] ------------------ 1620| | /*0 == num_of_H( at, n ) &&*/ 1621| 409| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 32| 9.87k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1621:33): [True: 397, False: 12] ------------------ 1622| 397| ion_el_group(at[n].el_number) == EL_NUMBER_N) ------------------ | | 14| 397|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1622:33): [True: 388, False: 9] ------------------ 1623| 388| { 1624| | /* found N(+)(IV)=N(-)(II); prepare conversion to N(V)#N(III) */ 1625| 388| num_neigh++; 1626| 388| pos_neigh = i1; 1627| 388| } 1628| 9.46k| } 1629| 4.57k| if (1 == num_neigh && ------------------ | Branch (1629:29): [True: 380, False: 4.19k] ------------------ 1630| 380| !has_other_ion_neigh(at, i, n = at[i].neighbor[i1 = pos_neigh]) && ------------------ | Branch (1630:29): [True: 357, False: 23] ------------------ 1631| 357| !has_other_ion_neigh(at, n, i)) ------------------ | Branch (1631:29): [True: 333, False: 24] ------------------ 1632| 333| { 1633| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1634| 333| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1635| 333| at[i].charge--; 1636| 333| at[n].charge++; 1637| 333| at[i].chem_bonds_valence++; 1638| 333| at[n].chem_bonds_valence++; 1639| 333| at[i].bond_type[i1]++; 1640| 333| at[n].bond_type[i2]++; 1641| 333| num_changes++; 1642| 333| num_N_minus--; 1643| 333| num_N_plus--; 1644| 333| num_All -= 2; 1645| 333| continue; 1646| 333| } 1647| 4.57k| } 1648| 32.9k| } 1649| 1.03M| else if (1 == at[i].charge && ------------------ | Branch (1649:26): [True: 173k, False: 860k] ------------------ 1650| 173k| 0 < num_O_plus && 0 < num_C_minus + num_N_minus && ------------------ | Branch (1650:26): [True: 58.0k, False: 115k] | Branch (1650:44): [True: 33.9k, False: 24.0k] ------------------ 1651| 33.9k| 3 >= nNoMetalNumBonds(at, i) && 3 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1651:26): [True: 27.8k, False: 6.08k] | Branch (1651:58): [True: 24.0k, False: 3.79k] ------------------ 1652| 24.0k| 0 == num_of_H(at, i) && ------------------ | Branch (1652:26): [True: 18.8k, False: 5.28k] ------------------ 1653| 18.8k| ion_el_group(at[i].el_number) == EL_NUMBER_O) ------------------ | | 15| 18.8k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1653:26): [True: 14.4k, False: 4.39k] ------------------ 1654| 14.4k| { 1655| | /* found non-terminal O(+)(III) */ 1656| 14.4k| if ((!type || 13 == type) && 0 < num_C_minus) ------------------ | Branch (1656:26): [True: 0, False: 14.4k] | Branch (1656:35): [True: 2.45k, False: 11.9k] | Branch (1656:50): [True: 1.93k, False: 524] ------------------ 1657| 1.93k| { 1658| 1.93k| int num_neigh = 0, pos_neigh = -1; 1659| 6.49k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1659:38): [True: 4.56k, False: 1.93k] ------------------ 1660| 4.56k| { 1661| 4.56k| n = at[i].neighbor[i1]; 1662| 4.56k| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH(at, n) && ------------------ | | 56| 6.25k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.68k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1662:33): [True: 1.74k, False: 2.82k] | Branch (1662:55): [True: 1.68k, False: 53] | Branch (1662:77): [True: 915, False: 774] ------------------ 1663| | /*0 == at[n].num_H &&*/ 1664| 915| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 32| 5.47k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1664:33): [True: 330, False: 585] ------------------ 1665| 330| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 330|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1665:33): [True: 304, False: 26] ------------------ 1666| 304| { 1667| | /* found O(+)(III)-C(-)(II); prepare conversion to O(IV)=C(IV) */ 1668| 304| num_neigh++; 1669| 304| pos_neigh = i1; 1670| 304| } 1671| 4.56k| } 1672| 1.93k| if (1 == num_neigh && ------------------ | Branch (1672:29): [True: 304, False: 1.62k] ------------------ 1673| 304| !has_other_ion_neigh(at, i, n = at[i].neighbor[i1 = pos_neigh]) && ------------------ | Branch (1673:29): [True: 248, False: 56] ------------------ 1674| 248| !has_other_ion_neigh(at, n, i)) ------------------ | Branch (1674:29): [True: 42, False: 206] ------------------ 1675| 42| { 1676| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1677| 42| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1678| 42| at[i].charge--; 1679| 42| at[n].charge++; 1680| 42| at[i].chem_bonds_valence++; 1681| 42| at[n].chem_bonds_valence++; 1682| 42| at[i].bond_type[i1]++; 1683| 42| at[n].bond_type[i2]++; 1684| 42| num_changes++; 1685| 42| num_C_minus--; 1686| 42| num_O_plus--; 1687| 42| num_All -= 2; 1688| 42| continue; 1689| 42| } 1690| 1.93k| } 1691| 14.3k| if ((!type || 14 == type) && 0 < num_C_minus) ------------------ | Branch (1691:26): [True: 0, False: 14.3k] | Branch (1691:35): [True: 2.41k, False: 11.9k] | Branch (1691:50): [True: 1.88k, False: 524] ------------------ 1692| 1.88k| { 1693| 1.88k| int num_neigh = 0, pos_neigh = -1; 1694| 6.32k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1694:38): [True: 4.43k, False: 1.88k] ------------------ 1695| 4.43k| { 1696| 4.43k| n = at[i].neighbor[i1]; 1697| 4.43k| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH(at, n) && ------------------ | | 56| 6.08k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.64k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1697:33): [True: 1.70k, False: 2.73k] | Branch (1697:55): [True: 1.64k, False: 53] | Branch (1697:77): [True: 873, False: 774] ------------------ 1698| | /*0 == at[n].num_H &&*/ 1699| 873| at[i].bond_type[i1] == BOND_TYPE_DOUBLE && ------------------ | | 33| 5.31k|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1699:33): [True: 583, False: 290] ------------------ 1700| 583| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 583|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1700:33): [True: 580, False: 3] ------------------ 1701| 580| { 1702| | /* found O(+)(III)=C(-)(III); prepare conversion to O(IV)#C(IV) */ 1703| 580| num_neigh++; 1704| 580| pos_neigh = i1; 1705| 580| } 1706| 4.43k| } 1707| 1.88k| if (1 == num_neigh && ------------------ | Branch (1707:29): [True: 580, False: 1.30k] ------------------ 1708| 580| !has_other_ion_neigh(at, i, n = at[i].neighbor[i1 = pos_neigh]) && ------------------ | Branch (1708:29): [True: 426, False: 154] ------------------ 1709| 426| !has_other_ion_neigh(at, n, i)) ------------------ | Branch (1709:29): [True: 226, False: 200] ------------------ 1710| 226| { 1711| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1712| 226| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1713| 226| at[i].charge--; 1714| 226| at[n].charge++; 1715| 226| at[i].chem_bonds_valence++; 1716| 226| at[n].chem_bonds_valence++; 1717| 226| at[i].bond_type[i1]++; 1718| 226| at[n].bond_type[i2]++; 1719| 226| num_changes++; 1720| 226| num_C_minus--; 1721| 226| num_O_plus--; 1722| 226| num_All -= 2; 1723| 226| continue; 1724| 226| } 1725| 1.88k| } 1726| 14.1k| if ((!type || 15 == type) && 0 < num_N_minus) ------------------ | Branch (1726:26): [True: 0, False: 14.1k] | Branch (1726:35): [True: 2.18k, False: 11.9k] | Branch (1726:50): [True: 833, False: 1.35k] ------------------ 1727| 833| { 1728| 833| int num_neigh = 0, pos_neigh = -1; 1729| 2.70k| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1729:38): [True: 1.87k, False: 833] ------------------ 1730| 1.87k| { 1731| 1.87k| n = at[i].neighbor[i1]; 1732| 1.87k| if (-1 == at[n].charge && 2 >= nNoMetalNumBonds(at, n) && ------------------ | Branch (1732:33): [True: 957, False: 914] | Branch (1732:55): [True: 901, False: 56] ------------------ 1733| 901| 2 == nNoMetalBondsValence(at, n) + NUMH(at, n) && ------------------ | | 56| 2.77k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 901|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1733:33): [True: 595, False: 306] ------------------ 1734| | /*0 == num_of_H( at, n ) &&*/ 1735| 595| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 32| 2.46k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1735:33): [True: 503, False: 92] ------------------ 1736| 503| ion_el_group(at[n].el_number) == EL_NUMBER_N) ------------------ | | 14| 503|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1736:33): [True: 474, False: 29] ------------------ 1737| 474| { 1738| | /* found O(+)(III)=N(-)(II); prepare conversion to O(IV)#N(III) */ 1739| 474| num_neigh++; 1740| 474| pos_neigh = i1; 1741| 474| } 1742| 1.87k| } 1743| 833| if (1 == num_neigh && ------------------ | Branch (1743:29): [True: 474, False: 359] ------------------ 1744| 474| !has_other_ion_neigh(at, i, n = at[i].neighbor[i1 = pos_neigh]) && ------------------ | Branch (1744:29): [True: 320, False: 154] ------------------ 1745| 320| !has_other_ion_neigh(at, n, i)) ------------------ | Branch (1745:29): [True: 258, False: 62] ------------------ 1746| 258| { 1747| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1748| 258| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1749| 258| at[i].charge--; 1750| 258| at[n].charge++; 1751| 258| at[i].chem_bonds_valence++; 1752| 258| at[n].chem_bonds_valence++; 1753| 258| at[i].bond_type[i1]++; 1754| 258| at[n].bond_type[i2]++; 1755| 258| num_changes++; 1756| 258| num_N_minus--; 1757| 258| num_O_plus--; 1758| 258| num_All -= 2; 1759| 258| continue; 1760| 258| } 1761| 833| } 1762| 14.1k| } 1763| 1.06M| } 1764| 196k| } 1765| | 1766| | /**************************************************************************/ 1767| | /*********************** NON-Terminal ion triples *************************/ 1768| | /**************************************************************************/ 1769| | /*------------------------------------------------------------------------- 1770| | Non-Terminal triple types: 16, 17, 18 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1771| | ======================================== 1772| | 16: C(+)(III)-O-N(-)(II) => C(IV)=O=N(III) (allow terminal H on N(-)) 1773| | | | 1774| | 17: C(+)(III)-N-C(-)(III) => C(IV)=N=C(IV) 1775| | 1776| | 18: C(-)(III)-N=C(+)(III) => C(IV)=N#C(IV) (may have two or no charges) 1777| | C(IV)=N-C(II) => C(IV)=N#C(IV) 1778| | 1779| | */ 1780| | 1781| 589k| if ((!type || 16 == type) && 0 < num_C_plus && 0 < num_N_minus) ------------------ | Branch (1781:14): [True: 0, False: 589k] | Branch (1781:23): [True: 32.7k, False: 556k] | Branch (1781:38): [True: 7.80k, False: 24.9k] | Branch (1781:56): [True: 3.20k, False: 4.60k] ------------------ 1782| 3.20k| { 1783| 3.20k| int m[2], j[2], k; 1784| 21.4k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1784:25): [True: 18.2k, False: 3.20k] ------------------ 1785| 18.2k| { 1786| 18.2k| if (0 == at[i].charge && 2 == nNoMetalNumBonds(at, i) && 2 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1786:21): [True: 9.27k, False: 9.00k] | Branch (1786:42): [True: 3.67k, False: 5.59k] | Branch (1786:74): [True: 1.56k, False: 2.10k] ------------------ 1787| 1.56k| 0 == num_of_H(at, i) && ------------------ | Branch (1787:21): [True: 1.42k, False: 140] ------------------ 1788| 1.42k| 0 <= (j[0] = nNoMetalNeighIndex(at, i)) && ------------------ | Branch (1788:21): [True: 1.33k, False: 92] ------------------ 1789| 1.33k| at[m[0] = at[i].neighbor[j[0]]].charge && ------------------ | Branch (1789:21): [True: 1.11k, False: 220] ------------------ 1790| 1.11k| 0 <= (j[1] = nNoMetalOtherNeighIndex(at, i, m[0])) && ------------------ | Branch (1790:21): [True: 864, False: 248] ------------------ 1791| 864| 0 == at[m[0]].charge + at[m[1] = at[i].neighbor[j[1]]].charge && ------------------ | Branch (1791:21): [True: 543, False: 321] ------------------ 1792| 543| 5 >= nNoMetalBondsValence(at, m[0]) + nNoMetalBondsValence(at, m[1]) && ------------------ | Branch (1792:21): [True: 276, False: 267] ------------------ 1793| | /*5 >= at[m[0]].chem_bonds_valence + at[m[1]].chem_bonds_valence &&*/ 1794| 276| ion_el_group(at[i].el_number) == EL_NUMBER_O) ------------------ | | 15| 276|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1794:21): [True: 57, False: 219] ------------------ 1795| 57| { 1796| | /* found non-terminal A(+)-O-B(-); chem_bond_val of A+B <= 5 */ 1797| 57| int n_N = -1, n_C = -1, i_C = -1; 1798| 171| for (k = 0; k < 2; k++) ------------------ | Branch (1798:33): [True: 114, False: 57] ------------------ 1799| 114| { 1800| 114| n = m[k]; 1801| 114| if (-1 == at[n].charge && 2 == nNoMetalNumBonds(at, n) + NUMH(at, n) && ------------------ | | 56| 171|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 57|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1801:29): [True: 57, False: 57] | Branch (1801:51): [True: 23, False: 34] ------------------ 1802| | /*0 == num_of_H( at, n ) &&*/ 1803| 23| ion_el_group(at[n].el_number) == EL_NUMBER_N) ------------------ | | 14| 23|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1803:29): [True: 22, False: 1] ------------------ 1804| 22| { 1805| 22| n_N = n; 1806| 22| } 1807| 92| else if (1 == at[n].charge && 3 == at[n].chem_bonds_valence + NUMH(at, n) && ------------------ | | 56| 149|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 57|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1807:34): [True: 57, False: 35] | Branch (1807:55): [True: 42, False: 15] ------------------ 1808| 42| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 42|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1808:34): [True: 19, False: 23] ------------------ 1809| 19| { 1810| 19| n_C = n; 1811| 19| i_C = k; 1812| 19| } 1813| 114| } 1814| 57| if (n_C < 0 || n_N < 0 || ------------------ | Branch (1814:25): [True: 38, False: 19] | Branch (1814:36): [True: 3, False: 16] ------------------ 1815| 16| has_other_ion_in_sphere_2(at, n_C, n_N) || ------------------ | Branch (1815:25): [True: 6, False: 10] ------------------ 1816| 10| has_other_ion_in_sphere_2(at, n_N, n_C)) ------------------ | Branch (1816:25): [True: 0, False: 10] ------------------ 1817| 47| { 1818| 47| continue; 1819| 47| } 1820| | 1821| | /* C(+)(III)-O-N(-)(II) => C(IV)=O=N(III) */ 1822| 30| for (k = 0; k < 2; k++) ------------------ | Branch (1822:33): [True: 20, False: 10] ------------------ 1823| 20| { 1824| 20| n = k ? n_C : n_N; ------------------ | Branch (1824:29): [True: 10, False: 10] ------------------ 1825| 20| i1 = k ? j[i_C] : j[1 - i_C]; ------------------ | Branch (1825:30): [True: 10, False: 10] ------------------ 1826| 20| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1827| 20| at[i].bond_type[i1]++; 1828| 20| at[n].bond_type[i2]++; 1829| 20| at[i].chem_bonds_valence++; 1830| 20| at[n].chem_bonds_valence++; 1831| 20| at[n].charge += (k ? -1 : 1); ------------------ | Branch (1831:42): [True: 10, False: 10] ------------------ 1832| 20| } 1833| 10| num_changes++; 1834| 10| num_N_minus--; 1835| 10| num_C_plus--; 1836| 10| num_All -= 2; 1837| 10| } 1838| 18.2k| } 1839| 3.20k| } 1840| | 1841| 589k| if ((!type || 17 == type) && 0 < num_C_plus && 0 < num_C_minus) ------------------ | Branch (1841:14): [True: 0, False: 589k] | Branch (1841:23): [True: 32.7k, False: 556k] | Branch (1841:38): [True: 7.79k, False: 24.9k] | Branch (1841:56): [True: 2.18k, False: 5.60k] ------------------ 1842| 2.18k| { 1843| 2.18k| int m[3], c[3], j[3], k; 1844| 14.4k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1844:25): [True: 12.2k, False: 2.18k] ------------------ 1845| 12.2k| { 1846| 12.2k| if (0 == at[i].charge && 3 == nNoMetalNumBonds(at, i) && 3 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1846:21): [True: 5.91k, False: 6.29k] | Branch (1846:42): [True: 1.70k, False: 4.20k] | Branch (1846:74): [True: 770, False: 937] ------------------ 1847| 770| 0 == num_of_H(at, i) && ------------------ | Branch (1847:21): [True: 658, False: 112] ------------------ 1848| 658| 0 <= (j[0] = nNoMetalNeighIndex(at, i)) && ------------------ | Branch (1848:21): [True: 657, False: 1] ------------------ 1849| 657| 0 <= (j[1] = nNoMetalOtherNeighIndex(at, i, m[0] = at[i].neighbor[j[0]])) && ------------------ | Branch (1849:21): [True: 650, False: 7] ------------------ 1850| 650| 0 <= (j[2] = nNoMetalOtherNeighIndex2(at, i, m[0], m[1] = at[i].neighbor[j[1]])) && ------------------ | Branch (1850:21): [True: 501, False: 149] ------------------ 1851| 501| 1 == !(c[0] = at[m[0]].charge) + !(c[1] = at[m[1]].charge) + !(c[2] = at[m[2] = at[i].neighbor[j[2]]].charge) && ------------------ | Branch (1851:21): [True: 183, False: 318] ------------------ 1852| 183| 0 == c[0] + c[1] + c[2] && ------------------ | Branch (1852:21): [True: 182, False: 1] ------------------ 1853| 182| 2 == (3 == (c[0] ? at[m[0]].chem_bonds_valence + NUMH(at, m[0]) : 0)) + (3 == (c[1] ? at[m[1]].chem_bonds_valence + NUMH(at, m[1]) : 0)) + (3 == (c[2] ? at[m[2]].chem_bonds_valence + NUMH(at, m[2]) : 0)) && ------------------ | | 56| 113|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 113|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 2 == (3 == (c[0] ? at[m[0]].chem_bonds_valence + NUMH(at, m[0]) : 0)) + (3 == (c[1] ? at[m[1]].chem_bonds_valence + NUMH(at, m[1]) : 0)) + (3 == (c[2] ? at[m[2]].chem_bonds_valence + NUMH(at, m[2]) : 0)) && ------------------ | | 56| 167|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 167|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 2 == (3 == (c[0] ? at[m[0]].chem_bonds_valence + NUMH(at, m[0]) : 0)) + (3 == (c[1] ? at[m[1]].chem_bonds_valence + NUMH(at, m[1]) : 0)) + (3 == (c[2] ? at[m[2]].chem_bonds_valence + NUMH(at, m[2]) : 0)) && ------------------ | | 56| 84|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 84|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1853:21): [True: 11, False: 171] | Branch (1853:33): [True: 113, False: 69] | Branch (1853:100): [True: 167, False: 15] | Branch (1853:167): [True: 84, False: 98] ------------------ 1854| 11| ion_el_group(at[i].el_number) == EL_NUMBER_N) ------------------ | | 14| 11|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1854:21): [True: 0, False: 11] ------------------ 1855| 0| { 1856| | /* found non-terminal A(+)-O-B(-) */ 1857| 0| int n_Cp = -1, n_Cm = -1, i_Cp = -1, i_Cm = -1; /* p = positive, m = negatice ion C */ 1858| 0| for (k = 0; k < 3; k++) ------------------ | Branch (1858:33): [True: 0, False: 0] ------------------ 1859| 0| { 1860| 0| if (c[k]) ------------------ | Branch (1860:29): [True: 0, False: 0] ------------------ 1861| 0| { 1862| 0| n = m[k]; 1863| 0| if (-1 == at[n].charge && ------------------ | Branch (1863:33): [True: 0, False: 0] ------------------ 1864| 0| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 0|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1864:33): [True: 0, False: 0] ------------------ 1865| 0| { 1866| 0| n_Cm = n; 1867| 0| i_Cm = k; 1868| 0| } 1869| 0| else if (1 == at[n].charge && ------------------ | Branch (1869:38): [True: 0, False: 0] ------------------ 1870| 0| ion_el_group(at[n].el_number) == EL_NUMBER_C) ------------------ | | 13| 0|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1870:38): [True: 0, False: 0] ------------------ 1871| 0| { 1872| 0| n_Cp = n; 1873| 0| i_Cp = k; 1874| 0| } 1875| 0| } 1876| 0| } 1877| 0| if (n_Cp < 0 || n_Cm < 0 || ------------------ | Branch (1877:25): [True: 0, False: 0] | Branch (1877:37): [True: 0, False: 0] ------------------ 1878| 0| has_other_ion_in_sphere_2(at, n_Cp, n_Cm) || ------------------ | Branch (1878:25): [True: 0, False: 0] ------------------ 1879| 0| has_other_ion_in_sphere_2(at, n_Cm, n_Cp)) ------------------ | Branch (1879:25): [True: 0, False: 0] ------------------ 1880| 0| { 1881| 0| continue; 1882| 0| } 1883| | 1884| | /* | | */ 1885| | /* C(+)(III)-N-C(-)(III) => C(IV)=N=C(IV) */ 1886| 0| for (k = 0; k < 2; k++) ------------------ | Branch (1886:33): [True: 0, False: 0] ------------------ 1887| 0| { 1888| 0| n = k ? n_Cp : n_Cm; ------------------ | Branch (1888:29): [True: 0, False: 0] ------------------ 1889| 0| i1 = k ? j[i_Cp] : j[i_Cm]; ------------------ | Branch (1889:30): [True: 0, False: 0] ------------------ 1890| 0| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1891| 0| at[i].bond_type[i1]++; 1892| 0| at[n].bond_type[i2]++; 1893| 0| at[i].chem_bonds_valence++; 1894| 0| at[n].chem_bonds_valence++; 1895| 0| at[n].charge += (k ? -1 : 1); ------------------ | Branch (1895:42): [True: 0, False: 0] ------------------ 1896| 0| } 1897| 0| num_changes++; 1898| 0| num_C_minus--; 1899| 0| num_C_plus--; 1900| 0| num_All -= 2; 1901| 0| } 1902| 12.2k| } 1903| 2.18k| } 1904| | 1905| 589k| if ((!type || 18 == type) && ((0 < num_C_plus && 0 < num_C_minus) || 0 < num_C_II)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (1905:14): [True: 0, False: 589k] | Branch (1905:23): [True: 32.7k, False: 556k] | Branch (1905:40): [True: 7.79k, False: 24.9k] | Branch (1905:58): [True: 2.18k, False: 5.60k] | Branch (1905:78): [True: 1.52k, False: 29.0k] ------------------ 1906| 3.71k| { 1907| 3.71k| int m[2], v[2], j[2], k; 1908| 23.7k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1908:25): [True: 20.0k, False: 3.71k] ------------------ 1909| 20.0k| { 1910| 20.0k| if (0 == at[i].charge && 2 == nNoMetalNumBonds(at, i) && 3 == nNoMetalBondsValence(at, i) && ------------------ | Branch (1910:21): [True: 12.7k, False: 7.26k] | Branch (1910:42): [True: 4.21k, False: 8.56k] | Branch (1910:74): [True: 2.07k, False: 2.14k] ------------------ 1911| 2.07k| 0 == num_of_H(at, i) && ------------------ | Branch (1911:21): [True: 2.03k, False: 44] ------------------ 1912| 2.03k| 0 <= (j[0] = nNoMetalNeighIndex(at, i)) && ------------------ | Branch (1912:21): [True: 1.93k, False: 97] ------------------ 1913| 1.93k| 0 <= (j[1] = nNoMetalOtherNeighIndex(at, i, m[0] = at[i].neighbor[j[0]])) && ------------------ | Branch (1913:21): [True: 1.58k, False: 352] ------------------ 1914| 1.58k| 0 == at[m[0]].charge + at[m[1] = at[i].neighbor[j[1]]].charge && ------------------ | Branch (1914:21): [True: 1.42k, False: 160] ------------------ 1915| 1.42k| 6 == (v[0] = at[m[0]].chem_bonds_valence + NUMH(at, m[0])) + (v[1] = at[m[1]].chem_bonds_valence + NUMH(at, m[1])) && ------------------ | | 56| 1.42k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.42k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 6 == (v[0] = at[m[0]].chem_bonds_valence + NUMH(at, m[0])) + (v[1] = at[m[1]].chem_bonds_valence + NUMH(at, m[1])) && ------------------ | | 56| 1.42k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.42k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1915:21): [True: 167, False: 1.25k] ------------------ 1916| 167| 2 >= abs(v[0] - v[1]) && ------------------ | Branch (1916:21): [True: 166, False: 1] ------------------ 1917| 166| ion_el_group(at[i].el_number) == EL_NUMBER_N && ------------------ | | 14| 20.2k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1917:21): [True: 83, False: 83] ------------------ 1918| 83| ion_el_group(at[m[0]].el_number) == EL_NUMBER_C && ------------------ | | 13| 20.1k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1918:21): [True: 39, False: 44] ------------------ 1919| 39| ion_el_group(at[m[1]].el_number) == EL_NUMBER_C) ------------------ | | 13| 39|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (1919:21): [True: 6, False: 33] ------------------ 1920| 6| { 1921| | /* n_Cm i n_Cp */ 1922| | /* found non-terminal C(-)(III)-N=C(+)(III) or C(IV)=N-C(II): Cm-N-Cp */ 1923| | /* convert to C(IV)=N#C(IV) */ 1924| 6| int n_Cp = -1, n_Cm = -1, i_Cp = -1, i_Cm = -1; /* p = positive, m = negatice ion C */ 1925| 18| for (k = 0; k < 2; k++) ------------------ | Branch (1925:33): [True: 12, False: 6] ------------------ 1926| 12| { 1927| 12| n = m[k]; 1928| 12| if (v[k] == 4 || (v[k] == 3 && at[i].bond_type[j[k]] == BOND_TYPE_SINGLE)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 32| 4|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1928:29): [True: 4, False: 8] | Branch (1928:43): [True: 4, False: 4] | Branch (1928:56): [True: 2, False: 2] ------------------ 1929| 6| { 1930| 6| n_Cm = n; 1931| 6| i_Cm = k; 1932| 6| } 1933| 6| else if (v[k] == 2 || (v[k] == 3 && at[i].bond_type[j[k]] == BOND_TYPE_DOUBLE)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 33| 2|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1933:34): [True: 4, False: 2] | Branch (1933:48): [True: 2, False: 0] | Branch (1933:61): [True: 2, False: 0] ------------------ 1934| 6| { 1935| 6| n_Cp = n; 1936| 6| i_Cp = k; 1937| 6| } 1938| 12| } 1939| 6| if (n_Cp < 0 || n_Cm < 0 || at[n_Cp].valence + NUMH(at, n_Cp) != 2) ------------------ | | 56| 6|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 6|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (1939:25): [True: 0, False: 6] | Branch (1939:37): [True: 0, False: 6] | Branch (1939:49): [True: 4, False: 2] ------------------ 1940| 4| { 1941| 4| continue; /* guarantees at[n_Cp].valence <= 2 */ 1942| 4| } 1943| 2| if (v[i_Cp] == 2 || !at[n_Cp].charge) ------------------ | Branch (1943:25): [True: 0, False: 2] | Branch (1943:41): [True: 0, False: 2] ------------------ 1944| 0| { 1945| 0| if (at[n_Cp].valence == 2) ------------------ | Branch (1945:29): [True: 0, False: 0] ------------------ 1946| 0| { 1947| | /* neighbor of at[n_Cp] opposite to at[i] */ 1948| 0| k = at[n_Cp].neighbor[at[n_Cp].neighbor[0] == i]; 1949| 0| if (ion_el_group(at[k].el_number) == EL_NUMBER_N) ------------------ | | 14| 0|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1949:33): [True: 0, False: 0] ------------------ 1950| 0| { 1951| 0| continue; 1952| 0| } 1953| 0| } 1954| 0| } 1955| 2| else if (at[n_Cp].charge) ------------------ | Branch (1955:30): [True: 2, False: 0] ------------------ 1956| 2| { 1957| 2| if (has_other_ion_in_sphere_2(at, n_Cp, n_Cm) || ------------------ | Branch (1957:29): [True: 0, False: 2] ------------------ 1958| 2| has_other_ion_in_sphere_2(at, n_Cm, n_Cp)) ------------------ | Branch (1958:29): [True: 0, False: 2] ------------------ 1959| 0| { 1960| 0| continue; 1961| 0| } 1962| 2| } 1963| 0| else 1964| 0| { 1965| 0| continue; /* unknown case */ 1966| 0| } 1967| | 1968| | /* */ 1969| | /* C(-)(III)-N=C(+)(III) => C(IV)=N#C(IV) */ 1970| | /* C(IV)=N-C(II) => C(IV)=N#C(IV) */ 1971| 2| if (at[n_Cp].charge) ------------------ | Branch (1971:25): [True: 2, False: 0] ------------------ 1972| 2| { 1973| 2| num_C_minus--; 1974| 2| num_C_plus--; 1975| 2| num_All -= 2; 1976| 2| } 1977| 0| else 1978| 0| { 1979| 0| num_C_II--; 1980| 0| num_All--; 1981| 0| } 1982| | 1983| 6| for (k = 0; k < 2; k++) ------------------ | Branch (1983:33): [True: 4, False: 2] ------------------ 1984| 4| { 1985| 4| n = k ? n_Cp : n_Cm; ------------------ | Branch (1985:29): [True: 2, False: 2] ------------------ 1986| 4| i3 = k ? i_Cp : i_Cm; /* added to fix the bug */ ------------------ | Branch (1986:30): [True: 2, False: 2] ------------------ 1987| | /*i1 = k? j[i_Cp] : j[i_Cm];*/ /* replaced with next line */ 1988| 4| i1 = j[i3]; 1989| 4| if (v[i3 /*was i1*/] < 4) ------------------ | Branch (1989:29): [True: 4, False: 0] ------------------ 1990| 4| { 1991| | /* WDI found a bug here: bounds violation */ 1992| 4| int delta = 4 - v[i3 /*was i1*/]; 1993| 4| i2 = (int)(is_in_the_list(at[n].neighbor, (AT_NUMB)i, at[n].valence) - at[n].neighbor); 1994| 4| at[i].bond_type[i1] += delta; 1995| 4| at[n].bond_type[i2] += delta; 1996| 4| at[i].chem_bonds_valence += delta; 1997| 4| at[n].chem_bonds_valence += delta; 1998| 4| at[n].charge = 0; 1999| 4| at[n].radical = 0; 2000| 4| } 2001| 4| } 2002| 2| at[i].charge = 0; 2003| 2| at[i].radical = 0; 2004| 2| num_changes++; 2005| 2| } 2006| 20.0k| } 2007| 3.71k| } 2008| 589k| } 2009| | 2010| 32.7k| return num_changes; 2011| 216k|} RemoveInpAtBond: 2017| 2.24k|{ 2018| 2.24k| int i, j, m, m2; /* djb-rwth: removing redundant variables */ 2019| 2.24k| inp_ATOM *at = atom + iat; 2020| 2.24k| inp_ATOM *at2 = NULL; 2021| 2.24k| int val = at->valence - 1; 2022| | 2023| 2.24k| if (val >= 0) ------------------ | Branch (2023:9): [True: 2.24k, False: 0] ------------------ 2024| 2.24k| { 2025| 2.24k| int bond = at->bond_type[k]; 2026| 2.24k| if (bond > BOND_TYPE_TRIPLE) ------------------ | | 34| 2.24k|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (2026:13): [True: 0, False: 2.24k] ------------------ 2027| 0| bond = BOND_TYPE_SINGLE; /* added 08-06-2003 */ ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ 2028| | 2029| | /* update CML tetrahedral atom parity. */ 2030| 2.24k| if (at->p_parity) ------------------ | Branch (2030:13): [True: 13, False: 2.22k] ------------------ 2031| 13| { 2032| 45| for (m = 0; m < MAX_NUM_STEREO_ATOM_NEIGH; m++) ------------------ | | 877| 45|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2032:25): [True: 37, False: 8] ------------------ 2033| 37| { 2034| 37| if (at->p_orig_at_num[m] == at->orig_at_number) ------------------ | Branch (2034:21): [True: 5, False: 32] ------------------ 2035| 5| { 2036| 5| at->p_parity = 0; 2037| 5| break; /* only 3 bonds are present; removing one bond removes stereo */ 2038| 5| } 2039| 37| } 2040| 13| if (at->p_parity /* at->valence == MAX_NUM_STEREO_ATOM_NEIGH*/) ------------------ | Branch (2040:17): [True: 8, False: 5] ------------------ 2041| 8| { 2042| | /* p_orig_at_num is a fixed size array of MAX_NUM_STEREO_ATOM_NEIGH (4) elements */ 2043| 18| for (m = 0; m < at->valence && m < MAX_NUM_STEREO_ATOM_NEIGH; m++) /* djb-rwth: fixing GH PR #72 */ ------------------ | | 877| 18|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2043:29): [True: 18, False: 0] | Branch (2043:48): [True: 18, False: 0] ------------------ 2044| 18| { 2045| 18| if (atom[(int)at->neighbor[k]].orig_at_number == at->p_orig_at_num[m]) ------------------ | Branch (2045:25): [True: 8, False: 10] ------------------ 2046| 8| { 2047| 8| break; 2048| 8| } 2049| 18| } 2050| 8| if (m < at->valence && m < MAX_NUM_STEREO_ATOM_NEIGH) /* djb-rwth: fixing GH PR #72 */ ------------------ | | 877| 8|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2050:21): [True: 8, False: 0] | Branch (2050:40): [True: 8, False: 0] ------------------ 2051| 8| { 2052| 8| at->p_orig_at_num[m] = at->orig_at_number; 2053| 8| } 2054| 0| else 2055| 0| { 2056| 0| at->p_parity = 0; /* wrong neighbors: at->neighbor[k] is not in the list of a stereo neighbors */ 2057| 0| } 2058| 8| } 2059| 13| } 2060| | 2061| | /* update CML stereogenic bond parities; at this point no removed explicit H exist yet */ 2062| 2.24k| if (at->sb_parity[0]) ------------------ | Branch (2062:13): [True: 15, False: 2.22k] ------------------ 2063| 15| { 2064| 34| for (m = 0; m < MAX_NUM_STEREO_BONDS && at->sb_parity[m];) ------------------ | | 873| 68|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2064:25): [True: 34, False: 0] | Branch (2064:53): [True: 19, False: 15] ------------------ 2065| 19| { 2066| 19| if (k == at->sb_ord[m] || (k == at->sn_ord[m] && val < 2 && ATOM_PARITY_WELL_DEF(at->sb_parity[m]))) /* djb-rwth: addressing LLVM warning */ ------------------ | | 259| 5|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 5|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 5|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 5, False: 0] | | | Branch (259:75): [True: 3, False: 2] | | ------------------ ------------------ | Branch (2066:21): [True: 4, False: 15] | Branch (2066:44): [True: 13, False: 2] | Branch (2066:66): [True: 5, False: 8] ------------------ 2067| 7| { 2068| | /* !!! FLAW: does take into account removed H !!! */ 2069| | /* stereogenic bond is being removed OR */ 2070| | /* remove stereogenic bond because its only neighbor is being removed */ 2071| 7| int pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; 2072| 7| int len = get_opposite_sb_atom(atom, iat, at->sb_ord[m], &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord); 2073| 7| if (len) ------------------ | Branch (2073:25): [True: 7, False: 0] ------------------ 2074| 7| { 2075| 7| i = pinxt_sb_parity_ord; 2076| 7| at2 = atom + pnxt_atom; 2077| | /* djb-rwth: removing redundant code */ 2078| 7| } 2079| 0| else 2080| 0| { 2081| 0| i = MAX_NUM_STEREO_BONDS; ------------------ | | 873| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2082| 0| } 2083| | /* 2084| | at2 = atom + at->neighbor[ (int)at->sb_ord[m] ]; 2085| | for ( i = 0; i < MAX_NUM_STEREO_BONDS && at2->sb_parity[i]; i ++ ) 2086| | { 2087| | if ( iat == at2->neighbor[ (int)at2->sb_ord[i] ] ) 2088| | break; 2089| | } 2090| | */ 2091| 7| if (i < MAX_NUM_STEREO_BONDS && at2->sb_parity[i]) ------------------ | | 873| 14|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2091:25): [True: 7, False: 0] | Branch (2091:53): [True: 7, False: 0] ------------------ 2092| 7| { 2093| 7| m2 = i; 2094| | /* remove bond parity from at */ 2095| 7| if (m < MAX_NUM_STEREO_BONDS - 1) ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2095:29): [True: 7, False: 0] ------------------ 2096| 7| { 2097| 7| memmove(at->sb_parity + m, at->sb_parity + m + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m) * sizeof(at->sb_parity[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2098| 7| memmove(at->sb_ord + m, at->sb_ord + m + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m) * sizeof(at->sb_ord[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2099| 7| memmove(at->sn_ord + m, at->sn_ord + m + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m) * sizeof(at->sn_ord[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2100| 7| memmove(at->sn_orig_at_num + m, at->sn_orig_at_num + m + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m) * sizeof(at->sn_orig_at_num[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2101| 7| } 2102| 7| at->sb_parity[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2103| 7| at->sb_ord[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2104| 7| at->sn_ord[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2105| 7| at->sn_orig_at_num[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2106| | /* remove bond parity from at2 */ 2107| 7| if (m2 < MAX_NUM_STEREO_BONDS - 1) ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2107:29): [True: 6, False: 1] ------------------ 2108| 6| { 2109| 6| memmove(at2->sb_parity + m2, at2->sb_parity + m2 + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m2) * sizeof(at2->sb_parity[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 6|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2110| 6| memmove(at2->sb_ord + m2, at2->sb_ord + m2 + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m2) * sizeof(at2->sb_ord[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 6|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2111| 6| memmove(at2->sn_ord + m2, at2->sn_ord + m2 + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m2) * sizeof(at2->sn_ord[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 6|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2112| 6| memmove(at2->sn_orig_at_num + m2, at2->sn_orig_at_num + m2 + 1, (MAX_NUM_STEREO_BONDS - 1 - (long long)m2) * sizeof(at2->sn_orig_at_num[0])); /* djb-rwth: cast operator added */ ------------------ | | 873| 6|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2113| 6| } 2114| 7| at2->sb_parity[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2115| 7| at2->sb_ord[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2116| 7| at2->sn_ord[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2117| 7| at2->sn_orig_at_num[MAX_NUM_STEREO_BONDS - 1] = 0; ------------------ | | 873| 7|#define MAX_NUM_STEREO_BONDS 3 ------------------ 2118| | /* do not increment m here because the array elements have been shifted */ 2119| 7| } 2120| 0| else 2121| 0| { 2122| 0| m++; /* program error: inconsistent stereobond parity */ 2123| 0| } 2124| 7| } 2125| 12| else if (k == at->sn_ord[m]) ------------------ | Branch (2125:26): [True: 10, False: 2] ------------------ 2126| 10| { 2127| | /* stereogenic bond neighbor is being removed; another neighbor remains */ 2128| | /* !!! FLAW: does take into account removed H !!! */ 2129| 27| for (j = 0, i = -1; j < at->valence; j++) ------------------ | Branch (2129:41): [True: 25, False: 2] ------------------ 2130| 25| { 2131| 25| if (j != k && j != at->sb_ord[m]) ------------------ | Branch (2131:29): [True: 15, False: 10] | Branch (2131:39): [True: 8, False: 7] ------------------ 2132| 8| { 2133| 8| i = j; 2134| 8| break; 2135| 8| } 2136| 25| } 2137| | 2138| | /* i is the position of the neighbor that will become a new neighbor */ 2139| | /*************************************************************************** 2140| | * at->sb_parity[m] is the direction (EVEN=clockwise, ODD=counterclockwise) 2141| | * from stereobond to the neighbor. If the neighbor is removed then 2142| | * the parity should invert, otherwise it should be unchanged. 2143| | ***************************************************************************/ 2144| 10| if (i < 0) ------------------ | Branch (2144:25): [True: 2, False: 8] ------------------ 2145| 2| { 2146| | /* no alternative neighbor is available */ 2147| 2| if (ATOM_PARITY_WELL_DEF(at->sb_parity[m])) ------------------ | | 259| 2|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 2|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 2|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 2, False: 0] | | | Branch (259:75): [True: 0, False: 2] | | ------------------ ------------------ 2148| 0| { 2149| | /* parity cannot be not well-defined anymore */ 2150| 0| int pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; 2151| 0| int len = get_opposite_sb_atom(atom, iat, at->sb_ord[m], &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord); 2152| 0| if (len > 0) ------------------ | Branch (2152:33): [True: 0, False: 0] ------------------ 2153| 0| { 2154| 0| atom[pnxt_atom].sb_parity[pinxt_sb_parity_ord] = at->sb_parity[m] = AB_PARITY_UNDF; ------------------ | | 222| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2155| 0| } 2156| 0| } 2157| 2| at->sn_ord[m] = -99; /* sb neighbor has been disconnected */ 2158| 2| at->sb_ord[m] -= (at->sb_ord[m] > k); /* same as above */ 2159| 2| at->sn_orig_at_num[m] = 0; 2160| 2| } 2161| 8| else if (i < at->valence) ------------------ | Branch (2161:30): [True: 8, False: 0] ------------------ 2162| 8| { 2163| | /* choose another stereogenic bond neighbor, its ord. number is i before bond removal */ 2164| 8| if (ATOM_PARITY_WELL_DEF(at->sb_parity[m])) ------------------ | | 259| 8|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 8|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 8|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 8, False: 0] | | | Branch (259:75): [True: 2, False: 6] | | ------------------ ------------------ 2165| 2| { 2166| | /* ALL WRONG: 'move' previous stereo bond neighbor to the last position (pos. 2 out of 0,1,2) */ 2167| | /* the parity of the transpositions is (2 - at->sn_ord[m])%2 = at->sn_ord[m] % 2 */ 2168| | /* and replace the neighbor with another; the contribution to the parity is 1 */ 2169| | 2170| | /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + at->sn_ord[m] + 1 ) % 2;*/ 2171| | 2172| | /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + k + i + 2173| | (i > k) + (i > at->sb_ord[m]) ) % 2;*/ 2174| | /*=== parity should be INVERTED ===*/ 2175| 2| at->sb_parity[m] = 3 - at->sb_parity[m]; 2176| 2| } 2177| 8| at->sn_ord[m] = i - (i > k); /* ord. number shifted because preceding bond is removed */ 2178| 8| at->sb_ord[m] -= (at->sb_ord[m] > k); /* same as above */ 2179| 8| at->sn_orig_at_num[m] = atom[(int)at->neighbor[i]].orig_at_number; 2180| | /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + 1 ) % 2;*/ 2181| 8| } 2182| 0| else 2183| 0| { 2184| 0| at->sb_parity[m] = 0; /* program error: inconsistent stereobond parity */ 2185| 0| } 2186| 10| m++; 2187| 10| } 2188| 2| else 2189| 2| { 2190| | /* removing another neighbor, k: first move it to the last position (pos. 2 out of 0,1,2) */ 2191| 2| if (k < 2 && ATOM_PARITY_WELL_DEF(at->sb_parity[m])) ------------------ | | 259| 1|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 237| 1|#define AB_MIN_WELL_DEFINED_PARITY 1 /* min(AB_PARITY_ODD, AB_PARITY_EVEN) */ | | ------------------ | | #define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 236| 1|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (259:38): [True: 1, False: 0] | | | Branch (259:75): [True: 1, False: 0] | | ------------------ ------------------ | Branch (2191:25): [True: 1, False: 1] ------------------ 2192| 1| { 2193| | /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + k ) % 2;*/ 2194| | /*at->sb_parity[m] = 2 - ( at->sb_parity[m] + (at->sn_ord[m] > k) + (at->sb_ord[m] > k) ) % 2;*/ 2195| 1| ; /*==== Parity should remain UNCHANGED ===*/ 2196| 1| } 2197| 2| if (at->sb_ord[m] > k) ------------------ | Branch (2197:25): [True: 1, False: 1] ------------------ 2198| 1| { 2199| 1| at->sb_ord[m]--; 2200| 1| } 2201| 2| if (at->sn_ord[m] > k) ------------------ | Branch (2201:25): [True: 0, False: 2] ------------------ 2202| 0| { 2203| 0| at->sn_ord[m]--; 2204| 0| } 2205| 2| m++; 2206| 2| } 2207| 19| } 2208| 15| } 2209| | 2210| 2.24k| if (k < val) ------------------ | Branch (2210:13): [True: 962, False: 1.27k] ------------------ 2211| 962| { 2212| 962| memmove(at->neighbor + k, at->neighbor + k + 1, sizeof(at->neighbor[0]) * ((long long)val - (long long)k)); /* djb-rwth: cast operators added */ 2213| 962| memmove(at->bond_stereo + k, at->bond_stereo + k + 1, sizeof(at->bond_stereo[0]) * ((long long)val - (long long)k)); /* djb-rwth: cast operators added */ 2214| 962| memmove(at->bond_type + k, at->bond_type + k + 1, sizeof(at->bond_type[0]) * ((long long)val - (long long)k)); /* djb-rwth: cast operators added */ 2215| 962| } 2216| | 2217| 2.24k| at->neighbor[val] = 0; 2218| 2.24k| at->bond_stereo[val] = 0; 2219| 2.24k| at->bond_type[val] = 0; 2220| 2.24k| at->valence = val; 2221| 2.24k| at->chem_bonds_valence -= bond; 2222| 2.24k| return 1; 2223| 2.24k| } 2224| | 2225| 0| return 0; 2226| 2.24k|} DisconnectInpAtBond: 2233| 1.12k|{ 2234| 1.12k| int neigh, i, ret = 0; 2235| 1.12k| int component; 2236| 1.12k| neigh = at[iat].neighbor[neigh_ord]; 2237| | 2238| 1.89k| for (i = 0; i < at[neigh].valence; i++) ------------------ | Branch (2238:17): [True: 1.89k, False: 0] ------------------ 2239| 1.89k| { 2240| 1.89k| if (iat == (int)at[neigh].neighbor[i]) ------------------ | Branch (2240:13): [True: 1.12k, False: 772] ------------------ 2241| 1.12k| { 2242| 1.12k| break; 2243| 1.12k| } 2244| 1.89k| } 2245| | 2246| 1.12k| if (i < at[neigh].valence) ------------------ | Branch (2246:9): [True: 1.12k, False: 0] ------------------ 2247| 1.12k| { 2248| 1.12k| ret += RemoveInpAtBond(at, iat, neigh_ord); 2249| 1.12k| ret += RemoveInpAtBond(at, neigh, i); 2250| 1.12k| if (nOldCompNumber && ret) ------------------ | Branch (2250:13): [True: 0, False: 1.12k] | Branch (2250:31): [True: 0, False: 0] ------------------ 2251| 0| { 2252| 0| if ((component = at[iat].component)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2252:17): [True: 0, False: 0] ------------------ 2253| 0| { 2254| 0| nOldCompNumber[component - 1] = 0; 2255| 0| } 2256| 0| if ((component = at[neigh].component)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2256:17): [True: 0, False: 0] ------------------ 2257| 0| { 2258| 0| nOldCompNumber[component - 1] = 0; 2259| 0| } 2260| 0| } 2261| 1.12k| } 2262| | 2263| 1.12k| return (ret == 2); 2264| 1.12k|} bIsAmmoniumSalt: 2272| 187k|{ 2273| | /* NH4(+charge)-O(-charge)-C -> NH3 + HO-C; any charge including 0, */ 2274| | /* any C except charged or radical F, Cl, Br, I */ 2275| | 2276| 187k| int num_H, num_non_iso_H, num_impl_iso_H, bDisconnect = 1; 2277| 187k| int j, val, neigh, iO = -1, iC, k = -1; 2278| | 2279| 187k| if (at[i].el_number != EL_NUMBER_N) ------------------ | | 14| 187k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (2279:9): [True: 168k, False: 19.0k] ------------------ 2280| 168k| { 2281| 168k| return 0; 2282| 168k| } 2283| | 2284| | /* check for NH4-O-C... -> NH3 + HO-C... */ 2285| 19.0k| val = at[i].valence; 2286| 19.0k| num_impl_iso_H = NUM_ISO_H(at, i); ------------------ | | 55| 19.0k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) ------------------ 2287| 19.0k| num_non_iso_H = at[i].num_H; 2288| 19.0k| num_H = num_non_iso_H + num_impl_iso_H; 2289| 19.0k| if (val + num_H == 5) ------------------ | Branch (2289:9): [True: 65, False: 18.9k] ------------------ 2290| 65| { 2291| 65| int num_O = 0; 2292| 65| memset(num_explicit_H, 0, (NUM_H_ISOTOPES + 1) * sizeof(num_explicit_H[0])); /* djb-rwth: memset_s C11/Annex K variant? */ ------------------ | | 25| 65|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ 2293| 89| for (j = 0; j < val; j++) ------------------ | Branch (2293:21): [True: 89, False: 0] ------------------ 2294| 89| { /* looking for O: H4N-O-C... */ 2295| 89| neigh = at[i].neighbor[j]; 2296| 89| if (at[neigh].num_H || ------------------ | Branch (2296:17): [True: 6, False: 83] ------------------ 2297| 83| (at[neigh].charge && (at[neigh].el_number != EL_NUMBER_O || at[neigh].charge + at[i].charge)) || ------------------ | | 15| 54|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2297:18): [True: 27, False: 56] | Branch (2297:39): [True: 25, False: 2] | Branch (2297:77): [True: 2, False: 0] ------------------ 2298| 56| (at[neigh].radical && at[neigh].radical != RADICAL_SINGLET)) /* djb-rwth: addressing LLVM warnings */ ------------------ | | 75| 1|#define RADICAL_SINGLET 1 ------------------ | Branch (2298:18): [True: 1, False: 55] | Branch (2298:39): [True: 1, False: 0] ------------------ 2299| 34| { 2300| 34| bDisconnect = 0; 2301| 34| break; /* reject */ 2302| 34| } 2303| 55| if (at[neigh].el_number == EL_NUMBER_H && at[neigh].valence == 1 && ------------------ | | 11| 110|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (2303:17): [True: 4, False: 51] | Branch (2303:55): [True: 2, False: 2] ------------------ 2304| 2| !at[neigh].charge && !at[neigh].radical) ------------------ | Branch (2304:17): [True: 2, False: 0] | Branch (2304:38): [True: 2, False: 0] ------------------ 2305| 2| { 2306| 2| num_H++; /* at this point at[].num_H does not include explicit H count */ 2307| 2| num_non_iso_H += (0 == at[neigh].iso_atw_diff); 2308| 2| num_explicit_H[at[neigh].iso_atw_diff]++; /* explicit H on N */ 2309| 2| } 2310| 53| else if (at[neigh].el_number == EL_NUMBER_O && at[neigh].valence == 2 && !num_O) ------------------ | | 15| 106|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2310:22): [True: 10, False: 43] | Branch (2310:60): [True: 10, False: 0] | Branch (2310:86): [True: 8, False: 2] ------------------ 2311| 8| { 2312| 8| num_O++; /* found O: N-O- */ 2313| 8| iO = neigh; 2314| 8| k = j; 2315| 8| iC = at[iO].neighbor[at[iO].neighbor[0] == i]; 2316| 8| if (at[iC].el_number != EL_NUMBER_C || /* ------------------ | | 13| 16|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (2316:21): [True: 4, False: 4] ------------------ 2317| | at[iC].num_H || 2318| | at[iC].chem_bonds_valence != 4 || */ 2319| 4| at[iC].charge || ------------------ | Branch (2319:21): [True: 0, False: 4] ------------------ 2320| 4| (at[iC].radical && at[iC].radical != RADICAL_SINGLET) /*|| ------------------ | | 75| 2|#define RADICAL_SINGLET 1 ------------------ | Branch (2320:22): [True: 2, False: 2] | Branch (2320:40): [True: 2, False: 0] ------------------ 2321| | at[iC].valence == at[iC].chem_bonds_valence*/ 2322| 8| ) /* djb-rwth: addressing LLVM warning */ 2323| 6| { 2324| 6| bDisconnect = 0; 2325| 6| break; /* reject */ 2326| 6| } 2327| 8| } 2328| 45| else if ((at[neigh].el_number == EL_NUMBER_F || ------------------ | | 16| 90|#define EL_NUMBER_F ((U_CHAR)9) ------------------ | Branch (2328:23): [True: 8, False: 37] ------------------ 2329| 37| at[neigh].el_number == EL_NUMBER_CL || ------------------ | | 20| 82|#define EL_NUMBER_CL ((U_CHAR)17) ------------------ | Branch (2329:23): [True: 0, False: 37] ------------------ 2330| 37| at[neigh].el_number == EL_NUMBER_BR || ------------------ | | 24| 82|#define EL_NUMBER_BR ((U_CHAR)35) ------------------ | Branch (2330:23): [True: 6, False: 31] ------------------ 2331| 31| at[neigh].el_number == EL_NUMBER_I) && ------------------ | | 27| 31|#define EL_NUMBER_I ((U_CHAR)53) ------------------ | Branch (2331:23): [True: 13, False: 18] ------------------ 2332| 27| at[neigh].valence == 1 && at[neigh].chem_bonds_valence == 1 && ------------------ | Branch (2332:22): [True: 22, False: 5] | Branch (2332:48): [True: 22, False: 0] ------------------ 2333| 22| !at[neigh].charge && !NUMH(at, neigh) && !num_O) ------------------ | | 56| 67|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 22|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2333:22): [True: 22, False: 0] | Branch (2333:43): [True: 22, False: 0] | Branch (2333:63): [True: 20, False: 2] ------------------ 2334| 20| { 2335| 20| num_O++; /* found O: N-O- */ 2336| 20| iO = neigh; 2337| 20| k = j; 2338| | /* djb-rwth: removing redundant code */ 2339| 20| } 2340| 25| else 2341| 25| { 2342| 25| bDisconnect = 0; 2343| 25| break; /* reject */ 2344| 25| } 2345| 55| } 2346| 65| if (bDisconnect && (num_O != 1 || num_H != 4)) ------------------ | Branch (2346:13): [True: 0, False: 65] | Branch (2346:29): [True: 0, False: 0] | Branch (2346:43): [True: 0, False: 0] ------------------ 2347| 0| { 2348| 0| bDisconnect = 0; /* reject */ 2349| 0| } 2350| 65| } 2351| 18.9k| else 2352| 18.9k| { 2353| 18.9k| bDisconnect = 0; 2354| 18.9k| } 2355| 19.0k| if (bDisconnect) ------------------ | Branch (2355:9): [True: 0, False: 19.0k] ------------------ 2356| 0| { 2357| 0| *piO = iO; 2358| 0| *pk = k; 2359| 0| } 2360| | 2361| 19.0k| return bDisconnect; 2362| 187k|} bIsMetalSalt: 2478| 28.4k|{ 2479| 28.4k| int type, val, k, iO, iC, j, neigh; 2480| 28.4k| int bDisconnect = 1; 2481| | 2482| | /* check for a metal atom: 2483| | metal atom should be connected and be a metal */ 2484| 28.4k| if (!(val = at[i].valence) || ------------------ | Branch (2484:9): [True: 12, False: 28.4k] ------------------ 2485| 28.4k| !(type = get_el_type(at[i].el_number)) || ------------------ | Branch (2485:9): [True: 22.8k, False: 5.59k] ------------------ 2486| 5.59k| !(type & IS_METAL)) ------------------ | | 82| 5.59k|#define IS_METAL 3 /* metal bitmap */ ------------------ | Branch (2486:9): [True: 0, False: 5.59k] ------------------ 2487| 22.8k| { 2488| 22.8k| bDisconnect = 0; /* reject */ 2489| 22.8k| } 2490| 5.59k| else if (at[i].num_H) ------------------ | Branch (2490:14): [True: 8, False: 5.58k] ------------------ 2491| | /* metal atom should not have adjacent H or multiple bonds or radical */ 2492| 8| { 2493| 8| bDisconnect = 0; /* reject */ 2494| 8| } 2495| 5.58k| else 2496| 5.58k| { 2497| | /* check valence */ 2498| 5.58k| if ((at[i].charge == 0 && ------------------ | Branch (2498:14): [True: 3.83k, False: 1.74k] ------------------ 2499| 3.83k| (((type & 1) && val == get_el_valence(at[i].el_number, 0, 0)) || ------------------ | Branch (2499:16): [True: 3.83k, False: 0] | Branch (2499:30): [True: 908, False: 2.92k] ------------------ 2500| 2.92k| ((type & 2) && val == get_el_valence(at[i].el_number, 0, 1)))) || ------------------ | Branch (2500:16): [True: 1.23k, False: 1.69k] | Branch (2500:30): [True: 267, False: 967] ------------------ 2501| 4.40k| (at[i].charge > 0 && ------------------ | Branch (2501:14): [True: 1.06k, False: 3.34k] ------------------ 2502| 1.06k| (type & 1) && val == get_el_valence(at[i].el_number, at[i].charge, 0))) /* djb-rwth: addressing LLVM warnings */ ------------------ | Branch (2502:14): [True: 1.06k, False: 0] | Branch (2502:28): [True: 0, False: 1.06k] ------------------ 2503| 1.17k| { 2504| 1.17k| ; /* accept */ 2505| 1.17k| } 2506| 4.40k| else 2507| 4.40k| { 2508| 4.40k| bDisconnect = 0; /* reject */ 2509| 4.40k| } 2510| 5.58k| } 2511| | 2512| 28.4k| if (bDisconnect) ------------------ | Branch (2512:9): [True: 1.17k, False: 27.2k] ------------------ 2513| 1.17k| { 2514| | /************************************************************************* 2515| | * | * 2516| | * check M neighbors. Disconnect if all neighbors are M-O-C# or M-O-C= * 2517| | * | * 2518| | *************************************************************************/ 2519| 1.17k| for (k = 0; k < at[i].valence; k++) ------------------ | Branch (2519:21): [True: 1.17k, False: 1] ------------------ 2520| 1.17k| { 2521| 1.17k| iO = at[i].neighbor[k]; 2522| | /* halogenide 2004-07-08 */ 2523| 1.17k| if ((at[iO].el_number == EL_NUMBER_F || ------------------ | | 16| 2.35k|#define EL_NUMBER_F ((U_CHAR)9) ------------------ | Branch (2523:18): [True: 5, False: 1.17k] ------------------ 2524| 1.17k| at[iO].el_number == EL_NUMBER_CL || ------------------ | | 20| 2.34k|#define EL_NUMBER_CL ((U_CHAR)17) ------------------ | Branch (2524:18): [True: 0, False: 1.17k] ------------------ 2525| 1.17k| at[iO].el_number == EL_NUMBER_BR || ------------------ | | 24| 2.34k|#define EL_NUMBER_BR ((U_CHAR)35) ------------------ | Branch (2525:18): [True: 1, False: 1.17k] ------------------ 2526| 1.17k| at[iO].el_number == EL_NUMBER_I) && ------------------ | | 27| 1.17k|#define EL_NUMBER_I ((U_CHAR)53) ------------------ | Branch (2526:18): [True: 6, False: 1.16k] ------------------ 2527| 12| at[iO].valence == 1 && at[iO].chem_bonds_valence == 1 && ------------------ | Branch (2527:17): [True: 2, False: 10] | Branch (2527:40): [True: 2, False: 0] ------------------ 2528| 2| !at[iO].charge && !(at[iO].radical && at[iO].radical != RADICAL_SINGLET) && !NUMH(at, iO)) ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ !at[iO].charge && !(at[iO].radical && at[iO].radical != RADICAL_SINGLET) && !NUMH(at, iO)) ------------------ | | 56| 1|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2528:17): [True: 1, False: 1] | Branch (2528:37): [True: 0, False: 1] | Branch (2528:55): [True: 0, False: 0] | Branch (2528:93): [True: 1, False: 0] ------------------ 2529| 1| { 2530| 1| ; /* found */ 2531| 1| } 2532| 1.17k| else 2533| 1.17k| { 2534| | /* -O-C= */ 2535| 1.17k| if (at[iO].el_number != EL_NUMBER_O || ------------------ | | 15| 2.35k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (2535:21): [True: 1.08k, False: 89] ------------------ 2536| 89| NUMH(at, iO) || ------------------ | | 56| 1.26k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 89|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ | | | Branch (56:21): [True: 0, False: 89] | | ------------------ ------------------ 2537| 89| at[iO].valence != 2 || ------------------ | Branch (2537:21): [True: 12, False: 77] ------------------ 2538| 77| at[iO].charge || ------------------ | Branch (2538:21): [True: 71, False: 6] ------------------ 2539| 6| (at[iO].radical && at[iO].radical != RADICAL_SINGLET) || ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2539:22): [True: 0, False: 6] | Branch (2539:40): [True: 0, False: 0] ------------------ 2540| 6| at[iO].valence != at[iO].chem_bonds_valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2540:21): [True: 0, False: 6] ------------------ 2541| 1.16k| { 2542| 1.16k| bDisconnect = 0; /* reject */ 2543| 1.16k| break; 2544| 1.16k| } 2545| 6| iC = at[iO].neighbor[at[iO].neighbor[0] == i]; 2546| 6| if (at[iC].el_number != EL_NUMBER_C || ------------------ | | 13| 12|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (2546:21): [True: 4, False: 2] ------------------ 2547| 2| at[iC].num_H || ------------------ | Branch (2547:21): [True: 0, False: 2] ------------------ 2548| 2| at[iC].chem_bonds_valence != 4 || ------------------ | Branch (2548:21): [True: 0, False: 2] ------------------ 2549| 2| at[iC].charge || ------------------ | Branch (2549:21): [True: 0, False: 2] ------------------ 2550| 2| (at[iC].radical && at[iC].radical != RADICAL_SINGLET) || ------------------ | | 75| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2550:22): [True: 0, False: 2] | Branch (2550:40): [True: 0, False: 0] ------------------ 2551| 2| at[iC].valence == at[iC].chem_bonds_valence) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (2551:21): [True: 0, False: 2] ------------------ 2552| 4| { 2553| 4| bDisconnect = 0; /* reject */ 2554| 4| break; 2555| 4| } 2556| 6| for (j = 0; j < at[iC].valence; j++) ------------------ | Branch (2556:29): [True: 5, False: 1] ------------------ 2557| 5| { 2558| 5| neigh = at[iC].neighbor[j]; 2559| 5| if (at[neigh].el_number == EL_NUMBER_H) ------------------ | | 11| 5|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (2559:25): [True: 1, False: 4] ------------------ 2560| 1| { 2561| 1| break; 2562| 1| } 2563| 5| } 2564| 2| if (j != at[iC].valence) ------------------ | Branch (2564:21): [True: 1, False: 1] ------------------ 2565| 1| { 2566| 1| bDisconnect = 0; /* reject */ 2567| 1| break; 2568| 1| } 2569| 2| } 2570| 1.17k| } 2571| 1.17k| } 2572| | 2573| 28.4k| return bDisconnect; 2574| 28.4k|} bIsMetalToDisconnect: 2683| 66.5k|{ 2684| 66.5k| int type, at_valence, num_H; 2685| | 2686| | /* 2687| | if ( !at[i].valence ) 2688| | */ 2689| | 2690| 66.5k| if (!(type = get_el_type(at[i].el_number)) || ------------------ | Branch (2690:9): [True: 58.3k, False: 8.21k] ------------------ 2691| 8.21k| !(type & IS_METAL)) ------------------ | | 82| 8.21k|#define IS_METAL 3 /* metal bitmap */ ------------------ | Branch (2691:9): [True: 0, False: 8.21k] ------------------ 2692| 58.3k| { 2693| 58.3k| return 0; 2694| 58.3k| } 2695| | 2696| 8.21k| num_H = NUMH(at, i); ------------------ | | 56| 8.21k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 8.21k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 2697| 8.21k| at_valence = num_H + at[i].chem_bonds_valence; 2698| | 2699| 8.21k| if (!at_valence) ------------------ | Branch (2699:9): [True: 0, False: 8.21k] ------------------ 2700| 0| { 2701| 0| return 0; /* nothing to disconnect */ 2702| 0| } 2703| | 2704| 8.21k| if (bCheckMetalValence) ------------------ | Branch (2704:9): [True: 0, False: 8.21k] ------------------ 2705| 0| { 2706| 0| if (abs(at[i].charge) > 1) ------------------ | Branch (2706:13): [True: 0, False: 0] ------------------ 2707| 0| { 2708| 0| return 1; /* multiple charges */ 2709| 0| } 2710| | 2711| 0| for (i = 0; i < 2 && (i & type); i++) ------------------ | Branch (2711:21): [True: 0, False: 0] | Branch (2711:30): [True: 0, False: 0] ------------------ 2712| 0| { 2713| 0| if (at_valence == get_el_valence( at[i].el_number, at[i].charge, i )) /* djb-rwth: fixing coverity ID #499532 -- unresolved issue -- revision required */ ------------------ | Branch (2713:17): [True: 0, False: 0] ------------------ 2714| 0| { 2715| 0| return 2; /* atom has normal valence */ 2716| 0| } 2717| 0| } 2718| 0| } 2719| | 2720| 8.21k| return 1; 2721| 8.21k|} bMayDisconnectMetals: 2727| 70.4k|{ 2728| 70.4k| int i, j, k, iO, num_changes, val, bRadOrMultBonds, num_impl_H = 0; 2729| 70.4k| S_CHAR num_explicit_H[NUM_H_ISOTOPES + 1]; 2730| 70.4k| inp_ATOM *at = orig_inp_data->at; 2731| 70.4k| int num_at = orig_inp_data->num_inp_atoms; 2732| 70.4k| int *nNumImplH = &orig_inp_data->bDisconnectCoord; 2733| | 2734| | /* check each atom */ 2735| 229k| for (i = 0, num_changes = 0; i < num_at; i++) ------------------ | Branch (2735:34): [True: 159k, False: 70.4k] ------------------ 2736| 159k| { 2737| | 2738| 159k| if (!(val = at[i].valence) && !NUMH(at, i)) ------------------ | | 56| 92.6k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 92.6k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (2738:13): [True: 92.6k, False: 66.5k] | Branch (2738:39): [True: 92.6k, False: 7] ------------------ 2739| 92.6k| { 2740| 92.6k| continue; /* disconnected atom */ 2741| 92.6k| } 2742| | 2743| 66.5k| bRadOrMultBonds = (val == 0) || ------------------ | Branch (2743:27): [True: 7, False: 66.5k] ------------------ 2744| 66.5k| (val != at[i].chem_bonds_valence) || /* a bond has higher multiplicity than 1 */ ------------------ | Branch (2744:27): [True: 35.0k, False: 31.4k] ------------------ 2745| 31.4k| (at[i].radical && at[i].radical != RADICAL_SINGLET); /* radical */ ------------------ | | 75| 3.00k|#define RADICAL_SINGLET 1 ------------------ | Branch (2745:28): [True: 3.00k, False: 28.4k] | Branch (2745:45): [True: 3.00k, False: 0] ------------------ 2746| | 2747| 66.5k| if (!bRadOrMultBonds && bIsAmmoniumSalt(at, i, &iO, &k, num_explicit_H)) ------------------ | Branch (2747:13): [True: 28.4k, False: 38.0k] | Branch (2747:33): [True: 0, False: 28.4k] ------------------ 2748| 0| { 2749| 0| ; 2750| 0| } 2751| 66.5k| else if (!bRadOrMultBonds && bIsMetalSalt(at, i)) ------------------ | Branch (2751:18): [True: 28.4k, False: 38.0k] | Branch (2751:38): [True: 1, False: 28.4k] ------------------ 2752| 1| { 2753| 1| ; 2754| 1| } 2755| 66.5k| else if (1 == (j = bIsMetalToDisconnect(at, i, bCheckMetalValence))) ------------------ | Branch (2755:18): [True: 8.21k, False: 58.3k] ------------------ 2756| 8.21k| { 2757| 8.21k| num_impl_H += NUMH(at, i); ------------------ | | 56| 8.21k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 8.21k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 2758| 8.21k| num_changes++; 2759| 8.21k| } 2760| 58.3k| else if (2 == j && bTautFlagsDone) ------------------ | Branch (2760:18): [True: 0, False: 58.3k] | Branch (2760:28): [True: 0, False: 0] ------------------ 2761| 0| { 2762| 0| *bTautFlagsDone |= TG_FLAG_CHECK_VALENCE_COORD_DONE; ------------------ | | 976| 0|#define TG_FLAG_CHECK_VALENCE_COORD_DONE 0x00000200 /* did not disconnect "coord. centers" with usual valence */ ------------------ 2763| 0| } 2764| 66.5k| } 2765| | 2766| 70.4k| if (nNumImplH) ------------------ | Branch (2766:9): [True: 70.4k, False: 0] ------------------ 2767| 70.4k| { 2768| 70.4k| *nNumImplH = num_changes ? num_impl_H + 1 : 0; ------------------ | Branch (2768:22): [True: 6.57k, False: 63.8k] ------------------ 2769| 70.4k| } 2770| | 2771| 70.4k| return num_changes; 2772| 70.4k|} add_DT_to_num_H: 3660| 106k|{ 3661| 106k| int i, j; 3662| 258k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3662:17): [True: 152k, False: 106k] ------------------ 3663| 152k| { 3664| 610k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 25| 610k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3664:21): [True: 458k, False: 152k] ------------------ 3665| 458k| { 3666| 458k| at[i].num_H += at[i].num_iso_H[j]; 3667| 458k| } 3668| 152k| } 3669| 106k| return 0; 3670| 106k|} remove_terminal_HDT: 3711| 106k|{ 3712| 106k| AT_NUMB *new_ord; 3713| 106k| inp_ATOM *new_at; 3714| 106k| char *p; 3715| 106k| static const char szHDT[] = "HDT"; 3716| 106k| static const int kMax = sizeof(szHDT); /* = 4 */ 3717| 106k| int ret = -1; 3718| 106k| int num_hydrogens = 0, num_H = 0; /* number of terminal H, D, T */ 3719| 106k| int i, j, k, n, m; 3720| 106k| int val; 3721| 106k| AT_RANK new_HydrogenAt_order[NUM_H_ISOTOPES + 1]; 3722| 106k| AT_RANK new_OtherNeigh_order[MAXVAL]; 3723| 106k| S_CHAR old_trans[MAX_NUM_STEREO_BONDS]; 3724| | 3725| 106k| int num_OtherNeigh, num_HydrogenAt; 3726| | 3727| 106k| new_ord = (AT_NUMB *)inchi_calloc(num_atoms, sizeof(new_ord[0])); /* changed malloc to calloc 9-11-2003 */ ------------------ | | 1146| 106k|#define inchi_calloc calloc ------------------ 3728| 106k| new_at = (inp_ATOM *)inchi_malloc(sizeof(new_at[0]) * num_atoms); ------------------ | | 1143| 106k|#define inchi_malloc malloc ------------------ 3729| 106k| if (!new_ord || !new_at) ------------------ | Branch (3729:9): [True: 0, False: 106k] | Branch (3729:21): [True: 0, False: 106k] ------------------ 3730| 0| { 3731| 0| goto exit_function; 3732| 0| } 3733| | 3734| | /* move H. D, T to the end of the list of atoms */ 3735| 265k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3735:17): [True: 159k, False: 106k] ------------------ 3736| 159k| { 3737| 159k| at[i].component = i; /* temporarily save original numbering */ 3738| | /* get k = temp. hydrogen isotope/non-hydrogen atom type: */ 3739| | /* k=0:H, k=2:D, k=3:T, k=4=kMax: not a hydrogen */ 3740| 159k| k = at[i].elname[1] ? kMax : (p = (char *)strchr(szHDT, at[i].elname[0])) ? (int)(p - szHDT) ------------------ | Branch (3740:13): [True: 40.9k, False: 118k] | Branch (3740:38): [True: 55.8k, False: 62.4k] ------------------ 3741| 118k| : kMax; 3742| | /* set hydrogen isotope atw differences */ 3743| | /* Notes: k-value of isotopic H is incremented to correct iso_atw_diff value later. */ 3744| | /* 1H isotope cannot be detected here. */ 3745| 159k| if (k == ATW_H || k == ATW_H + 1) ------------------ | | 26| 318k|#define ATW_H 1 /* hydrogen atomic weight */ ------------------ if (k == ATW_H || k == ATW_H + 1) ------------------ | | 26| 159k|#define ATW_H 1 /* hydrogen atomic weight */ ------------------ | Branch (3745:13): [True: 0, False: 159k] | Branch (3745:27): [True: 0, False: 159k] ------------------ 3746| 0| { 3747| | /* D or T, k = 1 or 2 */ 3748| 0| at[i].elname[0] = 'H'; /* hydrogen isotope */ 3749| 0| at[i].iso_atw_diff = ++k; /* increment k to make k = iso_atw_diff ( 2 for D, 3 for T ) */ 3750| 0| } 3751| 159k| num_H += (k != kMax && at[i].valence == 1 && at[i].chem_bonds_valence == 1 && !NUMH(at, i)); ------------------ | | 56| 7.24k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 7.24k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (3751:19): [True: 55.8k, False: 103k] | Branch (3751:32): [True: 7.24k, False: 48.5k] | Branch (3751:54): [True: 7.24k, False: 0] | Branch (3751:87): [True: 7.24k, False: 2] ------------------ 3752| 159k| } 3753| | 3754| | /* special case: HD, HT, DT, HH: the only non-isotopic H or 3755| | * the lightest isotopic H out of two is removed 3756| | * to become implicit (make the heavier H the "central atom"). 3757| | * Note: This must be consistent with MOL_FMT_to_atom() 3758| | * treatment of isotopic Hn aliases. 3759| | */ 3760| 106k| if (2 == num_H && 2 == num_atoms && ------------------ | Branch (3760:9): [True: 1.24k, False: 104k] | Branch (3760:23): [True: 4, False: 1.24k] ------------------ 3761| 4| !NUMH(at, 0) && !NUMH(at, 1) && ------------------ | | 56| 106k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 4|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ !NUMH(at, 0) && !NUMH(at, 1) && ------------------ | | 56| 106k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 4|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ | Branch (3761:9): [True: 4, False: 0] | Branch (3761:25): [True: 4, False: 0] ------------------ 3762| 4| (!keep_explicit_HDT || ------------------ | Branch (3762:10): [True: 4, False: 0] ------------------ 3763| 0| (!keep_explicit_HDT[0] && ------------------ | Branch (3763:11): [True: 0, False: 0] ------------------ 3764| 0| !keep_explicit_HDT[1]))) ------------------ | Branch (3764:14): [True: 0, False: 0] ------------------ 3765| 4| { 3766| | 3767| 4| if (at[0].iso_atw_diff >= at[1].iso_atw_diff) ------------------ | Branch (3767:13): [True: 4, False: 0] ------------------ 3768| 4| { 3769| 4| new_ord[0] = 0; 3770| 4| new_ord[1] = 1; 3771| 4| } 3772| 0| else 3773| 0| { 3774| 0| new_ord[0] = 1; 3775| 0| new_ord[1] = 0; 3776| 0| } 3777| 4| if (at[new_ord[1]].charge) ------------------ | Branch (3777:13): [True: 0, False: 4] ------------------ 3778| 0| { 3779| 0| at[new_ord[0]].charge += at[new_ord[1]].charge; 3780| 0| at[new_ord[1]].charge = 0; 3781| 0| } 3782| 4| new_at[new_ord[0]] = at[0]; 3783| 4| new_at[new_ord[1]] = at[1]; 3784| 4| num_hydrogens = 1; 3785| 4| } 3786| 106k| else 3787| 106k| { 3788| | /* general case except H-H */ 3789| 265k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3789:21): [True: 159k, False: 106k] ------------------ 3790| 159k| { 3791| 159k| k = (at[i].elname[1] || NUMH(at, i)) ? kMax : (at[i].elname[0] == 'H') ? at[i].iso_atw_diff ------------------ | | 56| 118k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 118k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ | | | Branch (56:21): [True: 537, False: 117k] | | ------------------ ------------------ | Branch (3791:18): [True: 40.9k, False: 118k] | Branch (3791:59): [True: 55.8k, False: 61.8k] ------------------ 3792| 117k| : kMax; 3793| 159k| n = (int)at[i].neighbor[0]; 3794| 159k| if (k < kMax && at[i].valence == 1 && at[i].chem_bonds_valence == 1 && ------------------ | Branch (3794:17): [True: 55.8k, False: 103k] | Branch (3794:29): [True: 7.23k, False: 48.5k] | Branch (3794:51): [True: 7.23k, False: 0] ------------------ 3795| 7.23k| (!keep_explicit_HDT || !keep_explicit_HDT[i]) && ------------------ | Branch (3795:18): [True: 7.23k, False: 0] | Branch (3795:40): [True: 0, False: 0] ------------------ 3796| | /* the order of comparison is important */ 3797| 7.23k| ((n > i) /* at[n] has not been encountered yet*/ || ------------------ | Branch (3797:18): [True: 708, False: 6.52k] ------------------ 3798| 6.52k| (int)new_ord[n] < num_atoms - num_hydrogens) /* at[n] might have been encountered; it has not been moved */ && ------------------ | Branch (3798:21): [True: 6.52k, False: 0] ------------------ 3799| 7.23k| (!is_el_a_metal(at[n].el_number) || is_only_HDT_neighbors(at, num_atoms, n))/*@nnuk*/) ------------------ | Branch (3799:18): [True: 6.11k, False: 1.11k] | Branch (3799:53): [True: 337, False: 782] ------------------ 3800| 6.45k| { 3801| | /* found an explicit terminal hydrogen */ 3802| 6.45k| num_hydrogens++; 3803| 6.45k| if (k == 0 && ATW_H <= at[i].iso_atw_diff && at[i].iso_atw_diff < ATW_H + NUM_H_ISOTOPES) ------------------ | | 26| 6.40k|#define ATW_H 1 /* hydrogen atomic weight */ ------------------ if (k == 0 && ATW_H <= at[i].iso_atw_diff && at[i].iso_atw_diff < ATW_H + NUM_H_ISOTOPES) ------------------ | | 26| 0|#define ATW_H 1 /* hydrogen atomic weight */ ------------------ if (k == 0 && ATW_H <= at[i].iso_atw_diff && at[i].iso_atw_diff < ATW_H + NUM_H_ISOTOPES) ------------------ | | 25| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3803:21): [True: 6.40k, False: 44] | Branch (3803:31): [True: 0, False: 6.40k] | Branch (3803:62): [True: 0, False: 0] ------------------ 3804| 0| { 3805| 0| k = at[i].iso_atw_diff; /* H isotope has already been marked above or elsewhere */ /* djb-rwth: ignoring LLVM warning: variable used */ 3806| 0| } 3807| 6.45k| if (at[i].charge) ------------------ | Branch (3807:21): [True: 2, False: 6.44k] ------------------ 3808| 2| { 3809| | /* transfer charge from the hydrogen */ 3810| 2| at[n].charge += at[i].charge; 3811| 2| at[i].charge = 0; 3812| 2| if (bFixTermHChrg) ------------------ | Branch (3812:25): [True: 2, False: 0] ------------------ 3813| 2| { 3814| | /* Fixed bug (July 6, 2008 IPl) : 3815| | if terminal H was charged (not neutralized before call of remove_terminal_HDT) 3816| | and had an ordering number > than that of heavy-atom neighbour, then 3817| | charge on neighbour atom was not adjusted (though charge on H was removed). */ 3818| 2| if (i > n) ------------------ | Branch (3818:29): [True: 2, False: 0] ------------------ 3819| | /* new_at[new_ord[n]] has been created and filled already */ 3820| 2| new_at[new_ord[n]].charge = at[n].charge; 3821| 2| } 3822| 2| } 3823| 6.45k| new_ord[i] = num_atoms - num_hydrogens; /* move hydrogens to the end of the list */ 3824| 6.45k| } 3825| 152k| else 3826| 152k| { 3827| | /* atom is not an explicit terminal hydrogen */ 3828| 152k| new_ord[i] = i - num_hydrogens; /* adjust non-hydrogens positions */ 3829| 152k| } 3830| | 3831| | /* copy atom to the new position */ 3832| 159k| new_at[new_ord[i]] = at[i]; 3833| 159k| } /* i */ 3834| 106k| } /* general case except H-H */ 3835| | 3836| 106k| if (num_hydrogens) ------------------ | Branch (3836:9): [True: 5.00k, False: 101k] ------------------ 3837| 5.00k| { 3838| 5.00k| int num_others = num_atoms - num_hydrogens; /* atoms which are not terminal H, D, T */ 3839| 5.00k| if (num_hydrogens > 1) ------------------ | Branch (3839:13): [True: 1.28k, False: 3.71k] ------------------ 3840| 1.28k| { 3841| | /* sort hydrogen isotopes in ascending order, */ 3842| | /* orig, numbers being the secondary sorting key */ 3843| 1.28k| qsort(new_at + num_others, num_hydrogens, sizeof(new_at[0]), cmp_iso_atw_diff_component_no); 3844| 1.28k| } 3845| | /* save new numbering of hydrogen atoms using temporarily saved orig numbering */ 3846| 11.4k| for (i = num_others; i < num_atoms; i++) ------------------ | Branch (3846:30): [True: 6.45k, False: 5.00k] ------------------ 3847| 6.45k| { 3848| 6.45k| new_ord[(int)new_at[i].component] = i; 3849| 6.45k| } 3850| | 3851| | /* renumber neighbors according to new_ord[] and detach terminal hydrogens */ 3852| 25.7k| for (i = 0; i < num_others; i++) ------------------ | Branch (3852:21): [True: 20.7k, False: 5.00k] ------------------ 3853| 20.7k| { 3854| 20.7k| memset(new_HydrogenAt_order, 0, sizeof(new_HydrogenAt_order)); /* djb-rwth: memset_s C11/Annex K variant? */ 3855| 20.7k| memset(new_OtherNeigh_order, 0, sizeof(new_OtherNeigh_order)); /* djb-rwth: memset_s C11/Annex K variant? */ 3856| 20.7k| num_OtherNeigh = 0; 3857| 20.7k| num_HydrogenAt = 0; 3858| 20.7k| num_H = 0; 3859| | 3860| 20.9k| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 873| 41.9k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3860:25): [True: 20.9k, False: 0] | Branch (3860:53): [True: 186, False: 20.7k] ------------------ 3861| 186| { 3862| 186| old_trans[m] = 2 - (new_at[i].sn_ord[m] + new_at[i].sb_ord[m] + (new_at[i].sn_ord[m] > new_at[i].sb_ord[m])) % 2; 3863| 186| } 3864| | 3865| 62.7k| for (k = val = 0; k < new_at[i].valence; k++) /* djb-rwth: removing redundant variables/code */ ------------------ | Branch (3865:31): [True: 41.9k, False: 20.7k] ------------------ 3866| 41.9k| { 3867| 41.9k| if (num_others <= (n = new_ord[new_at[i].neighbor[k]])) ------------------ | Branch (3867:21): [True: 6.45k, False: 35.5k] ------------------ 3868| 6.45k| { 3869| | /* discovered neighbor = disconnected explicit hydrogen 3870| | * i = new atom new_at[i] ordering number 3871| | * n = new number of the explicit H 3872| | * k = ordering number of the explicit H in new_at[i] adjacency list 3873| | */ 3874| 6.45k| if (0 < new_at[n].iso_atw_diff && new_at[n].iso_atw_diff < ATW_H + NUM_H_ISOTOPES) ------------------ | | 26| 35|#define ATW_H 1 /* hydrogen atomic weight */ ------------------ if (0 < new_at[n].iso_atw_diff && new_at[n].iso_atw_diff < ATW_H + NUM_H_ISOTOPES) ------------------ | | 25| 35|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3874:25): [True: 35, False: 6.41k] | Branch (3874:55): [True: 35, False: 0] ------------------ 3875| 35| { 3876| | /* make explicit isotopic H implicit */ 3877| 35| new_at[i].num_iso_H[new_at[n].iso_atw_diff - 1]++; /* isotopic H */ 3878| 35| num_HydrogenAt += !new_HydrogenAt_order[new_at[n].iso_atw_diff]; 3879| 35| new_HydrogenAt_order[new_at[n].iso_atw_diff] = k + 1; 3880| 35| } 3881| 6.41k| else 3882| 6.41k| { 3883| | /* make explicit non-isotopic H implicit */ 3884| 6.41k| new_at[i].num_H++; /* non-isotopic H */ 3885| 6.41k| num_HydrogenAt += !num_H; 3886| 6.41k| num_H++; 3887| 6.41k| new_HydrogenAt_order[0] = k + 1; 3888| 6.41k| } 3889| | /* decrement chem. bonds valence because one bond is removed */ 3890| 6.45k| new_at[i].chem_bonds_valence = inchi_max(0, new_at[i].chem_bonds_valence - 1); ------------------ | | 138| 6.45k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 6.45k] | | ------------------ ------------------ 3891| 6.45k| new_at[n].neighbor[0] = i; /* update removed hydrogen neighbor number */ 3892| 6.45k| if (new_at[i].sb_parity[0]) ------------------ | Branch (3892:25): [True: 103, False: 6.35k] ------------------ 3893| 103| { 3894| | /* if the removed H is an SB neighbor then mark it as removed */ 3895| 206| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 873| 412|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3895:37): [True: 206, False: 0] | Branch (3895:65): [True: 103, False: 103] ------------------ 3896| 103| { 3897| 103| if (k == (int)new_at[i].sn_ord[m]) ------------------ | Branch (3897:33): [True: 84, False: 19] ------------------ 3898| 84| { 3899| 84| new_at[i].sn_ord[m] = -(new_at[n].iso_atw_diff + 1); 3900| | /* means the SB neighbor has been removed; (-4)=H, (-3)=1H, (-2)=D, (-1)=T */ 3901| 84| } 3902| 103| } 3903| 103| } 3904| 6.45k| } 3905| 35.5k| else 3906| 35.5k| { 3907| | /* discovered a regular (not an explicit H) neighbor */ 3908| 35.5k| if (new_at[i].sb_parity[0]) ------------------ | Branch (3908:25): [True: 298, False: 35.2k] ------------------ 3909| 298| { 3910| 298| if (num_OtherNeigh < MAX_NUM_STEREO_BONDS) ------------------ | | 873| 298|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3910:29): [True: 298, False: 0] ------------------ 3911| 298| { 3912| 298| new_OtherNeigh_order[num_OtherNeigh] = k + 1; 3913| 298| } 3914| 298| num_OtherNeigh++; /* increment outside of if() to detect overflow */ 3915| 298| if (val != k) ------------------ | Branch (3915:29): [True: 57, False: 241] ------------------ 3916| 57| { 3917| | /* store new stereobond and sb-neighbor ordering numbers */ 3918| 114| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 873| 228|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3918:41): [True: 114, False: 0] | Branch (3918:69): [True: 57, False: 57] ------------------ 3919| 57| { 3920| 57| if (k == (int)new_at[i].sb_ord[m]) ------------------ | Branch (3920:37): [True: 45, False: 12] ------------------ 3921| 45| new_at[i].sb_ord[m] = val; 3922| 12| else if (k == (int)new_at[i].sn_ord[m]) ------------------ | Branch (3922:42): [True: 0, False: 12] ------------------ 3923| 0| new_at[i].sn_ord[m] = val; 3924| 57| } 3925| 57| } 3926| 298| } 3927| 35.5k| new_at[i].neighbor[val] = new_ord[new_at[i].neighbor[k]]; 3928| 35.5k| new_at[i].bond_type[val] = new_at[i].bond_type[k]; 3929| 35.5k| new_at[i].bond_stereo[val] = new_at[i].bond_stereo[k]; 3930| 35.5k| val++; 3931| 35.5k| } 3932| 41.9k| } 3933| 20.7k| if (new_at[i].valence > val && new_at[i].sb_parity[0]) ------------------ | Branch (3933:17): [True: 6.11k, False: 14.6k] | Branch (3933:44): [True: 85, False: 6.02k] ------------------ 3934| 85| { 3935| 85| if (num_HydrogenAt == new_at[i].valence - val && num_HydrogenAt + num_OtherNeigh <= MAXVAL) ------------------ | | 60| 74|#define MAXVAL 50 /* maximum valence */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (3935:21): [True: 74, False: 11] | Branch (3935:66): [True: 74, False: 0] ------------------ 3936| 74| { 3937| | /* recalculate parity so that it would describe neighbor sequence H,1H,D,T,neigh[0],neigh[1]... */ 3938| 74| memmove(new_OtherNeigh_order + num_HydrogenAt, new_OtherNeigh_order, num_OtherNeigh * sizeof(new_OtherNeigh_order[0])); 3939| 370| for (k = 0, j = 1; k <= NUM_H_ISOTOPES; k++) ------------------ | | 25| 370|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3939:40): [True: 296, False: 74] ------------------ 3940| 296| { 3941| 296| if (new_HydrogenAt_order[k] && (num_HydrogenAt - j < MAXVAL) && (num_HydrogenAt - j >= 0)) /* djb-rwth: fixing buffer overruns */ ------------------ | | 60| 81|#define MAXVAL 50 /* maximum valence */ /* @nnuk : Changed from 20 -> 50 for testing purposes, to account for some structures with one atom having more than 20 bonds */ ------------------ | Branch (3941:29): [True: 81, False: 215] | Branch (3941:56): [True: 81, False: 0] | Branch (3941:89): [True: 81, False: 0] ------------------ 3942| 81| { 3943| 81| new_OtherNeigh_order[num_HydrogenAt - j] = new_HydrogenAt_order[k]; 3944| 162| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 873| 324|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3944:41): [True: 162, False: 0] | Branch (3944:69): [True: 81, False: 81] ------------------ 3945| 81| { 3946| 81| if ((int)new_at[i].sn_ord[m] == -(k + 1)) ------------------ | Branch (3946:37): [True: 71, False: 10] ------------------ 3947| 71| { 3948| 71| new_at[i].sn_ord[m] = -j; 3949| | /* negative means explicit H isotope ord are 3950| | (contiguously) in front of the adjacency list */ 3951| 71| } 3952| 81| } 3953| 81| j++; 3954| 81| } 3955| 296| } 3956| | /* at this point new_OtherNeigh_order[] contains 3957| | incremented old ordering numbers in new order */ 3958| 74| k = insertions_sort_AT_RANK(new_OtherNeigh_order, num_HydrogenAt + num_OtherNeigh); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 3959| | /* djb-rwth: removing redundant code */ 3960| | /*if ( k ) {*/ 3961| | /* 3962| | for ( m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m ++ ) { 3963| | if ( PARITY_WELL_DEF(new_at[i].sb_parity[m]) ) { 3964| | if ( old_trans[m] != 2 - (4 + new_at[i].sn_ord[m] + new_at[i].sb_ord[m] + (new_at[i].sn_ord[m] > new_at[i].sb_ord[m]))%2 ) { 3965| | new_at[i].sb_parity[m] = 3 - new_at[i].sb_parity[m]; 3966| | } 3967| | } 3968| | } 3969| | */ 3970| | /*}*/ 3971| 74| } 3972| 85| } 3973| 20.7k| new_at[i].valence = val; 3974| 20.7k| } 3975| 5.00k| memcpy(at, new_at, sizeof(at[0]) * num_atoms); 3976| 5.00k| ret = num_others; 3977| 5.00k| } 3978| 101k| else 3979| 101k| { 3980| 101k| ret = num_atoms; 3981| 101k| } 3982| | 3983| 106k|exit_function: 3984| | 3985| 106k| if (new_ord) ------------------ | Branch (3985:9): [True: 106k, False: 0] ------------------ 3986| 106k| { 3987| 106k| inchi_free(new_ord); ------------------ | | 1152| 106k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 106k, False: 0] | | | Branch (1152:50): [Folded, False: 106k] | | ------------------ ------------------ 3988| 106k| } 3989| 106k| if (new_at) ------------------ | Branch (3989:9): [True: 106k, False: 0] ------------------ 3990| 106k| { 3991| 106k| inchi_free(new_at); ------------------ | | 1152| 106k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 106k, False: 0] | | | Branch (1152:50): [Folded, False: 106k] | | ------------------ ------------------ 3992| 106k| } 3993| | 3994| 106k| return ret; 3995| 106k|} get_iat_number: 4018| 1.06M|{ 4019| 1.06M| switch (el_number) 4020| 1.06M| { 4021| 109k| case EL_NUMBER_H: ------------------ | | 11| 109k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (4021:5): [True: 109k, False: 951k] ------------------ 4022| 109k| return IAT_H; 4023| 106k| case EL_NUMBER_C: ------------------ | | 13| 106k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (4023:5): [True: 106k, False: 954k] ------------------ 4024| 106k| return IAT_C; 4025| 108k| case EL_NUMBER_N: ------------------ | | 14| 108k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (4025:5): [True: 108k, False: 951k] ------------------ 4026| 108k| return IAT_N; 4027| 19.5k| case EL_NUMBER_P: ------------------ | | 18| 19.5k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (4027:5): [True: 19.5k, False: 1.04M] ------------------ 4028| 19.5k| return IAT_P; 4029| 194k| case EL_NUMBER_O: ------------------ | | 15| 194k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (4029:5): [True: 194k, False: 865k] ------------------ 4030| 194k| return IAT_O; 4031| 42.6k| case EL_NUMBER_S: ------------------ | | 19| 42.6k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (4031:5): [True: 42.6k, False: 1.01M] ------------------ 4032| 42.6k| return IAT_S; 4033| 2.49k| case EL_NUMBER_SE: ------------------ | | 23| 2.49k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (4033:5): [True: 2.49k, False: 1.05M] ------------------ 4034| 2.49k| return IAT_Se; 4035| 3.75k| case EL_NUMBER_TE: ------------------ | | 26| 3.75k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (4035:5): [True: 3.75k, False: 1.05M] ------------------ 4036| 3.75k| return IAT_Te; 4037| 11.3k| case EL_NUMBER_F: ------------------ | | 16| 11.3k|#define EL_NUMBER_F ((U_CHAR)9) ------------------ | Branch (4037:5): [True: 11.3k, False: 1.04M] ------------------ 4038| 11.3k| return IAT_F; 4039| 438| case EL_NUMBER_CL: ------------------ | | 20| 438|#define EL_NUMBER_CL ((U_CHAR)17) ------------------ | Branch (4039:5): [True: 438, False: 1.06M] ------------------ 4040| 438| return IAT_Cl; 4041| 1.06k| case EL_NUMBER_BR: ------------------ | | 24| 1.06k|#define EL_NUMBER_BR ((U_CHAR)35) ------------------ | Branch (4041:5): [True: 1.06k, False: 1.05M] ------------------ 4042| 1.06k| return IAT_Br; 4043| 10.6k| case EL_NUMBER_I: ------------------ | | 27| 10.6k|#define EL_NUMBER_I ((U_CHAR)53) ------------------ | Branch (4043:5): [True: 10.6k, False: 1.04M] ------------------ 4044| 10.6k| return IAT_I; 4045| 448k| default: ------------------ | Branch (4045:5): [True: 448k, False: 611k] ------------------ 4046| 448k| return -1; 4047| 1.06M| } 4048| 1.06M|} getElValenceforMolecularInorganics: 4069| 8.64k|{ 4070| 8.64k| if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || val_num >= MAX_NUM_VALENCES) ------------------ | | 571| 17.2k|#define MIN_ATOM_CHARGE (-2) ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || val_num >= MAX_NUM_VALENCES) ------------------ | | 572| 17.2k|#define MAX_ATOM_CHARGE 2 ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || val_num >= MAX_NUM_VALENCES) ------------------ | | 575| 8.64k|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (4070:9): [True: 0, False: 8.64k] | Branch (4070:37): [True: 0, False: 8.64k] | Branch (4070:65): [True: 0, False: 8.64k] ------------------ 4071| 0| { 4072| 0| return 0; 4073| 0| } 4074| | 4075| 8.64k| return (int) MolecularInorganicsArray[nPeriodicNum > 1 ? nPeriodicNum + 1 : 0].cValence[NEUTRAL_STATE + charge][val_num]; ------------------ | | 573| 8.64k|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) | | ------------------ | | | | 571| 8.64k|#define MIN_ATOM_CHARGE (-2) | | ------------------ ------------------ | Branch (4075:43): [True: 8.64k, False: 0] ------------------ 4076| 8.64k|} getElTypeforMolecularInorganics: 4083| 6.37k|{ 4084| 6.37k| return MolecularInorganicsArray[nPeriodicNum + 1].nType; 4085| 6.37k|} MolecularInorganicsIsMetalToDisconnect: 4093| 6.37k|{ 4094| | 4095| 6.37k| int at_valence, num_H; 4096| 6.37k| int type = getElTypeforMolecularInorganics(at[atom_idx].el_number); 4097| 6.37k| int j; 4098| | 4099| | /* Calculate the actual valence of the atom 4100| | * It means that the total bounding capacity 4101| | * of the atom has to be taken into account 4102| | * which will further get equated within the 4103| | * elements array to a metal atom(neutral or an ion) */ 4104| 6.37k| num_H = NUMH(at, atom_idx); ------------------ | | 56| 6.37k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 6.37k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 4105| 6.37k| at_valence = num_H + at[atom_idx].chem_bonds_valence; 4106| | 4107| 6.37k| if (!at_valence || (abs(at[atom_idx].charge) > 1)) ------------------ | Branch (4107:9): [True: 2, False: 6.37k] | Branch (4107:24): [True: 707, False: 5.66k] ------------------ 4108| 709| { 4109| 709| return 0; /* Isolated metal atom or Atom has multiple charges */ 4110| 709| } 4111| | 4112| | /* Check if the valence matches a known normal valence */ 4113| 24.9k| for (j = 0; j < 4; j++) ------------------ | Branch (4113:17): [True: 20.1k, False: 4.75k] ------------------ 4114| 20.1k| { 4115| 20.1k| const int bitmask = (1 << j); /* Create bitmask for the j-th bit */ 4116| 20.1k| const bool is_valence_state_valid = (bitmask & type) != 0; /* Check if the j-th valence state is allowed */ 4117| | 4118| 20.1k| if (is_valence_state_valid && at_valence == getElValenceforMolecularInorganics(at[atom_idx].el_number, at[atom_idx].charge, j)) ------------------ | Branch (4118:13): [True: 8.64k, False: 11.5k] | Branch (4118:39): [True: 911, False: 7.73k] ------------------ 4119| 911| { 4120| 911| return 1; /* Atom has normal valence follows disconnection logic if applicable */ 4121| 911| } 4122| 20.1k| } 4123| | 4124| | /* Default: Valence greater than usual or the atom is isolated hence no disconnection */ 4125| 4.75k| return 0; 4126| 5.66k|} shouldBondBeCut: 4137| 747|{ 4138| 747| int index1, index2, binaryValue; 4139| | 4140| | /* Bounds-check the 1-based periodic numbers before indexing the 4141| | * NUM_ELEMENTS x NUM_ELEMENTS table. An out-of-range value (e.g. a 4142| | * pseudo-atom with el_number 0, or a number beyond the table) would 4143| | * otherwise read out of bounds. Default to 0 = keep the bond. */ 4144| 747| if (atom1 < 1 || atom1 > NUM_ELEMENTS || atom2 < 1 || atom2 > NUM_ELEMENTS) ------------------ | | 12| 1.49k|#define NUM_ELEMENTS 118 /* Adjust according to the number of elements in the array */ ------------------ if (atom1 < 1 || atom1 > NUM_ELEMENTS || atom2 < 1 || atom2 > NUM_ELEMENTS) ------------------ | | 12| 747|#define NUM_ELEMENTS 118 /* Adjust according to the number of elements in the array */ ------------------ | Branch (4144:9): [True: 0, False: 747] | Branch (4144:22): [True: 0, False: 747] | Branch (4144:46): [True: 0, False: 747] | Branch (4144:59): [True: 0, False: 747] ------------------ 4145| 0| { 4146| 0| return 0; 4147| 0| } 4148| | 4149| | /* Get the indices corresponding to the atomic numbers */ 4150| 747| index1 = atom1 - 1; 4151| 747| index2 = atom2 - 1; 4152| | 4153| | /* Retrieve the binary value from the binary array */ 4154| 747| binaryValue = binaryArrayMolecularInorganics[index1][index2]; 4155| | 4156| | /* Output for debugging purposes */ 4157| | /*printf("Electronegativity binary value between the atom and it's neighbour is: %d\n", binaryValue); */ 4158| | 4159| 747| return binaryValue; 4160| 747|} updateNeighborListMolecularInorganics: 4168| 358|{ 4169| | 4170| 358| int valence = at[atom_idx].valence; 4171| 358| int i, j; 4172| | 4173| 721| for (i = 0; i < valence; i++) ------------------ | Branch (4173:17): [True: 363, False: 358] ------------------ 4174| 363| { 4175| 363| if (at[atom_idx].neighbor[i] == neighbor_idx) ------------------ | Branch (4175:13): [True: 0, False: 363] ------------------ 4176| 0| { 4177| | /* Shift remaining neighbors to fill the gap */ 4178| 0| for (j = i; j < valence - 1; j++) ------------------ | Branch (4178:25): [True: 0, False: 0] ------------------ 4179| 0| { 4180| 0| at[atom_idx].neighbor[j] = at[atom_idx].neighbor[j + 1]; 4181| 0| } 4182| 0| at[atom_idx].valence--; /* Reduce the valence (number of neighbors) */ 4183| | 4184| 0| break; 4185| 0| } 4186| 363| } 4187| 358|} MolecularInorganicsPreprocessing: 4393| 70.4k|{ 4394| 70.4k| int ret_code = 0; 4395| | 4396| 70.4k| if (!ip || !orig_at_data || !orig_at_data->at) ------------------ | Branch (4396:9): [True: 0, False: 70.4k] | Branch (4396:16): [True: 0, False: 70.4k] | Branch (4396:33): [True: 0, False: 70.4k] ------------------ 4397| 0| { 4398| 0| return -1; 4399| 0| } 4400| | 4401| 70.4k| if (!ip->bMolecularInorganics) ------------------ | Branch (4401:9): [True: 0, False: 70.4k] ------------------ 4402| 0| { 4403| 0| return -1; 4404| 0| } 4405| | 4406| 70.4k| ip->bMolecularInorganicsReconnectedInChI = 0; /*@nnuk: flag reset*/ 4407| | 4408| | /* Pointer to the array of input atoms from the original atom data structure */ 4409| 70.4k| inp_ATOM *at = orig_at_data->at; 4410| | 4411| | /* Total number of input atoms present in the molecular structure */ 4412| 70.4k| int num_at = orig_at_data->num_inp_atoms; 4413| | 4414| | /* Pointer to the array storing the old component numbers for each atom, used for tracking connectivity */ 4415| 70.4k| AT_NUMB *nOldCompNumber = orig_at_data->nOldCompNumber; 4416| | 4417| | /* Track number of disconnections */ 4418| 70.4k| int num_disconnected = 0; 4419| | 4420| | /* variables declared */ 4421| 70.4k| int i, j, n, k; 4422| 70.4k| int binaryValue; 4423| 70.4k| int disconnectDecision; 4424| 70.4k| int neigh_pos; 4425| 70.4k| int neighbor_idx; 4426| 70.4k| int num_metals; 4427| 70.4k| int all_metal_atoms_terminal; 4428| 70.4k| int has_single_bond_to_metal; 4429| 70.4k| int keep_all_metal_bonds; 4430| | 4431| | /* memory allocation */ 4432| 70.4k| S_CHAR* dfs_visited = (S_CHAR*)inchi_calloc(num_at, sizeof(S_CHAR)); ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 4433| 70.4k| int* dfs_stack = (int*)inchi_malloc(num_at * sizeof(int)); ------------------ | | 1143| 70.4k|#define inchi_malloc malloc ------------------ 4434| | 4435| 70.4k| if (!dfs_visited || !dfs_stack) ------------------ | Branch (4435:9): [True: 0, False: 70.4k] | Branch (4435:25): [True: 0, False: 70.4k] ------------------ 4436| 0| { 4437| 0| ret_code = -1; 4438| 0| goto cleanup; 4439| 0| } 4440| | 4441| | /* Before disconnection, invoke ammonium salt functions */ 4442| 229k| for (j = 0; j < num_at; j++) ------------------ | Branch (4442:17): [True: 159k, False: 70.4k] ------------------ 4443| 159k| { 4444| 159k| int piO, pk; 4445| 159k| S_CHAR num_explicit_H[NUM_H_ISOTOPES + 1]; 4446| | 4447| 159k| if (bIsAmmoniumSalt(at, j, &piO, &pk, num_explicit_H)) ------------------ | Branch (4447:13): [True: 0, False: 159k] ------------------ 4448| 0| { 4449| 0| DisconnectAmmoniumSalt(at, j, piO, pk, num_explicit_H); 4450| 0| } 4451| 159k| } 4452| | 4453| | /* 4454| | * Detect ring systems before the charge-separated bond pass so that a 4455| | * qualifying metal-containing chelate ring is not disconnected before 4456| | * the chelate protection rule can be applied. 4457| | */ 4458| 70.4k| MarkRingSystemsInp(at, num_at, 0); 4459| | 4460| | /* Disconnect charge-separated metal-ligand bonds, preserving the drawn 4461| | * formal charges. A metal and ligand carrying opposite formal charges 4462| | * across a single (type 1) or coordinative (type 9) bond depict an ionic 4463| | * interaction (e.g. M(2+) ... L(2-)) and must split into the drawn ions 4464| | * regardless of the metal's nominal valence or the presence of other 4465| | * metals in the same component - the heuristics in the disconnection loop 4466| | * below would otherwise keep these bonds connected. DisconnectInpAtBond 4467| | * also decrements valence and chem_bonds_valence on both atoms (a type-9 4468| | * bond counts as single), so no charge is added or removed here: each ion 4469| | * keeps exactly the charge drawn in the input. Higher-order bonds (e.g. a 4470| | * drawn M=O double bond) are genuine covalent bonds and are left intact. 4471| | * 4472| | * 4473| | * An exception is made for non-Group-1/2 metals that belong to a ring 4474| | * containing at least three carbon, nitrogen, or oxygen atoms. Such bonds 4475| | * form part of a qualifying chelate ring and must remain connected.*/ 4476| 229k| for (i = 0; i < num_at; i++) ------------------ | Branch (4476:17): [True: 159k, False: 70.4k] ------------------ 4477| 159k| { 4478| 282k| for (k = 0; k < at[i].valence; ) ------------------ | Branch (4478:21): [True: 123k, False: 159k] ------------------ 4479| 123k| { 4480| 123k| int metal_idx; 4481| 123k| int ring_cno_count = 0; 4482| | 4483| 123k| j = at[i].neighbor[k]; 4484| | 4485| | /* Process each undirected bond once, from its lower-indexed atom, 4486| | * and only charge-separated metal/non-metal single or coordinative 4487| | * bonds. */ 4488| 123k| if (j <= i || j >= num_at || ------------------ | Branch (4488:17): [True: 61.0k, False: 62.0k] | Branch (4488:27): [True: 0, False: 62.0k] ------------------ 4489| 62.0k| (at[i].bond_type[k] != COORDINATIVE_BOND && ------------------ | | 264| 124k|#define COORDINATIVE_BOND 9 /* (@nnuk) introduction of bond_type = 9 (Coordinative Bond) */ ------------------ | Branch (4489:18): [True: 62.0k, False: 0] ------------------ 4490| 62.0k| at[i].bond_type[k] != BOND_TYPE_SINGLE) || ------------------ | | 32| 62.0k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (4490:21): [True: 19.7k, False: 42.3k] ------------------ 4491| 42.3k| is_el_a_metal(at[i].el_number) == ------------------ | Branch (4491:17): [True: 32.1k, False: 10.1k] ------------------ 4492| 42.3k| is_el_a_metal(at[j].el_number) || 4493| 10.1k| !((at[i].charge > 0 && at[j].charge < 0) || ------------------ | Branch (4493:20): [True: 2.63k, False: 7.53k] | Branch (4493:40): [True: 691, False: 1.94k] ------------------ 4494| 9.47k| (at[i].charge < 0 && at[j].charge > 0))) ------------------ | Branch (4494:22): [True: 981, False: 8.49k] | Branch (4494:42): [True: 321, False: 660] ------------------ 4495| 122k| { 4496| 122k| k++; 4497| 122k| continue; 4498| 122k| } 4499| | 4500| 1.01k| metal_idx = is_el_a_metal(at[i].el_number) ? i : j; ------------------ | Branch (4500:25): [True: 445, False: 567] ------------------ 4501| | 4502| | /* 4503| | * Deliberately apply the chelate-ring protection in this preliminary 4504| | * charge-separated bond pass. Without this check, an explicitly charged 4505| | * chelate of a non-Group-1/2 metal could be disconnected before the main 4506| | * decision-tree pass evaluates whether its metal bonds must be retained. 4507| | * 4508| | * The ring criterion follows the 2026-07-16 Molecular Inorganics decision 4509| | * tree: the metal-containing ring system must contain at least three atoms 4510| | * selected from C, N, and O. 4511| | */ 4512| 1.01k| ring_cno_count = MolecularInorganicsCountRingCNOAtoms(at, num_at, metal_idx); 4513| | 4514| 1.01k| if (ring_cno_count >= 3) ------------------ | Branch (4514:17): [True: 71, False: 941] ------------------ 4515| 71| { 4516| 71| k++; 4517| 71| continue; 4518| 71| } 4519| | 4520| 941| DisconnectInpAtBond(at, nOldCompNumber, i, k); 4521| 941| num_disconnected++; 4522| 941| ip->bMolecularInorganicsReconnectedInChI = 1; 4523| 941| } 4524| 159k| } 4525| | 4526| | /* Realize the remaining (uncharged) coordinative (type 9) bonds as single 4527| | * bonds, so the rest of the pipeline treats them like the equivalent 4528| | * single-bonded structure. 4529| | */ 4530| 70.4k| ConvertCoordinativeBondsToSingle(at, num_at); 4531| | 4532| | /* 4533| | * Re-perceive ring systems after the charge-separated bond disconnections, 4534| | * because those graph changes may alter the ring membership used by the 4535| | * main Molecular Inorganics decision-tree evaluation. 4536| | */ 4537| 70.4k| MarkRingSystemsInp(at, num_at, 0); 4538| | 4539| | /* Compute the number of metals and whether every metal is terminal. */ 4540| 70.4k| num_metals = 0; 4541| 70.4k| all_metal_atoms_terminal = 1; 4542| | 4543| 229k| for (i = 0; i < num_at; i++) ------------------ | Branch (4543:17): [True: 159k, False: 70.4k] ------------------ 4544| 159k| { 4545| 159k| if (is_el_a_metal(at[i].el_number)) ------------------ | Branch (4545:13): [True: 10.1k, False: 149k] ------------------ 4546| 10.1k| { 4547| 10.1k| num_metals++; 4548| | 4549| 10.1k| if (at[i].valence != 1 || at[i].bond_type[0] != BOND_TYPE_SINGLE) ------------------ | | 32| 4.22k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (4549:17): [True: 5.91k, False: 4.22k] | Branch (4549:39): [True: 602, False: 3.61k] ------------------ 4550| 6.51k| { 4551| 6.51k| all_metal_atoms_terminal = 0; 4552| 6.51k| } 4553| 10.1k| } 4554| 159k| } 4555| | 4556| 70.4k| if (!num_metals) ------------------ | Branch (4556:9): [True: 61.9k, False: 8.48k] ------------------ 4557| 61.9k| { 4558| 61.9k| goto cleanup; 4559| 61.9k| } 4560| | 4561| | /* Check whether at least one single bond remains attached to a metal. */ 4562| 8.48k| has_single_bond_to_metal = 0; 4563| | 4564| 30.0k| for (i = 0; i < num_at && !has_single_bond_to_metal; i++) ------------------ | Branch (4564:17): [True: 27.3k, False: 2.71k] | Branch (4564:31): [True: 21.6k, False: 5.77k] ------------------ 4565| 21.6k| { 4566| 21.6k| if (!is_el_a_metal(at[i].el_number)) ------------------ | Branch (4566:13): [True: 12.9k, False: 8.69k] ------------------ 4567| 12.9k| { 4568| 12.9k| continue; 4569| 12.9k| } 4570| | 4571| 11.5k| for (n = 0; n < at[i].valence; n++) ------------------ | Branch (4571:21): [True: 9.09k, False: 2.40k] ------------------ 4572| 9.09k| { 4573| 9.09k| if (at[i].bond_type[n] == BOND_TYPE_SINGLE) ------------------ | | 32| 9.09k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (4573:17): [True: 6.28k, False: 2.81k] ------------------ 4574| 6.28k| { 4575| 6.28k| has_single_bond_to_metal = 1; 4576| 6.28k| break; 4577| 6.28k| } 4578| 9.09k| } 4579| 8.69k| } 4580| | 4581| 8.48k| if (!has_single_bond_to_metal) ------------------ | Branch (4581:9): [True: 2.20k, False: 6.28k] ------------------ 4582| 2.20k| { 4583| 2.20k| goto cleanup; 4584| 2.20k| } 4585| | 4586| | /* Evaluate the complete decision tree before changing any remaining 4587| | * metal-ligand bond. If one bond must be retained, all remaining bonds to 4588| | * metal atoms are retained. */ 4589| 6.28k| keep_all_metal_bonds = 0; 4590| | 4591| 22.7k| for (i = 0; i < num_at && !keep_all_metal_bonds; i++) ------------------ | Branch (4591:17): [True: 22.1k, False: 664] | Branch (4591:31): [True: 16.4k, False: 5.61k] ------------------ 4592| 16.4k| { 4593| 16.4k| int ring_cno_count = 0; 4594| 16.4k| int current_metal_is_group_1_or_2; 4595| | 4596| 16.4k| if (!is_el_a_metal(at[i].el_number)) ------------------ | Branch (4596:13): [True: 10.1k, False: 6.37k] ------------------ 4597| 10.1k| { 4598| 10.1k| continue; 4599| 10.1k| } 4600| | 4601| 6.37k| current_metal_is_group_1_or_2 = MolecularInorganicsIsGroup1or2Metal(at[i].el_number); 4602| | 4603| | /* 4604| | * Count C, N, and O atoms in the same ring system as the metal. 4605| | * Group 1 and Group 2 metals are excluded from chelate protection. 4606| | */ 4607| 6.37k| ring_cno_count = MolecularInorganicsCountRingCNOAtoms(at, num_at, i); 4608| | 4609| 6.37k| disconnectDecision = MolecularInorganicsIsMetalToDisconnect(at, i); 4610| | 4611| 6.65k| for (n = 0; n < at[i].valence; n++) ------------------ | Branch (4611:21): [True: 6.39k, False: 258] ------------------ 4612| 6.39k| { 4613| 6.39k| int bond_has_stereo = 0; 4614| 6.39k| int bond_links_to_other_metal = 0; 4615| 6.39k| int dfs_stack_size; 4616| | 4617| 6.39k| neighbor_idx = at[i].neighbor[n]; 4618| | 4619| 6.39k| if (neighbor_idx < 0 || neighbor_idx >= num_at) ------------------ | Branch (4619:17): [True: 0, False: 6.39k] | Branch (4619:37): [True: 0, False: 6.39k] ------------------ 4620| 0| { 4621| 0| continue; 4622| 0| } 4623| | 4624| 6.39k| bond_has_stereo = MolecularInorganicsBondHasStereo(at, i, n); 4625| | 4626| | /* The actual bond must be a non-stereogenic single bond. */ 4627| 6.39k| if (at[i].bond_type[n] != BOND_TYPE_SINGLE || bond_has_stereo) ------------------ | | 32| 12.7k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (4627:17): [True: 1.76k, False: 4.62k] | Branch (4627:59): [True: 0, False: 4.62k] ------------------ 4628| 1.76k| { 4629| 1.76k| keep_all_metal_bonds = 1; 4630| 1.76k| break; 4631| 1.76k| } 4632| | 4633| 4.62k| if (disconnectDecision != 1) ------------------ | Branch (4633:17): [True: 3.88k, False: 747] ------------------ 4634| 3.88k| { 4635| 3.88k| keep_all_metal_bonds = 1; 4636| 3.88k| break; 4637| 3.88k| } 4638| | 4639| | /* The bonded atom pair must satisfy the binary disconnection table. */ 4640| 747| binaryValue = shouldBondBeCut(at[i].el_number, at[neighbor_idx].el_number); 4641| | 4642| 747| if (binaryValue != 1) ------------------ | Branch (4642:17): [True: 467, False: 280] ------------------ 4643| 467| { 4644| 467| keep_all_metal_bonds = 1; 4645| 467| break; 4646| 467| } 4647| | 4648| | /* Determine whether the actual bond is part of a path from this 4649| | * metal atom to another metal atom. The current metal is excluded 4650| | * from the traversal so that only paths starting through this bond 4651| | * are considered. */ 4652| 280| memset(dfs_visited, 0, num_at * sizeof(*dfs_visited)); 4653| 280| dfs_stack_size = 0; 4654| 280| dfs_visited[i] = 1; 4655| 280| dfs_visited[neighbor_idx] = 1; 4656| 280| dfs_stack[dfs_stack_size++] = neighbor_idx; 4657| | 4658| 1.22k| while (dfs_stack_size && !bond_links_to_other_metal) ------------------ | Branch (4658:20): [True: 1.04k, False: 183] | Branch (4658:38): [True: 1.04k, False: 0] ------------------ 4659| 1.04k| { 4660| 1.04k| int current_atom = dfs_stack[--dfs_stack_size]; 4661| | 4662| 1.04k| if (is_el_a_metal(at[current_atom].el_number)) ------------------ | Branch (4662:21): [True: 97, False: 946] ------------------ 4663| 97| { 4664| 97| bond_links_to_other_metal = 1; 4665| 97| break; 4666| 97| } 4667| | 4668| 2.90k| for (neigh_pos = 0; neigh_pos < at[current_atom].valence; neigh_pos++) ------------------ | Branch (4668:37): [True: 1.96k, False: 946] ------------------ 4669| 1.96k| { 4670| 1.96k| int neighbor_atom = at[current_atom].neighbor[neigh_pos]; 4671| | 4672| 1.96k| if (neighbor_atom < 0 || neighbor_atom >= num_at || dfs_visited[neighbor_atom]) ------------------ | Branch (4672:25): [True: 0, False: 1.96k] | Branch (4672:46): [True: 0, False: 1.96k] | Branch (4672:73): [True: 1.17k, False: 784] ------------------ 4673| 1.17k| { 4674| 1.17k| continue; 4675| 1.17k| } 4676| | 4677| 784| dfs_visited[neighbor_atom] = 1; 4678| 784| dfs_stack[dfs_stack_size++] = neighbor_atom; 4679| 784| } 4680| 946| } 4681| | 4682| | /* 4683| | * Retain a linkage to another metal unless: 4684| | * 1) all metal atoms are terminal, or 4685| | * 2) the current metal belongs to Group 1 or Group 2. 4686| | */ 4687| 280| if (bond_links_to_other_metal && !all_metal_atoms_terminal && !current_metal_is_group_1_or_2) ------------------ | Branch (4687:17): [True: 97, False: 183] | Branch (4687:46): [True: 89, False: 8] | Branch (4687:75): [True: 2, False: 87] ------------------ 4688| 2| { 4689| 2| keep_all_metal_bonds = 1; 4690| 2| break; 4691| 2| } 4692| | 4693| | /* 4694| | * Protect a qualifying chelate ring. Group 1 and Group 2 metals return 4695| | * zero from MolecularInorganicsCountRingCNOAtoms(). 4696| | */ 4697| 278| if (ring_cno_count >= 3) ------------------ | Branch (4697:17): [True: 2, False: 276] ------------------ 4698| 2| { 4699| 2| keep_all_metal_bonds = 1; 4700| 2| break; 4701| 2| } 4702| 278| } 4703| 6.37k| } 4704| | 4705| 6.28k| if (keep_all_metal_bonds) ------------------ | Branch (4705:9): [True: 6.11k, False: 164] ------------------ 4706| 6.11k| { 4707| 6.11k| ip->bMolecularInorganicsReconnectedInChI = 1; 4708| 6.11k| goto cleanup; 4709| 6.11k| } 4710| | 4711| | /* All remaining metal bonds satisfy the complete decision tree and may be 4712| | * disconnected. 4713| | **/ 4714| 1.06k| for (i = 0; i < num_at; i++) ------------------ | Branch (4714:17): [True: 896, False: 164] ------------------ 4715| 896| { 4716| 896| if (!is_el_a_metal(at[i].el_number)) ------------------ | Branch (4716:13): [True: 729, False: 167] ------------------ 4717| 729| { 4718| 729| continue; 4719| 729| } 4720| | 4721| 346| for (n = at[i].valence - 1; n >= 0; n--) ------------------ | Branch (4721:37): [True: 179, False: 167] ------------------ 4722| 179| { 4723| 179| neighbor_idx = at[i].neighbor[n]; 4724| | 4725| 179| if (neighbor_idx < 0 || neighbor_idx >= num_at) ------------------ | Branch (4725:17): [True: 0, False: 179] | Branch (4725:37): [True: 0, False: 179] ------------------ 4726| 0| { 4727| 0| continue; 4728| 0| } 4729| | 4730| 179| DisconnectInpAtBond(at, nOldCompNumber, i, n); 4731| | 4732| | /* Updating the metal as well as neighbor list */ 4733| 179| updateNeighborListMolecularInorganics(at, i, neighbor_idx); 4734| 179| updateNeighborListMolecularInorganics(at, neighbor_idx, i); 4735| | 4736| 179| at[i].charge += 1; /* Metal atom loses an electron -> +1 charge */ 4737| 179| at[neighbor_idx].charge -= 1; /* Neighbor atom gains an electron -> -1 charge */ 4738| | 4739| 179| num_disconnected++; 4740| 179| } 4741| 167| } 4742| | 4743| 70.4k|cleanup: 4744| 70.4k| if (dfs_visited) inchi_free(dfs_visited); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ | Branch (4744:9): [True: 70.4k, False: 0] ------------------ 4745| 70.4k| if (dfs_stack) inchi_free(dfs_stack); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ | Branch (4745:9): [True: 70.4k, False: 0] ------------------ 4746| | 4747| 70.4k| return (ret_code < 0) ? ret_code : num_disconnected; ------------------ | Branch (4747:12): [True: 0, False: 70.4k] ------------------ 4748| 164|} bHeteroAtomMayHaveXchgIsoH: 4754| 3.38k|{ 4755| 3.38k| inp_ATOM *at = atom + iat, *at2; 4756| 3.38k| int j, val, is_H = 0, num_H, iat_numb, bAccept; /* djb-rwth: removing redundant variables */ 4757| | 4758| 3.38k| if (0 > (iat_numb = get_iat_number(at->el_number))) ------------------ | Branch (4758:9): [True: 125, False: 3.26k] ------------------ 4759| 125| { 4760| 125| return 0; 4761| 125| } 4762| | 4763| 3.26k| if (abs(at->charge) > 1 || (at->radical && RADICAL_SINGLET != at->radical)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 75| 227|#define RADICAL_SINGLET 1 ------------------ | Branch (4763:9): [True: 9, False: 3.25k] | Branch (4763:33): [True: 227, False: 3.02k] | Branch (4763:48): [True: 227, False: 0] ------------------ 4764| 236| { 4765| 236| return 0; 4766| 236| } 4767| | 4768| 3.02k| val = -1; 4769| 3.02k| switch (iat_numb) ------------------ | Branch (4769:13): [True: 2.93k, False: 88] ------------------ 4770| 3.02k| { 4771| 1.21k| case IAT_N: ------------------ | Branch (4771:5): [True: 1.21k, False: 1.80k] ------------------ 4772| 1.23k| case IAT_P: ------------------ | Branch (4772:5): [True: 14, False: 3.01k] ------------------ 4773| | /* djb-rwth: removing redundant code */ 4774| 1.23k| val = 3 + at->charge; 4775| 1.23k| break; 4776| | 4777| 134| case IAT_O: ------------------ | Branch (4777:5): [True: 134, False: 2.89k] ------------------ 4778| 203| case IAT_S: ------------------ | Branch (4778:5): [True: 69, False: 2.95k] ------------------ 4779| 204| case IAT_Se: ------------------ | Branch (4779:5): [True: 1, False: 3.02k] ------------------ 4780| 209| case IAT_Te: ------------------ | Branch (4780:5): [True: 5, False: 3.01k] ------------------ 4781| | /* djb-rwth: removing redundant code */ 4782| 209| val = 2 + at->charge; 4783| 209| break; 4784| | 4785| 11| case IAT_F: ------------------ | Branch (4785:5): [True: 11, False: 3.01k] ------------------ 4786| 35| case IAT_Cl: ------------------ | Branch (4786:5): [True: 24, False: 3.00k] ------------------ 4787| 37| case IAT_Br: ------------------ | Branch (4787:5): [True: 2, False: 3.02k] ------------------ 4788| 82| case IAT_I: ------------------ | Branch (4788:5): [True: 45, False: 2.97k] ------------------ 4789| 82| if (at->charge == 0) ------------------ | Branch (4789:13): [True: 51, False: 31] ------------------ 4790| 51| { 4791| | /* djb-rwth: removing redundant code */ 4792| 51| val = 1; 4793| 51| } 4794| 82| break; 4795| | 4796| 1.41k| case IAT_H: ------------------ | Branch (4796:5): [True: 1.41k, False: 1.61k] ------------------ 4797| 1.41k| if (at->valence == 0 && ------------------ | Branch (4797:13): [True: 657, False: 757] ------------------ 4798| 657| at->charge == 1) ------------------ | Branch (4798:13): [True: 651, False: 6] ------------------ 4799| 651| { 4800| 651| is_H = 1; /* isolated proton */ 4801| 651| val = 0; 4802| 651| } 4803| 3.02k| } 4804| 3.02k| if (val < 0) ------------------ | Branch (4804:9): [True: 882, False: 2.14k] ------------------ 4805| 882| { 4806| 882| return 0; 4807| 882| } 4808| 2.14k| num_H = NUMH(at, 0); ------------------ | | 56| 2.14k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 2.14k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 4809| 2.14k| if (val != at->chem_bonds_valence + num_H) ------------------ | Branch (4809:9): [True: 1.16k, False: 976] ------------------ 4810| 1.16k| { 4811| 1.16k| return 0; 4812| 1.16k| } 4813| 976| if (is_H) ------------------ | Branch (4813:9): [True: 651, False: 325] ------------------ 4814| 651| { 4815| 651| return 2; /* H atom */ 4816| 651| } 4817| 325| else 4818| 325| { 4819| | /* djb-rwth: removing redundant code */ 4820| 765| for (j = 0, bAccept = 1; j < at->valence && bAccept; j++) ------------------ | Branch (4820:34): [True: 516, False: 249] | Branch (4820:53): [True: 516, False: 0] ------------------ 4821| 516| { 4822| 516| at2 = atom + (int)at->neighbor[j]; 4823| 516| if ((at2->charge && at->charge) || ------------------ | Branch (4823:18): [True: 64, False: 452] | Branch (4823:33): [True: 49, False: 15] ------------------ 4824| 467| (at2->radical && RADICAL_SINGLET != at2->radical)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 75| 27|#define RADICAL_SINGLET 1 ------------------ | Branch (4824:18): [True: 27, False: 440] | Branch (4824:34): [True: 27, False: 0] ------------------ 4825| 76| { 4826| 76| return 0; /* adjacent charged/radical atoms: do not neutralizate */ 4827| 76| } 4828| 516| } 4829| 325| } 4830| | 4831| 249| return 1; 4832| 976|} bNumHeterAtomHasIsotopicH: 4838| 216k|{ 4839| 216k| int i, j, val, is_H = 0, num_H, iat_numb, bAccept, num_iso_H, cur_num_iso_H, num_iso_atoms; /* djb-rwth: removing redundant variables */ 4840| 216k| inp_ATOM *at, *at2; 4841| | 4842| 216k| num_iso_H = 0; 4843| 216k| num_iso_atoms = 0; 4844| | 4845| 1.27M| for (i = 0, at = atom; i < num_atoms; i++, at++) ------------------ | Branch (4845:28): [True: 1.05M, False: 216k] ------------------ 4846| 1.05M| { 4847| | 4848| 1.05M| num_iso_atoms += (at->iso_atw_diff != 0 || NUM_ISO_H(at, 0)); ------------------ | | 55| 1.05M|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ | | | Branch (55:26): [True: 869, False: 1.05M] | | ------------------ ------------------ | Branch (4848:27): [True: 982, False: 1.05M] ------------------ 4849| | /* isotopic atoms and implicit isotopic H */ 4850| | 4851| 1.05M| if (0 > (iat_numb = get_iat_number(at->el_number))) ------------------ | Branch (4851:13): [True: 448k, False: 608k] ------------------ 4852| 448k| { 4853| 448k| continue; 4854| 448k| } 4855| | 4856| 608k| if (abs(at->charge) > 1 || (at->radical && RADICAL_SINGLET != at->radical)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 75| 20.4k|#define RADICAL_SINGLET 1 ------------------ | Branch (4856:13): [True: 755, False: 607k] | Branch (4856:37): [True: 20.4k, False: 587k] | Branch (4856:52): [True: 20.4k, False: 0] ------------------ 4857| 21.1k| { 4858| 21.1k| continue; 4859| 21.1k| } 4860| | 4861| 587k| val = -1; 4862| 587k| switch (iat_numb) ------------------ | Branch (4862:17): [True: 489k, False: 97.6k] ------------------ 4863| 587k| { 4864| 100k| case IAT_N: ------------------ | Branch (4864:9): [True: 100k, False: 486k] ------------------ 4865| 118k| case IAT_P: ------------------ | Branch (4865:9): [True: 17.2k, False: 570k] ------------------ 4866| | /* djb-rwth: removing redundant code */ 4867| 118k| val = 3 + at->charge; 4868| 118k| break; 4869| | 4870| 193k| case IAT_O: ------------------ | Branch (4870:9): [True: 193k, False: 393k] ------------------ 4871| 235k| case IAT_S: ------------------ | Branch (4871:9): [True: 41.5k, False: 545k] ------------------ 4872| 237k| case IAT_Se: ------------------ | Branch (4872:9): [True: 2.29k, False: 585k] ------------------ 4873| 241k| case IAT_Te: ------------------ | Branch (4873:9): [True: 3.70k, False: 583k] ------------------ 4874| | /* djb-rwth: removing redundant code */ 4875| 241k| val = 2 + at->charge; 4876| 241k| break; 4877| | 4878| 11.0k| case IAT_F: ------------------ | Branch (4878:9): [True: 11.0k, False: 576k] ------------------ 4879| 11.2k| case IAT_Cl: ------------------ | Branch (4879:9): [True: 151, False: 587k] ------------------ 4880| 12.2k| case IAT_Br: ------------------ | Branch (4880:9): [True: 993, False: 586k] ------------------ 4881| 22.4k| case IAT_I: ------------------ | Branch (4881:9): [True: 10.1k, False: 577k] ------------------ 4882| 22.4k| if (at->charge == 0) ------------------ | Branch (4882:17): [True: 17.1k, False: 5.25k] ------------------ 4883| 17.1k| { 4884| | /* djb-rwth: removing redundant code */ 4885| 17.1k| val = 1; 4886| 17.1k| } 4887| 22.4k| break; 4888| | 4889| 108k| case IAT_H: ------------------ | Branch (4889:9): [True: 108k, False: 479k] ------------------ 4890| 108k| if (at->valence == 0 && ------------------ | Branch (4890:17): [True: 66.5k, False: 41.4k] ------------------ 4891| 66.5k| at->charge == 1) ------------------ | Branch (4891:17): [True: 35.0k, False: 31.4k] ------------------ 4892| 35.0k| { 4893| 35.0k| is_H = 1; /* isolated proton */ 4894| 35.0k| val = 0; 4895| 35.0k| } 4896| 587k| } 4897| 587k| if (val < 0) ------------------ | Branch (4897:13): [True: 175k, False: 411k] ------------------ 4898| 175k| { 4899| 175k| continue; 4900| 175k| } 4901| | 4902| 411k| num_H = NUMH(at, 0); ------------------ | | 56| 411k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 411k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 4903| 411k| if (val != at->chem_bonds_valence + num_H) ------------------ | Branch (4903:13): [True: 284k, False: 127k] ------------------ 4904| 284k| { 4905| 284k| continue; 4906| 284k| } 4907| | 4908| 127k| if (is_H) ------------------ | Branch (4908:13): [True: 35.0k, False: 92.1k] ------------------ 4909| 35.0k| { 4910| 35.0k| bAccept = 1; 4911| 35.0k| cur_num_iso_H = (at->iso_atw_diff != 0); 4912| 35.0k| } 4913| 92.1k| else 4914| 92.1k| { 4915| 92.1k| cur_num_iso_H = 0; 4916| 212k| for (j = 0, bAccept = 1; j < at->valence && bAccept; j++) ------------------ | Branch (4916:38): [True: 137k, False: 75.2k] | Branch (4916:57): [True: 137k, False: 0] ------------------ 4917| 137k| { 4918| 137k| at2 = atom + (int)at->neighbor[j]; 4919| 137k| if ((at2->charge && at->charge) || ------------------ | Branch (4919:22): [True: 35.1k, False: 101k] | Branch (4919:37): [True: 11.5k, False: 23.6k] ------------------ 4920| 125k| (at2->radical && RADICAL_SINGLET != at2->radical)) /* djb-rwth: addressing LLVM warning */ ------------------ | | 75| 5.38k|#define RADICAL_SINGLET 1 ------------------ | Branch (4920:22): [True: 5.38k, False: 120k] | Branch (4920:38): [True: 5.38k, False: 0] ------------------ 4921| 16.9k| { 4922| 16.9k| bAccept = 0; /* adjacent charged/radical atoms: do not neutralizate */ 4923| 16.9k| break; 4924| 16.9k| } 4925| 120k| else if (at2->el_number == EL_NUMBER_H && ------------------ | | 11| 240k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ | Branch (4925:26): [True: 14.6k, False: 105k] ------------------ 4926| 14.6k| at2->valence == 1 && at2->iso_atw_diff) ------------------ | Branch (4926:26): [True: 6.04k, False: 8.62k] | Branch (4926:47): [True: 70, False: 5.97k] ------------------ 4927| 70| { 4928| 70| cur_num_iso_H++; /* isotopic explicit H */ 4929| 70| } 4930| 137k| } 4931| | 4932| 92.1k| if (bAccept) ------------------ | Branch (4932:17): [True: 75.2k, False: 16.9k] ------------------ 4933| 75.2k| { 4934| 75.2k| num_iso_atoms -= cur_num_iso_H; /* avoid counting explicit H as isotopic atom */ 4935| 75.2k| cur_num_iso_H += NUM_ISO_H(at, 0); ------------------ | | 55| 75.2k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) ------------------ 4936| 75.2k| } 4937| 92.1k| } 4938| | 4939| 127k| num_iso_H += (bAccept && cur_num_iso_H); /* number of acceptable heteroatoms that have isotopic H */ ------------------ | Branch (4939:23): [True: 110k, False: 16.9k] | Branch (4939:34): [True: 740, False: 109k] ------------------ 4940| 127k| } 4941| | 4942| 216k| return ((num_iso_H ? 1 : 0) | (num_iso_atoms ? 2 : 0)); ------------------ | Branch (4942:14): [True: 176, False: 216k] | Branch (4942:36): [True: 853, False: 215k] ------------------ 4943| 216k|} cmp_components: 4950| 225k|{ 4951| 225k| int ret; 4952| 225k| AT_NUMB n1; 4953| 225k| AT_NUMB n2; 4954| | 4955| 225k| n1 = ((const AT_NUMB *)a1)[0]; 4956| | /* number of atoms in the component -- descending order */ 4957| 225k| n2 = ((const AT_NUMB *)a2)[0]; 4958| | 4959| 225k| if ((ret = (int)n2 - (int)n1)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (4959:9): [True: 700, False: 225k] ------------------ 4960| 700| { 4961| 700| return ret; 4962| 700| } 4963| | 4964| | /* stable sort */ 4965| 225k| n1 = ((const AT_NUMB *)a1)[1]; 4966| | /* component ordering number -- ascending order */ 4967| 225k| n2 = ((const AT_NUMB *)a2)[1]; 4968| | 4969| 225k| ret = (int)n1 - (int)n2; 4970| | 4971| 225k| return ret; 4972| 225k|} MarkDisconnectedComponents: 5170| 70.4k|{ 5171| 70.4k| typedef AT_NUMB AT_TRIPLE[3]; 5172| | 5173| 70.4k| inp_ATOM *at = orig_at_data->at; 5174| 70.4k| int num_at = orig_at_data->num_inp_atoms; 5175| 70.4k| AT_NUMB *nCurAtLen = NULL; 5176| | 5177| 70.4k| AT_NUMB *nNewCompNumber = NULL; 5178| 70.4k| AT_NUMB *nPrevAtom = NULL; 5179| 70.4k| S_CHAR *iNeigh = NULL; 5180| | 5181| 70.4k| AT_NUMB *nOldCompNumber = NULL; 5182| 70.4k| int i, j, num_components, ret; 5183| 70.4k| int new_comp_no; 5184| 70.4k| AT_NUMB old_comp_no, another_comp_no, no_component; 5185| | 5186| | /* component_nbr[i][0] = number of atoms in the component i-1 5187| | * component_nbr[i][1] = original component number (id-1) = i 5188| | * after sorting: 5189| | * component_nbr[j][2] = new number of component #(component_nbr[i][1]+1) 5190| | */ 5191| 70.4k| AT_TRIPLE *component_nbr = NULL; 5192| 70.4k| int fst_at, nxt_at, cur_at, cur_neq_fst; /* moved from below 2024-09-01 DT */ 5193| | 5194| | /* initialize */ 5195| 70.4k| if (bProcessOldCompNumbers && !orig_at_data->nOldCompNumber) ------------------ | Branch (5195:9): [True: 0, False: 70.4k] | Branch (5195:35): [True: 0, False: 0] ------------------ 5196| 0| { 5197| 0| bProcessOldCompNumbers = 0; 5198| 0| } 5199| 70.4k| num_components = 0; 5200| | 5201| | /* 5202| | for ( j = 0; j < num_at; j ++ ) 5203| | { 5204| | at[j].component = 0; 5205| | } 5206| | */ 5207| | 5208| 70.4k| ret = -1; 5209| 70.4k| if (!num_at) ------------------ | Branch (5209:9): [True: 0, False: 70.4k] ------------------ 5210| 0| { 5211| 0| return 0; 5212| 0| } 5213| | 5214| 70.4k| nNewCompNumber = (AT_NUMB *)inchi_calloc(num_at, sizeof(nNewCompNumber[0])); ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 5215| 70.4k| nPrevAtom = (AT_NUMB *)inchi_calloc(num_at, sizeof(nPrevAtom[0])); ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 5216| 70.4k| iNeigh = (S_CHAR *)inchi_calloc(num_at, sizeof(iNeigh[0])); ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 5217| | 5218| 70.4k| if (!nNewCompNumber || !nPrevAtom || !iNeigh) /* nNewCompNumber: for non-recursive DFS only: */ ------------------ | Branch (5218:9): [True: 0, False: 70.4k] | Branch (5218:28): [True: 0, False: 70.4k] | Branch (5218:42): [True: 0, False: 70.4k] ------------------ 5219| 0| { 5220| 0| goto exit_function; 5221| 0| } 5222| | 5223| | /*printf("\nnum_at = %d\n", num_at);*/ 5224| | 5225| | /* Mark and count; avoid deep DFS recursion: it may make verifying software unhappy */ 5226| | /* nNewCompNumber[i] will contain new component number for atoms at[i], i=0..num_at-1 */ 5227| | 5228| 229k| for (j = 0; j < num_at; j++) ------------------ | Branch (5228:17): [True: 159k, False: 70.4k] ------------------ 5229| 159k| { 5230| 159k| if (!nNewCompNumber[j]) ------------------ | Branch (5230:13): [True: 106k, False: 53.1k] ------------------ 5231| 106k| { 5232| | /* mark starting with at[j] */ 5233| 106k| fst_at = 0; 5234| 106k| nxt_at = 0; 5235| 106k| cur_at = j; 5236| 106k| cur_neq_fst = 1; 5237| 106k| num_components++; 5238| | 5239| | /* first time at at[j] */ 5240| 106k| fst_at = cur_at; 5241| 106k| nNewCompNumber[fst_at] = (AT_NUMB)num_components; 5242| | 5243| | /* find next neighbor */ 5244| 106k| do 5245| 281k| { 5246| 281k| if (iNeigh[cur_at] < at[cur_at].valence) ------------------ | Branch (5246:21): [True: 121k, False: 159k] ------------------ 5247| 121k| { 5248| 121k| int ineigh_incr = (int)iNeigh[cur_at]; 5249| 121k| nxt_at = at[cur_at].neighbor[ineigh_incr]; 5250| 121k| iNeigh[cur_at]++; 5251| | 5252| 121k| if (!nNewCompNumber[nxt_at]) ------------------ | Branch (5252:25): [True: 53.1k, False: 68.6k] ------------------ 5253| 53.1k| { 5254| | /* forward edge: found new atom */ 5255| 53.1k| nNewCompNumber[nxt_at] = (AT_NUMB)num_components; 5256| 53.1k| nPrevAtom[nxt_at] = (AT_NUMB)cur_at; 5257| 53.1k| cur_at = nxt_at; 5258| 53.1k| } 5259| 121k| } 5260| 159k| else if (cur_at == fst_at) ------------------ | Branch (5260:26): [True: 106k, False: 53.1k] ------------------ 5261| 106k| { 5262| 106k| cur_neq_fst = 0; 5263| | /* break; done */ 5264| 106k| } 5265| 53.1k| else 5266| 53.1k| { 5267| 53.1k| cur_at = nPrevAtom[cur_at]; /* retract */ 5268| 53.1k| } 5269| 281k| } while (cur_neq_fst); ------------------ | Branch (5269:22): [True: 174k, False: 106k] ------------------ 5270| 106k| } 5271| 159k| } 5272| | 5273| 70.4k| inchi_free(nPrevAtom); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 5274| 70.4k| nPrevAtom = NULL; 5275| 70.4k| inchi_free(iNeigh); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 5276| 70.4k| iNeigh = NULL; 5277| | 5278| | /* Allocate more memory */ 5279| 70.4k| i = inchi_max(num_components, orig_at_data->num_components); ------------------ | | 138| 70.4k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 70.4k, False: 0] | | ------------------ ------------------ 5280| | 5281| 70.4k| nCurAtLen = (AT_NUMB *)inchi_calloc((long long)num_components + 1, sizeof(nCurAtLen[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 5282| 70.4k| nOldCompNumber = (AT_NUMB *)inchi_calloc((long long)i + 1, sizeof(nOldCompNumber[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 5283| 70.4k| component_nbr = (AT_TRIPLE *)inchi_calloc((long long)num_components + 1, sizeof(component_nbr[0])); /* djb-rwth: cast operator added */ ------------------ | | 1146| 70.4k|#define inchi_calloc calloc ------------------ 5284| | 5285| 70.4k| if (!nCurAtLen || !nOldCompNumber || !component_nbr) ------------------ | Branch (5285:9): [True: 0, False: 70.4k] | Branch (5285:23): [True: 0, False: 70.4k] | Branch (5285:42): [True: 0, False: 70.4k] ------------------ 5286| 0| { 5287| 0| goto exit_function; 5288| 0| } 5289| | 5290| | /* Count atoms per component and renumber the components */ 5291| 176k| for (i = 0; i < num_components; i++) ------------------ | Branch (5291:17): [True: 106k, False: 70.4k] ------------------ 5292| 106k| { 5293| 106k| component_nbr[i][0] = 0; /* number of atoms in the component */ 5294| 106k| component_nbr[i][1] = i; /* component ordering number */ 5295| 106k| } 5296| | 5297| 229k| for (j = 0; j < num_at; j++) ------------------ | Branch (5297:17): [True: 159k, False: 70.4k] ------------------ 5298| 159k| { 5299| 159k| component_nbr[(int)nNewCompNumber[j] - 1][0]++; /* count atoms in each component */ 5300| 159k| } 5301| | 5302| | /* Sort settings 5303| | key: number of atoms 5304| | order: descending 5305| | stable sort 5306| | */ 5307| | 5308| 70.4k| qsort( (void*) component_nbr[0], num_components, sizeof( component_nbr[0] ), cmp_components ); /* djb-rwth: fixed buffer overrun */ 5309| | 5310| | /* Invert the transposition */ 5311| 176k| for (i = 0; i < num_components; i++) ------------------ | Branch (5311:17): [True: 106k, False: 70.4k] ------------------ 5312| 106k| { 5313| 106k| nCurAtLen[i] = component_nbr[i][0]; 5314| 106k| component_nbr[component_nbr[i][1]][2] = i + 1; 5315| 106k| } 5316| | 5317| | /* Renumber the components so that the component with the greatest number of atoms is the first */ 5318| 70.4k| no_component = num_at + 1; 5319| | 5320| 229k| for (j = 0; j < num_at; j++) ------------------ | Branch (5320:17): [True: 159k, False: 70.4k] ------------------ 5321| 159k| { 5322| | /* new component number for at[j] */ 5323| 159k| new_comp_no = component_nbr[(int)nNewCompNumber[j] - 1][2] - 1; /* starts from 0 */ 5324| 159k| if (bProcessOldCompNumbers) ------------------ | Branch (5324:13): [True: 0, False: 159k] ------------------ 5325| 0| { 5326| | /* old component number for at[j] */ 5327| 0| old_comp_no = at[j].component; 5328| | /* fill out nOldCompNumber[]; initially it contains zeroes */ 5329| 0| if (!old_comp_no) ------------------ | Branch (5329:17): [True: 0, False: 0] ------------------ 5330| 0| { 5331| 0| nOldCompNumber[new_comp_no] = no_component; /* atom did not have component number */ 5332| 0| } 5333| 0| else if (nOldCompNumber[new_comp_no] != old_comp_no) ------------------ | Branch (5333:22): [True: 0, False: 0] ------------------ 5334| 0| { 5335| 0| if (!nOldCompNumber[new_comp_no]) ------------------ | Branch (5335:21): [True: 0, False: 0] ------------------ 5336| 0| { 5337| 0| nOldCompNumber[new_comp_no] = old_comp_no; 5338| 0| } 5339| 0| else 5340| 0| { 5341| | /* at[j] moved from old comp #old_comp_no to old comp #nOldCompNumber[new_comp_no] 5342| | Both components cannot be equal to any current component */ 5343| 0| another_comp_no = nOldCompNumber[new_comp_no]; 5344| 0| for (i = 0; i < num_components; i++) ------------------ | Branch (5344:33): [True: 0, False: 0] ------------------ 5345| 0| { 5346| 0| if (nOldCompNumber[i] == old_comp_no || ------------------ | Branch (5346:29): [True: 0, False: 0] ------------------ 5347| 0| nOldCompNumber[i] == another_comp_no) ------------------ | Branch (5347:29): [True: 0, False: 0] ------------------ 5348| 0| { 5349| 0| nOldCompNumber[i] = no_component; 5350| 0| } 5351| 0| } 5352| | /* nOldCompNumber[new_comp_no] = num_at+1; */ 5353| 0| } 5354| 0| } 5355| 0| } 5356| | 5357| | /* orig_at_data->nOldCompNumber */ 5358| | 5359| | /* Finally, set the new component number for atom j (NB: starts from 1 ) */ 5360| 159k| at[j].component = new_comp_no + 1; 5361| 159k| } 5362| | 5363| 70.4k| if (bProcessOldCompNumbers) ------------------ | Branch (5363:9): [True: 0, False: 70.4k] ------------------ 5364| 0| { 5365| 0| for (j = 0; j < num_components; j++) ------------------ | Branch (5365:21): [True: 0, False: 0] ------------------ 5366| 0| { 5367| 0| if (nOldCompNumber[j] == no_component) ------------------ | Branch (5367:17): [True: 0, False: 0] ------------------ 5368| 0| { 5369| | /* the component has atom from another component */ 5370| 0| nOldCompNumber[j] = 0; 5371| 0| } 5372| 0| else if (nOldCompNumber[j] && ------------------ | Branch (5372:22): [True: 0, False: 0] ------------------ 5373| 0| !orig_at_data->nOldCompNumber[nOldCompNumber[j] - 1]) ------------------ | Branch (5373:22): [True: 0, False: 0] ------------------ 5374| 0| { 5375| | /* the component has changed in the previous processing */ 5376| 0| nOldCompNumber[j] = 0; 5377| 0| } 5378| 0| } 5379| 0| } 5380| 70.4k| else 5381| 70.4k| { 5382| 176k| for (j = 0; j < num_components; j++) ------------------ | Branch (5382:21): [True: 106k, False: 70.4k] ------------------ 5383| 106k| { 5384| 106k| nOldCompNumber[j] = j + 1; 5385| 106k| } 5386| 70.4k| } 5387| | 5388| 70.4k| ret = num_components; 5389| | 5390| 70.4k|exit_function: 5391| | 5392| 70.4k| if (nNewCompNumber) ------------------ | Branch (5392:9): [True: 70.4k, False: 0] ------------------ 5393| 70.4k| { 5394| 70.4k| inchi_free(nNewCompNumber); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 5395| 70.4k| } 5396| 70.4k| if (component_nbr) ------------------ | Branch (5396:9): [True: 70.4k, False: 0] ------------------ 5397| 70.4k| { 5398| 70.4k| inchi_free(component_nbr); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 5399| 70.4k| } 5400| | 5401| 70.4k| if (ret < 0) ------------------ | Branch (5401:9): [True: 0, False: 70.4k] ------------------ 5402| 0| { 5403| 0| if (nPrevAtom) ------------------ | Branch (5403:13): [True: 0, False: 0] ------------------ 5404| 0| { 5405| 0| inchi_free(nPrevAtom); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5406| 0| nPrevAtom = NULL; 5407| 0| } 5408| 0| if (iNeigh) ------------------ | Branch (5408:13): [True: 0, False: 0] ------------------ 5409| 0| { 5410| 0| inchi_free(iNeigh); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5411| 0| iNeigh = NULL; 5412| 0| } 5413| 0| if (nCurAtLen) ------------------ | Branch (5413:13): [True: 0, False: 0] ------------------ 5414| 0| { 5415| 0| inchi_free(nCurAtLen); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5416| 0| nCurAtLen = NULL; 5417| 0| } 5418| 0| if (nOldCompNumber) ------------------ | Branch (5418:13): [True: 0, False: 0] ------------------ 5419| 0| { 5420| 0| inchi_free(nOldCompNumber); ------------------ | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 0, False: 0] | | | Branch (1152:50): [Folded, False: 0] | | ------------------ ------------------ 5421| 0| nOldCompNumber = NULL; 5422| 0| } 5423| 0| num_components = ret; 5424| 0| } 5425| | 5426| | /* avoid memory leaks */ 5427| 70.4k| if (orig_at_data->nCurAtLen) ------------------ | Branch (5427:9): [True: 70.4k, False: 0] ------------------ 5428| 70.4k| { 5429| 70.4k| inchi_free(orig_at_data->nCurAtLen); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 5430| 70.4k| } 5431| 70.4k| if (orig_at_data->nOldCompNumber) ------------------ | Branch (5431:9): [True: 70.4k, False: 0] ------------------ 5432| 70.4k| { 5433| 70.4k| inchi_free(orig_at_data->nOldCompNumber); ------------------ | | 1152| 70.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 70.4k, False: 0] | | | Branch (1152:50): [Folded, False: 70.4k] | | ------------------ ------------------ 5434| 70.4k| } 5435| | 5436| 70.4k| orig_at_data->nCurAtLen = nCurAtLen; 5437| 70.4k| orig_at_data->nOldCompNumber = nOldCompNumber; 5438| | 5439| 70.4k| orig_at_data->num_components = num_components; 5440| | 5441| 70.4k| return ret; /* number of disconnected components; 5442| | 1=>single connected structure */ 5443| 70.4k|} ExtractConnectedComponent: 5452| 106k|{ 5453| 106k| int i, j, num_component_at; 5454| 106k| AT_NUMB *number; 5455| | 5456| 106k| if (NULL == (number = (AT_NUMB *)inchi_calloc(num_at, sizeof(AT_NUMB)))) ------------------ | | 1146| 106k|#define inchi_calloc calloc ------------------ | Branch (5456:9): [True: 0, False: 106k] ------------------ 5457| 0| { 5458| 0| return CT_OUT_OF_RAM; /* out of memory */ /* */ ------------------ | | 21| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 18| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5459| 0| } 5460| | 5461| | /* copy atoms */ 5462| 585M| for (i = 0, num_component_at = 0; i < num_at; i++) ------------------ | Branch (5462:39): [True: 585M, False: 106k] ------------------ 5463| 585M| { 5464| 585M| if (at[i].component == component_number) ------------------ | Branch (5464:13): [True: 159k, False: 585M] ------------------ 5465| 159k| { 5466| 159k| number[i] = num_component_at; 5467| 159k| component_at[num_component_at++] = at[i]; 5468| 159k| } 5469| 585M| } 5470| | 5471| | /* renumber neighbors */ 5472| 265k| for (i = 0; i < num_component_at; i++) ------------------ | Branch (5472:17): [True: 159k, False: 106k] ------------------ 5473| 159k| { 5474| 159k| component_at[i].orig_compt_at_numb = (AT_NUMB)(i + 1); 5475| 281k| for (j = 0; j < component_at[i].valence; j++) ------------------ | Branch (5475:21): [True: 121k, False: 159k] ------------------ 5476| 121k| { 5477| 121k| component_at[i].neighbor[j] = number[(int)component_at[i].neighbor[j]]; 5478| 121k| } 5479| 159k| } 5480| | 5481| 106k| inchi_free(number); ------------------ | | 1152| 106k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 106k, False: 0] | | | Branch (1152:50): [Folded, False: 106k] | | ------------------ ------------------ 5482| | 5483| 106k| return num_component_at; 5484| 106k|} SetConnectedComponentNumber: 5488| 252k|{ 5489| 252k| int i; 5490| 1.30M| for (i = 0; i < num_at; i++) ------------------ | Branch (5490:17): [True: 1.05M, False: 252k] ------------------ 5491| 1.05M| { 5492| 1.05M| at[i].component = (AT_NUMB)component_number; 5493| 1.05M| } 5494| | 5495| 252k| return 0; 5496| 252k|} Free_INChI_Stereo: 5500| 1.54M|{ 5501| 1.54M| if (pINChI_Stereo) ------------------ | Branch (5501:9): [True: 360k, False: 1.18M] ------------------ 5502| 360k| { 5503| 360k| qzfree(pINChI_Stereo->nNumber); ------------------ | | 1176| 360k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 351k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 351k, False: 0] | | | | | Branch (1152:50): [Folded, False: 351k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 351k, False: 9.37k] | | | Branch (1176:61): [Folded, False: 360k] | | ------------------ ------------------ 5504| 360k| qzfree(pINChI_Stereo->t_parity); ------------------ | | 1176| 360k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 351k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 351k, False: 0] | | | | | Branch (1152:50): [Folded, False: 351k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 351k, False: 9.37k] | | | Branch (1176:61): [Folded, False: 360k] | | ------------------ ------------------ 5505| 360k| qzfree(pINChI_Stereo->nNumberInv); ------------------ | | 1176| 360k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 298k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 298k, False: 0] | | | | | Branch (1152:50): [Folded, False: 298k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 298k, False: 62.1k] | | | Branch (1176:61): [Folded, False: 360k] | | ------------------ ------------------ 5506| 360k| qzfree(pINChI_Stereo->t_parityInv); ------------------ | | 1176| 360k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 298k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 298k, False: 0] | | | | | Branch (1152:50): [Folded, False: 298k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 298k, False: 62.1k] | | | Branch (1176:61): [Folded, False: 360k] | | ------------------ ------------------ 5507| 360k| qzfree(pINChI_Stereo->nBondAtom1); ------------------ | | 1176| 360k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 61.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 61.4k, False: 0] | | | | | Branch (1152:50): [Folded, False: 61.4k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 61.4k, False: 299k] | | | Branch (1176:61): [Folded, False: 360k] | | ------------------ ------------------ 5508| 360k| qzfree(pINChI_Stereo->nBondAtom2); ------------------ | | 1176| 360k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 61.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 61.4k, False: 0] | | | | | Branch (1152:50): [Folded, False: 61.4k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 61.4k, False: 299k] | | | Branch (1176:61): [Folded, False: 360k] | | ------------------ ------------------ 5509| 360k| qzfree(pINChI_Stereo->b_parity); ------------------ | | 1176| 360k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 61.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 61.4k, False: 0] | | | | | Branch (1152:50): [Folded, False: 61.4k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 61.4k, False: 299k] | | | Branch (1176:61): [Folded, False: 360k] | | ------------------ ------------------ 5510| 360k| } 5511| | 5512| 1.54M| return 0; 5513| 1.54M|} Alloc_INChI_Stereo: 5517| 298k|{ 5518| | 5519| 298k| INChI_Stereo *pINChI_Stereo = (INChI_Stereo *) 5520| 298k| inchi_calloc(1, sizeof(INChI_Stereo)); ------------------ | | 1146| 298k|#define inchi_calloc calloc ------------------ 5521| | 5522| 298k| if (pINChI_Stereo) ------------------ | Branch (5522:9): [True: 298k, False: 0] ------------------ 5523| 298k| { 5524| 298k| if (num_at && ------------------ | Branch (5524:13): [True: 298k, False: 0] ------------------ 5525| 298k| (pINChI_Stereo->nNumber = (AT_NUMB *)inchi_calloc(num_at, sizeof(pINChI_Stereo->nNumber[0]))) && ------------------ | | 1146| 298k|#define inchi_calloc calloc ------------------ | Branch (5525:13): [True: 298k, False: 0] ------------------ 5526| 298k| (pINChI_Stereo->t_parity = (S_CHAR *)inchi_calloc(num_at, sizeof(pINChI_Stereo->t_parity[0]))) && ------------------ | | 1146| 298k|#define inchi_calloc calloc ------------------ | Branch (5526:13): [True: 298k, False: 0] ------------------ 5527| 298k| (pINChI_Stereo->nNumberInv = (AT_NUMB *)inchi_calloc(num_at, sizeof(pINChI_Stereo->nNumberInv[0]))) && ------------------ | | 1146| 298k|#define inchi_calloc calloc ------------------ | Branch (5527:13): [True: 298k, False: 0] ------------------ 5528| 298k| (pINChI_Stereo->t_parityInv = (S_CHAR *)inchi_calloc(num_at, sizeof(pINChI_Stereo->t_parityInv[0])))) ------------------ | | 1146| 298k|#define inchi_calloc calloc ------------------ | Branch (5528:13): [True: 298k, False: 0] ------------------ 5529| 298k| { 5530| 298k| ; 5531| 298k| } 5532| 0| else if (num_at) ------------------ | Branch (5532:18): [True: 0, False: 0] ------------------ 5533| 0| { 5534| 0| goto out_of_RAM; 5535| 0| } 5536| | 5537| 298k| if (num_bonds && ------------------ | Branch (5537:13): [True: 51.7k, False: 247k] ------------------ 5538| 51.7k| (pINChI_Stereo->nBondAtom1 = (AT_NUMB *)inchi_calloc(num_bonds, sizeof(pINChI_Stereo->nBondAtom1[0]))) && ------------------ | | 1146| 51.7k|#define inchi_calloc calloc ------------------ | Branch (5538:13): [True: 51.7k, False: 0] ------------------ 5539| 51.7k| (pINChI_Stereo->nBondAtom2 = (AT_NUMB *)inchi_calloc(num_bonds, sizeof(pINChI_Stereo->nBondAtom2[0]))) && ------------------ | | 1146| 51.7k|#define inchi_calloc calloc ------------------ | Branch (5539:13): [True: 51.7k, False: 0] ------------------ 5540| 51.7k| (pINChI_Stereo->b_parity = (S_CHAR *)inchi_calloc(num_bonds, sizeof(pINChI_Stereo->b_parity[0])))) ------------------ | | 1146| 51.7k|#define inchi_calloc calloc ------------------ | Branch (5540:13): [True: 51.7k, False: 0] ------------------ 5541| 51.7k| { 5542| 51.7k| ; 5543| 51.7k| } 5544| 247k| else if (num_bonds) ------------------ | Branch (5544:18): [True: 0, False: 247k] ------------------ 5545| 0| { 5546| 0| goto out_of_RAM; 5547| 0| } 5548| | 5549| 298k| return pINChI_Stereo; 5550| | 5551| 0| out_of_RAM: 5552| | 5553| 0| Free_INChI_Stereo(pINChI_Stereo); 5554| 0| qzfree(pINChI_Stereo); ------------------ | | 1176| 0|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 0, False: 0] | | | Branch (1176:61): [Folded, False: 0] | | ------------------ ------------------ 5555| 0| } /* if ( pINChI_Stereo ) */ 5556| | 5557| 0| return NULL; 5558| 298k|} Free_INChI: 5562| 1.28M|{ 5563| | 5564| 1.28M| INChI *pINChI; 5565| | 5566| 1.28M| if ((pINChI = *ppINChI)) /* djb-rwth: addressing LLVM warning */ ------------------ | Branch (5566:9): [True: 387k, False: 893k] ------------------ 5567| 387k| { 5568| | 5569| 387k|#if (bREUSE_INCHI == 1) 5570| 387k| if (pINChI->nRefCount-- > 0) ------------------ | Branch (5570:13): [True: 0, False: 387k] ------------------ 5571| 0| return 1; 5572| 387k|#endif 5573| | 5574| 387k| Free_INChI_Members(pINChI); 5575| 387k| qzfree(pINChI); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 387k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 387k, False: 0] | | | | | Branch (1152:50): [Folded, False: 387k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 387k, False: 0] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5576| 387k| *ppINChI = NULL; 5577| 387k| } 5578| | 5579| 1.28M| return 0; 5580| 1.28M|} Free_INChI_Members: 5584| 773k|{ 5585| 773k| if (pINChI) ------------------ | Branch (5585:9): [True: 773k, False: 0] ------------------ 5586| 773k| { 5587| 773k| Free_INChI_Stereo(pINChI->Stereo); 5588| 773k| Free_INChI_Stereo(pINChI->StereoIsotopic); 5589| 773k| qzfree(pINChI->nAtom); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 721k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 721k, False: 0] | | | | | Branch (1152:50): [Folded, False: 721k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 721k, False: 51.5k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5590| 773k| qzfree(pINChI->nConnTable); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 682k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 682k, False: 0] | | | | | Branch (1152:50): [Folded, False: 682k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 682k, False: 90.8k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5591| 773k| qzfree(pINChI->nTautomer); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 296k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 296k, False: 0] | | | | | Branch (1152:50): [Folded, False: 296k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 296k, False: 476k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5592| 773k| qzfree(pINChI->nNum_H); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 697k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 697k, False: 0] | | | | | Branch (1152:50): [Folded, False: 697k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 697k, False: 75.7k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5593| 773k| qzfree(pINChI->nNum_H_fixed); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 388k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 388k, False: 0] | | | | | Branch (1152:50): [Folded, False: 388k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 388k, False: 384k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5594| 773k| qzfree(pINChI->IsotopicAtom); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 37.9k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 37.9k, False: 0] | | | | | Branch (1152:50): [Folded, False: 37.9k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 37.9k, False: 735k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5595| 773k| qzfree(pINChI->IsotopicTGroup); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 2.24k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 2.24k, False: 0] | | | | | Branch (1152:50): [Folded, False: 2.24k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 2.24k, False: 771k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5596| 773k| qzfree(pINChI->nPossibleLocationsOfIsotopicH); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 9.05k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 9.05k, False: 0] | | | | | Branch (1152:50): [Folded, False: 9.05k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 9.05k, False: 764k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5597| 773k| qzfree(pINChI->Stereo); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 317k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 317k, False: 0] | | | | | Branch (1152:50): [Folded, False: 317k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 317k, False: 456k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5598| 773k| qzfree(pINChI->StereoIsotopic); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 43.8k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 43.8k, False: 0] | | | | | Branch (1152:50): [Folded, False: 43.8k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 43.8k, False: 729k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5599| 773k| qzfree(pINChI->szHillFormula); ------------------ | | 1176| 773k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 685k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 685k, False: 0] | | | | | Branch (1152:50): [Folded, False: 685k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 685k, False: 88.0k] | | | Branch (1176:61): [Folded, False: 773k] | | ------------------ ------------------ 5600| 773k| } 5601| | 5602| 773k| return 0; 5603| 773k|} Alloc_INChI: 5611| 289k|{ 5612| 289k| int i, num_bonds, num_isotopic_atoms; 5613| 289k| INChI *pINChI; 5614| 289k| int bIsotopic = (nAllocMode & REQ_MODE_ISO); ------------------ | | 17| 289k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 5615| | /* int bTautomeric = (nAllocMode & REQ_MODE_TAUT); */ 5616| | 5617| 289k| if (num_at <= 0 || ------------------ | Branch (5617:9): [True: 0, False: 289k] ------------------ 5618| 289k| NULL == (pINChI = (INChI *)inchi_calloc(1, sizeof(INChI)))) ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ | Branch (5618:9): [True: 0, False: 289k] ------------------ 5619| 0| { 5620| 0| return NULL; 5621| 0| } 5622| | 5623| 1.40M| for (i = 0, num_bonds = 0, num_isotopic_atoms = 0; i < num_at; i++) ------------------ | Branch (5623:56): [True: 1.11M, False: 289k] ------------------ 5624| 1.11M| { 5625| 1.11M| num_bonds += at[i].valence; 5626| | /* if ( bIsotopic ) { */ 5627| 1.11M| num_isotopic_atoms += (0 != at[i].iso_atw_diff || ------------------ | Branch (5627:32): [True: 1.68k, False: 1.10M] ------------------ 5628| 1.10M| !strcmp(at[i].elname, "D") || ------------------ | Branch (5628:32): [True: 0, False: 1.10M] ------------------ 5629| 1.10M| !strcmp(at[i].elname, "T") || ------------------ | Branch (5629:32): [True: 0, False: 1.10M] ------------------ 5630| 1.10M| at[i].num_iso_H[0] || ------------------ | Branch (5630:32): [True: 554, False: 1.10M] ------------------ 5631| 1.10M| at[i].num_iso_H[1] || ------------------ | Branch (5631:32): [True: 189, False: 1.10M] ------------------ 5632| 1.10M| at[i].num_iso_H[2]); ------------------ | Branch (5632:32): [True: 214, False: 1.10M] ------------------ 5633| | /* } */ 5634| 1.11M| } 5635| 289k| num_bonds /= 2; 5636| | 5637| 289k| *found_num_bonds = num_bonds; 5638| 289k| *found_num_isotopic = num_isotopic_atoms; 5639| | 5640| 289k| if ((pINChI->nAtom = (U_CHAR *)inchi_calloc(num_at, sizeof(pINChI->nAtom[0]))) && ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ | Branch (5640:9): [True: 289k, False: 0] ------------------ 5641| 289k| (pINChI->nConnTable = (AT_NUMB *)inchi_calloc((long long)num_at + (long long)num_bonds, sizeof(pINChI->nConnTable[0]))) && /* djb-rwth: cast operator added */ ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ | Branch (5641:9): [True: 289k, False: 0] ------------------ 5642| 289k| (pINChI->nTautomer = (AT_NUMB *)inchi_calloc(((3 + INCHI_T_NUM_MOVABLE) * (long long)num_at) / 2 + 1, sizeof(pINChI->nTautomer[0]))) && /* djb-rwth: cast operator added */ ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ (pINChI->nTautomer = (AT_NUMB *)inchi_calloc(((3 + INCHI_T_NUM_MOVABLE) * (long long)num_at) / 2 + 1, sizeof(pINChI->nTautomer[0]))) && /* djb-rwth: cast operator added */ ------------------ | | 749| 289k|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (5642:9): [True: 289k, False: 0] ------------------ 5643| 289k| (pINChI->nNum_H = (S_CHAR *)inchi_calloc(num_at, sizeof(pINChI->nNum_H[0]))) && ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ | Branch (5643:9): [True: 289k, False: 0] ------------------ 5644| 289k| (pINChI->nNum_H_fixed = (S_CHAR *)inchi_calloc(num_at, sizeof(pINChI->nNum_H_fixed[0])))) ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ | Branch (5644:9): [True: 289k, False: 0] ------------------ 5645| 289k| { 5646| 289k| ; 5647| | /* nTautomer length: max. number of tautomeric groups is num_at/2 5648| | 5649| | 1 word -> number of t-groups 5650| | 5651| | each group has: 5652| | 5653| | 1 word -> number of endpoints+INCHI_T_NUM_MOVABLE 5654| | INCHI_T_NUM_MOVABLE words -> number(s) of moveable attachments 5655| | numbers of endpoints words -> canon. numbers 5656| | 5657| | max. occurs if each t-group has 2 atoms (num_at/2 t-groups) and all atoms 5658| | belong to t-groups (num_at endpoints) 5659| | 5660| | Total: 1 + (number of t-groups)*(1+INCHI_T_NUM_MOVABLE) + (number of endpoints) <= 5661| | 1 + (num_at/2) * (1+INCHI_T_NUM_MOVABLE) + num_at <= 5662| | 1 + (3+INCHI_T_NUM_MOVABLE)*num_at/2 words. 5663| | */ 5664| 289k| } 5665| 0| else 5666| 0| { 5667| 0| goto out_of_RAM; 5668| 0| } 5669| | 5670| 289k| pINChI->szHillFormula = NULL; /* the length is unknown */ 5671| | 5672| 289k| if (bIsotopic) ------------------ | Branch (5672:9): [True: 9.05k, False: 280k] ------------------ 5673| 9.05k| { 5674| 9.05k| if (num_isotopic_atoms && ------------------ | Branch (5674:13): [True: 2.24k, False: 6.81k] ------------------ 5675| 2.24k| (pINChI->IsotopicAtom = (INChI_IsotopicAtom *)inchi_calloc(num_isotopic_atoms, sizeof(INChI_IsotopicAtom))) && ------------------ | | 1146| 2.24k|#define inchi_calloc calloc ------------------ | Branch (5675:13): [True: 2.24k, False: 0] ------------------ 5676| 2.24k| (pINChI->IsotopicTGroup = (INChI_IsotopicTGroup *)inchi_calloc(num_isotopic_atoms, sizeof(INChI_IsotopicTGroup)))) ------------------ | | 1146| 2.24k|#define inchi_calloc calloc ------------------ | Branch (5676:13): [True: 2.24k, False: 0] ------------------ 5677| 2.24k| { 5678| 2.24k| ; 5679| 2.24k| } 5680| 6.81k| else if (num_isotopic_atoms) ------------------ | Branch (5680:18): [True: 0, False: 6.81k] ------------------ 5681| 0| { 5682| 0| goto out_of_RAM; 5683| 0| } 5684| 9.05k| if (!(pINChI->nPossibleLocationsOfIsotopicH = (AT_NUMB *)inchi_calloc((long long)num_at + 1, sizeof(pINChI->nPossibleLocationsOfIsotopicH[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 9.05k|#define inchi_calloc calloc ------------------ | Branch (5684:13): [True: 0, False: 9.05k] ------------------ 5685| 0| { 5686| 0| goto out_of_RAM; 5687| 0| } 5688| 9.05k| } 5689| | 5690| 289k| if ((pINChI->Stereo = Alloc_INChI_Stereo(num_at, num_bonds))) ------------------ | Branch (5690:9): [True: 289k, False: 0] ------------------ 5691| 289k| { 5692| 289k| ; 5693| 289k| } 5694| 0| else 5695| 0| { 5696| 0| goto out_of_RAM; 5697| 0| } 5698| | 5699| 289k| if (bIsotopic) ------------------ | Branch (5699:9): [True: 9.05k, False: 280k] ------------------ 5700| 9.05k| { 5701| 9.05k| if ((pINChI->StereoIsotopic = Alloc_INChI_Stereo(num_at, num_bonds))) ------------------ | Branch (5701:13): [True: 9.05k, False: 0] ------------------ 5702| 9.05k| { 5703| 9.05k| ; 5704| 9.05k| } 5705| 0| else 5706| 0| { 5707| 0| goto out_of_RAM; 5708| 0| } 5709| 9.05k| } 5710| | 5711| 289k| return pINChI; 5712| | 5713| 0|out_of_RAM: 5714| 0| if (pINChI) ------------------ | Branch (5714:9): [True: 0, False: 0] ------------------ 5715| 0| { 5716| 0| Free_INChI(&pINChI); 5717| | /* 5718| | inchi_free(pINChI); 5719| | */ 5720| 0| } 5721| | 5722| | return NULL; 5723| 289k|} Free_INChI_Aux: 5727| 1.28M|{ 5728| 1.28M| INChI_Aux *pINChI_Aux = *ppINChI_Aux; 5729| 1.28M| if (pINChI_Aux) ------------------ | Branch (5729:9): [True: 387k, False: 893k] ------------------ 5730| 387k| { 5731| | 5732| 387k|#if (bREUSE_INCHI == 1) 5733| 387k| if (pINChI_Aux->nRefCount-- > 0) ------------------ | Branch (5733:13): [True: 0, False: 387k] ------------------ 5734| 0| return 1; 5735| 387k|#endif 5736| | 5737| 387k| qzfree(pINChI_Aux->nOrigAtNosInCanonOrd); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 289k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 289k, False: 0] | | | | | Branch (1152:50): [Folded, False: 289k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 289k, False: 97.5k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5738| 387k| qzfree(pINChI_Aux->nIsotopicOrigAtNosInCanonOrd); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 9.05k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 9.05k, False: 0] | | | | | Branch (1152:50): [Folded, False: 9.05k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 9.05k, False: 378k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5739| 387k| qzfree(pINChI_Aux->nOrigAtNosInCanonOrdInv); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 289k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 289k, False: 0] | | | | | Branch (1152:50): [Folded, False: 289k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 289k, False: 97.5k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5740| 387k| qzfree(pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 9.05k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 9.05k, False: 0] | | | | | Branch (1152:50): [Folded, False: 9.05k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 9.05k, False: 378k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5741| 387k| qzfree(pINChI_Aux->szOrigCoord); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 0, False: 0] | | | | | Branch (1152:50): [Folded, False: 0] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 0, False: 387k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5742| 387k| qzfree(pINChI_Aux->OrigInfo); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 289k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 289k, False: 0] | | | | | Branch (1152:50): [Folded, False: 289k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 289k, False: 97.5k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5743| | /* 5744| | qzfree( pINChI_Aux->nOriginalAtomNumber ); 5745| | qzfree( pINChI_Aux->nCanonicalTGroupNumbers ); 5746| | qzfree( pINChI_Aux->nIsotopicCanonicalTGroupNumbers); 5747| | qzfree( pINChI_Aux->nTautomer ); 5748| | qzfree( pINChI_Aux->nNontautomericCanonicalNumbers ); 5749| | qzfree( pINChI_Aux->nIsotopicCanonicalNumbers ); 5750| | qzfree( pINChI_Aux->nNontautomericIsotopicCanonicalNumbers ); 5751| | qzfree( pINChI_Aux->nNontautomericEquNumbers ); 5752| | qzfree( pINChI_Aux->nNontautomericIsotopicEquNumbers ); 5753| | */ 5754| 387k| qzfree(pINChI_Aux->nConstitEquNumbers); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 289k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 289k, False: 0] | | | | | Branch (1152:50): [Folded, False: 289k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 289k, False: 97.5k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5755| 387k| qzfree(pINChI_Aux->nConstitEquTGroupNumbers); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 104k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 104k, False: 0] | | | | | Branch (1152:50): [Folded, False: 104k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 104k, False: 282k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5756| 387k| qzfree(pINChI_Aux->nConstitEquIsotopicNumbers); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 9.05k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 9.05k, False: 0] | | | | | Branch (1152:50): [Folded, False: 9.05k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 9.05k, False: 378k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5757| 387k| qzfree(pINChI_Aux->nConstitEquIsotopicTGroupNumbers); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 9.05k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 9.05k, False: 0] | | | | | Branch (1152:50): [Folded, False: 9.05k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 9.05k, False: 378k] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5758| 387k| qzfree(pINChI_Aux); ------------------ | | 1176| 387k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1152| 387k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1152:31): [True: 387k, False: 0] | | | | | Branch (1152:50): [Folded, False: 387k] | | | | ------------------ | | ------------------ | | | Branch (1176:27): [True: 387k, False: 0] | | | Branch (1176:61): [Folded, False: 387k] | | ------------------ ------------------ 5759| 387k| *ppINChI_Aux = NULL; 5760| 387k| } 5761| | 5762| 1.28M| return 0; 5763| 1.28M|} Alloc_INChI_Aux: 5770| 289k|{ 5771| 289k| INChI_Aux *pINChI_Aux; 5772| 289k| int bIsotopic = (nAllocMode & REQ_MODE_ISO); ------------------ | | 17| 289k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 5773| 289k| int num_at_tg = num_at + num_at / 2; 5774| | /* int bTautomeric = (nAllocMode & REQ_MODE_TAUT); */ 5775| | 5776| 289k| if (num_at <= 0 || ------------------ | Branch (5776:9): [True: 0, False: 289k] ------------------ 5777| 289k| NULL == (pINChI_Aux = (INChI_Aux *)inchi_calloc(1, sizeof(INChI_Aux)))) ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ | Branch (5777:9): [True: 0, False: 289k] ------------------ 5778| 0| { 5779| 0| return NULL; 5780| 0| } 5781| | 5782| 289k| if ((pINChI_Aux->nOrigAtNosInCanonOrd = (AT_NUMB *) ------------------ | Branch (5782:9): [True: 289k, False: 0] ------------------ 5783| 289k| inchi_calloc(num_at_tg, sizeof(pINChI_Aux->nOrigAtNosInCanonOrd[0]))) && ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ 5784| 289k| (pINChI_Aux->nOrigAtNosInCanonOrdInv = (AT_NUMB *) ------------------ | Branch (5784:9): [True: 289k, False: 0] ------------------ 5785| 289k| inchi_calloc(num_at_tg, sizeof(pINChI_Aux->nOrigAtNosInCanonOrd[0]))) && ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ 5786| 289k| (pINChI_Aux->nConstitEquNumbers = (AT_NUMB *) ------------------ | Branch (5786:9): [True: 289k, False: 0] ------------------ 5787| 289k| inchi_calloc(num_at_tg, sizeof(pINChI_Aux->nConstitEquNumbers[0])))) ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ 5788| 289k| { 5789| 289k| ; 5790| 289k| } 5791| 0| else 5792| 0| { 5793| 0| goto out_of_RAM; 5794| 0| } 5795| | 5796| 289k| if (num_at > 1 && ------------------ | Branch (5796:9): [True: 104k, False: 184k] ------------------ 5797| 104k| (pINChI_Aux->nConstitEquTGroupNumbers = (AT_NUMB *)inchi_calloc((long long)num_at / 2 + 1, sizeof(pINChI_Aux->nConstitEquTGroupNumbers[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 104k|#define inchi_calloc calloc ------------------ | Branch (5797:9): [True: 104k, False: 0] ------------------ 5798| 104k| { 5799| 104k| ; 5800| 104k| } 5801| 184k| else 5802| 184k| { 5803| 184k| if (num_at > 1) ------------------ | Branch (5803:13): [True: 0, False: 184k] ------------------ 5804| 0| { 5805| 0| goto out_of_RAM; 5806| 0| } 5807| 184k| } 5808| | 5809| 289k| if (num_at > 0) ------------------ | Branch (5809:9): [True: 289k, False: 0] ------------------ 5810| 289k| { 5811| 289k| pINChI_Aux->OrigInfo = (ORIG_INFO *)inchi_calloc(num_at, sizeof(pINChI_Aux->OrigInfo[0])); ------------------ | | 1146| 289k|#define inchi_calloc calloc ------------------ 5812| 289k| if (!pINChI_Aux->OrigInfo) ------------------ | Branch (5812:13): [True: 0, False: 289k] ------------------ 5813| 0| goto out_of_RAM; 5814| 289k| } 5815| | 5816| 289k| if (bOrigCoord && num_at > 0) ------------------ | Branch (5816:9): [True: 0, False: 289k] | Branch (5816:23): [True: 0, False: 0] ------------------ 5817| 0| { 5818| 0| pINChI_Aux->szOrigCoord = (MOL_COORD *)inchi_calloc(num_at, sizeof(pINChI_Aux->szOrigCoord[0])); ------------------ | | 1146| 0|#define inchi_calloc calloc ------------------ 5819| 0| if (!pINChI_Aux->szOrigCoord) ------------------ | Branch (5819:13): [True: 0, False: 0] ------------------ 5820| 0| goto out_of_RAM; 5821| 0| } 5822| | 5823| 289k| if (bIsotopic) ------------------ | Branch (5823:9): [True: 9.05k, False: 280k] ------------------ 5824| 9.05k| { 5825| 9.05k| if (/*num_isotopic_atoms &&*/ 5826| 9.05k| (pINChI_Aux->nIsotopicOrigAtNosInCanonOrd = (AT_NUMB *)inchi_calloc(num_at_tg, sizeof(pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0]))) && ------------------ | | 1146| 9.05k|#define inchi_calloc calloc ------------------ | Branch (5826:13): [True: 9.05k, False: 0] ------------------ 5827| 9.05k| (pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv = (AT_NUMB *)inchi_calloc(num_at_tg, sizeof(pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0]))) && ------------------ | | 1146| 9.05k|#define inchi_calloc calloc ------------------ | Branch (5827:13): [True: 9.05k, False: 0] ------------------ 5828| 9.05k| (pINChI_Aux->nConstitEquIsotopicNumbers = (AT_NUMB *)inchi_calloc(num_at_tg, sizeof(pINChI_Aux->nConstitEquIsotopicNumbers[0])))) ------------------ | | 1146| 9.05k|#define inchi_calloc calloc ------------------ | Branch (5828:13): [True: 9.05k, False: 0] ------------------ 5829| 9.05k| { 5830| 9.05k| ; 5831| 9.05k| } 5832| 0| else if (num_isotopic_atoms) ------------------ | Branch (5832:18): [True: 0, False: 0] ------------------ 5833| 0| { 5834| 0| goto out_of_RAM; 5835| 0| } 5836| | 5837| 9.05k| if ( /*num_isotopic_atoms && num_at > 1 &&*/ 5838| 9.05k| (pINChI_Aux->nConstitEquIsotopicTGroupNumbers = (AT_NUMB *)inchi_calloc((long long)num_at / 2 + 1, sizeof(pINChI_Aux->nConstitEquIsotopicTGroupNumbers[0])))) /* djb-rwth: cast operator added */ ------------------ | | 1146| 9.05k|#define inchi_calloc calloc ------------------ | Branch (5838:13): [True: 9.05k, False: 0] ------------------ 5839| 9.05k| { 5840| 9.05k| ; 5841| 9.05k| } 5842| 0| else if (num_isotopic_atoms && num_at > 1) ------------------ | Branch (5842:18): [True: 0, False: 0] | Branch (5842:40): [True: 0, False: 0] ------------------ 5843| 0| { 5844| 0| goto out_of_RAM; 5845| 0| } 5846| 9.05k| } 5847| | 5848| 289k| return pINChI_Aux; 5849| | 5850| 0|out_of_RAM: 5851| | 5852| 0| if (pINChI_Aux) ------------------ | Branch (5852:9): [True: 0, False: 0] ------------------ 5853| 0| { 5854| 0| Free_INChI_Aux(&pINChI_Aux); 5855| | /* 5856| | inchi_free(pINChI_Aux); 5857| | */ 5858| 0| } 5859| | 5860| | return NULL; 5861| 289k|} imat_new: 5885| 890|{ 5886| 890| int i; 5887| 890| if (m == 0 || n == 0) ------------------ | Branch (5887:9): [True: 770, False: 120] | Branch (5887:19): [True: 0, False: 120] ------------------ 5888| 770| { 5889| 770| return 0; 5890| 770| } 5891| 120| if (*a) ------------------ | Branch (5891:9): [True: 0, False: 120] ------------------ 5892| 0| { 5893| 0| imat_free(m, *a); 5894| 0| *a = NULL; 5895| 0| } 5896| 120| *a = (int **)inchi_calloc(m, sizeof(int *)); ------------------ | | 1146| 120|#define inchi_calloc calloc ------------------ 5897| 120| if (NULL == *a) ------------------ | Branch (5897:9): [True: 0, False: 120] ------------------ 5898| 0| { 5899| 0| return 1; 5900| 0| } 5901| 937| for (i = 0; i < m; i++) ------------------ | Branch (5901:17): [True: 817, False: 120] ------------------ 5902| 817| { 5903| 817| (*a)[i] = (int *)inchi_calloc(n, sizeof(int)); ------------------ | | 1146| 817|#define inchi_calloc calloc ------------------ 5904| 817| if (NULL == (*a)[i]) ------------------ | Branch (5904:13): [True: 0, False: 817] ------------------ 5905| 0| { 5906| 0| return 1; 5907| 0| } 5908| 817| } 5909| 120| return 0; 5910| 120|} imat_free: 5916| 120|{ 5917| 120| int i; 5918| 120| if (NULL != a) ------------------ | Branch (5918:9): [True: 120, False: 0] ------------------ 5919| 120| { 5920| 937| for (i = 0; i < m; i++) ------------------ | Branch (5920:21): [True: 817, False: 120] ------------------ 5921| 817| { 5922| 817| if (NULL != a[i]) /* djb-rwth: unresolved issue -- revision required? -- false positive as this function just does the clean-up job */ ------------------ | Branch (5922:17): [True: 817, False: 0] ------------------ 5923| 817| { 5924| 817| inchi_free(a[i]); ------------------ | | 1152| 817|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 817, False: 0] | | | Branch (1152:50): [Folded, False: 817] | | ------------------ ------------------ 5925| 817| } 5926| 817| } 5927| 120| inchi_free(a); ------------------ | | 1152| 120|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1152:31): [True: 120, False: 0] | | | Branch (1152:50): [Folded, False: 120] | | ------------------ ------------------ 5928| 120| a = NULL; 5929| 120| } 5930| | 5931| 120| return; 5932| 120|} strutil.c:is_only_HDT_neighbors: 3681| 1.11k|{ 3682| 1.11k| int v; 3683| | 3684| 1.11k| if (!at || metal_idx < 0 || metal_idx >= num_atoms) ------------------ | Branch (3684:9): [True: 0, False: 1.11k] | Branch (3684:16): [True: 0, False: 1.11k] | Branch (3684:33): [True: 0, False: 1.11k] ------------------ 3685| 0| { 3686| 0| return 0; 3687| 0| } 3688| | 3689| 1.79k| for (v = 0; v < at[metal_idx].valence; v++) ------------------ | Branch (3689:17): [True: 1.46k, False: 337] ------------------ 3690| 1.46k| { 3691| 1.46k| int nb = at[metal_idx].neighbor[v]; 3692| | 3693| 1.46k| if (nb < 0 || nb >= num_atoms) ------------------ | Branch (3693:13): [True: 0, False: 1.46k] | Branch (3693:23): [True: 0, False: 1.46k] ------------------ 3694| 0| { 3695| 0| continue; 3696| 0| } 3697| | 3698| 1.46k| if (!(at[nb].elname[0] == 'H' && at[nb].elname[1] == '\0')) ------------------ | Branch (3698:15): [True: 682, False: 779] | Branch (3698:42): [True: 679, False: 3] ------------------ 3699| 782| { 3700| 782| return 0; 3701| 782| } 3702| 1.46k| } 3703| | 3704| 337| return 1; 3705| 1.11k|} strutil.c:MolecularInorganicsCountRingCNOAtoms: 4320| 7.38k|{ 4321| 7.38k| int atom_idx; 4322| 7.38k| int ring_cno_count = 0; 4323| 7.38k| AT_NUMB ring_id; 4324| | 4325| 7.38k| if (!MolecularInorganicsIsGroup1or2Metal(at[metal_idx].el_number) && at[metal_idx].nRingSystem) ------------------ | Branch (4325:9): [True: 4.69k, False: 2.69k] | Branch (4325:74): [True: 4.69k, False: 0] ------------------ 4326| 4.69k| { 4327| 4.69k| ring_id = at[metal_idx].nRingSystem; 4328| | 4329| 29.1k| for (atom_idx = 0; atom_idx < num_at; atom_idx++) ------------------ | Branch (4329:28): [True: 24.4k, False: 4.69k] ------------------ 4330| 24.4k| { 4331| 24.4k| if (at[atom_idx].nRingSystem == ring_id && ------------------ | Branch (4331:17): [True: 8.53k, False: 15.8k] ------------------ 4332| 8.53k| (at[atom_idx].el_number == 6 || /* C */ ------------------ | Branch (4332:18): [True: 394, False: 8.14k] ------------------ 4333| 8.14k| at[atom_idx].el_number == 7 || /* N */ ------------------ | Branch (4333:21): [True: 1.38k, False: 6.76k] ------------------ 4334| 6.76k| at[atom_idx].el_number == 8)) /* O */ ------------------ | Branch (4334:21): [True: 441, False: 6.32k] ------------------ 4335| 2.21k| { 4336| 2.21k| ring_cno_count++; 4337| 2.21k| } 4338| 24.4k| } 4339| 4.69k| } 4340| | 4341| 7.38k| return ring_cno_count; 4342| 7.38k|} strutil.c:ConvertCoordinativeBondsToSingle: 4211| 70.4k|{ 4212| 70.4k| int i, k, k2, j; 4213| | 4214| 229k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4214:17): [True: 159k, False: 70.4k] ------------------ 4215| 159k| { 4216| 281k| for (k = 0; k < at[i].valence; k++) ------------------ | Branch (4216:21): [True: 122k, False: 159k] ------------------ 4217| 122k| { 4218| 122k| j = at[i].neighbor[k]; 4219| 122k| if (j < 0 || j >= num_atoms) ------------------ | Branch (4219:17): [True: 0, False: 122k] | Branch (4219:26): [True: 0, False: 122k] ------------------ 4220| 0| { 4221| 0| continue; 4222| 0| } 4223| | 4224| | /* Visit each undirected bond once, from the lower-indexed atom, so 4225| | * a multiply-charged pair cannot be neutralized once from each end. */ 4226| 122k| if (j <= i) ------------------ | Branch (4226:17): [True: 61.0k, False: 61.0k] ------------------ 4227| 61.0k| { 4228| 61.0k| continue; 4229| 61.0k| } 4230| | 4231| | /* Only coordinative (type 9) bonds are converted; plain single 4232| | * bonds keep their intrinsic formal charges untouched. */ 4233| 61.0k| if (at[i].bond_type[k] != COORDINATIVE_BOND) ------------------ | | 264| 61.0k|#define COORDINATIVE_BOND 9 /* (@nnuk) introduction of bond_type = 9 (Coordinative Bond) */ ------------------ | Branch (4233:17): [True: 61.0k, False: 0] ------------------ 4234| 61.0k| { 4235| 61.0k| continue; 4236| 61.0k| } 4237| | 4238| | /* Realize the bond as single on both endpoints so the rest of the 4239| | * pipeline sees a plain single bond from either atom. */ 4240| 0| at[i].bond_type[k] = BOND_TYPE_SINGLE; ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ 4241| | 4242| 0| for (k2 = 0; k2 < at[j].valence; k2++) ------------------ | Branch (4242:26): [True: 0, False: 0] ------------------ 4243| 0| { 4244| 0| if (at[j].neighbor[k2] == i) ------------------ | Branch (4244:21): [True: 0, False: 0] ------------------ 4245| 0| { 4246| 0| at[j].bond_type[k2] = BOND_TYPE_SINGLE; ------------------ | | 32| 0|#define BOND_TYPE_SINGLE 1 ------------------ 4247| 0| break; 4248| 0| } 4249| 0| } 4250| | 4251| | /* Cancel the paired +/- charges: the lone pair becomes the bonding 4252| | * pair, so each atom moves one unit toward neutral. */ 4253| 0| if (at[i].charge > 0 && at[j].charge < 0) ------------------ | Branch (4253:17): [True: 0, False: 0] | Branch (4253:37): [True: 0, False: 0] ------------------ 4254| 0| { 4255| 0| at[i].charge--; 4256| 0| at[j].charge++; 4257| 0| } 4258| 0| else if (at[i].charge < 0 && at[j].charge > 0) ------------------ | Branch (4258:22): [True: 0, False: 0] | Branch (4258:42): [True: 0, False: 0] ------------------ 4259| 0| { 4260| 0| at[i].charge++; 4261| 0| at[j].charge--; 4262| 0| } 4263| 0| } 4264| 159k| } 4265| 70.4k|} strutil.c:MolecularInorganicsIsGroup1or2Metal: 4279| 13.7k|{ 4280| 13.7k| switch (el_number) 4281| 13.7k| { 4282| | /* Group 1 */ 4283| 2| case 3: /* Li */ ------------------ | Branch (4283:5): [True: 2, False: 13.7k] ------------------ 4284| 98| case 11: /* Na */ ------------------ | Branch (4284:5): [True: 96, False: 13.6k] ------------------ 4285| 4.37k| case 19: /* K */ ------------------ | Branch (4285:5): [True: 4.27k, False: 9.49k] ------------------ 4286| 4.37k| case 37: /* Rb */ ------------------ | Branch (4286:5): [True: 7, False: 13.7k] ------------------ 4287| 4.39k| case 55: /* Cs */ ------------------ | Branch (4287:5): [True: 17, False: 13.7k] ------------------ 4288| 4.40k| case 87: /* Fr */ ------------------ | Branch (4288:5): [True: 8, False: 13.7k] ------------------ 4289| | 4290| | /* Group 2 */ 4291| 4.40k| case 4: /* Be */ ------------------ | Branch (4291:5): [True: 2, False: 13.7k] ------------------ 4292| 4.41k| case 12: /* Mg */ ------------------ | Branch (4292:5): [True: 6, False: 13.7k] ------------------ 4293| 4.41k| case 20: /* Ca */ ------------------ | Branch (4293:5): [True: 6, False: 13.7k] ------------------ 4294| 4.95k| case 38: /* Sr */ ------------------ | Branch (4294:5): [True: 540, False: 13.2k] ------------------ 4295| 4.96k| case 56: /* Ba */ ------------------ | Branch (4295:5): [True: 6, False: 13.7k] ------------------ 4296| 5.01k| case 88: /* Ra */ ------------------ | Branch (4296:5): [True: 48, False: 13.7k] ------------------ 4297| 5.01k| return 1; 4298| | 4299| 8.75k| default: ------------------ | Branch (4299:5): [True: 8.75k, False: 5.01k] ------------------ 4300| 8.75k| return 0; 4301| 13.7k| } 4302| 13.7k|} strutil.c:MolecularInorganicsBondHasStereo: 4357| 6.39k|{ 4358| 6.39k| int neigh_pos; 4359| 6.39k| int neighbor_idx; 4360| 6.39k| int bond_has_stereo; 4361| | 4362| 6.39k| neighbor_idx = at[atom_idx].neighbor[bond_pos]; 4363| 6.39k| bond_has_stereo = (at[atom_idx].bond_stereo[bond_pos] != 0); 4364| | 4365| 9.31k| for (neigh_pos = 0; !bond_has_stereo && neigh_pos < at[neighbor_idx].valence; neigh_pos++) ------------------ | Branch (4365:25): [True: 9.31k, False: 3] | Branch (4365:45): [True: 9.31k, False: 0] ------------------ 4366| 9.31k| { 4367| 9.31k| if (at[neighbor_idx].neighbor[neigh_pos] == atom_idx) ------------------ | Branch (4367:13): [True: 6.39k, False: 2.92k] ------------------ 4368| 6.39k| { 4369| 6.39k| bond_has_stereo = (at[neighbor_idx].bond_stereo[neigh_pos] != 0); 4370| 6.39k| break; 4371| 6.39k| } 4372| 9.31k| } 4373| | 4374| 6.39k| return bond_has_stereo; 4375| 6.39k|} get_element_chemical_symbol: 43| 1.68M|{ 44| 1.68M| nAtNum -= 1; 45| | 46| 1.68M| if ( 0 < nAtNum ) ------------------ | Branch (46:10): [True: 1.60M, False: 78.2k] ------------------ 47| 1.60M| { 48| 1.60M| nAtNum += 2; /* bypass D, T */ 49| 1.60M| } 50| | 51| 1.68M| if ( 0 <= nAtNum && nAtNum < nElDataLen ) ------------------ | Branch (51:10): [True: 1.68M, False: 0] | Branch (51:25): [True: 1.68M, False: 0] ------------------ 52| 1.68M| { 53| | /* valid element symbol found */ 54| 1.68M| strcpy(szElement, ElData[nAtNum].szElName); 55| 1.68M| return 0; 56| 1.68M| } 57| | 58| | /* not found */ 59| 0| strcpy(szElement, "??"); 60| 0| return -1; 61| 1.68M|} get_element_or_pseudoelement_symbol: 71| 1.97M|{ 72| 1.97M| nAtNum -= 1; 73| | 74| 1.97M| if ( 0 < nAtNum ) ------------------ | Branch (74:10): [True: 1.82M, False: 148k] ------------------ 75| 1.82M| { 76| 1.82M| nAtNum += 2; /* bypass D, T */ 77| 1.82M| } 78| | 79| 1.97M| if ( 0 <= nAtNum && nAtNum < nElDataLen ) ------------------ | Branch (79:10): [True: 1.97M, False: 0] | Branch (79:25): [True: 1.97M, False: 0] ------------------ 80| 1.97M| { 81| | /* valid element symbol found */ 82| 1.97M| strcpy(szElement, ElData[nAtNum].szElName); 83| | 84| 1.97M| if (!strcmp( szElement, "Zy" )) ------------------ | Branch (84:13): [True: 1.96k, False: 1.96M] ------------------ 85| 1.96k| { 86| 1.96k| strcpy(szElement, "Zz"); 87| 1.96k| } 88| | 89| 1.97M| return 0; 90| 1.97M| } 91| | 92| | /* not found */ 93| 0| strcpy(szElement, "??"); 94| | 95| 0| return -1; 96| 1.97M|} el_number_in_internal_ref_table: 101| 632k|{ 102| 632k| int i; 103| 632k| const char* p; 104| | 105| 31.1M| for (i = 0; ( p = ElData[i].szElName )[0] && strcmp( p, elname ); i++) ------------------ | Branch (105:17): [True: 31.1M, False: 29] | Branch (105:50): [True: 30.5M, False: 632k] ------------------ 106| 30.5M| { 107| 30.5M| ; 108| 30.5M| } 109| | 110| 632k| return p[0] ? i : ERR_ELEM; ------------------ | Branch (110:12): [True: 632k, False: 29] ------------------ 111| 632k|} get_periodic_table_number: 118| 1.24M|{ 119| 1.24M| int num; 120| | 121| 1.24M| if (elname == NULL) ------------------ | Branch (121:9): [True: 0, False: 1.24M] ------------------ 122| 0| { 123| 0| return ERR_ELEM; 124| 0| } 125| | 126| 1.24M| if (strlen(elname) == 0) ------------------ | Branch (126:9): [True: 0, False: 1.24M] ------------------ 127| 0| { 128| 0| return ERR_ELEM; 129| 0| } 130| | 131| | /* the single letter (common) elements */ 132| 1.24M| if (!elname[1]) ------------------ | Branch (132:9): [True: 1.04M, False: 198k] ------------------ 133| 1.04M| { 134| 1.04M| switch (elname[0]) ------------------ | Branch (134:17): [True: 743k, False: 300k] ------------------ 135| 1.04M| { 136| 144k| case 'H': ------------------ | Branch (136:13): [True: 144k, False: 900k] ------------------ 137| 144k| return EL_NUMBER_H; ------------------ | | 11| 144k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 138| 0| break; 139| 44.6k| case 'B': ------------------ | Branch (139:13): [True: 44.6k, False: 1.00M] ------------------ 140| 44.6k| return EL_NUMBER_B; ------------------ | | 12| 44.6k|#define EL_NUMBER_B ((U_CHAR)5) ------------------ 141| 0| break; 142| 115k| case 'C': ------------------ | Branch (142:13): [True: 115k, False: 929k] ------------------ 143| 115k| return EL_NUMBER_C; ------------------ | | 13| 115k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ 144| 0| break; 145| 121k| case 'N': ------------------ | Branch (145:13): [True: 121k, False: 923k] ------------------ 146| 121k| return EL_NUMBER_N; ------------------ | | 14| 121k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ 147| 0| break; 148| 212k| case 'O': ------------------ | Branch (148:13): [True: 212k, False: 832k] ------------------ 149| 212k| return EL_NUMBER_O; ------------------ | | 15| 212k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ 150| 0| break; 151| 24.0k| case 'P': ------------------ | Branch (151:13): [True: 24.0k, False: 1.02M] ------------------ 152| 24.0k| return EL_NUMBER_P; ------------------ | | 18| 24.0k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ 153| 0| break; 154| 54.9k| case 'S': ------------------ | Branch (154:13): [True: 54.9k, False: 989k] ------------------ 155| 54.9k| return EL_NUMBER_S; ------------------ | | 19| 54.9k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ 156| 0| break; 157| 13.1k| case 'F': ------------------ | Branch (157:13): [True: 13.1k, False: 1.03M] ------------------ 158| 13.1k| return EL_NUMBER_F; ------------------ | | 16| 13.1k|#define EL_NUMBER_F ((U_CHAR)9) ------------------ 159| 0| break; 160| 13.3k| case 'I': ------------------ | Branch (160:13): [True: 13.3k, False: 1.03M] ------------------ 161| 13.3k| return EL_NUMBER_I; ------------------ | | 27| 13.3k|#define EL_NUMBER_I ((U_CHAR)53) ------------------ 162| 0| break; 163| 1.04M| } 164| 1.04M| } 165| | 166| 499k| num = el_number_in_internal_ref_table( elname ); 167| | 168| 499k| if ( num < ERR_ELEM ) ------------------ | Branch (168:10): [True: 499k, False: 29] ------------------ 169| 499k| { 170| | /* account for D,T in internal table (but not Mendeleev's table) */ 171| 499k| num = inchi_max( 1, num - 1 ); ------------------ | | 138| 499k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 7.90k, False: 491k] | | ------------------ ------------------ 172| 499k| } 173| | 174| 499k| return num; 175| 1.24M|} if_skip_add_H: 183| 1.52M|{ 184| 1.52M| return 185| 1.52M| ElData[nPeriodicNum > 1 ? nPeriodicNum + 1 : 0].bSkipAddingH; ------------------ | Branch (185:16): [True: 1.43M, False: 87.9k] ------------------ 186| 1.52M|} get_el_valence: 193| 18.6M|{ 194| 18.6M| int idx = ( nPeriodicNum > 1 ) ? nPeriodicNum + 1 : 0; ------------------ | Branch (194:15): [True: 16.5M, False: 2.10M] ------------------ 195| | 196| | /* Bounds-check every index before touching ElData[].cValence[][]. 197| | * The original code guarded only the upper bound of val_num and the 198| | * charge range; a negative nPeriodicNum/val_num or an element number 199| | * beyond the table would read out of bounds. Return 0 (no known 200| | * valence) for any out-of-range input. */ 201| 18.6M| if ( nPeriodicNum < 0 || idx > nElDataLen || ------------------ | Branch (201:10): [True: 0, False: 18.6M] | Branch (201:30): [True: 0, False: 18.6M] ------------------ 202| 18.6M| val_num < 0 || val_num >= MAX_NUM_VALENCES || ------------------ | | 575| 37.3M|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (202:10): [True: 0, False: 18.6M] | Branch (202:25): [True: 0, False: 18.6M] ------------------ 203| 18.6M| charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE ) ------------------ | | 571| 37.3M|#define MIN_ATOM_CHARGE (-2) ------------------ charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE ) ------------------ | | 572| 18.6M|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (203:10): [True: 22, False: 18.6M] | Branch (203:38): [True: 312, False: 18.6M] ------------------ 204| 334| { 205| 334| return 0; 206| 334| } 207| | 208| 18.6M| return ElData[idx].cValence[NEUTRAL_STATE + charge][val_num]; ------------------ | | 573| 18.6M|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) | | ------------------ | | | | 571| 18.6M|#define MIN_ATOM_CHARGE (-2) | | ------------------ ------------------ 209| 18.6M|} get_unusual_el_valence: 221| 263k|{ 222| 263k| int i, num_found, chem_valence, rad_adj, known_chem_valence, exact_found; 223| | 224| 263k| if ( !num_bonds && !num_H ) ------------------ | Branch (224:10): [True: 1.84k, False: 261k] | Branch (224:24): [True: 0, False: 1.84k] ------------------ 225| 0| { 226| 0| return 0; 227| 0| } 228| | 229| 263k| if ( charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE ) ------------------ | | 571| 527k|#define MIN_ATOM_CHARGE (-2) ------------------ if ( charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE ) ------------------ | | 572| 263k|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (229:10): [True: 221, False: 263k] | Branch (229:38): [True: 1.31k, False: 262k] ------------------ 230| 1.53k| { 231| 1.53k| if ( bonds_valence == num_bonds ) ------------------ | Branch (231:14): [True: 1.38k, False: 151] ------------------ 232| 1.38k| { 233| 1.38k| return 0; /* all single bonds */ 234| 1.38k| } 235| 151| return bonds_valence; 236| 1.53k| } 237| | 238| 262k| if (!get_el_valence( nPeriodicNum, charge, 0 ) && bonds_valence == num_bonds) ------------------ | Branch (238:9): [True: 11.1k, False: 250k] | Branch (238:55): [True: 7.17k, False: 3.96k] ------------------ 239| 7.17k| { 240| 7.17k| return 0; 241| 7.17k| } 242| | 243| 254k| chem_valence = bonds_valence + num_H; 244| 254k| rad_adj = 0; 245| 254k| num_found = 0; 246| 254k| exact_found = 0; 247| | 248| | /* Take into account a radical */ 249| 254k| if ( radical == RADICAL_DOUBLET ) ------------------ | | 76| 254k|#define RADICAL_DOUBLET 2 ------------------ | Branch (249:10): [True: 17.2k, False: 237k] ------------------ 250| 17.2k| { 251| 17.2k| rad_adj = 1; 252| 17.2k| } 253| 237k| else if ( radical == RADICAL_TRIPLET ) ------------------ | | 77| 237k|#define RADICAL_TRIPLET 3 ------------------ | Branch (253:15): [True: 5.75k, False: 231k] ------------------ 254| 5.75k| { 255| 5.75k| rad_adj = 2; 256| 5.75k| } 257| | 258| 532k| for ( i = 0; i < MAX_NUM_VALENCES; i++ ) ------------------ | | 575| 532k|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (258:18): [True: 483k, False: 48.8k] ------------------ 259| 483k| { 260| 483k| if (0 < ( known_chem_valence = get_el_valence( nPeriodicNum, charge, i ) - rad_adj ) && ------------------ | Branch (260:13): [True: 300k, False: 182k] ------------------ 261| 300k| num_bonds <= known_chem_valence && known_chem_valence <= chem_valence) ------------------ | Branch (261:14): [True: 254k, False: 45.8k] | Branch (261:49): [True: 233k, False: 21.2k] ------------------ 262| 233k| { 263| 233k| num_found++; 264| 233k| if ( known_chem_valence == chem_valence ) ------------------ | Branch (264:18): [True: 206k, False: 27.6k] ------------------ 265| 206k| { 266| 206k| exact_found = 1; 267| 206k| break; 268| 206k| } 269| 233k| } 270| 483k| } 271| | 272| 254k| return ( exact_found && 1 == num_found ) ? 0 : chem_valence; ------------------ | Branch (272:14): [True: 206k, False: 48.8k] | Branch (272:29): [True: 189k, False: 16.5k] ------------------ 273| 262k|} needed_unusual_el_valence: 286| 318k|{ 287| 318k| int chem_valence, num_H_expected; /* djb-rwth: ignoring LLVM warning: variable used to store function return value */ 288| 318k| char szElement[4]; 289| | 290| | /* 291| | if ( !num_bonds && !num_H ) 292| | return 0; 293| | */ 294| | 295| 318k| if (num_bonds && get_element_chemical_symbol( nPeriodicNum, szElement ) != -1) ------------------ | Branch (295:9): [True: 133k, False: 184k] | Branch (295:22): [True: 133k, False: 0] ------------------ 296| 133k| { 297| 133k| num_H_expected = get_num_H( szElement, 0, NULL, charge, radical, actual_bonds_valence, 0, 0, 0, 0 ); 298| 133k| } 299| 184k| else 300| 184k| { 301| 184k| num_H_expected = num_H; 302| 184k| } 303| | 304| 318k| chem_valence = bonds_valence + num_H; 305| | 306| |#if ( (BUILD_WITH_ENG_OPTIONS==1) && (SDF_OUTPUT_HETERO_VALENCE==1) ) 307| | if ((nPeriodicNum == 1 && chem_valence != 1) /* H */ || (nPeriodicNum == 6 && chem_valence != 4) /* C */ || 308| | (nPeriodicNum != 1 && nPeriodicNum != 6) || charge || radical) /* djb-rwth: addressing LLVM warning */ 309| | { 310| | return chem_valence ? chem_valence : -1; 311| | } 312| | else 313| | { 314| | return 0; 315| | } 316| |#else 317| 318k| { 318| 318k| int i, num_found, num_found_known, rad_adj, known_chem_valence, exact_found; 319| | 320| 318k| if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || ------------------ | | 571| 637k|#define MIN_ATOM_CHARGE (-2) ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || ------------------ | | 572| 637k|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (320:13): [True: 46, False: 318k] | Branch (320:41): [True: 812, False: 317k] ------------------ 321| 317k| !get_el_valence( nPeriodicNum, charge, 0 ) || ------------------ | Branch (321:14): [True: 75.7k, False: 241k] ------------------ 322| 241k| if_skip_add_H( nPeriodicNum ) || bonds_valence != actual_bonds_valence || ------------------ | Branch (322:14): [True: 75.7k, False: 166k] | Branch (322:47): [True: 0, False: 166k] ------------------ 323| 166k| num_H_expected != num_H) ------------------ | Branch (323:14): [True: 820, False: 165k] ------------------ 324| 153k| { 325| 153k| if ( !num_H && !num_H_expected && bonds_valence == actual_bonds_valence ) ------------------ | Branch (325:18): [True: 152k, False: 236] | Branch (325:28): [True: 152k, False: 606] | Branch (325:47): [True: 152k, False: 0] ------------------ 326| 152k| { 327| 152k| return 0; /* no H */ 328| 152k| } 329| 842| return chem_valence; /* needs to add H-atoms */ 330| 153k| } 331| | 332| | /* take into account radical */ 333| 165k| if ( radical == RADICAL_DOUBLET ) ------------------ | | 76| 165k|#define RADICAL_DOUBLET 2 ------------------ | Branch (333:14): [True: 6.24k, False: 159k] ------------------ 334| 6.24k| { 335| 6.24k| rad_adj = 1; 336| 6.24k| } 337| 159k| else if ( radical == RADICAL_TRIPLET ) ------------------ | | 77| 159k|#define RADICAL_TRIPLET 3 ------------------ | Branch (337:19): [True: 3.10k, False: 156k] ------------------ 338| 3.10k| { 339| 3.10k| rad_adj = 2; 340| 3.10k| } 341| 156k| else 342| 156k| { 343| 156k| rad_adj = 0; 344| 156k| } 345| | 346| 165k| num_found_known = 0; 347| 165k| num_found = 0; 348| 165k| exact_found = 0; 349| | 350| 504k| for ( i = 0; i < MAX_NUM_VALENCES; i++ ) ------------------ | | 575| 504k|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (350:22): [True: 439k, False: 64.9k] ------------------ 351| 439k| { 352| 439k| if (0 < ( known_chem_valence = get_el_valence( nPeriodicNum, charge, i ) ) && ------------------ | Branch (352:17): [True: 219k, False: 219k] ------------------ 353| 219k| bonds_valence <= ( known_chem_valence -= rad_adj )) ------------------ | Branch (353:18): [True: 187k, False: 31.8k] ------------------ 354| 187k| { 355| | /* found known valence that fits without H */ 356| 187k| num_found_known++; 357| 187k| if ( known_chem_valence <= chem_valence ) ------------------ | Branch (357:22): [True: 100k, False: 87.3k] ------------------ 358| 100k| { 359| | /* known valence is large enough to accommodate (implicit) H */ 360| 100k| num_found++; 361| 100k| } 362| 187k| if ( known_chem_valence == chem_valence ) ------------------ | Branch (362:22): [True: 100k, False: 87.3k] ------------------ 363| 100k| { 364| 100k| exact_found = 1; 365| 100k| break; 366| 100k| } 367| 187k| } 368| 439k| } 369| | 370| 165k| return ( exact_found && 1 == num_found && 1 == num_found_known ) ------------------ | Branch (370:18): [True: 100k, False: 64.9k] | Branch (370:33): [True: 100k, False: 0] | Branch (370:51): [True: 100k, False: 0] ------------------ 371| 165k| ? 0 372| 165k| : chem_valence ? chem_valence : -1; /* needs zero */ ------------------ | Branch (372:15): [True: 14.9k, False: 49.9k] ------------------ 373| 318k| } 374| 318k|#endif 375| 318k|} detect_unusual_el_valence: 387| 2.11M|{ 388| 2.11M| int i, chem_valence, rad_adj, known_chem_valence; 389| | 390| 2.11M| if ( !num_bonds && !num_H ) ------------------ | Branch (390:10): [True: 556k, False: 1.55M] | Branch (390:24): [True: 555k, False: 483] ------------------ 391| 555k| { 392| 555k| return 0; 393| 555k| } 394| | 395| 1.55M| if ( charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE ) ------------------ | | 571| 3.11M|#define MIN_ATOM_CHARGE (-2) ------------------ if ( charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE ) ------------------ | | 572| 1.55M|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (395:10): [True: 20, False: 1.55M] | Branch (395:38): [True: 350, False: 1.55M] ------------------ 396| 370| { 397| 370| if ( bonds_valence == num_bonds ) ------------------ | Branch (397:14): [True: 332, False: 38] ------------------ 398| 332| { 399| 332| return 0; /* all single bonds */ 400| 332| } 401| 38| return bonds_valence; 402| 370| } 403| | 404| 1.55M| if (!get_el_valence( nPeriodicNum, charge, 0 ) && bonds_valence == num_bonds) ------------------ | Branch (404:9): [True: 38.7k, False: 1.52M] | Branch (404:55): [True: 17.1k, False: 21.5k] ------------------ 405| 17.1k| { 406| 17.1k| return 0; 407| 17.1k| } 408| | 409| 1.54M| chem_valence = bonds_valence + num_H; 410| 1.54M| rad_adj = 0; 411| | 412| | /* take into account radical */ 413| 1.54M| if ( radical == RADICAL_DOUBLET ) ------------------ | | 76| 1.54M|#define RADICAL_DOUBLET 2 ------------------ | Branch (413:10): [True: 42.9k, False: 1.49M] ------------------ 414| 42.9k| { 415| 42.9k| rad_adj = 1; 416| 42.9k| } 417| 1.49M| else if ( radical == RADICAL_TRIPLET || radical == RADICAL_SINGLET ) ------------------ | | 77| 2.99M|#define RADICAL_TRIPLET 3 ------------------ else if ( radical == RADICAL_TRIPLET || radical == RADICAL_SINGLET ) ------------------ | | 75| 1.49M|#define RADICAL_SINGLET 1 ------------------ | Branch (417:15): [True: 5.53k, False: 1.49M] | Branch (417:45): [True: 0, False: 1.49M] ------------------ 418| 5.53k| { 419| 5.53k| rad_adj = 2; 420| 5.53k| } 421| | 422| 2.92M| for ( i = 0; i < MAX_NUM_VALENCES; i++ ) ------------------ | | 575| 2.92M|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (422:18): [True: 2.70M, False: 218k] ------------------ 423| 2.70M| { 424| 2.70M| if (0 < ( known_chem_valence = get_el_valence( nPeriodicNum, charge, i ) - rad_adj )) ------------------ | Branch (424:13): [True: 1.85M, False: 849k] ------------------ 425| 1.85M| { 426| 1.85M| if ( known_chem_valence == chem_valence ) ------------------ | Branch (426:18): [True: 1.32M, False: 531k] ------------------ 427| 1.32M| { 428| 1.32M| return 0; 429| 1.32M| } 430| 1.85M| } 431| 2.70M| } 432| | 433| 218k| return chem_valence; 434| 1.54M|} get_el_type: 441| 95.0k|{ 442| 95.0k| return ElData[nPeriodicNum + 1].nType; 443| 95.0k|} is_el_a_metal: 450| 6.67M|{ 451| 6.67M| return 0 != ( ElData[nPeriodicNum + 1].nType & IS_METAL ); ------------------ | | 82| 6.67M|#define IS_METAL 3 /* metal bitmap */ ------------------ 452| 6.67M|} get_num_H: 633| 133k|{ 634| 133k| int val, i, el_number, num_H = 0, num_iso_H; 635| 133k| static int intl_el_number_N = 0, intl_el_number_S=0, intl_el_number_O=0, intl_el_number_C=0; 636| | 637| 133k| if ( !intl_el_number_N ) ------------------ | Branch (637:10): [True: 1, False: 133k] ------------------ 638| 1| { 639| 1| intl_el_number_N = el_number_in_internal_ref_table( "N" ); 640| 1| } 641| 133k| if ( !intl_el_number_S ) ------------------ | Branch (641:10): [True: 1, False: 133k] ------------------ 642| 1| { 643| 1| intl_el_number_S = el_number_in_internal_ref_table( "S" ); 644| 1| } 645| 133k| if ( !intl_el_number_O ) ------------------ | Branch (645:10): [True: 1, False: 133k] ------------------ 646| 1| { 647| 1| intl_el_number_O = el_number_in_internal_ref_table( "O" ); 648| 1| } 649| 133k| if ( !intl_el_number_C ) ------------------ | Branch (649:10): [True: 1, False: 133k] ------------------ 650| 1| { 651| 1| intl_el_number_C = el_number_in_internal_ref_table( "C" ); 652| 1| } 653| | 654| | 655| | /* atom_input_valence (cValence) cannot be specified in case of */ 656| | /* aliased MOLFile atom with known inp_num_H or inp_num_iso_H[] */ 657| | 658| 133k| if ( bAliased ) ------------------ | Branch (658:10): [True: 0, False: 133k] ------------------ 659| 0| { 660| 0| num_H = inp_num_H; 661| 0| } 662| 133k| else if (atom_input_valence && atom_input_valence != 15) ------------------ | Branch (662:14): [True: 0, False: 133k] | Branch (662:36): [True: 0, False: 0] ------------------ 663| 0| { 664| 0| num_H = inchi_max( 0, atom_input_valence - chem_bonds_valence ); ------------------ | | 138| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 0, False: 0] | | ------------------ ------------------ 665| 0| } 666| 133k| else if ( atom_input_valence == 15 ) ------------------ | Branch (666:15): [True: 0, False: 133k] ------------------ 667| 0| { 668| | /* Explicit zero valence (V3000 VAL=-1 / V2000 valence field 15): the */ 669| | /* atom must carry neither implicit H nor (chemically) any bonds. Honour */ 670| | /* the zero valence regardless of whether bonds were drawn, instead of */ 671| | /* treating 15 as a literal target valence and adding 15 - chem_bonds_valence */ 672| | /* hydrogens (github #105). */ 673| 0| num_H = 0; 674| 0| } 675| 133k| else if (MIN_ATOM_CHARGE <= charge && ------------------ | | 571| 133k|#define MIN_ATOM_CHARGE (-2) ------------------ | Branch (675:14): [True: 133k, False: 44] ------------------ 676| 133k| MAX_ATOM_CHARGE >= charge && ------------------ | | 572| 133k|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (676:15): [True: 133k, False: 812] ------------------ 677| 133k| ERR_ELEM != ( el_number = el_number_in_internal_ref_table( elname ) ) && ------------------ | Branch (677:15): [True: 133k, False: 0] ------------------ 678| 133k| !ElData[el_number].bSkipAddingH && !bDoNotAddH) ------------------ | Branch (678:15): [True: 116k, False: 16.4k] | Branch (678:50): [True: 116k, False: 0] ------------------ 679| 116k| { 680| | /* add hydrogen atoms according to standard element valence */ 681| 116k| if ( radical && radical != RADICAL_SINGLET ) ------------------ | | 75| 9.75k|#define RADICAL_SINGLET 1 ------------------ | Branch (681:14): [True: 9.75k, False: 106k] | Branch (681:25): [True: 9.75k, False: 0] ------------------ 682| 9.75k| { 683| 9.75k| if ( (val = ElData[el_number].cValence[NEUTRAL_STATE + charge][0]) ) /* djb-rwth: addressing LLVM warning */ ------------------ | | 573| 9.75k|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) | | ------------------ | | | | 571| 9.75k|#define MIN_ATOM_CHARGE (-2) | | ------------------ ------------------ | Branch (683:18): [True: 9.65k, False: 102] ------------------ 684| 9.65k| { 685| 9.65k| val -= ( radical == RADICAL_DOUBLET ) ? 1 ------------------ | | 76| 9.65k|#define RADICAL_DOUBLET 2 ------------------ | Branch (685:24): [True: 6.25k, False: 3.40k] ------------------ 686| 9.65k| : ( radical == RADICAL_SINGLET || radical == RADICAL_TRIPLET ) ? 2 : val; ------------------ | | 75| 6.80k|#define RADICAL_SINGLET 1 ------------------ : ( radical == RADICAL_SINGLET || radical == RADICAL_TRIPLET ) ? 2 : val; ------------------ | | 77| 3.40k|#define RADICAL_TRIPLET 3 ------------------ | Branch (686:25): [True: 0, False: 3.40k] | Branch (686:55): [True: 3.12k, False: 278] ------------------ 687| | /* if unknown radical then do not add H */ 688| 9.65k| num_H = inchi_max( 0, val - chem_bonds_valence ); ------------------ | | 138| 9.65k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 902, False: 8.75k] | | ------------------ ------------------ 689| 9.65k| } 690| 9.75k| } 691| 106k| else 692| 106k| { 693| | /* find the smallest valence that is greater than the sum of the chemical bond valences */ 694| 106k| for (i = 0; 695| 138k| ( val = ElData[el_number].cValence[NEUTRAL_STATE + charge][i] ) && ------------------ | | 573| 138k|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) | | ------------------ | | | | 571| 138k|#define MIN_ATOM_CHARGE (-2) | | ------------------ ------------------ | Branch (695:18): [True: 123k, False: 14.5k] ------------------ 696| 123k| val < chem_bonds_valence; ------------------ | Branch (696:18): [True: 31.5k, False: 92.4k] ------------------ 697| 106k| i++) 698| 31.5k| { 699| 31.5k| ; 700| 31.5k| } 701| | 702| | /* special case: do not add H to N(IV), S(III), S+(II), S-(II) */ /* S ions added 2004-05-10 */ 703| 106k| if ( el_number == intl_el_number_N && !charge && !radical && val == 5 ) ------------------ | Branch (703:18): [True: 25.0k, False: 81.9k] | Branch (703:51): [True: 15.2k, False: 9.75k] | Branch (703:62): [True: 15.2k, False: 0] | Branch (703:74): [True: 3.29k, False: 11.9k] ------------------ 704| 3.29k| { 705| 3.29k| val = 3; 706| 3.29k| } 707| | /*else if ( el_number == el_number_N && !charge && !radical && val == 3 && 708| | chem_bonds_valence == 2 && bHasMetalNeighbor ) 709| | { 710| | val = 2; 711| | } 712| | */ 713| 103k| else if ( el_number == intl_el_number_S && !charge && !radical && val == 4 && chem_bonds_valence == 3 ) ------------------ | Branch (713:23): [True: 8.13k, False: 95.5k] | Branch (713:56): [True: 4.86k, False: 3.27k] | Branch (713:67): [True: 4.86k, False: 0] | Branch (713:79): [True: 1.13k, False: 3.73k] | Branch (713:91): [True: 54, False: 1.07k] ------------------ 714| 54| { 715| 54| val = 3; 716| 54| } 717| 103k| else if ( bHasMetalNeighbor && el_number != intl_el_number_C && val > 0 ) ------------------ | Branch (717:23): [True: 0, False: 103k] | Branch (717:44): [True: 0, False: 0] | Branch (717:77): [True: 0, False: 0] ------------------ 718| 0| { 719| 0| val--; 720| 0| } 721| | /* 722| | if ( (el_number == el_number_S || el_number == el_number_O) && 723| | abs(charge)==1 && !radical && val == 3 && chem_bonds_valence == 2 && bHasMetalNeighbor ) 724| | { 725| | val = 2; 726| | } 727| | else 728| | */ 729| | 730| 106k| num_H = inchi_max( 0, val - chem_bonds_valence ); ------------------ | | 138| 106k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (138:26): [True: 17.8k, False: 89.1k] | | ------------------ ------------------ 731| 106k| } 732| | 733| 116k| num_iso_H = 0; 734| 116k| if ( inp_num_iso_H ) ------------------ | Branch (734:14): [True: 0, False: 116k] ------------------ 735| 0| { 736| 0| for ( i = 0; i < NUM_H_ISOTOPES; i++ ) ------------------ | | 25| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (736:26): [True: 0, False: 0] ------------------ 737| 0| { 738| 0| num_iso_H += inp_num_iso_H[i]; 739| 0| } 740| 0| } 741| | 742| | /* should not happen because atom here is not aliased */ 743| 116k| if ( num_iso_H ) ------------------ | Branch (743:14): [True: 0, False: 116k] ------------------ 744| 0| { 745| 0| if ( num_H >= num_iso_H ) ------------------ | Branch (745:18): [True: 0, False: 0] ------------------ 746| 0| { 747| 0| num_H -= num_iso_H; 748| 0| } 749| 0| else 750| 0| { 751| 0| num_H = inp_num_H; /* as requested in the alias */ 752| | /* num_H = (num_iso_H - num_H) % 2; */ /* keep unchanged parity of the total number of H atoms */ 753| 0| } 754| 0| } 755| | 756| | /* should not happen because atom here is not aliased */ 757| 116k| if ( inp_num_H > num_H ) ------------------ | Branch (757:14): [True: 0, False: 116k] ------------------ 758| 0| { 759| 0| num_H = inp_num_H; /* as requested in the alias */ 760| | /* num_H = inp_num_H + (inp_num_H - num_H)%2; */ /* keep unchanged parity of the number of non-isotopic H atoms */ 761| 0| } 762| 116k| } 763| 17.2k| else 764| 17.2k| { 765| 17.2k| num_H = inp_num_H; 766| 17.2k| } 767| | 768| 133k| return num_H; 769| 133k|} get_atomic_mass_from_elnum: 774| 1.46k|{ 775| 1.46k| nAtNum -= 1; 776| | 777| 1.46k| if ( 0 < nAtNum ) ------------------ | Branch (777:10): [True: 186, False: 1.27k] ------------------ 778| 186| { 779| 186| nAtNum += 2; /* bypass D, T */ 780| 186| } 781| | 782| 1.46k| if ( 0 <= nAtNum && nAtNum < nElDataLen ) ------------------ | Branch (782:10): [True: 1.46k, False: 0] | Branch (782:25): [True: 1.46k, False: 0] ------------------ 783| 1.46k| { 784| 1.46k| return (int) ElData[nAtNum].nAtMass; 785| 1.46k| } 786| | 787| 0| return 0; 788| 1.46k|} is_in_the_list: 826| 138k|{ 827| 242k| for ( ; nPathLen && *pathAtom != nNextAtom; nPathLen--, pathAtom++ ) ------------------ | Branch (827:13): [True: 242k, False: 292] | Branch (827:25): [True: 104k, False: 138k] ------------------ 828| 104k| { 829| 104k| ; 830| 104k| } 831| 138k| return nPathLen ? pathAtom : NULL; ------------------ | Branch (831:12): [True: 138k, False: 292] ------------------ 832| 138k|} num_of_H: 895| 372k|{ 896| 372k| static int el_number_H = (int)EL_NUMBER_H; ------------------ | | 11| 372k|#define EL_NUMBER_H ((U_CHAR)1) ------------------ 897| 372k| int i, n, num_explicit_H = 0; 898| 372k| inp_ATOM *a = at + iat; 899| | 900| 1.07M| for (i = 0; i < a->valence; i++) ------------------ | Branch (900:17): [True: 700k, False: 372k] ------------------ 901| 700k| { 902| 700k| n = a->neighbor[i]; 903| 700k| num_explicit_H += ( 1 == at[n].valence && el_number_H == at[n].el_number ); ------------------ | Branch (903:29): [True: 210k, False: 489k] | Branch (903:51): [True: 33.2k, False: 177k] ------------------ 904| 700k| } 905| | 906| 372k| return num_explicit_H + NUMH( at, iat ); ------------------ | | 56| 372k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 372k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 907| 372k|} ion_el_group: 917| 517k|{ 918| 517k| switch ( el ) 919| 517k| { 920| 47.3k| case EL_NUMBER_C: /* fallthrough */ ------------------ | | 13| 47.3k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ | Branch (920:9): [True: 47.3k, False: 470k] ------------------ 921| |#if ( FIX_REM_ION_PAIRS_Si_BUG == 1 ) 922| | case EL_NUMBER_SI: 923| |#endif 924| 47.3k| return EL_NUMBER_C; ------------------ | | 13| 47.3k|#define EL_NUMBER_C ((U_CHAR)6) ------------------ 925| 132k| case EL_NUMBER_N: /* fallthrough */ ------------------ | | 14| 132k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (925:9): [True: 132k, False: 385k] ------------------ 926| 167k| case EL_NUMBER_P: ------------------ | | 18| 167k|#define EL_NUMBER_P ((U_CHAR)15) ------------------ | Branch (926:9): [True: 35.1k, False: 482k] ------------------ 927| 174k| case EL_NUMBER_AS: ------------------ | | 22| 174k|#define EL_NUMBER_AS ((U_CHAR)33) ------------------ | Branch (927:9): [True: 7.57k, False: 509k] ------------------ 928| 175k| case EL_NUMBER_SB: ------------------ | | 25| 175k|#define EL_NUMBER_SB ((U_CHAR)51) ------------------ | Branch (928:9): [True: 784, False: 516k] ------------------ 929| 175k| return EL_NUMBER_N; ------------------ | | 14| 175k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ 930| 112k| case EL_NUMBER_O: /* fallthrough */ ------------------ | | 15| 112k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (930:9): [True: 112k, False: 404k] ------------------ 931| 178k| case EL_NUMBER_S: ------------------ | | 19| 178k|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (931:9): [True: 66.3k, False: 451k] ------------------ 932| 186k| case EL_NUMBER_SE: ------------------ | | 23| 186k|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (932:9): [True: 7.36k, False: 510k] ------------------ 933| 198k| case EL_NUMBER_TE: ------------------ | | 26| 198k|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (933:9): [True: 11.7k, False: 505k] ------------------ 934| 198k| return EL_NUMBER_O; ------------------ | | 15| 198k|#define EL_NUMBER_O ((U_CHAR)8) ------------------ 935| 96.4k| default: ------------------ | Branch (935:9): [True: 96.4k, False: 421k] ------------------ 936| 96.4k| return 0; 937| 517k| } 938| 517k|} has_other_ion_neigh: 943| 3.21k|{ 944| 3.21k| int charge = at[iat_ion_neigh].charge; 945| 3.21k| int i, neigh; 946| | 947| 9.05k| for ( i = 0; i < at[iat].valence; i++ ) ------------------ | Branch (947:18): [True: 6.74k, False: 2.31k] ------------------ 948| 6.74k| { 949| 6.74k| neigh = at[iat].neighbor[i]; 950| | 951| 6.74k| if (neigh != iat_ion_neigh && at[neigh].charge == charge && ------------------ | Branch (951:13): [True: 3.82k, False: 2.91k] | Branch (951:39): [True: 1.01k, False: 2.81k] ------------------ 952| 1.01k| ion_el_group( at[neigh].el_number )) ------------------ | Branch (952:13): [True: 902, False: 112] ------------------ 953| 902| { 954| 902| return 1; 955| 902| } 956| 6.74k| } 957| | 958| 2.31k| return 0; 959| 3.21k|} has_other_ion_in_sphere_2: 968| 30|{ 969| 30|#define MAXQ 16 970| 30| AT_NUMB q[MAXQ]; 971| 30| int lenq = 0, lenq2, dist = 0, i = 0, iq, neigh, j, nRet = 0; 972| 30| q[lenq++] = iat; 973| 30| at[iat].cFlags = 1; 974| | 975| 30| iq = 0; 976| 30| dist = 1; 977| | /* use at->cFlags as an indicator */ 978| | 979| 90| while ( dist <= 2 ) ------------------ | Branch (979:13): [True: 60, False: 30] ------------------ 980| 60| { 981| 130| for ( lenq2 = lenq; iq < lenq2; iq++ ) ------------------ | Branch (981:29): [True: 70, False: 60] ------------------ 982| 70| { 983| 70| i = q[iq]; 984| | 985| 214| for ( j = 0; j < at[i].valence; j++ ) ------------------ | Branch (985:26): [True: 144, False: 70] ------------------ 986| 144| { 987| 144| neigh = at[i].neighbor[j]; 988| | 989| 144| if (!at[neigh].cFlags && ------------------ | Branch (989:21): [True: 104, False: 40] ------------------ 990| 104| at[neigh].valence <= 3 && ------------------ | Branch (990:22): [True: 95, False: 9] ------------------ 991| 95| ion_el_group( at[neigh].el_number )) ------------------ | Branch (991:22): [True: 79, False: 16] ------------------ 992| 79| { 993| 79| q[lenq++] = neigh; 994| 79| at[neigh].cFlags = 1; 995| 79| if (neigh != iat_ion_neigh && ------------------ | Branch (995:25): [True: 49, False: 30] ------------------ 996| 49| at[iat_ion_neigh].charge == at[neigh].charge) ------------------ | Branch (996:26): [True: 6, False: 43] ------------------ 997| 6| { 998| 6| nRet++; 999| 6| } 1000| 79| } 1001| 144| } 1002| 70| } 1003| | 1004| 60| dist++; 1005| 60| } 1006| | 1007| 139| for ( iq = 0; iq < lenq; iq++ ) ------------------ | Branch (1007:19): [True: 109, False: 30] ------------------ 1008| 109| { 1009| 109| i = q[iq]; 1010| 109| at[i].cFlags = 0; 1011| 109| } 1012| | 1013| 30| return nRet; 1014| 30|} nNoMetalNumBonds: 1019| 1.33M|{ 1020| 1.33M| int i; 1021| | 1022| 1.33M| inp_ATOM *a = at + at_no; 1023| 1.33M| int num_H = NUMH( a, 0 ); ------------------ | | 56| 1.33M|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 1.33M|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 1024| 1.33M| int std_chem_bonds_valence = get_el_valence( a->el_number, a->charge, 0 ); 1025| | 1026| 1.33M| if ( a->chem_bonds_valence + num_H > std_chem_bonds_valence ) ------------------ | Branch (1026:10): [True: 356k, False: 977k] ------------------ 1027| 356k| { 1028| 356k| int valence_to_metal = 0; 1029| 356k| int num_bonds_to_metal = 0; 1030| | 1031| 1.40M| for ( i = 0; i < a->valence; i++ ) ------------------ | Branch (1031:22): [True: 1.04M, False: 356k] ------------------ 1032| 1.04M| { 1033| 1.04M| if (is_el_a_metal( at[(int) a->neighbor[i]].el_number )) ------------------ | Branch (1033:17): [True: 91.7k, False: 956k] ------------------ 1034| 91.7k| { 1035| 91.7k| if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 189| 91.7k|#define BOND_TYPE_MASK 0x0f ------------------ if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 35| 91.7k|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (1035:21): [True: 0, False: 91.7k] ------------------ 1036| 0| { 1037| 0| return a->valence; /* fall back */ 1038| 0| } 1039| 91.7k| num_bonds_to_metal++; 1040| 91.7k| valence_to_metal += ( a->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 189| 91.7k|#define BOND_TYPE_MASK 0x0f ------------------ 1041| 91.7k| } 1042| 1.04M| } 1043| | 1044| 356k| if ( a->chem_bonds_valence + num_H - valence_to_metal == std_chem_bonds_valence ) ------------------ | Branch (1044:14): [True: 31.2k, False: 325k] ------------------ 1045| 31.2k| { 1046| | /* removing bonds to metal produces standard valence */ 1047| 31.2k| return a->valence - num_bonds_to_metal; 1048| 31.2k| } 1049| 356k| } 1050| | 1051| 977k|#if ( S_VI_O_PLUS_METAL_FIX_BOND == 1 ) 1052| 977k| else 1053| 977k| { 1054| 977k| if (1 == a->charge && 2 == get_endpoint_valence( a->el_number ) && ------------------ | Branch (1054:13): [True: 92.1k, False: 884k] | Branch (1054:31): [True: 40.6k, False: 51.5k] ------------------ 1055| 40.6k| a->chem_bonds_valence + num_H == std_chem_bonds_valence) ------------------ | Branch (1055:17): [True: 40.1k, False: 488] ------------------ 1056| 40.1k| { 1057| 40.1k| int valence_to_metal = 0; 1058| 40.1k| int num_bonds_to_metal = 0; 1059| 134k| for ( i = 0; i < a->valence; i++ ) ------------------ | Branch (1059:26): [True: 94.3k, False: 40.1k] ------------------ 1060| 94.3k| { 1061| 94.3k| if (is_el_a_metal( at[(int) a->neighbor[i]].el_number )) ------------------ | Branch (1061:21): [True: 4.77k, False: 89.5k] ------------------ 1062| 4.77k| { 1063| 4.77k| if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 189| 4.77k|#define BOND_TYPE_MASK 0x0f ------------------ if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 35| 4.77k|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (1063:25): [True: 0, False: 4.77k] ------------------ 1064| 0| { 1065| 0| return a->valence; /* fall back */ 1066| 0| } 1067| 4.77k| num_bonds_to_metal++; 1068| 4.77k| valence_to_metal += ( a->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 189| 4.77k|#define BOND_TYPE_MASK 0x0f ------------------ 1069| 4.77k| } 1070| 94.3k| } 1071| 40.1k| if ( 1 == valence_to_metal ) ------------------ | Branch (1071:18): [True: 1.89k, False: 38.2k] ------------------ 1072| 1.89k| { 1073| | /* removing bonds to metal produces standard valence */ 1074| 1.89k| return a->valence - num_bonds_to_metal; 1075| 1.89k| } 1076| 40.1k| } 1077| 977k| } 1078| 1.30M|#endif 1079| | 1080| 1.30M| return a->valence; 1081| 1.33M|} nNoMetalBondsValence: 1086| 756k|{ 1087| 756k| int i; 1088| | 1089| 756k| inp_ATOM *a = at + at_no; 1090| 756k| int num_H = NUMH( a, 0 ); ------------------ | | 56| 756k|#define NUMH(AT, N) (AT[N].num_H + NUM_ISO_H(AT, N)) | | ------------------ | | | | 55| 756k|#define NUM_ISO_H(AT, N) (AT[N].num_iso_H[0] + AT[N].num_iso_H[1] + AT[N].num_iso_H[2]) | | ------------------ ------------------ 1091| 756k| int std_chem_bonds_valence = get_el_valence( a->el_number, a->charge, 0 ); 1092| | 1093| 756k| if ( a->chem_bonds_valence + num_H > std_chem_bonds_valence ) ------------------ | Branch (1093:10): [True: 149k, False: 606k] ------------------ 1094| 149k| { 1095| 149k| int valence_to_metal = 0; 1096| | /*int num_bonds_to_metal = 0;*/ 1097| | 1098| 550k| for ( i = 0; i < a->valence; i++ ) ------------------ | Branch (1098:22): [True: 401k, False: 149k] ------------------ 1099| 401k| { 1100| 401k| if (is_el_a_metal( at[(int) a->neighbor[i]].el_number )) ------------------ | Branch (1100:17): [True: 59.7k, False: 341k] ------------------ 1101| 59.7k| { 1102| 59.7k| if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 189| 59.7k|#define BOND_TYPE_MASK 0x0f ------------------ if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 35| 59.7k|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (1102:21): [True: 0, False: 59.7k] ------------------ 1103| 0| { 1104| 0| return a->valence; /* fall back */ 1105| 0| } 1106| | /* num_bonds_to_metal ++;*/ 1107| 59.7k| valence_to_metal += ( a->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 189| 59.7k|#define BOND_TYPE_MASK 0x0f ------------------ 1108| 59.7k| } 1109| 401k| } 1110| | 1111| 149k| if ( a->chem_bonds_valence + num_H - valence_to_metal == std_chem_bonds_valence ) ------------------ | Branch (1111:14): [True: 32.1k, False: 117k] ------------------ 1112| 32.1k| { 1113| | /* removing bonds to metal produces standard valence */ 1114| 32.1k| return a->chem_bonds_valence - valence_to_metal; 1115| 32.1k| } 1116| 149k| } 1117| | 1118| 606k|#if ( S_VI_O_PLUS_METAL_FIX_BOND == 1 ) 1119| 606k| else if (1 == a->charge && 2 == get_endpoint_valence( a->el_number ) && ------------------ | Branch (1119:14): [True: 89.3k, False: 517k] | Branch (1119:32): [True: 40.0k, False: 49.2k] ------------------ 1120| 40.0k| a->chem_bonds_valence + num_H == std_chem_bonds_valence) ------------------ | Branch (1120:10): [True: 39.6k, False: 433] ------------------ 1121| 39.6k| { 1122| | 1123| 39.6k| int valence_to_metal = 0; 1124| | /* int num_bonds_to_metal = 0;*/ 1125| | 1126| 133k| for ( i = 0; i < a->valence; i++ ) ------------------ | Branch (1126:22): [True: 93.4k, False: 39.6k] ------------------ 1127| 93.4k| { 1128| 93.4k| if (is_el_a_metal( at[(int) a->neighbor[i]].el_number )) ------------------ | Branch (1128:17): [True: 4.68k, False: 88.7k] ------------------ 1129| 4.68k| { 1130| 4.68k| if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 189| 4.68k|#define BOND_TYPE_MASK 0x0f ------------------ if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 35| 4.68k|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (1130:21): [True: 0, False: 4.68k] ------------------ 1131| 0| { 1132| 0| return a->valence; /* fall back */ 1133| 0| } 1134| | /* num_bonds_to_metal ++;*/ 1135| 4.68k| valence_to_metal += ( a->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 189| 4.68k|#define BOND_TYPE_MASK 0x0f ------------------ 1136| 4.68k| } 1137| 93.4k| } 1138| | 1139| 39.6k| if (1 == valence_to_metal) ------------------ | Branch (1139:13): [True: 1.82k, False: 37.7k] ------------------ 1140| 1.82k| {/* removing bonds to metal produces standard valence */ 1141| 1.82k| return a->chem_bonds_valence - valence_to_metal; 1142| 1.82k| } 1143| 39.6k| } 1144| 722k|#endif 1145| | 1146| 722k| return a->chem_bonds_valence; 1147| 756k|} nNoMetalNeighIndex: 1152| 185k|{ 1153| 185k| int i; 1154| | 1155| 185k| inp_ATOM* a = at + at_no; 1156| | 1157| 194k| for ( i = 0; i < a->valence; i++ ) ------------------ | Branch (1157:18): [True: 186k, False: 8.19k] ------------------ 1158| 186k| { 1159| 186k| if (!is_el_a_metal( at[(int) a->neighbor[i]].el_number )) ------------------ | Branch (1159:13): [True: 177k, False: 9.22k] ------------------ 1160| 177k| { 1161| 177k| return i; 1162| 177k| } 1163| 186k| } 1164| | 1165| 8.19k| return -1; 1166| 185k|} nNoMetalOtherNeighIndex: 1171| 17.7k|{ 1172| 17.7k| int i, neigh; 1173| | 1174| 17.7k| inp_ATOM* a = at + at_no; 1175| | 1176| 36.8k| for ( i = 0; i < a->valence; i++ ) ------------------ | Branch (1176:18): [True: 35.7k, False: 1.16k] ------------------ 1177| 35.7k| { 1178| 35.7k| neigh = (int) a->neighbor[i]; 1179| | 1180| 35.7k| if (neigh != cur_neigh && !is_el_a_metal( at[neigh].el_number )) ------------------ | Branch (1180:13): [True: 18.3k, False: 17.3k] | Branch (1180:35): [True: 16.5k, False: 1.79k] ------------------ 1181| 16.5k| { 1182| 16.5k| return i; 1183| 16.5k| } 1184| 35.7k| } 1185| | 1186| 1.16k| return -1; 1187| 17.7k|} nNoMetalOtherNeighIndex2: 1195| 10.7k|{ 1196| 10.7k| int i, neigh; 1197| | 1198| 10.7k| inp_ATOM* a = at + at_no; 1199| | 1200| 33.1k| for ( i = 0; i < a->valence; i++ ) ------------------ | Branch (1200:18): [True: 32.0k, False: 1.10k] ------------------ 1201| 32.0k| { 1202| 32.0k| neigh = (int) a->neighbor[i]; 1203| | 1204| 32.0k| if (neigh != cur_neigh && neigh != cur_neigh2 && !is_el_a_metal( at[neigh].el_number )) ------------------ | Branch (1204:13): [True: 21.3k, False: 10.6k] | Branch (1204:35): [True: 10.7k, False: 10.6k] | Branch (1204:58): [True: 9.61k, False: 1.10k] ------------------ 1205| 9.61k| { 1206| 9.61k| return i; 1207| 9.61k| } 1208| 32.0k| } 1209| | 1210| 1.10k| return -1; 1211| 10.7k|} get_endpoint_valence: 1275| 7.06M|{ 1276| 7.06M| switch (el_number) 1277| 7.06M| { 1278| 1.36M| case EL_NUMBER_O: /* fallthrough */ ------------------ | | 15| 1.36M|#define EL_NUMBER_O ((U_CHAR)8) ------------------ | Branch (1278:9): [True: 1.36M, False: 5.70M] ------------------ 1279| 1.65M| case EL_NUMBER_S: ------------------ | | 19| 1.65M|#define EL_NUMBER_S ((U_CHAR)16) ------------------ | Branch (1279:9): [True: 291k, False: 6.77M] ------------------ 1280| 1.67M| case EL_NUMBER_SE: ------------------ | | 23| 1.67M|#define EL_NUMBER_SE ((U_CHAR)34) ------------------ | Branch (1280:9): [True: 20.0k, False: 7.04M] ------------------ 1281| 1.70M| case EL_NUMBER_TE: ------------------ | | 26| 1.70M|#define EL_NUMBER_TE ((U_CHAR)52) ------------------ | Branch (1281:9): [True: 29.9k, False: 7.03M] ------------------ 1282| 1.70M| return 2; 1283| 982k| case EL_NUMBER_N: ------------------ | | 14| 982k|#define EL_NUMBER_N ((U_CHAR)7) ------------------ | Branch (1283:9): [True: 982k, False: 6.08M] ------------------ 1284| 982k| return 3; 1285| 4.37M| default: ------------------ | Branch (1285:9): [True: 4.37M, False: 2.69M] ------------------ 1286| 4.37M| return 0; 1287| 7.06M| } 1288| 7.06M|} extract_inchi_substring: 1626| 6.35k|{ 1627| 6.35k| size_t i; 1628| 6.35k| const char *p; 1629| 6.35k| char* bufp; 1630| 6.35k| char pp; 1631| | 1632| 6.35k| bufp = *buf; 1633| 6.35k| *buf = NULL; 1634| | 1635| 6.35k| if ( str == NULL ) ------------------ | Branch (1635:10): [True: 0, False: 6.35k] ------------------ 1636| 0| { 1637| 0| return; 1638| 0| } 1639| 6.35k| if (strlen( str ) < 1) ------------------ | Branch (1639:9): [True: 0, False: 6.35k] ------------------ 1640| 0| { 1641| 0| return; 1642| 0| } 1643| | 1644| 6.35k| p = strstr( str, "InChI=" ); 1645| 6.35k| if (NULL == p) ------------------ | Branch (1645:9): [True: 0, False: 6.35k] ------------------ 1646| 0| return; 1647| | 1648| 4.20M| for ( i = 0; i < slen; i++ ) ------------------ | Branch (1648:18): [True: 4.20M, False: 6.16k] ------------------ 1649| 4.20M| { 1650| 4.20M| pp = p[i]; 1651| | 1652| 4.20M| if (pp >= 'A' && pp <= 'Z') continue; ------------------ | Branch (1652:13): [True: 2.34M, False: 1.86M] | Branch (1652:26): [True: 530k, False: 1.81M] ------------------ 1653| 3.67M| if (pp >= 'a' && pp <= 'z') continue; ------------------ | Branch (1653:13): [True: 1.81M, False: 1.86M] | Branch (1653:26): [True: 1.81M, False: 0] ------------------ 1654| 1.86M| if (pp >= '0' && pp <= '9') continue; ------------------ | Branch (1654:13): [True: 956k, False: 904k] | Branch (1654:26): [True: 881k, False: 74.7k] ------------------ 1655| 979k| switch (pp) 1656| 979k| { 1657| 219k| case '(': ------------------ | Branch (1657:13): [True: 219k, False: 760k] ------------------ 1658| 419k| case ')': ------------------ | Branch (1658:13): [True: 200k, False: 779k] ------------------ 1659| 454k| case '*': ------------------ | Branch (1659:13): [True: 35.3k, False: 944k] ------------------ 1660| 456k| case '+': ------------------ | Branch (1660:13): [True: 1.46k, False: 977k] ------------------ 1661| 563k| case ',': ------------------ | Branch (1661:13): [True: 107k, False: 872k] ------------------ 1662| 705k| case '-': ------------------ | Branch (1662:13): [True: 142k, False: 837k] ------------------ 1663| 713k| case '.': ------------------ | Branch (1663:13): [True: 8.11k, False: 971k] ------------------ 1664| 904k| case '/': ------------------ | Branch (1664:13): [True: 190k, False: 788k] ------------------ 1665| 908k| case ';': ------------------ | Branch (1665:13): [True: 4.24k, False: 975k] ------------------ 1666| 974k| case '=': ------------------ | Branch (1666:13): [True: 65.5k, False: 913k] ------------------ 1667| 979k| case '?': ------------------ | Branch (1667:13): [True: 4.76k, False: 974k] ------------------ 1668| 979k| case '@': continue; ------------------ | Branch (1668:13): [True: 198, False: 979k] ------------------ 1669| | 1670| 185| default: break; ------------------ | Branch (1670:13): [True: 185, False: 979k] ------------------ 1671| 979k| } 1672| | 1673| 185| break; 1674| 979k| } 1675| | 1676| 6.35k| *buf = (char*) inchi_calloc( i + 1, sizeof( char ) ); ------------------ | | 1146| 6.35k|#define inchi_calloc calloc ------------------ 1677| 6.35k| memcpy(*buf, p, i); 1678| 6.35k| if ( *buf ) ------------------ | Branch (1678:10): [True: 6.35k, False: 0] ------------------ 1679| 6.35k| (*buf)[i] = '\0'; 1680| | 1681| 6.35k| return; 1682| 6.35k|} inchi_memicmp: 1737| 101k|{ 1738| 101k| const U_CHAR *s1 = (const U_CHAR*) p1; 1739| 101k| const U_CHAR *s2 = (const U_CHAR*) p2; 1740| 101k| while (length--) ------------------ | Branch (1740:12): [True: 101k, False: 0] ------------------ 1741| 101k| { 1742| 101k| if (*s1 == *s2 || ------------------ | Branch (1742:13): [True: 0, False: 101k] ------------------ 1743| 101k| __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1732| 101k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 101k, False: 0] | | | Branch (1732:42): [True: 101k, False: 0] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1732| 101k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 101k, False: 0] | | | Branch (1732:42): [True: 101k, False: 0] | | ------------------ ------------------ | Branch (1743:15): [True: 0, False: 101k] ------------------ 1744| 0| { 1745| 0| s1++; 1746| 0| s2++; 1747| 0| } 1748| 101k| else 1749| 101k| { 1750| 101k| return 1751| 101k| __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1732| 101k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 101k, False: 0] | | | Branch (1732:42): [True: 101k, False: 0] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1732| 101k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 101k, False: 0] | | | Branch (1732:42): [True: 101k, False: 0] | | ------------------ ------------------ 1752| 101k| } 1753| 101k| } 1754| | 1755| 0| return 0; 1756| 101k|} inchi_stricmp: 1761| 694k|{ 1762| 904k| while ( *s1 ) ------------------ | Branch (1762:13): [True: 891k, False: 12.7k] ------------------ 1763| 891k| { 1764| 891k| if (*s1 == *s2 || ------------------ | Branch (1764:13): [True: 197k, False: 694k] ------------------ 1765| 694k| __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1732| 694k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 694k, False: 0] | | | Branch (1732:42): [True: 681k, False: 12.7k] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1732| 694k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 681k, False: 12.7k] | | | Branch (1732:42): [True: 668k, False: 12.7k] | | ------------------ ------------------ | Branch (1765:15): [True: 12.7k, False: 681k] ------------------ 1766| 210k| { 1767| 210k| s1++; 1768| 210k| s2++; 1769| 210k| } 1770| 681k| else 1771| 681k| { 1772| 681k| return 1773| 681k| __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1732| 681k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 681k, False: 0] | | | Branch (1732:42): [True: 681k, False: 0] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1732| 681k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1732:26): [True: 668k, False: 12.7k] | | | Branch (1732:42): [True: 656k, False: 12.7k] | | ------------------ ------------------ 1774| 681k| } 1775| 891k| } 1776| | 1777| 12.7k| if ( *s2 ) ------------------ | Branch (1777:10): [True: 0, False: 12.7k] ------------------ 1778| 0| { 1779| 0| return -1; 1780| 0| } 1781| | 1782| 12.7k| return 0; 1783| 12.7k|} inchi__strdup: 1801| 12.7k|{ 1802| 12.7k| char* p = NULL; 1803| 12.7k| if ( string ) ------------------ | Branch (1803:10): [True: 0, False: 12.7k] ------------------ 1804| 0| { 1805| 0| size_t length = strlen( string ); 1806| 0| p = (char *) inchi_malloc( length + 1 ); ------------------ | | 1143| 0|#define inchi_malloc malloc ------------------ 1807| 0| if (p) ------------------ | Branch (1807:13): [True: 0, False: 0] ------------------ 1808| 0| { 1809| 0| strcpy(p, string); 1810| 0| } 1811| 0| } 1812| | 1813| 12.7k| return p; 1814| 12.7k|} LLVMFuzzerTestOneInput: 27| 6.37k|int LLVMFuzzerTestOneInput(const uint8_t *data, size_t size) { 28| | 29| 6.37k| if (size == kSizeMax) ------------------ | Branch (29:7): [True: 0, False: 6.37k] ------------------ 30| 0| return 0; 31| | 32| 6.37k| char *szINCHISource = malloc(sizeof(char) * (size + 1)); 33| 6.37k| memcpy(szINCHISource, data, size); 34| 6.37k| szINCHISource[size] = '\0'; // InChI string must be null-terminated 35| | 36| | // Buffer lengths taken from InChI API reference, located at 37| | // https://www.inchi-trust.org/download/104/InChI_API_Reference.pdf, page 24 38| 6.37k| char szINCHIKey[28], szXtra1[65], szXtra2[65]; 39| 6.37k| GetINCHIKeyFromINCHI(szINCHISource, 0, 0, szINCHIKey, szXtra1, szXtra2); 40| | 41| 6.37k| inchi_InputINCHI inpInChI; 42| 6.37k| inpInChI.szInChI = szINCHISource; 43| 6.37k| inpInChI.szOptions = NULL; 44| | 45| 6.37k| inchi_Output out; 46| 6.37k| GetINCHIfromINCHI(&inpInChI, &out); 47| | 48| 6.37k| inchi_OutputStruct outStruct; 49| 6.37k| GetStructFromINCHI(&inpInChI, &outStruct); 50| | 51| 6.37k| free(szINCHISource); 52| 6.37k| FreeINCHI(&out); 53| 6.37k| FreeStructFromINCHI(&outStruct); 54| | 55| 6.37k| return 0; 56| 6.37k|}